title: U21_Sol

description: nAnTi-CAGE

value: unloading 7 days; recovery 24 hours


title: U2932, Scr_Rep3

status: Public on Jun 17 2021

type: SRA

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: total RNA

organism: Homo sapiens

growth_protocol: U2932 cells were grown in Iscove's DMEM supplemented with 10% FBS and Penn/Strep at 37C, 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the Rneasy Plus Mini Kit (Qiagen).
Nextera libraries were prepared by the Weill Cornell Epigenomics Core

treatment_protocol: U2932 cells were lentivirally infected using a 3rd generation packaging system. MISSION shRNA expression constructs targeting ROCK2 or a scrambled shRNA control were generated in pLKO.1 vectors containing puromycin resistance cassettes and tGFP were obtained from Sigma. Lentiviral particles were produced by transient transfection of 293T cells.

tag: cell line

tag: genotype

value: control


title: control HEL RNA-seq rep2

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

country: China

institute: Shanghai Jiao Tong University

description:
RLib26_CTTGTA_L003
processed data file: HEL.RNA-seq.read_count.txt

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: control HEL RNA-seq

growth_protocol: Human cells HEL cells were cultured in RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin + 2 mM L-Glutamine + 55 μM β-mercaptoethanol. Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: HEL

tag: genotype/variation


title: U21_EDL

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: nAnTi-CAGE

data_processing:
Reads were trimmed using fastx_trimmer and removeN scripts from Moirai pipeline (http://fantom.gsc.riken.jp/software/). Adapters were removed by using Trimmomatic-0.38
Trimmed reads mapped on Rnor_6.0 Ensembl genome assembly for Rattus norvegicus using BWA, unmapped reads remapped by Hisat2 and merged into processed BAM files
BAM files used to generate CTSS (CAGE transcription start site) tables in OSC format (https://zenbu-wiki.gsc.riken.jp/zenbu/wiki/index.php/OSCtable) using PromoterPipeline script level1.py (https://github.com/Population-Transcriptomics/C1-CAGE-preview/blob/master/tutorial.md)
OSC files merged into Level2_table.osc by using level2.py from PromoterPipeline.
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: OSC files contain information about position and strand of mapped CAGE reads, column for raw and TPM (tags per million) normalized counts included. Level2_table.osc table contains clustered CAGE signal representing putative promoter regions with expression level within all experiments in raw and TPM normalized counts for these clusters.

organism: Rattus norvegicus

source_name: hindlimb

extract_protocol:
Total RNA was extracted from EDL and Soleus muscles using RNeasy Fibrous Tissue Mini Kit QIAGEN
5 µg of total RNA RIN≥7 processed into cDNA by reverse transcriptase. CAGE libraries prepared according to Murata et al., 2014 (doi: 10.1007/978-1-4939-0805-9_7).

tag: tissue

value: EDL muscle

tag: protocol


title: U2932, Scr_Rep2


title: shCHD4_1%_1

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: TXT

molecule: polyA RNA

source_name: MDA-MB-231 cells

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a  KAPA mRNA  Hyper Library Preparation kit.

treatment_protocol: Cells were exposed to 20% or 1% O2 for 24 hrs

value: MDA-MB-231 cells

tag: treatment

tag: knockdown


title: U20_Sol

description: nAnTi-CAGE

value: soleus muscle


title: shCHD4_1%_2


title: U2932, Scr_Rep1


title: U20_EDL

description: nAnTi-CAGE


title: U12_Sol

description: nAnTi-CAGE

value: unloading 7 days; recovery 7 days


title: U3_Sol

description: nAnTi-CAGE

value: unloading 7 days


title: U2932, ROCK2 KD_Rep3

value: ROCK2 knockdown


title: U2_Sol

description: nAnTi-CAGE


title: U2932, ROCK2 KD_Rep2


title: U18_Sol

description: nAnTi-CAGE


title: U2_EDL

description: nAnTi-CAGE


title: U1_Sol

description: nAnTi-CAGE


title: U1_EDL

description: nAnTi-CAGE


title: U11_Sol

description: nAnTi-CAGE

value: unloading 3 days


title: 140729JH3

city: Glasgow

first: Julia

last: Cordero

state: Please select your county

address: Garscube Estate. Switchback Road

country: United Kingdom

institute: University of Glasgow

data_processing:
Fastq files were generated from the sequencer output using illumina’s bcl2fastq and quality checks on the raw data were done using FastQC (Andrews S., 2018, Available online at: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and Fastq Screen (Wingett, S. and Andrews, S., 2018, Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Alignment of the RNA-Seq paired-end reads was to the BDGP6 (Adams, M.D., et al., 2000 and Celniker, S.E., et al., 2002) version of the Drosophila melanogaster genome and annotation using Tophat with Bowtie (Trapnell, C., et al, 2009).
Expression levels were determined and statistically analysed by a workflow combining HTSeq (Anders S. et al, 2015), the R environment (R Core Team, 2018, https://www.R-project.org/), utilising packages from the Bioconductor data analysis suite (Huber, W., et al, 2015) and differential gene expression analysis based on the negative binomial distribution using the DESeq2 package (Love, M.I., et al, 2014).
Genome_build: BDGP6
Supplementary_files_format_and_content: xls. File including: gene id, symbol, gene name, accession id, base Mean, base Mean (tumor free), base Mean(tumor bearing animal), fold Change (tumor bearing vs tumor free), log2FoldChange (tumor bearing vs tumor free), pval (tumor bearing vs tumor free), padj (tumor bearing vs tumor free), gene symbol, fold change for each replicate in each condition

organism: Drosophila melanogaster

source_name: cuticle

growth_protocol: Larvae grown on standard fly food medium for 7 days at 25 degree for the controls (w1118) and for 10 days for the tumor bearing animals (y,w,ey-flp;act5C>y+>GFP/UAS-RasV12;FRT82B,tub-gal80/FRT82B,scrib1)

extract_protocol:
Cuticles were isolated by removing all internal organs, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: body wall skeletal muscles

tag: timing

value: 7 days after egg laying

tag: replicate number


title: 140729JH6

value: 10 days after egg laying


title: 140729JH4


title: M73

city: Atlanta

first: James

last: Dahlman

state: ga

address: 311 Ferst dr

institute: Georgia Institute of Technology

description:
Separate replicates
Humanized_counts_rep.txt

data_processing:
Used FastProNGS for preprocessing of reads, used standard preamters
Samples were mapped to both mouse and human genomes using RNAstar, paramters used "SortedByCoordinate --twopassMode None '' --quantMode - --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --outBAMsortingThreadN ${GALAXY_SLOTS:-4} --outBAMsortingBinsN 50 --limitBAMsortRAM "
htseq-cout was used to create determine counts, parameters used "--mode=union --stranded=no --minaqual=5 --type='exon' --idattr='gene_id'"
iDep9.1 was used to normalize and analyze dataset
Genome_build: MM10 and GRCh38
Supplementary_files_format_and_content: tab delimited table of raw counts

organism: Mus musculus

extract_protocol:
Tween20 whole cell without RNA extraction
SMART-seq2 protocol scaled up to 1000 cells

value: Liver

tag: iv injection

value: LNP

tag: pooled replicates

value: No

tag: repopulated

value: Yes


title: U11_EDL

description: nAnTi-CAGE


title: U9_Sol

description: nAnTi-CAGE


title: 140729JH2


title: U9_EDL

description: nAnTi-CAGE


title: 140729JH5


title: U18_EDL

description: nAnTi-CAGE

value: unloading 7 days; recovery 24 hours


title: M72


title: U26_Sol

description: nAnTi-CAGE

value: unloading 24 hours


title: U26_EDL

description: nAnTi-CAGE


title: U2932, ROCK2 KD_Rep1


title: U25_Sol

description: nAnTi-CAGE


title: M71


title: 6hpf_IgG

city: Athens

first: Mary

last: Goll

state: GA

address: 120 East Green Street

department: Genetics

institute: University of Goergia

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Reads were trimmed using TrimGalore (version 0.6.5) with the following paramters: --phred33 --fastqc --illumina --length 20. For Pol2 and IgG samples, --paired was also used
Trimmed reads were aligned to the zebrafish genome and the spike-in using Bowtie2 (version 2.4.1)  with the following paramters: --local --very-sensitive-local --phred33 --no-unal
Aligned reads were filtered using SAMTools (version 1.10) for a MAPQ score of 20
Spike-in and library-size normalization was performed using Bedtools (version 2.29.2) "genomecov". This outputs a bedgraph file which was converted to a bed file for peak-calling.
Bedgraphs were converted to bigwigs for data visualization using ucsc “bedGraphToBigWig” (version 359)
HOMER (version 4.11) was used for peak calling with the following paramters for histone modifications: -style histone -minDist 1000 -F 6 -gsize 1.5e9 -fdr 0.0001 with IgG as input file. Pol2 peaks were called with the following paramters: -style factor  -gsize 1.5e9 with IgG as input file.
Bedtools intersect was used to identify peaks present in both replicates
Genome_build: GRCz11
Supplementary_files_format_and_content: peak BED files
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Danio rerio

source_name: 6 hpf embryos

extract_protocol:
CUT&RUN: a fusion of micrococcal nuclease and protein A/G selectively cleaves antibody-bound chromatin in unfixed permeabilized cells. Released fragments are then isolated from solution and used for sequencing.
CUT&RUN libraries were prepared for sequencing using illimuna guidelines and adaptors

tag: spike in dna

value: E. coli

tag: antibody

value: IgG (abcam ab46540)

value: AB


title: M67

value: PBS


title: U25_EDL

description: nAnTi-CAGE

value: EDL muscle


title: U8_Sol

description: nAnTi-CAGE

value: soleus muscle

value: control


title: 6hpf_pol2_rep2

value: RNA pol-II CTD repeat phospho S5 (abcam ab5408)


title: M66


title: 6hpf_pol2_rep1


title: M65


title: U8_EDL

description: nAnTi-CAGE


title: 6hpf_H3K9me3_rep2

value: S. cerevisiae

value: H3K9me3 (abcam ab8898)


title: U7_EDL

description: nAnTi-CAGE


title: U6_Sol

description: nAnTi-CAGE


title: U7_Sol

description: nAnTi-CAGE


title: 6hpf_H3K9me3_rep1


title: U6_EDL

description: nAnTi-CAGE


title: 6hpf_H3K27me3_rep2

value: H3K27me3 (millipore 07-449)


title: U10_Sol

description: nAnTi-CAGE

value: unloading 3 days


title: 6hpf_H3K27me3_rep1


title: U24_Sol

description: nAnTi-CAGE


title: LNCAP sgNC rep1 [ATAC-Seq]

city: San Francisco

first: Raunak

last: Shrestha

state: CA

department: Radiation Oncology

institute: University of California, San Francisco

data_processing:
The ATAC-seq paired-end fastq files were trimmed to remove Illumina Nextera adapter sequence using Cutadapt v2.6. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Bowtie2 was then used to align the ATAC-seq reads against the Human reference genome build hg38 using. The uniquely mapped reads were obtained in SAM format. Samtools was used to convert SAM to BAM file as well as sort the BAM file. Picard was then used to flag duplicates using the MarkDuplicates tool. The resulting BAM file reads position were then corrected by a constant offset to the read start using deepTools2. This resulted in the final aligned, de-duplicated BAM file that was used in all downstream analyses. ATAC-seq peak calling was performed using MACS2 to obtain narrow peaks. The resulting peaks that map to the mitochondrial genome or genomic regions listed in the ENCODE hg38 blacklist or peaks that extend beyond the ends of chromosomes were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: peaks bed file

source_name: castration resistant prostate cancer

extract_protocol: ATAC-Seq on LNCaP and C42B cells were performed following knockdown of KIF4A or control (GAL4). The experiment was carried out as described in the previously reported optimized ATAC-seq protocol. Briefly, cells were resuspended in buffer, incubated on ice for 10 minutes, and lysed using a dounce homogenizer. 50,000 nuclei were incubated with 25uL 2X TD Buffer and 1.25uL Transposase shaking at 300rpm at 37C for 30 minutes. Zymo DNA Clean and Concentrator 5 kit was then used to purify DNA. Transposed DNA was amplified using PCR master mix and indexes from Nextera DNA Library Prep kit for 5 cycles and then assessed using qPCR. Final cleanup was performed using 1.8X AMPure XP beads and libraries quantified using the DNA High Sensitivity Agilent 2100 Bioanalyzer System. Paired end sequencing were performed on the Illumina NovaSeq platform. The entire experimental setup was performed in two technical replicates.

tag: cell type

value: castration resistant prostate cancer

value: LNCaP

value: sgNC


title: LNCAP sgNC rep2 [ATAC-Seq]


title: 6hpf_H3K4me3_rep2

value: H3K4me3 (abcam ab8580)


title: LNCAP sgKIF4A rep1 [ATAC-Seq]


title: LNCAP sgKIF4A rep2 [ATAC-Seq]


title: 6hpf_H3K4me3_rep1


title: C42B sgKIF4A rep2 [ATAC-Seq]


title: C42B sgNC rep2 [ATAC-Seq]


title: C42B sgKIF4A rep1 [ATAC-Seq]


title: C42B sgNC rep1 [ATAC-Seq]


title: PAO1161 BsrA_3 RNA-seq

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: gene expression data from BsrA (PA2121) overproducer

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Genome_build: CP032126
Supplementary_files_format_and_content: Raw counts of sequencing (FeatureCounts output summarized for all samples).
Supplementary_files_format_and_content: A table with DE data for all genes and normalized abundance measurements (EdgeR output).

organism: Pseudomonas aeruginosa

source_name: BsrA overproducer (BsrA), biological rep3

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pMEB63 carrying lacIQ-tacp-bsrA and empty vector pAMB9.37 (lacIQ-tacp) to obtain PAO1161/pMEB63 (lacIQ-tacp-bsrA) and PAO1161/pAMB9.37 (lacIQ-tacp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml-1 chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 mg/ml-1 chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 mg/ml-1) and IPTG (0.05 mM) and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
Ribosomal RNA was depleted using RiboZero Bacteria kit (Illumina). Obtained mRNA was used for cDNA library construction using KAPA Stranded RNASeq kit. Library was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

treatment_protocol: All cultures were incubated at 37°C in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG with shaking until reaching exponential phase of growth (OD600= 0.5).

tag: strain

value: PAO1161/pMEB63 (lacIQ-tacp-bsrA)

value: BsrA overproducer (BsrA)

value: logarithmic phase of liquid culture


title: U2OS_Input_DMSO_1

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
biological replicates of each input and IP were pooled prior to peak calling with MACS2 v2.2.7.1 with q-value cutoff 0.05. MACS2 was executed in both available modes utilizing either the learned or a customized shifting model parameterized according to the assumed mean fragment length of 150bp as extension size. The resulting peak sets were merged by overlap with BEDTools v2.29.2. Per interval, the strongest enrichment signal under the associated peak summits as well as the lowest p-value and q-value was kept. ENCODE blacklist regions were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak file contains the RFX7 ChIP peaks that have been called by MACS2

extract_protocol:
ChIP was performed with the SimpleChIP Kit (Cell Signaling Technology) following the manufacturer instructions. 3 µg of RFX7 (#A303-062A Bethyl Laboratories) antibody was used per IP
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Frankfurt am Main, Germany) following the manufacturer's description.

treatment_protocol: Treated for 24h with 10 µM Nutlin-3a or DMSO solvent control

value: DMSO


title: CROP-Seq Day 8 iTF-Microglia sgRNA enrichment Lane 04

last: Kampmann

address: 675 Nelson Rising Ln

institute: UCSF

data_processing:
Library strategy: CROP-seq (CRISPR interference + single-cell RNA sequencing)
QuantSeq: Alignment and mapping were performed using Salmon version 1.4.0 (Patro et al., 2017), with the --noLengthCorrection flag and either the human reference genome GRCh38 (Gencode, release 37), or a custom GRCh38 reference genome containing the references for each 3TF transgene integrated in iTF-iPSCs, to obtain transcript abundance counts. CROP-Seq: Alignment and gene expression quantification was performed on scRNAseq libraries and sgRNA-enriched libraries using Cell Ranger (version 5.0.1, 10X Genomics) with default parameters and reference genome GRCh38-3.0.0. Cellranger aggr was used to aggregate counts belonging to the same sample across different GEM wells. The resulting gene vs. cell barcode matrix contained 58,302 cells which had on average 41,827 reads per cell, and a median of 3,346 genes per cell.
QuantSeq: Tximport version 1.18.0 (Soneson et al., 2015) was used to obtain gene-level count estimates. Genes with zero counts across all samples were removed from the analysis. CROP-seq: sgRNA unique molecular identifier (UMI) counts for each cell barcode were obtained using a previously described mapping workflow (Hill et al., 2018). To facilitate sgRNA identity assignment, a combination of demuxEM (Gaublomme et al., 2019) and a z-score cut-off method we previously described (Tian et al., 2019) were used such that only cells with a single sgRNA as determined by both methods were carried forward in the analysis.
QuantSeq: For differential gene expression analysis of LPS-treated vs. PBS-treated iTF-Microglia samples, DESeq2 version 1.30.1 (Love et al., 2014) was used to calculate the log-fold-change and p-values and perform shrinkage of log-fold-change for downstream visualization using ggplot2 version 3.3.3. CROP-seq: The raw gene vs. barcode matrix outputted by Cell Ranger was converted into a SingleCellExperiment (SCE) object using the read10xCounts function from the DropletUtils package version 1.10.3 (Lun et al., 2019) in R (v 4.0.3). sgRNA assignments were appended to the SCE metadata and filtered to only include cells with a single sgRNA, resulting in 28,905 cells. The SCE was converted into a Seurat object using Seurat::as.Seurat version 4.0.1 (Hao et al., 2020).
CROP-Seq: The data was normalized and highly variable genes were identified using Seurat::SCTransform (Hafemeister and Satija, 2019). For initial data exploration, principal-component analysis was performed using Seurat::RunPCA to determine the number of principal components to retain. UMAP dimensional reduction using Seurat::RunUMAP and clustering using Seurat::FindNeighbors and Seurat::FindClusters were performed on the retained principal components with resolution = 0.7.
CROP-Seq: To determine the differentially expressed genes between UMAP clusters, Seurat::FindAllMarkers was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files for CROP-seq are hdf5 formatted matrices of UMI counts, with rows as genes and columns as cell barcodes, obtained from running cellranger count.

source_name: Day 8 iTF-Microglia

growth_protocol: For CROP-seq, inducible CRISPRi-iTF-iPSCs were infected with the pooled sgRNA library at <0.15 MOI and then selected for lentiviral integration. For both QuantSeq and CROP-seq, iTF-iPSCs were differentiated into iTF-microglia and cultured with the addition of TMP with the following conditions: iTF-iPSCs were grown in StemFlex until reaching at least 50% confluency and were grown for at least 24h without ROCK inhibitor. They were dissociated with Accutase and centrifuged and pelleted cells were resuspended in Day 0 differentiation medium containing the following: Essential 8™ Basal Medium (Gibco; Cat. No. A15169-01) as a base, 10nM ROCK inhibitor, and 2 mg/ml Doxycycline (Clontech; Cat. No. 631311). iTF-iPSCs were counted and seeded onto double coated plates (Poly-D-Lysine-precoated Bio plates (Corning, assorted Cat. No.) + Matrigel coating) with the following seeding densities: 10,000 cells/well for 96-well plate, 0.1 Mio/well for 12-well plate, 0.15 Mio/well for 6-well plate, 2 Mio/dish for 10-cm dish, and 8 Mio/dish for 15-cm dish. On day 2, media was replaced with Day 2 differentiation media containing Advanced DMEM/F12 Medium (Gibco; Cat. No. 12634-010) as a base medium containing the following: 1X Antibiotic-Antimycotic (Anti-Anti) (Gibco; Cat. No. 15240-062), 1X GlutaMAX™ (Gibco; Cat. No. 35050-061), 2 mg/ml doxycycline, 100 ng/ml Human IL34 (Peprotech; Cat. No. 200-34) and 10 ng/ml Human GM-CSF (Peprotech; Cat. No. 300-03). On day 4 and day 6, the medium was replaced with iTF-Microglia medium, containing Advanced DMEM/F12 as a base medium and the following: 1X Anti-Anti, 1X GlutaMAX, 2 mg/ml doxycycline, 100 ng/ml Human IL-34 and 10 ng/ml Human GM-CSF, 50 ng/ml Human M-CSF (Peprotech; Cat. No. 300-25) and 50 ng/ml Human TGFB1 (Peprotech; Cat. No. 100-21C).

extract_protocol:
For QuantSeq, cell culture medium was aspirated, cells were washed once with DPBS, and RNA lysis buffer was added directly to wells containing either Day 0 iTF-iPSCs, Day 9 iTF-Microglia or Brownjohn-iMG +/- 100 ng/ml 24h LPS treatment, or Day 15 iTF-Microglia. Biological triplicates for each condition (approximately 0.15 Mio cells each) were pelleted, snap frozen, and stored at -80°C. RNA was extracted using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1055). For CROP-seq, Day 8 iTF-Microglia were washed 3X with DPBS, dissociated with TrypLE, and resuspended in nuclease-free water before loading onto four wells of the 10x Chromium Controller (10x Genomics, v3.1) according to the manufacturer’s protocol, with 35,000 cells recovered per sample as the target.
For QuantSeq, libraries were prepared from total RNA (473 ng per sample) using the QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen; Cat. No. 015UG009V0252) following the manufacturer’s instructions. Library amplification was performed with 14 total PCR cycles. mRNA-seq library concentrations (mean of 1.13 ± 0.66 ng/uL) were measured with the Qubit dsDNA HS Assay Kit (Invitrogen; Cat. No. Q32851) on a Qubit 2.0 Fluorometer. Library fragment-length distributions (mean of 287 ± 28 bp) were quantified with High Sensitivity D5000 Reagents (Agilent Technologies; Cat. No. 5067-5593) on the 4200 TapeStation System. The libraries were sequenced on an Illumina NextSeq 2000 instrument with single-end reads. For CROP-seq, sample preparation was performed using the Chromium Next GEM Single Cell 3′ Reagent Kits version 3.1 (10x Genomics, cat. no. PN-1000121) according to the manufacturer’s protocol, reserving 10-30 ng full-length cDNA to facilitate sgRNA assignment by amplifying sgRNA-containing transcripts using hemi-nested PCR reactions adapted from a previously published approach (Hill et al., 2018; Tian et al., 2019). cDNA fragment analysis was performed using the 4200 TapeStation System and sgRNA enrichment libraries were separately indexed and sequenced as spike-ins alongside the whole-transcriptome scRNA-seq libraries using a NovaSeq 6000 using the following configuration: Read 1: 28; i7 index: 8; i5 index: 0; Read 2: 91.

treatment_protocol: For QuantSeq, treatment with PBS (control) or 100 ng/ml 24h LPS treatment on Day 8 iTF-Microglia or Brownjohn-iMicroglia

value: iTF-Microglia


title: CROP-Seq Day 8 iTF-Microglia sgRNA enrichment Lane 03


title: CROP-Seq Day 8 iTF-Microglia sgRNA enrichment Lane 02


title: CROP-Seq Day 8 iTF-Microglia sgRNA enrichment Lane 01


title: CROP-Seq Day 8 iTF-Microglia 10X Lane 03


title: CROP-Seq Day 8 iTF-Microglia 10X Lane 02


title: CROP-Seq Day 8 iTF-Microglia 10X Lane 04


title: CROP-Seq Day 8 iTF-Microglia 10X Lane 01


title: PAO1161 BsrA_2 RNA-seq

source_name: BsrA overproducer (BsrA), biological rep2


title: ENL KO K562 RNA-seq rep3

source_name: K562 cell line

value: ENL-/-


title: ENL KO K562 RNA-seq rep2


title: HCT116_siRFX7_Nutlin_3_RNAseq

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
Read quantification was performed on exon level using featureCounts v1.6.5, parametrized according to the strand specificity inferred through RSeQC v3.0.0. Differential gene expression and its statistical significance was identified using DeSeq2 v1.20.0.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv DESeq2 output

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol.
Libraries were constructed from 500 ng of total RNA using NEBNext Ultra II RNA - polyA+ (mRNA) Library Preparation Kit following the manufacturer's description.


title: PAO1161 BsrA_1 RNA-seq

source_name: BsrA overproducer (BsrA), biological rep1


title: HCT116_siRFX7_Nutlin_2_RNAseq


title: ENL KO K562 RNA-seq rep1


title: HFD rep3_Ribo [Ribo_HF12]

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

description: processed data file: Ribo_RC_RPKM

data_processing:
We used cutadapt and bowtie2 software to process raw data to obtain high-quality clean data.
The FANSE3 series algorithm was used for quantitative genetic analysis. The mRNA and RPFs in each sample were normalized using reads per kilobase per million reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HFD liver_Ribo

extract_protocol:
RNA-seq:Total RNA was isolated using TRIzol reagent. Equal amounts of total RNA or RFPs from the HFD and LYC groups were pooled for subsequent library construction and high-throughput sequencing.Ribo-seq: Liver was pretreated with 100 mg/ml cycloheximide for 15 min, washed with prechilled phosphate-buffered saline, then treated with cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer, 20 mM HEPES–KOH (pH 7.4), 15 mM MgCI2, 200 mM KCl, 100 ug/ml cycloheximide and 2 mM dithiothreitol)]. Cell debris was removed by centrifugation at 16,200 × g for 10 min at 4°C. Supernatants were transferred into new prechilled 1.5-ml tubes with the addition of 2 μl Ribolock RNase Inhibitor (40 U/μl, Fermentas) in each tube. RNase I (10 U/μl, Fermentas) was added at 0.2 μl per tube, followed by incubation at 37°C for 15 min and reaction termination with 1% sodium dodecyl sulfate (1/10 volume per tube). The digested samples were pooled and layered on the surface of 15 ml sucrose buffer (30% sucrose in RB buffer). The ribosomes were pelleted by ultracentrifugation at 185,000 × g for 5 h at 4°C. Ribosome protected fragment (RPF) extraction was performed using the TRIzol method and rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Mouse) (Epicenter).
RNA libraries were prepared according to the protocol of the VAHTS mRNA-seq v.3 Library Prep Kit for Illumina (Vazyme Biotech Co. Ltd., Nanjing, Jiangsu, China), and the raw sequencing reads were generated on an Illumina HiSeqX Ten sequencer.

tag: age

value: 16 weeks

tag: Sex

value: male

value: eight-week-old male mouse was fed high-fat diet for 8 weeks

value: liver


title: HFD rep2_Ribo [Ribo_HF10]

description: processed data file: Ribo_RC_RPKM


title: LYC rep2_Ribo [Ribo_HF-Lyc28]

description: processed data file: Ribo_RC_RPKM

source_name: LYC liver_Ribo


title: PAO1161 BsrA-F_2 ChIP-seq

description: ChIP DNA data from BsrA-FLAG overproducer

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
BsrA peaks were identified by comparing combined replicates of IP samples (BsrA-F) for each strain with negative control (empty vector EV-F) samples using the callpeak function of MACS2 ver 2.1.2 with default options for paired-end .BAM files, and 0.05 as false discovery rate (FDR) cut off.
Genome_build: CP032126
Supplementary_files_format_and_content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome.
Supplementary_files_format_and_content: Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed).
Supplementary_files_format_and_content: A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

source_name: BsrA overproducer (BsrA-F), replicate 2

growth_protocol: P. aeruginosa PAO1161 ΔbsrA strain carrying pMEB99 (lacIQ-tacp-bsrA-flag) as well as control strain carrying pABB28.1 (lacIQ-tacp-flag) were obtained by conjugation of PAO1161 (leu-, r-, RifR) and E. coli S-17 donor strain carrying appropriate plasmid. Conjugants were selected on L agar plates supplemented with 300 μg/mL rifampicin and 150 μg/mL chloramphenicol. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37oC. After that they were diluted 1:100 in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG to induce the expression of bsrA-flag and grown with shaking at 37oC until reaching exponential phase with optical density about 0.5 (OD600).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-FLAG mouse antibodies (1-10 μg per reaction, 3 and 6 μL for this procedure) [DYKDDDDK Tag polyclonal  antibodies; 1 mg/mL; PA1-985B; Invitrogen] diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

value: PAO1161/pMEB99 (lacIQ-tacp-bsrA-flag)

tag: genotype

value: BsrA overproducer (BsrA-F)


title: HFD rep1_Ribo [Ribo_HF2]

description: processed data file: Ribo_RC_RPKM


title: LYC rep3_Ribo [Ribo_HF-Lyc29]

description: processed data file: Ribo_RC_RPKM


title: HCT116_siRFX7_Nutlin_1_RNAseq

tag: cell line


title: K562_ENL KO TBP ChIP-seq rep2

description: TZlane9-1-TZ_lib106_FKDL190757050-1a-4_H3JYHCCX2_L5

source_name: K562_ENL KO TBP ChIP-seq

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
ChIP-seq libraries: The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

treatment_protocol: For double fixation with EGS (Thermo, cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For double fixation with DMA (Thermo, cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

tag: genotype/variation

tag: fixation

value: EGS + FA

tag: chip antibody

value: TBP


title: PAO1161 BsrA-F_1 ChIP-seq

source_name: BsrA overproducer (BsrA-F), replicate 1


title: K562_ENL KO TBP ChIP-seq rep1


title: K562_control TBP ChIP-seq rep4

description: TZlane9-1-TZ_lib103_FKDL190757050-1a-1_H3JYHCCX2_L5

source_name: K562_control TBP ChIP-seq

value: wild type


title: HCT116_siRFX7_DMSO_2_RNAseq

tag: treatment


title: HCT116_siRFX7_DMSO_3_RNAseq


title: 140729JH1

tag: tissue

value: body wall skeletal muscles

tag: timing

value: 7 days after egg laying


title: K562_control TBP ChIP-seq rep3


title: HCT116_siRFX7_DMSO_1_RNAseq


title: LYC rep3_mRNA [RNA_HF-Lyc29]

description: processed data file: RNA_RC_RPKM

source_name: LYC liver_mRNA


title: LYC rep1_Ribo [Ribo_HF-Lyc25]

description: processed data file: Ribo_RC_RPKM


title: PAO1161 EV-F_1 ChIP-seq

description: ChIP DNA data from empty vector control

source_name: empty vector control (EV-F), replicate 1

value: PAO1161/pABB28.1 (lacIQ-tacp-flag)

value: empty vector control (EV-F)


title: K562_ENL KO ChIP-seq input

source_name: K562_ENL KO ChIP-seq input

value: input


title: LYC rep1_mRNA [RNA_HF-Lyc25]

description: processed data file: RNA_RC_RPKM


title: HFD rep3_mRNA [RNA_HF12]

description: processed data file: RNA_RC_RPKM

source_name: HFD liver_mRNA


title: NLS1_120519

city: Haifa

first: Marina

last: Katsman

address: Technion City

department: Biotechnology and Food Engineering

country: Israel

institute: Technion

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adaepter trimming: trim galore (uses cutadapt version 1.10)
Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: Htseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.18.1
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: raw count text file

source_name: MEFs_expressing NLS-N-VEGF

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Library preparation kit v2 was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To study the effect of nuclear NLS-N-VEGF on cellular transcriptome profile, RNA was extracted from cells expressing either N-VEGF or NLS-N-VEGF prior or following exposure to dox and subjected in triplicates to RNA-Seq using next-generation sequencing (NGS).

value: mouse embryonic fibroblasts

tag: genotype/treatment

value: expressing NLS-N-VEGF


title: HCT116_siControl_Nutlin_2_RNAseq


title: HFD rep2_mRNA [RNA_HF10]

description: processed data file: RNA_RC_RPKM


title: K562_DOT1L KO ChIP-seq input -3

source_name: K562_DOT1L KO ChIP-seq input

value: FA


title: U3_EDL

description: nAnTi-CAGE

source_name: hindlimb

value: EDL muscle

tag: protocol

value: unloading 7 days


title: K562_control ChIP-seq input - 4

source_name: K562_control ChIP-seq input


title: HFD rep1_mRNA [RNA_HF2]

description: processed data file: RNA_RC_RPKM

value: 16 weeks

value: male

value: eight-week-old male mouse was fed high-fat diet for 8 weeks


title: HCT116_siControl_DMSO_2_RNAseq

value: DMSO


title: K562_DOT1L KO ChIP-seq input -2

value: EGS + FA


title: Early lesions Pool #8

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.6.0) using Bioconductor package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-deliminated data matrix of normalized gene counts

source_name: Indolent lesions

extract_protocol:
Tumor cells were homogenized using a Bullet Blender (Next Advance) and RNA extracted (Qiagen RNeasy Kit). RNA was treated with DNase (Turbo DNA-Free Kit), and then cleaned and concentrated (Zymo RNA Cleanup Kit), per manufacturers’ instructions
RNA libraries were prepared according to manufacturer's instructions for NEBNext® Ultra™ RNA Library Prep Kit for Illumina, NEBNext® Poly(A) mRNA Magnetic Isolation Module

tag: source name abbreviation

value: EL

value: FVB

value: Mammary gland

tag: pool

tag: batch (sample prep)

tag: sequence id


title: HCT116_siControl_Nutlin_1_RNAseq


title: Tumor Pool #8

source_name: Aggressive lesions

value: AL

tag: strain


title: HCT116_siControl_DMSO_3_RNAseq


title: K562_DOT1L KO K562 Pol II ChIP-seq

source_name: K562_DOT1L KO K562 Pol II ChIP-seq

value: DMA + FA

value: Pol II


title: K562_control ChIP-seq input -2

value: wild type

value: input


title: HEL ChIP-seq input

source_name: HEL ChIP-seq input

value: HEL

value: control

value: DMA


title: HCT116_siControl_Nutlin_3_RNAseq


title: Early lesions Pool #7


title: RPE-1_RFX7_Nutlin_1

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2fastq v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
biological replicates of each input and IP were pooled prior to peak calling with MACS2 v2.2.7.1 with q-value cutoff 0.05. MACS2 was executed in both available modes utilizing either the learned or a customized shifting model parameterized according to the assumed mean fragment length of 150bp as extension size. The resulting peak sets were merged by overlap with BEDTools v2.29.2. Per interval, the strongest enrichment signal under the associated peak summits as well as the lowest p-value and q-value was kept. ENCODE blacklist regions were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak file contains the RFX7 ChIP peaks that have been called by MACS2


title: E17.5

city: Oxford

first: Steve

last: Twigg

address: John Radcliffe Hospital

institute: University of Oxford

description: E17.5 alone

data_processing:
Quality control of raw reads was performed with FastQC version 0.11.7, fastq_screen version 0.7.0 and multiqc (Ewels et al., 2016) version 0.9. Samples were counted individually and aggregated with cellranger (10X Genomics) version 2.1.1. All other parameters were set to their default values.
Data analysis was performed with Seurat (Stuart et al., 2019) version 3.2.0. The aggregate gene/barcode matrix (`raw_gene_bc_matrices_mex`) was loaded using `CreateSeuratObject` and `Read10X` with `min.cells = 10, min.genes = 200`. Cells were filtered to exclude cells with fewer than 1000 UMIs, fewer than 1000 genes, more than 7.5% mitochondrial content (calculated as the fraction of reads assigned to a gene on the chromosome `MT`), and more 3% Hbb/Hba centent (to remove red blood cells, and cells with high contamination for red blood cell specific genes). Filtered cells were normalized with SCTransform, and cell cycle scoring and regression was performed for each dataset with the default list of human cell-cycle genes (converted to mouse gene symbols). Datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat. In brief, an object list including both datasets was created, 3000 features were selected using the SelectIntegrationFeatures following by PrepSCTIntegration, anchors were identified using FindIntegrationAnchors, and the data was integrated using IntegrateData.
Dimensionality reduction was performed using the first 30 principal components (PCs) with UMAP (McInnes et al., 2018) (`min_dist = 0.5, n_neighbors = 50`). Clustering was performed with `FindClusters` and `resolution=1`. Cluster marker genes were identified with `FindAllMarkers` using parameters `min.pct  = 0.2, logfc.threshold = 0.5, max.cells.per.ident = 1000, min.cells.gene = 5`. Secondary dimensionality reduction and clustering of the osteogenic and mesenchymal subset was performed as above, after subsetting for cluster numbers 0, 1, 2, 4, 5, 7, and 9.
Genome_build: mm10
Supplementary_files_format_and_content: The matrix, genes are barcode files for the E15.5 and E17.5 datasets are respectively: E15_matrix.mtx,  E15_barcodes.tsv, E15_features.tsv, and E17_matrix.mtx, E17_barcodes.tsv, E17_genes.tsv.
Supplementary_files_format_and_content: composite_full_clusters.rds - this is an R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS`. It contains the gene counts, sample metadata, and feature metadata of the full E15.5-E17.5 composite datset.
Supplementary_files_format_and_content: composite_mesenchyme_bone_subset.rds - this contains the gene counts, sample metadata, and feature metadata of the osteogenic-mesenchyme subset of E15.5-E17.5 composite datset.
Supplementary_files_format_and_content: the 'E15_17_composite_data' and 'E15_17_composite_metadata' files contain respectively, the Seurat SCT expression data (3000 genes x 12,170 cells) and metadata from the osteogenic-mesenchyme subset.

source_name: wildtype_coronal suture

extract_protocol:
E15.5 and E17.5 embryos were isolated, and the skin, the brain, and some of the meningeal layers were peeled away, leaving the bony skull. For E15.5 embryos the coronal suture was dissected away from the skull cap using microdissection scissors, and 10 coronal sutures were rinsed in PBS and enzymatically dissociated with a final concentration of 3 mg/mL of Collagenase II (Worthington) and 4 units/mL of Dispase (COMPANY) in DMEM/F12 (company) for 45 min. For E17.5 embryos coronal sutures were dissected out in ice cold PBS using a scalpel blade, isolating a strip containing the overlapping frontal and parietal bone fronts (which appears opaque compared to adjacent regions) and avoiding the most apical and basal aspects of the suture. Isolated sutural strips from embryos from two litters in 3 batches (batch 1, 10 sutures from litter 1; batch 2 and 3, 3 sutures each from litter 2) were cut into small fragments in HBBS and digested using Collagenase IV (Worthington, USA; final concentration in HBBS of 2 mg/mL) for 30 min. Dissociation was terminated with 2% Fetal Bovine Serum and cells were passed through a 0.35 µM filter (E15.5) or Pluri-strainer Mini 70 µm (E17.5; pluriSelect Life Science, Germany). For E15.5 sample preparation, dead cells were removed using the Dead Cell Removal kit (Miltenyi Biotec 130-090-101) and cells counts were determined with a hemocytometer. The three batches of E17.5 dissociated cells were separately sorted by FACs to remove debris, cell doublets and likely dead cells (BD FACSAria Fusion; 100 µM nozzle) prior to library preparation.
Transcriptome libraries  for single cells were captured using 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v2 following manufacturer’s guidelines. Sequencing for E15.5 coronal sutures was performed with Illumina’s HiSeq 3000/4000 PE Cluster Kit at the Children’s Hospital Los Angeles’ Molecular Genomics Core, and for E17.5 cells, PE sequencing was run on an Illumina HiSeq 4000 at the Oxford Genomics Centre Wellcome Centre for Human Genetics, Oxford achieving an average of  ~150,000 mean reads per cell for E15.5 and ~92,000 mean reads per cell for E17.5.
scRNAseq

value: Coronal suture

tag: developmental stage


title: K562_control K562  Pol II ChIP-seq

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: K562_control K562  Pol II ChIP-seq


title: Tumor #6


title: HCT116_siControl_DMSO_1_RNAseq


title: K562_DOT1L KO ChIP-seq input -1


title: Tumor Pool #7


title: RPE-1_RFX7_DMSO_2


title: K562_control ChIP-seq input -3

value: FA


title: K562_control ChIP-seq input -1


title: LYC rep2_mRNA [RNA_HF-Lyc28]

description: processed data file: RNA_RC_RPKM

tag: age

value: 16 weeks

tag: Sex

value: male

value: liver


title: M66 (JD69)

description:
Pooled Replicates (JD69)
Humanized_counts.txt

value: Liver

tag: iv injection

value: LNP

tag: pooled replicates

value: Yes

tag: repopulated

value: No


title: RPE-1_RFX7_DMSO_1

value: DMSO

tag: cell line


title: RPE-1_Input_Nutlin_2

tag: treatment


title: Tumor #5

value: AL

value: FVB

tag: tissue

value: Mammary gland


title: RPE-1_RFX7_Nutlin_2


title: H71


title: Early lesions #5

value: EL


title: Tumor #4


title: RPE-1_Input_DMSO_2


title: H67

value: PBS


title: H65


title: M36


title: M44


title: Early lesions #4


title: RPE-1_Input_Nutlin_1


title: RPE-1_Input_DMSO_1


title: LNCAP sgWDR62 rep2

data_processing:
The RNA-seq single-end fastq data generated by Illumina HiSeq 4000 sequencing system were first trimmed to remove adapter sequence using Cutadapt. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Using splice-aware aligner STAR, RNA-seq reads were aligned onto the Human reference genome build hg38 and exon-exon junctions, according to the known Human gene model annotation from the GENCODE v30. Apart from protein coding genes, non-coding RNA types, and pseudogenes are further annotated and classified. Furthermore, based on the reads that can only be mapped to a single genomic location, the gene expression quantification was performed using featurecount function within Rsubread R-package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: castration resistant prostate cancer

extract_protocol: LNCaPi cells were viral transduced with sgRNA targeting KIF4A or control sgRNA for 3 days and selected with puromycin for pure population for 3 days. Post-selection RNA was extracted from the cells as described above for library preparation to generate Illumina compatible libraries of sequences and to perform qPCR to determine the sgRNA knockdown efficiency. QuantSeq 3’mRNA-Seq library prep kit FWD for Illumina was used to prepare the library as per the manufacturer’s protocol. Quality control was performed by using the Agilent Bioanalyzer 2100 system and the samples were sequenced in Illumina HiSeq 4000. The entire set of the experiment was done in two biological replicates.

tag: cell type

value: castration resistant prostate cancer

value: LNCaP


title: H73


title: HCT116_RFX7_Nutlin_1


title: M29

source_name: C57BL6/J PBS


title: Tumor Pool #3


title: M34


title: H72


title: M31

source_name: C57BL6/J LNP


title: HCT116_RFX7_Nutlin_2


title: LNCAP sgKIF4A rep2


title: Tumor Pool #1


title: LNCAP sgWDR62 rep1


title: Early lesions #6


title: LNCAP sgKIF4A rep1


title: HCT116_RFX7_DMSO_1


title: LNCAP sgAR rep2

value: sgAR


title: HCT116_RFX7_DMSO_2


title: Tumor Pool #2


title: 120min_with_auxin_with_triptolide rep1

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For each biological replicate, paired end reads were aligned to the mouse reference genome mm9 using bowtie2 (global parameters: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder) through the Hi-C Pro software 41. PCR duplicates were removed and uniquely mapped reads were paired to generate a validPair file. The output validPair file was converted into “.hic” file using the hicpro2juicebox utility. For merged samples, similar steps were taken on reads merged from each biological replicate.
Genome_build: mm9
Supplementary_files_format_and_content: .hic formated files of each individual biological replicate of hic data are provided

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
In-situ Hi-C experiments were performed as previously described 1. Briefly, sorted cells (5 million for prometaphase and ana/telophase and 10million for early- and mid-G1 phase) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Cells were pelleted at 4℃ and washed with 1.2 x DpnII buffer. Nuclei were permeabilized with 0.3% SDS for 1h at 37℃ and quenched with 1.8% Triton X-100 for 1h at 37℃. Chromatin was digested with 300U DpnII restriction enzyme (NEB, R0543M) in-situ at 37℃ over night with shaking. 300U DpnII restriction enzyme was added for an additional 4h at 37℃ with shaking. Nuclei were incubated at 65℃ for 20min to inactivate DpnII. After cool down, digested chromatin fragments were blunted with pCTP, pGTP, pTTP and Biotin-14-dATP (Thermal Fisher Scientific, 19524016) using 40U DNA Polymerase I, Large (Klenow) fragment (NEB, M0210). DNA was ligated in-situ with 4000U T4 DNA ligase (NEB, M0202M) for 4h at 16℃ followed by further incubation for 2h at RT. Nuclei were then incubated in 10% SDS containing proteinase K (3115879 BMB) at 65℃ overnight to reverse crosslinking. RNA was then digested with DNase-free RNase at 37℃ for 30min. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in nuclease free water. DNA was sonicated to 200-300bp fragments (Epishear, Active Motif, 100% amplitude, 30s ON and 30s OFF, 25-30min) and purified with AMPure XP beads (Beckman Coulter).
For hic library construction, biotin-labeled DNA after extraction was purified by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, 65002) at RT for 15min. DNA libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040, M0543L, E7335S). To elute DNA, streptavidin bead- bound DNA was incubated in 0.1% SDS at 98℃ for 10min. DNA was purified with AMPure XP beads and index labeled with NEBNext multiplex oligos for 6 cycles on a thermal cycler, using the NEBNext Q5 Hot Start HIFI PCR master mix. Index labeled PCR products were then purified with AMPure XP beads and sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: Cells were synchronized to pro-metaphase with 200ng/ml nocodazole for 7-8.5h. For post-mitotic enrichment, cells were released from nocodazole for 0, 25min, 60min, 120min and 240min for pro-meta, ana/telo, early-G1, mid-G1 and late-G1 respectively.

value: erythroid

value: auxin

tag: time point


title: Early lesions Pool #1


title: HCT116_Input_Nutlin_2


title: LNCAP sgAR rep1


title: DS18: P4 Nmnat1-/- Retina

city: Morgantown

first: Saravanan

last: Kolandaivelu

state: WV

address: 1 Medical Center Dr.

department: Ophthalmology, Biochemistry

institute: West Virginia University Eye Institute

description: P4 knockout retina

data_processing:
bases were called using the integrated primary analysis software RTA (Real Time Analysis) from Illumina. Resulting BCL files were converted to FASTQ format using Illumina package bcl2fastq
read quality was verified using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Illumina adapters were trimmed using the Bbduk utility of the BBTools package (http://sourceforge.net/projects/bbmap/)
read alignment was performed using HISAT2 v2.1.0 and resulting SAM files were converted to BAM format using Samtools v1.9 (parameters were set following protocol from Pertea, et al 2016 Nature Protocols)
transcripts were assembled and quantified using StringTie v1.3.6 (following protocol from Pertea, et al 2016 Nature Protocols, quantifying transcripts directly from reference annotation file instead of de novo transcript assembly)
DESeq2 count matrices were generated from StringTie output using prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq) and differential gene expression analysis was performed in R using the DESeq2 package
For E18.5 dataset, DS3 sample was removed as an outlier prior to differential gene expression analysis using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: matrix tables with raw gene counts for every gene in every sample (E18.5 and P4 datasets)
Supplementary_files_format_and_content: matrix tablse with normalized gene counts for every gene in every sample (E18.5 and P4 datasets)
Supplementary_files_format_and_content: matrix table with normalized gene counts for every gene in every sample, with DS3 outlier removed (E18.5 dataset)
Supplementary_files_format_and_content: matrix tables with gene identifiers, wild-type mean count, log2 fold change in Nmnat1-/- compared to control samples, and p-values (computed by DeSeq2, E18.5 and P4 datasets)
Supplementary_files_format_and_content: matrix table with gene identifiers, wild-type mean count, log2 fold change in Nmnat1-/- compared to control samples, and p-values (with DS3 outlier removed, E18.5 dataset)

source_name: P4 knockout retina

extract_protocol:
Retinas were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Total RNA resuspended in DEPC water was sent to Macrogen Corp. (now Psomagen Corp., Rockville, MD, USA) for library construction and sequencing
libraries were constructed by Psomagen Corp. using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit (part# 15031047 Rev. E)

value: retina

value: postnatal day 4 (P4)

tag: genotype


title: Early lesions Pool #2

tag: source name abbreviation


title: LNCAP sgNC rep2

value: sgNC


title: 120min_no_auxin_with_triptolide rep1

value: no auxin


title: HCT116_Input_Nutlin_1


title: 120min_with_auxin_rep3


title: DS17: P4 Nmnat1-/- Retina

description: P4 knockout retina


title: 120min_with_auxin_rep2


title: Donor 3 CD137 Low

city: Erlangen

first: Andrej

last: Stoll

address: Schwabachanlage 12

department: Department of Medicine 5 - Hematology and Oncology

institute: Friedrich-Alexander University Erlangen Nuremberg

data_processing:
Reads in FASTQ format were analysed withfastqc (v0.11.9) and remaining adapter sequences were trimmed by cutadapt (v2.8) with the following parameters: -j 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 40
Reads were mapped against the human genome (GENCODE GRCh38.p13 v33) using STAR v2.7.3a with the following parameters:  --runThreadN 4  --genomeLoad LoadAndKeep   --outSAMtype BAM SortedByCoordinate  --outSAMunmapped Within --outSAMattributes Standard
All non-multimapping and non-multi-overlapping reads mapping to exons were counted using featureCounts (v2.0.0) using the following parameters: featureCounts -T 4 -s 2 -t exon -g gene_id -a gencode.v33.annotation.gtf

source_name: Monocyte

growth_protocol: PBMC were isolated by density gradient centrifugation of peripheral blood of healthy donors. Monocytes were purified by MACS, flurescence labeled for CD137 and subsequently FACS sorted for CD137HI vs LO.

extract_protocol:
RNA was isolated from the cells using an innuPREP DNA/RNA Mini Kit (analytic Jena, 845-KS-2080250) according to the manufacturer’s recommended protocol. Approx. 300 ng RNA of each total RNA sample was used as template.
RNAseq and library construction was carried out by Eurofins/GATC Biotech (Product: INVIEW Transcriptome), RNA libraries were prepared for sequencing using standard Illumina protocols

value: Monocyte

tag: cd137 expression

value: Low

tag: donor

value: healthy donor


title: LNCAP sgNC rep1


title: DS15: P4 Nmnat1-/- Retina

description: P4 knockout retina


title: HCT116_Input_DMSO_1

value: DMSO


title: HCT116_Input_DMSO_2


title: 120min_with_auxin_with_triptolide rep2


title: 120min_with_auxin_rep1


title: Donor 2 CD137 Low


title: K562_ENL KO 4sU-DRB-seq 10min rep2

last: Wu

institute: Shanghai Jiao Tong University

description: TZlane18-2-4sU-DRB36_BKDL202599488-1a-12-AK4544

data_processing:
library strategy: 4sU-DRB-seq
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: K562_ENL KO 4sU-DRB-seq 10min

extract_protocol:
After RNA biotinylation and free biotin removal, biotinylated RNA was purified by streptavidin-coupled Dynabeads (Thermo, cat. no. 11205D). rRNA was depleted before library construction. Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.

treatment_protocol: 10 million cells were used for each experiment. After DRB (Sigma, cat. no. D1916) treatment and 4sU (Sigma, cat. no. T4509) incorporation, total RNA was extracted.

tag: genotype/variation

value: ENL-/-


title: DS14: P4 Nmnat1-/- Retina

description: P4 knockout retina

tag: strain


title: K562_ENL KO 4sU-DRB-seq 0min rep2

description: TZlane18-1-4sU-DRB33_BKDL202599487-1a-9-AK4544

source_name: K562_ENL KO 4sU-DRB-seq 0min


title: Donor 1 CD137 Low


title: 120min_no_auxin_with_triptolide rep2


title: 120min_no_auxin_rep2


title: K562_DOT1L KO 4sU-DRB-seq 10min rep2

description: TZlane18-2-4sU-DRB35_BKDL202599488-1a-11-AK4544

source_name: K562_DOT1L KO 4sU-DRB-seq 10min


title: 120min_no_auxin_rep3


title: DS12: P4 Nmnat1 fl/fl Retina

description: P4 control retina

source_name: P4 control retina

value: Nmnat1 fl/fl


title: Donor 3 CD137 High

value: High


title: DS13: P4 Nmnat1 fl/fl Retina

description: P4 control retina


title: K562_control 4sU-DRB-seq 10min rep2

description: TZlane18-2-4sU-DRB34_BKDL202599488-1a-10-AK4544

source_name: K562_control 4sU-DRB-seq 10min

value: wild type


title: Donor 1 CD137 High


title: DS16: P4 Nmnat1-/- Retina

description: P4 knockout retina


title: K562_DOT1L KO 4sU-DRB-seq 0min rep2

description: TZlane18-1-4sU-DRB32_BKDL202599487-1a-8-AK4544

source_name: K562_DOT1L KO 4sU-DRB-seq 0min


title: 120min_no_auxin_rep1


title: 60min_with_auxin_rep2


title: Donor 2 CD137 High


title: DS11: P4 Nmnat1 fl/fl Retina

description: P4 control retina


title: K562_ENL KO 4sU-DRB-seq 10min rep1

description: TZlane18-2-4sU-DRB30_BKDL202599488-1a-6-AK4544


title: 60min_with_auxin_rep1


title: DS8: E18.5 Nmnat1 fl/fl Retina

description: E18.5 control retina

source_name: E18.5 control retina

value: embryonic day 18.5 (E18.5)


title: DS9: P4 Nmnat1 fl/fl Retina

description: P4 control retina


title: HT29_CP_3_RNAseq

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

data_processing:
ATAC-seq:
Fastq read adaptor trimming by cutadapt 1.9.1.
Read alignment by Bowtie2 2.2.6.
Fraction of mitochondrial reads by SAMstats and postalignment filtering by SAMtools.
Duplicates filtering by mark-duplicate.
Peak calling by MACS2 macs2 callpeak --nomodel --shift -100 --extsize 200 --broad -t
RNA-seq:
Fastq read adaptor trimming by cutadapt 1.9.1.
Read alignment by Hisat2.
Duplicates were removed by SAMtools.
Count tables were generated by HTSeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bw: bigWig files
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include counts.

growth_protocol: Cells were incubated in a 95% air and 5% CO2 humidified atmosphere at 37°C, and the medium was replaced every 48hrs. In logarithmic phase CRC cells were obtained and resuspended in RPMI medium (Gibco) supplemented with 10% FBS (Hyclone, Logan, UT, USA).

extract_protocol:
Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific) with RNeasy (Qiagen) 300ng/ul.
RNA libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced using an Illumina.

value: Colon Primary

tag: morphology

value: epithelial


title: K562_control 4sU-DRB-seq 0min rep2

city: Shanghai

first: Aiwei

address: 800 Dongchuan Road

description: TZlane18-1-4sU-DRB31_BKDL202599487-1a-7-AK4544

source_name: K562_control 4sU-DRB-seq 0min


title: HT29_CP_2_RNAseq


title: 60min_no_auxin_rep2

value: erythroid


title: 60min_no_auxin_rep1


title: K562_ENL KO 4sU-DRB-seq 0min rep1

description: TZlane18-1-4sU-DRB27_BKDL202599487-1a-3-AK4544


title: DS7: E18.5 Nmnat1 fl/fl Retina

description: E18.5 control retina

tag: age


title: K562_DOT1L KO 4sU-DRB-seq 10min rep1

description: TZlane18-2-4sU-DRB29_BKDL202599488-1a-5-AK4544


title: 30min_with_auxin_rep2

value: auxin


title: 30min_with_auxin_rep1


title: K562_DOT1L KO 4sU-DRB-seq 0min rep1

description: TZlane18-1-4sU-DRB26_BKDL202599487-1a-2-AK4544


title: DS6: E18.5 Nmnat1 fl/fl Retina

description: E18.5 control retina

value: retina


title: HT29_LM_3_RNAseq

value: Liver Metastases


title: HT29_LM_2_RNAseq


title: DS10: P4 Nmnat1 fl/fl Retina

description: P4 control retina

value: postnatal day 4 (P4)


title: 30min_no_auxin_rep2

value: no auxin


title: K562_control 4sU-DRB-seq 10min rep1

description: TZlane18-2-4sU-DRB28_BKDL202599488-1a-4-AK4544


title: HT29_LM_1_RNAseq


title: DS5: E18.5 Nmnat1 fl/fl Retina

description: E18.5 control retina


title: K562_control 4sU-DRB-seq 0min rep1

description: TZlane18-1-4sU-DRB25_BKDL202599487-1a-1-AK4544


title: DS3: E18.5 Nmnat1-/- Retina

description: E18.5 knockout retina

source_name: E18.5 knockout retina


title: DS4: E18.5 Nmnat1-/- Retina

description: E18.5 knockout retina


title: HT29_CP_4

extract_protocol:
50,000 (viability >90%) cells were pelleted at 500 RCF at 4°C for 5 min. Cell pellet was resuspended in cold ATAC-Resuspension Buffer (RSB) (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and incubated on ice. RSB was washed out with cold ATAC-RSB (containing 0.1% Tween-20 but NO NP40 or digitonin). Nuclei were pelleted at 500 RCF for 10 min at 4°C. Cell pellet was resuspended in 50 ul of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O). Reaction was incubated 37°C for 30 minutes in a thermomixer with 1000 RPM mixing.
The tagmented nuclei was sequenced using an Illumina.


title: 0h_with_auxin_rep2


title: K562_ENL KO ATAC-seq rep2

description: JZlane3-JZAlib24_BKDL202586431-1A-N704-AK6925

source_name: K562_ENL KO ATAC-seq

extract_protocol:
ATAC-seq experiments were performed by following a published protocol(Corces, M.R. et al.). Briefly, 50,000 cells were used for each experiment. After nuclei preparation, tagmentation and termination, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.


title: DS1: E18.5 Nmnat1-/- Retina

description: E18.5 knockout retina


title: K562_ENL KO ATAC-seq rep1


title: 0h_no_auxin_rep2


title: HT29_CP_1


title: HT29_CP_3


title: DS2: E18.5 Nmnat1-/- Retina

description: E18.5 knockout retina


title: K562_DOT1L KO ATAC-seq rep2

description: JZlane3-JZAlib26_BKDL202586431-1A-N706-AK6925

source_name: K562_DOT1L KO ATAC-seq


title: 0h_no_auxin_rep1


title: HT29_CP_1_RNAseq


title: K562_DOT1L KO ATAC-seq rep1


title: HT29_LM_4


title: 30min_no_auxin_rep1


title: WT_IL10_S9

city: Zürich

first: Miquel

last: Anglada Girotto

address: Cäsar-Ritz-Strasse, 5/560

country: Switzerland

institute: Functional Genomics Center Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the gene annotation as provided by GENCODE M23 release.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: bone marrow-derived eosinophils

growth_protocol: bone marrow stem cells from donor mice were flushed from the femur and the tibia and were resuspended in RPMI-1640 medium upon red blood cell lysis. Cells were seeded at a density of 106 cells/ml in RPMI-1640 medium supplemented with 20% heat inactivated FBS, 25mM HEPES, 100 U ml−1 penicillin/streptomycin, 2 mM glutamine, 1× NEAA and 1mM sodium pyruvate, and cultured at 37°C. BM Eos were differentiated with 100 ng/mL mouse stem-cell factor (SCF; PeproTech) and 100 ng/mL mouse FLT3-Ligand (FLT3-L; PeproTech) from day 0 to day 4, followed by differentiation with 10 ng/mL mouse interleukin-5 (IL-5; PeproTech) only from day 4 onwards, as described (Dyer et al., 2008).

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) including an on-column DNA digestion step. Total RNA was submitted to the Functional Genomics Center Zurich.
TruSeq stranded mRNA library preparation (Illumina)

treatment_protocol: At day 13, eosinophils were purified using the Dead Cell Removal Kit (Miltenyi Biotech), seeded at a density of 1x106 cells/well in RPMI-1640 medium supplemented with 10% heat inactivated FBS, 100 U ml−1 penicillin/streptomycin and recombinant IL-5 (10ng/ml). Cell triplicates were stimulated overnight with 20ng/ml recombinant GM-CSF at 37°C or left untreated.

value: WT

value: recombinant mouse IL-10


title: WT_IL10_S12


title: K562_control ATAC-seq rep2

description: JZlane3-JZAlib21_BKDL202586431-1A-N701-AK6925

source_name: K562_control ATAC-seq


title: 0h_with_auxin_rep1


title: HT29_LM_3


title: K562_control ATAC-seq rep1


title: HT29_LM_2


title: WT_GM_S3

value: recombinant mouse GM-CSF


title: WT_IL10_S11


title: K562_DOT1L KO PCAF CUT&Tag

description: JZlane4-CTlib10_BKDL202603094-1a-A5-AK6925

data_processing:
library strategy: CUT&Tag
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
For ChIP-seq, ATAC-seq, PRO-seq, CUT&Tag and 4sUDRB-seq, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM. For RNA-seq, read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq, ChIP-seq, ATAC-seq, PRO-seq and CUT&Tag read mapping, hg19 for 4sUDRB-seq.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for ChIP-seq, PRO-seq, CUT&Tag and 4sUDRB-seq or normalized insertion count (CPM, in 50-bp bins) for ATAC-seq.

source_name: K562_DOT1L KO PCAF CUT&Tag

extract_protocol:
CUT&Tag experiments were performed as previously described with minor modifications(Kaya-Okur, H.S. et al. ). Briefly, 100,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.

tag: chip antibody

value: PCAF


title: HT29_LM_1


title: Input-Noc2h

data_processing:
Sequencing reads were mapped to mm9 using Bowtie2 (v2.2.9) with default parameters. Aligments with MAPQ score smaller than 10 were discarded. Duplicates were removed using Samtools (v0.1.19), and in addition, reads on mitochondria, contigs and blacklist regions were removed. BAM files were converted to BED files using Bedtools (v2.27.1). Peaks were called using MACS2 (v2.1.0) over corresponding input controls, with default parameters and 0.01 q-value cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files and peak files for each biologica replicate is provided

source_name: G1E-ER4 cells

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using anti-RNA Polymerase II antibody (Cell Signaling, 14958) as described previously 1. Briefly, following sorting, cells were re-suspended in 1ml pre-cooled Cell Lysis Buffer supplemented with protease inhibitors (PI) and PMSF for 20min on ice. Nuclei were pelleted and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 10min on ice. 0.6ml IP dilution buffer (20mM Tris pH 8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS, fresh supplemented with PI and PMSF) was added followed by sonication (Epishear, Active Motif, 100% amplitude, 30s ON and 30s OFF) for 45min. Samples were pelleted at 15000rpm for 10min at 4℃ to remove cell debris. Supernatant was supplemented with 3.4ml IP dilution buffer fresh supplemented with PI and PMSF, 50g isotope-matched IgG and 50l protein A/G agarose beads (A:G = 1:1, ThermoFisher 15918014 and ThermoFisher 15920010) and rotated at 4℃ for 8h to preclear the chromatin. 200μl, chromatin was set aside as input chromatin. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with anti-RNA PolII antibody (5μg/IP) at 4℃ for overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to RT and eluted in 200μl fresh made Elution Buffer (100mM NaHCO3, 1%SDS). 12μl of 5M NaCl, 2μl RNaseA (10mg/ml) was added to IP and input samples and incubated at 65℃ for 2h, followed by addition of 3μl protease K (20mg/ml) and incubated at 65℃ overnight to reverse crosslinking. Finally, IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with QIAquick PCR purification kit (QIAGEN 28106).
ChIP-seq libraries were constructed using the Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012). Libraries were size selected using the SPRIselect beads (Beckman Coulter, catalog no. B23318) before PCR amplification. Libraries were then quantified through real-time PCR with the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Finally, libraries were pooled and sequenced on a Illumina NextSeq 500 platform using Illumina sequencing reagents.

treatment_protocol: Cells were synchronized to pro-metaphase with 200ng/ml nocodazole for 7-8.5h. For post-mitotic enrichment, cells were released from nocodazole for 0,  60min, 120min and 240min for pro-meta, early-G1, mid-G1 and late-G1 respectively.


title: Input-Noc1h


title: Input-Noc4h


title: WT_GM_S2


title: HT29_CP_2


title: K562_control PCAF CUT&Tag

description: JZlane4-CTlib9_BKDL202603094-1a-AK1971-AK6925

source_name: K562_control PCAF CUT&Tag


title: Rat xiphoid cartilage 2

city: Changchun

first: Baojin

last: Yao

address: 1035 Boshuo Road

institute: Changchun University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
using HISAT2 (v2.0.4) and StringTie (v1.2.1) to mapping reads to genome and to reconstruct transcirpts
using bowtie2 (v2.2.6) and RSEM (v1.2.12) to mapping reads to gene and to calculate gene expression
Functional enrichment analyses including Gene Ontology (GO) and KEGG were performed to identify which DEGs were signifcantly enriched in GO terms or metabolic pathways
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text file includes expression values for each Sample

source_name: xiphoid cartilage

extract_protocol:
Cartilages were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: xiphoid cartilage

value: Sprague-Dawley


title: Rat xiphoid cartilage 1


title: K562_DOT1L KO H2BUb1 ChIP-seq

source_name: K562_DOT1L KO H2BUb1 ChIP-seq

tag: fixation

value: FA


title: WT_GM_S1


title: K562_control H2BUb1 ChIP-seq

source_name: K562_control H2BUb1 ChIP-seq

value: wild type


title: Rat articular cartilage 2

source_name: articular cartilage

value: articular cartilage


title: WT_GM_IL10_S8

value: recombinant mouse IL-10+GM-CSF


title: polii_4h_with_A.rep2

tag: antibody

value: anti-RNA Polymerase II antibody (Cell Signaling, 14958)


title: polii_4h_no_A.rep3

value: erythroid


title: WT_GM_IL10_S5


title: Input-Noc0h


title: K562_DOT1L KO PCAF ChIP-seq

description: TZlane17-TZlib160_BKDL202596503-1a-16-AK4544

source_name: K562_DOT1L KO PCAF ChIP-seq

value: EGS + FA


title: EZH1 KO rep2

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
A custom Danio rerio reference genome containing a GFP transcript was generated using Ensembl Release 101 (ftp://ftp.ensembl.org/pub/release-101/gtf/danio_rerio/) with the mkref command from cellranger v2.1 (10X Genomics)
The raw sequencing files were aligned to the custom reference processed with the Cellranger count pipeline.
Cellranger count matrices for each library were read into R (v3.5) and analyzed with Seurat v3.2. High-quality cells were retained for subsequent analyses based on technical metrics: <5% mitochondrial reads, >1000 UMI counts, and >500 genes detected. A Seurat object of all unfiltered cells across all libraries is provided as a supplementary file.
Genome_build: GRCz11-101
Supplementary_files_format_and_content: Cells by genes count matrices produced from the cellranger pipeline

source_name: kdrl:GFP+ cells 30hpf

extract_protocol:
Pools of fluorescent zebrafish embryos/larvae were dissociated using Liberase TM (Sigma) in a 34C circulating water bath and resuspended in 1X PBS/1mM EDTA. kdrl:GFP+ cells were FACS sorted on a FACSAria II (BD) at the BCH Flow Cytometry Core into 1X PBS containing 2% fetal bovine serum.
Single-cell RNA-seq was performed on the 10X Genomics Chromium platform using the single cell expression 3’ v2 profiling chemistry. Following kdrl:GFP+ FACS, cells from each ezh1 genotype were loaded across two lanes in a 10X Genomics Single Cell 3’ Chip as independent technical replicates and libraries were constructed according to the manufacturer’s protocol. Cells were loaded into 10X lanes at cell concentrations to maintain an estimated doublet rate below 5%. The final libraries were assayed via an Agilent High Sensitivity dsDNA Bioanalyzer, normalized, pooled and shallow sequenced (Illumina MiniSeq), identifying ~11,000 high confidence cell barcodes in total across all libraries. The libraries were subsequently renormalized per the distribution of reads/library from the shallow sequencing run and deep sequenced on a NovaSeq S4 (Illumina) to a depth of ~100,000 reads per cell with cycle configuration 151-8-8-151.

value: kdrl:GFP+ cells


title: Rat articular cartilage 1


title: K562_DOT1L KO TFIIB ChIP-seq rep2

description: TZlane17-TZlib158_BKDL202596503-1a-14-AK4544

source_name: K562_DOT1L KO TFIIB ChIP-seq

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
ChIP-seq libraries: The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: TFIIB


title: K562_control PCAF ChIP-seq

description: TZlane17-TZlib159_BKDL202596503-1a-15-AK4544

source_name: K562_control PCAF ChIP-seq


title: polii_2h_with_A.rep3


title: EZH1 KO rep1


title: polii_4h_no_A.rep2


title: polii_4h_with_A.rep1


title: EZH1 HET rep2


title: K562_control TFIIB ChIP-seq rep2

description: TZlane17-TZlib157_BKDL202596503-1a-13-AK4544

source_name: K562_control TFIIB ChIP-seq


title: polii_2h_with_A.rep2


title: WT_GM_IL10_S7


title: K562_DOT1L KO GTF2A2 ChIP-seq rep2

description: TZlane17-TZlib156_BKDL202596503-1a-12-AK4544

source_name: K562_DOT1L KO GTF2A2 ChIP-seq


title: EZH1 WT rep1


title: EZH1 WT rep2


title: IRF5_GM_S20


title: K562_control TFIIB ChIP-seq rep1


title: WT_ctrl_S16

value: untreated


title: WT_ctrl_S13


title: WT_ctrl_S15


title: polii_2h_no_A.rep3


title: polii_2h_no_A.rep2


title: IRF5_GM_S18


title: K562_DOT1L KO TFIIB ChIP-seq rep1


title: polii_2h_with_A.rep1


title: K562_DOT1L KO GTF2A2 ChIP-seq rep1


title: K562_control GTF2A2 ChIP-seq rep2

description: TZlane17-TZlib155_BKDL202596503-1a-11-AK4544

source_name: K562_control GTF2A2 ChIP-seq


title: K562_control GTF2A2 ChIP-seq rep1


title: EZH1 HET rep1


title: IRF5_GM_S19


title: polii_1h_with_A.rep2


title: polii_2h_no_A.rep1


title: K562_DOT1L KO TBP ChIP-seq rep2

description: TZlane17-TZlib154_BKDL202596503-1a-10-AK4544

source_name: K562_DOT1L KO TBP ChIP-seq

value: TBP


title: polii_1h_no_A.rep2


title: IRF5_ctrl_S21

source_name: bone marrow-derived eosinophils


title: IRF5_ctrl_S23


title: polii_1h_with_A.rep1


title: Csf2r_GM_S27


title: Csf2r_GM_S26


title: K562_DOT1L KO TBP ChIP-seq rep1


title: polii_1h_no_A.rep1


title: polii_0h_with_A.rep2


title: IRF5_ctrl_S24


title: K562_control TBP ChIP-seq rep2

description: TZlane17-TZlib153_BKDL202596503-1a-9-AK4544

source_name: K562_control TBP ChIP-seq


title: Csf2r_GM_S25


title: scOPC 10ng/ml PDGF-AA n3

type: RNA

city: Münster

first: Julia

last: Ghelman

address: Pottkamp 2

department: Institute of Neuropathology

institute: University Hospital Münster

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using genome studio V2011.1

label: biotin

source_name: mouse spinal cord

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using Rneasy Mini Kit (#74104, Qiagen)  in accordance with the prescribed protocol provided with the kit. Quality control was performed with a nanodrop spectrometer.

value: spinal cord

value: primary murine OPC


title: K562_control TBP ChIP-seq rep1


title: Well A12 Sample

city: San Antonio

first: Georgios

last: Kotsakis

address: 7703 Floyd Curl Dr.

department: Periodontics

institute: UT Health San Antonio

description: SST-RMA expression value derived from Transcriptome Analysis Console; exon analysis

hyb_protocol: Sample reads were loaded in the Transcriptome Analysis Console (TAC, Affymetrix) using the Summarization Signal Space Transformation - Robust Multichip Analysis (SST-RMA) algorithm.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Annotated reads of microarray data were loaded in the Transcriptome Analysis Console (TAC, Affymetrix) using the Summarization Signal Space Transformation - Robust Multichip Analysis (SST-RMA) algorithm. Samples were examined for quality control using Target Prep Controls. Hybridization Controls were used to ensure proper hybridization of tested samples. Processed microarray data was then further analyzed in TAC to determine any condition-specific changes in expression of select genes. The samples were analyzed by expression levels (determined by probe intensity) of all genes present in the samples.

source_name: Peri-implantitis patient

label_protocol: Used probes tiled through the most constitutively share exons across all known transcripts for a given gene.

growth_protocol: Healthy samples were obtained from procedures such as tissue excision for contour site development around healed implant provisional restorations as long as they included all components of the peri-implant soft tissue barrier. Diseased samples were obtained during peri-implantitis surgical therapy with care to also obtain the entire peri-implant soft tissue barrier. Immediately after harvesting the samples were trimmed to 2 x 3 mm dimensions and stored in RNAlater solution (Invitrogen, USA) and stored in -20°C in the Biospecimen repository of the Translational Periodontal Research Lab, UT Health San Antonio.

extract_protocol: gDNA was eliminated and RNA was extracted from samples using a RNeasy Plus mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instruction, treated using Proteinase K digestion and purified via a spin column using silica gel particles.

value: Peri-implant soft tissue barrier


title: Csf2r_ctrl_S30


title: DOT1L KO K562 RNA-seq rep3

description:
TZlane1-R15_TKR181201339-15
processed data file: K562.RNA-seq.fragment_count.txt

source_name: DOT1L KO K562 RNA-seq

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.


title: scOPC 10ng/ml PDGF-AA n2

description: replicate 2


title: scOPC 10ng/ml PDGF-AA n1

description: replicate 1


title: polii_0h_with_A.rep1

source_name: G1E-ER4 cells


title: cOPC 10ng/ml PDGF-AA n2

description: replicate 2

source_name: mouse cerebrum

value: cerebrum


title: cOPC 10ng/ml PDGF-AA n3

description: replicate 3


title: polii_0h_no_A.rep2


title: cOPC 10ng/ml PDGF-AA n1

description: replicate 1


title: Csf2r_ctrl_S29


title: DOT1L KO K562 RNA-seq rep1

description:
TZlane1-R05_TKR181201339-5
processed data file: K562.RNA-seq.fragment_count.txt


title: Csf2r_ctrl_S28


title: Well F04 Sample


title: CD45+ Advanced Lesions

data_processing:
cellranger V3.0.2 mkfastq
cellranger V3.0.2 count
reads are mapped to mm10
UMI counts are summarized are gene expression levels
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of normalized gene counts for tumor and CD45 Samples

source_name: Aggressive lesions

extract_protocol:
Single cells in suspension were evaluated for sample concentration and viability prior to 3' capture and library preparation
3’ capture and library preparation performed per manufacturer's intructions (5000 cells/sample, Chromium Single Cell 3' v2) using the Chromium Controller (10X Genomics) for sequencing (Illumina NextSeq500)

value: AL

value: FVB

value: Mammary gland

tag: pool


title: CD45+ Early Lesions

source_name: Indolent lesions

value: EL


title: GFP+ Advanced Lesions

value: GFP+


title: control K562 RNA-seq rep3

description:
TZlane1-R11_TKR181201339-11
processed data file: K562.RNA-seq.fragment_count.txt

source_name: control K562 RNA-seq

tag: cell line

value: wild type


title: control K562 RNA-seq rep1

description:
TZlane1-R01_TKR181201339-1
processed data file: K562.RNA-seq.fragment_count.txt


title: GFP+ Early Lesions