title: RNAseq_msh_4

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
3'RNA-seq: In our sequencing strategy read R1 contains UMI, barcode and first nucleotide of oligo(dT). We trim read R1 to keep only UMI and barcode. Our oligo(dT) primers have two parts of UMI split by barcode sequence - we move UMI sequences to be next to each other. For all of this, we use a single awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
3'RNA-seq: Fastq files for read R2 from the pools was demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
For ChIRP-seq and ChIDP-seq data analysis, Bowtie2 (v2.5.3) was used to align the reads to the reference genome (TAIR10, with default parameters). bamCoverage (v3.5.4) with CPM normalisation was used to create bigwig files.
Assembly: TAIR10
Supplementary files format and content: 3'RNA-seq: UMI counts per gene
Supplementary files format and content: ChIRP and ChIDP: bigwig

source_name: siliques (13-20 days after pollination)

growth_protocol: Arabidopsis thaliana plants were grown on soil in a greenhouse under long-day conditions (16 h light/8 h dark) at 22°C/18°C.

extract_protocol:
3'RNA-seq: After grinding in liquid nitrogen, samples were resuspended in 500 μl of homogenisation buffer (100 mM Tris pH 8.5, 5 mM EDTA, 100 mM NaCl, 0.5% SDS, 1% β-mercaptoethanol (Sigma)) and centrifuged for 5 min at RT at 8000 g. The supernatant was transferred to the new tubes containing 250 μl of chloroform. After 15 min of shaking, 250 μl of phenol was added, and shaking was repeated, followed by centrifugation for 10 min at 10000 g. The upper phase was transferred to new tubes, and an equal volume of phenol:chloroform:isoamyl alcohol was added. Shaking and centrifugation steps were repeated. The upper phase was mixed with 10% of the volume of 3 M sodium acetate (pH 5.2), and an equal volume of isopropanol was added. After centrifugation for 30 min at 20000g at 4°C the pellet was washed with 70% EtOH and resuspended in water.
ChIRP-seq and ChIDP-seq: To uncover RNA-DNA (Chromatin Isolation by RNA Purification) and DNA-DNA (Chromatin Isolation by DNA Purification Assay) interactions, we used 400 mg of fresh siliques (13-20 days after pollination), which were ground in liquid nitrogen and resuspended in 20 ml of crosslink buffer (10 mM HEPES-KOH pH 7.4, 50 mM NaCl, 100 mM sucrose, 1% formaldehyde (for RNA-RNA and RNA-DNA) or 0.5% glutaraldehyde (for ChIDP)). After 10 min incubation on a rotator at 4°C, the crosslinking reaction was quenched by adding 1.25 ml 2 M glycine. After an additional 5 min incubation on a rotator, samples were centrifuged at 4°C and 2,000 g for 15 min. The pellets were resuspended in 20 ml of cold Honda Buffer (20 mM HEPES-KOH pH 7.4, 0.44M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 10 mM MgCl2, 5 mM DTT, 0.5% Triton X-100, 10 mM β mercaptoethanol, 1 mM PMSF, 1x Complete protease inhibitors (Roche) and 5 U/ml murine RNase inhibitor (NEB)) and filtered through Miracloth. Subsequently, samples were centrifuged for 15 min at 2,000 g at 4°C. According to downstream assays, the nuclei pellets were resuspended in appropriate buffers (Element Zero Biolabs kit). To enrich specific RNA molecules or chromatin fragments, we used MagIC beads with custom probes targeting those sequences (Element Zero Biolabs). Element Zero Biololabs designed probes are delivered with kits and remain confidential as protected intellectual property.
For ChIRP-seq with MUSHER and lacZ probes, nuclei pellets were resuspended in 1.1 ml of MagIC Lysis Buffer FA (Element Zero Biolabs kit), supplemented with 1x Complete protease inhibitors (Roche) and 5 mM DTT. Next, samples were sonicated using a Bioruptor (Diagenode) and diluted two times with MagIC Lysate Dilution Buffer FA, with 1% of the volume saved as an input sample. MagIC beads were pre-cleared according to the producers' protocol and added to the samples that were next incubated at 40°C for 30 minutes with occasional shaking. This was followed by three washes using MagIC Wash Buffer I FA and nucleic acids elution by incubation at 92°C for 5 min with 10 mM Tris-HCl pH 7.5. After Proteinase K treatment (55°C, 90 min) and phenol:chloroform:isoamyl alcohol extraction, DNA was precipitated by adding 1 µl glycogen, 10% of the volume of 3 M LiCl, and an equal volume of isopropanol. Samples were centrifuged for 30 min at 4°C at 20,000 g. Pellets were washed with cold 80% ethanol and resuspended in water.
For ChIDP-seq, the nuclei pellet was resuspended in 1.1 ml of MagIC Lysis Buffer FA (Element Zero kit) supplemented with 1x Complete protease inhibitors (Roche) and 5 mM DTT. Samples were sonicated using Bioruptor (Diagenode), diluted with MagIC Lysate Dilution Buffer FA, and split into halves (treated with RNaseA at 37°C for 20 min and non-treated). MagIC beads recognising the PIR1 locus were mixed with the lysates that were next incubated at 81°C for 5 min with occasional shaking to denature DNA partially. Subsequently, samples were transferred to 40°C for 20 min to enable binding of the probes. This was followed by six washing steps with the MagIC Lysate Wash buffer I and II, and DNA was eluted with 10 mM Tris-HCl pH 7.5 at 92°C for 5 min. After adding an equal volume of MagIC Lysate Wash buffer I to eluted samples, proteinase K treatment (55°C, 120 min) was performed. To extract DNA fragments, an equal volume of phenol:chloroform:isoamyl alcohol was added. The upper phase was mixed with 1 µl of glycogen, 10% of the volume of 3 M LiCl and an equal amount of isopropanol. After centrifugation for 30 min at 20000g at 4°C, the pellet was washed with 80% EtOH and resuspended in water.
3'RNA-seq: 500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled and pools were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence).
For ChIRP-seq and ChIDP-seq, DNA fragments eluted from MagIC beads were used to prepare libraries with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina using NEBNext Multiplex Dual Index Primers.

treatment_protocol: Siliques were collected 13-20 days after pollination.

value: siliques (13-20 days after pollination)

tag: experiment type


title: UUATAC-seq datasets of Axolotl_GallBladder_A

status: Public on Jul 14 2025

type: SRA

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

description: single-nucleus ATAC profile of Axolotl_GallBladder_A

library_source: genomic single cell

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of axolotl (AmexG_v6.0-DD) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: AmexG_v6.0-DD
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

molecule: genomic DNA

organism: Ambystoma mexicanum

source_name: GallBladder

extract_protocol:
Whole organs were then dissected in the following order: heart, lung, gill, gall bladder, pancreas, liver, cloaca, stomach, intestine, bladder, brain, kidney, spleen, limb and gonad. The samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The NIB's formulation and permeabilization time for each tissue were listed in Supplementary Table 2. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 5,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: The axolotl was anesthetized by 0.1% ethyl 3-aminobenzoate methanesulfonate salt (Sigma-Aldrich) in water prior to heart perfusion with 0.8× PBS.

tag: strain

value: d/dA. mexicanumstrain

tag: tissue

value: GallBladder

tag: genotype

value: d/d

tag: treatment


title: RNAseq_msh_2

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana


title: RNAseq_msh_3


title: RNAseq_msh_1


title: UUATAC-seq datasets of Axolotl_Cloaca_B

description: single-nucleus ATAC profile of Axolotl_Cloaca_B

source_name: Cloaca

value: Cloaca


title: RNAseq_wt_4


title: UUATAC-seq datasets of Axolotl_GallBladder_B

description: single-nucleus ATAC profile of Axolotl_GallBladder_B


title: UUATAC-seq datasets of Axolotl_Cloaca_C

description: single-nucleus ATAC profile of Axolotl_Cloaca_C


title: UUATAC-seq datasets of Axolotl_Kidney_B

description: single-nucleus ATAC profile of Axolotl_Kidney_B

source_name: Kidney

value: Kidney


title: UUATAC-seq datasets of Axolotl_Brain_C

description: single-nucleus ATAC profile of Axolotl_Brain_C

source_name: Brain

value: Brain


title: RNAseq_wt_2


title: UUATAC-seq datasets of Axolotl_Brain_B

description: single-nucleus ATAC profile of Axolotl_Brain_B


title: UUATAC-seq datasets of Axolotl_Cloaca_A

description: single-nucleus ATAC profile of Axolotl_Cloaca_A


title: cfDNA-Healthy-Z00000415

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description: Library name: cfDNA-Healthy-Z00000415

library_source: genomic

data_processing:
Paired-end FASTQ files were mapped to the human genome (hg19) using bwa-meth (V 0.2.0)
Duplicated reads were marked by Sambamba (V 0.6.5)
Reads with low (<10) mapping quality, duplicated, or not mapped in a proper pair were excluded
Reads were stripped from non-CpG nucleotides and converted to PAT files using wgbstools (V 0.1.0)
Assembly: hg19
Supplementary files format and content: bigwig - methylation levels (beta values) in a CpG resolution
Supplementary files format and content: beta - beta values in a CpG resolution in a compact binary representation compatible with wgbstools (https://github.com/nloyfer/wgbs_tools)
Supplementary files format and content: pat.gz - fragment-level CpG methylation patterns compatible with wgbstools
Supplementary files format and content: pat.gz.csi - index file matching the pat.gz files

organism: Homo sapiens

source_name: Cell-free DNA from plasma

extract_protocol:
Blood samples were collected in STRECK tubes and were processed within 10 days of collection. Tubes were centrifuged at 1500g for 10 minutes at 24°C. Plasma was then stored at −80°C until assay. cfDNA was extracted using the QIAsymphony SP instrument and its dedicated QIAsymphony Circulating DNA Kit (QIAGEN) according to the manufacturer’s instructions. DNA concentration was measured using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). DNA derived from all samples was treated with bisulfite using EZ DNA Methylation-Gold (Zymo Research) and eluted in 24 μL elution buffer.
Dual indexed sequencing libraries were prepared using Accel-NGS Methyl-Seq DNA library preparation kits (Swift BioSciences; Ann Arbor, MI) and custom liquid handling scripts executed on the Hamilton MicroLab STAR. Libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA). Four uniquely dual indexed libraries, along with 10% PhiX v3 library (Illumina; San Diego, CA), were pooled and clustered on an Illumina NovaSeq 6000 S2 flow cell followed by 150-bp paired-end sequencing.

value: Cell-free DNA from plasma

tag: disease

value: Healthy


title: RNAseq_wt_1


title: cfDNA-Healthy-Z00000414

description: Library name: cfDNA-Healthy-Z00000414


title: UUATAC-seq datasets of Axolotl_Brain_A

description: single-nucleus ATAC profile of Axolotl_Brain_A


title: cfDNA-Healthy-Z0000040P

description: Library name: cfDNA-Healthy-Z0000040P


title: cfDNA-Healthy-Z0000040Q

description: Library name: cfDNA-Healthy-Z0000040Q


title: UUATAC-seq datasets of Axolotl_Bladder_B

description: single-nucleus ATAC profile of Axolotl_Bladder_B

source_name: Bladder

value: Bladder


title: cfDNA-Healthy-Z0000040N

description: Library name: cfDNA-Healthy-Z0000040N


title: UUATAC-seq datasets of Axolotl_Bladder_C

description: single-nucleus ATAC profile of Axolotl_Bladder_C


title: cfDNA-Healthy-Z0000040M

description: Library name: cfDNA-Healthy-Z0000040M


title: Double mutant normal_3

city: Monrovia

first: Lili

last: Wang

state: California

address: 1218 South fifth avenue

department: Systems Biology

country: USA

institute: City of Hope

description: Library name: 5770

data_processing:
Raw FASTQ files were assessed with FastQC. Sequencing adapters and low-quality bases were trimmed using Trimmomatic, and the cleaned reads were mapped to the mouse reference genome (mm10) with STAR (default settings). MultiQC summarized trimming and alignment metrics. Differential mRNA expression was analyzed with DESeq2; genes showing |log2 fold-change| > 1 and FDR < 0.05 were deemed significantly dysregulated.RNA splicing was analyzed with our established pipeline (24, 46), which combines StringTie, LeafCutter, and rMATS to maximize detection power for splicing dysregulation.
Assembly: mm10
Supplementary files format and content: Normalized gene expression values

organism: Mus musculus

source_name: Mouse splenic B

extract_protocol:
Total RNA was extracted from splenic B cells isolated from murine CLL and normal mouse B cells. ~200-300 ng was used to prepare the RNAseq libraries
Total RNA libraries were prepared using Ultra Lowinput library NugGen Kit following manufacturer instructions

value: Spleen

tag: cell line

tag: cell type

value: Normal B

value: SF3B1 FW MDR FW


title: Double mutant  CLL_2

description: Library name: 4261

value: CLL B

value: SF3B1 WT MDR FW


title: cfDNA-COVID-19-Z0000040L

description: Library name: cfDNA-COVID-19-Z0000040L


title: SF3B1 wild type MDR Mutant CLL

description: Library name: 4470


title: cfDNA-COVID-19-Z0000040H

description: Library name: cfDNA-COVID-19-Z0000040H


title: RNAseq_wt_3


title: Double mutant normal _2

description: Library name: 811553

value: SF3B1 FW MDRFF


title: cfDNA-COVID-19-Z0000040J

description: Library name: cfDNA-COVID-19-Z0000040J


title: Double mutant CLL_3

description: Library name: 4380

value: SF3B1 FW MDR FF


title: UUATAC-seq datasets of Axolotl_Bladder_A

description: single-nucleus ATAC profile of Axolotl_Bladder_A


title: 2nd replicate of IgG CUT&RUN on SALE-RIT1 M90I + YAP8SA cells (negative control).

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: Library name: H12_SALE_RY_IgG_2

data_processing:
Trim Galore (https://github.com/FelixKrueger/TrimGalore) was used to examine read quality and trim adapters. Reads were aligned to the reference genome using Bowtie2. Genome coverage profiles were generated using bedtools genomecov. MACS2 was used to call peaks from each sample in both target-only and IgG-controlled modes. Reads from all IgG samples were pooled to create a common control for peak calling. For narrow peaks from transcription factors and H3K4me3, IgG-controlled peaks were kept for downstream analysis if they met the following criteria: overlapping with treatment-only peaks, q-value < 0.01 and enrichment > 2. For broad peaks from H3K27me3, target-only peaks were kept for downstream analysis if they met the follow criteria: overlapping with IgG-controlled peaks, q-value < 0.01 and enrichment > 2.
Assembly: hg38
Supplementary files format and content: .bw files are BigWig files normalized using the counts per millions (CPM) method.
Library strategy: CUT&Run

source_name: SALE

extract_protocol:
12 million cells per cell line were collected by trypsinization, washed extensively in Wash Buffer (20mM HEPES-NaOH pH 7.5, 150mM NaCl, 0.5mM Spermidine (Cell Signaling Technology), and 1 large Roche complete EDTA-free protease tablet per 50mL solution).
Concanavalin A beads (Bangs Laboratories, ca. no. BP531) were activated through repeated washing in Binding Buffer (20mM HEPES-KOS pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), and prepared at 10µL per sample. Beads were added under gentle vortex, and incubated rocking at room temperature for 8 minutes. Bead-cell complexes were collected by magnet separation, buffer removed, and bead-cell complexes were resuspended in Antibody Buffer (0.1% Triton-X 100, 2mM EDTA). Each cell line sample was then split into two technical replicates per cell line, per antibody. Primary antibodies were added to a final dilution of 1:100 (see Star Methods) and incubated for 2hrs rotating at 4 ºC. Samples were processed for AutoCUT&RUN by arraying in a 96-well PCR plate and processed on a Beckman Biomek i7 liquid handling instrument equipped with a 96S Super Magnet Plate (Alpaqua SKU A001322) for magnetic separation of samples during wash steps, and a QInstruments ColdPlate heater-cooler thermo block (QInstruments no. 2016-0110) with a 96 well PCR plate adapter (Qinstruments no. 2016-1041) to perform the MNase digestion reaction at 4 °C after the addition of 2 mM CaCl2. MNase digestion reactions are then stopped after 120 min by adding EGTA, which allows Mg2+ addition for subsequent enzymatic reactions. Chromatin fragments released into the supernatant during digestion are then used as the substrate for end-repair and ligation with barcoded Y-adapters. Prior to ligation, the A-tailing step is performed at 58 °C to preserve sub-nucleosomal fragments in the library. End-repair and adapter ligation reactions are performed on a separate thermocycler. Chromatin proteins are then digested with Proteinase K, and adapter ligated DNA fragments are purified on the Biomek i7 using two rounds of pre-PCR Ampure bead cleanup with size selection. PCR enrichment reactions are performed on a thermocycler using the KAPA PCR kit (KAPA Cat#KK2502). Two rounds of post-PCR Ampure bead cleanup with size selection are performed on the Biomek i7 to remove unwanted proteins and self-ligated adapters. The size distributions of AutoCUT&RUN libraries are analyzed on an Agilent 4200 TapeStation, and gated size and quantification values are used to calculate sample library yields for pooling. Up to 96 barcoded AutoCUT&RUN libraries are pooled at equimolar concentration for paired-end 50 × 50 bp sequencing on an Illumina NextSeq P2 platform at the Fred Hutchinson Cancer Center Genomics Shared Resource.

value: SALE

value: immortalized small airway lung epithelial cells

value: RIT1-M90I and YAP-8SA (RY)

tag: antibody

value: IgG:CST 3900


title: Double mutant normal

description: Library name: 811545


title: Double mutant normal_2

description: Library name: F1Q3


title: P11, TCRseq

city: Shanghai

first: Feixiang

state: Shanghai

address: Chongqing South Road 280

institute: Shanghai Jiaotong University School of Medicine

description:
Library name: sample22
10x Genomics

data_processing:
Raw reads of scRNA-seq were processed with the Cell Ranger v.6.0.1 and mapped to GRCh38 reference genome for human samples to generate matrices of gene counts by cell barcodes. Gene-barcodes matrices were analyzed with the R package Seurat v.4.4.0. Cells with ≥ 200 genes and genes expressed in ≥ 3 cells were used in subsequent analysis. Illumina bcl2fastq2 Conversion Software v2.20 was used to convert sequencing data into FASTQ format. FastQC v0.11.9 was used for data quality control. CellRanger v6.0.1was used to process, align to mapped to GRCh38 reference genome for human samples to generate matrices of gene counts by cell barcodes, and summarize unique molecular identifier (UMI) counts in feature-barcode matrices. The genes expressed in fewer than three cells were excluded. The cells with gene count over 7500 or fewer than 200 were filtered, as were cells that obtained more than 5% mitochondrial genes. Cells with ≥ 200 genes and genes expressed in ≥ 3 cells were used in subsequent analysis for human tumor tissues. A global-scaling method was applied to normalize the data matrix using the LogNormalize function in Seurat v4.4.0. A log-transformation normalized data matrix was employed for downstream analysis. The batch effect between groups is removed through the R package harmony v1.2.0. To identify T cell subpopulations, lineage markers such as Cd3g, Cd3d, and Cd3e are used to confirm whether a cell population consists of T cells. After removing contaminating cells, clustering and dimensionality reduction are performed again following the standard Seurat workflow to obtain T cell subsets for further analysis.
Assembly: GRCh38 reference genome for human samples
Supplementary files format and content: The *-Count.txt.gz file stores the gene expression count data from single-cell RNA sequencing. In this file, each row corresponds to a gene, and each column represents a cell. The values within the file denote the reads counts of genes in respective cells.
Supplementary files format and content: The *-Metadata.txt.gz file contains the metadata of single cells. Here, each row corresponds to a cell, and each column represents a metadata field (such as nFeature, nCount, sample id, etc.).
Supplementary files format and content: The *-TCR.txt.gz file stores the T-cell receptor (TCR) sequencing data of single cells. In this file, each row corresponds to a cell, and each column represents a TCR attribute field (such as clonetype, frequency, etc.).
Library strategy: TCR-Seq

source_name: tumor tissue

extract_protocol:
Fresh CRC tissue was washed with ice-cold PBS, cut into small pieces, and incubated in 10 mL of PBS containing DTT (65 mM) (supplemented with 10% FBS) at 37°C with shaking for 15 minutes. After two incubations with PBS, EDTA and DTT were removed. Small pieces of tissue were minced and digested with 0.38 mg/mL collagenase VIII and 0.1 mg/mL DNase I in complete RPMI 1640 medium (containing 10% FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin) for 1 hour at 37°C. After digestion, the tube was shaken vigorously for 5 minutes. The cells were mechanically dissociated using a 21-gauge syringe. The cells were filtered through a 100 μm filter and pelleted, and washed twice with PBS.
Freshly prepared cell suspensions were performed immediately according to the manufacturer’s protocol of 10 X Chromium 5’ v2 kit (10x Genomics, Pleasanton, CA) and 10x Chromium Single Cell V(D)J Reagent Kits v1.1.

treatment_protocol: all samples were freshly isolated from patients

value: tumor tissue

tag: age

value: tumor infiltrating CD8 T cells

tag: Sex

value: male


title: cfDNA-COVID-19-Z0000040F

description: Library name: cfDNA-COVID-19-Z0000040F

value: Cell-free DNA from plasma


title: 2nd replicate of ZEB1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H11_SALE_RY_ZEB1_2

value: ZEB1:Abcam ab155249


title: 2nd replicate of H3K27ac CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H10_SALE_RY_H3K27ac_2


title: P10, TCRseq

description:
Library name: sample21
10x Genomics

value: female


title: 2nd replicate of H3K27me3 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H9_SALE_RY_H3K27me3_2


title: P9, TCRseq

description:
Library name: sample20
10x Genomics


title: Double mutant  CLL

description: Library name: 811567

value: Spleen


title: P8, TCRseq

description:
Library name: sample19
10x Genomics


title: P6, TCRseq

description:
Library name: sample17
10x Genomics


title: P5, TCRseq

description:
Library name: sample16
10x Genomics


title: 2nd replicate of H3K4me3 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H8_SALE_RY_H3K4me3_2


title: P7, TCRseq

description:
Library name: sample18
10x Genomics


title: P3, TCRseq

description:
Library name: sample14
10x Genomics


title: ChIDPseq_input_1

value: siliques (13-20 days after pollination)

value: ChIDP-seq

value: input


title: ChIDPseq_input_2


title: 2nd replicate of H3K4me1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H7_SALE_RY_H3K4me1_2


title: cfDNA-COVID-19-Z0000040G

description: Library name: cfDNA-COVID-19-Z0000040G


title: P1, TCRseq

description:
Library name: sample12
10x Genomics


title: P2, TCRseq

description:
Library name: sample13
10x Genomics


title: ChIDPseq_1

value: PIR1 probes


title: 2nd replicate of cJUN CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H5_SALE_RY_cJUN_2

value: cJUN:CST 9165


title: P11, scRNAseq

description:
Library name: sample11
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads of scRNA-seq were processed with the Cell Ranger v.6.0.1 and mapped to GRCh38 reference genome for human samples to generate matrices of gene counts by cell barcodes. Gene-barcodes matrices were analyzed with the R package Seurat v.4.4.0. Cells with ≥ 200 genes and genes expressed in ≥ 3 cells were used in subsequent analysis. Illumina bcl2fastq2 Conversion Software v2.20 was used to convert sequencing data into FASTQ format. FastQC v0.11.9 was used for data quality control. CellRanger v6.0.1was used to process, align to mapped to GRCh38 reference genome for human samples to generate matrices of gene counts by cell barcodes, and summarize unique molecular identifier (UMI) counts in feature-barcode matrices. The genes expressed in fewer than three cells were excluded. The cells with gene count over 7500 or fewer than 200 were filtered, as were cells that obtained more than 5% mitochondrial genes. Cells with ≥ 200 genes and genes expressed in ≥ 3 cells were used in subsequent analysis for human tumor tissues. A global-scaling method was applied to normalize the data matrix using the LogNormalize function in Seurat v4.4.0. A log-transformation normalized data matrix was employed for downstream analysis. The batch effect between groups is removed through the R package harmony v1.2.0. To identify T cell subpopulations, lineage markers such as Cd3g, Cd3d, and Cd3e are used to confirm whether a cell population consists of T cells. After removing contaminating cells, clustering and dimensionality reduction are performed again following the standard Seurat workflow to obtain T cell subsets for further analysis.
Assembly: GRCh38 reference genome for human samples
Supplementary files format and content: The *-Count.txt.gz file stores the gene expression count data from single-cell RNA sequencing. In this file, each row corresponds to a gene, and each column represents a cell. The values within the file denote the reads counts of genes in respective cells.
Supplementary files format and content: The *-Metadata.txt.gz file contains the metadata of single cells. Here, each row corresponds to a cell, and each column represents a metadata field (such as nFeature, nCount, sample id, etc.).
Supplementary files format and content: The *-TCR.txt.gz file stores the T-cell receptor (TCR) sequencing data of single cells. In this file, each row corresponds to a cell, and each column represents a TCR attribute field (such as clonetype, frequency, etc.).


title: ChIDPseq_2


title: 2nd replicate of FOSL1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H6_SALE_RY_FOSL1_2

value: FOSL1:Abcam ab252421


title: 2nd replicate of panTEAD CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H4_SALE_RY_panTEAD_2

value: SALE

value: panTEAD:CST 13295


title: Double mutant CLL_2

description: Library name: 4330

value: CLL B

value: SF3B1 FW MDR FF


title: P8, scRNAseq

description:
Library name: sample8
10x Genomics

value: tumor tissue


title: 2nd replicate of TAZ CUT&RUN onSALE-RIT1 M90I + YAP8SA cells.

description: Library name: H3_SALE_RY_TAZ_2

value: immortalized small airway lung epithelial cells

value: RIT1-M90I and YAP-8SA (RY)

value: TAZ:CST 4883


title: P7, scRNAseq

description:
Library name: sample7
10x Genomics

value: tumor infiltrating CD8 T cells

value: male


title: ChIRPseq_lacZ_2

value: ChIRP-seq

value: lacZ probes


title: P10, scRNAseq

description:
Library name: sample10
10x Genomics

value: female


title: P6, scRNAseq

description:
Library name: sample6
10x Genomics


title: ChIRPseq_lacZ_1

value: siliques (13-20 days after pollination)


title: 2nd replicate of YAP1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: H2_SALE_RY_YAP1_2

value: YAP1:Abcam ab52771


title: P4, TCRseq

description:
Library name: sample15
10x Genomics


title: ChIRPseq_msh_input_2

value: input


title: P4, scRNAseq

description:
Library name: sample4
10x Genomics


title: P3, scRNAseq

description:
Library name: sample3
10x Genomics


title: ChIRPseq_msh_input_1


title: P2, scRNAseq

description:
Library name: sample2
10x Genomics


title: P1, scRNAseq

description:
Library name: sample1
10x Genomics


title: 1st replicate of IgG CUT&RUN on SALE-RIT1 M90I + YAP8SA cells (negative control).

description: Library name: G12_SALE_RY_IgG_1

value: IgG:CST 3900


title: ChIRPseq_msh_2

value: MUSHER probes


title: P9, scRNAseq

description:
Library name: sample9
10x Genomics


title: AD-NC+Ang II-4

city: Ethnicity

first: Xiaohan

last: Liu

address: 44#, Whenhua Xi Road

institute: Shandong University

description: Library name: Sample 9

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.108 genome assembly using Tophat version 2.0.5 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: GRCh38.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: cell line

growth_protocol: Human umbilical vein endothelial cells (HUVECs)  were cultured under growth permissive conditions in DMEM/F12  supplemented with 10% fetal bovine serum (FBS) , and then the human  endothelial cells were transfected with NC-adenovirus or mydgf-adenovirus for 24 hours to construct AD-NC or AD-MYDGF endothelial cell line,  and treated with1 μmol/L Ang II for 48 hours for this study

extract_protocol:
According to the manufacturer’s instruction, RNA of cells was isolated using AG RNAex Pro Reagent （AG21102， Accurate Biology）.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ang II at a final concentration of 1 μmol/L in culture medium

value: cell line

value: HUVEC

value: endothelial cells

value: WT

value: Ang II treatment for 48h


title: ChIRPseq_msh_1


title: AD-NC+Ang II-2

description: Library name: Sample 7


title: 1st replicate of ZEB1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G11_SALE_RY_ZEB1_1

value: SALE

value: immortalized small airway lung epithelial cells

value: RIT1-M90I and YAP-8SA (RY)

value: ZEB1:Abcam ab155249


title: 1st replicate of H3K27ac CUT&RUN on SALE-RIT1 M90I + YAP8SAcells.

description: Library name: G10_SALE_RY_H3K27ac_1


title: AD-NC+Ang II-3

description: Library name: Sample 8


title: ChIRPseq_wt_input_2

value: ChIRP-seq


title: 1st replicate of H3K27me3 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G9_SALE_RY_H3K27me3_1


title: AD-MYDGF+Ang II-5

description: Library name: Sample 5

value: MYDGF overexpression


title: P5, scRNAseq

description:
Library name: sample5
10x Genomics

value: tumor tissue

value: tumor infiltrating CD8 T cells

value: female


title: 1st replicate of H3K4me3 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G8_SALE_RY_H3K4me3_1


title: AD-MYDGF+Ang II-3

description: Library name: Sample 3


title: ChIRPseq_wt_input_1

value: siliques (13-20 days after pollination)

value: input


title: AD-NC+Ang II-1

description: Library name: Sample 6


title: AD-MYDGF+Ang II-2

description: Library name: Sample 2


title: AD-MYDGF+Ang II-4

description: Library name: Sample 4


title: 2nd replicate of PolII CUT&RUN on SALE-RIT1 M90I + YAP8SA cells (positive control).

description: Library name: H1_SALE_RY_PolII_2

value: PolII:CST 13523


title: 1st replicate of H3K4me1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G7_SALE_RY_H3K4me1_1


title: AD-MYDGF+Ang II-1

description: Library name: Sample 1

value: cell line


title: ChIRPseq_wt_1

value: MUSHER probes


title: WIBR3 organoids, S. cerevisiae infected at MOI 1:2, Day7, replicate 2

city: Boston

first: Jatin

last: Vyas

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

description: Library name: Sc2Day7

data_processing:
Data was processed using the nextflow RNA-seq pipeline
Assembly: hg38
Supplementary files format and content: excel sheet detailing the normalized read counts for each sample

source_name: Cerebral organoid

extract_protocol:
Rna was harvested and extracted using the standard protocol from Qiagen's Rneasy miniprep kit
Libraries were constructed using the RNA-Seq 3' Digital Gene Expression (3'-DGE) library preparation

value: Cerebral organoid

value: Cerebral


title: AD-NC+Ang II-5

description: Library name: Sample 10

value: HUVEC

value: endothelial cells

value: WT

value: Ang II treatment for 48h


title: 1st replicate of FOSL1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G6_SALE_RY_FOSL1_1

value: SALE

value: immortalized small airway lung epithelial cells

value: RIT1-M90I and YAP-8SA (RY)

value: FOSL1:Abcam ab252421


title: 1st replicate of cJUN CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G5_SALE_RY_cJUN_1

value: cJUN:CST 9165


title: MNASEseq_GAL60

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

data_processing:
NET-seq: Sequencing reads were aligned, processed and subtracted of background signal (signal that is not specific to immunoprecipitation of Pol2 via its tagged Rpb3 subunit) as described in Fischl et al., 2017;
RNA-seq: Sequencing reads were aligned to the sacCer3 genome build using the Ion Torrent Server TMAP aligner with default alignment settings (-tmap mapall stage1 map4). Non-uniquely mapped reads were removed using Samtools (samtools view -bq 1). Bigwig files were generated by normalizing to reads per million (RPM)
MNASE-seq: Sequencing reads were aligned to the sacCer3 genome build using the Ion Torrent Server TMAP aligner with default alignment settings (-tmap mapall stage1 map4). Bam files were further processed using DANPOS2 (Chen et al., 2015) (dpos -a 1) to give genome-wide maps of the centre point of each nucleosome.
Genome_build: sacCer3
Supplementary_files_format_and_content: RNA-seq: Fastq raw sequencing data, bed file of uniquely aligned reads, bigwigs of RPM normalized read pile up; MNASE-seq: bam file of tmap aligned reads, DANPOS processed bigwigs of bam file data, DANPOS processed bigwigs showing the centre point of each nucleosome; NET-seq data bam file of bowtie aligned reads – raw reads have been clipped of adapter sequences, bigwigs of reads narrowed to their 3’ nucleotide before no tag signal subtration, bigwigs of reads narrowed to their 3’ nucleotide after no tag signal subtraction.

organism: Saccharomyces cerevisiae BY4741

extract_protocol:
NET-seq/RNA-seq: Cells were harvested by filtration followed by flash-freezing and grinding; MNASE-seq: Cells were cross-linked by incubation with 1 % formadehyde for 10 min. Cells were then incubated for 5 min with glycine (0.125 M final). Cells were then harvested by filtration, washed with 1 % cold PBS, followed by flash-freezing in liquid nitrogen and grinding.
NET-seq: Libraries were generated as described in Fischl et., al 2017 and Nguyen et al., 2014; RNA-seq: RNA was extracted using phenol:chloroform, extracted RNA was depleted of ribosomal RNA using Ribominus kit (Invitrogen) as per the manufacturer's instructions, libraries for RNA-seq were constructed using the Ion Total RNA-seq kit v2 (ThermoFisher) as per the manufacturer's instructions. MNASE-seq: yeast grindate was digested with MNASE, digested DNA was purified and size selected, libraries for MNASE-seq using the NEBNext Fast DNA library prep set for Ion Torrent as per the manufacturer's instructions.

value: Wild type

tag: growth condition

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then switched to galactose (YPG) for 60 minutes

tag: molecule

value: MNASE digested DNA


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day7, replicate 2

description: Library name: Cau2Day7


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day3, replicate 3

description: Library name: Cau3Day3


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day3, replicate 2

description: Library name: Cau2Day3


title: MNASEseq_GAL5

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then switched to galactose (YPG) for 5 minutes


title: 1st replicate of panTEAD CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G4_SALE_RY_panTEAD_1

value: panTEAD:CST 13295


title: 1st replicate of TAZ CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G3_SALE_RY_TAZ_1

value: TAZ:CST 4883


title: ChIRPseq_wt_2

value: siliques (13-20 days after pollination)

value: ChIRP-seq

value: MUSHER probes


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day7, replicate 3

description: Library name: CNhigh3Day7

value: Cerebral organoid

value: Cerebral


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day3, replicate 1

description: Library name: Cau1Day3


title: 1st replicate of YAP1 CUT&RUN on SALE-RIT1 M90I + YAP8SA cells.

description: Library name: G2_SALE_RY_YAP1_1

value: YAP1:Abcam ab52771


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day7, replicate 1

description: Library name: CNhigh1Day7


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day7, replicate 2

description: Library name: CNhigh2Day7


title: RNAseq_GAL60_Rep2

value: RNA


title: 1st replicate of PolII CUT&RUN on SALE-RIT1 M90I + YAP8SA cells (positive control).

description: Library name: G1_SALE_RY_PolII_1

value: SALE

value: immortalized small airway lung epithelial cells

value: PolII:CST 13523


title: RNAseq_GAL60_Rep1


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day3, replicate 1

description: Library name: CNhigh1Day3


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day3, replicate 2

description: Library name: CNhigh2Day3


title: 2nd replicate of IgG CUT&RUN on SALE-YAP8SA cells (negative control).

description: Library name: F12_SALE_Y_IgG_2

value: IgG:CST 3900


title: WIBR3 organoids, S. cerevisiae infected at MOI 1:2, Day7, replicate 1

description: Library name: Sc1Day7


title: WIBR3 organoids, C. neformans infected at MOI 1:2, Day3, replicate 3

description: Library name: CNhigh3Day3


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day7, replicate 3

description: Library name: Cau3Day7


title: WIBR3 organoids, C. neformans infected at MOI 0.1:2, Day7, replicate 3

description: Library name: CNlow3Day7


title: 2nd replicate of ZEB1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: F11_SALE_Y_ZEB1_2

value: ZEB1:Abcam ab155249


title: WIBR3 organoids, C. auris infected at MOI 1:2, Day7, replicate 1

description: Library name: Cau1Day7


title: WIBR3 organoids, C. neformans infected at MOI 0.1:2, Day7, replicate 2

description: Library name: CNlow2Day7


title: RNAseq_GAL15_Rep2

value: Wild type

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then switched to galactose (YPG) for 15 minutes


title: WIBR3 organoids, C. neformans infected at MOI 0.1:2, Day7, replicate 1

description: Library name: CNlow1Day7


title: MNASEseq_GAL15

value: MNASE digested DNA


title: RNAseq_GAL15_Rep1


title: MNASEseq_GLU

value: Exponential growth in glucose (YPD) to OD600 = 0.65


title: 2nd replicate of H3K27me3 CUT&RUN on SALE-YAP8SA cells.

description: Library name: F9_SALE_Y_H3K27me3_2


title: WIBR3 organoids, C. neformans infected at MOI 0.1:2, Day3, replicate 1

description: Library name: CNlow1Day3


title: RNAseq_GAL5_Rep2

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then switched to galactose (YPG) for 5 minutes


title: WIBR3 organoids, uninfected, Day7, replicate 3

description: Library name: CTRL3Day7


title: 2nd replicate of H3K27ac CUT&RUN on SALE-YAP8SA cells.

description: Library name: F10_SALE_Y_H3K27ac_2


title: RNAseq_GAL5_Rep1


title: WIBR3 organoids, uninfected, Day7, replicate 1

description: Library name: CTRL1Day7


title: WIBR3 organoids, uninfected, Day7, replicate 2

description: Library name: CTRL2Day7


title: RNAseq_GLU_Rep2


title: 2nd replicate of H3K4me3 CUT&RUN on SALE-YAP8SA cells.

description: Library name: F8_SALE_Y_H3K4me3_2


title: 2nd replicate of H3K4me1 CUT&RUN on SALE-YAP8SAcells.

description: Library name: F7_SALE_Y_H3K4me1_2


title: WIBR3 organoids, uninfected, Day3, replicate 2

description: Library name: CTRL2Day3


title: WIBR3 organoids, uninfected, Day3, replicate 1

description: Library name: CTRL1Day3


title: 2nd replicate of FOSL1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: F6_SALE_Y_FOSL1_2

value: FOSL1:Abcam ab252421


title: Substantia nigra, monomer, hypoxia, rep12

first: Vamsi

last: Mootha

address: 185 Cambridge Street 6th Floor

description: Library name: m218

data_processing:
First, any rDNA-derived transcripts remaining after polyA selection were filtered out by aligning the reads to the mouse rDNA reference and annotation (GenBank ID: BK000964.3) with the STAR aligner (v 2.7.5a), and keeping only the unaligned reads.
After this in silico rRNA depletion step, STAR was used again to align the remaining reads to the mouse reference genome (mm10 with GENCODE annotation v M24) with the options --outSAMattributes NH HI NM MD AS XS nM, and –twopassMode Basic.
Next, for any reads that mapped equally well to the nuclear genome and the mitochondrial genome, the mitochondrial alignment was set as the primary alignment.
Duplicate reads were removed with the Picard MarkDuplicates tool (Picard v 2.21.9, as distributed in GATK v 4.1.5.0-9-g227bef6-SNAPSHOT)
Reads were assigned to genes using featureCounts (v 2.0.1) with options -p, -M, and –primary
The read counts per gene were aggregated from the featureCounts output files into a single read count matrix with a row for each sample and a column for each gene for downstream analysis
The raw count matrix was joined with the metadata about the samples and genes using AnnData (v 0.7.5), and Scanpy (v 1.8.1) was used to conduct a principal components analysis (PCA). The raw counts were first normalized using transcripts per million (TPM), then log-scaled with the scanpy.pp.log1p function. The gene list was filtered to only contain protein-coding genes, and then highly variable genes were identified with the scanpy.pp.highly_variable_genes function with min_mean=1.25, max_mean=7, and min_disp=1.5. Finally, the normalized and logged counts were z-score scaled using the scanpy.pp.scale function with max_value=10, and the scanpy.tl.pca function with svd_solver=’arpack’ was used to perform PCA, using the scaled highly variable genes as the features. This initial PCA highlighted some outlier samples, so an iterative procedure of removing outliers and updating the PCA was used until there were no outliers dominating the variance in PC1 or PC2. Six of forty eight samples were removed in this way.
The ComBat-seq tool was applied on the 42 non-outlier samples to adjust for the batch effect, while specifying the O2 status (hypoxia or normoxia) and injection type (PFF or monomer) as additional covariates to preserve the signal associated with our experimental variables. A final PCA on the batch-corrected count matrix returned by ComBat-seq confirmed that the batch effects were successfully mitigated.
Assembly: mm10
Supplementary files format and content: csv files contain raw counts, transcripts per million (TPM) normalized counts, and filtered/batch-corrected raw and TPM-normalized counts

molecule: polyA RNA

source_name: substantia nigra

growth_protocol: C57Bl/6J male mice were purchased and housed in a specific pathogen-free room of the animal facirity at Massachusetts General Hospital for 1 week before PFF/monomeric alpha-syn injection. After PFF/monomeric alpha-syn injection, mice cages were housed in plastic chambers to breathe air or hypoxic gas . Humidity or carbon dioxide levels in the plastic chambers were monitored continuously and maintained at 30-50% or below 2000 ppm, respectively. Mice were fed regular diet and drinking water supplied by the animal facirity. The room light was maintained with 12h/12h day/night cycles.

extract_protocol:
Total RNA was extracted from dissected fresh frozen SN samples using Qiagen RNeasy Plus Universal mini kit following the manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with 13 cycles.

treatment_protocol: Mice were subjected to intrastriatal injection of PFF or monomeric alpha-syn under isoflurane anesthesia. Mice, that were received the injection of PFF or monomeric alpha-syn and recovered from anesthesia, were housed in plastic chambers to breathe 21% O2 or 11% O2. SN tissues were harvested 12 weeks after injection of PFF/monomeric alpha-syn.

value: substantia nigra

value: monomer

tag: oxygen level

value: hypoxia

tag: injection date

tag: date of_birth

tag: date of_harvest

tag: batch


title: PC3 cells, siPRMT74

city: Wuxi

first: Hongyuan

last: Wan

state: Jiangsu

address: Wuxi Medical College, Jiangnan University, Wuxi 214122, Jiangsu Province, China

description: Library name: shPRMT7_4

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: PC3 cells were cultured in RPMI-1640 (Cytiva) medium supplemented with 10% fetal bovine serum (Ausbian). All cells were incubated at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
Atotal amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5  min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

treatment_protocol: 4×105 PC3 cells were seeded in each well of a 6-well plate. Upon reaching 60-–70% confluency, transfections were performed using Lipofectamine™ 3000 reagent (Thermo, Inc.) according to the manufacturer’s instructions, including synthetic RNA mimics and negative controls. The cells were cultured for another 48 h. The transfection efficiency was >80% based on green protein fluorescence.

value: prostate cncer cells

value: PRMT7 knockdown


title: PC3 cells, siPRMT73

institute: Wuxi Medical College, Jiangnan University

description: Library name: shPRMT7_3


title: 2nd replicate of cJUN CUT&RUN on SALE-YAP8SA cells.

description: Library name: F5_SALE_Y_cJUN_2

value: cJUN:CST 9165


title: PC3 cells, siPRMT72

description: Library name: shPRMT7_2


title: Substantia nigra, monomer, hypoxia, rep11

description: Library name: m217


title: PC3 cells, siPRMT71

description: Library name: shPRMT7_1


title: 2nd replicate of panTEAD CUT&RUN on SALE-YAP8SA cells.

description: Library name: F4_SALE_Y_panTEAD

value: SALE

value: panTEAD:CST 13295


title: PC3 cells, siCtrl4

description: Library name: shCtrl_4

value: WT


title: Substantia nigra, monomer, hypoxia, rep10

description: Library name: m215


title: WIBR3 organoids, C. neformans infected at MOI 0.1:2, Day3, replicate 2

description: Library name: CNlow2Day3

value: Cerebral organoid

value: Cerebral


title: PC3 cells, siCtrl2

description: Library name: shCtrl_2


title: PC3 cells, siCtrl1

description: Library name: shCtrl_1


title: 2nd replicate of YAP1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: F2_SALE_Y_YAP1_2

value: immortalized small airway lung epithelial cells

value: YAP1:Abcam ab52771


title: Substantia nigra, monomer, hypoxia, rep8

description: Library name: m213


title: 2nd replicate of TAZ CUT&RUN on SALE-YAP8SA cells.

description: Library name: F3_SALE_Y_TAZ_2

value: TAZ:CST 4883


title: PolII CUT&RUN on SALE-YAP8SA cells (positive control).

description: Library name: F1_SALE_Y_PolII_1

value: PolII:CST 13523


title: RNAseq_GLU_Rep1

value: Wild type

value: Exponential growth in glucose (YPD) to OD600 = 0.65

value: RNA


title: WIBR3 organoids, uninfected, Day3, replicate 3

description: Library name: CTRL3Day3


title: Substantia nigra, monomer, hypoxia, rep7

description: Library name: m212

value: substantia nigra

value: monomer


title: Substantia nigra, monomer, hypoxia, rep6

description: Library name: m211

value: hypoxia


title: wild type hESC, H2AK119ub, rep2

city: Irvine

first: Minji

last: Byun

state: CA

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

description: Library name: CUT_RUN, H2AK119ub_g3-2

data_processing:
The output data is preprocessed using FastQC, then aligned with Bowtie2 and deduplicated using gatk markduplicates.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
Nuclei were extracted from cells and conjugated to ConA beads, which were then treated with Mnase.
CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina and NEBNext Mutiple Oligos for Illumina (Dual index). 5ng of DNA was used as starting material. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraires were purified with SPRIselect beads. Libraries were validated using Agilent High Sensitivity dsDNA kit.

value: human embryonic stem cell

value: wild type


title: wild type hESC, H2AK119ub, rep3

description: Library name: CUT_RUN, H2AK119ub_g1-14


title: 1st replicate of IgG CUT&RUN on SALE-YAP8SA cells (negative control).

description: Library name: E12_SALE_Y_IgG_1

value: SALE

value: IgG:CST 3900


title: wild type hESC, H3K4me3, rep2

description: Library name: CUT_RUN, H3K4me3_g3-2


title: wild type hESC, H2AK119ub, rep1

description: Library name: CUT_RUN, H2AK119ub_H1


title: wild type hESC, H3K27me3, rep3

description: Library name: CUT_RUN, H3K27me3_g1-14


title: PC3 cells, siCtrl3

description: Library name: shCtrl_3

value: prostate cncer cells

value: WT


title: wild type hESC, H3K27me3, rep1

description: Library name: CUT_RUN, H3K27me3_H1


title: Substantia nigra, monomer, hypoxia, rep5

description: Library name: m210


title: wild type hESC, H3K4me3, rep3

description: Library name: CUT_RUN, H3K4me3_g1-14


title: 1st replicate of ZEB1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E11_SALE_Y_ZEB1_1

value: ZEB1:Abcam ab155249


title: 1st replicate of H3K27me3 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E9_SALE_Y_H3K27me3_1

value: immortalized small airway lung epithelial cells


title: Substantia nigra, PFF, hypoxia, rep12

description: Library name: m208

value: PFF


title: wild type hESC, H3K4me3, rep1

description: Library name: CUT_RUN, H3K4me3_H1


title: wild type hESC, H3K4me1, rep2

description: Library name: CUT_RUN, H3K4me1_g3-2


title: wild type hESC, H3K4me1, rep3

description: Library name: CUT_RUN, H3K4me1_g1-14


title: Substantia nigra, monomer, hypoxia, rep9

description: Library name: m214


title: 1st replicate of H3K27ac CUT&RUN on SALE-YAP8SA cells.

description: Library name: E10_SALE_Y_H3K27ac_1


title: Substantia nigra, PFF, hypoxia, rep11

description: Library name: m207


title: Substantia nigra, PFF, hypoxia, rep10

description: Library name: m206


title: wild type hESC, IgG, rep2

description: Library name: CUT_RUN, IgG_g3-2


title: 1st replicate of H3K4me3 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E8_SALE_Y_H3K4me3_1


title: wild type hESC, H3K27me3, rep2

description: Library name: CUT_RUN, H3K27me3_g3-2


title: 1st replicate of H3K4me1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E7_SALE_Y_H3K4me1_1


title: wildtype hESC, IgG, rep3

description: Library name: CUT_RUN, IgG_g1-14


title: wildtype hESC, IgG, rep1

description: Library name: CUT_RUN, IgG_H1


title: Substantia nigra, PFF, hypoxia, rep9

description: Library name: m205


title: 1st replicate of FOSL1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E6_SALE_Y_FOSL1_1

value: FOSL1:Abcam ab252421


title: dCas9-cdPRDM9 + sgRNA_acFOXC1 rep2

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: Library name: cdPRDM9_rep2

data_processing:
Data were filtered for high‐quality reads using the fastq_quality_filter tool from FASTX‐Toolkit with parameters ‐p 80 ‐q 20 parameters.
Filtered libraries were aligned to the hg19 genome assembly using Bowtie2 with parameters --end‐to‐end --sensitive.
Aligned reads were filtered to get uniquely mapping reads without PCR duplicates using SAMtools with parameters -q 1 -f 3 -F 256.
Bigwig files were generated using the bamCoverage tool from deepTools.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: bed (.narrowPeak)

growth_protocol: DMEM, 10% fetal bovine serum, 2.5 ug/ml Plasmocin , 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
5 x 104 cells were harvested for each reaction.
ATAC-seq library preparation was carried out using the ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions.

value: Triple negative breast cancer

value: dCas9-cdPRDM9 + sgRNA_acFOXC1


title: 1st replicate of cJUN CUT&RUN on SALE-YAP8SA cells.

description: Library name: E5_SALE_Y_cJUN_1

value: cJUN:CST 9165


title: dCas9-PRDM9 + sgRNA_acFOXC1 rep2

description: Library name: PRDM9_rep2

value: dCas9-PRDM9 + sgRNA_acFOXC1


title: dCas9-PRDM9 + sgRNA_acFOXC1 rep1

description: Library name: PRDM9_rep1


title: Substantia nigra, PFF, normoxia, rep12

description: Library name: m204

value: substantia nigra

value: normoxia


title: Substantia nigra, PFF, normoxia, rep11

description: Library name: m203


title: dCas9-cdPRDM9 + sgRNA_acFOXC1 rep1

description: Library name: cdPRDM9_rep1


title: Substantia nigra, PFF, normoxia, rep10

description: Library name: m202


title: 8CLL8683D

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

description: Library name: 8CLL8683D

data_processing:
Paired end reads (100bp) were generated on NovaSeq 6000 (Illumina) instrument following manufacturer recommendations.
Reads from multiple lanes were merged and trimmed with Trimmomatic.
Reads were aligned to the hg38 GRCh38 reference genome using STAR aligner (v2.5.3a).
FeatureCounts (v1.6.4) was used to compute reads mapping on exons as annotated in GENCODE Homo sapiens basic gene annotation (version v31) and obtain transcript quantification summarized at the gene level, excluding multimapping reads.
Only genes with at least 1 CPM (Counts per million) in at least 3 samples were retained.
Assembly: GRCh38  (GENCODE v31)
Supplementary files format and content: Tab separated file of raw counts. Gizipped.

source_name: Chronic lymphocytic leukemia (CLL) B cells

growth_protocol: 2D and 3D cocultures were cultured in RPMI supplemented with 10% FBS and antibiotics

extract_protocol:
Spheroids were digested with LiberaseTM to obtain a single cell suspension, instead for 2D cultured was used trypsine. Then cells were purified and RNA was extracted using RNAeasy minikit protocol from Qiagen.
RNA-Seq libraries were prepared with the Illumina TruSeq Stranded mRNA kit. Sequencing was performed in PE mode on a Illumina NovaSeq 6000 machine.

tag: model

tag: patient


title: 7CLL8682D

description: Library name: 7CLL8682D

tag: tissue

value: Chronic lymphocytic leukemia (CLL) B cells


title: Substantia nigra, PFF, normoxia, rep9

description: Library name: m201

tag: treatment


title: 1st replicate of panTEAD CUT&RUN on SALE-YAP8SA cells.

description: Library name: E4_SALE_Y_panTEAD_1

tag: genotype

value: panTEAD:CST 13295


title: 1st replicate of TAZ CUT&RUN on SALE-YAP8SA cells.

description: Library name: E3_SALE_Y_TAZ_1

tag: cell line

value: TAZ:CST 4883


title: wild type hESC, H3K4me1, rep1

description: Library name: CUT_RUN, H3K4me1_H1

tag: cell type

value: human embryonic stem cell

value: wild type


title: 1st replicate of YAP1 CUT&RUN on SALE-YAP8SA cells.

description: Library name: E2_SALE_Y_YAP1_1

value: SALE

tag: antibody

value: YAP1:Abcam ab52771


title: 5CLL4962D

description: Library name: 5CLL4962D


title: 4CLL8413D

description: Library name: 4CLL8413D


title: 3CLL8412D

description: Library name: 3CLL8412D


title: SAT5 (snm3C)

city: Los Angeles

first: Asha

last: Kar

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

description: Library name: SAT5

data_processing:
The sequencing reads of snm3C-seq3 were mapped to the GRCh38 human genome reference with Gencode v34 gene annotations using Taurus-MH. Mapped reads were subsequently processed using scHicluster and ALLCools.
Assembly: hg38
Supplementary files format and content: Tab-separated text files for meta data, gene-body and 5-kb bin location, chromatin conformation contact patterns per cell, methylated CG counts, total coverage, normalized gene-body methylation fraction, 5kb-bin binarized hypo-methylation matrix
Supplementary files format and content: Tab-seperated text file with aggregate CG methylation patterns per cell-type
Supplementary files format and content: Text file with description of all files and their column identifiers

source_name: subcutaneous adipose tissue

extract_protocol:
For the snm3C data, the frozen tissue biopsies were Dounce homogenized in 2.4 mL of ice-cold NIMT buffer containing 250 mM Sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-Cl pH 8.0, 1% Triton X-100, 1 mM DTT and 1:100 diluted proteinase inhibitor, using 40 strokes each with the loose and tight pestles. The lysed solution was transferred to a 5 mL tube on ice and mixed with 1.5 mL of 50% Iodixanol (prepared as 5 parts OptiPrep and 1 part Diluent Buffer), and 1 mL of the resulting suspension was carefully layered over 500 μL of 25% iodixanol (prepared as 1:1 of 50% iodixanol and NIM) in four 2 mL tubes. Samples were centrifuged in swing rotor for 20 min at 10,000 x g at 4°C and prepared for library construction.
The snm3C-seq3 library preparation was performed using the snm3C-seq3 workflow.

value: subcutaneous adipose tissue

value: female

tag: ethnicity

value: Finnish


title: Substantia nigra, monomer, normoxia, rep12

description: Library name: m193

value: monomer


title: SAT4 (snm3C)

description: Library name: SAT4

tag: Sex


title: PolII CUT&RUN on SALE-RIT1 M90I cells (positive control).

description: Library name: E1_SALE_R_PolII_1

value: immortalized small airway lung epithelial cells

value: PolII:CST 13523


title: SAT3 (snm3C)

description: Library name: SAT3


title: Substantia nigra, monomer, normoxia, rep11

description: Library name: m192


title: SAT2 (snm3C)

description: Library name: SAT2


title: 2nd replicate of IgG CUT&RUN on SALE-RIT1 M90I cells (negative control).

description: Library name: D12_SALE_R_IgG_2

value: IgG:CST 3900


title: SAT1 (snm3C)

description: Library name: SAT1


title: 6CLL4963D

description: Library name: 6CLL4963D


title: SAT8

description:
Library name: SAT8
Chromium Single Cell 3’ v3.1

data_processing:
The sequencing reads of snRNA-seq were aligned to the GRCh38 human genome reference with Gencode v42 gene annotations using STARSolo in STAR v2.7.10b, using the ‘--soloFeatures GeneFull’ parameter to account for full pre-mRNA transcripts. Empty droplets and nuclei with high levels of ambient RNA were removed with DIEM v2.4.0. Read decontamination and doublet removal were performed with DecontX and DoubletFinder. Seurat v4.3.0 was used to cluster the data and perform reciprocal principal components analysis based integration.
Assembly: hg38
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names)

molecule: nuclear RNA

extract_protocol:
For samples profiled using snRNA-seq, frozen tissue biopsies were minced over dry ice and incubated for 10 minutes in ice-cold lysis buffer containing 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl₂. The resulting lysate was filtered through a 30 μm MACS SmartStrainer (Miltenyi Biotec, #130-110-915) and centrifuged at 500 × g for 5 minutes at 4 °C. The nuclei pellet was washed in 1 mL of wash buffer composed of 1X PBS, 1.0% BSA, and 0.2 U/μL RNase inhibitor (Sigma, #3335402001). Nuclei were subsequently filtered again through a 40 μm Flowmi cell strainer (Sigma-Aldrich, #BAH136800040), centrifuged at 500 × g for 5 minutes at 4 °C, and finally resuspended in wash buffer.  For the samples processed using the 10x multiome library, we combined 300 mg of the frozen biopsies into a gentleMACS C tube (Miltenyi Biotec) containing 3 mL of chilled 0.1X lysis, including 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL CA-630, 0.01% Digitonin, 1% BSA, 1 mM DTT, and 1 U/μL RNase inhibitor. We next dissociated the tissues by placing the gentleMACS C tube on the gentleMACS Dissociator (Miltenyi Biotec) and running the ‘4C_nuclei_1’ program. The tissues were incubated in the lysis buffer for a total of 15 minutes including the time on the dissociator. After the incubation period, we added 3 mL of chilled wash buffer, containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, and 1 U/μL RNase inhibitor, to the lysate and filtered the lysate mixture through a 70 μm MACS strainer, followed by a 30 μm MACS strainer. Next, the nuclei were centrifuged at 300 × g for 5 minutes at 4°C, and the supernatant was removed without disrupting the nuclei pellets. We then resuspended the nuclei pellet in 3 mL of chilled wash buffer and passed it through a 30 μm MACS strainer.
The snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 and the Single Cell Multiome ATAC + Gene Expression Reagent kits.


title: SAT7

description:
Library name: SAT7
Chromium Single Cell 3’ v3.1


title: 2nd replicate of ZEB1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D11_SALE_R_ZEB1_2

value: ZEB1:Abcam ab155249


title: Substantia nigra, monomer, normoxia, rep9

description: Library name: m190

value: substantia nigra


title: SAT6

description:
Library name: SAT6
Chromium Single Cell 3’ v3.1


title: 2nd replicate of H3K27ac CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D10_SALE_R_H3K27ac_2


title: Substantia nigra, monomer, normoxia, rep8

description: Library name: m189

value: normoxia


title: SAT5

description:
Library name: SAT5
Single Cell Multiome ATAC + Gene Expression


title: 2nd replicate of H3K27me3 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D9_SALE_R_H3K27me3_2


title: SAT3, biological rep 2

description:
Library name: SAT3, rep 2
Single Cell Multiome ATAC + Gene Expression


title: SAT3, biological rep 1

description:
Library name: SAT3, rep 1
Chromium Single Cell 3’ v3.1


title: Substantia nigra, monomer, normoxia, rep6

description: Library name: m187


title: 2nd replicate of H3K4me3 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D8_SALE_R_H3K4me3_2


title: Substantia nigra, monomer, normoxia, rep7

description: Library name: m188


title: SAT4

description:
Library name: SAT4
Single Cell Multiome ATAC + Gene Expression


title: cfDNA-COVID-19-Z0000040K

description: Library name: cfDNA-COVID-19-Z0000040K

value: Cell-free DNA from plasma

tag: disease


title: SAT1, biological rep 2

description:
Library name: SAT1, rep 2
Single Cell Multiome ATAC + Gene Expression


title: 2nd replicate of H3K4me1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D7_SALE_R_H3K4me1_2


title: SAT2, biological rep 1

description:
Library name: SAT2, rep 1
Chromium Single Cell 3’ v3.1


title: SAT2, biological rep 2

description:
Library name: SAT2, rep 2
Single Cell Multiome ATAC + Gene Expression


title: 2nd replicate of FOSL1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D6_SALE_R_FOSL1_2

value: FOSL1:Abcam ab252421


title: Substantia nigra, monomer, normoxia, rep5

description: Library name: m186


title: Substantia nigra, PFF, hypoxia, rep8

description: Library name: m185

value: PFF

value: hypoxia


title: SAT1, biological rep 1

description:
Library name: SAT1, rep 1
Chromium Single Cell 3’ v3.1


title: 2nd replicate of cJUN CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D5_SALE_R_cJUN_2

value: cJUN:CST 9165


title: Substantia nigra, PFF, hypoxia, rep7

description: Library name: m184


title: Substantia nigra, monomer, normoxia, rep10

description: Library name: m191


title: RNA-seq of THP-1 macrophages:F. novicida infected-b

city: COLLEGE STATION

first: Doyoung

last: Kwak

state: Texas

address: 302 Ball Street

institute: Texas A&M

description:
Library name: THP-F.novicida-b
RNA isolated from THP-1 macrophages cells infected with Francisella novicida U112 and collected at 1hour post infection (replicate 2)

data_processing:
Raw sequencing reads in FASTQ format were processed to remove adapter sequences, poly-N reads, and low-quality reads, generating high-quality clean reads. Clean reads from each sample were aligned to the Homo sapiens reference genome (GRCh38.p12) using STAR (v2.5.4b), along with the annotation reference gencode.v30.chr_patch_hapl_scaff.annotation.gff3. Alignment efficiency ranged from 73–87%, yielding 35.9–83.4 million uniquely mapped reads per sample. Uniquely mapped reads were used for gene-level quantification, ensuring that each read was assigned to a single, non-overlapping gene based on its genomic coordinates. Paired-end reads were checked for overlaps to improve mapping accuracy.
Assembly: Reads were aligned to the human reference genome sequence GRCh38.p12 along with the GENCODE annotation file gencode.v30.chr_patch_hapl_scaff.annotation.gff3.
Supplementary files format and content: Processed RNA-seq data files contain raw gene-level counts and are provided in comma-separated values (CSV) format. Each row corresponds to a gene, identified using Ensembl Gene IDs and annotated according to GENCODE v30.

extract_protocol:
Total RNA was extracted using TRIzol™ reagent (Invitrogen) following manufacturer protocols. RNA integrity (RIN) and concentration were assessed using the Agilent 4200 TapeStation system, and only RNA samples with RIN >8 were used for library preparation.
RNA-seq libraries were generated using the TruSeq Stranded Total RNA-Seq Library Kit (Illumina), incorporating rRNA depletion. cDNA synthesis was performed using random primers, and paired-end libraries were constructed following the manufacturer’s instructions.Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq6000 platform.

treatment_protocol: THP-1 monocytes were differentiated into macrophages using Phorbol 12-myristate 13-acetate (PMA, 100 ng/mL, 48 h) before infection with various bacterial strains. Infections were carried for 1 hour, after which cells were collected for RNA extraction. Bacterial Strains used,Pathogenic strains: Coxiella burnetii Nine Mile Phase II (NMII), Coxiella burnetii NMII dotA::Tn (T4SS mutant), Coxiella burnetii NMII dotB::Tn (T4SS mutant), Enterohemorrhagic Escherichia coli (O157, O157 Δstx), Francisella novicida U112, Pseudomonas aeruginosa PAO1, Staphylococcus aureus JE2, Salmonella enterica subsp. Typhimurium SL1344, Rhizobium radiobacter, Micrococcus luteus, Enterococcus faecalis, Brucella melitensis ΔvjbR. Non-pathogenic controls: Escherichia coli DH5α, Listeria innocua, Bacillus subtilis P31K6.

value: Monocytes

value: PMA differentiation, followed by infection-1h


title: RNA-seq of THP-1 macrophages:F. novicida infected-a

description:
Library name: THP-F.novicida-a
RNA isolated from THP-1 macrophages cells infected with Francisella novicida U112 and collected at 1hour post infection(replicate 1)


title: RNA-seq of THP-1 macrophages:F. novicida infected-d

description:
Library name: THP-F.novicida-d
RNA isolated from THP-1 macrophages cells infected with Francisella novicida U112 and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:F. novicida infected-c

description:
Library name: THP-F.novicida-c
RNA isolated from THP-1 macrophages cells infected with Francisella novicida U112 and collected at 1hour post infection (replicate 3


title: RNA-seq of THP-1 macrophages:Uninfected-16

description:
Library name: THP-Mock-16
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:P.aeruginosa infected-d

description:
Library name: THP-P.aeruginosa-d
RNA isolated from THP-1 macrophages cells infected with Pseudomonas aeruginosa PAO1 and collected at 1hour post infection (replicate 4)


title: Substantia nigra, PFF, hypoxia, rep5

description: Library name: m182


title: 2nd replicate of TAZ CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D3_SALE_R_TAZ_2

value: SALE

value: TAZ:CST 4883


title: RNA-seq of THP-1 macrophages:P.aeruginosa infected-c

description:
Library name: THP-P.aeruginosa-c
RNA isolated from THP-1 macrophages cells infected with Pseudomonas aeruginosa PAO1 and collected at 1hour post infection (replicate 3


title: 2nd replicate of YAP1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D2_SALE_R_YAP1_2

value: YAP1:Abcam ab52771


title: RNA-seq of THP-1 macrophages:P.aeruginosa infected-b

description:
Library name: THP-P.aeruginosa-b
RNA isolated from THP-1 macrophages cells infected with Pseudomonas aeruginosa PAO1 and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages:Uninfected-15

description:
Library name: THP-Mock-15
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:P.aeruginosa infected-a

description:
Library name: THP-P.aeruginosa-a
RNA isolated from THP-1 macrophages cells infected with Pseudomonas aeruginosa PAO1 and collected at 1hour post infection(replicate 1)


title: Substantia nigra, PFF, normoxia, rep8

description: Library name: m181


title: 2nd replicate of PolII CUT&RUN on parental SALE cells (positive control).

description: Library name: D1_SALE_par_PolII_2


title: RNA-seq of THP-1 macrophages:C.burnetiidotA infected-c

description:
Library name: THP-CoxielladotA-c
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II dotA::Tn and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:C.burnetiidotA infected-b

description:
Library name: THP-CoxielladotA-b
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II dotA::Tn and collected at 1hour post infection(replicate 2)


title: RNA-seq of THP-1 macrophages:C.burnetiidotA infected-a

description:
Library name: THP-CoxielladotA-a
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II dotA::Tn and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:S. Typhimurium SL1344 infected-d

description:
Library name: THP-S.Typhimurium-d
RNA isolated from THP-1 macrophages cells infected with Salmonella enterica subsp. Typhimurium SL1344 and collected at 1hour post infection (replicate 4)


title: Substantia nigra, PFF, normoxia, rep6

description: Library name: m179


title: 1st replicate of IgG CUT&RUN on SALE-RIT1 M90I cells (negative control).

description: Library name: C12_SALE_R_IgG_1


title: Substantia nigra, PFF, normoxia, rep5

description: Library name: m178


title: 1st replicate of ZEB1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C11_SALE_R_ZEB1_1


title: RNA-seq of THP-1 macrophages:S. Typhimurium SL1344 infected-c

description:
Library name: THP-S.Typhimurium-c
RNA isolated from THP-1 macrophages cells infected with Salmonella enterica subsp. Typhimurium SL1344 and collected at 1hour post infection (replicate 3)


title: 2nd replicate of panTEAD CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: D4_SALE_R_panTEAD_2

value: panTEAD:CST 13295


title: RNA-seq of THP-1 macrophages:C.burnetiidotA infected-d

description:
Library name: THP-CoxielladotA-d
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II dotA::Tn and collected at 1hour post infection (replicate 4)


title: Substantia nigra, PFF, hypoxia, rep6

description: Library name: m183


title: Substantia nigra, monomer, normoxia, rep4

description: Library name: m177

value: monomer


title: 1st replicate of H3K27me3 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C9_SALE_R_H3K27me3_1

value: immortalized small airway lung epithelial cells


title: 1st replicate of H3K27ac CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C10_SALE_R_H3K27ac_1


title: RNA-seq of THP-1 macrophages:Uninfected-13

description:
Library name: THP-Mock-13
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:Enterohemorrhagic E.coli stx infected-d

description:
Library name: THP-EHEC-NT-d
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 Δstx (nontoxicogenic) and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:S. Typhimurium SL1344 infected-a

description:
Library name: THP-S.Typhimurium-a
RNA isolated from THP-1 macrophages cells infected with Salmonella enterica subsp. Typhimurium SL1344 and collected at 1hour post infection(replicate 1)


title: 1st replicate of H3K4me3 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C8_SALE_R_H3K4me3_1


title: RNA-seq of THP-1 macrophages:Enterohemorrhagic E.coli stx infected-c

description:
Library name: THP-EHEC-NT-c
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 Δstx (nontoxicogenic) and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:Enterohemorrhagic E.coli stx infected-b

description:
Library name: THP-EHEC-NT-b
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 Δstx (nontoxicogenic) and collected at 1hour post infection(replicate 2)


title: Substantia nigra, PFF, normoxia, rep7

description: Library name: m180


title: RNA-seq of THP-1 macrophages:Enterohemorrhagic E.coli stx infected-a

description:
Library name: THP-EHEC-NT-a
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 Δstx (nontoxicogenic) and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:Uninfected-12

description:
Library name: THP-Mock-12
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: 1st replicate of FOSL1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C6_SALE_R_FOSL1_1


title: Substantia nigra, monomer, normoxia, rep2

description: Library name: m174


title: 1st replicate of H3K4me1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C7_SALE_R_H3K4me1_1


title: RNA-seq of THP-1 macrophages:S.aureus-c

description:
Library name: THP-S.aureus-c
RNA isolated from THP-1 macrophages cells infected with Staphylococcus aureus and collected at 1hour post infection (replicate 3)


title: Substantia nigra, monomer, hypoxia, rep4

description: Library name: m172


title: 1st replicate of cJUN CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C5_SALE_R_cJUN_1


title: RNA-seq of THP-1 macrophages:S.aureus-a

description:
Library name: THP-S.aureus-a
RNA isolated from THP-1 macrophages cells infected with Staphylococcus aureus and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:S.aureus-b

description:
Library name: THP-S.aureus-b
RNA isolated from THP-1 macrophages cells infected with Staphylococcus aureus and collected at 1hour post infection (replicate 2)


title: Substantia nigra, monomer, hypoxia, rep3

description: Library name: m171


title: 1st replicate of panTEAD CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C4_SALE_R_panTEAD_1_


title: Substantia nigra, monomer, normoxia, rep1

description: Library name: m173


title: Substantia nigra, monomer, hypoxia, rep2

description: Library name: m170


title: RNA-seq of THP-1 macrophages:Uninfected-11

description:
Library name: THP-Mock-11
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: Substantia nigra, monomer, normoxia, rep3

description: Library name: m175


title: RNA-seq of THP-1 macrophages:C.burnetii NMII infected-c

description:
Library name: THP-NMII-c
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:C.burnetii NMII infected-d

description:
Library name: THP-NMII-d
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II and collected at 1hour post infection (replicate 4)


title: 1st replicate of YAP1 CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C2_SALE_R_YAP1_1


title: 1st replicate of TAZ CUT&RUN on SALE-RIT1 M90I cells.

description: Library name: C3_SALE_R_TAZ_1


title: Substantia nigra, monomer, hypoxia, rep1

description: Library name: m167


title: Substantia nigra, PFF, hypoxia, rep4

description: Library name: m166


title: RNA-seq of THP-1 macrophages:C.burnetii NMII infected-a

description:
Library name: THP-NMII-a
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:C.burnetii NMII infected-b

description:
Library name: THP-NMII-b
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii Nine Mile Phase II and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages:Uninfected-10

description:
Library name: THP-Mock-10
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:S.aureus-d

description:
Library name: THP-S.aureus-d
RNA isolated from THP-1 macrophages cells infected with Staphylococcus aureus and collected at 1hour post infection (replicate 4)


title: Substantia nigra, PFF, hypoxia, rep2

description: Library name: m164


title: RNA-seq of THP-1 macrophages:B.subtilis infected-a

description:
Library name: THP-B.subtilis-a
RNA isolated from THP-1 macrophages cells infected with Bacillus subtilis and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:Uninfected-9

description:
Library name: THP-Mock-9
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:B.subtilis infected-d

description:
Library name: THP-B.subtilis-d
RNA isolated from THP-1 macrophages cells infected with Bacillus subtilis and collected at 1hour post infection (replicate4)


title: 1st replicate of PolII CUT&RUN on parental SALE cells (positive control).

description: Library name: C1_SALE_par_PolII_1

value: parental

value: PolII:CST 13523


title: Substantia nigra, PFF, hypoxia, rep3

description: Library name: m165

value: substantia nigra


title: 2nd replicate of IgG CUT&RUN on parental SALE cells (negative control).

description: Library name: B12_SALE_par_IgG_2

value: IgG:CST 3900


title: RNA-seq of THP-1 macrophages:B.subtilis infected-b

description:
Library name: THP-B.subtilis-b
RNA isolated from THP-1 macrophages cells infected with Bacillus subtilis and collected at 1hour post infection (replicate 2)


title: 2nd replicate of H3K27me3 CUT&RUN on parental SALE cells.

description: Library name: B9_SALE_par_H3K27me3


title: RNA-seq of THP-1 macrophages: Enterohemorrhagic E.coli O157:H7 infected-d

description:
Library name: THP-EHEC-d
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 and collected at 1hour post infection (replicate 4)


title: Substantia nigra, PFF, hypoxia, rep1

description: Library name: m163


title: RNA-seq of THP-1 macrophages: Enterohemorrhagic E. coli O157:H7 infected-b

description:
Library name: THP-EHEC-b
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages: Enterohemorrhagic E.coli O157:H7 infected-c

description:
Library name: THP-EHEC-c
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 and collected at 1hour post infection (replicate 3)


title: Substantia nigra, PFF, normoxia, rep4

description: Library name: m162

value: normoxia


title: Substantia nigra, PFF, normoxia, rep3

description: Library name: m161


title: RNA-seq of THP-1 macrophages:Uninfected-8

description:
Library name: THP-Mock-8
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:L.innocua infected-d

description:
Library name: THP-L.inoccua-d
RNA isolated from THP-1 macrophages cells infected with Listeria innocua and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:L.innocua infected-c

description:
Library name: THP-L.inoccua-c
RNA isolated from THP-1 macrophages cells infected with Listeria innocua  and collected at 1hour post infection (replicate 3)


title: 2nd replicate of H3K4me3 CUT&RUN on parental SALE cells.

description: Library name: B8_SALE_par_H3K4me3_2


title: 2nd replicate of H3K4me1 CUT&RUN on parental SALE cells.

description: Library name: B7_SALE_par_H3K4me1


title: Substantia nigra, PFF, normoxia, rep2

description: Library name: m160


title: Substantia nigra, PFF, normoxia, rep1

description: Library name: m159


title: RNA-seq of THP-1 macrophages:L.innocua infected-b

description:
Library name: THP-L.inoccua-b
RNA isolated from THP-1 macrophages cells infected with Listeria innocua and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages:L.innocua infected-a

description:
Library name: THP-L.inoccua-a
RNA isolated from THP-1 macrophages cells infected with Listeria innocua and collected at 1hour post infection (replicate 1)


title: 2nd replicate of ZEB1 CUT&RUN on parental SALE cells.

description: Library name: B11_SALE_par_ZEB1_2

value: ZEB1:Abcam ab155249


title: 2nd replicate of FOSL1 CUT&RUN on parental SALE cells.

description: Library name: B6_SALE_par_FOSL1_2

value: FOSL1:Abcam ab252421


title: 2nd replicate of H3K27ac CUT&RUN on parental SALE cells.

description: Library name: B10_SALE_par_H3K27ac_2


title: RNA-seq of THP-1 macrophages:B.melitensisvjbR infected-d

description:
Library name: THP-BrucellavjbR-d
RNA isolated from THP-1 macrophages cells infected with Brucella melitensis ΔvjbR and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:B.melitensisvjbR infected-c

description:
Library name: THP-BrucellavjbR-c
RNA isolated from THP-1 macrophages cells infected with Brucella melitensis ΔvjbR and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:Uninfected-7

description:
Library name: THP-Mock-7
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:B.melitensisvjbR infected-b

description:
Library name: THP-BrucellasvjbR-b
RNA isolated from THP-1 macrophages cells infected with Brucella melitensis ΔvjbR and collected at 1hour post infection (replicate 2)


title: NETseq_ResuspendedSameYPD

data_processing:
Library strategy: NET-seq
NET-seq: Sequencing reads were aligned, processed and subtracted of background signal (signal that is not specific to immunoprecipitation of Pol2 via its tagged Rpb3 subunit) as described in Fischl et al., 2017;
RNA-seq: Sequencing reads were aligned to the sacCer3 genome build using the Ion Torrent Server TMAP aligner with default alignment settings (-tmap mapall stage1 map4). Non-uniquely mapped reads were removed using Samtools (samtools view -bq 1). Bigwig files were generated by normalizing to reads per million (RPM)
MNASE-seq: Sequencing reads were aligned to the sacCer3 genome build using the Ion Torrent Server TMAP aligner with default alignment settings (-tmap mapall stage1 map4). Bam files were further processed using DANPOS2 (Chen et al., 2015) (dpos -a 1) to give genome-wide maps of the centre point of each nucleosome.
Genome_build: sacCer3
Supplementary_files_format_and_content: RNA-seq: Fastq raw sequencing data, bed file of uniquely aligned reads, bigwigs of RPM normalized read pile up; MNASE-seq: bam file of tmap aligned reads, DANPOS processed bigwigs of bam file data, DANPOS processed bigwigs showing the centre point of each nucleosome; NET-seq data bam file of bowtie aligned reads – raw reads have been clipped of adapter sequences, bigwigs of reads narrowed to their 3’ nucleotide before no tag signal subtration, bigwigs of reads narrowed to their 3’ nucleotide after no tag signal subtraction.

tag: growth condition

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then spun and resuspended in the same YPD in which it had been growing

tag: molecule

value: Nascent RNA


title: 2nd replicate of panTEAD CUT&RUN on parental SALE cells.

description: Library name: B4_SALE_par_panTEAD_2


title: RNA-seq of THP-1 macrophages: Enterohemorrhagic E.coli O157:H7 infected-a

description:
Library name: THP-EHEC-a
RNA isolated from THP-1 macrophages cells infected with Enterohemorrhagic Escherichia coli O157:H7 and collected at 1hour post infection (replicate 1)

value: Monocytes


title: NETseq_ResuspendedFreshYPD

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then spun and resuspended in fresh prewarmed YPD


title: NETseq_GAL180

value: Exponential growth in glucose (YPD) to OD600 = 0.65 then switched to galactose (YPG) for 180 minutes


title: RNA-seq of THP-1 macrophages:B.subtilis infected-c

description:
Library name: THP-B.subtilis-c
RNA isolated from THP-1 macrophages cells infected with Bacillus subtilis and collected at 1hour post infection (replicate 3)

value: PMA differentiation, followed by infection-1h


title: 2nd replicate of TAZ CUT&RUN on parental SALE cells.

description: Library name: B3_SALE_par_TAZ_2

value: SALE

value: TAZ:CST 4883


title: RNA-seq of THP-1 macrophages:E.faecalis infected-c

description:
Library name: THP-E.faecalis-c
RNA isolated from THP-1 macrophages cells infected with Enterococcus faecalis and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:E.faecalis infected-d

description:
Library name: THP-E.faecalis-d
RNA isolated from THP-1 macrophages cells infected with Enterococcus faecalis and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:B.melitensisvjbR infected-a

description:
Library name: THP-BrucellavjbR-a
RNA isolated from THP-1 macrophages cells infected with Brucella melitensis ΔvjbR and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:Uninfected-6

description:
Library name: THP-Mock-6
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: RNA-seq of THP-1 macrophages:E.faecalis infected-b

description:
Library name: THP-E.faecalis-b
RNA isolated from THP-1 macrophages cells infected with Enterococcus faecalis and collected at 1hour post infection (replicate 2)


title: MCF-7 cell,LINC00365 overexpression 3

city: changchun

first: long

last: xu

address: xinmin road

institute: jilin university

data_processing:
In this project, the mRNA with polyA structure in the total RNA was enriched by Oligo(dT) magnetic beads, and the RNA was broken down to 200-300bp fragments by ion interruption. The 200-300bp fragment length was chosen because the splice length is fixed and a shorter interrupted fragment length would result in a higher proportion of splice sequences, thus reducing the proportion of valid data; a longer interrupted fragment length would not be conducive to cluster generation during up-sequencing. The first strand of cDNA was synthesised using RNA as the template and a 6-base random primer and reverse transcriptase, and the first strand cDNA was used as the template for the second strand cDNA synthesis.    Translated with www.DeepL.com/Translator (free version)
After library construction, PCR amplification was used to enrich the library fragments, followed by library selection based on fragment size, which ranged from 300-400 bp. The libraries were then quality checked by an Agilent 2100 Bioanalyzer, and the total library concentration and the effective library concentration were tested. Libraries containing different Index sequences (each sample with a different Index, and finally the downstream data of each sample according to the Index) were mixed proportionally according to the effective concentration of the library and the amount of data required for the library. The mixed libraries are uniformly diluted to 2nM and denatured by alkali to form single-stranded libraries.    Translated with www.DeepL.com/Translator (free version)
After RNA extraction, purification and library construction, these libraries were sequenced using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform with Paired-end (PE) sequencing.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast cancer

extract_protocol:
RNA was harvested using RNeasy Mini Kits (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the ScriptSeq Complete Kit (Epicentre) following manufacturer's protocols.

value: breast cancer

value: MCF-7 cell

value: HER4-negative breast cancer cells

value: LINC00365 over expression

value: Inhibition of cell survival


title: MCF-7 cell,LINC00365 overexpression 2


title: RNA-seq of THP-1 macrophages:E.faecalis infected-a

description:
Library name: THP-E.faecalis-a
RNA isolated from THP-1 macrophages cells infected with Enterococcus faecalis and collected at 1hour post infection (replicate 1)


title: 2nd replicate of YAP1 CUT&RUN on parental SALE cells.

description: Library name: B2_SALE_par_YAP1_2

value: immortalized small airway lung epithelial cells

value: parental

value: YAP1:Abcam ab52771


title: MCF-7 cell,LINC00365 overexpression 1

value: HER6-negative breast cancer cells


title: RNA-seq of THP-1 macrophages:Uninfected-5

description:
Library name: THP-Mock-5
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: 1st replicate of IgG CUT&RUN on parental SALE cells (negative control).

description: Library name: A12_SALE_par_IgG_1

value: IgG:CST 3900


title: RNA-seq of THP-1 macrophages:C.burnetiidotB infected-d

description:
Library name: THP-CoxielladotB-d
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii dotB:: Tn and collected at 1hour post infection (replicate 4)


title: 1st replicate of ZEB1 CUT&RUN on parental SALE cells.

description: Library name: A11_SALE_par_ZEB1_1

value: ZEB1:Abcam ab155249


title: 2nd replicate of cJUN CUT&RUN on parental SALE cells.

description: Library name: B5_SALE_par_cJUN_2

value: cJUN:CST 9165


title: MCF-7 cell,nc 3

value: HER3-negative breast cancer cells

value: nc

value: Normal cells


title: RNA-seq of THP-1 macrophages:C.burnetiidotB infected-b

description:
Library name: THP-CoxielladotB-b
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii dotB:: Tn and collected at 1hour post infection (replicate 2)

value: Monocytes

value: PMA differentiation, followed by infection-1h


title: 1st replicate of H3K27ac CUT&RUN on parental SALE cells.

description: Library name: A10_SALE_par_H3K27ac_1

value: SALE


title: RNA-seq of THP-1 macrophages:Uninfected-4

description:
Library name: THP-Mock-4
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: 1st replicate of H3K27me3 CUT&RUN on parental SALE cells.

description: Library name: A9_SALE_par_H3K27me3


title: RNA-seq of THP-1 macrophages:M.luteus infected-d

description:
Library name: THP-M.luetus-d
RNA isolated from THP-1 macrophages cells infected with Micrococcus luteus and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:C.burnetiidotB infected-a

description:
Library name: THP-CoxielladotB-a
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii dotB:: Tn and collected at 1hour post infection (replicate 1)


title: RNA-seq of THP-1 macrophages:M.luteus infected-c

description:
Library name: THP-M.luetus-c
RNA isolated from THP-1 macrophages cells infected with Micrococcus luteus and collected at 1hour post infection (replicate 3)