title: Cav1-null_day17_sample3

city: Columbia

first: SUSANTA

last: BEHURA

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt. The fastp tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides). The quality reads were then mapped to the mouse reference genome GRCm39 using STAR. The read count data was then analyzed by edgeR to determine significance of differential expression.
The multi-sample 2-pass mapping approach of STAR was applied  to analyze splice variants in fetal brain of the three strains at each developmental time points.
The alternative splice variants were detected based on the presence or absence of mapped reads to the junction sites in the fetal brain. We defined a developmental time specific splice variant as a transcript which showed evidence of 10 or more reads mapped to the transcript junction in a specific strain at a specific developmental time point (i.e. zero read mapped to the same junction in the other strains and time points).
The genes associated with the detected splice junctions in the individual samples were identified by intersecting the detected junction sites with the exon coordinates of mouse genes by using BEDTools.
Assembly: GRCm39
Supplementary files format and content: CSV file (number of reads mapped to each gene in each sample)
Supplementary files format and content: CSV file (number of reads mapped to each splice junction in each sample). We defined a splice variant as an alternative form of a messenger RNA where 10 or more number of sequence reads mapped to ends (i.e. the acceptor and donor positions) of the splice junction.

source_name: Fetal brain

growth_protocol: The inbred mice strains C57BL/6J (Strain # 000664), AKR/J (Strain # 00064) and B6.Cg-Cav1tm1Mls/J (aka Cav1-null, Strain # 007083) used in this study were obtained from the Jackson Laboratory (Bar Harbor, ME USA). Approximately 8-weeks old mice of these strains were used to establish timed pregnancy separately. The vaginal plug was observed to keep a record of the start of pregnancy (day 1). On days (d) 12, 15 and 17, the pregnant mice were euthanized, and the fetuses were collected, washed in sterile PBS and snap frozen in liquid nitrogen. The whole brain was dissected from each fetus. Fetal sex was determined by polymerase chain reaction assay as described earlier.

extract_protocol:
Total RNA were isolated from the dissected fetal brain samples using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction. A total of 27 samples were used which included 3 strains x 3 time points x 3 replicates.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Fetal brain

tag: fetal sex

value: Female


title: Corn_oil (control) S01

status: Public on Jun 05 2024

type: SRA

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

description: Control - 8124

library_source: transcriptomic single cell

data_processing:
To generate gene-expression matrices, fastq files were processed and mapped to the GRCm39.109 reference genome, using the Parse Biosciences SplitPipe v1.0.4 with default parameters (Parse Biosciences, Seattle, WA).
The downstream analysis was performed using the R 4.2.2 and Seurat v4.3.0 R package
Low-quality cells with less than 200 genes detected and all genes expressed in less than 3 cells were removed, leaving 31,089 cells and 37,725 genes for further analysis. Data was normalized using Seurat’s NormalizeData function with LogNormalize as a method and a scale factor equal to 10,000.
Principal Component Analysis was performed on a submatrix of the top 2,000 most-variable genes, using the function FindVariableGenes from the Seurat package. The number of top Principal Components (PC) was evaluated by the elbow method keeping 20 PCs for clustering and data visualization. The batch effect between samples was removed using the package Harmony v0.1.1. The cells were clustered using a shared nearest-neighbor modularity optimization-based clustering algorithm (FindClusters in the Seurat package).
To visualize cells in two dimensions the Uniform Manifold Approximation and Projection was applied. The cluster-specific genes were computed using FindAllMarkers from the Seurat package, using the MAST test with the number of Unique Molecular Identifiers detected as a latent variable. The same test was used to compute differentially expressed genes between genotypes or treatment groups within cell clusters. Cell clusters were annotated by assessing known cell-type-specific markers. All plots were created using ggplot2 v3.4.1. Labels in the volcano plots were created using ggrepel v0.9.3.
Assembly: GRCm39
Supplementary files format and content: ExpressionMatrix.mtx.gz - a sparse matrix with read counts
Supplementary files format and content: CellIDs.txt.gz - a comma-separated archive of barcodes (columns of the expression matrix)
Supplementary files format and content: Genes.txt.gz - a tab-delimited archive of genes (rows of the expression matrix)
Supplementary files format and content: MetaData.txt.gz - a tab-delimited archive containing an additional description of the samples (columns of the expression matrix)

molecule: polyA RNA

organism: Mus musculus

source_name: retina

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle, fed ad libitum, and maintained using standard procedures.

extract_protocol:
Animals were sacrificed and eyes were enucleated. Under a microscope, the anterior chamber, consisting of the cornea, lens, and iris was removed. The retina then carefully peeled from the posterior eye cup. The retina was then disassociated into single cells with the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions. 2mL of papain solution was used per animal.
8 sublibraries were generated and sequenced independently on Illumina NovaSeq6000 at an average sequencing depth of 50,000 reads/cell, for a projected total of 5 billion reads for the entirety of the 100,000 cell barcoded library. Reads from identical cells from each of the 8 sublibraries were consolidated during analysis and processing of raw reads.

treatment_protocol: Animals were treated at post-natal day 28 (P28) for five consective days via intraperitoneal injection - control animals were administered corn oil vehicle, while dKO animals were treated with 75mg/kg of tamoxifen dissolved in corn oil. Tamoxifen was stored at 4 deg C in the dark.

tag: tissue

value: retina

tag: genotype

tag: time

value: 6 months

tag: treatment

value: Corn oil, P28


title: ACBI1 treated cells, 60min LipidA [Exp4_60min_ACBI1_rep2]

city: La Jolla

first: Jingwen

last: Liao

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute

library_source: transcriptomic

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using analyzeRepeats.pl within HOMER with -strand both -count exons -condenseGenes –noadj and then by getDiffExpression.pl within HOMER
Assembly: GRCm38 (mm10)
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-20) dataValue.
Supplementary files format and content: Exp2_ARID1AKO_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-18) dataValue.
Supplementary files format and content: Exp3_PBRM1KO_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-14) dataValue.
Supplementary files format and content: Exp4_early_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-26) dataValue.
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-20) normalized Log2 read count for experiment (21-23) Log2 fold change, p-value, adjusted p-value 1hr_Ctrl vs 0hr_Ctrl (24-26) Log2 fold change, p-value, adjusted p-value of 4hr_Ctrl vs 0hr_Ctrl (27-29) Log2 fold change, p-value, adjusted p-value of 4hr_ACBI1 vs 4hr_Ctrl (30-32) Log2 fold change, p-value, adjusted p-value of 4hr_BRM014 vs 4hr_Ctrl (33-35) Log2 fold change, p-value, adjusted p-value of 4hr_BRDK98 vs 4hr_Ctrl
Supplementary files format and content: Exp2_ARID1AKO_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-18) normalized Log2 read count for experiment (19-21) Log2 fold change, p-value, adjusted p-value 1hr_Ctrl vs 0hr_Ctrl (22-24) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (25-27) Log2 fold change, p-value, adjusted p-value of 1hr_ARID1AKO vs 1hr_Ctrl (28-30) Log2 fold change, p-value, adjusted p-value of 4hr_ARID1AKO vs 4hr_Ctrl
Supplementary files format and content: Exp3_PBRM1KO_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) normalized Log2 read count for experiment (15-17) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (18-20) Log2 fold change, p-value, adjusted p-value of 4hr_PBRM1KO vs 4hr_Ctrl
Supplementary files format and content: Exp4_early_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-26) normalized Log2 read count for experiment (27-29) Log2 fold change, p-value, adjusted p-value 20min_Ctrl vs 0min_Ctrl  (30-32) Log2 fold change, p-value, adjusted p-value 60min_Ctrl vs 0min_Ctrl  (33-35)  Log2 fold change, p-value, adjusted p-value of 20min_ACBI1 vs 20min_Ctrl  (36-38) Log2 fold change, p-value, adjusted p-value of 20min_BRM014 vs 20min_Ctrl  (39-41) Log2 fold change, p-value, adjusted p-value of 20min_BRDK98 vs 20min_Ctrl  (42-44) Log2 fold change, p-value, adjusted p-value of 60min_ACBI1 vs 60min_Ctrl (45-47) Log2 fold change, p-value, adjusted p-value of 60min_BRM014 vs 60min_Ctrl (48-50) Log2 fold change, p-value, adjusted p-value of 60min_BRDK98 vs 60min_Ctrl

source_name: BMDM

extract_protocol:
RNA was harvested using Zymo Research Quick-RNA miniprep kit and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded messenger ribonucleic acid (mRNA) kit following manufacturer's protocols.
RNA-seq 50bp single-end sequencing

tag: cell type

value: BMDM

value: ACBI1 treated

tag: stimulation

value: 60min LipidA

tag: molecule type

value: strand specific polyA+ RNA


title: Cav1-null_day17_sample2

state: MO

molecule: total RNA

tag: strain


title: KF-6h-1

city: Changsha

first: Jingheng

last: Zhang

address: 87 Xiangya Rd

country: China

institute: Xiangya Hospital, Central South Uniiversity

data_processing:
For RNA-seq data analysis, raw fastq files were processed with trim_galore (version 0.6.7).
Filtered reads were mapped with STAR (version 2.7.10b).
Mapped reads were quantified with featurecounts (version 2.0.5) . All steps were done in Linux (Red Hat 7.9).
Assembly: hg38
Supplementary files format and content: The csv file contains raw counts for each sample.

organism: Homo sapiens

source_name: Keloid

growth_protocol: Human foreskin fibroblasts (HFF, CTCC-001-0346) were isolated from human male foreskin biopsies. Keloid fibroblasts (KF, CTCC-185-HUM) were isolated from human keloid specimen. Both cell lines were cultured in Dulbecco’s MEM (C3113, Vivacell) with 10% fetal bovine serum (CTCC-002-001, Meisen) and 0.2% Primocin (ant-pm-05, Invivogen).

extract_protocol:
Total RNA was isolated using RNAiso plus (9109, Takara) and quantified using Nanodrop One. The quality of RNA was determined by Bioanalyzer 2100 (Agilent Technologies).
After the RNA was purified by poly-T magnetic beads, sequencing libraries was generated, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina) with PE150 strategy.

treatment_protocol: 8*10^4 cells were seeded into each elastomer and were allowed to adhere for 24 hours. Then, the elastomer was installed on the cell stretching device and stretched for the indicated time.

value: Keloid

tag: cell line

value: KF cells stretched for 6 hours


title: ACBI1 treated cells, 60min LipidA [Exp4_60min_ACBI1_rep1]


title: DGM-10161_Sample_32

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Raw reads from 240 sequenced samples pooled from the 3 healthy, nonsmoker subjects were processed with Salmon to obtain gene and transcript levels as estimated read counts and transcripts per million (TPM) using the Ensembl release 79 transcriptome.
Samples with <10e6 reads or for which less than 80% of fragments mapped to non-mitochondrial protein coding genes were excluded from the final analysis, leaving data from a total of 157 single cells.
For all analyses, TPM values were log transformed as log2(1+TPM). Genes which were not expressed in any sample were excluded, leaving a total of 21,757 genes after filtering. Eighteen samples with no visible cell captured and <10e6 mapped reads (“no cell” wells) were used to estimate background levels of RNA contamination for each gene detected. For 855 genes expressed in at least 20% of no cell wells, background levels were estimated from estimated read counts by fitting an exponential distribution. Estimated read counts for affected genes were corrected by subtracting background levels (to a minimum of 0) and TPM values were recalculated using the corrected read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: log TPM text files include the Ensembl unique ID and gene symbol and log2(1+TPM) values for all samples.

source_name: small airway epithelium brushing

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Fluidigm C1 system following the manufacturer’s protocol. To enrich the cell capture of club cells and basal cells, and minimize the inclusion with larger differentiated ciliated and mucin-secreting cells, the single cell suspension (15 μl; 400~600 cells/μl) were loaded into the medium-sized (10 to 17 μm in diameter) microfluidic RNA-seq chip after priming (Fluidigm). The cells were captured using an Olympus-phase contrast microscope to examine the cell numbers in each capture site. Only single cells in the capture site were used.
The Fluidigm C1 system was used for single cell RNA purification and cDNA synthesis by using the SMARTer Ultra Low RNA kit, and the single cell cDNAs were transferred to a 96 well-plate. The single cell library preparation and RNA sequencing were performed following a Fluidigm protocol.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

tag: individual id

tag: smoking status

value: nonsmoker

value: SAE


title: DGM-10161_Sample_40


title: HFF-12h-2

source_name: Skin

value: Skin

value: HFF cells stretched for 12 hours


title: Cav1-null_day17_sample1


title: DGM-10161_Sample_31


title: HFF-6h-2

value: HFF cells stretched for 6 hours


title: WT cells, 60min LipidA [Exp4_60min_Ctrl_rep2]

value: WT


title: Cav1-null_day15_sample3

value: Fetal brain


title: WT cells, 60min LipidA [Exp4_60min_Ctrl_rep1]


title: DGM-10161_Sample_30


title: HFF-6h-1


title: Cav1-null_day15_sample2

value: Female


title: HFF-ctr-2

value: Unstretched HFF cells


title: DGM-10161_Sample_34


title: BRDK98 treated cells, 20min LipidA [Exp4_20min_BRDK98_rep1]

value: BRDK98 treated

value: 20min LipidA


title: Cav1-null_day15_sample1


title: BRDK98 treated cells, 20min LipidA [Exp4_20min_BRDK98_rep2]

value: BMDM


title: Cav1-null_day12_sample3


title: DGM-10161_Sample_28


title: DGM-10161_Sample_27


title: DGM-10161_Sample_3


title: BRM014 treated cells, 20min LipidA [Exp4_20min_BRM014_rep2]

value: BRM014 treated


title: Cav1-null_day12_sample2


title: hc_pmn12

city: Seattle

first: Rayan

last: Najjar

address: 750 Republican Street

department: Medicine/Rheumatology

institute: University of Washington

data_processing:
Alignment by STAR then gene quantification by Rsubread featureCounts
Assembly: GRCh38.p13
Supplementary files format and content: Gene expression matrix

source_name: neutrophils

extract_protocol:
Gradient centrifugation on PolymorphPrep to isolate neutrophils
PolyA RNA

tag: disease state

value: healthy control

value: neutrophils


title: BRM014 treated cells, 20min LipidA [Exp4_20min_BRM014_rep1]

value: strand specific polyA+ RNA


title: HFF-12h-1


title: DGM-10161_Sample_25


title: hc_pmn11


title: ACBI1 treated cells, 20minLipidA [Exp4_20min_ACBI1_rep2]

value: ACBI1 treated


title: HFF-ctr-1


title: ACBI1 treated cells, 20min LipidA [Exp4_20min_ACBI1_rep1]


title: hc_pmn9


title: hc_pmn10


title: WT cells, 20min LipidA [Exp4_20min_Ctrl_rep2]


title: DGM-10161_Sample_24

value: nonsmoker


title: C57BL/6J_day17_sample3


title: DGM-10161_Sample_17

value: SAE


title: hc_pmn8


title: WT cells, 20min LipidA [Exp4_20min_Ctrl_rep1]


title: DGM-10161_Sample_16


title: C57BL/6J_day15_sample3


title: hc_pmn7


title: WT cells, 0min LipidA [Exp4_0min_Ctrl_rep2]

value: 0min LipidA


title: hc_pmn6


title: DGM-10161_Sample_15


title: WT cells, 0min LipidA [Exp4_0min_Ctrl_rep1]


title: Cav1-null_day12_sample1


title: C57BL/6J_day15_sample2


title: Arid1a-/- cells, 1hr LPS [Exp2_1hr_ARID1AKO_rep2]

value: 1hr LPS


title: hc_pmn5


title: C57BL/6J_day15_sample1


title: DGM-10161_Sample_10


title: DGM-10161_Sample_23


title: DGM-10161_Sample_12


title: C57BL/6J_day12_sample3


title: Arid1a-/- cells, 1hr LPS [Exp2_1hr_ARID1AKO_rep1]


title: hc_pmn4


title: hc_pmn3


title: Arid1af/f cells, 1hr LPS [Exp2_1hr_Ctrl_rep2]


title: C57BL/6J_day12_sample2


title: DGM-10161_Sample_1


title: C57BL/6J_day12_sample1


title: C57BL/6J_day17_sample1


title: hc_pmn2


title: Arid1af/f cells, 1hr LPS [Exp2_1hr_Ctrl_rep1]


title: hc_pmn1


title: BRDK98 treated cells, 1hr LipidA [Exp5_1hr_BRDK98_rep1]

library_source: genomic

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto". Differential ATAC peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5
Metaplots were generated using annotatePeaks.pl with parameters -size 1000 and -hist 25. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style dnase
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.

value: 1hr LipidA


title: AKR/J_day17_sample3

value: AKR/J


title: BRM014 treated cells, 1hr LipidA [Exp5_1hr_BRM014_rep2]


title: AKR/J_day17_sample2

value: Fetal brain


title: sle_pmn14

value: systemic lupus erythematosus


title: BRM014 treated cells, 1hr LipidA [Exp5_1hr_BRM014_rep1]


title: sle_pmn13


title: ACBI1 treated cells, 1hr LipidA [Exp5_1hr_ACBI1_rep2]


title: AKR/J_day15_sample3

value: Female


title: AKR/J_day17_sample1


title: C57BL/6J_day17_sample2


title: AKR/J_day15_sample2


title: AKR/J_day15_sample1


title: sle_pmn12


title: ACBI1 treated cells, 1hr LipidA [Exp5_1hr_ACBI1_rep1]


title: WT cells, 1hr LipidA [Exp5_1hr_Ctrl_rep2]

value: WT


title: AKR/J_day12_sample3


title: sle_pmn10


title: WT cells, 1hr LipidA [Exp5_1hr_Ctrl_rep1]


title: sle_pmn15


title: sle_pmn9


title: ACBI1 treated cells, 0hr LipidA [Exp5_0hr_ACBI1_rep1]

value: 0hr LipidA


title: sle_pmn11


title: WT cells, 0hr LipidA [Exp5_0hr_Ctrl_rep1]

value: BMDM


title: BRM014 treated cells, 4hr LipidA [Exp4_4hr_BRM014_rep2]

value: BRM014 treated

value: 4hr LipidA


title: AKR/J_day12_sample1


title: sle_pmn7

value: neutrophils


title: sle_pmn8


title: BRM014 treated cells, 4hr LipidA [Exp4_4hr_BRM014_rep1]


title: sle_pmn6


title: oocyte FSH30_7

city: Piscataway

first: Tingjie

last: Zhan

state: NJ

address: 499 Vernon Ct

institute: Rutgers university

description: oocyte FSH30_7

data_processing:
Sequenced reads were uploaded into Partek Flow software for data analyses. We first filtered out potential rDNA and mtDNA contaminants using Bowtie 2. Filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner. Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm. Raw read counts were then normalized based on the Transcripts Per Million (TPM) method, and differential expression analysis was performed by using the DESeq2(R).
Assembly: Ensembl Transcripts release 99
Supplementary files format and content: Raw_counts.xlsx contains the raw read counts that were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm.
Supplementary files format and content: Log2(TPM+1).xlsx contains the log2 transformed normalized counts  based on the Transcripts Per Million (TPM) method

source_name: Ovarian oocyte

growth_protocol: Secondary follicles with intact morphology were encapsulated in 0.5% (w/v) alginate and cultured in 96-well plates, with each well containing one bead and 100 μl growth media. The growth media consisted of 50% αMEM Glutamax (Thermo Fisher Scientific) and 50% F-12 Glutamax (Thermo Fisher Scientific) supplemented with 3 mg/ml bovine serum albumin (BSA; Sigma-Aldrich),  recombinant follicle stimulating hormone (rFSH; gifted by Organon, Jersey City, NJ, USA), 1 mg/ml bovine fetuin (Sigma-Aldrich), and 5 μg/ml insulin-transferrin-selenium (ITS, Sigma-Aldrich). Follicles were cultured for 6 days at 37 °C in a humidified environment of 5% CO2 .in air.

extract_protocol:
Total RNA of a single follicle was extracted using Arcturus PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA) following manufacturer’s instructions.
For follicles, the cDNA library construction and low-input mRNA-Seq were performed on an Illumina NovaSeq PE150 platform by Novogene (Novogene Corporation, Sacramento, CA). For oocytes, Smart-Seq2 cDNA synthesis was performed on isolated follicle RNA with Maxima H Minus reverse transcriptase (ThermoFisher). Whole transcriptome amplified (WTA) product was purified with AMPure XP beads (Beckman Coulter), quantified with Quanit-iT PicoGreen dsDNA Assay (ThermoFisher), normalized and used for preparing paired-end sequencing libraries with Nextera XT (Illumina, #FC-131) according to the manufacturer’s instructions.

treatment_protocol: Follicles were cultured with FSH of 5 mIU/mL on day 0-4, and then treated with FSH of 5, 10, 20 and 30 mIU/mLon day 4-6. On day 4 or day 6 of eIVFG,  follicles  were removed from alginate beads by incubation in L15 media containing 1% FBS and 10 IU/ml alginate lyase from Flavobacterium multivorum (Sigma-Aldrich) at 37 °C for 20 minutes. Follicles were collected and washed in 1X phosphate buffered saline (PBS; Invitrogen) three times. On day 6 of eIVFG, follicles treated with FSH of 10 and 30 mIU/mL were then transferred to the maturation media, and ovulation was induced by incubation in the maturation media containing 50% αMEM Glutamax and 50% F-12 Glutamax supplemented with 10%FBS, 1.5 IU/ml hCG (Sigma-Aldrich], 10 ng/ml epidermal growth factor (EGF; BD Biosciences). At 16-hours post-hCG treatment,  oocytes were collected and washed in 1X phosphate buffered saline (PBS; Invitrogen) three times.

value: Ovarian oocyte

value: CD-1 mouse strain

value: oocyte FSH 30


title: oocyte FSH30_9

description: oocyte FSH30_9


title: oocyte FSH30_5

description: oocyte FSH30_5


title: BRM014 treated cells, 0hr LipidA [Exp2_0hr_BRM014_rep1]


title: AKR/J_day12_sample2


title: sle_pmn4


title: oocyte FSH30_4

description: oocyte FSH30_4


title: BRDK98 treated cells, 0hr LipidA [Exp1_0hr_BRDK98_rep1]

value: BRDK98 treated


title: sle_pmn3


title: sle_pmn5


title: sle_pmn2


title: oocyte FSH30_3

description: oocyte FSH30_3


title: oocyte FSH30_2

description: oocyte FSH30_2


title: sle_pmn1


title: BR_127_CTR_full

city: Medford

first: rebecca

last: batorsky

state: MA

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

data_processing:
10x Data analysis and clustering: 10x scRNA-seq data was aligned with 10x Genomics Cell Ranger (v3.0) against the mm10 mouse reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fetal Brain

extract_protocol:
Uterine horns containing embryos were rapidly dissected and embryos were placed on ice in sterile PBS. Brains and placentas were isolated, and fetal forebrain and placenta were diced finely with sterile blade and placed into collagenase A (Millipore-Sigma; 11088793001) digestion solution on ice. Cd11b-positive cells were isolated from both placenta and brain tissue. Samples were serially dissociated into a single cell suspension using hand-flamed Pasteur pipettes, and the resultant suspension was enriched for macrophages and monocytes using a 70%/30% Percoll gradient (Millipore-Sigma; GE17-0891-01). This enriched macrophage/monocyte solution was incubated with human and mouse CD11b microbeads (Miltenyi Biotec; 130-093-634), and cells were further enriched for Cd11b-positive macrophages/monocytes using Miltenyi MACS Separation Columns (LS; 130-042-401) and a Miltenyi QuadroMACS Separator (130-090-976).
Fresh CD11b+ cells from biological replicates per diet group were prepared for single-cell RNA sequencing (10X Genomics v3.0 chip).
Paired fetal brain and placental samples were collected for 17 mice, giving 34 total samples. Approximately 5,900 cells/sample were sequenced, giving 197,000 sequenced cells with an average depth of approximately 22,000 reads/cell).

treatment_protocol: For diet-induced obesity versus lean control experiments, C57BL/6J females were placed on either an obesogenic diet (Research Diets D12492, 60% kcal from fat) for 10 weeks to induce maternal obesity, or a control diet (D12450J, 10% fat) matched for protein, fiber and sucrose content for the same duration of time, prior to breeding with C57BL/6J males on the control diet, as described in prior publications by our group.

value: CD11b+ cells

value: Fetal Brain

tag: age

tag: Sex

value: F

value: Control Dam


title: BRDK98 treated cells, 0hr LipidA [Exp1_0hr_BRDK98_rep2]


title: oocyte FSH30_15

description: oocyte FSH30_15


title: oocyte FSH30_12

description: oocyte FSH30_12


title: PL_127_CTR_full

source_name: Placenta

value: Placenta


title: PL_122_OBS_full

value: Obese Dam


title: 150-NSUN2, Input (MeRIP-Seq)

city: Zhengzhou

first: Liu

last: liwen

address: NO.101 Kexue Road High-Tech Development Zone Of States Zhengzhou

institute: Zhengzhou University

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC HG38) by STAR software.After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA,were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: HG38
Supplementary files format and content: The Excel table contains m5C methylation site identification information for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent
m5C RNA immunoprecipitation was performed with the GenSeqTM m5C RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m5C IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Novaseq instrument with 150bp paired-end reads.

value: esophageal squamous cell carcinoma (ESCC)

value: NSUN2 knockdown

tag: fraction

value: input


title: oocyte FSH30_10

description: oocyte FSH30_10

value: WT


title: BR_122_OBS_full


title: 150-NC, Input (MeRIP-Seq)

value: control


title: oocyte FSH30_1

description: oocyte FSH30_1


title: 150-NSUN2, IP (MeRIP-Seq)

value: IP


title: PL_118_OBS_full


title: 150-NC, IP (MeRIP-Seq)


title: oocyte FSH10_9

description: oocyte FSH10_9

value: oocyte FSH 10


title: BR_118_OBS_full


title: TA563_Control

city: San Francisco

first: Aartik

last: Sarma

address: 513 Parnassus Ave

institute: University of California, San Francisco

data_processing:
Sequencing reads were aligned with STAR
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport, with the scaledTPM method
Assembly: human protein coding genes (ENSEMBL v. 99), cytosolic and mitochondrial ribosomal RNA sequences, and the sequences of ERCC RNA standards

source_name: Tracheal aspirate

extract_protocol:
RNA was extracted using Zymo Pathogen Magbead Kit followed by DNase treatment. human cytosolic and mitochondrial ribosomal RNA was then depleted using Qiagen FastSelect
RNA was then fragmented and underwent library preparation using the NEBNext Ultra II RNASeq Kit (New England Biolabs)

value: Tracheal aspirate

value: Control


title: PL_115_CTR_full


title: oocyte FSH10_8

description: oocyte FSH10_8

value: Ovarian oocyte

value: CD-1 mouse strain


title: TA555_Control


title: oocyte FSH10_5

description: oocyte FSH10_5


title: BR_115_CTR_full

value: CD11b+ cells


title: TA477_Control


title: PL_56_OBS_full

value: M


title: TA463_SP only

value: SP only


title: BR_56_OBS_full

value: Fetal Brain


title: TA462_Control


title: PL_52_CTR_full

value: Placenta

value: Control Dam


title: oocyte FSH10_3

description: oocyte FSH10_3


title: DGM-00461 [genotype]

type: genomic

hyb_protocol: Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method.
CHP files were created from CEL files after running BRLMM_p

label: biotin

source_name: Blood from healthy nonsmokers or healthy smokers

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

extract_protocol: DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions

tag: ethnicity

value: Afr

tag: department of genetic medicine id

value: S


title: DGM-00194 [genotype]

value: Eur


title: non-smoker 141, genotype

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method. CHP files were created from CEL files after running BRLMM_p

source_name: DNA obtained from blood

tag: sex

tag: ethnic group

value: black

value: non-smoker


title: oocyte FSH10_2

description: oocyte FSH10_2

tag: tissue

tag: genotype

value: WT


title: oocyte FSH10_15

description: oocyte FSH10_15

tag: cell type

value: oocyte FSH 10

tag: treatment


title: BR_52_CTR_full


title: non-smoker 138, genotype


title: non-smoker 040, genotype

value: F


title: non-smoker 110, genotype


title: TA359_SP only

value: Tracheal aspirate


title: non-smoker 109, genotype

value: white


title: PL_51_CTR_full


title: oocyte FSH10_4

description: oocyte FSH10_4

value: Ovarian oocyte

value: CD-1 mouse strain


title: LOD-215, genotype

value: M

value: smoker, 40 pack-years


title: LOD-195, genotype

value: smoker, 30 pack-years


title: LOD-244, genotype

value: smoker, 19.5 pack-years


title: TA367_SP + steroids

value: SP + steroids


title: BR_51_CTR_full

value: CD11b+ cells

value: Fetal Brain

value: Control Dam


title: TA341_SP + steroids


title: oocyte FSH10_11

description: oocyte FSH10_11


title: TA337_SP + steroids


title: LOD-114, genotype

value: smoker, 50 pack-years


title: non-smoker 124, genotype

value: black

value: non-smoker


title: non-smoker 048, genotype


title: PL_50_CTR_full

value: Placenta


title: LOD-145, genotype

value: smoker, 20 pack-years


title: oocyte FSH10_1

description: oocyte FSH10_1

value: oocyte FSH 10

value: WT


title: LOD-132, genotype

value: smoker, 32 pack-years


title: BR_50_CTR_full


title: oocyte FSH10_13

description: oocyte FSH10_13

value: Ovarian oocyte

value: CD-1 mouse strain


title: LOD-053, genotype

value: M


title: LOD-054, genotype

value: smoker, 30 pack-years


title: TA319_Control

value: Tracheal aspirate

value: Control


title: follicle D6_30_7

description: follicle D6_30_7

source_name: Ovarian follicle

value: Ovarian follicle

value: FSH 30 D6


title: PL_45_OBS_full

value: CD11b+ cells

value: F

value: Obese Dam


title: TA315_SP + steroids

value: SP + steroids


title: follicle D6_30_6

description: follicle D6_30_6


title: BR_45_OBS_full

value: Fetal Brain


title: LOD-194, genotype

value: black

value: smoker, 49 pack-years


title: LOD-086, genotype

value: hispanic

value: smoker, 90 pack-years


title: LOD-131, genotype

value: smoker, 7 pack-years


title: TA314_SP only

value: SP only


title: PL_41_OBS_full

value: Placenta

value: M


title: follicle D6_30_5

description: follicle D6_30_5

value: CD-1 mouse strain

value: WT


title: TA311_SP + steroids

value: Tracheal aspirate


title: LOD-021, genotype

value: smoker, 23 pack-years


title: follicle D6_30_2

description: follicle D6_30_2

value: Ovarian follicle

value: FSH 30 D6


title: LOD-204, genotype

value: F

value: smoker, 35 pack-years


title: TA252_SP only


title: LOD-045, genotype

value: white

value: smoker, 31 pack-years


title: LOD-164, genotype

value: black

value: smoker, 15 pack-years


title: follicle D6_30_1

description: follicle D6_30_1


title: follicle D6_30_4

description: follicle D6_30_4


title: LOD-012, genotype

value: smoker, 20 pack-years


title: BR_41_OBS_full

value: CD11b+ cells

value: Fetal Brain

value: Obese Dam


title: TA334_SP only

value: SP only


title: HCC1143, CROPseq

first: Andrea

last: Califano

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

description: 10x Genomics

data_processing:
The barcoded processing, CRISPR guide capture analysis, gene counting and aggregation were made using the CellRanger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Fro CROPseq samples, CRISPR guide capture analysis via CellRanger provided sgRNA's UMI thresholds to identify cells detected with a sgRNA, using a gaussian mixture model.
For control samples, the scRNA-seq data were demultiplexed using Demuxlet, the poor quality cells were removed, and the count matrix for each cell line was saved, separately.
Supplementary files format and content: count matrix files (.mtx), cell ID-to-gRNA tables (.csv), and gRNA UMI threshold tables (.csv) for CROP-seq samples (HCC38 and HCC1143)
Supplementary files format and content: count matrix files (.csv) for negative controls (HCC38, HCC1143, HCC2157, and MCF7)

source_name: Breast; Mammary gland

growth_protocol: All cell lines were routinely tested for mycoplasma contamination. Cell lines were kept in a 37 °C humidity-controlled incubator with 5.0% CO2.

extract_protocol:
For scRNA-seq of control samples, cells were seeded into 15cm circular plates and incubated for 72 hours. After the incubation, the cells had a confluence <50% and were dissociated and subjected to scRNA-seq (10X Genomics).
For CROP-seq screening, sgRNA containing lentiviruses were transduced into Cas9 expressing breast cancer cell lines HCC1143 and HCC38 (in 15cm plate-format) in presence of 8ug/ml polybrene, at an estimated MOI < 0.2. After 24h, the lentivirus containing media was removed, cells were washed with PBS, and puromycin-containing media (3ug/ml) was added to the cells for 48-96h until all control cells (not virus-infected) were dead. The cells were grown for 14 days post sgRNA transduction to allow potential reprogramming effects to take place, before the scRNAseq (10X Genomics).
For control samples, the resulting suspension of human tumor cells (HCC38, HCC1143 in batch 1, and MCF7, HCC2157 in batch 2) was adjusted to a concentration appropriate for loading into a 10X genomics Chromium controller with an expected output of 5000 cells/each cell line. Samples within each batch were pooled into the same well and libraries constructed according to the manufacturer’s instructions. Libraries were sequenced on an Illumina Novaseq 6000, aiming for approximately 100,000 reads/cell.
For CROPseq, the CRISPR perturbed cell lines (HCC38, HCC1143) were adjusted to a concentration appropriate for loading into a 10X genomics with an expected output of 10,000 cells/each cell line. The 10x libraries were prepared based on manufacturer's instructions with feature barcode CRISPR screening protocol. Libraries were sequenced on an Illumina Novaseq 6000, aiming for approximately 100,000 reads/cell.

value: Breast; Mammary gland

value: TNBC


title: BR_39_CTR_full

value: Control Dam


title: follicle D6_20_8

description: follicle D6_20_8

value: CD-1 mouse strain

value: FSH 20 D6

value: WT


title: PL_38_CTR_full

value: Placenta

value: M


title: follicle D6_20_7

description: follicle D6_20_7

value: Ovarian follicle


title: follicle D6_20_5

description: follicle D6_20_5


title: scRNAseq of control sample (HCC2157 + MCF7)

description: 10x Genomics

value: HCC2157 and MCF7

value: TNBC and HR+


title: BR_38_CTR_full


title: PL_37_CTR_full


title: scRNAseq of control sample (HCC38 + HCC1143)

description: 10x Genomics

value: HCC38 and HCC1143

value: TNBCs


title: follicle D6_20_4

description: follicle D6_20_4


title: LOD-009, genotype

value: F

value: black

value: smoker, 30 pack-years


title: follicle D6_20_2

description: follicle D6_20_2


title: HCT116, shTCF7L1-2, Dox-treated to express pCW57.1-TCF7L1-MUT ChIP-Seq

city: Hershey

first: Gregory

middle: S

last: Yochum

state: PA

address: 700 HMC Cres Rd

institute: The Pennsylvania State University, College of Medicine

data_processing:
Raw reads were trimmed using skewer software (v0.1.126) by Novogene Co., Ltd
Quality control was assessed using FastQC by Novogene Co., Ltd
Clean reads were mapped against the human genome (GRCh38 /hg38) using BWA (v0.7.12) by Novogene Co., Ltd
Peaks were called for aligned reads using MACS2 (v2.1.0) by Novogene Co., Ltd
Peaks were annotated using PeakAnnotator_Cpp (v1.4) by Novogene Co., Ltd
Assembly: Homo sapien GRCh38/hg38
Supplementary files format and content: bigWig, BED, and narrowPeaks files for all samples

growth_protocol: Stable HCT116 cell lines were maintained in DMEM supplemented with 10% fetal bovine (FBS), antibiotics, and puromycin in 5% CO2 at 37C

extract_protocol:
Chromatin immunoprecipitation was conducted using Active Motive High-Sensitivity ChIP-IT Kit according to manufacturer guidelines
ChIP libraries were prepared by Novogene Co., Ltd

treatment_protocol:
Lentiviral delivery of shRNA targeting TCF7L1 to mediate TCF7L1 knockdown (shTF7L1-2)
1 µg/ml Doxycline to induce pCW57.1 plasmid expression

value: colon adenocarcinoma

value: TCF7L1 KD, pCW57.1-TCF7L1-MUT

value: doxycycline

tag: chip antibody

value: FLAG (Sigma 1804)


title: BR_37_CTR_full

value: CD11b+ cells

value: Fetal Brain

tag: strain

value: Control Dam


title: HCC38, CROPseq

description: 10x Genomics

value: Breast; Mammary gland

tag: cell line

value: TNBC


title: smoker 176, genotype

tag: Age

value: M

tag: Ethnic group

tag: Smoking status

value: smoker, 33 pack-years


title: follicle D6_20_1

description: follicle D6_20_1

value: Ovarian follicle

value: CD-1 mouse strain

value: FSH 20 D6

value: WT


title: HCT116, shTCF7L1-2, Dox-treated to express pCW57.1-TCF7L1-MUT

data_processing:
Clean reads were mapped using STAR v2.5 (Reference genome: GRCh38/hg38) by Novogene Co., Ltd
Aligned reads were counted using HTSeq (v0.6.1) by Novogene Co., Ltd
Read counts were adjusted by edgeR program package through one scaling normalized factor by Novogene Co., Ltd
Differential expression analysis was performed using the edgeR R package (v3.16.5) by Novogene Co., Ltd
Assembly: Homo sapien GRCh38/hg38
Supplementary files format and content: Excel file includes fpkm values for each sample
Supplementary files format and content: Excel file includes read counts for each sample

extract_protocol:
RNA was isolated using TRIzol reagent according to manufacturer guidelines
RNA libraries were prepared using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® by Novogene Co., Ltd

treatment_protocol:
Lentiviral delivery of shRNA targeting TCF7L1 to mediate TCF7L1 knockdown
1 µg/ml Doxycline to induce pCW57.1 plasmid expression


title: HCT116, shTCF7L1-2, Dox-treated to express pCW57.1-TCF7L1 ChIP-Seq

value: TCF7L1 KD, pCW57.1-TCF7L1


title: follicle D6_10_7

description: follicle D6_10_7

value: FSH 10 D6


title: PL_39_CTR_full

value: Placenta

tag: age

value: F


title: PL_35_CTR_full

tag: Sex


title: HCT116, shTCF7L1-2, Dox-treated to express pCW57.1-TCF7L1

value: colon adenocarcinoma

value: doxycycline


title: BR_35_CTR_full

value: CD11b+ cells


title: COPD 136, genotype

value: white

tag: smoking status

value: COPD, GOLD-I, 119 pack-years


title: follicle D6_10_6

description: follicle D6_10_6


title: PL_28_OBS_full

value: Obese Dam


title: COPD 134, genotype

value: COPD, GOLD-I, 24 pack-years


title: HCT116, shTCF7L1-2, Dox-treated to express pCW57.1-empty

value: TCF7L1 KD, pCW57.1-empty


title: follicle D6_10_5

description: follicle D6_10_5


title: BR_28_OBS_full

value: Fetal Brain

value: M


title: Input_CPT60_rep1

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

data_processing:
library strategy: DRIP-seq
DRIP-seq libraries were quality checked using Fastqc and reads were trimmed using Cutadapt.
Reads were aligned on both human genome (hg 19) and spike-in yeast genome (sacCer3) using BWA aligner.
Alignment sorting, filtering for ENCODE blacklist region and duplicated reads removal was performed using Samtools.
Peak calling and genomic signal computation for each library was performed using macs2.
DRIP-seq signal tracks for each condition were created using Deeptools bamCoverage function, using the normalization scaling factor computed using  library dimension and spike-in fraction for each library.
Assembly: hg19
Supplementary files format and content: .bw file contain the normalized genomic level of DRIP signal
Supplementary files format and content: .narrowPeak file contain the output of MACS peak caller in BED format

growth_protocol: HCT116 cells were cultured in a humidified incubator at 5% of CO2 and 37°C in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (FBS)

extract_protocol:
Cells were harvested by using accutase, pelleted, resuspended in 1X TE buffer (Tris HCl pH 7.6 10 mM, EDTA pH 8 1 mM) and lysed O/N at 37°C with 0.5% SDS and 62.5 μg/ml in 1X TE buffer. Chromatin was then precipited with isopropanolo and sodio acetato, washed with ethanol and resuspeded in 1X TE for 4h at 30°C. O/N digestion was performed with restriction enzymes cocktail
Library construction using the ThruPLEX DNA-Seq kit.

treatment_protocol: HCT116 cells were treated with 10 μM CPT for 5 and 60 minutes.

value: Human epithelial colorectal carcinoma

tag: antibody


title: PL_27_OBS_full


title: follicle D6_10_4

description: follicle D6_10_4

value: Ovarian follicle

value: CD-1 mouse strain


title: Input_CPT5_rep1


title: BR_27_OBS_full


title: follicle D6_10_2

description: follicle D6_10_2

value: WT


title: Input_Ctrl_rep1


title: COPD 074, genotype

value: asian

value: COPD, GOLD-III, 110 pack-years


title: follicle D6_10_1

description: follicle D6_10_1

value: FSH 10 D6


title: PL_6_OBS_full

value: Placenta


title: DGM-01346_am

type: RNA

description: alveolar macrophages obtained from bronchoalveolar lavage

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: alveolar macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

value: smoker

tag: disease state

value: HIV-

value: alveolar macrophage


title: DRIP+RH_CPT60_rep1


title: BR_6_OBS_full

value: CD11b+ cells


title: DGM-01342_am


title: DGM-01344_am


title: Pbrm1-/- cells, 4hr LipidA [Exp3_4hr_PRBM1KO_rep2 RNA-seq]

description: strand specific polyA+ RNA

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using analyzeRepeats.pl within HOMER with -strand both -count exons -condenseGenes –noadj and then by getDiffExpression.pl within HOMER
Assembly: GRCm38 (mm10)
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_tpm.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-20) dataValue.
Supplementary files format and content: Exp2_ARID1AKO_tpm.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-14) dataValue.
Supplementary files format and content: Exp3_PBRM1KO_tpm.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-14) dataValue.
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_DESeq2.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-20) normalized Log2 read count for experiment (21-23) Log2 fold change, p-value, adjusted p-value 1hr_Ctrl vs 0hr_Ctrl (24-26) Log2 fold change, p-value, adjusted p-value of 4hr_Ctrl vs 0hr_Ctrl (27-29) Log2 fold change, p-value, adjusted p-value of 4hr_ACBI1 vs 4hr_Ctrl (30-32) Log2 fold change, p-value, adjusted p-value of 4hr_BRM014 vs 4hr_Ctrl (33-35) Log2 fold change, p-value, adjusted p-value of 4hr_BRDK98 vs 4hr_Ctrl
Supplementary files format and content: Exp2_ARID1AKO_DESeq2.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) normalized Log2 read count for experiment (15-17) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (18-20) Log2 fold change, p-value, adjusted p-value of 4hr_ARID1AKO vs 4hr_Ctrl
Supplementary files format and content: Exp3_PBRM1KO_DESeq2.txt:
Supplementary files format and content: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) normalized Log2 read count for experiment (15-17) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (18-20) Log2 fold change, p-value, adjusted p-value of 4hr_PBRM1KO vs 4hr_Ctrl

value: BMDM

tag: stimulation

value: 4hr LipidA


title: follicle D6_5_6

description: follicle D6_5_6

value: FSH 5 D6


title: COPD 110, genotype

tag: sex

value: F

tag: ethnic group

value: black

value: COPD, GOLD-II, 15 pack-years


title: DGM-01347_am


title: Pbrm1-/- cells, 4hr LipidA [Exp3_4hr_PRBM1KO_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: DRIP+RH_CPT5_rep1

value: Human epithelial colorectal carcinoma


title: follicle D6_5_7

description: follicle D6_5_7

tag: tissue

value: Ovarian follicle

value: CD-1 mouse strain

tag: genotype


title: DRIP_CPT60_rep1

tag: cell type


title: Pbrm1f/f cells, 4hr LipidA [Exp3_4hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

tag: treatment

value: WT


title: follicle D6_5_4

description: follicle D6_5_4

tag: strain


title: DGM-01526_am


title: DGM-01326_am


title: DRIP_CPT5_rep1

tag: cell line


title: follicle D6_5_3

description: follicle D6_5_3


title: DGM-01485_am


title: Pbrm1f/f cells, 4hr LipidA [Exp3_4hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: DGM-10673_am


title: COPD 093, genotype

value: white

value: COPD, GOLD-II, 34 pack-years


title: COPD 068, genotype

value: M

value: COPD, GOLD-II, 60 pack-years


title: COPD 054, genotype

value: COPDex, GOLD-II, 90 pack-years


title: COPD 122, genotype

value: COPD, GOLD-I, 14 pack-years


title: COPD 114, genotype

value: COPD, GOLD-II, 29 pack-years


title: Pbrm1f/f cells, 0hr LipidA [Exp3_0hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: 0hr LipidA


title: COPD 046, genotype

value: COPD, GOLD-II, 75 pack-years


title: DGM-00522_am

value: smoker

value: HIV-

value: alveolar macrophage


title: Pbrm1f/f cells, 0hr LipidA [Exp3_0hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: follicle D4_8

description: follicle D4_8

value: FSH 5 D4


title: DGM-00951_am


title: follicle D4_7

description: follicle D4_7

value: Ovarian follicle


title: COPD 036, genotype

value: COPD, GOLD-I, 48 pack-years


title: Donor 5 NTHi  infected Day 1

city: St. Lucia

first: Ulrike

last: Kappler

state: Qld

address: Cooper Rd B76

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description:
D5_day1
NTHi_RPKM.txt
NHNE_RPKM.txt

data_processing:
CLC Genomics Workbench v 11
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork using default parameters.
Trimmed sequence reads were mapped to using CLC genomic workbench using default settings.
Read count extraction and normalization were performed using CLC genomic workbench
Supplementary files format and content: The procesed data files contains RPKM values for all samples
Supplementary files format and content: tab-delimited text files

source_name: NHNE

extract_protocol:
Samples for RNA isolation were collected prior to infection (day0) for uninfected NHNE and bacterial pre-cultures, and on day1, 3, 7 and 14 post-infection for NTHi-infected NHNE. RNA was extracted from 3 replicate NHNE per sample (samples 6-28) or from bacterial cell material collected following growth on BHI agar ( samples 1-5) using TRIZOL (Thermo Fisher), treated with EZDnase to remove remaining gDNA and concentrated usingRNA Clean and Concentrate Kits (Zymo). 2-3 microg total RNA (RIN >8.0) were ribodepleted using the RiboMinus kit (Termo Fisher) and the ribodepleted RNA used for library preparation. For all NHNE samples ~ 70 million reads were collected per sample and mapped to human and NTHi reference genomes. for NTHi infected NHNE samples, approximately 2 milion reads could be mapped to the bacterial genome.
RNA libraries were prepared using the Illumina TruSeq kit

value: NHNE

value: human

value: wt

value: infected


title: DRIP+RH_Ctrl_rep1

value: Human epithelial colorectal carcinoma


title: DRIP_Ctrl_rep1


title: DGM-01155_am


title: follicle D6_5_5

description: follicle D6_5_5

value: CD-1 mouse strain

value: FSH 5 D6

value: WT


title: follicle D4_6

description: follicle D4_6


title: follicle D6_5_2

description: follicle D6_5_2


title: Arid1af/f cells, 4hr LPS [Exp2_4hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: 4hr LPS


title: COPD 059, genotype

value: M

value: black

value: COPD, GOLD-II, 27 pack-years


title: follicle D4_4

description: follicle D4_4


title: Donor 4 NTHi infected Day 7

description:
D4_day7
NTHi_RPKM.txt
NHNE_RPKM.txt


title: DGM-01023_am

value: smoker

value: HIV-

value: alveolar macrophage


title: follicle D4_3

description: follicle D4_3

value: Ovarian follicle

value: FSH 5 D4


title: Donor 5 NTHi infected Day 7

description:
D5_day7
NTHi_RPKM.txt
NHNE_RPKM.txt

value: NHNE

value: human


title: COPD 008, genotype

value: white

value: COPD, GOLD-I, 50 pack-years


title: DGM-01025_am


title: Arid1af/f cells, 0hr LPS [Exp2_0hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: 0hr LPS


title: follicle D4_2

description: follicle D4_2

value: CD-1 mouse strain


title: Donor 4 NTHi  infected Day 1

description:
D4_day1
NTHi_RPKM.txt
NHNE_RPKM.txt

value: wt

value: infected


title: COPD 015, genotype

value: COPD, GOLD-II, 18 pack-years


title: COPD 014, genotype

value: M

value: COPD, GOLD-II, 35 pack-years


title: Arid1af/f cells, 0hr LPS [Exp2_0hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: WT


title: Arid1af/f cells, 4hr LPS [Exp2_4hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA

value: 4hr LPS


title: Donor 4 Day 0

description:
D4_day0
NHNE_RPKM.txt

value: uninfected


title: astrocytes, hyperglycemic, rep3

city: Seoul

first: Kyung-Seo

last: Lee

address: ABMRC,50-1, Yonsei-ro, Seodaemun-gu

department: College of Medicine

country: South Korea

institute: Yonsei University

data_processing:
Basecalling was done using Illumina bcl2fastq2-v2.20.0 software. Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0, based on the HISAT and Bowtie2 implementations. The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were osrted and indexed using SAMtools v 1.9.
The transcripts were then assembled and quantified using StringTie v2.1.3b.
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM and TPM.
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include read counts, TPM, and FPKM for each samples arranged in a matrix

source_name: astrocytes

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen). Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen). TapeStation RNA Screentape (Agilent) was used to assess the integrity of total RNA. Only high-quality RNA preparations, with RIN greater than 7.0 was used for RNA library construction.
RNA libraries for RNA seq were prepared using the SMART-SeqTM mRNA Kit, following the manufacturer's protocol.

value: astrocytes

value: streptozotocin


title: astrocytes, hyperglycemic, rep2


title: Donor 14NTHi infected Day 3

description:
D4_Day3
NTHi_RPKM.txt
NHNE_RPKM.txt

value: NHNE


title: DGM-00867_am

value: smoker

value: HIV-

value: alveolar macrophage


title: DGM-00332_am


title: Donor 3 NTHi infected Day 14

description:
D3_day14
NTHi_RPKM.txt
NHNE_RPKM.txt

value: human


title: DGM-01193_am


title: DGM-00153_am


title: DGM-00742_am


title: DGM-00823_am


title: astrocytes, hyperglycemic, rep1


title: Donor 3 NTHi infected Day 7

description:
D3_day7
NTHi_RPKM.txt
NHNE_RPKM.txt


title: DGM-00405_am


title: BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep1 RNA-seq]

description: strand specific polyA+ RNA

extract_protocol:
RNA was harvested using Zymo Research Quick-RNA miniprep kit and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded messenger ribonucleic acid (mRNA) kit following manufacturer's protocols.
RNA-seq 50bp single-end sequencing

value: BRDK98 treated

value: 4hr LipidA


title: astrocytes, normoglycemic, rep2

value: vehicle


title: BRM014 treated cells, 4hr LipidA [Exp1_4hr_BRM014_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: BRM014 treated


title: BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep2 RNA-seq]

description: strand specific polyA+ RNA


title: Donor 3 NTHi  infected Day 1

description:
D3_day1
NTHi_RPKM.txt
NHNE_RPKM.txt

value: wt

value: infected


title: astrocytes, normoglycemic, rep3


title: COPD 012, genotype

value: M

value: black

value: COPD, GOLD-II, 33 pack-years


title: astrocytes, normoglycemic, rep1

value: WT


title: ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: ACBI1 treated


title: BRM014 treated cells, 4hr LipidA [Exp1_4hr_BRM014_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: Donor 3 Day 0

description:
D3_day0
NHNE_RPKM.txt

value: NHNE

value: uninfected


title: ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: Donor 3 NTHi infected Day 3

description:
D3_day3
NTHi_RPKM.txt
NHNE_RPKM.txt


title: HC-5770, replicate 3, scRNAseq

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E 57th street

department: Medicine

institute: University of Chicago

description: 10x Genomics

data_processing:
Raw sequencing files were processed through the Rosalind (https://rosalind.bio/) pipeline with a HyperScale architecture (Rosalind). Quality scores were assessed using the FastQC tool
Cell Ranger was used to align reads to the Mus musculus genome build GRCm38, count unique molecular identifiers (UMIs), call cell barcodes, and perform default clustering. After initial processing, raw RNA matrices from each sample were then analyzed for quality control, “ambient” mRNA was removed using SoupX V1.6.1 and clustering utilizing Seurat v4.3.0 in R v4.2.2.
Basic filtering parameters included cells with unique features of minimum 200 and maximum 7500. Cells expressing less than 25 percent mitochondrial related genes were included. Cell cycle effect was regressed out using previously established methods in Seurat. After filtering, replicates from each condition were merged using standard SCTransform Seurat protocols using 3000 integration features. After clustering, cells were visualized using Uniform Manifold Approximation and Projection
Marker genes were determined using ‘FindAllMarkers’ function (Wilcoxon rank-sum test) in Seurat. Contaminating endothelial and neuronal cells were distinct from the other clusters and were subsequently removed from the final analysis.
Assembly: Grcm38

source_name: Pancreatic islets

extract_protocol: Single cell 3’ RNA-seq experiment was conducted using the Chromium controller (10x Genomics, Inc provided reagents and protocols). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium controller. Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v3 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA.

treatment_protocol: Female NOD mice were treated with vehicle or HC-5770 during pre-diabetic stage (6-8 weeks of age). At the end of the treatment, islets were isolated and scRNAseq was performed.

value: Female

value: NOD

value: Pancreatic islets

value: 8 week old

value: HC-5770 (PERK inhibitor)


title: Donor 2 NTHi infected Day 14

description:
D2_day14
NTHi_RPKM.txt
NHNE_RPKM.txt

value: human


title: WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

source_name: BMDM

value: 4hr LipidA


title: DGM-00083_am

value: smoker

value: HIV-

value: alveolar macrophage


title: DGM-02164_am


title: HC-5770, replicate 2, scRNAseq

description: 10x Genomics


title: DGM-00194_am


title: DGM-00365_HIV_am

value: HIV+


title: DGM-00309_HIV_am


title: WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: Donor 2 NTHi infected Day 7

description:
D2_day7
NTHi_RPKM.txt
NHNE_RPKM.txt

value: wt

value: infected


title: HC-5770, replicate 1, scRNAseq

description: 10x Genomics


title: Donor 2 NTHi infected Day 3

description:
D2_day3
NTHi_RPKM.txt
NHNE_RPKM.txt


title: WT cells, 1hr LipidA [Exp1_1hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: WT

value: 1hr LipidA


title: Vehicle, replicate 3, scRNAseq

description: 10x Genomics

value: vehicle


title: Vehicle, replicate 2, scRNAseq

description: 10x Genomics

value: Female


title: WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep2 RNA-seq]

description: strand specific polyA+ RNA

value: 0hr LipidA


title: Donor 2 Day 0

description:
D2_day0
NHNE_RPKM.txt

value: NHNE

value: uninfected


title: WT cells, 1hr LipidA [Exp1_1hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: Donor 2 NTHi  infected Day 1

description:
D2_day1
NTHi_RPKM.txt
NHNE_RPKM.txt


title: Vehicle, replicate 1, scRNAseq

description: 10x Genomics

value: NOD

value: Pancreatic islets

value: 8 week old


title: Donor 1 NTHi infected Day 14

description:
D1_day14
NTHi_RPKM.txt
NHNE_RPKM.txt

value: human


title: WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep1 RNA-seq]

description: strand specific polyA+ RNA


title: Pbrm1-/- cells, 4hr LipidA [Exp4_4hr__PBRM1KO_rep2 ATAC-seq]

value: 4hr LipidA


title: DGM-00298_HIV_am

value: smoker

value: alveolar macrophage


title: Donor 1 NTHi infected Day 7

description:
D1_day7
NTHi_RPKM.txt
NHNE_RPKM.txt

value: wt


title: L_IR_HSC_rep3

city: Chongqing

first: Xinliang

last: Chen

address: Gaotanyan street 30

institute: Army Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus GRCm38.
The mapped reads of each sample were then assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All the transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: All mice used were randomized, background-matched. All mice used were housed in individually ventilated specific pathogen-free (SPF) conditions and fed with autoclaved water and food.

extract_protocol:
HSCs  were sorted from the BM of WT mice at 3 days after IR.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
RNA libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: Hematopoietic stem cell


title: L_IR_HSC_rep2

value: WT


title: DGM-00271_HIV_am

value: HIV+


title: DGM-00265_HIV_am


title: DGM-00257_HIV_am


title: Donor 1 NTHi infected Day 3

description:
D1_day3
NTHi_RPKM.txt
NHNE_RPKM.txt

value: infected


title: DGM-00279_HIV_am


title: Pbrm1-/- cells, 4hr LipidA [Exp4_4hr_PBRM1KO_rep1 ATAC-seq]

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto". Differential ATAC peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5
Metaplots were generated using annotatePeaks.pl with parameters -size 1000 and -hist 25. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style dnase
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig

value: BMDM


title: L_IR_HSC_rep1


title: DGM-00243_HIV_am


title: WT cells, 4hr LipidA [Exp4_4hr_rep2 ATAC-seq]


title: Ab_IR_HSC_rep2


title: Ab_IR_HSC_rep3


title: Donor 1 Day 0

description:
D1_day0
NHNE_RPKM.txt


title: PCLD9, scRNAseq

city: London

first: Gillian

last: Tomlinson

address: Gower Street

department: Infection and Immunity

country: United Kingdom

institute: University College London

description: 10x Genomics

data_processing:
Raw sequencing files were demultiplexed using BCL Convert v3.7.5 (Illumina) or Cell Ranger version 6.1.1 using the “mkfastq” script. Transcript alignment and quantitation against the GRCh38 human genome assembly was performed using Cell Ranger “multi” for samples with gene expression and T cell VDJ data or Cell Ranger “count” for samples with gene expression data only.
Assembly: GRCh38
Supplementary files format and content: .h5 files are raw count matrices generated by Cell Ranger count or multi, rows are features and columns are cells; .csv files are TCR contig and clonotype annotations generated by Cell Ranger multi.

source_name: Bronchoalveolar cells

extract_protocol:
Flexible fibreoptic bronchoscopy was used to obtain bronchoalveolar lavage (BAL) samples by instillation of up to 240 ml of warmed normal saline into a lung segment affected by the predominant radiological abnormality. Aspirated BAL fluid was cooled to 4°C and filtered through a cell strainer to remove particulate debris before centrifugation. After removal of the supernatant, cells were resuspended in PBS. Cell count and viability were determined by Trypan blue staining and erythrocytes removed where indicated, using red cell lysis buffer. Cells were resuspended at 2 x10^6 per ml for downstream processing. 20,000 cells per sample were loaded on to the Chromium controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs).
Single-cell partitioning, reverse transcription, cDNA amplification and library construction were performed using the Chromium Single-cell 5’ Reagent kits v1.1 and v2 (10x Genomics) according to the manufacturer’s instructions. T cell receptor (TCR) V(D)J segments were enriched from amplified cDNA using Chromium Single-Cell V(D)J Enrichment kits v1.1 and v2 (10x Genomics) per the manufacturer’s protocol.

value: Bronchoalveolar cells

value: Post-COVID-19 lung disease

tag: radiology

value: Inflammatory


title: Donor 1 NTHi  infected Day 1

description:
D1_day1
NTHi_RPKM.txt
NHNE_RPKM.txt

value: NHNE


title: WT cells, 4hr LipidA [Exp4_4hr_rep1 ATAC-seq]

extract_protocol:
Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.


title: Ab_IR_HSC_rep1


title: WT cells, 0hr LipidA [Exp4_0hr_rep2 ATAC-seq]

value: 0hr LipidA


title: PCLD8, scRNAseq

description: 10x Genomics

value: Fibrotic


title: WT cells, 0hr LipidA [Exp4_0hr_rep1 ATAC-seq]


title: IR_HSC_rep3

value: IR


title: dBrd9 treated cells, 4hr LipidA [Exp3_4hr_dBrd9_rep2 ATAC-seq]

value: dBrd9 treated

value: 4hr LipidA


title: PCLD7, scRNAseq

description: 10x Genomics


title: IR_HSC_rep2


title: DGM-00093_HIV_am

value: smoker

value: alveolar macrophage


title: DGM-00020_HIV_am


title: dBrd9 treated cells, 4hr LipidA [Exp3_4hr_dBrd9_rep1 ATAC-seq]


title: DGM-00087_HIV_am


title: Donor 5 Day 0

description:
D5_day0
NHNE_RPKM.txt

value: human

value: wt

value: uninfected


title: qNHA cells, WGBS, DMSO, BR1

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Raw sequencing reads are trimmed using TrimGalore (v.0.6.1) with "-a AGATCGGAAGAGC".
Bismark (v.0.22.0) was used to prepare bisulfite-converted hg38 reference genome and to align trimmed reads to the prepared genome (-X 2000 --nucleotide_coverage).
Uniquely mapped, deduplicated reads were retained.
hg38
bed (methylC)

source_name: brain

extract_protocol:
We extracted genomic DNA with Quick-DNA Miniprep Kit (Zymo, D3024)
We bisulfite converted 200-400 ng of DNA spiked with 0.5% lambda DNA using EZ DNA Methylation-Direct kit (Zymo, D5020). For WGBS, we processed the bisulfite- converted DNA with Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024).

value: brain

value: HA

value: Human Astrocytes

value: DMSO


title: Ctrl_HSC_rep3

value: Bone marrow

value: Hematopoietic stem cell

value: WT

value: Ctrl


title: WT cells, 4hr LipidA [Exp3_4hr_Ctrl_rep1 ATAC-seq]

first: Jingwen

last: Liao

address: 10010 N Torrey Pines Rd

institute: Salk Institute

value: BMDM


title: WT cells, 4hr LipidA [Exp3_4hr_Ctrl_rep2 ATAC-seq]


title: qNHA cells, WGBS, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: qNHA cells, WGBS, DMSO, BR2


title: Ctrl_HSC_rep2


title: WT cells, 1hr LipidA [Exp3_1hr_Ctrl_rep2 ATAC-seq]

value: 1hr LipidA


title: qNHA cells, WGBS, DACPano, BR1


title: qhFB cells, WGBS, DMSO, BR2

source_name: skin

value: skin

value: HDFa

value: primary dermal fibroblast


title: DGM-00130 [gene_expr]

source_name: small airways

value: smoker

tag: disease status

value: healthy


title: WT cells, 1hr LipidA [Exp3_1hr_Ctrl_rep1 ATAC-seq]


title: IR_HSC_rep1

value: IR


title: DGM-00242 [gene_expr]


title: DGM-01270_hRBC_sm

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

tag: department of genetic medicine id

value: NS

tag: serum 25-oh-d

value: mid vitamin D


title: MEF PEDF (experiment 2)

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

country: Japan

institute: National Center for Geriatrics and Gerontology

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version 1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
The raw read counts were normalized with transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including TPM values for each sample

source_name: Embryonic fibroblasts

growth_protocol: MEF (passage 2) were maintained in DMEM supplemented with 10% fetal bovine serum, non-essential aminoacids and antibiotics in humiditified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA were extracted using NucleoSpin RNA (Maccherey Nagel), and poly A were purified form the total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module.
RNA libraries were prepared using NEBNext UltraTMII Directional RNA Library Prep Kit.

treatment_protocol: Cells were treated or untreated with 100 ng/mL of PEDF purified from mammalian cells for 24h.

value: Embryonic fibroblasts

value: Wild-type

value: Experiment_2 PEDF


title: qhFB cells, WGBS, DMSO, BR1

value: DMSO


title: WT cells, 0hr LipidA [Exp3_0hr_Ctrl_rep2 ATAC-seq]

city: La Jolla

value: WT

value: 0hr LipidA


title: MEF control (experiment 2)

value: Experiment_2 control


title: Donor 5 NTHi infected Day 3

description:
D5_day3
NTHi_RPKM.txt
NHNE_RPKM.txt

value: NHNE

value: human

value: wt

value: infected


title: DGM-10126 [gene_expr]

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College

value: nonsmoker


title: Arid1a-/- cells, 4hr LPS [Exp2_4hr_ARID1AKO_rep1 RNA-seq]

description: strand specific polyA+ RNA

value: BMDM

value: 4hr LPS


title: WT cells, 0hr LipidA [Exp3_0hr_Ctrl_rep1 ATAC-seq]


title: DGM-00701 [gene_expr]

value: smoker

value: healthy


title: Arid1a-/- cells, 4hr LPS [Exp2_4hr_ARID1AKO_rep2 RNA-seq]

description: strand specific polyA+ RNA


title: Arid1a-/- cells, 4hr LipidA [Exp2_4hr_ARID1AKO_rep1 ATAC-seq]

value: 4hr LipidA


title: DGM-02160 [gene_expr]


title: MEF control (experiment 1)

value: Embryonic fibroblasts

value: Experiment_1 control


title: Ctrl_HSC_rep1

value: Bone marrow

value: Hematopoietic stem cell

value: Ctrl


title: qhFB cells, WGBS, DACPano, BR1

value: skin

value: HDFa

value: primary dermal fibroblast

value: 1uM DAC 6 days, 100nM Pano 2 days


title: DGM-01134 [gene_expr]


title: DGM-01721 [gene_expr]


title: BRM014 treated cells, 4hr LipidA [Exp2_4hr_BRM014_rep1 ATAC-seq]

value: BRM014 treated


title: NHA cells, WGBS, DMSO, BR2

value: brain

value: HA

value: Human Astrocytes

value: DMSO


title: DGM-00355 [gene_expr]

value: smoker


title: DGM-01155 [gene_expr]

value: disease


title: NHA cells, WGBS, DMSO, BR1


title: MEF PEDF (experiment 1)

value: Wild-type

value: Experiment_1 PEDF


title: AOM/DSS WT - biol rep 6

city: Bonn

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

country: Germany

institute: University Clinics Bonn

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software:
Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Pre-alignment QA/QC - Version 10.0.21.1116
Alignment STAR - 2.5.3a - Version 10.0.21.1116
Post-alignment QA/QC - Version 10.0.21.1116
Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Gene counts were normalized
Gene Set Analysis was performed from normalized reads comparing AOM/DSS treated vs. naive
Gene list was filtered for significance (p<= 0.05)
Assembly: mm10 Ensembl Transcripts release 102
Supplementary files format and content: Excel with differentially expressed genes between naive and AOM/DSS treated samples with p<0.05

source_name: colon tissue

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using QuantSeq 3'-mRNA Library Prep Kit (Lexogen) following the manufacturer's instructions

treatment_protocol: Mice either underwent the AOM/DSS model or kept under naive conditions for the corresponding time span. For AOM/DSS treatment, mice were injected with an intraperitoneal injection of AOM at 10 mg/kg bodyweight on day 0. On day 7, mice received 1.5% dextran-sodium sulfate (DSS) in drinking water for 5 days, followed by 16 days of recovery. Mice underwent 3 DSS cycles in total in the same manner. After the last DSS cycle + recovery phase, mice were sacrificed on day 70.

value: colon tissue

tag: Sex

value: female

value: wildtype

value: AOM/DSS


title: NHA cells, WGBS, DACPano, BR2


title: WT cells, 4hr LipidA [Exp2_4hr_Ctrl_rep1 ATAC-seq]

value: BMDM

value: WT

value: 4hr LipidA


title: DGM-01088 [gene_expr]

city: New York

tag: smoking status


title: WT cells, 0hr LipidA [Exp2_0hr_Ctrl_rep1 ATAC-seq]

value: 0hr LipidA


title: AOM/DSS WT - biol rep 5


title: DGM-01052 [gene_expr]


title: AOM/DSS WT - biol rep 4


title: BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep2 ATAC-seq]

value: BRDK98 treated


title: hFB cells, WGBS, DMSO, BR2

value: skin

value: HDFa

value: primary dermal fibroblast


title: AOM/DSS WT - biol rep 7


title: AOM/DSS WT - biol rep 3


title: ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep2 ATAC-seq]

value: ACBI1 treated


title: hFB cells, WGBS, DMSO, BR1

value: DMSO


title: BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep1 ATAC-seq]


title: AOM/DSS WT - biol rep 2


title: DGM-01009 [gene_expr]

value: smoker

value: disease


title: hFB cells, WGBS, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: DGM-00702 [gene_expr]

source_name: large airways

value: healthy


title: NHA cells, WGBS, DACPano, BR1

value: brain

value: HA

value: Human Astrocytes


title: DGM-10410 [gene_expr]


title: ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep1 ATAC-seq]

value: BMDM


title: AOM/DSS WT - biol rep 1

value: colon tissue

value: female

value: wildtype

value: AOM/DSS


title: DGM-00595 [gene_expr]


title: hFB cells, WGBS, DACPano, BR1

value: skin


title: WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep2 ATAC-seq]

value: WT

value: 4hr LipidA


title: B66 cells, WGBS, DMSO, BR2

value: glioblastoma stem cell


title: WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep1 ATAC-seq]


title: naive WT - biol rep 3

value: naive


title: naive WT - biol rep 4


title: B66 cells, WGBS, DACPano, BR2


title: WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep1 ATAC-seq]

value: 0hr LipidA


title: WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep2 ATAC-seq]


title: B66 cells, WGBS, DMSO, BR1

value: DMSO


title: B66 cells, WGBS, DACPano, BR1

value: 1uM DAC 6 days, 100nM Pano 2 days


title: Retina, ONC, MBV_3

city: Pittsburgh

first: Takaaki

last: Kuwajima

address: 1622 Locus Street, 7.396

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

description:
[Matrix Bound Nanovesicles] [Optic Nerve Crush] [3]
MBV vs. Control.csv
MBV3_S6

data_processing:
FASTQ files were analyzed using CLC Genomics Grid Workbench v22.0.2.
For RNA sequencing analysis, sequenced reads were aligned to the mouse genome (GRCm39).
Parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Transcripts with at least 10 read events in two samples of either treatments or control PBS with a p-value lower than 0.05 among three were collected for further analysis.
Assembly: mm39
Supplementary files format and content: Each .csv file contains: Chromosome, Region, Max group mean, Log2 fold change, Fold change, P-value, FDR p-value, & Bonferroni for each gene name as well as the read number for the three experimental samples of a particular treatment and the three control as well as the average for each treatment.
Supplementary files format and content: The supplementary file contains all the .csv procesed data with extra formatting to enhance readability. This file is organized with each .csv file as a new page in the .xlsx workbook with all genes sorted by lowest to highest p-value.

source_name: Retina

extract_protocol:
Injured retinas treated with fluvastatin, MBVs, PBS or a combination of fluvastatin and MBVs in WT mice two days after ONC were collected, and RNA was extracted using TRIzol RNA isolation reagent.
Library preparation was conducted with TruSeq Total RNA library kit (Illumina) using at least 1 mg of total RNA following the manufacture’s instruction.
Libraries were sequenced using NextSeq500 (Illumina) with 75 base paired end reads resulting in 40M reads per sample.

treatment_protocol: The optic nerve in the left eye was crushed using #5 Dumont forceps, applying pressure for 5s at ~1 mm behind the optic disc in 8 week-old C57BL/6J mice. Single intravetral injection of MBVs, Fluvastatin, MBVs and a combination of MBVs and Fluvastatin, or PBS (Control) were administered after optic nerve crush. Tow days after injury, the whole retina were collected for collection of RNA and further RNA-seq anaysis.

value: Retina

tag: age

value: 8-10 weeks old

tag: protocol

value: optic nerve crush

value: MBV


title: naive WT - biol rep 2


title: HSC_IGF1 rep3

first: Weinian

extract_protocol:
HSCs were sorted from the BM of control or IR mice.RNA was extracted from sorted cells using a RNeasy Micro Kit (QIAGEN) following the manufacturer's procedure. The RNA amount and purity were quantified using NanoDrop ND-1000 (NanoDrop).
Libraries for RNA-seq were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Bone marrow

value: hematopoietic stem cell


title: Retina, ONC, MBV_2

description:
[Matrix Bound Nanovesicles] [Optic Nerve Crush] [2]
MBV vs. Control.csv
MBV2_S5


title: HSC_IGF1 rep2


title: B49 cells, WGBS, DMSO, BR1

value: brain


title: HSC_IGF1 rep1


title: DGM-00254 [gene_expr]

value: smoker

value: disease


title: DGM-00428 [gene_expr]

value: healthy


title: DGM-00601 [gene_expr]


title: B49 cells, WGBS, DACPano, BR2


title: DGM-00453 [gene_expr]


title: DGM-00130_lg [gene_expr]


title: Retina, ONC, Fluvastatin_3

description:
[Fluvastatin] [Optic Nerve Crush] [3]
Fluvastatin vs. Control.csv
Fluv3_S3

value: Fluvastatin


title: DGM-00132 [gene_expr]


title: HSC_Ctrl rep2

value: WT

value: control


title: B36 cells, WGBS, DMSO, BR2

value: glioblastoma stem cell


title: B49 cells, WGBS, DACPano, BR1


title: Retina, ONC, Fluvastatin_1

description:
[Fluvastatin] [Optic Nerve Crush] [1]
Fluvastatin vs. Control.csv
Fluv1_S1


title: Retina, ONC, Fluvastatin_2

description:
[Fluvastatin] [Optic Nerve Crush] [2]
Fluvastatin vs. Control.csv
Fluv2_S2


title: B36 cells, WGBS, DMSO, BR1


title: HSC_Ctrl rep1


title: Retina, ONC, MBV_1

description:
[Matrix Bound Nanovesicles] [Optic Nerve Crush] [1]
MBV vs. Control.csv
MBV1_S4


title: HSC_Ctrl rep3


title: Liver_Lpcat3_NASH_4 [1345R]

city: Urbana

first: Ye

last: Tian

address: 2001 South Lincoln Avenue, room 3612

department: Comparative Biosciences

institute: University of Illinois ar Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
The Fastq files were then mapped to the GRCm39 mouse genome from GENCODE using STAR2.7.10b
The count matrix were generated using Rsubread and the differentially expressed genes were analyzed using DESeq2
Assembly: GRCm39
Supplementary files format and content: csv file (read count table)

source_name: Liver

extract_protocol:
RNA were extracted from frozen liver samples using TRIzol following manufacturer's instruction. Ribosomal RNA was removed with the FastSelect HMR kit (Qiagen).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNAseq Sample Prep kit' (Roche). The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000.

value: Liver


title: DGM-00764_Tr

source_name: Trachea

value: S


title: DGM-00641_Tr


title: DGM-00626_Tr


title: DGM-00613_Tr


title: DGM-00567_Tr


title: B36 cells, WGBS, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: B49 cells, WGBS, DMSO, BR2

value: DMSO


title: DGM-00537_Tr


title: B36 cells, WGBS, DACPano, BR1


title: DGM-00515_Tr


title: Retina, ONC, Fluvastatin + MBV_1

description:
[MBV + Fluvastatin] [Optic Nerve Crush] [1]
MBV+F vs. Control.csv
Flu+MBV_1_S4

value: Retina

value: 8-10 weeks old

value: Fluvastatin + MBV


title: Liver_Lpcat3_NASH_3 [1344R]


title: Retina, ONC, Control_2

description:
[PBS] [Optic Nerve Crush] [2]
MBV+F vs. Control.csv
CTR_2_S2

value: optic nerve crush

value: PBS (control)


title: Ivermectin-treated, scRNAseq

description: 10x Genomics

data_processing:
The gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: H5 files and count matrix files

source_name: Triple-negative breast cancer

growth_protocol: Patient-derived xenograft (PDX) models were generated using dissociated tumor cells obtained from a patient with triple-negative breast carcinoma. Tumor cell suspensions were mixed (1:1) with Matrigel (Corning) and implanted into the mammary fat pad of 6-8 week old female NOD (NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ) SCID gamma (NSG) mice (Jackson Labs, Strain #005557).

extract_protocol:
Tumors were resected and stored in cold DMEM media on ice for transport. After necrotic tissue was removed using a scalpel, the samples were minced and dissociated in a gengleMACS Octo (Miltenyi, 130-096-427) to single-cell suspension using a human tumor dissociation kit (Miltenyi, 130-095-929) at 37C per the manufacturer's instructions with the following change: samples were checked after 30 min and the protocol was terminated if chunks of undissociated tissue were not visible. If a significant amount of undissociated sample remained, the program was run for 15min additional time. After dissociation, the samples were filtered through a 100uM strainer, the cells pelleted, the supernatant removed, and red blood cells were lysed using RBC lysis buffer (Invitrogen, 50-112-9751). RBC lysis buffer was diluted in DMEM, and the cells were washed prior to mouse cell depletion using magnetic beads (Miltenyi, 130-104-694).
The resulting suspension of human tumor cells was adjusted to a concentration appropriate for loading into a 10X genomics Chromium controller (3’ gene expression kit, #120267) with an expected output of 7,000 cells/sample. Samples were run in separate wells and libraries constructed according to the manufacturer’s instructions. Libraries were sequenced on an Illumina Novaseq 6000, aiming for approximately 100,000 reads/cell.

treatment_protocol: Treatments were initiated when TV was ~350-400 mm3 to enable collection of sufficient tumor material for analysis. Paclitaxel was formulated in sterile saline and dosed at 25 mg/kg intravenously every week. Ivermectin was formulated in 10% (v/v) NMP (N-methylpyrrolidone, Sigma) and 45% (w/v) cyclodextrin in sterile water and dosed at 3.3 mg/kg intraperitoneal 1 daily. Albendazole was formulated in 10% (v/v) DMSO (dimethylsulfoxide), 0.5% (w/v) carboxymethylcellulose, and 1% (v/v) Tween 80 in sterile water and dosed at 50 mg/kg IP 3 times weekly. The animals (n=2/arm) were treated for 15 days and tumors harvested 2 hours after administration of the last dose of vehicle or drug.

value: Triple-negative breast cancer

value: Ivermectin


title: Retina, ONC, Fluvastatin + MBV_3

description:
[MBV + Fluvastatin] [Optic Nerve Crush] [3]
MBV+F vs. Control.csv
Flu+MBV_3_S6


title: Liver_Lpcat3_NASH_2 [1344L]


title: Albendazole-treated, scRNAseq

description: 10x Genomics

value: Albendazole


title: Retina, ONC, Fluvastatin + MBV_2

description:
[MBV + Fluvastatin] [Optic Nerve Crush] [2]
MBV+F vs. Control.csv
Flu+MBV_2_S5


title: Paclitaxel-treated, scRNAseq

description: 10x Genomics

value: Paclitaxel


title: Retina, ONC, Control_3

description:
[PBS] [Optic Nerve Crush] [3]
MBV+F vs. Control.csv
CTR_3_S3


title: Liver_eGFP_NASH_2 [1290N]

description: 1290N_TACTCCACGG-GTTCTCATAG_L001_R1_001.fastq

value: eGFP


title: DGM-00446_Tr


title: DMSO-treated, scRNAseq

description: 10x Genomics


title: Liver_eGFP_NASH_1 [1290L]


title: Liver_eGFP_NASH_3 [1317N]


title: Retina, ONC, Control_1

description:
[PBS] [Optic Nerve Crush] [1]
MBV+F vs. Control.csv
CTR_1_S1


title: Liver_eGFP_NASH_4 [1345N]


title: END-seq, CPT 20 µM, Rep2

data_processing:
library strategy: END-seq
Adaptor sequences of paired-end reads in fastq format were trimmed, using Trim Galore.
Reads were aligned to the GRCh37 (hg19) reference human genome and to GRCm38 (mm10) reference mouse genome, using Bowtie2, default settings. Only properly-paired reads with MAPQ ≥ 30 were kept, including duplicated reads, using Samtools .
Prior peak calling, aligned paired-end reads in BAM format were splitted according to first-in pair orientation, so to potentially discriminate reads aligned on the left side (F2R1- reverse- minus strand) and on the right side (F1R2- forward-plus strand) respect with the DSB.
Peak calling was performed using MACS2 and using control samples as “input”.
Peak calling was performed separately for each replicate and according to first-in-pair reads orientation, using the parameters --nomodel --nolambda -q 0.05 --keep-dup all -f BAMPE as previously described in .
Assembly: hg19
Supplementary files format and content: .bw file contain the normalized genomic level of END-seq signal
Supplementary files format and content: .narrowPeak file contain the output of MACS peak caller in BED format

growth_protocol: HCT116 cells were cultured in a humidified incubator at 5% of CO2 and 37°C in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (FBS). Spike in pre-B murine cells: DMEM complemented with 10% FBS, 2mM L-Glutamine, 100 mg/ml Pen/Strep, 1mM Sodium Pyruvate, 1X NEAA, and 55 mM b-mercaptoethanol

extract_protocol:
Cells were embedded in agarose plugs and, after proteinase K and RNase A digestion, DSBs are recovered by ligation of a biotinylated adapter. DNA is then extracted from plug and sheared by sonication. Sheared fragments containing the biotinylated adapter are captured with streptavidin-coated beads. A second adapter is ligated to the other end of the fragments and library amplified with Illumina barcoded p5 and p7.
End-Seq libraries were prepared incorporating Illumina barcoded p5 and p7 with KAPA HiFi HotStart Ready Mix by PCR. All the recovered DNA fragments were used for amplification. Libraries were amplified using 16 cycles on the thermocycler.

treatment_protocol: Cells are treated for 10 or 20 minutes with Camptothecin 10 micromolar

value: Human epithelial colorectal carcinoma

value: CPT 20 µM


title: PMCRC19_PT_RNA-seq

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts.

source_name: Primary colorectal tumor

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed  by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation  reactions into a single step that greatly increases the efficiency of the library preparation process.  Adapter-ligated fragments are then PCR amplified and gel purified.

tag: subject

value: Primary colorectal tumor

tag: histologic type


title: Liver_Lpcat3_NASH_1 [1290B]

value: Liver


title: END-seq, CPT 20 µM, Rep1


title: PMCRC18_MT_RNA-seq

source_name: metastasized tumor into peritoneal

value: metastasized tumor into peritoneal


title: END-seq, CPT 10 µM, Rep2

value: CPT 10 µM


title: PMCRC18_PT_RNA-seq


title: END-seq, CPT 10 µM, Rep1