title: Ginigival mucosa, diabetic

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
CellRanger Software version 6.0.2 was use to generate the FASTQ files, aligned fastq files to the mouse reference genome (refdata-gex-mm10-2020-A)
Data filtering: mRNA contamination was moved using Soupx v1.3.0, nCount_RNA >= 500 & nFeature_RNA > 200 & nFeature_RNA < 6500 & percent.mt < 15
Assembly: mm10
Supplementary files format and content: Barcodes, features and matrix for each sample

source_name: Gingival tissue

extract_protocol:
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pCapture
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pLibraryPrep

treatment_protocol: Type-I diabetes mellitus was induced in mice using streptozotocin. Bacterial-induced inflammation was maintained for two weeks, followed by a two-week waiting period. Cells were isolated from the gingiva, pooled from 4 mice per group. Negative selection was performed to remove dead cells (DAPI+), endothelial cells (CD31+), and red blood cells (Ter-119+). Positive selection for CD45+ cells was conducted, with 20% enrichment of CD11c+CD45+ cells by FACS sorting. 10,000 FACS-sorted cells were loaded per lane of a 10x Genomics Chromium instrument for scRNA-seq analysis. For each experimental condition, a pool of four mice was used, with no replicates.

value: Gingival tissue

value: diabetic


title: Group B-16

status: Public on Nov 26 2025

type: SRA

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

country: China

institute: SUN YAT-SEN UNIVERSITY

library_source: transcriptomic

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer after quality filtering.
Firstly, Q30 was used to perform quality control.
The high quality reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl gtf gene annotation file with hisat2 software (v2.04).
Then, cuffdiff software (part of cufflinks, v2.2.1) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes.
Fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Assembly: UCSC hg19
Supplementary files format and content: processed_data.xlsx: Excel file includes raw counts and normalized counts for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: liver metastases

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

tag: tissue

value: liver metastases

tag: donor


title: Group A-16

source_name: CRC tissues

value: CRC tissues


title: A2 LTA treated replicate 2

city: Graz

first: Sebastian

last: Vosberg

address: Auenbruggerplatz 15

country: Austria

institute: Medical University of Graz

data_processing:
Sequencing reads were mapped using STAR with reference genome hg38. Gene expression counts were retreived using featureCounts. Default parameters have been used for all individual steps
Assembly: hg38
Supplementary files format and content: tab-separated values: gene_symbol / raw_count

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Total RNA were isolated using peq gold total RNA kit (VWR)
mRNA library was made with poly A enrichment using a kit developed by Novogene (Novogene GmbH)

treatment_protocol: The following reagents were used for treatment of AML cell lines: recombinant human LTα3 (5 ng/ml or 100 ng/ml rh-LTα3; R&D Systems), recombinant human TNF (5 ng/ml or 100 ng/ml rh-TNF; R&D Systems) for 24h, if indicated

value: bone marrow

tag: cell type

value: acute myeloid leukemia

tag: genotype

value: WT

tag: treatment

value: recombinant human Lymphotoxin A, 100 ng/ml


title: Group A-17


title: mES-E14-WT-PromoterBait_1

city: Oxford

first: James

last: Davies

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description:
Library name: Sample 1
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt

library_source: genomic

data_processing:
The raw FASTQ file is processed to reconstruct a single read from paired-end sequencing data. These reads are then mapped to the 800bp region surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This step allows the reads to be segmented into ‘slices’ based on their alignment to the sequence around the capture site, enabling the identification of ligation junctions with base-pair precision. After this, the resulting FASTQ file is aligned to the genome using Bowtie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes contact frequency
Library strategy: Capture-C

molecule: genomic DNA

organism: Mus musculus

source_name: Embryo

growth_protocol: This research was conducted under the project license PP3929317, adhering to the European Union directive 2010/63/EU and the UK Animals (Scientific Procedures) Act of 1986. All procedures were reviewed by the Animal Welfare and Ethical Review Body of the Department of Biomedical Services at the University of Oxford. Murine erythroid cells were purified using Ter119 selection (ter119-phycoerythrin antibodies (Biolegend 116208) and anti-PE MACS beads (Miltenyi, 130-048-801)) from the spleen of C57BL/6J mice following administration of phenylyhydrazine (40 mg/g body weight, 3 doses, 12 h apart). Murine HSPCs were extracted and cultured as previously described(Wilkinson et al., 2020). Murine ES cells (E14TG2a) were maintained in gelatin (Gibco 10131-035) coated flasks in Glasgow MEM x1 liquid (Gibco 21710-025) with 10% FCS (Gibco 10270-106), 1x Glutamine (Gibco 25030-024), 1 mM sodium pyruvate (Gibco 11360-039), 1x non-essential amino acids (Gibco 11140-035), mercaptoethanol (Gibco 31350-010) and LIF (Thermo Fisher PMC9484). RPE-1 cells were maintained in Dulbecco’s Modified Eagle’s Medium (Gibco, 11960044) supplemented with 10% fetal bovine serum, 1% GLUTmax (Gibco, 35050061), 1% non-essential amino acids, and 1% penicillin-streptomycin (Gibco, 15070063) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
3C library manufacture was undertaken as described previously(Hamley et al., 2023). In brief, aliquots of 1 x 107 cells were fixed 10 ml media with Formaldehyde, 37% (vol/vol) (Sigma, 47608-250ML) at a final of concentration 2% for 10 minutes at room temperature. This reaction was quenched with 1 M glycine to a final concentration 130 mM and centrifuged (5 min, 300 g). The supernatant was removed, and the cell pellet washed with cold PBS and reconstituted in 1 ml PBS. Cells were permeabilised with Digitonin (Sigma D-141; final concentration of 0.005% wt/vol). Cells were snap frozen and stored at -80 °C. Subsequently, defrosted, permeabilised cells were centrifuged (5 min, 300 g) the supernatant discarded, and resuspended in a reduced calcium content MNase buffer (Tris-HCl pH 7.5 10 mM; CaCl2 1 mM). Cells were split into 3 separate digests to allow titration of MNase (NEB M0247) concentration, which typically ranged from 5 to 20 Kunitz units per reaction. This reaction was incubated for 1 hour at 37 °C in an Eppendorf Thermomixer at 500 rpm and was quenched by adding ethylene glycol-bis(2-aminoethylether)-N,N,N’,N’-tetraacetic acid (EGTA) (Sigma E3889) to a final concentration of 5 mM. To evaluate digestion efficiency, 20% of the reaction was removed. The remaining reaction was centrifuged (5 min, 300 g) and the supernatant containing digestion buffer was discarded. The cell pellet was washed in 1 ml PBS and the cells were resuspended in DNA ligase buffer (Thermo Scientific; final concentrations Tris-HCl pH 7.5 40 mM, MgCl2 10 mM, DTT 10 mM, 5 mM ATP) supplemented with dNTPs (final concentration 400 µM of each of dATP, dCTP, dGTP and dTTP (Thermo Fisher R0191)) and EGTA 5 mM. The reaction mixture was then treated with T4 Polynucleotide Kinase PNK (NEB M0201L) and DNA Polymerase I Large (Klenow) Fragment (NEB M0210L) at final concentrations of 200 U/ml, and 100 U/ml respectively, T4 DNA ligase (Thermo Scientific, High Concentration Ligase (30 U/µl) EL0013) was added to a final concentration of 300 U/ml and the reaction was incubated at 20°C overnight using an Eppendorf Thermomixer at 500 rpm. Chromatin was decrosslinked (proteinase K, 65 °C, >2 hours) and DNA was purified using the Qiagen DNeasy blood and tissue kit (69506). Digestion and ligation efficiencies were assessed using the Agilent Tapestation (D1000 reagents).
Sequencing library preparation. Oligonucleotide capture was performed as previously described(Hamley et al., 2023; Hua et al., 2021a). Initially, 7-10 µg of each 3C library was sonicated to an averagefragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (3 cycles of 60 seconds, duty cycle 10%, intensity 5, 200 cycles per burst). After sonication, the size of library was evaluated using an Agilent TapeStation (DNA 1000). The sample was then cleaned using Ampure XP beads (Beckman Coulter A63881). To maximise library complexity, three separate aliquots of 2 µg each of the sonicated 3C library were processed simultaneously for the addition of sequencing adaptors (NEB Ultra II (NEB 7645S)) following the standard protocol with the following alternations: 7.5 µl adapter was used in ligation reactions; all Ampure XP bead clean ups were performed at a ratio of 1 : 1.8 and  the final PCR was carried out in triplicate using the Herculase II PCR reagents (Agilent) to enhance DNA yield.

value: Embryo

tag: cell line

value: Mouse embryonic stem cell


title: chiPSC_Primed,cHiC,Rep2

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

country: France

institute: Université Paris Cité

description:
chiPSC_rep2_ontarget.XIConly.q23.cool
chiPSC.ontarget.XIConly.q23.cool

data_processing:
Sequencing reads from both technical replicates were processed using the HiC-pro pipeline (Servant 2015), including, reads alignement on the human reference genome (hg38, mapping quality > 23) and valid interaction pairs detection. Raw contact matrices were built by binning in genomic windows of 2kb, 4kb, 6kb, 8kb and 10kb, using the allValidPairs2cooler.sh utility. Correlation analysis between the raw contact matrices of both replicates was done using the hicCorrelate package from the HiCExplorer toolbox (Wolff 2020). The 4kb binning was retained for the very good correlation score (R²=0,67) and the contact matrices of both replicates were merged. The raw contact interaction frequencies of the captured region were normalized using the Iterrative Correction approach (Imakaev 2012). Insulation score was computed on the normalized contact matrice using the hicFindTads package (Wolff 2020) with –minDepth 12000 –maxDepth 48000 –step 8000. Viewpoints data were extracted using the chicViewpoint package (Wolff 2020) with default parameters. Chromatin loops were called on ICE normalized contact matrices using the mustache software with default parameters (Ardakany 2020), non-significant loop interactions (FDR p.value < 0,05) were filtered before downstream analysis.
Assembly: rheMac10, panTro6
Supplementary files format and content: cool file containing the raw and the ICE normalized interaction frequency values binned at 4kb
Supplementary files format and content: Bigwig files for insulation score
Library strategy: Capture Hi-C

organism: Pan troglodytes

source_name: chiPSC-Sandra

extract_protocol:
In situ Capture HiC was performed as previously published (Davies 2016) with the following modifications. Cells were crosslinked with 2% formaldehyde. In short, 10x10⁶ cells were lysed on ice in 10 mM Tris-HCL pH8.0, 10 mM NaCl, 0,2% NP40, 1X complete protease inhibitor cocktail (Roche). De-crosslinking was performed in 100 µL 0,5% SDS at 37°C for 1h under agitation (1400 rpm). Nuclei permeabilization was done by adding 50 µL of 10% Triton X-100 and 290µL H2O and incubated for 15 minutes at 37°C and swirling at 1400 rpm. To prepare for digestion, 50µL of 10X DpnII buffer was added and 50µL were taken as an undigested control. At mid day, a first 10µL of DpnII (NEB, 50 000 U/ml) was added and incubated for 4 hours at 37°C, swirling at 1400 rpm. Another 10 µL was added and incubation was carried on overnight. A final 10µL of DpnII  was added the following morning and  left for 4 hours. DpnII was inactivated by heating at 65°C for 20 minutes and 50 µL were taken as an digested-unligated control. Ligation was carried by adding 800 µL of ligation cocktail containing 240U T4 ligase (ThermoScientific 30U/µL), 1X T4 ligase buffer, and incubated overnight at 16°C swirling at 1000 rpm. To prepare for DNA purification, samples and controls were incubated with 150µg of ProteinaseK (Eurobio) for 4 hours ar 65°C. Then, 0,1 vol. of NaAc 3M and 3 vol. of 100% EtOH were added and incubated overnight at -80°C. Precipitated DNA were pelleted by centrifugation, washed with 70% EtOH and finally air dryied. Samples and controls were resuspended in 100 µL and 20 µL H2O respectively and 1 µL of RNAse A (ThermoScientific) was added and incubated at 37°C for 1 hour.  DNA quantities in sample and controls were determined using the Qbit broad range kit (ThermoScientific) and 100 ng of each were loaded on an agarose gel as quality control of the digestion and ligation steps.
Other

value: chiPSC-Sandra

value: chimpanzee induced pluripotent stem cell


title: U1 untreated replicate 1

source_name: CD34+ HSPCs

value: CD34+ HSPCs


title: A2 LTA treated replicate 1


title: Ginigival mucosa, normoglycemic

country: USA

library_source: transcriptomic single cell

value: normoglycemic


title: Group C-15

source_name: normal intestinal mucosal tissues

value: normal intestinal mucosal tissues


title: A2 TNF treated replicate 3

value: recombinant human TNF, 100 ng/ml


title: Group B-18


title: chiPSC_Primed,cHiC,Rep1

description:
chiPSC_rep1_ontarget.XIConly.q23.cool
chiPSC.ontarget.XIConly.q23.cool


title: A2 untreated replicate 3


title: A2 untreated replicate 2


title: 053022-700

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

data_processing:
Sequence files were pre-processed and trimmed using fastp 0.23.2
Alignment was done using STAR 2.7.10b
Count matrices were imported into R 4.3.0 and Rstudio 2023.03.0.386 and analyzed with DESeq2 with design = ~ group + comparison, where “group” controlled for litter/sex and comparison was either genotype or sex, depending on the analysis
Assembly: mm10
Supplementary files format and content: Matrix with raw counts

source_name: kidney

extract_protocol:
Total RNA was isolated using Trizol (Fisher Scientific) and Qiagen RNeasy kit (Quiagen, #74034) using the manufacturer’s protocols
RNA libraries were generated, and RNA sequencing was conducted by a core laboratory at the Institute for Genome Sciences (University of Maryland)

value: kidney

tag: Sex

value: Male

tag: age

tag: body weight

tag: kidney weight_1

tag: kidney weight_2

tag: sex litter_group

value: Pkd2fl/fl; Pax8; Tet-O-Cre +

value: Doxycycline Hyclate 50mg/Kg


title: Kat6b KO pre-osteoblast bone, rep 4

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: PreO_KO_1721_1

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 2.2.4
Fragment (read pair) counts were summarized by Ensembl gene ID using Gencode annotation to the mouse genome vM24
Assembly: mm10
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Ensembl Gene Id, Gene Symbol, total gene length (total base count of all exons) and the number of fragments mapping to that gene.

source_name: Mouse embryonic fibroblasts

growth_protocol: E12.5 embryos were collected under a dissecting microscope. Limbs, head, tail and internal organs were removed. Dissected carcasses were triturated in 1 ml DMEM + 10% FCS and passed through a 40 µm cell sieve onto gelatine-coated plated. Cells were cultured in DMEM with 10% (vol/vol) foetal calf serum (FCS), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma, 15140122) and grown in 5% CO2, 3% O2 and 37oC.

extract_protocol:
Cells were washed in PBS and scraped in PBS. Cells were pelleted at 200 g for 5 min, supernatant was removed, and samples were processed using the Qiagen RNease Mini kit (Qiagen, 74104), according to the manufacturer’s instructions and including the optional DNase digest step. RNA quality and quantity was assessed using a Tapestation 4200 (Agilent).
500 ng total RNA was using to generate RNA libraries using the TruSeq RNA library prep kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: Passage 3 MEFs were plated onto gelatine-coated plates at 2.5x10^4 cells/cm2 and grown for 3 days at 37oC in 5% CO2 and 3% O2 in either (a) proliferation medium (DMEM (Gibco, 11885084) , 10% (vol/vol) FCS, 100 units/ml penicillin  and 100 µg/ml streptomycin (Gibco, 15140122), (b) osteogenic medium (Proliferation media, 2 mM GlutaMAXTM (Gibco, 35050061), 100 units/ml penicillin, 100 µg/ml streptomycin (Gibco, 15140122), 20 ng/ml BMP-2 (Sigma, B3555), 100 µg/ml ascorbic acid (Sigma, A4403) and 10 mM ß-glycerophosphate (Sigma, G9422) (Saeed et al., 2012) or (c) chondrogenic medium (DMEM F12 (Gibco, 11885084), 10% (vol/vol) FCS, 2 mM L-Glutamate, 100 units/ml penicillin, 100 µg/ml streptomycin (Gibco, 15140122), 100 ng/ml BMP-2 (Sigma, B3555), 50 µg/ml ascorbic acid (Sigma, A4403), 10 mM ß-glycerophosphate (Sigma, G9422), 10 ng/ml TGF-ß3 (Sigma, 19008721), 100 nM dexamethasone (Sigma, D4902), 100 ug/ml sodium pyruvate (Gibco, 11360070), 1x ITS (Sigma, I3146) and 1x NEAA (Gibco, 11140050)) (Saeed et al., 2012).

value: Mouse embryonic fibroblasts

tag: kat6b genotype

tag: litter

tag: embryo number


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

institute: Institute for Integrative Biology of the Cell (I2BC)

description: Library name: MKL1

data_processing:
Hi-C libraries were proccessed using the OHCA pipeline from Bioconductor: https://jserizay.com/OHCA/docs/devel/. Hi-C matrices were binned at 1Kb, plasmids were exluded of the analyses
For the ChIP-seq analysis, each read was aligned to the reference genome (Salmonella enterica serovar Typhimurium strain SL1344) using Bowtie2 (v 2.4.2).  Paired-end reads were then Merged and sorted with Samtools, and PCR duplicates were removed using the Picard MarkDuplicates tool. Subsequently, SAM files were converted to BAM files, indexed, and processed to generate bedGraph and bigWig files with using bamCompared from DeepTools2. This tool allowed us to compare the ChIP-seq data to the INPUT and normalize it in Bins Per Million mapped reads (BPM). For Hi-C correlations and determination of protein occupancy (H-NS and RNA polymerase), 1Kb bins were used. No binning was used for the rest of analyses.
For RNA-seq analysis, paired-end reads were mapped to the reference genome using Bowtie2 (v 2.4.2). After alignment, SAM files were sorted, converted to BAM format, and indexed. BAM files were subsequently converted to WIG format using bamCoverage or Galaxy with CPM normalization. Read quantification in sense and antisense orientations was performed using featureCounts program (v 2.0.1)70. Differential gene expression analysis was conducted in R using the SARTools pipeline (Statistical Analysis of RNA-Seq data Tools, v1.8.1), which is based on DESeq2. Quality controls, raw count normalization, and identification of differentially expressed genes were systematically performed. Principal Component Analysis (PCA) and hierarchical clustering were applied to data transformed using Variance Stabilizing Transformation (VST) to ensure homoscedasticity. The Benjamini-Hochberg method was used for p-value adjustment with a statistical significance threshold of 0.05. The condition "GFP negative" was defined as the reference for comparisons. Genes with null counts across all samples and predefined low-quality features were excluded prior to analysis.  Additionally, to facilitate correlations with Hi-C data, DESeq2-normalized counts per kilobase for each gene under all experimental conditions were determined
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium SL1344 complete genome, GenBank: FQ312003.1
Supplementary files format and content: 4879x4879 Hi-C contact matrices in txt format

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacteria

growth_protocol: Bacteria were cultured in Lennox Broth (LB) medium at 37°C with shaking at 180 rpm. Overnight cultures were diluted 1:1000 and grown to an OD600 of 0.1 (early exponential phase, EEP) or OD600 of 2 (early stationary phase, ESP). When required, antibiotics were added to the liquid medium or agar plates at the following final concentrations: 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 30 μg/mL chloramphenicol (Cm). Include oxygen shock and microanaerobiosis

extract_protocol:
Hi-C: Frozen pellets were thawed on ice, resuspended in 200 μL of 1× Tris-EDTA (TE) buffer (Sigma-Aldrich, Cat# T928) containing a complete protease inhibitor cocktail (Roche, Cat# 11873580001). Then, 1 µl of ready-lyse lysozyme (LGC Biosearch, Cat# LU-R1804M) was added and the mixture was incubated at RT for 20 minutes.  Next, 10 µl of 10% SDS (Sigma-Aldrich, Cat#  05030) was added to the cells and incubated for 10 minutes at RT. Subsequently, the lysed cells were transferred into a 2 mL Eppendorf tube containing 800 μL of digestion mix: 100 μL of 10× NEB1 buffer (New England Biolabs, Cat# B7001S), 100 μL of 10% Triton (Sigma-Aldrich, Cat# T8787), and 600 μL of sterile water. After removing 80 μL of non-digested control, 20 μL of HpaII enzyme (New England Biolabs, Cat# R0171L) were added to the digestion mix. Both tubes were then incubated for 3 hours at 37°C with agitation. Following DNA digestion, 80 μL of the digested control were removed and kept on ice with the non-digested control. The remaining digestion mix was centrifuged for 20 minutes at 16,000 × g, 4°C, and the pellet was re-suspended in 80 µL of sterile water. The 80 µL of digested DNA was then added to the biotinylation mix containing 10 µL of 10× ligation buffer, 1 µL of 10 mM dAGTP mix, 3 µL of 1 mM biotin-14-dCTP (Jena Biosciences, Cat# E-NU-956-BIO14-S), and 2 µL of DNA polymerase I, large (Klenow) fragment (New England Biolabs, Cat# M0210L), and incubated for 1 hour at 37°C with agitation. Following biotinylation, proximity ligation of DNA fragments was performed by adding the ligation mix: 24 µL of 10× ligation buffer (without ATP), 2.4 µL of 100 mM ATP, 2.4 µL of 10 mg/mL BSA (New England Biolabs, Cat# B9000S), and 3.2 µL of of T4 DNA ligase (Thermo Fisher Scientific, Cat# EL0013). Ligation was performed at 25°C for 3 hours with gentle agitation. The crosslink was then reversed by incubating the samples (including the non-digested and digested controls) overnight at 65°C in the presence of proteinase K (20 mg/mL; Eurobio Scientific, Cat# GEXPROK01-B5), EDTA (500 mM; Sigma-Aldrich, Cat# 03690), and 10% SDS. The next day, DNA was purified by phenol extraction and ethanol precipitation. Briefly, one volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Thermo Fisher Scientific, Cat# 10308293) was added to the samples. Following centrifugation, the upper aqueous phase was transferred to a new 1.5 mL tube, and DNA was precipitated with 1/10 volume of 3 M Na-acetate (pH 5.2) and two and a half volumes of cold ethanol. After incubation at −80°C for 30 minutes, the DNA was pelleted, washed once with 70% ethanol, and dried using an Eppendorf concentrator plus speed vac. The DNA was resuspended in 130 µL of 1× TE buffer containing 10 μg/mL RNase A (Thermo Fisher Scientific, Cat# EN0531) ChIP-seq: frozen cell pellets, fixed with 1% formaldehyde, were thawed on ice and re-suspended in 500 μl of lysis buffer I: 20% sucrose (Sigma-Aldrich, Cat# S7903), 10 mM Tris-HCl (pH 8), 50 mM NaCl, and 10 mM EDTA, supplemented with 4 μl of ready-lyse lysozyme. The mixture was incubated at 37°C for 30 minutes. Next, 500 μl of lysis buffer II (50 mM Tris-HCl (pH8), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 and complete protease inhibitor cocktail) was added. The cells were transferred to a 1 mL Covaris tube and sonicated using a Covaris S220 focused Ultrasonicator. Sonication parameters were set to 210 seconds for EEP samples and 270 seconds for ESP samples (peak power = 140 W; duty factor = 5%; cycles per burst = 200). Following sonication, the samples were centrifuged at 18,000 × g for 30 minutes at 4°C. The supernatant was transferred into a new 1.5 mL tube, with 50 μL set aside as input and stored at −20°C until further use. Immunoprecipitation of FLAG-tagged proteins was performed by incubating the cell extracts with 100 μL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich, Cat# A2220) overnight at 4°C on a rotator. The beads were washed twice with 400 μL of TBS (Tris-HCl 50mM pH 7.4, 150mM NaCl) containing 0.05% Tween 20, followed by three washes with 400 μL of cold TBS. Each wash step was performed under rotation for 10 minutes at 4°C. The 3xFLAG-protein-DNA complexes were eluted by adding 2.5 volumes of 3xFLAG peptide solution (Sigma-Aldrich, Cat# F4799) relative to the total packed gel volume. The samples were incubated for 90 minutes on a rotator at 4°C, centrifuged for 30 seconds at 5000 × g at 4°C, and the supernatant was transferred to 1.5 mL LoBind DNA tubes. A second elution step was performed similarly. The IP and input samples were treated with RNase A (10 μg/mL) for 1 hour at 37°C and then incubated overnight at 65°C with proteinase K (final concentration: 50 μg/mL) to reverse the formaldehyde crosslinks. DNA was then purified using a Qiagen MinElute PCR Purification Kit (Qiagen, Cat# 28004) and stored at -20°C until further processing. RNA-seq:Frozen pellets of sorted cells were thawed on ice and resuspended in 1 mL of TRIzol (Qiagen, Cat# 79306), followed by the addition of 400 µL of chloroform. After a 3-minute incubation, the mixture was centrifuged at 20,000 × g for 15 minutes at 4°C. The upper aqueous phase containing RNA was carefully transferred to a new tube, and 600 µL of isopropanol was added to precipitate the RNA at room temperature. Following a 30-minute centrifugation at 20,000 × g at 4°C, the supernatant was discarded. The RNA pellet was washed with 500 µL of 70% ethanol, air-dried, and resuspended in RNase-free water by shaking at 900 rpm for 5 minutes. RNA was treated with DNase according to the manufacturer’s instructions (Invitrogen™ TURBO DNA-free™ Kit, Cat# AM1907). RNA concentrations were determined using either a Nanodrop spectrophotometer or a Qubit fluorometer (Invitrogen). RNA quality was assessed with an Agilent 2100 Bioanalyzer, and samples were stored at −20°C.
For Hi-C and ChIP-seq libraries preparation, samples were first sheared to a target fragment size of 300 bp using a Covaris S220 instrument. Then, Hi-C libraries were prepared as described in (Ckrockram et al, STAR protocol, 2021). For ChIP-seq libraries, after sonication, IP and input samples were purified using 1.6x volume of AMPure XP beads according to manufacturer instructions (Beckman Coulter, Cat# A63881). DNA was eluted into 40 μL of elution buffer (EB, 10 mM Tris-HCl pH 7.5). After adjusting the volume of the samples to 80 μL with sterile water, DNA fragments were end-repaired by adding 40 μL of the following mix: 12 μL 10× T4 DNA ligase buffer (New England Biolabs, Cat# B0202S), 4 μL 10 mM dNTP mix, 5 μL T4 DNA polymerase (3 U/μL, New England Biolabs, Cat# M0203L), 5 μL T4 Polynucleotide Kinase (10 U/μL, Thermo Fisher Scientific, Cat# EK0032), 1 μL DNA polymerase I, large (Klenow) fragment (5 U/μL, New England Biolabs, Cat# M0210L), and 13 μL H2O . The reaction was incubated at room temperature (RT) for 30 minutes, purified using 1.6× AMPure XP beads, and DNA was eluted in 30 μL of EB. Purified DNA was then dA-tailed by adding 5 μL of 10× NEBuffer 2 (New England Biolabs, Cat# B7002S), 10 μL of 1 mM dATP (Sigma-Aldrich, Cat# D4788), 3 μL of Klenow Fragment (3'–5' exo-), (5 U/μL, New England Biolabs, Cat# M0212L), and 2 μL of H2O. The reaction was incubated at 37 °C for 30 minutes, followed by heat inactivation at 65 °C for 20 minutes to deactivate the Klenow Fragment (3’–5’ exo-). After purification with 1.6× volume of AMPure XP beads, DNA was eluted in 12 μL of EB. Illumina adapters were ligated using the NEBNext Quick Ligation Module (New England Biolabs, Cat# E6056S) for 15 minutes at RT. The ligation reaction was then purified using AMPure XP beads. First, the sample volume was adjusted to 50 μL with water, and a double size selection step was performed with the beads at a ratio of 0.7×-1.1×. For 3xFLAG-H-NS and 3xFLAG-RpoC libraries, PCR amplification was performed in a single 15-cycle reaction using  5 µl of library, 10 µl of 2 µM Illumina primers P1 and P2 mix, 10 µl Phusion 2× High Fidelity Master Mix (New England Biolabs, Cat#  M0531S) and 10 µl of H2O (for both IP and input). For the 3xFLAG-HilD and 3xFLAG-H-NS on sorted populations, three PCR reactions were performed for IP samples and one for the input sample. PCR products were purified using Qiagen MinElute PCR purification columns, and primer dimers were removed using AMPure XP beads. The concentration of Hi-C and ChIP-seq libraries was quantified using a Qubit fluorometer (Invitrogen) with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Cat# 10606433). Libraries were diluted to 0.5 ng/μL, and their quality was assessed on an Agilent 4150 TapeStation system using Agilent High Sensitivity D5000 ScreenTape (Agilent, Cat# 5067-5592). RNA-seq libraries.....

value: bacteria


title: A2 LTA treated replicate 3

value: bone marrow

value: acute myeloid leukemia


title: Group C-14


title: 053022-400

value: Female

value: Control


title: A2 untreated replicate 1

value: WT


title: 053022-1000


title: Kat6b KO pre-osteoblast bone, rep 3

description: Library name: PreO_KO_1720_6


title: Kat6b KO pre-osteoblast bone, rep 2

description: Library name: PreO_KO_1720_2


title: Group A-14

value: CRC tissues


title: 053022-100


title: Group A-13


title: Kat6b KO pre-osteoblast bone, rep 1

description: Library name: PreO_KO_1720_1


title: 050322-70


title: A1 TNF high treated replicate 3


title: Group C-12


title: WT pre-osteoblast bone, rep 4

description: Library name: PreO_WT_1721_5


title: A1 TNF high treated replicate 1


title: A1 TNF high treated replicate 2


title: Group A-15


title: Group B-15

value: liver metastases


title: 050322-7


title: Group B-12


title: WT pre-osteoblast bone, rep 3

description: Library name: PreO_WT_1721_4


title: 050322-4000


title: A1 TNF low treated replicate 2

value: recombinant human TNF, 5 ng/ml


title: Group A-12


title: mES-E14-WT-PromoterBait_5

description:
Library name: Sample 5
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt

value: Embryo

value: Mouse embryonic stem cell


title: 050322-400


title: WT pre-osteoblast bone, rep 2

description: Library name: PreO_WT_1720_7


title: A1 TNF low treated replicate 1


title: WT pre-osteoblast bone, rep 1

description: Library name: PreO_WT_1720_4


title: Group B-11


title: 050322-4


title: Kat6b KO pre-chondrocyte cartilage, rep 4

description: Library name: PreC_KO_1721_1


title: Group A-11


title: 050322-200


title: Kat6b KO pre-chondrocyte cartilage, rep 3

description: Library name: PreC_KO_1720_6


title: 050322-2


title: A1 LTA high treated replicate 2

value: recombinant human Lymphotoxin A, 100 ng/ml


title: Kat6b KO pre-chondrocyte cartilage, rep 2

description: Library name: PreC_KO_1720_2


title: Group B-10


title: A1 LTA high treated replicate 1


title: A1 TNF low treated replicate 3


title: A1 LTA low treated replicate 3

value: recombinant human Lymphotoxin A, 5 ng/ml


title: Kat6b KO pre-chondrocyte cartilage, rep 1

description: Library name: PreC_KO_1720_1


title: 050322-1

value: kidney


title: Group A-10


title: 050322-10

value: Male

value: Pkd2fl/fl; Pax8; Tet-O-Cre +


title: Group C-10

value: normal intestinal mucosal tissues


title: A1 LTA low treated replicate 2


title: Group C-11


title: 042922-70

value: Doxycycline Hyclate 50mg/Kg


title: WT pre-chondrocyte cartilage, rep 4

description: Library name: PreC_WT_1721_5

value: Mouse embryonic fibroblasts


title: Group B-9


title: A1 LTA low treated replicate 1

value: bone marrow

value: acute myeloid leukemia


title: A1 LTA high treated replicate 3


title: Group A-9


title: A1 untreated replicate 3


title: 042922-4


title: WT pre-chondrocyte cartilage, rep 2

description: Library name: PreC_WT_1720_7


title: A1 untreated replicate 2


title: Group C-8


title: WT pre-chondrocyte cartilage, rep 1

description: Library name: PreC_WT_1720_4


title: 042922-2


title: Kat6b KO pre-adipocyte fat, rep 4

description: Library name: PreA_KO_1721_1


title: A1 untreated replicate 1


title: 042922-100

value: Female

value: Control


title: Group A-8

value: CRC tissues


title: Kat6b KO pre-adipocyte fat, rep 3

description: Library name: PreA_KO_1720_6


title: OCIAML3 TNF treated replicate 3

source_name: cell line

value: cell line

value: WT

value: recombinant human TNF, 100 ng/ml


title: 042922-10


title: Group C-7


title: OCIAML3 TNF treated replicate 2


title: Group B-7

value: liver metastases


title: OCIAML3 TNF treated replicate 1


title: 042922-7


title: Group A-7


title: WT pre-chondrocyte cartilage, rep 3

description: Library name: PreC_WT_1721_4


title: OCIAML3 LTA treated replicate 3

value: recombinant human Lymphotoxin A, 100 ng/ml


title: WT pre-adipocyte fat, rep 4

description: Library name: PreA_WT_1721_5


title: Group C-6


title: OCIAML3 LTA treated replicate 2


title: Bone marrow, Control, Rep2

city: Heidelberg

first: Maximilian

last: Schönung

address: Im Neuenheimer Feld 280

department: Division Translational Medical Oncology

country: Germany

institute: German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg

data_processing:
Cell Ranger version 4.0.0 (10x Genomics) was used for generation of feature count matrices.
Data was processed using Seurat (version 4.0). Low quality cells were removed from the analysis based on a cutoff of more than 5% of mitochondrial genes. Additionally, only cells with more than 500 and less than 5800 detected genes were included. Furthermore, only genes that were expressed in a minimum of 10 cells were considered.
Potential cell doublets were removed using DoubletFinder (PMID 30954475).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated count matrices, features and cell barcodes.

source_name: Bone marrow

extract_protocol:
Bone marrow cells from three hematopoietic compartments (LSK, LK and total hematopoietic cells) were FACS-isolated 18 week after tamoxifen injection.
Library preparation was performed according to the manufacturers instructions using the Single Cell 3’ Reagent Kit v2 (10x Genomics).

value: Bone marrow

value: Ptpn11+/+ Scl-CreERT

value: Tamoxifen


title: Group B-8


title: WT pre-adipocyte fat, rep 3

description: Library name: PreA_WT_1721_4


title: Group B-6


title: OCIAML3 LTA treated replicate 1


title: OCIAML3 untreated replicate 3


title: WT pre-adipocyte fat, rep 1

description: Library name: PreA_WT_1720_4


title: Group A-6


title: Group C-5


title: OCIAML3 untreated replicate 2


title: 042922-1

value: kidney

value: Male


title: Kat6b KO proliferating, rep 4

description: Library name: Prof_KO_1721_1

value: Proliferating


title: Kat6b KO pre-adipocyte fat, rep 1

description: Library name: PreA_KO_1720_1

value: Mouse embryonic fibroblasts


title: WT pre-adipocyte fat, rep 2

description: Library name: PreA_WT_1720_7


title: Bone marrow, Mutant, Rep2

value: Ptpn11E76K/+ Scl-CreERT


title: Bone marrow, Control, Rep3


title: Group B-5


title: Bone marrow, Mutant, Rep1


title: Group A-5


title: Kat6b KO pre-adipocyte fat, rep 2

description: Library name: PreA_KO_1720_2


title: Kat6b KO proliferating, rep 3

description: Library name: Prof_KO_1720_6


title: CMES40-WGS

description: CMES-40.SRR11996369.ASE.GENEID.10Reads.tab corresponds the   processed file produced from CMES40-WGS raw data. We crossed those   processed data with data from the GSM4610404 record we re-analyzed hence   the SRA ID in the file name.

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the rhesus macaque genome (rheMac10) or to the marmoset genome (calJac4) using BWA-MEM 0.7.17 (Li et al 2013) with the default parameters
Aligned reads pre-processing and variant calling were performed by following the Genome Analysis Tool Kit (GATK) Best Practices for short germline variant discovery pipeline.
Variant calling was performed using GATK HaplotypeCaller with --stand-cal-conf=10, Single Nucleotide Variants (SNV) were selected using GATK SelectVariants. The vcf were then filtered with stringent parameters to avoid false positive in SNP calling with VariantFiltration: -FS>60.0 -QD<6.0 -SOR>3.0 -MQ<50.0 -MQRankSum<-12.5 -MQPosRankSum<-8.0  -DP<10.
Assembly: rheMac10, calJac4
Supplementary files format and content: vcf, tab

organism: Callithrix jacchus

extract_protocol:
Genomic DNA from 5x10⁶ rhESC and maESC were extracted using the DNeasy Blood and Tissue kit following the manufacturer instructions.
WGS libraries were prepared by the Institut Curie Next Generation Sequencing Core Facility using the KAPA Hyper Prep PCR-free Library Kit according to manufacturer’s instructions and sequenced on an Illumina HiSeq 2500 (PE100)
Whole Genome Sequencing

value: marmoset embryonic stem cells


title: OCIAML3 untreated replicate 1

value: acute myeloid leukemia


title: MOLM13 TNF treated replicate 3


title: Bone marrow, Mutant, Rep3


title: Kat6b KO proliferating, rep 2

description: Library name: Prof_KO_1720_2


title: Group B-4


title: MOLM13 TNF treated replicate 2


title: CD90+ HSC resorted after 7 day culture with DMSO - Replicate 1

city: Rye

first: Larry

middle: L

last: Luchsinger

state: NY

address: 601 Midland Ave

department: Stem Cell Regenerative Research

institute: New York Blood Center

description:
Library name: D1
processed data file column assignment: Column A-E

data_processing:
Paired-end 150 bp sequencing was performed on an Illumina HiSeq 4000.
Trimmed sequence reads were aligned to the human genome (hg37) and expression counts (STAR) was performed BasePair (https://basepairtech.com).
Read counts were extracted and normalized (FPKM) followed by statistical analyses.
Assembly: hg19 (GRCh37)
Supplementary files format and content: Normalized STAR Expression Analysis (NCBI RefSeq ID, Gene Symbol, count, FPKM and TPM)

source_name: Cord Blood

growth_protocol: HSCs were cultured in StemSpan SFM with 100ng SCF, TPO, FLT3L, 50ng/mL IL-3, 20ng/mL IL-6 in 5% CO2 and 5% O2 humidified chamber.

extract_protocol:
RNA was extracted with LS Trizol in the presence of linear acrylamide, according to manufacturer's instructions.
Sequencing libraries were prepared using an SMartR 2 RNA-seq system V2 kit following manufacturer's protocols.

treatment_protocol: Cultures were treated with 0.01% DMSO or 5nM Compound B.  Half media was refreshed every day for 7 days.

value: Cord Blood

value: CD90+ HSC

tag: batch


title: Larynx, TdTomato Red sorted cells isolated from 10 murine larynges, rep 2 (5x males and 5x females)

city: Madison

first: Yujia

last: Cai

address: 425 Henry Mall

institute: University of Wisconsin-Madison

description:
Library name: BR 2
10x Genomics

data_processing:
Raw sequencing reads were processed using Cell Ranger v8.0.1 (10x Genomics)
Assembly: Mouse mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: larynges

extract_protocol:
Mouse larynges were collected from Lrig1CreERT2/+; ROSA26CAG−LSL−tdTomato/+ , WT, and ROSA26CAG−LSL−tdTomato/+ mice. Tissues were minced into 0.5 mm pieces under a dissection scope and dissociated using the protocol by An et al. Dissociation buffer contained Accumax, Bacillus lichenformis protease, collagenase I, and DNase I in Ca/Mg-free PBS. Each larynx was digested in 300 μL solution at room temperature for 5 min, followed by 15 min vortexing on ice with gentle trituration. Cells were pooled, centrifuged, resuspended in DPBS with 10% FBS, and filtered through 40 μm strainers. ACK lysis buffer was used to remove erythrocytes. For FACS, cells were washed, filtered again, and sorted using a FACSAria2 (BD Biosciences). WT and background controls were used to set gates. Sorted cells were analyzed using J Flow software.
Library construction was performed following the manufacturer’s protocol using the Chromium GEM-X Single Cell 3' v4 Reagent Kit (10x Genomics). Cells in single-cell suspensions were delivered on ice to the sequencing center, where cell concentration and viability were measured with the Luna-FX7 (Logos Biosystems) using acridine orange/propidium iodide staining. Single cells were encapsulated in GEMs, and reverse transcription and barcoding were carried out using an Eppendorf MasterCycler Pro thermocycler. Amplified cDNA was purified using SPRIselect beads (Beckman Coulter), quantified using a Bioanalyzer 2100 (Agilent Technologies) with the High Sensitivity DNA kit, and used for library preparation. Sequencing was performed on the Illumina NovaSeq X Plus system with 150 bp paired-end reads.

value: larynges


title: Bone marrow, Control, Rep1


title: Larynx, TdTomato Red sorted cells isolated from 10 murine larynges, rep 3 (5x males and 5x females)

description:
Library name: BR 3
10x Genomics


title: WT proliferating, rep 4

description: Library name: Prof_WT_1721_5

value: WT


title: MOLM13 TNF treated replicate 1

value: cell line

value: recombinant human TNF, 100 ng/ml


title: Larynx, TdTomato Red sorted cells isolated from 10 murine larynges, rep 1 (5x males and 5x females)

description:
Library name: BR 1
10x Genomics


title: Group A-4

value: CRC tissues


title: Group C-3

value: normal intestinal mucosal tissues


title: WT proliferating, rep 3

description: Library name: Prof_WT_1721_4


title: MOLM13 LTA treated replicate 3

value: recombinant human Lymphotoxin A, 100 ng/ml


title: ARC_scATAC_WT_E1205_rep2

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

description: Library name: ARC_scATAC_WT_E1205_rep2

library_source: genomic single cell

data_processing:
Raw fastq files were aligned to the mouse mm10 reference genome using CellRanger ARC (v2.0.2). ATAC fragments were processed with Signac (v1.13.0), while RNA data were processed using Seurat (v4.4.0). Quality control filtering retained nuclei meeting the following criteria: TSS enrichment > 4, number of fragments > 1,000, 500 < nFeature_RNA < 8,000, 1,000 < nCount_RNA < 40,000, and mitochondrial gene percentage < 15%. Post-quality control nuclei underwent doublet removal using DoubletFinder (v2.0.4). Raw RNA counts were normalized and scaled with SCTransform, incorporating regression of mitochondrial read percentage and nCount_RNA. Subsequent analyses in Seurat included PCA, CCA-based batch integration (stratified by sample), nearest neighbor clustering, and UMAP embedding construction. Cell types were annotated using differential expression and knowledge of canonical gene markers. The RNA-derived annotations, normalized gene expression matrix, and UMAP embeddings were added to the Signac project onto the nuclei with the same barcodes. Following the Signac documentation, after constructing a unified peak set, we normalized the single-nucleus ATAC-seq data using the 'RunTFIDF' function. Subsequently, we employed the 'FindTopFeatures' function to calculate highly variable features and used the 'RunSVD' function for linear dimensionality reduction, selecting the 2nd to 50th dimensions for UMAP visualization. We utilized the 'GeneActivity' function in Signac to compute gene activity in the scATAC-seq dataset by counting the chromatin fragments overlapping the gene body and a 2-kilobase upstream region for each gene. To generate a joint RNA/ATAC embedding, we calculate a WNN graph, representing a weighted combination of RNA and ATAC-seq modalities. We use this graph for UMAP visualization.
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix for scRNA
Supplementary files format and content: fragment files for scATAC

source_name: lung

extract_protocol:
Timed-pregnant mice were sacrificed at the indicated time points. The uterus was removed, and embryos were harvested on ice. The embryonic lung was incubated in digestion medium [DMEM (Hyclone, SH30243.01) + 100 U/mL DNase I (NEB, M0303S) + 100 μg/mL Liberase™ (Roche, 5401119001)] for 20 min at 37°C at 300 rpm. After digestion, lung tissue was dissociated into single cells via pipetting. The cells were washed and resuspended in 1×PBS + 2% FBS (Hyclone, SH30096.03).
Single-cell multi-omics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) for 2 independent biological replicates according to the manufacturer’s protocol. Briefly, after dissociation, cells (sorted epithelial cells: whole lung cells = 1:10) were collected and resuspended in a chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing transposase. The transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. Finally, the snATAC-seq libraries were sequenced on the Element AVITI instrument. Conversely, the snRNA-seq libraries were loaded on the NovaSeq 6000 platform using a 150 bp paired-end read configuration.

value: lung

value: whole lung cells


title: MOLM13 LTA treated replicate 2


title: Group B-3

value: liver metastases


title: virus and drug-High3

first: liu

last: lifu

address: Panyu xinzao NO.1 Road

institute: Guangzhou Medical University

description: Library name: B7-300-3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 1.5 or fold change <2/3.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Lung

value: tumor pericytes

value: H1N1 virus infection + EA-High


title: ARC_scATAC_WT_E1205_rep1

description: Library name: ARC_scATAC_WT_E1205_rep1


title: WT proliferating, rep 2

description: Library name: Prof_WT_1720_7

value: Mouse embryonic fibroblasts

value: Proliferating


title: Kat6b KO proliferating, rep 1

description: Library name: Prof_KO_1720_1


title: Group B-2


title: mES-E14-WT-PromoterBait-optimized_4

description:
Library name: Sample 10
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt

value: Embryo

value: Mouse embryonic stem cell


title: Group C-2


title: virus and drug-High2

description: Library name: B7-300-2


title: MOLM13 LTA treated replicate 1

value: acute myeloid leukemia


title: MOLM13 untreated replicate 1

value: WT


title: Group A-2


title: WT proliferating, rep 1

description: Library name: Prof_WT_1720_4


title: MOLM13 untreated replicate 3

value: cell line


title: MOLM13 untreated replicate 2


title: E72 human distal femur ATAC

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
the Cell Ranger pipeline was used to process the fastq files
the Cell Ranger-ARC pipeline v2.0.0 was used to generate the count matrix
Assembly: hg38
Supplementary files format and content: Cell ranger output files - barcodes.tsv, features.tsv, matrix.mtx, atac_fragments.tsv

source_name: distal femur

extract_protocol:
collagenase digestion
RNA and ATAC seq libraries were prepared using the 10x Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer's protocols

value: distal femur

value: Collagenase digestion


title: virus and drug-High1

description: Library name: B7-300-1


title: Group C-1

value: normal intestinal mucosal tissues


title: SCAP cKO circulating csMBC_2

city: Indianapolis

first: Wei

last: Luo

state: Indiana

address: 950 W Walnut Street - R2 E302c

department: Microbiology and Immunology

institute: Indiana University

description:
Library name: sample 22
CIR6

data_processing:
Raw FASTQ files underwent initial quality control with FastQC. Reads were aligned to the Mus musculus reference genome (mm39) using STAR, and gene-level quantification was performed with Salmon against GENCODE vM34 annotations (gencode.vM34.annotation.gtf). Only genes with a raw read count greater than 5 in at least three samples were retained for downstream analyses.
Assembly: Mus musculus reference genome (mm39)
Supplementary files format and content: CSV files with raw counts

source_name: Lung B cell

extract_protocol:
RNA was extracted using the Zymo Quick-RNA Microprep kit (Zymo Research).
Library construction was performed with the xGen Broad-range RNA library prep kit (Integrated DNA Technologies), adapted for low cell input.

value: Lung B cell

value: B cells

value: SCAP fl/fl hCD20-TamCre


title: virus and drug-Medium3

description: Library name: B7-200-3

value: H1N1 virus infection + EA-Medium


title: SCAP cKO circulating csMBC_4

description:
Library name: sample 24
CIR9


title: SCAP cKO circulating csMBC_1

description:
Library name: sample 21
CIR5


title: Group A-3

source_name: CRC tissues

value: CRC tissues


title: SCAP cKO CCR6-CD69- csMBC_4

description:
Library name: sample 20
NON9


title: Group B-1

source_name: liver metastases

value: liver metastases


title: SCAP cKO circulating csMBC_3

description:
Library name: sample 23
CIR7


title: E72 human distal femur RNA


title: SCAP cKO CCR6-CD69- csMBC_2

description:
Library name: sample 18
NON6


title: virus and drug-Medium1

description: Library name: B7-200-1

value: Lung

value: tumor pericytes


title: SCAP cKO CCR6-CD69- csMBC_3

description:
Library name: sample 19
NON7


title: HeLa_24hHpx_sicRel_N2

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

institute: University of Liverpool

data_processing:
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle
Reads were aligned to the human genome version hg38 (GRCh38, Ensembl) using and the resulting binary alignment mapped (bam) files were indexed using Samtools
Read counts for each transcript (GRCh38, Ensembl) were generated using Subread (featureCounts)
Assembly: Genome_build: GRCh38
Supplementary files format and content: tab-delimited text file which contains raw counts for each sample

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultured for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen).
RNAseq libraries (unstranded, polyA selection) were prepared using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Cells were transfected with 27 nM of small interfering RNA (siRNA) oligonucleotides (Eurofins) for 48h using Interferin (Polyplus) transfection reagent according to manufacturer’s instructions. Hypoxia treatments were performed by incubating cells in an InvivO2 300 Hypoxia Workstation (Baker Ruskinn) at 1% O2, 5% CO2 and 37 °C.

value: HeLa

value: 24h 1% oxygen and cRel siRNA


title: HeLa_24hHpx_siRelB_N2

value: 24h 1% oxygen and RelB siRNA


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 21 day harvest, rep5

city: Cambridge

first: Richard

last: Lee

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description:
Library name: Puck_220928_39_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

data_processing:
Raw sequencing data were processed using the Slide-seqV2 protocol described in (Stickels R.R., et al., Nature Biotechnology, 2020)
Assembly: GRCr8 for rat genes/GRCh38 for human genes
Supplementary files format and content: .matched.digital_expression_barcodes.tsv: list of spatial barcodes
Supplementary files format and content: .matched.digital_expression_features.tsv: list of gene IDs
Supplementary files format and content: .matched.digital_expression_matrix.mtx: gene expression counts
Supplementary files format and content: Puck_ID_barcode_xy.txt: spatial bead coordinates
Library strategy: Spatial Transcriptomics

organism: Homo sapiens/Rattus norvegicus xenograft

source_name: Left Ventricular Anterior Wall

extract_protocol:
Fresh-frozen samples were cut to expose the left anterior ventricular wall (transverse) before a 10um section was cut and mounted on a Slide-seqV2 puck
Spatial transcriptome sequencing libraries were prepared according to the Slide-seqV2 protocol as described in (Stickels et al. 2021, Nature Biotechnology)

treatment_protocol: Cyclosporine injection: Rats received cyclosporine injections (15 mg/ml) as an immunosuppressant a day before the injection and every day after surgery.  Cell injection: We used RNU nude rats (8-10 weeks old, male, 250-350g). Rats received cyclosporine injections (15 mg/ml) as an immunosuppressant a day before the injection and every day after surgery. Rats were sedated using Isoflurane (initial at 3%, maintenance at 1-2%), secured to an electrode-heating platform. A long-axis heart image was obtained with an ultrasound transducer (Vevo 3100, FUJIFILM, Japan) applied to the chest. Using a syringe and 30-gauge needle attached to a mount/injection guide, 100 ml of cell suspension (hiPS-CM suspension or hiPS-CM with RADA16 suspension) prepared in advance was injected (ultrasound-guided) into the anterior wall of the left ventricle for immunostaining, cell retention analysis, and slide-seq. After ultrasound-guided intramyocardial injection, rats were returned to their cages and allowed to recover. Cyclosporine (15 mg/ml) was administered intraperitoneally on a daily basis to suppress immune reactions until the heart was harvested.

value: Left Ventricular Anterior Wall

value: UCSD 142i-86-1 iPSCs

value: iPSC-derived ventricular cardiomyocyte

value: Cardiomyocytes only; 21 day post-injection harvest

value: total RNA

value: single


title: HeLa_24hHpx_siRelA_N2

value: 24h 1% oxygen and RelA siRNA


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 21 day harvest, rep4

description:
Library name: Puck_220928_38_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2


title: virus and drug-Low2

description: Library name: B7-100-2

value: H1N2 virus infection + EA-Low


title: virus and drug-Low3

description: Library name: B7-100-3

value: H1N1 virus infection + EA-Low


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 21 day harvest, rep4

description:
Library name: Puck_220928_34_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: RADA16+Cardiomyocyte injection; 21 day post-injection harvest


title: SCAP cKO CCR6+CD69+ csMBC_4

description:
Library name: sample 16
BRM9

value: Lung B cell

value: B cells

value: SCAP fl/fl hCD20-TamCre


title: HeLa_24hHpx_siControl_N2

value: 24h 1% oxygen and Control siRNA


title: virus-3

description: Library name: IAV-3

value: Lung

value: tumor pericytes

value: H1N1 virus infection


title: HeLa_Nx_siControl_N2

value: HeLa

value: Control siRNA


title: SCAP cKO CCR6+CD69+ csMBC_2

description:
Library name: sample 14
BRM6


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 21 day harvest, rep3

description:
Library name: Puck_220928_33_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Left Ventricular Anterior Wall

value: UCSD 142i-86-1 iPSCs

value: iPSC-derived ventricular cardiomyocyte


title: SCAP cKO CCR6-CD69- csMBC_1

description:
Library name: sample 17
NON5


title: HeLa_24hHpx_sicRel_N1

value: 24h 1% oxygen and cRel siRNA


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 21 day harvest, rep2

description:
Library name: Puck_220928_30_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Cardiomyocytes only; 21 day post-injection harvest

value: total RNA

value: single


title: virus-2

description: Library name: IAV-2


title: SCAP cKO CCR6+CD69+ csMBC_1

description:
Library name: sample 13
BRM5


title: HeLa_24hHpx_siRelB_N1

value: 24h 1% oxygen and RelB siRNA


title: virus and drug-Medium2

description: Library name: B7-200-2

value: H1N1 virus infection + EA-Medium


title: virus and drug-Low1

description: Library name: B7-100-1

value: H1N1 virus infection + EA-Low


title: Group A-1

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer after quality filtering.
Firstly, Q30 was used to perform quality control.
The high quality reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl gtf gene annotation file with hisat2 software (v2.04).
Then, cuffdiff software (part of cufflinks, v2.2.1) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes.
Fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Assembly: UCSC hg19
Supplementary files format and content: processed_data.xlsx: Excel file includes raw counts and normalized counts for each Sample.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

value: CRC tissues


title: virus-1

description: Library name: IAV-1


title: WT circulating csMBC_4

description:
Library name: sample 12
CIR4

value: Lung B cell

value: B cells

value: SCAP +/+ hCD20-TamCre


title: WT circulating csMBC_3

description:
Library name: sample 11
CIR3


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 21 day harvest, rep1

description:
Library name: Puck_220928_29_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2


title: HeLa_24hHpx_siControl_N1

value: 24h 1% oxygen and Control siRNA


title: HeLa_24hHpx_siRelA_N1

value: HeLa

value: 24h 1% oxygen and RelA siRNA


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 21 day harvest, rep2

description:
Library name: Puck_220928_27_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Left Ventricular Anterior Wall

value: RADA16+Cardiomyocyte injection; 21 day post-injection harvest


title: WT circulating csMBC_2

description:
Library name: sample 10
CIR2


title: control-2

description: Library name: NC-2

value: Lung

value: tumor pericytes

value: control


title: SCAP cKO CCR6+CD69+ csMBC_3

description:
Library name: sample 15
BRM7

value: SCAP fl/fl hCD20-TamCre


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 7 day harvest, rep4

description:
Library name: Puck_220928_23_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: UCSD 142i-86-1 iPSCs

value: iPSC-derived ventricular cardiomyocyte

value: RADA16+Cardiomyocyte injection; 7 day post-injection harvest

value: total RNA

value: single


title: control-1

description: Library name: NC-1


title: HeLa_Nx_siControl_N1

value: Control siRNA


title: WT circulating csMBC_1

description:
Library name: sample 9
CIR1

value: Lung B cell

value: B cells


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 7 day harvest, rep3

description:
Library name: Puck_220928_22_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2


title: AD3-205-0A

city: Richland

first: Predictive Phenomics

last: Initiative

state: WA

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description: Library name: sample 23

data_processing:
Rsubread v2.16.1
Assembly: NC007604.1 (16-NOV-2022), NC_007595.1 (16-NOV-2022), NC_004990.1 (29-OCT-2022)
Supplementary files format and content: .csv counts

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: axenic

growth_protocol: Synechococcus elongatus PCC 7942 CscB/SPS strain, engineered to overexpress sucrose phosphate synthase (SPS) and sucrose permease (CscB), was obtained from Dr. Daniel Ducat. Cultures were maintained in BG11 medium supplemented with chloramphenicol (12.5 mg L⁻¹) and kanamycin (25 mg L⁻¹). Standard growth conditions were maintained at 29±2°C with nitrogen gas sparging supplemented with 2% CO₂ under 200 μmol photons m⁻² s⁻¹ illumination from LED lights. Culture mixing was facilitated using PFTE Octagon Spinbar Magnetic Stirring Bars (9.5 mm x 25.4 mm) at 200 r.p.m. Antibiotics were removed prior to experimental procedures. During the experiment, continuous cultivation was performed in 6.5-L New Brunswick Bioflo 310 fermentors (Eppendorf, Inc.) equipped with custom LED photobioreactors. Steady-state cultures (5.5-L) were maintained in turbidostat mode at OD₇₃₀ of 0.08, with constant conditions of 250 rpm agitation, 30°C, and pH 8.0 (controlled by 2 M NaOH or HCl addition). Illumination was provided at 760 μmol photons m⁻² s⁻¹ using 630 and 680 nm narrow-band LED illuminator chips (Marubeni America Corporation). Photosynthetically active radiation (PAR, 400-700 nm) was monitored using three quantum sensors (LI-210SA, LI-COR Biosciences). Initial conditions utilized a baseline sparging rate of 2.04 L min⁻¹ with 98:2 N2/CO2 gas mixture. Oxidative stress was implemented through stepwise increases in O2 content while maintaining constant total gas flow and CO2 concentratio, with corresponding N₂ reduction. Dissolved O₂ was measured using a Clark-type electrode (InPro® 6800Series, Mettler Toledo). Turbidostat operation was maintained by correlating transmitted irradiance measurements with spectrophotometer-verified OD750 values to control medium addition and removal.

extract_protocol:
Total RNA was extracted using RNeasy kit with QiaShredder columns (QIAGEN). Cells were lysed in RLT buffer containing 1% β-mercaptoethanol, homogenized through QiaShredder, then processed following manufacturer's protocol with 70% ethanol addition.
Library construction and sequencing was done by Azenta Life Sciences. Two technical replicates were processed per condition. Samples underwent DNase treatment and rRNA depletion before paired-end sequencing (2x150bp, ~350M reads, ~105GB) with single indexing on Illumina platform.

treatment_protocol: To assess How S. elongatus calibrate response to oxidative stress and to evolve stress-adapted cell-lines the dissolved oxygen (oxidative stress level) was varied in culture by elevating oxygen content in sparged gas phase.  First, oxygen content was increased stepwise from 0 to 78% and RNA-seq samples were collected in order to assess the response of non-adapted S. elongatus PCC 7942 CscB/SPS strain (called WT for short). Highest stress level was followed by long recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 1 (AD1), sample of AD1 was collected for DNA extraction and resequencing. Second, we repeated the oxygen stress campaign by testing oxygen levels from 0% to 93% with collection of RNAseq data for stress response of AD1 population. Highest stress level was followed by long recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 2 (AD2), sample of AD2 was collected for DNA extraction and resequencing.  Third, the oxygen stress campaign was repeated again by increasing the oxygen content from 0 to 99.8% with collection of RNAseq data for stress response of AD2 population. Highest stress level was followed by recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 3 (AD3), sample of AD3 was collected for DNA extraction and resequencing.

value: axenic

value: cscB-sps

value: AD3 high light 0% O2 air saturation


title: WT CCR6-CD69- csMBC_3

description:
Library name: sample 7
NON3

value: SCAP +/+ hCD20-TamCre


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 21 day harvest, rep1

description:
Library name: Puck_220928_19_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Left Ventricular Anterior Wall

value: RADA16+Cardiomyocyte injection; 21 day post-injection harvest


title: WT CCR6-CD69- csMBC_4

description:
Library name: sample 8
NON4


title: hESC_Primed,IgG,Rep2

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the rhesus macaque genome (rheMac10) or to the human genome (hg38) using bowtie 2 (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40.
Assembly: rheMac10, hg38
Supplementary files format and content: bigWig
Library strategy: Cut & Run

extract_protocol:
Digested chromatin was treated with proteinase K and  eluted using phenol chloroform extraction as described in Skene et al.,2017.
High-throughput sequencing libraries were constructed using the TruSeq ChIP Library Preparation Kit according to the manufacturer’s recommendation. Paired-end sequencing was done on the Illumina NovaSeq 6000  with a read length of 100 bp.

value: human embryonic stem cell


title: AD2-205-998A

description: Library name: sample 22

value: AD2 high light 476% O2 air saturation


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 21 day harvest, rep3

description:
Library name: Puck_220928_32_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Cardiomyocytes only; 21 day post-injection harvest


title: hESC_Primed,IgG,Rep1


title: hESC_Primed,H3K27ac,Rep2


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 7 day harvest, rep3

description:
Library name: Puck_220928_13_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: UCSD 142i-86-1 iPSCs

value: Cardiomyocytes only; 7 day post-injection harvest


title: AD2-205-98A

description: Library name: sample 21

value: AD2 high light 468% O2 air saturation


title: WT CCR6-CD69- csMBC_2

description:
Library name: sample 6
NON2


title: control-3

description: Library name: NC-3

value: Lung

value: tumor pericytes

value: control


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 7 day harvest, rep2

description:
Library name: Puck_220928_12_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: iPSC-derived ventricular cardiomyocyte

value: total RNA

value: single


title: AD2-205-0A

description: Library name: sample 20

value: axenic

value: cscB-sps

value: AD2 high light 0% O2 air saturation


title: WT CCR6-CD69- csMBC_1

description:
Library name: sample 5
NON1

value: Lung B cell

value: B cells

value: SCAP +/+ hCD20-TamCre


title: hESC_Primed,H3K27ac,Rep1

value: human embryonic stem cell


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 7 day harvest, rep2

description:
Library name: Puck_220928_10_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Left Ventricular Anterior Wall

value: RADA16+Cardiomyocyte injection; 7 day post-injection harvest


title: WT CCR6+CD69+ csMBC_4

description:
Library name: sample 4
BRM4


title: pAD205-93A

description: Library name: sample 18

value: AD1 planktonic high light 445% O2 air saturation


title: hESC_Primed,H3K4me1,Rep1


title: hESC_Primed,H3K4me1,Rep2


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, RADA16+Cardiomyocytes, 7 day harvest, rep1

description:
Library name: Puck_220928_09_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: UCSD 142i-86-1 iPSCs


title: WT CCR6+CD69+ csMBC_3

description:
Library name: sample 3
BRM3


title: Rat Myocardium with injected iPSC-derived cardiomyocytes, cardiomyocytes only, 7 day harvest, rep1

description:
Library name: Puck_220928_03_deep
Fresh-Frozen Spatial Transcriptomic Sequencing using Slide-seqV2

value: Cardiomyocytes only; 7 day post-injection harvest


title: fAD205-93A

description: Library name: sample 19

value: AD1 biofilm high light 445% O2 air saturation


title: AD205-93A

description: Library name: sample 17

value: AD1 high light 445% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, Nutlin, 6hr, rep1

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: IAA_12hr_Nutlin_rep1

data_processing:
Sequence reads were mapped to hg38 using STAR version 2.7.10b with default parameters. For differential gene expression analysis, we analyzed raw read counts using RSEM (Li et al., 2011), and then calculated statistics of differential expression via DESeq2 version 1.48.1 (Love et al., 2014) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tap-delimited text files include gene id, transcript id, length, effective length, expected count, TPM and FPKM for each replicates.

extract_protocol:
Total RNA was extracted by Trizol extraction. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold Kit following manufacture's protocols.


title: Ng rep3

city: Jingzhou

first: Jinmeng

last: Li

address: Chengnan

institute: Yangtze University

description:
Library name: Sample 6
Ng3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: tab-delimited text file includes FPKM values and gene count for each Sample

organism: Picromerus lewisi

source_name: venom glands

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: venom glands

tag: developmental stage

value: Nymph gland


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, control, 12hr, rep2

description: Library name: IAA_12hr_control_rep2


title: AD205-60A

description: Library name: sample 15

value: AD1 high light 281% O2 air saturation


title: WT CCR6+CD69+ csMBC_1

description:
Library name: sample 1
BRM1

tag: tissue


title: Ng rep2

description:
Library name: Sample 5
Ng2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, Nutlin, 6hr, rep2

description: Library name: IAA_12hr_Nutlin_rep2


title: WT CCR6+CD69+ csMBC_2

description:
Library name: sample 2
BRM2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, control, 12hr, rep1

description: Library name: IAA_12hr_control_rep1


title: Ng rep1

description:
Library name: Sample 4
Ng1


title: Ag rep3

description:
Library name: Sample 3
Ag3

value: Adult gland


title: AD205-80A

description: Library name: sample 13

value: axenic

value: cscB-sps

value: AD1 high light 374% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, Nutlin, 6hr, rep2

description: Library name: DMSO_Nutlin_rep2


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 4

description:
Library name: MKL142
ChIP-seq merge rep1 to rep4

value: hisG46, rpoC-3xFLAG:Cm

value: bacteria


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 4

description:
Library name: MKL141
ChIP-seq merge rep1 to rep4


title: AD205-70A

description: Library name: sample 14

value: AD1 high light 328% O2 air saturation


title: Ag rep2

description:
Library name: Sample 2
Ag2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, Nutlin, 6hr, rep1

description: Library name: DMSO_Nutlin_rep1


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 3

description: Library name: MKL140


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 3

description: Library name: MKL139


title: AD205-0A

description: Library name: sample 12

value: AD1 high light 0% O2 air saturation


title: WT205-80A

description: Library name: sample 11

value: WT high light 374% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, control, rep2

description: Library name: DMSO_control_rep2


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 4

description:
Library name: MKL138
ChIP-seq merge rep1& rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, control, rep1

description: Library name: DMSO_control_rep1


title: Male slide M2 slice D2

type: RNA

city: Mountain View

first: Daniel

last: Berg

state: CA

address: 2005 California Street

institute: Stanford University

description: Resolve Biosciences Molecular Cartography technology was used to spatially resolve distinct cell populations by using 98 specific gene markers in amygdala of mouse brain.

data_processing:
Cell nuclei segmentation masks were obtained using the DAPI channel as input to Cellpose with diameter set to 65 and mask threshold -0.1. This mask was used as prior segmentation information to Baysor (confidence: 0.9; scale: 45; scale_sfd: 50%) to obtain final segmentation counts and cell metadata.
transcript per cell

label: fluorescence

source_name: amygdala brain tissue

label_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 100-plex combinatorial single molecule fluorescence in-situ hybridization

extract_protocol: Mouse brain was dissected and right hemisphere immersed in OCT with cryo-mold in isopentane dry ice bath and stored at -80.  The frozen brains were sectioned into 10 μm coronal slices on a cryostat at -20°C.

value: amygdala brain tissue

value: male

tag: bregma coordinate


title: AD205-50A

description: Library name: sample 16

tag: cell type

value: AD1 high light 234% O2 air saturation


title: WT205-60A

description: Library name: sample 9

tag: genotype

value: WT high light 281% O2 air saturation


title: Male slide M2 slice D1


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 4

description:
Library name: MKL137
ChIP-seq merge rep1 to rep4

data_processing:
Hi-C libraries were proccessed using the OHCA pipeline from Bioconductor: https://jserizay.com/OHCA/docs/devel/. Hi-C matrices were binned at 1Kb, plasmids were exluded of the analyses
For the ChIP-seq analysis, each read was aligned to the reference genome (Salmonella enterica serovar Typhimurium strain SL1344) using Bowtie2 (v 2.4.2).  Paired-end reads were then Merged and sorted with Samtools, and PCR duplicates were removed using the Picard MarkDuplicates tool. Subsequently, SAM files were converted to BAM files, indexed, and processed to generate bedGraph and bigWig files with using bamCompared from DeepTools2. This tool allowed us to compare the ChIP-seq data to the INPUT and normalize it in Bins Per Million mapped reads (BPM). For Hi-C correlations and determination of protein occupancy (H-NS and RNA polymerase), 1Kb bins were used. No binning was used for the rest of analyses.
For RNA-seq analysis, paired-end reads were mapped to the reference genome using Bowtie2 (v 2.4.2). After alignment, SAM files were sorted, converted to BAM format, and indexed. BAM files were subsequently converted to WIG format using bamCoverage or Galaxy with CPM normalization. Read quantification in sense and antisense orientations was performed using featureCounts program (v 2.0.1)70. Differential gene expression analysis was conducted in R using the SARTools pipeline (Statistical Analysis of RNA-Seq data Tools, v1.8.1), which is based on DESeq2. Quality controls, raw count normalization, and identification of differentially expressed genes were systematically performed. Principal Component Analysis (PCA) and hierarchical clustering were applied to data transformed using Variance Stabilizing Transformation (VST) to ensure homoscedasticity. The Benjamini-Hochberg method was used for p-value adjustment with a statistical significance threshold of 0.05. The condition "GFP negative" was defined as the reference for comparisons. Genes with null counts across all samples and predefined low-quality features were excluded prior to analysis.  Additionally, to facilitate correlations with Hi-C data, DESeq2-normalized counts per kilobase for each gene under all experimental conditions were determined
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium SL1344 complete genome, GenBank: FQ312003.1
Supplementary files format and content: 4879x4879 Hi-C contact matrices in txt format

extract_protocol:
Hi-C: Frozen pellets were thawed on ice, resuspended in 200 μL of 1× Tris-EDTA (TE) buffer (Sigma-Aldrich, Cat# T928) containing a complete protease inhibitor cocktail (Roche, Cat# 11873580001). Then, 1 µl of ready-lyse lysozyme (LGC Biosearch, Cat# LU-R1804M) was added and the mixture was incubated at RT for 20 minutes.  Next, 10 µl of 10% SDS (Sigma-Aldrich, Cat#  05030) was added to the cells and incubated for 10 minutes at RT. Subsequently, the lysed cells were transferred into a 2 mL Eppendorf tube containing 800 μL of digestion mix: 100 μL of 10× NEB1 buffer (New England Biolabs, Cat# B7001S), 100 μL of 10% Triton (Sigma-Aldrich, Cat# T8787), and 600 μL of sterile water. After removing 80 μL of non-digested control, 20 μL of HpaII enzyme (New England Biolabs, Cat# R0171L) were added to the digestion mix. Both tubes were then incubated for 3 hours at 37°C with agitation. Following DNA digestion, 80 μL of the digested control were removed and kept on ice with the non-digested control. The remaining digestion mix was centrifuged for 20 minutes at 16,000 × g, 4°C, and the pellet was re-suspended in 80 µL of sterile water. The 80 µL of digested DNA was then added to the biotinylation mix containing 10 µL of 10× ligation buffer, 1 µL of 10 mM dAGTP mix, 3 µL of 1 mM biotin-14-dCTP (Jena Biosciences, Cat# E-NU-956-BIO14-S), and 2 µL of DNA polymerase I, large (Klenow) fragment (New England Biolabs, Cat# M0210L), and incubated for 1 hour at 37°C with agitation. Following biotinylation, proximity ligation of DNA fragments was performed by adding the ligation mix: 24 µL of 10× ligation buffer (without ATP), 2.4 µL of 100 mM ATP, 2.4 µL of 10 mg/mL BSA (New England Biolabs, Cat# B9000S), and 3.2 µL of of T4 DNA ligase (Thermo Fisher Scientific, Cat# EL0013). Ligation was performed at 25°C for 3 hours with gentle agitation. The crosslink was then reversed by incubating the samples (including the non-digested and digested controls) overnight at 65°C in the presence of proteinase K (20 mg/mL; Eurobio Scientific, Cat# GEXPROK01-B5), EDTA (500 mM; Sigma-Aldrich, Cat# 03690), and 10% SDS. The next day, DNA was purified by phenol extraction and ethanol precipitation. Briefly, one volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Thermo Fisher Scientific, Cat# 10308293) was added to the samples. Following centrifugation, the upper aqueous phase was transferred to a new 1.5 mL tube, and DNA was precipitated with 1/10 volume of 3 M Na-acetate (pH 5.2) and two and a half volumes of cold ethanol. After incubation at −80°C for 30 minutes, the DNA was pelleted, washed once with 70% ethanol, and dried using an Eppendorf concentrator plus speed vac. The DNA was resuspended in 130 µL of 1× TE buffer containing 10 μg/mL RNase A (Thermo Fisher Scientific, Cat# EN0531) ChIP-seq: frozen cell pellets, fixed with 1% formaldehyde, were thawed on ice and re-suspended in 500 μl of lysis buffer I: 20% sucrose (Sigma-Aldrich, Cat# S7903), 10 mM Tris-HCl (pH 8), 50 mM NaCl, and 10 mM EDTA, supplemented with 4 μl of ready-lyse lysozyme. The mixture was incubated at 37°C for 30 minutes. Next, 500 μl of lysis buffer II (50 mM Tris-HCl (pH8), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 and complete protease inhibitor cocktail) was added. The cells were transferred to a 1 mL Covaris tube and sonicated using a Covaris S220 focused Ultrasonicator. Sonication parameters were set to 210 seconds for EEP samples and 270 seconds for ESP samples (peak power = 140 W; duty factor = 5%; cycles per burst = 200). Following sonication, the samples were centrifuged at 18,000 × g for 30 minutes at 4°C. The supernatant was transferred into a new 1.5 mL tube, with 50 μL set aside as input and stored at −20°C until further use. Immunoprecipitation of FLAG-tagged proteins was performed by incubating the cell extracts with 100 μL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich, Cat# A2220) overnight at 4°C on a rotator. The beads were washed twice with 400 μL of TBS (Tris-HCl 50mM pH 7.4, 150mM NaCl) containing 0.05% Tween 20, followed by three washes with 400 μL of cold TBS. Each wash step was performed under rotation for 10 minutes at 4°C. The 3xFLAG-protein-DNA complexes were eluted by adding 2.5 volumes of 3xFLAG peptide solution (Sigma-Aldrich, Cat# F4799) relative to the total packed gel volume. The samples were incubated for 90 minutes on a rotator at 4°C, centrifuged for 30 seconds at 5000 × g at 4°C, and the supernatant was transferred to 1.5 mL LoBind DNA tubes. A second elution step was performed similarly. The IP and input samples were treated with RNase A (10 μg/mL) for 1 hour at 37°C and then incubated overnight at 65°C with proteinase K (final concentration: 50 μg/mL) to reverse the formaldehyde crosslinks. DNA was then purified using a Qiagen MinElute PCR Purification Kit (Qiagen, Cat# 28004) and stored at -20°C until further processing. RNA-seq:Frozen pellets of sorted cells were thawed on ice and resuspended in 1 mL of TRIzol (Qiagen, Cat# 79306), followed by the addition of 400 µL of chloroform. After a 3-minute incubation, the mixture was centrifuged at 20,000 × g for 15 minutes at 4°C. The upper aqueous phase containing RNA was carefully transferred to a new tube, and 600 µL of isopropanol was added to precipitate the RNA at room temperature. Following a 30-minute centrifugation at 20,000 × g at 4°C, the supernatant was discarded. The RNA pellet was washed with 500 µL of 70% ethanol, air-dried, and resuspended in RNase-free water by shaking at 900 rpm for 5 minutes. RNA was treated with DNase according to the manufacturer’s instructions (Invitrogen™ TURBO DNA-free™ Kit, Cat# AM1907). RNA concentrations were determined using either a Nanodrop spectrophotometer or a Qubit fluorometer (Invitrogen). RNA quality was assessed with an Agilent 2100 Bioanalyzer, and samples were stored at −20°C.
For Hi-C and ChIP-seq libraries preparation, samples were first sheared to a target fragment size of 300 bp using a Covaris S220 instrument. Then, Hi-C libraries were prepared as described in (Ckrockram et al, STAR protocol, 2021). For ChIP-seq libraries, after sonication, IP and input samples were purified using 1.6x volume of AMPure XP beads according to manufacturer instructions (Beckman Coulter, Cat# A63881). DNA was eluted into 40 μL of elution buffer (EB, 10 mM Tris-HCl pH 7.5). After adjusting the volume of the samples to 80 μL with sterile water, DNA fragments were end-repaired by adding 40 μL of the following mix: 12 μL 10× T4 DNA ligase buffer (New England Biolabs, Cat# B0202S), 4 μL 10 mM dNTP mix, 5 μL T4 DNA polymerase (3 U/μL, New England Biolabs, Cat# M0203L), 5 μL T4 Polynucleotide Kinase (10 U/μL, Thermo Fisher Scientific, Cat# EK0032), 1 μL DNA polymerase I, large (Klenow) fragment (5 U/μL, New England Biolabs, Cat# M0210L), and 13 μL H2O . The reaction was incubated at room temperature (RT) for 30 minutes, purified using 1.6× AMPure XP beads, and DNA was eluted in 30 μL of EB. Purified DNA was then dA-tailed by adding 5 μL of 10× NEBuffer 2 (New England Biolabs, Cat# B7002S), 10 μL of 1 mM dATP (Sigma-Aldrich, Cat# D4788), 3 μL of Klenow Fragment (3'–5' exo-), (5 U/μL, New England Biolabs, Cat# M0212L), and 2 μL of H2O. The reaction was incubated at 37 °C for 30 minutes, followed by heat inactivation at 65 °C for 20 minutes to deactivate the Klenow Fragment (3’–5’ exo-). After purification with 1.6× volume of AMPure XP beads, DNA was eluted in 12 μL of EB. Illumina adapters were ligated using the NEBNext Quick Ligation Module (New England Biolabs, Cat# E6056S) for 15 minutes at RT. The ligation reaction was then purified using AMPure XP beads. First, the sample volume was adjusted to 50 μL with water, and a double size selection step was performed with the beads at a ratio of 0.7×-1.1×. For 3xFLAG-H-NS and 3xFLAG-RpoC libraries, PCR amplification was performed in a single 15-cycle reaction using  5 µl of library, 10 µl of 2 µM Illumina primers P1 and P2 mix, 10 µl Phusion 2× High Fidelity Master Mix (New England Biolabs, Cat#  M0531S) and 10 µl of H2O (for both IP and input). For the 3xFLAG-HilD and 3xFLAG-H-NS on sorted populations, three PCR reactions were performed for IP samples and one for the input sample. PCR products were purified using Qiagen MinElute PCR purification columns, and primer dimers were removed using AMPure XP beads. The concentration of Hi-C and ChIP-seq libraries was quantified using a Qubit fluorometer (Invitrogen) with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Cat# 10606433). Libraries were diluted to 0.5 ng/μL, and their quality was assessed on an Agilent 4150 TapeStation system using Agilent High Sensitivity D5000 ScreenTape (Agilent, Cat# 5067-5592). RNA-seq libraries.....


title: Male slide M2 slice C1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, rep2

description: Library name: IAA_12hr_2


title: Male slide M2 slice B2


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 3

description: Library name: MKL136


title: WT205-70A

description: Library name: sample 10

tag: treatment

value: WT high light 328% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, rep2

description: Library name: IAA_3hr_2

tag: cell line


title: WT205-40A

description: Library name: sample 7

value: WT high light 187% O2 air saturation


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 3

description: Library name: MKL135


title: ΔlexA ΔsidA_MMC_0_replicate2

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

description: Library name: ΔlexA ΔsidA_MMC_0_replicate2

data_processing:
Raw reads for the RNA-seq were obtained as fastq files. BWA was used in order to align the reads to the Caulobacter genome (accession number: NC_011916.1).
The aligned reads in .bam format were converted into a .bed file format using the bamtobed option of Bedtools. Coverage was further calculated using BEDTools. FPKM was further calculated for the samples from the read counts.
Assembly: NC_011916.1
Supplementary files format and content: csv file includes raw counts for all samples
Supplementary files format and content: csv file includes FPKM values for all samples

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N

growth_protocol: Overnight cultures of Caulobacter grown in PYE media were diluted to 0.025 OD600 and grown for ~3 hours.

extract_protocol:
The samples were then centrifuged at 10000g for 5 minutes following which supernatant was discarded and the pellets were snap frozen and stored at -80°C until further processed. mRNA was isolated from the collected pellets. Pre-heated trizol (65°C) was added to each pellet and cells were lysed using a Thermomixer (65°C, 2000rpm, for 10 minutes). Total RNA was extracted from the lysed cells using the Direct-zol RNA MiniPrep kit. Any DNA contamination was then removed via DNAse treatment and  RNA was purified using RNA Clean & Concentrator-25 kit. Integrity of the total RNA was tested by the Tapestation instrument. Ribosomal RNA was then depleted using the Thermo RiboMinus kit. mRNA was purified using RNA Clean & Concentrator-5 kit and submitted for RNA-seq.
NEBNext Ultra II Directional RNA Library Prep kit was used for library preparation and samples were sequenced via the Illumina NovaSeq 6000 platform.

treatment_protocol: 3 hours post back-dilution, when OD600 reached ~0.1, 0.25 μg/mL MMC damage was introduced in to these cultures. Caulobacter cells were harvested (2mL/sample) for RNA-seq at 0, 20, 40 minutes post damage exposure.

value: exponential phase

value: CB15N; delta-lexA delta-sidA


title: WT205-30A

description: Library name: sample 6

value: WT high light 140% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, rep1

description: Library name: IAA_12hr_1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, rep1

description: Library name: IAA_3hr_1


title: Male slide M2 slice B1

tag: Sex


title: Male slide M2 slice A1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, rep2

description: Library name: DMSO_2


title: WT205-20A

description: Library name: sample 5

value: axenic

value: WT high light 94% O2 air saturation


title: Ag rep1

description:
Library name: Sample 1
Ag1

value: venom glands

value: Adult gland


title: WT205-10A

description: Library name: sample 4

value: cscB-sps

value: WT high light 47% O2 air saturation


title: ΔrecA_MMC_40_replicate1

description: Library name: ΔrecA_MMC_40_replicate1

value: CB15N; delta-recA


title: Female slide F4 slice D2

value: female


title: WT205-5A

description: Library name: sample 3

value: WT high light 23% O2 air saturation


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, rep1

description: Library name: DMSO_1


title: Female slide F4 slice C2

value: amygdala brain tissue


title: ΔrecA_MMC_40_replicate2

description: Library name: ΔrecA_MMC_40_replicate2


title: E67_knee_spatial01

description:
Library name: D1_k67_spatialHD
10X Genomics Visium HD

data_processing:
The raw files were mapped to the Human genome Hg38 using the Space Ranger v.4.0 software, available via the 10X Genomics website.
Assembly: hg38
Supplementary files format and content: space ranger output files: fragments, matrix and barcodes are provided.
Supplementary files format and content: Loupe file.
Library strategy: Spatial Transcriptomics

source_name: knee

extract_protocol:
Fresh knee tissues were dissected, flash frozen in OCT, sectioned at 10um, permeabalized, and follwed the 10X Genomics spatial Visium HD manufactureres protocol. cDNA was made, amplified and the DNA was purified using Ampure beads.
Libraries were constructed following 10X Genomics visium manufactures protocols. Quality was checked using the tapestation, libraries were pooled and eventually sequenced using the NovaSeq X.

value: knee

tag: age


title: ΔrecA_MMC_20_replicate1

description: Library name: ΔrecA_MMC_20_replicate1


title: Female slide F4 slice B2