title: pLN WT stromal cell

data_processing:
Data were demultiplexed using Cell Ranger software (version 6.0.0) based on 8 bp 10X sample indexes and paired-end FASTQ files generated. The cell barcodes and transcript UMIs were processed as previously described (Zheng et al., 2017). Subsequently, read 2, which contains the transcript insert sequence, was aligned to mouse UCSC mm10 reference genome using STAR aligner with default parameters (Dobin and Gingeras, 2015). The alignment results were used to quantify the expression level of mouse genes and generation of gene-barcode matrix, which were further processed with Seurat (version 4.0.1). All cells received an identifier which was used as common meta-data throughout the analysis including differentiation trajectories and dynamic gene regulatory networks (see below).
All cells with less than 750 or more than 4,500 detected genes per cell were filtered out. Moreover, cells with more than 6 % reads mapping to mitochondrial genes were removed yielding 18.048 cells passing QC. After filtering, data were default normalized and the 2,000 most variable genes identified. The expression levels of these genes were scaled before performing PCA. The following covariates were regressed out: number of UMIs, number of genes , percent of mitochondrial reads and percent of ribosomal reads. t SNE and UMAP dimensionality reduction was performed using the first 30 dimensions of the PCA and resolution set to 0.4.
Only non-endothelial SC clusters were used for the further analysis amounting to 11.040 cells which were re-embedded as described above (dimsuse = 13, resolution = 0.9).
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger processed fastq output yielding RMCs and gene annotation

growth_protocol: LNs of IRF3KO and WT mice were harvested for stromal cell isolation.

extract_protocol:
Single CD45‑CD24‑ cells were sorted by FACS ARIA III (BD) and collected in PBS containing 0.04 % w/v BSA at a density of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs)
Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics, Cat. #120236). The detailed protocol was provided by 10xGenomics. SimpliAmp Thermal Cycler was used for amplification and incubation steps (Applied Biosystems). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality checked using Fragmentanalyzer with High Sensitivity DNA kit (Agilent).
Sequencing was performed in asynchronous paired-end mode (28-10-10-91 cycles) using a NovaSeq6000 sequencer (Illumina) to attain approximately 80,000 reads per single cell.

value: pLN

tag: sorted cell

value: ex vivo isolated cells CD24-CD45-

tag: genotype/variation

value: WT


title: Morulae, 6% EtOH sire, M216

status: Public on Oct 07 2022

type: SRA

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Fast QC/Multi QC
Trim universal Illumina adapters
Fast QC/Multi QC
Mapping genome
counts file, DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: featureCounts, tabular file

molecule: total RNA

organism: Mus musculus

source_name: embryo

growth_protocol: Nakagata IVF protocol with CARD media

extract_protocol:
Quick Biololgy Inc. RNA isolation protocol
Quick Biololgy Inc. library construction protocol
Illumina sequencing of 15Mpair reads

tag: tissue

value: embryo

tag: strain

tag: developmental stage

value: Morula stage embryos

tag: treatment

value: 6% EtOH


title: Neanderthal_updated_pool2B_input_rep2

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

data_processing:
Alignment of MaPSy input/output paired-end reads to either input/output custom reference genomes with STAR (2.7.9a) with parameters (--runThreadN 8 --genomeDir [DIR] --readFilesIn [FASTQ_R1] [FASTQ_R2] --readFilesCommand zcat -c --outSAMtype BAM Unsorted --outFileNamePrefix [PREFIX] --alignIntronMax 1 --outFilterMismatchNmax 5 --alignEndsType EndToEnd --outFilterMultimapNmax 1)
Get unique reads with samtools view (1.7) with parameters (-@ 16 -hbq 10 [BAM_UNSORTED] >| [BAM_UNIQUE]])
Sort reads with samtools sort (1.7) with parameters (-@ 16 -o [BAM_SORTED] [BAM_UNSORTED])
Index reads with samtools index (1.7) with parameters (-@ 16 -b [BAM_SORTED])
Count reads with samtools idxstats (1.7) with parameters ([BAM_SORTED] >| [IDXSTATS])
Join read counts by seq id to reference table
genome build: Custom minigene reference genomes based on hg19 (neanderthal_updated_input.fasta.gz for input libraries, neanderthal_updated_output.fasta.gz for output libraries)
processed data files format and content: txt - samtools idxstats read counts

organism: Homo sapiens

source_name: HEK 293T cells

extract_protocol:
Forty-eight hours after transfection, RNA was extracted using TRIzol (ThermoFisher) and DNase treated (Invitrogen). Random 9-mers were used to generate cDNA with SuperScript IV Reverse Transcriptase (Invitrogen) followed by 25 cycles of PCR amplification (GoTaq, Promega), resulting in output libraries of spliced exon inclusion and exon skipped species.
Primers were designed to amplify the region of the input and output library sequences immediately surrounding the variable region of interest. For the input libraries, the primers matched AD81 and ACTN1 intronic regions, and for the output libraries, the primers matched exonic regions of AD81 and ACTN1. Replicates were identified using NEXTflex DNA Barcodes (PerkinElmer).

treatment_protocol: The input library was transfected into human embryonic kidney HEK 293T cells obtained from the American Type Culture Collection (ATCC CRL-316) in three cell culture replicates using Lipofectamine 3000 (Invitrogen) in a 6-well plate.

tag: cell line

value: HEK 293T cells

tag: genotype

value: wildtype


title: INPUT_Lbx1-FS

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

library_source: genomic

data_processing:
mapping (bowtie v2.26)
filtered MAPQ ≥10
remove duplicates (SAMTOOLS v1.6 rmdup)
peak-calling (Q (Hansen et al. 2015), default parameters)
Assembly: mm9
Supplementary files format and content: peaks for Lbx1 wt or FS proteins in narrowpeak format

molecule: genomic DNA

source_name: P19 cells

growth_protocol: P19 murine embryonic teracarcinoma cells were obtained from ATTC (CRL-1825TM) and differentiated into neurons using 1 μM retinoic acid (Sigma) as follows: P19 cell suspension cultures were incubated for 4 days in neuronal differentiation media (94%DMEM, 5% FBS, 1% Pep/Strep and 1 μM retinoic acid) to allow for the formation of embryoid bodies. The embryoid bodies were treated with trypsin on the fourth day of differentiation and plated as a monolayer on laminin (10mg/ml) coated dishes for terminal neuronal differentiation. Cytosine β-D-arabinoside (AraC, 12μM; Sigma) was added to the differentiation media on the sixth day to eliminate proliferative cells and enrich for postmitotic neurons. Neurons were collected for chromatin and RNA extraction on the seventh day of differentiation.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody. We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate with anti-FLAG M2 (SIGMA) antibody. ChIP-seq was then performed as in Ibrahim et al. 2013.
ChIP-seq Libraries were prepared using the TruSeq protocol

value: P19 cells

tag: cell type

value: embryonic carcinoma cell line (RA-induced)

tag: chip antibody

value: Lbx1-fs-FLAG transduced

value: RA induced neural differentiation


title: pLN IRF3KO stromal cell

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

source_name: speripheral skin-draining lymph node

treatment_protocol: For stromal cell isolation, LNs were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase D (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by autoMACS separation after direct magnetic labeling of CD45+ cells using CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort bulk CD45-CD24- non-hematopoietic cells (Aria III, 70 μm nozzle) for scRNA‑seq.


title: Neanderthal_updated_pool2B_input_rep1


title: Neanderthal_updated_pool2B_input_rep3


title: mLN WT stromal cell

source_name: mesenteric lymph node

value: mLN


title: VCaP_CRPC_rep1

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

description: polyA RNA

data_processing:
The reads were aligned to the GRCh37 (hg19) human genome (Ensembl release 75), provided as reference fasta file "genome.fa", using STAR (v2.7.5)
Read alignments were merged and disambiguated, and a single BAM file output per library or sample was used. BAM files were then additionally filtered to remove reads with a mapping quality (MAPQ) less than 13, and all ribosomal and mitochondrial RNA reads.
Alignments were assembled using Cufflinks (v2.2.1) using the –g parameter to construct a genome annotation file against the reference gene model (Ensembl release 75) and to identify novel transcripts
Raw read counts were obtained by mapping reads at the gene level using the Cufflinks assembled transcript annotation file with the featureCounts tool from the SubRead package (version 2.0.0) using the exon counting mode
EdgeR R-package (v3.12.1) was then used to normalize the data, calculate transcript abundance (as counts per million reads (CPM)) and perform statistical analysis
Genome_build: hg19
Supplementary_files_format_and_content: Excel table (.xlsx) containing CPM values for each gene and sample, and EdgeR normalization output.

molecule: polyA RNA

source_name: Prostate cancer cell line

growth_protocol: VCaP, VCaP-CRPC and VCaP-ER (Enzalutamide-resistant cell line) were cultivated in DMEM F12 10% FBS with 1mM sodium pyruvate. ENZ-resistant cell lines were maintained in 10 µM ENZ (enzalutamide).

extract_protocol:
Total RNA: VCaP, VCaP-CRPC and VCaP-ER were flash frozen on dry ice, and RNA was harvested using Trizol reagent according to the manufacturer's instructions.
Polysomes RNA: VCaP-CRPC and VCaP-ER were incubated in a cytoplasmic lysis buffer and nuclei were excluded by centrifugation. Cytoplasmic RNA was then loaded on a sucrose gradient and ultracentrifuged to allow for sorting according to the number of associated ribosomes. RNA fractions corresponding to 3 ribosomes or more (Heavy polysomes) were pooled and harvested using Phenol/chloroform extraction.
Paired-ends RNA libraries were constructed from 0.2 ug of RNA in accordance with the TruSeq stranded mRNA kit protocol (Illumina; # 20020594) and TruSeq RNA Single Indexes Set A and B (Illumina, # 20020492 and 20020493).

treatment_protocol: VCaP-ER were cultivated with ENZ (10uM)

tag: media

value: DMEM F12 media + 10% FBS


title: INPUT_Lbx1-WT

value: Lbx1-wt-FLAG transduced


title: Morulae, 6% EtOH sire, M2110


title: Lbx1-FS_ChIPseq_Rep2

value: anit-FLAG M2 (Sigma)


title: Neanderthal_updated_pool2A_output_rep3


title: mLN IRF3KO stromal cell


title: Neanderthal_updated_pool2A_output_rep2


title: Lbx1-FS_ChIPseq_Rep1


title: HiMyc

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
The library purity and size was validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies)
The library quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen
The libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to a depth of ~100k reads per cell. Raw sequencing data were processed using the 10x Genomics’ Cell Ranger pipeline (version 3.1.0) to generate FASTQ files and were aligned to the mm10 genome with added hARtg and mGFP sequences to generate gene expression counts
Genome_build: mm10 reference genome with added hMYCTg sequence
Supplementary_files_format_and_content: Txt file with counts for each cell corresponding to each gene

source_name: Prostatic intraepithelial neoplasia

extract_protocol:
Prostate tissues were trimmed and dissociated to single cells using collagenase and TrypLE (Gibco)
The library was prepared using 10x Genomics Chromium Single Cell 3' Solution with v2 chemistry following manufacturer protocols (10x Genomics)

value: HiMyc

value: Prostate

tag: normal/modified

value: Prostatic intraepithelial neoplasia


title: HiMyc-ARKO

value: HiMyc-ARKO


title: SRI_37618_4h_2

city: Birmingham

first: Anupam

last: Agarwal

state: AL

address: 703 19th St S

institute: University of Alabama at Birmingham

data_processing:
STAR alignment
Assembly: hg18
Supplementary files format and content: counts

extract_protocol: RNA was isolated according to manufacturer's instructions with Trizol

value: SRI-37618_4 hours

value: kidney

tag: time

value: 4 hours


title: Neanderthal_updated_pool2A_input_rep3

value: HEK 293T cells


title: Lbx1-WT_ChIPseq_Rep2


title: Neanderthal_updated_pool2A_output_rep1

value: wildtype


title: mLN_day56_2

data_processing:
Data were demultiplexed using Cell Ranger software (version 2.0.0) based on 8 bp 10X sample indexes and paired-end FASTQ files generated. The cell barcodes and transcript UMIs were processed as previously described (Zheng et al., 2017). Subsequently, read 2, which contains the transcript insert sequence, was aligned to mouse UCSC mm10 reference genome using STAR aligner with default parameters (Dobin and Gingeras, 2015). The alignment results were used to quantify the expression level of mouse genes and generation of gene-barcode matrix, which were further processed with Seurat (version 2.3.3). All cells received an identifier which was used as common meta-data throughout the analysis including differentiation trajectories and dynamic gene regulatory networks (see below).
All cells with less than 1,000 or more than 4,600 detected genes per cell were filtered out. Moreover, cells with more than 4.5 % read mapping to mitochondrial genes were removed yielding 15,659 cells passing QC. All cells across all developmental stages were subjected to canonical correlation analysis and regressed against the variables, number of UMIs, percent of mitochondrial reads, percent of ribosomal reads and scores for the proliferation S.Score and G2M.Score computed with CellCycleScoring(). t‑SNE dimensionality reduction was performed using the first 12 dimensions of the CCA and resolution set to 1.1. Only clusters (non-endothelial MC) with expression for Pecam < 1 were used for the further analysis amounting to 9,323 cells which were re-embedded as described above (resolution = 1.0). The perivascular mesenchymal cell (PvMC) cluster and clusters classified as adjacent cells were excluded and the remainder cells, numbering 5,658 mesenchymal cells were re-embedded as described above (resolution = 1.0). For subsetting the Prog. subset, 259 cells were re-embedded as described above (resolution = 0.5, dimsuse = 10). Gene ontology (GO) analysis was performed for differentially upregulated genes per cluster using TopGO (Alexa and Rahnenfuhrer, 2010).
Differentiation trajectories were analyzed using Monocle (version 2.18.0) (Trapnell et al., 2014). Unsupervised ordering was performed on the 5,658 mesenchymal cells using Monocle2’s DDRTree algorithm based on genes with a mean expression >0.1. The trajectory containing all mesenchymal cells, was split based on marker gene expression Vcam1 and Cd34 and the annotation of cells belonging to the ProgCxcl13+ or ProgCD34+ subset to distinct terminal branches. Two separate unsupervised orderings were performed as described above and are referred to as CD34+SC or FRC trajectory.
Gene regulatory networks were inferred with the dynGENIE3 algorithm, where the input expression values were based on ordering the genes according to physiological age per branch for each of the two trajectories being CD34+SC or FRC (Huynh-Thu and Geurts, 2018). The list of candidate TFs was derived from TFBS from ATAC-seq profiling or DMRs within the proximity of TFs. For network visualization with Cytoscape (version 3.6.0)(Shannon et al., 2003), only the top 500 links ranked by weight assigned by dynGENIE3 were used. Node centrality and betweenness were calculated with the degree and betweenness functions from the igraph (version 1.2.2) package.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger processed fastq output yielding RMCs and gene annotation

source_name: gut-draining mesenteric lymph node

growth_protocol: Mice were housed under specific pathogen free conditions.

extract_protocol:
Single CD45‑CD24‑ cells were sorted by FACS ARIA III (BD) and collected in PBS containing 0.04 % w/v BSA at a density of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs)
Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics, Cat. #120236). The detailed protocol was provided by 10xGenomics. SimpliAmp Thermal Cycler was used for amplification and incubation steps (Applied Biosystems). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).
Sequencing was performed in paired-end mode (2 x 75 cycles) using NextSeq 500 sequencer (Illumina) to attain approximately 75,000 +/- 25,000 reads per single cell.

treatment_protocol: For stromal cell isolation, mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco, Cat. #72400021) containing 0.2 mg/ml collagenase P (Roche, Cat. #11213865001), 0.15 U/ml dispase (Roche, Cat. #4942078001) and 0.2 mg/ml DNase I (Roche, Cat. #4536282001) as described previously (Malhotra et al., 2012). After digestion, cells were kept at 4 °C in PBS containing 0.2 % BSA (Merck, Cat. #A2058) and 5 mM EDTA (Roth, Cat. #8043.1). CD45- cells were enriched by autoMACS separation after magnetic labeling of CD45+ cells using anti‑CD45‑APC followed by anti‑APC microbeads (Miltenyi Biotec, Cat. #130-090-855) or anti-CD45 Nanobeads (Biolegend, Cat. #480028). Subsequently, the CD45- fraction was stained using fluorochrome-coupled antibodies and used to sort CD45‑CD24‑CD31‑gp38+ FSCs (Aria II, 100 μm nozzle) and bulk CD45‑CD24‑ non-hematopoietic cells (Aria III, 70 μm nozzle) for RNA‑seq/ATAC‑seq and scRNA‑seq, respectively.

value: BALB/c

value: ex vivo isolated cells CD24-CD45-

value: gut-draining mesenteric lymph node

tag: housing

value: specific pathogen free


title: Neanderthal_updated_pool2A_input_rep2


title: Lbx1-WT_ChIPseq_Rep1

value: P19 cells

value: embryonic carcinoma cell line (RA-induced)

value: RA induced neural differentiation


title: Neanderthal_updated_pool2A_input_rep1


title: ATAC_pLNSPF3

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR (version 2.5.3a)(Dobin and Gingeras, 2015) with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 (assembly: GRCm38). Duplicates were removed using picard MarkDuplicates (https://broadinstitute.github.io/picard/). Peaks were called on de-duplicated bam-files using macs2 callpeak with the parameters --broad -g mm -q 0.05 for each replicate (Zhang et al., 2008).
Heatmaps of fragment distribution around the TSS were computed using computeMatrix with the reference-point -a 3000 -b 3000 and plotted using plotHeatmap. The regions identified via macs2 were merged across all replicates into one set of regions, by combining peaks over-lapping with at least one base-pair and removing peaks that overlapped with blacklisted regions (Yue et al., 2014).
Differential accessibility of raw ATAC-seq counts for each region/peak across all replicates of all samples were normalized across replicates with size factors computed with DESeq2 (version 1.22) (Love et al., 2014). Pairwise comparisons were performed with DESeq2 and differentially accessible regions (DARs) were called with an FDR adjusted p-value of less than 0.05 and a fold change (FC) of at least 2. Genomic features were identified via getAnnotation from ChIPpeakANNO (Zhu et al., 2010). The cumulative FC of all DARs for one respective gene is represented as the mean of all the FC of all respective DARs. Transcription factor motif enrichment was computed using homer (version 4.9)(Heinz et al., 2010). Graphics were generated in R using pheatmap and ggplot2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig-files for track visulaization of peaks in Genome-browsers (e.g. IGV, UCSC)

source_name: skin-draining mesenteric lymph node

growth_protocol: Mice were housed either under germ-free or specific pathogen free conditions.

extract_protocol:
For stromal cell isolation, skin-draining pLNs (inguinal and axillary or popliteal) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco, Cat. #72400021) containing 0.2 mg/ml collagenase P (Roche, Cat. #11213865001), 0.15 U/ml dispase (Roche, Cat. #4942078001) and 0.2 mg/ml DNase I (Roche, Cat. #4536282001) as described previously (Malhotra et al., 2012). After digestion, cells were kept at 4 °C in PBS containing 0.2 % BSA (Merck, Cat. #A2058) and 5 mM EDTA (Roth, Cat. #8043.1). CD45- cells were enriched by autoMACS separation after magnetic labeling of CD45+ cells using anti‑CD45‑APC followed by anti‑APC microbeads (Miltenyi Biotec, Cat. #130-090-855) or anti-CD45 Nanobeads (Biolegend, Cat. #480028). Subsequently, the CD45- fraction was stained using fluorochrome-coupled antibodies and used to sort CD45‑CD24‑CD31‑gp38+ FSCs (Aria II, 100 μm nozzle) and bulk CD45‑CD24‑ non-hematopoietic cells (Aria III, 70 μm nozzle) for RNA‑seq/ATAC‑seq and scRNA‑seq, respectively.
CD45‑CD24‑CD31‑gp38+ cells FACS isolated into PBS, containing 0.2% BSA. Cells were washed once with PBS before DNA transposition was performed with the Nextera DNA Library Prep Kit (Illumina, Cat. #FC-121-1031). Per sample, 25 µl TD, 2.5 µl TDE1 and 22 µl nuclease free water were combined and placed at 37°C for 3 min before 0.5 µl of 1% Digitonin (Promega, Cat. #G9441) was added to the master mix. Samples were resuspended in the transposition reaction mix and incubated for 30 min at 37°C at 300 rpm. After transposition, DNA was purified with the MinElute PCR Purification kit (Qiagen, Cat. #28006) according to manufacturer’s instructions and eluted in 50 µl nuclease free water. Transposed DNA fragments were pre-amplified using 10 μl transposed DNA, 10 μl nuclease free water, 2.5 μl 25 μM custom Nextera PCR primer 1, 2.5 μl 25 μM custom Nextera PCR primer 2, 25 μl NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs, Cat. #M0541L) per reaction and amplified via a 6-cycle PCR program (1 cycle of 72°C for 5 min, 98°C for 30 s; 5 cycles of 98°C for 10 s, 63°C for 30 s, 72°C for 1 min). The forward primer was identical for all samples 5′-AATGATACG GCGACCACCGA GATCTACACTC GTCGGCAGCGT CAGATGTG-3′, whereas the reverse primer contained distinct barcodes (example underlined) used for demultiplexing 5′-CAAGCAGAAGA CGGCATACGAG ATTCGCCTTA GTCTCGTGGGC TCGGAGATGT‑3′ (Buenrostro et al., 2015). The appropriate amount of further amplification cycles was determined by qPCR using 5 µl of the pre-amplified product. Final amplification was carried out with 45 μl of previously PCR amplified DNA, 39.7 μl nuclease free water, 2.25 μl 25 μM customized Nextera PCR primer 1, 2.25 μl 25 μM customized Nextera PCR Primer 2, 0.81 μl 100x SYBR Green I and 45 μl NEBNext High-Fidelity 2x PCR Master Mix with the PCR program of 1 cycle of 98°C for 30 s; 8-10 cycles (depending on qPCR results) of 98°C for 10 s, 63°C for 30 s, 72°C for 1 min. PCR purification was carried out using the MinElute PCR Purification kit. Finally, size selection was performed with SPRIselect beads (Beckmann-Coulter, Cat. #B23317) with 1.2x for left-side and 0.55x for right-side selection according to manufacturer’s instructions. DNA quality, content and fragment size was assessed with Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements.
Sequencing of libraries was carried out at the sequencing facility on Illumina using 50 bp paired-end reads

treatment_protocol: Cells isolated from lymph nodes of wild-type specific pathogen free or germ-free housed BALB/c mice.

value: ex vivo isolated cells non-endothelial stromal cells

value: skin-draining mesenteric lymph node


title: Mll3-null CD44+CD104-/low, biological replicate 3 [M 3]

city: Bronx

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

data_processing:
Base calling were conducted by illumina HiSeq Control Software.
After investigating the quality of raw data by FASTQC, we used bbduk.sh from BBMap to trim the raw reads (adapter timming and quality trimming with the parameters k=21 ktrim=r mink=8 qtrim=rl trimq=10 minlength=28).
Quasi-alignment of the reads was performed using salmon 1.3.0 to perform transcript-level quantification using GRCh38/hg38 (GENCODE v.34 ) in mapping-based mode.
The salmon index was built using the whole genome as decoy.
The data was then imported in to R using the Bioconductor package tximeta, to generate a count matrix summarized by gene.
Differential expression was performed using this count matrix with ExpressSurv, using DESeq2 for differential expression analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mll3-null CD44+CD104-/low

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10%FBS.

extract_protocol:
Cells were sorted based on the level of CD104. RNA was extracted using Quick-RNA microprep kit (Cat# R1050).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Foskolin treament, cells were treated with 10 μM foskolin for 14 days. Medium was freshed every 2 days.

value: Triple-negative breast cancer line

tag: tissue source

value: Beast

value: Forskolin 10 μM for 14 days


title: ATAC_pLNSPF2


title: Mll3-null CD44+CD104-/low, biological replicate 2 [M 2]


title: ATAC_pLNSPF1


title: ATAC_pLNGF3

value: germ-free


title: ATAC_pLNGF2


title: Mll3-null CD44+CD104-/low, biological replicate 1 [M 1]


title: Mll3-null CD44+CD104high, biological replicate 3 [E/M 3]

source_name: Mll3-null CD44+CD104high


title: Mll3-null CD44+CD104high, biological replicate 2 [E/M 2]


title: ATAC_pLNGF1


title: ATAC_mLNSPF3


title: Mll3-null CD44+CD104high, biological replicate 1 [E/M 1]


title: ATAC_mLNSPF1


title: ATAC_mLNSPF2


title: ATAC_mLNGF3


title: ATAC_mLNGF2


title: ND-75 knockdown heads 3

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

country: United Kingdom

institute: King's College London

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Paired-end clean reads were mapped to the Drosophila_melanogaster ensemble 102 genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene, then RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions was performed using DESeq2 R package. P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. GO enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.
Assembly: Drosophila_melanogaster ensemble 102 genome
Supplementary files format and content: Excel files include RPKM values for each sample

organism: Drosophila melanogaster

source_name: Adult head, 2 days old

extract_protocol:
20 snap frozen fly heads (10 male and 10 female, 2 days old) were used for each replicate and placed into 100 µL of lysis buffer + β-mercaptoethanol from the Absolutely RNA Microprep kit (Agilent Technologies). Each genotype was prepared in quadruplicate. RNA was extracted from using the Absolutely RNA Microprep kit according to the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: Adult head, 2 days old

value: nSybGal4/ND-75 RNAi


title: ND-75 knockdown heads 2


title: ND-75 knockdown heads 4


title: ND-75 knockdown heads 1


title: ATAC_mLNGF1


title: Control heads replicate 4


title: E1_GFP_47

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were aligned to the mouse genome using HISAT2. The average mapping rates for neuron and oligodendrocytes studies were 84% and 89%, respectively.
Quality control was performed using FastQC and principal component analysis was used to identify outliers.
Normalization and differential expression analysis were performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files

source_name: Brain

extract_protocol:
Total RNA was extracted using the total RNA Purification Kit (Norgen Biotek) including on-column DNase treatment. All samples were tested for concentration and purity using a NanoDrop (Thermo Fisher). Samples used for RNA-seq were analyzed using a bioanalyzer RNA Nano chips (Agilent) for integrity.
RNA libraries were prepared from female mouse mPFC infected with Neuro-FEDORA or Neuro-GFP as well as from Oligo-FEDORA and Oligo-GFP. The successful manipulation of FEDORA was confirmed in the samples used for sequencing by qPCR. Libraries were made using 1 µg of purified RNA form neuron sequencing using the ScriptSeq Complete Kit (Epicentre) and 500 ng RNA for oligodendrocyte with the TruSeq Stranded Total RNA (Illumina). Library preparation kits were changes due to discontinuous production of the Epicenter kit. For library prep, the cDNA was synthesized from ribosomal depleted RNA and then fragmented total RNA using random hexamers, followed by terminal tagging. The libraries were PCR amplified and then purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases were introduced at the end of the adaptors during PCR amplification steps. Quality and concentration of libraries were confirmed on a Bioanalyzer (Agilent)

tag: gender

value: Female

tag: virus

value: Oligodendrocytes

tag: region

value: PFC


title: E3_GFP_2


title: Control heads replicate 2


title: D3_GFP_16


title: Control heads replicate 1


title: 5512-13_LCK

type: RNA

city: ANKARA

first: Ömer

last: Bayır

address: Gölbaşı

country: Turkey

institute: University of Health Sciences

hyb_protocol: The hybridization process of aRNA fragments required 16 h at 45°C, and streptavidin phycoerythrin dye was used to stain the array.

scan_protocol: After staining, GeneChips (Affymetrix, Catolog no: 901838) were scanned with the Affymetrix GeneChip Scanner 3000 to obtain raw data.

data_processing:
After analysis, differentially expressed genes between groups that had a fold change of >2 and a P-value of <0.05 were considered statistically significant.
Sample table created from data in the *.rma.chp files

label: biotin

source_name: Mucosa

label_protocol: The Transcriptor First Strand cDNA Synthesis Kit (Roche, Mannheim, Germany) was used to obtain cDNA from total RNAs. Some cDNAs were used for real-time polymerase chain reaction (RT-PCR) experiments. The prepared solution included Oligo dT, hexamer RNase inhibitor, dNTP, and reverse transcriptase incubated for 1 h at 16°C and 10 min at 65°C. After incubation with double-stranded cDNA, aRNA was synthesized using the in vitro transcription (IVT, Affymetrix, catalog no: 901229) method. IVT biotin label, buffer, enzyme mixture, and double-stranded cDNA were added to this solution. IVT reaction occurs at 40°C for 16 h. The aRNA was subsequently purified using magnetic microparticles. Magnetic microbeads bind to aRNAs with a binding buffer, and after washing, RNA is eluted with elution buffer. After elution, aRNAs were incubated with Mg ions for aRNA fragmentation.

extract_protocol: The tissues from paraffin blocks were treated with the PureLink FFPE RNA Isolation Kit (Thermo Scientific, Waltham, MA, USA) to isolate RNA. Following deparaffinization, the samples were treated with proteinase K and centrifuged in spin colons to remove cell debris. Isolated total RNA was eluted from the spin colons and stored at 4°C.

tag: patient diagnosis

value: laryngeal squamous cell carcinoma (LSCC)

value: Mucosa

tag: lymph node metastasis

value: positiive


title: 5512-13_2x1

source_name: Lymph node

tag: tissue

value: Lymph node

value: positive


title: 5512-13_RPS

source_name: Tumor

value: Tumor


title: D1_GFP_28


title: 5662-11_1SCK


title: sgMLL3 CD44+CD104high, biological replicate 2 [sgMLL3#9-E/M]

data_processing:
Basecalls were performed using bcl2fastq.
After investigating the quality of raw data by FASTQC, raw reads were trimmed with BBduk.sh, with the parameters minlen=50 qtrim=r  trimq=6 ktrim=r k=25 mink=11.
Alignment to the human genome (GENCODE v.34) was done with  bowtie2 (v. 2.4.1) with the parameters  mm  no-mixed  no-discordant  very-sensitive -X 1000,  duplicates were removed with samblaster, and reads from chrM were removed with sambamba
Differential ATAC-seq peaks were called using Genrich (v. 0.6; https://github.com/yejg2017/Genrich).
Blacklisted regions were _x001C_ltered out in the process.
Assembly: GRCh38/hg38
Supplementary files format and content: Normalized coverage track in bigWig format

source_name: breast cancer cell

extract_protocol:
100,000 cells were sorted based on the level of CD104. Nuclei are extracted from samples.
Nuclei pellet is resuspended in the Tn5 transposase reaction mix. The transposition reaction is incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 are added after transposition, PCR is then performed to amplify the library. After the PCR reaction, libraries are purified with the AMPure beads.

value: Triple-negative breast cancer line MDA-MB-233

value: sgMLL3 CD44+CD104high


title: 5970-12_1LCK-3


title: 5662-11_1K


title: 5818-13_RBV

value: negative


title: 5662-11_5-2


title: C3_GFP_1


title: sgMLL3 CD44+CD104-/low, biological replicate 2 [sgMLL3#9-M]

value: Triple-negative breast cancer line MDA-MB-232

value: Beast

value: sgMLL3 CD44+CD104-/low


title: sgMLL3 CD44+CD104high, biological replicate 1 [sgMLL3#3-E/M]

value: Triple-negative breast cancer line MDA-MB-231

value: Forskolin 10 μM for 14 days


title: Control heads replicate 3

value: Adult head, 2 days old


title: 5818-13_T2


title: 5970-12_5-2


title: 9463-10_8x1


title: 5970-12_T4A-1


title: C1_298_25

value: Female

value: Oligodendrocytes


title: 9463-10_L2B

value: laryngeal squamous cell carcinoma (LSCC)


title: 5818-13_6x3


title: sgMLL3 CD44+CD104-/low, biological replicate 1 [sgMLL3#3-M]


title: B3_298_7

value: PFC


title: Y79 cells-1,shNSUN2

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

country: China

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
none provided by the submitter
Assembly: Ensembl genes as provided in the processed data files

extract_protocol: none provided by the submitter

value: Human retinoblastoma

value: NSUN2 knockdown


title: Y79 cells-3,shNSUN2


title: Y79 cells-2,shNSUN2


title: Y79 cells-3,shControl

value: WT


title: 9463-10_R1C

value: Mucosa

value: positiive


title: 9787-13_3-4

value: Lymph node

value: positive


title: B1_298_24


title: sgNT CD44+CD104high, biological replicate 2 [sgNT2-E/M]

value: sgNT CD44+CD104high


title: Y79 cells-2,shControl


title: sgNT CD44+CD104-/low, biological replicate 2 [sgNT2-M]

value: Beast

value: sgNT CD44+CD104-/low


title: 9787-13_L3

value: Tumor


title: A3_298_6


title: Y79-2.m5C-IP


title: A1_298_11


title: Y79 cells-1,shControl


title: sgNT CD44+CD104high, biological replicate 1 [gNT1-E/M]

value: Triple-negative breast cancer line MDA-MB-231

value: Forskolin 10 μM for 14 days


title: sgNT CD44+CD104-/low, biological replicate 1 [sgNT1-M]


title: Y79-1.m5C-IP


title: D3_S9

value: Female

value: Neurons


title: E1_S5


title: MDA-MB-231 sgMLL3, UTX, biological replicate1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
The raw read were quality assessed using FastQC v0.11.9, then quality trimmed using Trimmomatic 0.40 with illumina adaptor file and default values.
The surviving paired reads post quality trimming were then aligned against the human reference genome (GRCh38) with bwa-mem(arXiv:1303.3997v2), then sorted and indexed with samtools.The resulting BAM alignments were then processed through PICARD (https://github.com/broadinstitute/picard) tools for ‘MarkDuplicates’.
BigWig files were generated from the Markduplicated bam files using bamCoverage with RPKM normalization. The resulting BigWig files were then passed to computeMatrix, which generates a matrix of scores per genomic region for visualization.
Peaks were called using MACS2 with a p value of 1e-3.
The regions of interested, including IFNγ signature genes and enhancers, were curated from UCSC table browser and BEDOPS v2.4.40.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were cultured in DMEM medium with 10%FBS.

extract_protocol:
Around 2 x 107 MLL3-WT or -mutant MCF7 and MDA-MB-231 cells were cross-linked with 1% formaldehyde for 10min, quenched by 125 mM glycine for 10 min and rinsed twice with 1X PBS. Fixed cells were incubated in the lysis buffer containing 5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 and protease inhibitors on ice for 10 min and centrifuged at 3000 rpm for 5min at 4°C. Nuclear pellets were resuspended with cold TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and sonicated into 200-500 bp fragments at 4°C. The experimental chromatins mixed with 20 ng drosophila spike-in chromatin (Active Motif, #53083) were incubated overnight at 4°C with Dynabeads Protein A (Invitrogen, 10002D), which had been pre-coated with 1 µg Drosophila-specific histone variant H2Av spike-in antibody (Active Motif, #61686) and 8 µg primary target antibody. The beads were washed twice with RIPA buffer, twice with RIPA buffer containing 300 mM NaCl, twice with LiCl buffer (50 mM Tris-Cl pH 7.5/250 mM LiCl/0.5% NP-40/0.5% Na-DOC) and twice with PBS. DNA was then eluted with 100 μl elution buffer (0.1 M NaHCO3, 1%SDS and 20 μg proteinase K) and reverse crosslinked at 65°C overnight. DNA was purified using QIAquick PCR purification kit (Qiagen) and quantified.
The ChIP DNA and input DNA were used to construct libraries using NEBNext Ultra™ II DNA Library Prep kit for Illumina (NEB, E7645) following the manufacturer’s instructions. The final libraries were sequenced on Illumina NovaSeq 6000.

treatment_protocol: No treatment

value: Breast cancer cell line

value: UTX (home-made)


title: 12398-12_5-1

value: laryngeal squamous cell carcinoma (LSCC)


title: 12398-12_RPK


title: RPE-2.m5C-IP

value: Human retina pigment epithelium


title: D1_S4

value: PFC


title: C3_S8


title: 13431-14_8D-2

value: negative


title: 13431-14_LPS


title: MDA-MB-231 sgNT1, UTX, biological replicate1


title: MDA-MB-231 sgMLL3, input, biological replicate1


title: Y79-2.Input

value: Human retinoblastoma

value: WT


title: 9787-13_RCK

value: Mucosa

value: positiive


title: 13475-15_2C-A


title: 13431_14-RPS


title: MDA-MB-231 sgNT1, MLL4, biological replicate1

value: MLL4 (home-made)


title: B3_S7


title: MDA-MB-231 sgNT1, input, biological replicate1


title: 13475-15_15

value: Lymph node


title: B1_S2


title: MDA-MB-231 sgMLL3, MLL4, biological replicate1


title: RPE-1.m5C-IP


title: 13475-15_6

value: Tumor


title: RPE-1.Input


title: MCF7 sgMLL3, UTX, biological replicate1


title: C1_S3


title: A1_S1


title: MCF7 sgMLL3, MLL4, biological replicate1


title: P. syringae-treated Arabidopsis leaf (scRNAseq)

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

description: DC3000-treated cells from scRNAseq

library_source: transcriptomic single cell

data_processing:
cellranger (6.0.1) was used to map and quantify transcripts per cell
The Seurat R package was used to further process and integrate data, filtering cells containing > 1% mitochondrial transcripts, and having fewer UMI than a dataset-dependent threshold
The monocle3 package was used to infer pseudotime for mesophyll cells
Assembly: Arabidopsis thaliana TAIR10 assembly, Araport11 gene models
Supplementary files format and content: tab-delimited text files (.tsv), comma delimited text files (.csv) and matrix files (.mtx) contain single-cell counts and cell metadata

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis plants were grown on soil in controlled conditions (22 deg. C, 70% RH, 10h light/14h dark, 100 uE intensity)

extract_protocol:
Protoplasts were isolated from Arabidopsis leaves infiltrated by bacteria and 10 mM MgCl 2 (mock) using the Tape-Arabidopsis Sandwich method. Peeled leaves were immediately immersed in a petri dish containing 10 mL of enzyme solution (1.5% Cellulase Onuzuka R-10 (Yakult, Japan), 0.3% Macerozyme R-10, (Yakult, Japan), 0.4 M Mannitol, 20 mM KCl, 20 mM MES (2-(N-Morpholino)ethanesulfonic acid hydrate) pH 5.7, 10 mM CaCl2, and 0.1%, BSA). After digesting for 100 min with gentle shaking, the protoplast suspension was filtered through 40 μm cell strainer (BD Falcon 352340) into a round-bottomed 50 mL tube and centrifuged at 100 x g for 1 min at 22°C using a swinging rotor. Protoplast pellets were gently resuspended in 10 mL of CS-sucrose buffer (0.4 M sucrose, 20 mM MES pH 5.7, 20 mM KCl) and centrifuged at 100 x g for 2 min at 22°C. Intact and healthy protoplasts remained suspended in the upper layer. The upper layer suspension was then transferred into a clean round-bottomed tube and gently mixed with 10 mL of protoplast buffer (0.4 M Mannitol, 20 mM KCl, 20 mM MES pH 5.7, and 0.1%, BSA). After centrifuging at 100 x g for 2 min at 4°C using a swinging rotor, the supernatant was removed without disturbing the loosely packed protoplast pellets. The protoplast concentration was determined using a hemocytometer and the viability was checked using trypan blue solution.
The protoplast suspension was diluted to a final concentration of 1000 cells/ µL. A total of 40, 000 cells were loaded into a microfluidic chip (10X Genomics) with v3 chemistry to capture ~10,000 cells per sample.

treatment_protocol: Leaves of four-week-old A. thaliana were syringe infiltrated with a bacterial suspension of OD 600 = 0.0001. Inoculated plants were kept under ambient humidity for 1 h to allow evaporation of excess water on the leaf surface. Then plants were covered with a transparent dome to maintain high humidity and incubated in growth chamber for 24 h.

value: Leaf

tag: ecotype

value: P. syringae DC3000


title: Y79-1.Input


title: MCF7 sgMLL3, input, biological replicate1


title: 16993-14_SCK-3


title: Mock-treated Arabidopsis leaf (scRNAseq)

description: Mock-treated cells from scRNAseq

tag: treatment

value: Mock


title: 4C_AdC3KO_4

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E. Young Drive South, MRL 6619

department: Pathology and Laboratory Medicine

institute: UCLA

data_processing:
FastQC was used to analyze FASTQ files before and after trimming.
Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic.
Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR.
HTSeq-count was used to extract gene counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Gene counts in CSV format

extract_protocol:
Total RNA was extracted using TRIzol and the RNeasy Mini Kit with on-column DNase I digestion (Qiagen).
Library preparation was done at GENEWIZ using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: brown adipose tissue (BAT)


title: 16993-14_T5S


title: MCF7 sgNT1, UTX, biological replicate1

tag: cell line

value: Breast cancer cell line


title: pLN_SPF_FSC_2 (WGBS)

data_processing:
The sequenced 2x100 bp paired-end libraries of bisulfite-treated reads were quality assessed and trimmed with the FastQC (version 0.11.1) (Andrews, 2010) and Cutadapt (version 1.4) (Martin, 2011) tools. Trimmed libraries were aligned with the bisulfite short read mapping program BSMAP (version 2.4.3) (Xi & Li, 2009) versus the mouse reference genome (assembly: GRCm38), and the methylation status of each CpG site was called.
Methylation profiles of CpGs with a minimum coverage of five mapped reads in at least two replicates of one condition and significant (based on t-statistics) change in their methylation status, served as input for the detection.
Differentially methylated regions were identified using bsmooth with default settings (Hansen et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with the methylation values per CpG with genomic coordinates.

extract_protocol:
Genomic DNA was isolated from purified CD45‑CD31‑Ter119‑gp38+ using the AllPrep DNA/RNA Micro Kit (Qiagen, Cat. #80284) according to the manufacturer’s instructions.
Concentration and quality of the purified genomic DNA (gDNA) was determined by using NanoDrop (Thermo Fisher Scientific). Fragmentation of gDNA was carried out via Covaris S2 (Covaris), at duty cycle 10 %, intensity 4 and 200 cycles per burst during 80 sec, to obtain fragments with an average length of 300 bp. The size of the fragments was verified with Agilent Technologies 2100 Bioanalyzer. DNA sequencing libraries were generated from fragmented gDNA using the TruSeq DNA Sample Prep Kit v2 (Illumina, Cat. #15026486) according to the manufacturer's instructions and extending the workflow by adding one additional step: Subsequent to ligation of the adapter molecules to the DNA fragments, the sample was subjected to bisulfite conversion reaction using the EZ DNA Methylation Kit (Zymo Research, Cat. #D5001). The protocol for the True Seq DNA generation was then followed. The bisulfite-converted library was amplified by performing a PCR reaction (10 cycles, 98°C for 10 s, 63°C for 30 s, 72°C for 1 min) including the TruSeq primer mix and the KAPA Hifi Uracil+ Poly-merase Master Mix (Kapa Biosystems, Cat. #KK2801). The PCR product was purified and size controlled by Agilent Technologies 2100 Bioanalyzer (High Sensitivity DNA Chip).
The libraries were sequenced on an Illumina HiSeq2500 sequencer using the TruSeq SBS Kit v3-HS (200 cycles, paired end run) with an average of 2*108 reads per replicate.

treatment_protocol: For stromal cell isolation, skin-draining pLNs (inguinal and axillary or popliteal) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco, Cat. #72400021) containing 0.2 mg/ml collagenase P (Roche, Cat. #11213865001), 0.15 U/ml dispase (Roche, Cat. #4942078001) and 0.2 mg/ml DNase I (Roche, Cat. #4536282001) as described previously (Malhotra et al., 2012). After digestion, cells were kept at 4 °C in PBS containing 0.2 % BSA (Merck, Cat. #A2058) and 5 mM EDTA (Roth, Cat. #8043.1). CD45- cells were enriched by autoMACS separation after magnetic labeling of CD45+ cells using anti‑CD45‑APC followed by anti‑APC microbeads (Miltenyi Biotec, Cat. #130-090-855) or anti-CD45 Nanobeads (Biolegend, Cat. #480028). Subsequently, the CD45- fraction was stained using fluorochrome-coupled antibodies and used to sort CD45‑CD24‑CD31‑gp38+ FSCs (Aria II, 100 μm nozzle) and bulk CD45‑CD24‑ non-hematopoietic cells (Aria III, 70 μm nozzle) for RNA‑seq/ATAC‑seq and scRNA‑seq, respectively.

tag: strain

value: BALB/c

value: ex vivo isolated cells non-endothelial stromal cells

value: skin-draining mesenteric lymph node

value: specific pathogen free


title: 4C_AdC3KO_3

tag: genotype


title: 17848-13_1D

value: laryngeal squamous cell carcinoma (LSCC)

value: negative


title: A3_S6

value: Female

tag: cell type

value: Neurons

value: PFC


title: pLN_SPF_FSC_1 (WGBS)


title: MCF7 sgNT1, MLL4, biological replicate1

tag: chip antibody

value: MLL4 (home-made)


title: 4C_AdC3KO_2


title: MCF7 sgNT1, input, biological replicate1


title: 4C_AdC3KO_1


title: wt (control for IT325) 3

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

institute: Max Planck Institute for Immunobiology and Epigenetics

data_processing:
Reads were aligned to the reference genome with STAR 2.5.2b-1 (Dobin, A., et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013)
Resulting alignments were quantified at the gene level with featureCounts version 1.6.0.1 (Liao, Y., et al. (2013) Feature Counts: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features. Bioinformatics, 30, 923-930 (2014)
Differential gene expression analysis was performed using DESeq2 version 2.11.40.1 (Love, M.I., et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014)
Assembly: Zv10.85 (http://www.ensembl.org/info/data/ftp/index.html)
Supplementary files format and content: Excel file containing normalized counts and FC log2
Supplementary files format and content: Tab-separated text file containing counts for genes for all samples

organism: Danio rerio

source_name: whole body  (5 days post fertilization)

extract_protocol:
Zebrafish embryos (5 days post fertilisation) were homogenized in Tri Reagent (Sigma), DNA was removed using TURBO DNA-free kit (Invitrogen).
cDNA libraries were prepared from 1 µg of mRNA following poly-A selection using TrueSeqstranded mRNA Library Prep (Illumina) according to manufacturer's instructions.

value: whole body  (5 days post fertilization)

value: mixture of different wt strains

value: wild type


title: 4C_WT_4

value: WT


title: pLN_SPF_FSC_3 (WGBS)


title: 17848-13_1LPS

value: Mucosa


title: 22880-14__UCS

value: positiive


title: pLN_GF_FSC_1 (WGBS)

value: germ-free


title: pLN_GF_FSC_2 (WGBS)

value: BALB/c


title: 4C_WT_3

value: brown adipose tissue (BAT)


title: 17848-13_5x2

value: Lymph node


title: mLN_SPF_FSC_3 (WGBS)

value: ex vivo isolated cells non-endothelial stromal cells

value: gut-draining mesenteric lymph node

value: specific pathogen free


title: mLN_SPF_FSC_2 (WGBS)


title: 22880-14_3-2

value: laryngeal squamous cell carcinoma (LSCC)

value: positive


title: wt (control for IT325) 2


title: wt (control for IT325) 1


title: IT325 mut 3

value: IT325 (allele #t24980) homozygous mutant


title: mLN_SPF_FSC_1 (WGBS)


title: 4C_WT_2


title: mLN_GF_FSC_2 (WGBS)


title: 22970-14_9-1


title: IT325 mut 2


title: 30C_AdC3KO_3


title: 4C_WT_1


title: mLN_GF_FSC_1 (WGBS)


title: IT325 mut 1


title: 30C_AdC3KO_2


title: pLN_SPF_FSC_3 (RNAseq)

data_processing:
Libraries were aligned versus the mouse reference genome assembly GRCm38 using the splice junction mapper Tophat2 v1.2.0 with default parameterization (Kim et al., 2013).
Reads aligned to annotated genes were quantified with the HTSeq (version 0.12.4)(Anders et al., 2015) and determined read counts served as input to DESeq2 (Love et al., 2014) for pairwise detection and quantification of differential gene expression. RPKM (reads per kilobase of exon length per million mapped reads) values were computed for each library from the raw read counts.
For scatterplots and heatmaps only genes with an annotated official Gene Symbol were included. Gene ontology analyses were performed using the R package TopGo (Alexa and Rahnenfuhrer, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: XLSX of RPKM values per sample, q-Value and foldchange

extract_protocol:
Total RNA was extracted from FACS-sorted CD45‑CD24‑CD31‑gp38+ using the RNeasy Plus Micro Kit (Qiagen, Cat. #74034).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Cat. #R400752), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter, Cat. #A63880). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.
Deep sequencing was carried out on Illumina HiSeq2500 using 50 bp single reads. Sequenced libraries were assessed for read quality using the FastQC tool.

value: skin-draining mesenteric lymph node


title: 22970-14_EP


title: KP-1 SDS treated replicate 3

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

data_processing:
The raw reads from 48 samples were processed using cutadapt (version 1.2.1) with default parameters, except --overlap 10 -m 10 -q 20.
Each fastq file was mapped to rRNA sequences of the corresponding genomes (P. aeruginosa PAO1, P. protegens Pf-5 and K. pneumoniae KP-1 with GenBank accession numbers  NC_002516.2, CP000076.1 and CP012883.1 respectively)  or combined rRNA sequences from all the 3 genomes ( in case of mixed samples), using bowtie2 (version 2.2.6, running default parameters except -t -q -p 5 --un ). The unmapped reads from each sample were mapped to all the three genomes separately using bowtie2 (version 2.2.6, running default parameters except -t -q -p 5 --un ). Reads having multiple alignments within each genomes were removed (reads with "XS:i:" flag in the SAM file). The SAM files were further filtered for uniquely mapped reads (reads not mapping to muti-genomes ).
Transcript abundance estimation was subsequently performed by HTSeq v0.13.5 (Anders et al 2015) followed by differential expression analysis by DESeq2 v1.30.1 (Love et al 2014).  Genes with absolute value of log2 fold change (log2FC) ≥1 and adjusted p-value <=0.05 were considered as DEGs in comparative two-group analyses
Assembly: P. aeruginosa PAO1, P. protegens Pf-5 and K. pneumoniae KP-1 reference genomes (GenBank accession numbers:  AE004091, CP000076 and CP012883, respectively)
Supplementary files format and content: tab-delimited text files include RPKM values

organism: Klebsiella pneumoniae KP-1

source_name: WT

growth_protocol: Bacteria were cultured in M9 minimal medium (48 mM Na2HPO4; 22 mM KH2PO4; 9 mM NaCl; 19 mM NH4Cl; 2 mM MgSO4; 0.1 mM CaCl2; and 0.04% w/v glucose) supplemented with 0.2% w/v casamino acids (supplemented M9 minimal medium).

extract_protocol:
Stabilized RNA from the biofilm was extracted from the cells using the RNeasy Protect Bacteria Mini Kit (Qiagen, Netherlands). Extracted RNA was treated with TURBO DNA-freeTM Kit (Ambion, USA) to remove any DNA before purification by RNA Clean & ConcentratorTM-5 (ZYMO Research Corporation, USA).
Libraries for total RNA were prepared using the TruSeq RNA Sample Preparation Kit (Illumina, USA) and sequenced on the HiSeq 2500 sequencer (Illumina, USA) according to the manufacturer's protocols.

treatment_protocol: Single and mixed species biofilms were cultivated in three-channel flow cells for 4, 5 and 6 d. Biofilms on day 4 were also treated with 0.1% w/v SDS as described (Lee et al 2014) (Table 1). Biomass from each flow cell was extracted by first flushing ice cold PBS through the channels several times followed by a validation of biomass removal efficiency by confocal laser scanning microscopy. Subsequently, the RNAprotect Bacteria reagent (Qiagen, Netherlands) was added immediately to the extracted biomass according to the protocols suggested by the manufacturer to stabilize the RNA before extraction.

value: SDS treated

tag: biol rep

value: replicate 3


title: 30C_WT_3


title: 24348-14_3-3

value: negative


title: pLN_SPF_FSC_2 (RNAseq)


title: 22880-14_REP2

value: Tumor


title: KP-1 SDS treated replicate 1

value: WT

tag: time

value: replicate 1


title: 22970-14_PREP-1


title: 24348-14_ECK4

value: Mucosa


title: 24348-14_T3P


title: pLN_SPF_FSC_1 (RNAseq)

value: BALB/c

tag: housing


title: 30C_WT_2

value: brown adipose tissue (BAT)


title: 30C_AdC3KO_1


title: pLN_GF_FSC_3 (RNAseq)

value: germ-free


title: pLN_GF_FSC_2 (RNAseq)

value: ex vivo isolated cells non-endothelial stromal cells


title: KP-1 Day 6 Replicate 2

value: Day 6

value: Replicate 2


title: 24729-14_8x1

value: laryngeal squamous cell carcinoma (LSCC)

value: Lymph node


title: 30C_WT_1


title: KP-1 SDS treated replicate 2

value: replicate 2


title: Pooled protoplasts from P. syringae-treated Arabidopsis leaf (replicate 1)

data_processing:
STAR (v 2.7.2a) was used to map and quantify reads from each library
the edgeR (R) package was used to determine differential expression features for each locus
Assembly: Arabidopsis thaliana TAIR10 assembly, Araport11 gene models
Supplementary files format and content: gzipped tab-delimited text files (.tab.gz), digital gene expression matrix (counts.tsv.gz)

extract_protocol:
Protoplasts were isolated from Arabidopsis leaves infiltrated by bacteria and 10 mM MgCl 2 (mock) using the Tape-Arabidopsis Sandwich method. Peeled leaves were immediately immersed in a petri dish containing 10 mL of enzyme solution (1.5% Cellulase Onuzuka R-10 (Yakult, Japan), 0.3% Macerozyme R-10, (Yakult, Japan), 0.4 M Mannitol, 20 mM KCl, 20 mM MES (2-(N-Morpholino)ethanesulfonic acid hydrate) pH 5.7, 10 mM CaCl2, and 0.1%, BSA). After digesting for 100 min with gentle shaking, the protoplast suspension was filtered through 40 μm cell strainer (BD Falcon 352340) into a round-bottomed 50 mL tube and centrifuged at 100 x g for 1 min at 22°C using a swinging rotor. Protoplast pellets were gently resuspended in 10 mL of CS-sucrose buffer (0.4 M sucrose, 20 mM MES pH 5.7, 20 mM KCl) and centrifuged at 100 x g for 2 min at 22°C. Intact and healthy protoplasts remained suspended in the upper layer. The upper layer suspension was then transferred into a clean round-bottomed tube and gently mixed with 10 mL of protoplast buffer (0.4 M Mannitol, 20 mM KCl, 20 mM MES pH 5.7, and 0.1%, BSA). After centrifuging at 100 x g for 2 min at 4°C using a swinging rotor, the supernatant was removed without disturbing the loosely packed protoplast pellets. Leaf samples were processed
cDNA libraries were prepared with NEBNext Multiplex Oligos for Illumina sequencing

value: Leaf

value: P. syringae DC3000


title: pLN_GF_FSC_1 (RNAseq)

value: skin-draining mesenteric lymph node


title: KP-1 Day 6 Replicate 1

value: Replicate 1


title: 27586-12_1L-CK

value: negative


title: KP-1 Day 5 Replicate 3

value: WT

value: Day 5

value: Replicate 3


title: mLN_SPF_FSC_3 (RNAseq)

value: BALB/c

value: gut-draining mesenteric lymph node

value: specific pathogen free


title: KP-1 Day 6 Replicate 3


title: P. syringae-treated Arabidopsis leaf (bulk, replicate 1)


title: wt (control for CRISPR ikzf1) 5

value: whole body  (5 days post fertilization)

value: mixture of different wt strains

value: wild type


title: mLN_SPF_FSC_2 (RNAseq)

value: ex vivo isolated cells non-endothelial stromal cells


title: KP-1 Day 5 Replicate 2

value: Replicate 2


title: KP-1 Day 5 Replicate 1


title: P. syringae-treated Arabidopsis leaf (bulk, replicate 2)


title: 27586-12_1TL4

value: laryngeal squamous cell carcinoma (LSCC)

value: Tumor


title: mLN_SPF_FSC_1 (RNAseq)


title: wt (control for CRISPR ikzf1) 4


title: Pooled protoplasts from mock-treated Arabidopsis leaf (replicate 1)

value: Leaf

value: Mock


title: 24729-14_L3


title: 27586-12_9x7

value: Lymph node


title: 24729-14_L6

value: Mucosa

value: negative


title: wt (control for CRISPR ikzf1) 6


title: mLN_GF_FSC_3 (RNAseq)

value: germ-free


title: KP-1 Day 4 Replicate 2

value: WT

value: Day 4


title: CRISPR ikzf1 mut 3

value: CRISPR ikzf1 (allele #fr105) homozygous mutant


title: Mock-treated Arabidopsis leaf (bulk, replicate 3)


title: mLN_GF_FSC_2 (RNAseq)

value: BALB/c

value: gut-draining mesenteric lymph node


title: CRISPR ikzf1 mut 2

value: whole body  (5 days post fertilization)

value: mixture of different wt strains


title: KP-1 Day 4 Replicate 1

value: Replicate 1


title: Mock-treated Arabidopsis leaf (bulk, replicate 2)


title: P. syringae-treated Arabidopsis leaf (bulk, replicate 3)

value: P. syringae DC3000


title: mLN_GF_FSC_1 (RNAseq)

value: ex vivo isolated cells non-endothelial stromal cells


title: Mock-treated Arabidopsis leaf (bulk, replicate 1)


title: CRISPR ikzf1 mut 1


title: monocytes_rep B

status: Public on Oct 06 2022

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
monocytes from peripheral blood of healthy donors
r27

data_processing:
Sequenced reads were aligned to GRCh38 genome with hisat2 2.1.0 (standard options)
Aligned reads with not proper pair and secondary alignments were filtered out with samtools (samtools view -h -f 0x2 $file | samtools view -h -b -f 0x100 -U $file".filter.bam" > discarded.bam)
Reads were asigned to genes using featureCounts v1.6.4 with options -B -p
Differential expressed genes and VST values for representation were obtained from counts matrix with the R package DESeq2 (version 1.26.0). Ashr was used in the lfcShrink function.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and cultured 7 days in Roswell Park Memorial Institute (RPMI) Medium 1640 + GlutaMAX™ containing 10% fetal bovine serum, 100 units/mL penicillin, 100 mg/mL streptomycin

extract_protocol:
Total RNA was isolated utilising Maxwell® RSC simplyRNA Cells Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in RPMI with 10ng/mL Granulocyte Macrophage Colony-Stimulating Factor and 10ng/mL Interleukin 4 with or without vitamin C (500uM). On day 5, lypopolysaccharide (10ng/mL) was added to obtain mature dendritic cells

value: MO

tag: donor

value: B


title: monocytes_rep C

description:
monocytes from peripheral blood of healthy donors
r28

value: C


title: monocytes_re pA

description:
monocytes from peripheral blood of healthy donors
r26

value: A


title: mature_dendritic_cell_vitC_repC

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS (mDCvitC)
r24

value: mDCvitC


title: KP-1 Day 4 Replicate 3

value: Replicate 3


title: mature_dendritic_cell_repC

description:
monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS (mDC)
r23

value: mDC


title: immature_dendritic_cell_repC

description:
monocytes differentiated to dendritic cells for 7 days (iDC)
r21

value: iDC


title: dendritic_cell_vitC_day2_repC

description:
monocytes differentiated to dendritic cells for 2 days + vitamin C ( DC_d2vitC)
r20


title: dendritic_cell_day2_repC

description:
monocytes differentiated to dendritic cells for 2 days ( DC_d2)
r19


title: mature_dendritic_cell_repB

description:
monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS (mDC)
r17


title: dendritic_cell_vitC_day2_repB

description:
monocytes differentiated to dendritic cells for 2 days + vitamin C ( DC_d2vitC)
r14


title: immature_dendritic_cell_vitC_repB

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C (iDCvitC)
r16

value: iDCvitC


title: mature_dendritic_cell_vitC_repB

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS (mDCvitC)
r18


title: mature_dendritic_cell_vitC_repA

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS (mDCvitC)
r12


title: mature_dendritic_cell_repA

description:
monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS (mDC)
r11


title: dendritic_cell_vitC_day2_repA

description:
monocytes differentiated to dendritic cells for 2 days + vitamin C ( DC_d2vitC)
r8


title: dendritic_cell_day2_repB

description:
monocytes differentiated to dendritic cells for 2 days ( DC_d2)
r13


title: immature_dendritic_cell_vitC_repA

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C (iDCvitC)
r10


title: immature_dendritic_cell_repA

description:
monocytes differentiated to dendritic cells for 7 days (iDC)
r9


title: dendritic_cell_day2_repA

description:
monocytes differentiated to dendritic cells for 2 days ( DC_d2)
r7


title: immature_dendritic_cell_vitC_repC

description:
monocytes differentiated to dendritic cells for 7 days + vitamin C (iDCvitC)
r22


title: immature_dendritic_cell_repB

description:
monocytes differentiated to dendritic cells for 7 days (iDC)
r15


title: immature_dendritic_cell_repD

type: genomic

description: monocytes differentiated to dendritic cells for 7 days (iDC)

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project
Normalized (minfi preprocessNoob + preprocessQuantile) Beta values

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was isolated utilising Maxwell® RSC Cultured Cells DNA Kit (Promega)

value: DC d7

value: D


title: mature_dendritic_cell_repB

description: monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS (mDC)

value: DC LPS d7


title: RPE-2.Input

value: Human retina pigment epithelium

value: WT


title: dendritic_cell_vitC_day2_repA

description: monocytes differentiated to dendritic cells for 2 days ( DC_d2)

value: DC d2


title: mature_dendritic_cell_vitC_repD

description: monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS (mDCvitC)

value: DC VitC +LPS d7


title: monocyte_repC

description: monocytes from peripheral blood of healthy donors


title: monocyte_repA

source_name: monocytes from peripheral blood of healthy donors

value: F


title: immature_dendritic_cell_vitC_repD

description: monocytes differentiated to dendritic cells for 7 days + vitamin C (iDCvitC)

value: DC VitC d7


title: dendritic_cell_vitC_day2_repB

description: monocytes differentiated to dendritic cells for 2 days + vitamin C ( DC_d2vitC)

value: DC VitC d2

value: B


title: dendritic_cell_day2_repD

source_name: monocytes differentiated to dendritic cells for 2 days ( DC_d2)


title: dendritic_cell_vitC_day2_vrepC

source_name: monocytes differentiated to dendritic cells for 2 days + vitamin C ( DC_d2vitC)

value: A


title: immature_dendritic_cell_repA

source_name: monocytes differentiated to dendritic cells for 7 days (iDC)


title: mature_dendritic_cell_vitC_repC

source_name: monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS (mDCvitC)

value: C


title: mature_dendritic_cell_vitC_repB


title: immature_dendritic_cell_vitC_repC

source_name: monocytes differentiated to dendritic cells for 7 days + vitamin C (iDCvitC)


title: monocyte_repD

value: MO

value: E


title: immature_dendritic_cell_repC


title: dendritic_cell_vitC_day2_repC


title: mature_dendritic_cell_repC

source_name: monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS (mDC)


title: immature_dendritic_cell_vitC_repB


title: 16993-14_9LN-5

value: laryngeal squamous cell carcinoma (LSCC)

value: Lymph node

value: negative


title: dendritic_cell_day2_repB

source_name: monocytes differentiated to dendritic cells for 2 days ( Ø)


title: monocyte_repB


title: immature_dendritic_cell_vitC_repA


title: mature_dendritic_cell_repA


title: HSC AAV only Mouse 4

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Data analyzed withthe CRISPResso2 pipeline:
reads were trimmed using the Trimmomatic
paired-end reads were merged using the FLASh and aligned against the reference vector
quantification around the guide cut site was performed for each found allele
Assembly: Custom reference vector sequences (AAV and IDLV) and sgRNA
Supplementary files format and content: Tab-separated results of the different allele found with corresponding quantifications
Library strategy: amplicon sequencing

source_name: Human Splenocytes xenotransplanted mouse

extract_protocol:
gDNA was isolated with QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
PCR amplicons for individual samples were generated by nested PCR using primers listed in the related manuscript and starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’min, (95°C x 0.5 min, 60°C x 0.5 min, 72°C x 0.2 5min) x 20 cycles, 72°C x 5 min. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5μl of the first-step PCR product and the following amplification protocol: 95°C x 5min, (95°C x 0.5 min, 60°C x 0.5 min, 72°C x 0.3 min) x 20 cycles, 72°C x 5 min. Second-step PCR primers were endowed with tails containing P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites (Supplementary Table 5). PCR amplicons were separately purified performing double-side selection with AmpPure XP beads (Beckman Coulter) or QIAquick PCR Purification Kit (QIAGEN). Amplicons concentration and quality was assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 36 differently tagged samples were multiplexed at equimolar ratios and run

tag: celltype

value: Cord Blood HSC

tag: vector

value: AAV only

tag: target locus


title: immature_dendritic_cell_repB

value: DC d7


title: HSC AAV only Mouse 3


title: HSC AAV only Mouse 2


title: HSC AAV only Mouse 1


title: UT for AAV only mice


title: dendritic_cell_day2_repC


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 15

data_processing:
Library strategy: amplicon sequencing
Data analyzed withthe CRISPResso2 pipeline:
reads were trimmed using the Trimmomatic
paired-end reads were merged using the FLASh and aligned against the reference vector
quantification around the guide cut site was performed for each found allele
Genome_build: Custom reference vector sequences (AAV and IDLV) and sgRNA
Supplementary_files_format_and_content: Tab-separated results of the different allele found with corresponding quantifications

value: Mobilized Peripheral Blood HSC

value: IDLV

value: + GSE56/Ad5-E4orf6/7 (2 hits)


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 13


title: HSC AAV only Mouse 5


title: mature_dendritic_cell_vitC_repA

value: DC VitC +LPS d7


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 12


title: mature_dendritic_cell_repD

value: DC LPS d7

value: D


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 11


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 10

value: + GSE56 (2 hits)


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 8


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 7


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 6


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 9


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 14


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 5

value: + GSE56 (1 hit)


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 4


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 3


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 2


title: Mobilized PB HSC on AAVS1 with IDLV Mouse 1


title: HSC on AAVS1 with IDLV Mouse 25

value: + CSH + GSE56


title: HSC on AAVS1 with IDLV Mouse 26


title: HSC on AAVS1 with IDLV Mouse 24


title: HSC on AAVS1 with IDLV Mouse 22


title: HSC on AAVS1 with IDLV Mouse 23


title: HSC on AAVS1 with IDLV Mouse 21


title: HSC on AAVS1 with IDLV Mouse 18


title: HSC on AAVS1 with IDLV Mouse 17


title: HSC on AAVS1 with IDLV Mouse 14

value: + GSE56


title: HSC on AAVS1 with IDLV Mouse 12


title: HSC on AAVS1 with IDLV Mouse 15


title: HSC on AAVS1 with IDLV Mouse 16


title: HSC on AAVS1 with IDLV Mouse 9

value: + CSH


title: HSC on AAVS1 with IDLV Mouse 20


title: mature_dendritic_cell_VitaminC_NF-kB inhibitor(Bay) 32

description:
mature_dendritic_cell_VitaminC_NF-kB inhibitor(Bay)
monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS and the p65 inhibitor (Bay)

data_processing: iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project

source_name: monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS and the NF-kB inhibitor (Bay)

treatment_protocol: Cells were cultured in RPMI with 10ng/mL Granulocyte Macrophage Colony-Stimulating Factor and 10ng/mL Interleukin 4 with or without vitamin C (500uM). On day 5, lypopolysaccharide (10ng/mL) was added to obtain mature dendritic cells and a NF-kB inhibitor (Bay 11-7082) (50mM) or dimethylsulphoxide (DMSO)

value: DC VitC +LPS +Bay

value: A


title: mature_dendritic_cell_VitaminC_NF-kB inhibitor(Bay) 16

value: C


title: HSC on AAVS1 with IDLV Mouse 8

value: Cord Blood HSC


title: HSC on AAVS1 with IDLV Mouse 7


title: mature_dendritic_cell_VitaminC_DMSO 22

description:
mature_dendritic_cell_VitaminC_DMSO
monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS and DMSO

value: DC VitC +LPS +DMSO


title: mature_dendritic_cell_DMSO 3

description:
mature_dendritic_cell_DMSO
monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS DMSO

value: DC +LPS +DMSO

value: B


title: mature_dendritic_cell_NF-kB inhibitor(Bay) 28

description:
mature_dendritic_cell_NF-kB inhibitor(Bay)
monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS and the p65 inhibitor (Bay)

source_name: monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS and the NF-kB inhibitor (Bay)

value: DC +LPS +Bay


title: HSC on AAVS1 with IDLV Mouse 4

value: IDLV


title: mature_dendritic_cell_DMSO 26

source_name: monocytes differentiated to dendritic cells for 7 days, last 2 days with LPS DMSO


title: dendritic_cell_vitC_day2_repD

value: DC VitC d2


title: mature_dendritic_cell_VitaminC_DMSO 7

source_name: monocytes differentiated to dendritic cells for 7 days + vitamin C, last 2 days with LPS and DMSO


title: mature_dendritic_cell_NF-kB inhibitor(Bay) 4


title: HSC on AAVS1 with IDLV Mouse 19


title: mature_dendritic_cell_DMSO 18


title: mature_dendritic_cell_VitaminC_NF-kB inhibitor(Bay) 24


title: mature_dendritic_cell_NF-kB inhibitor(Bay) 12


title: HSC on AAVS1 with IDLV Mouse 3


title: T cells on CD40L with AAV Mouse 27

source_name: Human T cells xenotransplanted mouse

value: T cells

value: AAV

value: RNP + ssAAV


title: HSC on AAVS1 with IDLV Mouse 5


title: HSC on AAVS1 with IDLV Mouse 1


title: HSC on AAVS1 with IDLV Mouse 6


title: T cells on CD40L with AAV Mouse 26


title: T cells on CD40L with AAV Mouse 25


title: T cells on CD40L with AAV Mouse 28


title: T cells on CD40L with AAV Mouse 24


title: T cells on CD40L with AAV Mouse 23


title: HSC on AAVS1 with IDLV Mouse 11


title: mature_dendritic_cell_NF-kB inhibitor(Bay) 20

value: D


title: T cells on CD40L with AAV Mouse 22


title: T cells on CD40L with AAV Mouse 20


title: T cells on CD40L with AAV Mouse 18

value: UT


title: T cells on CD40L with AAV Mouse 17


title: T cells on CD40L with AAV Mouse 19


title: mature_dendritic_cell_VitaminC_DMSO 15


title: T cells on CD40L with AAV Mouse 16


title: T cells on CD40L with AAV Mouse 15


title: mature_dendritic_cell_VitaminC_DMSO 30


title: HSC on CD40L with AAV Mouse 14

value: + GSE56


title: HSC on CD40L with AAV Mouse 11


title: mature_dendritic_cell_DMSO 11


title: HSC on CD40L with AAV Mouse 13


title: HSC on CD40L with AAV Mouse 10


title: HSC on CD40L with AAV Mouse 12


title: HSC on CD40L with AAV Mouse 7


title: HSC on CD40L with AAV Mouse 9


title: HSC on CD40L with AAV Mouse 5


title: HSC on CD40L with AAV Mouse 6


title: HSC on CD40L with AAV Mouse 8


title: T cells on CD40L with AAV Mouse 21


title: HSC on CD40L with AAV Mouse 4


title: HSC on CD40L with AAV Mouse 1


title: HSC on CD40L with AAV Mouse 2


title: HSC on CD40L with AAV Mouse 3


title: Mobilized PB HSC on AAVS1 with AAV Mouse 5

value: Mobilized Peripheral Blood HSC


title: Mobilized PB HSC on AAVS1 with AAV Mouse 4


title: Mobilized PB HSC on AAVS1 with AAV Mouse 3


title: Mobilized PB HSC on AAVS1 with AAV Mouse 2


title: Mobilized PB HSC on AAVS1 with AAV Mouse 1


title: HSC on AAVS1 with AAV Mouse 97


title: HSC on AAVS1 with AAV Mouse 96


title: mature_dendritic_cell_VitaminC_NF-kB inhibitor(Bay) 8

value: DC VitC +LPS +Bay


title: HSC on AAVS1 with AAV Mouse 95


title: HSC on AAVS1 with AAV Mouse 90


title: HSC on AAVS1 with AAV Mouse 91


title: HSC on AAVS1 with AAV Mouse 92


title: HSC on AAVS1 with AAV Mouse 94


title: HSC on AAVS1 with AAV Mouse 89


title: HSC on AAVS1 with AAV Mouse 87


title: HSC on AAVS1 with AAV Mouse 85


title: HSC on AAVS1 with AAV Mouse 86


title: HSC on AAVS1 with AAV Mouse 84


title: HSC on AAVS1 with AAV Mouse 82


title: HSC on AAVS1 with AAV Mouse 81


title: HSC on AAVS1 with AAV Mouse 80


title: HSC on AAVS1 with AAV Mouse 78


title: HSC on AAVS1 with AAV Mouse 79


title: HSC on AAVS1 with AAV Mouse 77


title: HSC on AAVS1 with AAV Mouse 76


title: HSC on AAVS1 with AAV Mouse 75


title: HSC on AAVS1 with AAV Mouse 98


title: HSC on AAVS1 with AAV Mouse 93


title: HSC on AAVS1 with AAV Mouse 74


title: HSC on AAVS1 with AAV Mouse 72


title: HSC on AAVS1 with AAV Mouse 88


title: HSC on AAVS1 with AAV Mouse 70


title: HSC on AAVS1 with AAV Mouse 69


title: HSC on AAVS1 with AAV Mouse 71


title: HSC on AAVS1 with AAV Mouse 66


title: HSC on AAVS1 with AAV Mouse 68


title: HSC on AAVS1 with AAV Mouse 73


title: HSC on AAVS1 with AAV Mouse 65


title: HSC on AAVS1 with AAV Mouse 83


title: HSC on AAVS1 with AAV Mouse 67


title: HSC on AAVS1 with AAV Mouse 63


title: HSC on AAVS1 with AAV Mouse 64


title: HSC on AAVS1 with AAV Mouse 62


title: HSC on AAVS1 with AAV Mouse 61


title: HSC on AAVS1 with AAV Mouse 60


title: HSC on AAVS1 with AAV Mouse 59


title: HSC on AAVS1 with AAV Mouse 58


title: HSC on AAVS1 with AAV Mouse 55


title: HSC on AAVS1 with AAV Mouse 54


title: HSC on AAVS1 with AAV Mouse 53


title: HSC on AAVS1 with AAV Mouse 56


title: HSC on AAVS1 with AAV Mouse 52


title: HSC on AAVS1 with AAV Mouse 51


title: HSC on AAVS1 with IDLV Mouse 10

value: + CSH


title: HSC on AAVS1 with IDLV Mouse 13


title: HSC on AAVS1 with AAV Mouse 48


title: HSC on AAVS1 with AAV Mouse 50


title: HSC on AAVS1 with AAV Mouse 49


title: HSC on AAVS1 with AAV Mouse 43


title: HSC on AAVS1 with AAV Mouse 44


title: HSC on AAVS1 with AAV Mouse 47


title: HSC on AAVS1 with AAV Mouse 38


title: HSC on AAVS1 with AAV Mouse 40


title: HSC on AAVS1 with AAV Mouse 46


title: HSC on AAVS1 with AAV Mouse 45


title: HSC on AAVS1 with AAV Mouse 36


title: HSC on AAVS1 with AAV Mouse 42


title: HSC on AAVS1 with AAV Mouse 33

value: RNP + scAAV


title: HSC on AAVS1 with AAV Mouse 34

value: Cord Blood HSC


title: HSC on AAVS1 with AAV Mouse 39


title: HSC on AAVS1 with AAV Mouse 57


title: HSC on AAVS1 with AAV Mouse 32


title: HSC on AAVS1 with AAV Mouse 37


title: HSC on AAVS1 with AAV Mouse 41


title: HSC on AAVS1 with AAV Mouse 31


title: HSC on AAVS1 with AAV Mouse 35


title: HSC on AAVS1 with AAV Mouse 29


title: HSC on AAVS1 with AAV Mouse 30


title: HSC on AAVS1 with AAV Mouse 27

value: RNP + ssAAV (2x10^4)


title: HSC on AAVS1 with AAV Mouse 28


title: HSC on AAVS1 with AAV Mouse 26


title: HSC on AAVS1 with AAV Mouse 24


title: HSC on AAVS1 with AAV Mouse 25


title: HSC on AAVS1 with AAV Mouse 23


title: HSC on AAVS1 with AAV Mouse 21


title: HSC on AAVS1 with AAV Mouse 16

value: RNP + ssAAV (2x10^3)


title: HSC on AAVS1 with AAV Mouse 19


title: HSC on AAVS1 with AAV Mouse 17


title: HSC on AAVS1 with AAV Mouse 15


title: HSC on AAVS1 with AAV Mouse 10


title: HSC on AAVS1 with AAV Mouse 18


title: HSC on AAVS1 with AAV Mouse 11


title: HSC on AAVS1 with AAV Mouse 8

value: RNP + empty


title: HSC on AAVS1 with AAV Mouse 6


title: HSC on AAVS1 with AAV Mouse 5


title: HSC on AAVS1 with AAV Mouse 13


title: HSC on AAVS1 with AAV Mouse 3


title: HSC on AAVS1 with AAV Mouse 2


title: HSC on AAVS1 with AAV Mouse 9


title: HSC on AAVS1 with AAV Mouse 12


title: HSC on AAVS1 with AAV Mouse 7


title: HSC on AAVS1 with AAV Mouse 4


title: HSC on AAVS1 with AAV Mouse 1


title: HSC on AAVS1 control Mouse 1

source_name: Cultured Human HSCs


title: HSC on AAVS1 control Mouse 2


title: HSC on AAVS1 control Mouse 3


title: HSC on AAVS1 with AAV Mouse 20


title: HSC on AAVS1 with AAV Mouse 22


title: Delta H-NS Input Bead A Rep 2

city: Madison

first: Robert

last: Landick

state: WI

address: 5445 Microbial Science Building 1550 Linden Dr.

department: Biochemistry

institute: University of Wisconsin-Madison

description:
Pooled input for H-NS, StpA IPs delta hns CFT073 rep 2
Δhns

data_processing:
Paired-end reads were trimmed of adapter sequences using CutAdapt version 2.10 (16) with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’. Quality trimming was performed using trimmomatic (version 0.39) with parameters " -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15". The reads were aligned to the CFT073 genome (NC_004431.1 for CFT073 or GenBank accession no. U00096.3 for RL3000) using bowtie2 (version 2.4.2) under parameters “--end-to-end --very-sensitive --phred33”. Read coverage per five bp bin was scaled to the median coverage over all bins for each sample. Read coverage was calculated using (deepTools version 3.5.0; (20)) with the parameters ‘--binSize 5 –samFlagInclude 66 –extendReads' for paired end samples and ‘--binSize 5’ for single end samples. Normalization of the coverage based on the input (IP/Input) or log2(IP/input)) was calculated with custom python scripts included in the coverage and norm module of the pipeline. Read quality control was performed using fastqc version 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and multiqc version 1.11.0. RfaH regions were called using macs2 (version 2.27.1) using the parameters ‘–broad’ with the corresponding input used as a control sample.
Assembly: NC_004431.1 for CFT073 and U00963.3 for RL3000.
Supplementary files format and content: bigWig files

organism: Escherichia coli CFT073

source_name: NA-bacteria

growth_protocol: Strains were grown aerobically in Niehardt MOPs rich defined media supplemented with 0.2% glucose at 37° C with shaking at 140 RPM.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 minutes at an apparent OD600 ~0.4. After quenching with 500 mM glycine, cells were lysed and chromatin sonicated using a Misonix Ultrasonic Liquid Processor to fragments with a median size of ~200-600 nt in length. H-NS, StpA, RfaH, Beta, and σ70 IPs and input controls were performed with modifications as described in Davis SE et al. 2011. Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide. Methods Enzymol 498:449-71. DNA was quantified with QuBit dsDNA HS assay (ThermoFisher) on a QuBit 3.0 fluorimeter.
DNA sequencing paired-end libraries were prepared using the NEBNext Ultra II DNA library reagents with NEBNext sample purification beads according to the manufacturer’s protocols without size selection. Quality and size ranges of libraries were determined using HS DNA Screentape (Agilent) on a TapeStation 4200 system (Agilent). Libraries were sequenced on Illumina MiSeq or NovaSeq 6000 sequencers.

value: NA-bacteria

value: <delta>hns


title: HSC on AAVS1 with AAV Mouse 14


title: HSC on AAVS1 with IDLV Mouse 2

value: IDLV


title: Delta H-NS StpA Rep 1

description:
StpA ChIP in delta hns CFT073 rep 1
Δhns

value: Polyclonal, Covance, Final bleed, WI631


title: Delta H-NS Input Bead A Rep 1

description:
Pooled input for H-NS, StpA IPs delta hns CFT073 rep 1
Δhns


title: Delta H-NS H-NS Rep 2

description:
HNS ChIP in delta hns CFT073 rep 2
Δhns

value: Polyclonal, Harlan, Final bleed, ID R10041, Cat POL001


title: Delta H-NS H-NS Rep 1

description:
HNS ChIP in delta hns CFT073 rep 1
Δhns


title: Delta H-NS Delta StpA Delta RfaH Input Bead G Rep 2

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns delta rfaH CFT073 rep 2
ΔhnsΔstpAΔrfaH

value: <delta>hns<delta>stpA<delta>rfaH


title: Delta H-NS Delta StpA Delta RfaH Input Bead G Rep 1

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns delta rfaH CFT073 rep 1
ΔhnsΔstpAΔrfaH


title: Delta H-NS Delta StpA Delta RfaH Sigma70 Rep 3

description:
Sigma 70 ChIP in delta stpA delta hns delta rfaH CFT073 rep 3
ΔhnsΔstpAΔrfaH

value: Monoclonal, Biolegend, 663207


title: Delta H-NS Delta StpA Delta RfaH Input Bead G Rep 3

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns delta rfaH CFT073 rep 3
ΔhnsΔstpAΔrfaH


title: Delta H-NS Delta StpA Input Bead G Rep 3

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns CFT073 rep 3
ΔhnsΔstpA

value: <delta>hns<delta>stpA


title: hBM-MSC_TNF_18h

city: Seoul

first: Soon Young

last: Shin

address: 120, Neungdong-ro, Gwangjin-gu

department: Department of Biological Sciences

country: South Korea

institute: Konkuk University

description: Gene expression of TNF-α-treated MSCs

hyb_protocol: Hybridization and washing steps were performed using Agilent’s Gene Expression Hybridization Kit and Agilent’s Gene Expression Wash Buffer Kit, respectively.

scan_protocol: Microarrays were scanned using Agilent’s DNA microarray scanner and Feature Extraction Software.

data_processing: Raw data were processed and normalized using Agilent's GeneSpring Software. First, noise data with signal intensity less than 0.01 were adjusted to 0.01. For normalization, Each probes are divided by the 50th percentile (median) value of all probes. To optain reliable genes, spots with signal intensity lower than the background or insignificant standard deviation of each pixel value were removed by applying flag values.

source_name: Human bone marrow mesenchymal stem cell, 18 h, TNF-α

label_protocol: Amplification and babeling were performed using Agilent’s Low RNA Input Linear Amplification kit PLUS.

growth_protocol: Mesenchymal stem cells are cultured in complete MSCGM2 (Promocell) and serum-starved in DMEM containing 0.5% fetal bovine serum for 24 h before treating TNF-a.

extract_protocol: Total RNA was isolated using NucleoZOL (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: Serum-starved MSCs are treated with or without 5 ng/mL TNF-a for 18 h.

value: bone marrow

value: TNFalpha, 5ng/mL, 18h


title: Mobilized PB HSC on AAVS1 control Mouse 1

value: Mobilized Peripheral Blood HSC

value: UT


title: Delta H-NS Delta StpA Input Bead G Rep 1

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA


title: hBM-MSC_NT

description: Gene expression of nontreated MSCs

source_name: Human bone marrow mesenchymal stem cell, nontreated

value: nontreated


title: T cell on CD40L control Mouse 1

source_name: Human T cells

value: T cells


title: Delta H-NS Delta StpA Delta RfaH Sigma70 Rep 1

description:
Sigma 70 ChIP in delta stpA delta hns delta rfaH CFT073 rep 1
ΔhnsΔstpAΔrfaH


title: Delta H-NS Delta StpA Delta RfaH RNAP Rep 1

description:
Beta ChIP in delta stpA delta hns delta rfaH CFT073 rep 1
ΔhnsΔstpAΔrfaH

value: Monoclonal, Biolegend, Beta subunit, 663905


title: Delta H-NS Delta StpA Input Bead G Rep 2

description:
Pooled input for RNAP and Sigma70 IPs delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta H-NS Delta StpA Delta RfaH RNAP Rep 3

description:
Beta ChIP in delta stpA delta hns delta rfaH CFT073 rep 3
ΔhnsΔstpAΔrfaH


title: Delta H-NS Delta StpA Input Bead A Rep 2

description:
Pooled input for H-NS, StpA, and RfaH IPs delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta H-NS Delta StpA Input Bead A Rep 3

description:
Pooled input for H-NS, StpA, and RfaH IPs delta stpA delta hns CFT073 rep 3
ΔhnsΔstpA


title: Delta H-NS Delta StpA Input Bead A Rep 1

description:
Pooled input for H-NS, StpA, and RfaH IPs delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA


title: Delta H-NS Delta StpA Sigma70 Rep 1

description:
Sigma 70 ChIP in delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA


title: Delta H-NS Delta StpA Sigma70 Rep 3

description:
Sigma 70 ChIP in delta stpA delta hns CFT073 rep 3
ΔhnsΔstpA


title: Delta H-NS Delta StpA RNAP Rep 3

description:
Beta ChIP in delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta H-NS Delta StpA RNAP Rep 1

description:
Beta ChIP in delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA


title: Delta H-NS StpA Rep 2

description:
StpA ChIP in delta hns CFT073 rep 2
Δhns


title: Delta H-NS Delta StpA RfaH Rep 1

description:
RfaH ChIP in delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA

value: Polyclonal PAS 552, Final bleed


title: Delta H-NS Delta StpA StpA Rep 1

description:
StpA ChIP in delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA


title: Delta H-NS Delta StpA RfaH Rep 2 (actually rep 4)

description:
RfaH ChIP in delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta H-NS Delta StpA H-NS Rep 2

description:
H-NS ChIP in delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta H-NS Delta StpA Sigma70 Rep 2

description:
Sigma 70 ChIP in delta stpA delta hns CFT073 rep 2
ΔhnsΔstpA


title: Delta StpA Delta RfaH Sigma70 Rep 3

description:
Sigma 70 ChIP in delta stpA delta rfaH CFT073 rep 3
ΔstpAΔrfaH

value: <delta>stpA<delta>rfaH


title: Delta H-NS Delta StpA H-NS Rep 1

description:
H-NS ChIP in delta stpA delta hns CFT073 rep 1
ΔhnsΔstpA

value: NA-bacteria


title: Delta StpA Delta RfaH RNAP Rep 3

description:
Beta ChIP in delta stpA delta rfaH CFT073 rep 3
ΔstpAΔrfaH


title: Delta H-NS Delta StpA Delta RfaH Sigma70 Rep 2

description:
Sigma 70 ChIP in delta stpA delta hns delta rfaH CFT073 rep 2
ΔhnsΔstpAΔrfaH


title: Delta StpA Delta RfaH Sigma70 Rep 1

description:
Sigma 70 ChIP in delta stpA delta rfaH CFT073 rep 1
ΔstpAΔrfaH


title: Delta H-NS Delta StpA H-NS Rep 3

description:
H-NS ChIP in delta stpA delta hns CFT073 rep 3
ΔhnsΔstpA


title: Delta StpA Input Bead G Rep 3

description:
Pooled input for RNAP and Sigma70 IPs
ΔstpA

value: <delta>stpA


title: Delta StpA Delta RfaH Input Bead G Rep 2

description:
Pooled input for RNAP and Sigma70 IPs
ΔstpAΔrfaH


title: Delta StpA Delta RfaH Sigma70 Rep 2

description:
Sigma 70 ChIP in delta stpA delta rfaH CFT073 rep 2
ΔstpAΔrfaH


title: Delta StpA Sigma70 Rep 1

description:
Sigma 70 ChIP in delta stpA CFT073 rep 1
ΔstpA


title: Delta StpA Delta RfaH Input Bead G Rep 3


title: Delta StpA Sigma70 Rep 2

description:
Sigma 70 ChIP in delta stpA CFT073 rep 2
ΔstpA


title: Delta StpA RNAP Rep 3

description:
Beta ChIP in delta stpA CFT073 rep 3
ΔstpA


title: Delta StpA Delta RfaH RNAP Rep 2

description:
Beta ChIP in delta stpA delta rfaH CFT073 rep 2
ΔstpAΔrfaH


title: Delta StpA Input Bead G Rep 1


title: Delta StpA Input Bead G Rep 2


title: Delta StpA Delta RfaH RNAP Rep 1

description:
Beta ChIP in delta stpA delta rfaH CFT073 rep 1
ΔstpAΔrfaH


title: Delta StpA RfaH Rep 1

description:
RfaH ChIP in delta stpA CFT073 rep 1
ΔstpA


title: Delta StpA StpA Rep 2

description:
StpA ChIP in delta stpA CFT073 rep 2
ΔstpA


title: Delta StpA Input Bead A Rep 1

description:
Pooled input for H-NS, StpA, and RfaH IPs
ΔstpA


title: Delta StpA RNAP Rep 1

description:
Beta ChIP in delta stpA CFT073 rep 1
ΔstpA


title: Delta StpA StpA Rep 1

description:
StpA ChIP in delta stpA CFT073 rep 1
ΔstpA


title: Delta StpA H-NS Rep 1

description:
HNS ChIP in delta stpA CFT073 rep 1
ΔstpA


title: Delta RfaH Input Bead G Rep 3

description:
Pooled input for RNAP and Sigma70 IPs
ΔrfaH

value: <delta>rfaH


title: Delta StpA H-NS Rep 2

description:
HNS ChIP in delta stpA CFT073 rep 2
ΔstpA


title: Delta RfaH Input Bead G Rep 2


title: Delta StpA Input Bead A Rep 2


title: Delta RfaH Input Bead G Rep 1


title: Delta StpA Sigma70 Rep 3

description:
Sigma 70 ChIP in delta stpA CFT073 rep 3
ΔstpA


title: Delta RfaH Input Bead A Rep 2

description:
Pooled input for H-NS, StpA, and RfaH IPs
ΔrfaH


title: Delta RfaH Input Bead A Rep 1


title: Delta RfaH Sigma70 Rep 3

description:
Sigma 70 ChIP in delta rfaH CFT073 rep 3
ΔrfaH


title: Delta StpA RNAP Rep 2

description:
Beta ChIP in delta stpA CFT073 rep 2
ΔstpA


title: Delta RfaH Sigma70 Rep 1

description:
Sigma 70 ChIP in delta rfaH CFT073 rep 1
ΔrfaH


title: Delta RfaH Sigma70 Rep 2

description:
Sigma 70 ChIP in delta rfaH CFT073 rep 2
ΔrfaH


title: Delta RfaH RNAP Rep 3

description:
Beta ChIP in delta rfaH CFT073 rep 3
ΔrfaH


title: Delta RfaH RNAP Rep 2

description:
Beta ChIP in delta rfaH CFT073 rep 2
ΔrfaH


title: Delta RfaH RfaH Rep 1

description:
RfaH ChIP in delta rfaH CFT073 rep 1
ΔrfaH


title: Delta RfaH StpA Rep 3

description:
StpA ChIP in delta rfaH CFT073 rep 3
ΔrfaH

value: Polyclonal, Covance, Final bleed, WI631


title: Delta RfaH StpA Rep 1

description:
StpA ChIP in delta rfaH CFT073 rep 1
ΔrfaH


title: Delta RfaH H-NS Rep 2

description:
HNS ChIP in delta rfaH CFT073 rep 2
ΔrfaH

value: Polyclonal, Harlan, Final bleed, ID R10041, Cat POL001


title: WT Input Bead G Rep 1

description: Pooled input for RNAP and Sigma70 IPs

value: WT


title: WT Input Bead A Rep 3

description: Pooled input for H-NS, StpA, and RfaH IPs


title: WT Input Bead G Rep 2

description: Pooled input for RNAP and Sigma70 IPs


title: Delta RfaH H-NS Rep 1

description:
HNS ChIP in delta rfaH CFT073 rep 1
ΔrfaH


title: Delta RfaH Input Bead A Rep 3


title: WT Input Bead A Rep 1


title: WT Input Bead G Rep 3

description: Pooled input for RNAP and Sigma70 IPs


title: WT Input Bead A Rep 2


title: WT Sigma70 Rep 3

description: Sigma 70 ChIP in WT CFT073 rep 3

value: Monoclonal, Biolegend, 663207


title: WT Sigma70 Rep 1

description: Sigma 70 ChIP in WT CFT073 rep 1


title: Delta RfaH H-NS Rep 3

description:
HNS ChIP in delta rfaH CFT073 rep 3
ΔrfaH


title: WT RNAP Rep 3

description: Beta ChIP in WT CFT073 rep 3


title: WT Sigma70 Rep 2

description: Sigma 70 ChIP in WT CFT073 rep 2


title: Delta RfaH StpA Rep 2

description:
StpA ChIP in delta rfaH CFT073 rep 2
ΔrfaH


title: WT RfaH Rep 1

description: RfaH ChIP in WT CFT073 rep 1


title: WT RNAP Rep 1

description: Beta ChIP in WT CFT073 rep 1


title: WT StpA Rep 3

description: StpA ChIP in WT CFT073 rep 3


title: Delta RfaH RNAP Rep 1

description:
Beta ChIP in delta rfaH CFT073 rep 1
ΔrfaH


title: WT RfaH Rep 2

description: RfaH ChIP in WT CFT073 rep 2


title: WT RNAP Rep 2

description: Beta ChIP in WT CFT073 rep 2


title: WT StpA Rep 1

description: StpA ChIP in WT CFT073 rep 1


title: WT StpA Rep 2

description: StpA ChIP in WT CFT073 rep 2


title: Delta StpA Delta RfaH Input Bead G Rep 1

description:
Pooled input for RNAP and Sigma70 IPs
ΔstpAΔrfaH


title: WT H-NS Rep 1

description: HNS ChIP in WT CFT073 rep 1


title: C646 + 4hr WO Rep 3

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

country: Sweden

institute: Stockholm University

description: C646 + 4hr WO Rep 3

data_processing:
RNA-seq reads were mapped to the Drosophila dm6 genome assembly using the STAR RNA-seq aligner with the default parameters. Coverage tracks of the mean RPKM signal from the three biological replicates were produced using deepTools. Reads mapping to the exons of genes were counted using featureCounts and differential gene expression analysis performed on the count data using the DESeq2 Bioconductor package.
Assembly: dm6
Supplementary files format and content: bigwig for coverage

source_name: Schneider 2 (S2) cells

growth_protocol: S2 cells were cultured at 25°C in Schneider's Drosophila medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Total RNA corresponding to 0.5-1 million control or drug treated S2 cells were homogenized in TRIzol LS (Ambion) and purified and concentrated using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturer's instructions. RNA extractions were performed on three independent biological replicates.
RNA libraries were prepared from total RNA using the Illumina Stranded mRNA Prep kit and sequenced single-end (1 x 75 bp) on the Illumina NextSeq 2000 platform.

treatment_protocol: Experiments were conducted on cells at 80-90% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 for 30 minutes, with or without a drug washout (WO) in media without C646 for either 1 hr or 4 hr.

value: Oregon R

tag: developmental stage

value: Late embryonic stage


title: WT H-NS Rep 2

description: HNS ChIP in WT CFT073 rep 2


title: C646 + 4hr WO Rep 2

description: C646 + 4hr WO Rep 2