title: Differentiation day 25

data_processing:
Raw 10X single-cell RNA-seq data from three time points (expansion, early differentiation, and late differentiation) were demultiplexed, aligned (GRCm38), and feature-counted by Cellranger using the default settings
Cell barcode processing, feature-barcode matrix were generated by cellranger.
Genome_build: hg38
Supplementary_files_format_and_content: csv files (barcodes.csv.gz, features.tsv.gz.gz) and mtx.gz files (matrix.mtx.gz.gz)

extract_protocol:
Organoids from passage 2 (day 8) in expansion medium, from differentiated day 5, and from differentiated day 25 were collected and incubating with 0.125% trypsin for 25 min and dissociated into single cells by mechanical pipetting. Nuclei were stained with DAPI (Sigma) on ice for 10 minutes, then cells were sorted using a MoFlo® SX FACS cytometer (Beckman Coulter). Sorted single, living cells were resuspended in 40 mL of fresh cell media.
Single-cell transcriptomic profiling was performed using the Single Cell 3’ Reagent v3 kits according to the manufacturer’s recommendations (10X Genomics

value: Organoids derived from cochlear progenitor cells

value: Lgr5+ progenitor cells were initially expanded in 3D culture system in expansion medium based on DMEM/F-12, GlutaMAX culture medium, supplemented with penicillin/streptomycin, N2, B27, EGF (20 ng/mL), bFGF (10 ng/mL), and IGF (50 ng/mL), CHIR99021 (3um), Y27-632  (10um) and LPA (2.5um) and then shifted to differentiation medium composed of bFGF, BDNF, Shh, A83-01, RA, and LY4115775 during the initial 5 days, and removed LY4115775 aterward


title: KO_1

status: Public on Jul 21 2024

type: SRA

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

library_source: transcriptomic

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow monocytes

extract_protocol:
Rank_cre mice, previously described (Maeda K, et al., Nature Medicine 18, 405-412, 2012), were generously provided by Prof. Kobayashi (Matsumoto Dental University). Sik3_flox mice, also previously described (Yahara Y, et al., Nature Communications 7, 10959, 2016), were provided by Prof. Tsumaki (Osaka University). Bone marrow monocytes from C57BL/6J, Rank_Cre/+, and Rank_Cre/+; Sik3_flox/flox mice were seeded at a density of 2x10⁵ cells/well in 6-well plates and cultured in α-MEM with 50 ng/ml M-CSF for two days. After the initial incubation, the cells were further cultured for two days with 50 ng/ml M-CSF and RANKL.    C57BL/6J mice were obtained from Japan SLC Inc. Bone marrow cells were isolated from mice and seeded in 10 cm dishes. One day after seeding, non-adherent bone marrow cells were re-seeded at a density of 20,000 cells per well in a 48-well plate. The cells were cultured in α-MEM with 10% FBS containing 50 ng/ml M-CSF (Peprotech) for two days to differentiate into bone marrow monocytes. Subsequently, the cells were cultured in the presence of 50 ng/ml RANKL and 50 ng/ml M-CSF for three days to induce osteoclast differentiation. Pterosin B was synthesized by i-Chemical Lab Corporation, Japan, as previously described (Yahara Y, et al., Nature Communications 7, 10959, 2016). Bone marrow monocytes were differentiated into mature osteoclasts with or without pterosin B at final concentrations of 300 μM.    Total RNA was extracted using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: Bone marrow

tag: genotype

value: osteoclast-specific Sik3 conditional knockout


title: THP-1 cells, si-NC, CSE for 48h_2

city: Guangzhou

first: Erkang

last: Yi

state: Guangdong

address: 195 Dongfeng Xi Road

department: State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
Sequencing fragments are randomly broken from mRNA. To determine which regions on the genome these fragments correspond to, we used HISAT2 software to align the quality controlled clean data reads to the reference genome (parameter: -- dta (preparation for downstream assembly), generating. sam or. bam files that contain alignment records between clean data reads and the genome. We then used the Qualimap RNA seq software process to evaluate the comparison situation (parameter: -- paid)
Calculate the gene count (gene_count. xls) using the featureCounts software in the subRead package, with the key calculation parameters being - p - t exon - g gene_id. The count here refers to the fragment count, which means that a pair of reads are counted as a whole (fragment).
Using gene_count.xls as input, genes with a detection rate (proportion of count not 0) less than 0.25 were screened out. The corrected expression levels of gene_deseq2.xls and geneuedger-TMM.xls were calculated using R language DESeq2 package and edgeR package [, respectively; These two expression tables can be used to compare the expression differences between samples or groups, but cannot be used to compare the expression differences between genes. Please note that these two files cannot be used as direct input files for DESeq2 and edger, nor can they be used to calculate FoldChange for DESeq2 and edger. DESeq2 and edger can only use gene_count.xls as input files, as they have already encoded the calibration process into the model. Please refer to the formula in the literature for the calculation of TPM
Assembly: hg38

organism: Homo sapiens

source_name: Thp-1 cells

growth_protocol: THP-1 cells, sourced from Procell (Wuhan, China), were cultured in RPMI-1640 medium enriched with 0.05 mM β-mercaptoethanol, 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin/streptomycin (P/S, Invitrogen, USA).

extract_protocol:
Total RNA was isolated from lung tissues and cells using the SteadyPure RNA kit (AG21022, AG, China) following an established protocol
After the construction of the library is completed, initial quantification is performed using Qubit2.0 Fluorometer to dilute the library to 1.5ng/ul. Then, Agilent 2100 bioanalyzer is used to detect the insert size of the library. Once the insert size meets expectations, qRT PCR accurately quantifies the effective concentration of the library (the effective concentration of the library is higher than 2nM) to ensure the quality of the library.

treatment_protocol: Differentiation into M0 macrophages was induced with 100 ng/ml phorbol 12-myristate 13-acetate (PMA), following established protocols.

tag: cell line

value: Thp-1 cells

tag: cell type

value: mononuclear macrophage

value: WT

tag: treatment

value: PMA and CSE stimulated


title: Patient_4 pre-AZA

city: NY

first: Christopher

middle: Y.

last: Park

address: 550 First Avenue

country: USA

institute: NYU Grossman School of Medicine

data_processing:
Following demultiplexing, data quality control, alignment, and generation of a read count matrix, DESeq2 was used for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab limited text file contains raw count for each sample

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were isolated from BM samples using Ficoll-Paque Plus (GE Healthcare, Massachusetts, US) density gradients per manufacturer’s instructions. CD34+ cells were isolated by immunomagnetic separation using an autoMACs Pro Separator (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) following the manufacturer´s instructions. Sorted cells were snap-frozen and stored at -80ºC. Total RNA was extracted using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol. RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Assay kit. RNA quantities were assessed by qubit 2.0 (ThermoFisher Scientific, Massachusetts, U.S.A.) using an RNA kit (high/broad sensitivity).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech, California, U.S.), and sequenced on a HiSeq400 sequencer (Illumina) according to manufacturer´s protocol with a read length of 2 × 150 nucleotides.

value: Bone marrow mononuclear cells (BMMCs)

value: CD34+ HSPC

value: no treatment


title: Patient_4 post-AZA

value: AZA treatment


title: P_432_5

city: tartu

first: Maire

last: Peters

department: Dept. of Obstetrics and gynecology

country: Estonia

institute: University of Tartu

library_source: transcriptomic single cell

data_processing:
barcode processing, sequence alignment, gene counting and aggregation was done using Cellranger software v7.0.0
Seurat R package was used to preprocessing, quality control/checks, sample integration, clustering analysis.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: tsv, mtx and rds files

source_name: Ectopic endometrium

extract_protocol:
Cryopreserved samples of EuE and EcE were enzymatically dissociated to obtain single-cell suspensions with viability >90%.
ScRNA libraries were constructed using 10X chromium Next GEM Single cell 3′ reagent v3.1 kit.

value: Ectopic endometrium

tag: condition

value: peritoneal lesions from ectopic endometrium


title: WT_2

value: wild type control


title: Lane F, P3-9-11-24-30, scRNAseq

city: New York

first: Rachel

last: Glenn

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Raw sequencing read data were processed using the Dropseq computational pipeline with default parameters. Raw reads were aligned to the Mouse reference genome GRCm38 with, giving a matrix representing unique molecular identifers (UMI’s) per cell barcode per gene. To demultiplex the donor pool, we used VCF files containing genotype information as input for the Dropseq AssignCellsToSamples function. Based on the output from Dropseqs DetectDoublets function, we developed a custom assignment method. By applying the Rosner Test for outliers and analyzing the absolute distances of previously calculated donor likelihoods, we categorized each cell as a singlet or doublet. Only singlets were utilized for downstream analysis. The raw UMI matrices for each sample were processed using R v4.3.1 with the Seurat package v5.0.1. Matrices were filtered to remove cells with less than 200 genes detected and cells with >10% of reads mapping to mitochondrial RNA. Data from all samples was then integrated to combine and account for batch effects using the IntegrateLayers function using CCAIntegration as integration method.
Unsupervised clustering: The top 2k  most variably expressed genes were used for dimensionality reduction, firstly by principal component analysis (PCA) and subsequently by uniform manifold projection (UMAP), selecting PCs 1:20 that explained the majority of the variance observed (assessed by elbow plots). A shared nearest-neighbour graph was constructed in PCA-space using PCs 1:20 with Seurat FindNeighbors function. Clusters are identifed within
this graph using Seurat FindClusters function, optimizing the modularity with the Louvain algorithm. The resolution parameter to control cluster granularity was manually selected at 0.5. Cluster marker genes were identifed with FindAllMarkers function only testing genes that are detected in a minimum fraction of 0.1 cells and using a logFC cutoff of 0.1. Pseudo-bulk expression was generated using Seurat AggregateExpression function and counts were log-normalized before downstream analysis. Limma removeBatchEffect effect was utilized to account for lane dependent batch effects.
Differential gene expression analysis: Genes differentially expressed between groups were identifed per cluster using Seurats fndMarkers utilizing Wilcoxon Rank Sum test with default parameters.
Assembly: GRCm38

source_name: EpiSC

extract_protocol:
EpiSCs were collected using collagenase and Accutase as per the EpiSC 48 hours post-thaw. The resulting cell suspension was used for 10x scRNA-seq (10x Genomics, Single Cell 3′ Kit v3.1, dual index) following the manufacturer's directions. We combined four cell villages in equal number to a total of 30,000 cells per sequencing channel.
We targeted a sequencing depth of 40,000 reads per cell (1.2e9 total reads per sequencing channel) for genetic demultiplexing. Libraries were prepared according to manufacturer's instructions (10x Genomics, Single Cell 3′ Kit v3.1, dual index).

value: EpiSC

value: Diversity Outbred


title: WT indisulam 1

city: Hiroshima

first: Toshinori

last: Ando

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University Hospital

data_processing:
For each sample, paired-end sequencing reads were mapped using HISAT2 version 2.1.0 to the hg38 reference human genome downloaded from Ensembl
To compute transcript abundance, uniquely mapped reads were quantified using featureCounts version 1.6.3.
Assembly: hg38 reference human genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

extract_protocol:
RNA was harvested by using Rneasy mini kit (Qiagen). One μg of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTMII Directional RNA Library Prep Kit following manufacture's protocol.

value: head and neck squamous cell carcinoma

value: LATS1/2 KO

value: indisulam


title: WT_3

value: Bone marrow


title: P_398_4


title: P_002_4


title: Patient_3 post-AZA


title: Patient_5 pre-AZA


title: E_432_1

source_name: Eutopic endometrium

value: Eutopic endometrium

value: eutopic endometrium


title: Patient_5 post-AZA


title: Patient_3 pre-AZA


title: Patient_2 post-AZA


title: CMML_Non_cachexia2_Inf_Mo_bulkRNAseq

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.0)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Assembly: mm10
Supplementary files format and content: raw counts with genes in rows and samples in columns

source_name: Ly6Chigh BM monocytes

extract_protocol:
Bone marrow cells were harvested from individual mice. Ly6C+CD115+ monocytes were then FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ly6Chigh BM monocytes

tag: disease state

value: CMML without cachexia


title: Patient_2 pre-AZA

value: Bone marrow mononuclear cells (BMMCs)


title: E_398_1


title: Lingo1 KO MLE-12 cells, unscratched

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

data_processing:
base-calling with Illumina basespace FASTQ generation (1.0.0)
reads trimmed to remove adapters using Trimmomatic  (0.39)
reads aligned usings STAR (2.7.9a)
reads counted using htseq-count (0.11.3)
counts filtered to remove genes with less than 5 counts per condition, using R (4.0.2), counts normalized and RPKM calculated using edgeR (3.32.1)
Genome_build: mm10
Supplementary_files_format_and_content: tables of count or normalized count (RPKM) values for each gene as text (.tsv) files

source_name: mouse alveolar epithelial cell line, MLE-12

extract_protocol:
RNA extracted with Qiagen RNAeasy plus kit
Illumina stranded mRNA-seq library prep

value: Lingo1 KO

value: unscratched


title: CMML_Non_cachexia1_Inf_Mo_bulkRNAseq


title: Lane C, P2-5-11-25-30, scRNAseq

description: 10X Genomics


title: Lingo1 KO MLE-12 cells, 24 hours post-scratch

value: 24 hours post scratch


title: WT_1


title: CMML_cachexia1_Inf_Mo_bulkRNAseq

value: CMML with cachexia


title: Patient_1 post-AZA

value: CD34+ HSPC

value: AZA treatment


title: Patient_1 pre-AZA

value: no treatment


title: Lane E, P1-2-6-26-28, scRNAseq

description: 10X Genomics

value: EpiSC

value: Diversity Outbred


title: E_002_1


title: Ctrl2_Inf_Mo_bulkRNAseq

value: control


title: Marjolin ulcer

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: Recovered cells: 40,000 cells

data_processing:
All raw FASTQs reads were aligned to Homo sapiens (GRCh38) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Assembly: Homo_sapiens : GRCh38
Supplementary files format and content: Filtered gene - barcode matrix output from CellRanger

extract_protocol:
The subject was recruited through a tertiary outpatient burn clinic. The Health Research Ethics Board of Alberta Cancer Committee determined that a full ethics review was not necessary for the study because the samples harvested (scar tissue and Marjolin's ulcer tumor tissue) were considered surgical wastes (HREBA.CC-23-0003). Following post-surgical harvest, samples were minced and incubated in dispase (StemCell Technologies) for 10-15 minutes at 37°C to remove epidermis. Remaining dermis tissue was minced and digested using collagenase (0.2%, Sigma) in 37 degree C water bath for 1-3 hours. To further dissociate the tissue and liberate single cells, DNase I (1x - Sigma) was added to the tissue for the last 30 minutes in the water bath. Single cell suspensions were resuspended in cold FACS staining buffer (1% bovine serum albumin in Hank’s Buffered Salt Solution, HBSS;Life Technologies), strained through 100 µm and 70 µm filters (Falcon) and centrifuged at 1200 rpm for 6 minutes. Cell pellets were resuspended in FACS staining buffer and quantified. Viability dye eFlour780 (eBiosciences) was used to exclude dead cells using FACSAria III (BD Biosciences).
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

tag: subject

value: Marjolin ulcer

tag: facs strategy

value: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3


title: Tumour free scar tissue

description: Recovered cells: 10,000 cells

value: Tumour free scar tissue


title: Ctrl1_Inf_Mo_bulkRNAseq

value: Ly6Chigh BM monocytes


title: WT MLE-12 cells, unscratched

value: WT


title: Burn_Scar_MU_Interface_Section

type: RNA

description: Human Multi-Tissue and Cancer Pre-designed Panel (377 genes)

hyb_protocol: The Xenium samples went through 15 cycles of hybridization, imaging, and probe removal. The Xenium Analyzer took Z-stack images each cycle in multiple channels, which were processed to create a spatial transcript map in the tissue. Transcript decoding used a Xenium codebook linking codewords to genes. mRNA localization in cells was determined by identifying cell boundaries through nuclear expansion.

scan_protocol: Xenium In Situ Analyzer

data_processing: Xenium In Situ Analyzer

source_name: FFPE Marjolin ulcers, Xenium In Situ Spatial Gene Expression

label_protocol: Xenium In situ manufacter's protocol

extract_protocol: The subject was recruited through a tertiary outpatient burn clinic. The Health Research Ethics Board of Alberta Cancer Committee determined that a full ethics review was not necessary for the study because the samples harvested (scar tissue and Marjolin's ulcer tumor tissue) were considered surgical wastes (HREBA.CC-23-0003). One 15 μm section was analyzed as per Xenium In situ manufacter's protocol.

value: Marjolin's ulcer


title: E_421_1

value: Eutopic endometrium

value: eutopic endometrium


title: WCM2549_Z6, H3K27me3, CUT&Tag

status: Public on Jul 20 2024

city: Boston

first: Kei

last: Mizuno

state: MASSACHUSETTS

address: 450 Brookline Avenue

institute: Dana-Farber Cancer institute

library_source: genomic

data_processing:
We used Bowtie2  to map the paired-end Illumina reads to hg19. We extracted fragments from properly paired reads.
Assembly: hg19
Supplementary files format and content: bam
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Liver

extract_protocol:
CUT&Tag was performed according to the manufacturer’s protocol.
Library preparation for CUT&Tag samples was performed according to the manufacturer’s protocol

value: Liver

value: prostate cancer


title: Lane D, P7-9-12-26-27, scRNAseq

description: 10X Genomics


title: WCM2848_X1, H3K27me3, CUT&Tag

source_name: Prostate

value: Prostate


title: WCM2549_Z5, H3K27me3, CUT&Tag


title: WCM2549_Z3, H3K27me3, CUT&Tag

source_name: Lymph node

value: Lymph node


title: CMML_cachexia2_Inf_Mo_bulkRNAseq

value: CMML with cachexia


title: WCM2549_Z4, H3K27me3, CUT&Tag

source_name: Adrenal gland

value: Adrenal gland


title: WCM1070_Z8, H3K27me3, CUT&Tag

source_name: Bone

value: Bone


title: WCM1358_Z3, H3K27me3, CUT&Tag


title: WCM2549_Z1, H3K27me3, CUT&Tag


title: WCM1070_Z4, H3K27me3, CUT&Tag


title: WCM1070_Z7, H3K27me3, CUT&Tag


title: WCM1070_Z5, H3K27me3, CUT&Tag


title: WCM493_Z1, H3K27me3, CUT&Tag

source_name: Brain

value: Brain


title: DFCI24_Z2, H3K27me3, CUT&Tag


title: DFCI24_Z4, H3K27me3, CUT&Tag


title: siMLL3_rep2_RNA-Seq

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
Pair-end 150bp reads were aligned to the hg19 reference genome using Hisat2 (version 7.2.0).
Reads were counted with htseq-count program (version 0.11.3) by default and normalized to gene levels by Fragments Per Kilobase per Million mapped fragments (FPKM).
Assembly: hg19
Supplementary files format and content: Raw reads count tab file and combined FPKM tab file

growth_protocol: KYSE510 cells were cultured in RPMI-1640 medium (Corning, #10-040-CV) supplemented with 10% Fetal Bovine Serum (FBS) (Omega, Tarzna, #FB-02), 1% Penicillin/Streptomycin (Thermofisher Scientific, 30-002-CI).

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol

treatment_protocol: KYSE510 cells were transfected with siRNA scramble, siMLL3, or siGRHL2 by lipofectamine RNAiMAX (Thermofisher Scientific, 13778150) and incubated for 48 hours.

value: Esophageal squamous cell carcinoma cell line

tag: transfection


title: WT MLE-12 cells, 24 hours post scratch

value: 24 hours post scratch


title: Nafion byproduct 2_96h_replicate-5 [s100]

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

department: Environmental Molecular toxicology

institute: Oregon State University

description:
Total RNA isolated from zebrafish embryos treated with 73 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-96 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC

data_processing:
STAR for genome mapping and alignment (parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate).
HTSeq for gene-level counts (parameters: -m intersection-nonempty -s yes -f bam -r pos).
For experiments A&B, genes with low counts were removed (i.e., genes with zero counts for all samples (9.9% of 32,521 genes), genes that were in the lowest 35th percentile of counts for all samples (4.8%)). Multidimensional scaling analysis in R (metaMDS function, vegan package) identified 1 outlier (PFAS-5_replicate-1) that was removed.
For experiment C, all genes with zero count were removed but low count genes were not removed. Control-C_48h_replicate-2 and Nafion byproduct 2_48h_replicate-3 were identified as outliers and removed.
DESeq2 for differential expression analysis (experiments A&B analyzed together, with sequencing runs collapsed by sample and samples contrasted to appropriate controls).
Assembly: GRCz11
Supplementary files format and content: .xlsx with read counts, filtered files and gene expression for all samples.

organism: Danio rerio

source_name: Zebrafish embyonic total RNA

growth_protocol: Animals were dechorionated at 4 hours post-fertilization (hpf) and then kept in 96-well plates in 100µLembryo medium consisting of 15 mM NaCl, 0.5 mM KCl, 1 mM MgSO4, 0.15 mM KH2PO4, 0.05 mM Na2HPO4, and 0.7 mM NaHCO3(Westerfield, 2000) at 28°C in the dark.

extract_protocol:
Total RNA was isolated from pooled animals in Eppendorf safe-lock tubes by euthanizing on ice, immediately removing excess water, homogenizing in 200 µL RNAzol®RT (Molecular Research Center) with 100 µL 0.5 mm zirconium oxide beads (Next Advance) using a Bullet Blender® (Next Advance) at speed 8 for 3 minutes. After homogenization, 300 µL RNAzol® was added, and samples were stored at -80 °C. Isolation was performed using Direct-zol RNA MiniPrep kit (Zymo, Cat no. R2052) and optional DNase I digestion step.
RNA libraries for RNA-seq were prepared usingLexogen QuantSeq 3' mRNA-seq FWD kit following manufacturer's protocols.

treatment_protocol: At 6 hours post-fertilization (hpf), animals were statically exposed to chemicalsusing an HP D300 digital dispenser to dispense stocks into individual wells of the 96-well plates, all normalized to 1% DMSO, and plates were sealed.

value: Tropical 5D Wildtype

tag: age

value: 96 hours post fertilization

tag: pooled organisms

value: 8 whole embryos


title: siGRHL2_rep2_RNA-seq


title: siMLL3_rep1_RNA-seq


title: WCM2549_Z2, H3K27me3, CUT&Tag


title: siNC_rep1_RNA-seq

value: siNC


title: DFCI23_Z3, H3K27me3, CUT&Tag


title: Nafion byproduct 2_96h_replicate-4 [s099]


title: Nafion byproduct 2_96h_replicate-3 [s098]


title: WCM1358_Z2, H3K27me3, CUT&Tag


title: KYSE510_ GRHL2_ChIP-Seq

data_processing:
Pair-end 150bp reads were trimmed for adaptor sequence, and then mapped to hg19 reference genome using BWA
PCR duplicate reads were removed using Picard MarkDuplicates in ChIP-seq.
Blacklist regions were removed using ENCODE blacklist file in ChIP-seq.
Peaks were called subsequently using macs2.
Bigwig files were generated by deepTools bamCompare function (version 3.1.3) with “--operation subtract --normalizeUsing CPM --extendReads 146 --binSize 20” parameters.
KYSE510 ChIP-seq input file was downloaded from GSM2039113, which was conducted as part of our previous research.
Assembly: hg19
Supplementary files format and content: bigwig files

extract_protocol:
DNA framgents were collected after reverse crosslink using 5M NaCl and purified using Qiaquick PCR purification kit (Qiagen, #28104) according to manufacturer's protocol
Standard Illumina library preparation protocol

treatment_protocol: KYSE510 cell line was harvested and fixed using 1% formalin. Sample then sonicated using sonicator and pulled down uisng either MLL3 (Millipore sigma, ABE1851, 5ug) or GRHL2 (Genetex, GTX109410, 5ug) antibodies and Dynabeads. DNA framgents were collected after reverse crosslink using 5M NaCl and purified using Qiaquick PCR purification kit (Qiagen, #28104) according to manufacturer's protocol

tag: antibody


title: siGRHL2_rep1_RNA-seq


title: Control-C_96h_replicate-5 [s095]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-96 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC

value: untreated (Control-C)


title: amox500, 60min, pectin, rep3

city: Providence

first: Rachael

last: Nilson

state: RI

address: 171 Meeting St

institute: Brown University

data_processing:
Transcriptomic reads were trimmed and decontaminated using KneadData (version 0.6.1); trimming was done using Trimmomatic (version 0.39) with a SLIDINGWINDOW of 4:20
Contaminating reads from the SILVA 128 database containing LSU and SSU ribosomal RNA sequenceswere removed using Bowtie2 (version 2.3.5.1)
Processed reads were aligned to NCBI GenBank Assembly GCF_000011065.1 using Bowtie2 (version 2.3.4.5.1)
Aligned reads were counted using the featureCounts command in the subread program (version 1.6.2)
Counts were input into DESeq2 (version 1.40.2) for differential expression analysis with multiple hypothesis testing correction using the Benjamini-Hochberg method
Assembly: NCBI GenBank Assembly GCF_000011065.1
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

organism: Bacteroides thetaiotaomicron VPI-5482

growth_protocol: Bacteroides thetaiotaomicron cells were grown in minimal media containing either glucose or pectin as a carbon source, at 37C inside a Coy anaerobic chamber under an atmosphere of 2.5% H2, 5% CO2, 92.5% N2

extract_protocol:
Cultures were pelleted and resuspended in RNAlater until extraction using the Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research, Irvine, CA, USA)
Libraries were prepared from total RNA (~500 ng) using the NEBNext®rRNA Depletion Kit (Bacteria) and the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s instructions for intact RNA.

treatment_protocol: Cultures were grown to early log phase (0.1 OD600) in either minimal media + glucose or minimal media + pectin and treated with three different doses of AMX (62.5, 200, 500 𝝻g/ml) or vehicle control for sixty minutes

value: WT

value: amoxicillin 500 ug/ml

tag: time

value: 60 minutes

tag: carbon source

value: pectin


title: Nafion byproduct 2_96h_replicate-2 [s097]

tag: strain


title: Nafion byproduct 2_96h_replicate-1 [s096]


title: amox500, 60min, pectin, rep4


title: siNC_rep2_RNA-seq


title: Control-C_96h_replicate-4 [s094]


title: Control-C_96h_replicate-2 [s092]


title: Control-C_96h_replicate-3 [s093]


title: amox500, 60min, pectin, rep2


title: amox200, 60min, pectin, rep3

value: amoxicillin 200 ug/ml


title: Control-C_96h_replicate-1 [s091]


title: Nafion byproduct 2_72h_replicate-4 [s089]

description:
Total RNA isolated from zebrafish embryos treated with 73 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-72 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC

value: 72 hours post fertilization


title: amox200, 60min, pectin, rep1


title: Nafion byproduct 2_72h_replicate-5 [s090]


title: Nafion byproduct 2_72h_replicate-2 [s087]


title: Control-C_72h_replicate-5 [s085]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-72 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC


title: amox62.5, 60min, pectin, rep3

value: amoxicillin 62.5 ug/ml


title: amox62.5, 60min, pectin, rep1


title: WCM1070_Z6, H3K27me3, CUT&Tag

tag: tissue

value: Liver

value: prostate cancer


title: amox200, 60min, pectin, rep2

tag: genotype


title: Nafion byproduct 2_72h_replicate-1 [s086]


title: Control-C_72h_replicate-2 [s082]


title: amox500, 60min, pectin, rep1


title: Control-C_72h_replicate-3 [s083]


title: control, 60min, pectin, rep3

value: vehicle control


title: control, 60min, pectin, rep2


title: control, 60min, pectin, rep1


title: Control-C_72h_replicate-1 [s081]


title: Nafion byproduct 2_48h_replicate-5 [s080]

description:
Total RNA isolated from zebrafish embryos treated with 73 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-48 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC

value: 48 hours post fertilization


title: amox62.5, 60min, pectin, rep4


title: Nafion byproduct 2_48h_replicate-3 [s078]


title: amox500, 0 min, pectin rep4

value: 0 minutes


title: amox500, 0 min, pectin rep3


title: amox62.5, 60min, pectin, rep2


title: Nafion byproduct 2_48h_replicate-4 [s079]

value: Tropical 5D Wildtype


title: control, 60min, pectin, rep4


title: amox500, 0 min, pectin rep1


title: amox500, 0 min, pectin rep2


title: Nafion byproduct 2_48h_replicate-1 [s076]


title: amox200, 0min, pectin, rep4


title: Control-C_48h_replicate-5 [s075]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-48 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC


title: Control-C_48h_replicate-4 [s074]


title: Control-C_48h_replicate-3 [s073]


title: Control-C_48h_replicate-2 [s072]


title: amox200, 0min, pectin, rep3


title: amox200, 0min, pectin, rep2


title: amox62.5, 0min, pectin, rep4


title: Control-C_48h_replicate-1 [s071]


title: amox200, 0min, pectin, rep1


title: PFAS-8_replicate-4 [run66_s070]

description:
Total RNA isolated from zebrafish embryos treated with 53 µM 1H,1H,11H,11H-Perfluorotetraethylene glycol (PFAS-8; CAS 330562-44-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: 10 whole embryos


title: amox62.5, 0min, pectin, rep2


title: amox62.5, 0min, pectin, rep3


title: amox62.5, 0min, pectin, rep1


title: PFAS-4_replicate-4 [run66_s069]

description:
Total RNA isolated from zebrafish embryos treated with 50 µM Perfluoro-3,6,9-trioxatridecanoic acid (PFAS-4; CAS 330562-41-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Nafion byproduct 2_48h_replicate-2 [s077]

value: 8 whole embryos


title: control, 0min, pectin, rep4


title: PFAS-9_replicate-4 [run66_s068]

description:
Total RNA isolated from zebrafish embryos treated with 62 µM 2,2,3,3-Tetrafluoropropyl acrylate (PFAS-9; CAS 7383-71-3; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-12_replicate-4 [run66_s067]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM 3H-Perfluoro-2,2,4,4-tetrahydroxypentane (PFAS-12; CAS 77953-71-0; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-7_replicate-4 [run66_s066]

description:
Total RNA isolated from zebrafish embryos treated with 39.7 µM 1-(Perfluorofluorooctyl)propane-2,3-diol (PFAS-7; CAS 94159-84-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: control, 0min, pectin, rep3


title: control, 0min, pectin, rep2


title: control, 0min, pectin, rep1


title: PFAS-13_replicate-4 [run66_s063]

description:
Total RNA isolated from zebrafish embryos treated with 25 µM 1H,1H,10H,10H-Perfluorodecane-1,10-diol (PFAS-13; CAS 754-96-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-15_replicate-4 [run66_s064]

description:
Total RNA isolated from zebrafish embryos treated with 20 µM 1H,1H,6H,6H-Perfluorohexane-1,6-diol diacrylate (PFAS-15; CAS 2264-01-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: amox500, 60min, glucose, rep4

value: glucose


title: amox500, 60min, glucose, rep3


title: PFAS-14_replicate-4 [run66_s062]

description:
Total RNA isolated from zebrafish embryos treated with 20 µM 1H,1H,5H,5H-Perfluoro-1,5-pentanediol diacrylate (PFAS-14; CAS 678-95-5; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Control-A_replicate-6 [run66_s061]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: untreated (Control-A)


title: amox500, 60min, glucose, rep2

value: WT


title: amox200, 60min, glucose, rep4


title: amox500, 60min, glucose, rep1

value: amoxicillin 500 ug/ml


title: PFAS-2_replicate-4 [run66_s059]

description:
Total RNA isolated from zebrafish embryos treated with 30 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-6_replicate-4 [run66_s058]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM N-Ethylperfluorooctanesulfonamide (PFAS-6; CAS 4151-50-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: amox200, 60min, glucose, rep2

value: 60 minutes


title: PFAS-3_replicate-4 [run66_s056]

description:
Total RNA isolated from zebrafish embryos treated with 13.8 µM Potassium perfluorooctanesulfonate (PFAS-3; CAS 2795-39-3; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-5_replicate-4 [run66_s057]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM Perfluoroheptanesulfonic acid (PFAS-5; CAS 375-92-8; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluoroheptanesulfonic acid (PFAS-5)


title: PFAS-11_replicate-4 [run66_s055]

description:
Total RNA isolated from zebrafish embryos treated with 28 µM Perfluorohexanesulfonamide (PFAS-11; CAS 41997-13-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluorohexanesulfonamide (PFAS-11)


title: PFAS-10_replicate-4 [run66_s054]

description:
Total RNA isolated from zebrafish embryos treated with 8 µM Perfluorooctanesulfonamide (PFAS-10; CAS 754-91-6; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluorooctanesulfonamide (PFAS-10)


title: amox62.5, 60min, glucose, rep4

value: amoxicillin 62.5 ug/ml


title: amox200, 60min, glucose, rep1

value: amoxicillin 200 ug/ml


title: PFAS-8_replicate-3 [run66_s065]


title: amox62.5, 60min, glucose, rep2


title: WT DMSO 1

tag: cell line

value: head and neck squamous cell carcinoma

value: DMSO


title: amox62.5, 60min, glucose, rep3


title: amox62.5, 60min, glucose, rep1


title: PFAS-4_replicate-3 [run66_s053]

value: 48 hours post fertilization


title: control, 60min, glucose, rep4

value: vehicle control


title: PFAS-1_replicate-4 [run66_s052]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM 9-Chloro-perfluorononanoic acid (PFAS-1; CAS 865-79-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Tropical 5D Wildtype


title: Control-A_replicate-5 [run66_s051]

value: 10 whole embryos


title: Control-B_replicate-4 [run66_s060]

value: untreated (Control-B)


title: control, 60min, glucose, rep3

value: glucose


title: amox200, 60min, glucose, rep3


title: PFAS-2_replicate-3 [run66_s050]


title: PFAS-5_replicate-3 [run66_s048]


title: PFAS-6_replicate-3 [run66_s049]


title: control, 60min, glucose, rep1


title: control, 60min, glucose, rep2


title: PFAS-3_replicate-3 [run66_s047]


title: amox500, 0min, glucose, rep3

value: 0 minutes


title: PFAS-11_replicate-3 [run66_s046]


title: amox500, 0min, glucose, rep2

value: WT


title: amox200, 0min, glucose, rep3


title: amox200, 0min, glucose, rep4


title: PFAS-1_replicate-3 [run66_s043]


title: amox500, 0min, glucose, rep1

value: amoxicillin 500 ug/ml


title: PFAS-9_replicate-3 [run66_s042]


title: PFAS-12_replicate-3 [run66_s041]


title: amox200, 0min, glucose, rep1


title: PFAS-7_replicate-3 [run66_s040]


title: amox500, 0min, glucose, rep4


title: PFAS-8_replicate-2 [run66_s039]


title: amox62.5, 0min, glucose, rep4


title: amox62.5, 0min, glucose, rep3


title: PFAS-13_replicate-3 [run66_s037]


title: PFAS-15_replicate-3 [run66_s038]


title: control, 0min, glucose, rep3


title: PFAS-10_replicate-3 [run66_s045]


title: amox62.5, 0min, glucose, rep1


title: Control-A_replicate-4 [run66_s035]

value: untreated (Control-A)


title: Control-B_replicate-3 [run66_s034]


title: amox62.5, 0min, glucose, rep2


title: control, 0min, glucose, rep2


title: control, 0min, glucose, rep4


title: PFAS-14_replicate-3 [run66_s036]


title: PFAS-4_replicate-2 [run66_s044]


title: PFAS-6_replicate-2 [run66_s031]


title: PFAS-2_replicate-2 [run66_s032]


title: Control-A_replicate-3 [run66_s033]


title: amox200, 0min, glucose, rep2


title: PFAS-5_replicate-2 [run66_s030]

value: Perfluoroheptanesulfonic acid (PFAS-5)


title: PFAS-3_replicate-2 [run66_s029]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36030_rep1

city: Houston

first: James

middle: M.

last: Musser

state: Texas

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

institute: Houston Methodist Hospital and Research Institute

data_processing:
Multiplexed libraries were sequenced on an Illumina NextSeq 500 instrument.
Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNA-seq reads from all strains were mapped to reference strain MGCS36044 [National Center for Biotechnology Information (NCBI) Bioproject accession number PRJNA925803], using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Differential expression (DE) analysis was performed with DESeq2 using pcaExplorer and Ideal to streamline RStudio.
DE genes were identified in each of the 38 strains compared to a common reference strain (MGCS36044).
Assembly: MGCS36044, NCBI GenBank accession GCA_029234115.1
Supplementary files format and content: EDGEpro output listing 6 space separated columns: geneID, start_coord, end_coord, average_cov, and RPKM -- determined relative to the reference MGCS36044 genome

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using NEBNext rRNA depletion kit (NEB)
Resultant RNAs were processed using the NEBNext Ultra II directional RNA library prep kit for Illumina (NEB), reverse transcribed to cDNA, tagged with the NEBNext multiplex oligos for Illumina (NEB), pooled and sequenced

treatment_protocol: At the desired growth stage, mid-exponential phase (OD 600nm 1.0), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36030_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36030_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36021_rep3


title: PFAS-11_replicate-2 [run66_s028]

value: Perfluorohexanesulfonamide (PFAS-11)


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36021_rep2


title: PFAS-10_replicate-2 [run66_s027]

value: Perfluorooctanesulfonamide (PFAS-10)


title: control, 0min, glucose, rep1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS36021_rep1


title: PFAS-4_replicate-1 [run66_s026]


title: PFAS-9_replicate-2 [run66_s024]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS35977_rep1


title: PFAS-12_replicate-2 [run66_s023]


title: PFAS-1_replicate-2 [run66_s025]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS35977_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGGS35977_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36086_rep3


title: PFAS-7_replicate-2 [run66_s022]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36071_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36086_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36086_rep1


title: PFAS-13_replicate-2 [run66_s020]


title: PFAS-15_replicate-2 [run66_s021]


title: Control-A_replicate-2 [run66_s018]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36071_rep1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36067_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36067_rep3


title: Control-B_replicate-2 [run66_s017]


title: PFAS-2_replicate-1 [run66_s016]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36067_rep1


title: PFAS-14_replicate-2 [run66_s019]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36061_rep3


title: PFAS-6_replicate-1 [run66_s015]


title: KYSE510_MLL3_ ChIP-Seq

tag: cell type

value: Esophageal squamous cell carcinoma cell line


title: PFAS-11_replicate-1 [run66_s012]

tag: treatment


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36061_rep1


title: PFAS-5_replicate-1 [run66_s014]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36061_rep2


title: BMM Mtb-MGO rep2

city: Solna

first: Martin

last: Rottenberg

address: Solna vägen 9

country: Sweden

institute: Karolinska Institutet

data_processing:
Pre-processed reads were aligned to the standard mouse reference genome mm10 using the HISAT2 program
Hypergeometric Optimization of Motif EnRichment (HOMER, http://homer.salk.edu/homer) was used to create the tag directory and count tags in all exons.
For the gene expression analysis, unsupervised hierarchical clustering and principal component analysis of genes were performed in Qlucore Omics Explorer 3.2
Assembly: mm10
Supplementary files format and content: tab delimited txt data include RPKM values for each sample

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow cells were flushed from tibia and femurs with PBS, filtered through a 70μm cell strainer, resuspended in DMEM supplemented with 10% FCS and 30% L929 cell-conditioned medium (as a source of macrophage-colony stimulating factor) and incubated for 6 days at 37°C, 5% CO2. Bone marrow-derived macrophage (BMM) cultures were then washed with PBS, detached with 1%trypsin, and 5.105 cells were seeded to each well at (using 24 well plates). BMM were further incubated for 24 h at 37°C before infections or treatment with diverse compounds. BMM were F4/80+, CD11b+, CD11c- and SiglecF-.

extract_protocol:
RNA was isolated using miRNeasy micro kit (QIAGEN, Hilden, Germany)
Illumina TruSeq RNA Library Preparation Kit

treatment_protocol: triplicate independent cultures of BMM treated or not with 200 mM MGO and infected 4 h after with M. tuberculosis at a MOI of 3:1. RNA was extracted 4h after infection.

value: Bone marrow derived macrophage

value: M. tuberculosis- MGO


title: BMM Mtb-MGO rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36071_rep2


title: Control-C_72h_replicate-4 [s084]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-72 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC

value: 72 hours post fertilization

value: 8 whole embryos

value: untreated (Control-C)


title: PFAS-10_replicate-1 [run66_s011]

value: Tropical 5D Wildtype

value: 48 hours post fertilization


title: Nafion byproduct 2_72h_replicate-3 [s088]

description:
Total RNA isolated from zebrafish embryos treated with 73 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-72 hpf
NormalizedGeneExpression_DEGs_gProfiler_ExperimentC


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36051_rep3


title: BMM Mtb rep3

value: M. tuberculosis


title: BMM Mtb-MGO rep1


title: PFAS-9_replicate-1 [run66_s009]

value: 10 whole embryos


title: amox200, 60min, pectin, rep4

value: amoxicillin 200 ug/ml

value: 60 minutes

value: pectin


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36051_rep1


title: PFAS-1_replicate-1 [run66_s010]


title: BMM rep2

value: Untreated


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36051_rep2


title: BMM rep1


title: BMM Mtb rep1


title: PFAS-7_replicate-1 [run66_s007]


title: BMM rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36046_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36046_rep1


title: PFAS-8_replicate-1 [run66_s006]

description:
Total RNA isolated from zebrafish embryos treated with 53 µM 1H,1H,11H,11H-Perfluorotetraethylene glycol (PFAS-8; CAS 330562-44-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-3_replicate-1 [run66_s013]


title: BMM Mtb rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36046_rep2


title: PFAS-15_replicate-1 [run66_s005]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36035_rep3


title: PFAS-12_replicate-1 [run66_s008]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36035_rep2


title: PFAS-14_replicate-1 [run66_s003]


title: Organoid D120 D120_01

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

description:
Organoid D120
Bulk RNAseq, Neuropathology panel

hyb_protocol: RNA was hybridized with the gene panel Codeset at 65 °C for 16 hr.

scan_protocol: The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, with subsequent data analysis performed using nSolver.

data_processing: Raw data was first normalized to internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Gene expression variability of less than 20% within a single organoid was the criterion for acceptance.

source_name: LMNSC01 neural stem cell

label_protocol: We utilized the NanoString Neuropathology Profiling panel, consisting of genes targeting six fundamental themes: neurotransmission, neuron-glia interactions, neuroplasticity, cell structure integrity, neuroinflammation, and metabolism

growth_protocol: Organoids generated in vitro initiated with neural stem cell line LMNSC01 (previously referred to as LM-NSC008) with 1000 cells per 6 µL matrigel cultured under hypoxia (4% O2) in NeuroCult Proliferation media (NC.Prol) and harvested at 6 time points

extract_protocol: mRNA was extracted using the miRNeasy mini kit (HB-1277-066,Qiagen). Concentration was assessed by Nanodrop spectrophotometer ND-1000 and Qubit 3.0 Fluorometer , with mRNA fragmentation and quality assessed by 2100 Bioanalyzer

treatment_protocol: Neurocult Proliferation medium 4% oxygen, Neurocult differntiation medium 20% oxygen, BrainPhys medium 4% oxygen.

tag: culture time (days)

tag: number of organoids

tag: experimental run

tag: culture medium, o2 concentration (%)

value: Neurocult Proliferation medium, 4% O2 environment


title: Organoid D120 D120_03


title: Organoid D120 D120_02


title: Control-A_replicate-1 [run66_s002]

value: untreated (Control-A)


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36035_rep1


title: Organoid D94 D94_03

description:
Organoid D94
Bulk RNAseq, Neuropathology panel


title: Organoid D94 D94_01


title: Organoid D94 D94_02


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36023_rep3


title: Organoid D90 D90_1O_05

description:
Organoid D90
Bulk RNAseq, Neuropathology panel


title: Organoid D90 D90_1O_06


title: Organoid D94 D94_04


title: Organoid D90 D90_1O_04


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36023_rep2


title: Organoid D90 D90_5O_01


title: Organoid D90 D90_1O_03


title: PFAS-13_replicate-1 [run66_s004]

description:
Total RNA isolated from zebrafish embryos treated with 25 µM 1H,1H,10H,10H-Perfluorodecane-1,10-diol (PFAS-13; CAS 754-96-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36023_rep1


title: PFAS-8_replicate-4 [run64_s070]


title: Organoid D90 D90_1O_01


title: Organoid D90 D90_1O_02


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36020_rep3


title: PFAS-4_replicate-4 [run64_s069]

description:
Total RNA isolated from zebrafish embryos treated with 50 µM Perfluoro-3,6,9-trioxatridecanoic acid (PFAS-4; CAS 330562-41-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36020_rep2


title: PFAS-12_replicate-4 [run64_s067]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM 3H-Perfluoro-2,2,4,4-tetrahydroxypentane (PFAS-12; CAS 77953-71-0; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Organoid D60 D60_1O_08

description:
Organoid D60
Bulk RNAseq, Neuropathology panel


title: Organoid D65 D65_03

description:
Organoid D65
Bulk RNAseq, Neuropathology panel


title: Organoid D65 D65_02


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS36020_rep1


title: PFAS-7_replicate-4 [run64_s066]

description:
Total RNA isolated from zebrafish embryos treated with 39.7 µM 1-(Perfluorofluorooctyl)propane-2,3-diol (PFAS-7; CAS 94159-84-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Organoid D60 D60 5O_01


title: Organoid D65 D65_01


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35987_rep3


title: Organoid D60 D60 5O_02


title: Control-B_replicate-1 [run66_s001]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: untreated (Control-B)


title: PFAS-8_replicate-3 [run64_s065]


title: Organoid D60 D60_1O_07


title: Organoid D60 D60_1O_04


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35987_rep2


title: Organoid D60 D60_1O_05


title: PFAS-15_replicate-4 [run64_s064]

description:
Total RNA isolated from zebrafish embryos treated with 20 µM 1H,1H,6H,6H-Perfluorohexane-1,6-diol diacrylate (PFAS-15; CAS 2264-01-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-9_replicate-4 [run64_s068]

description:
Total RNA isolated from zebrafish embryos treated with 62 µM 2,2,3,3-Tetrafluoropropyl acrylate (PFAS-9; CAS 7383-71-3; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35987_rep1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35983_rep3


title: Organoid D60 D60_1O_02


title: Organoid D60 D60_1O_06


title: Organoid D34 D34_04

description:
Organoid D34
Bulk RNAseq, Neuropathology panel


title: Control-A_replicate-6 [run64_s061]


title: Organoid D60 D60_1O_01


title: Organoid D34 D34_02


title: Control-B_replicate-4 [run64_s060]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35983_rep1


title: Organoid D34 D34_03


title: CK-30-BM

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing analysis was carried out using 10X Genomics’ CellRanger software. Fastq files were generated using the CellRanger mkfastq pipeline.
Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger count pipeline. The expression matrices from different samples were concatenated.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Bone Marrow

extract_protocol:
FACS-purified live BM MNCs or Lin-CD34+ cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: Bone Marrow Mononuclear cells

value: Pre-canakinumab


title: CK-43-BM

value: Canakinumab C2D29


title: CK-38-BM


title: CK-33-BM


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35978_rep3


title: Organoid D34 D34_01


title: PFAS-2_replicate-4 [run64_s059]

description:
Total RNA isolated from zebrafish embryos treated with 30 µM 7H-Perfluoro-4-methyl-3,6-dioxaoctanesulfonic acid (PFAS-2; CAS 749836-20-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML051, blood, time point 1, Batch 3

city: Zuerich

first: Yannik

last: Severin

state: ZH

address: Otto-Stern-Weg 3

department: Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).
Assembly: GRCh38, v.93
Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv

source_name: blood

growth_protocol: primary samples

extract_protocol:
Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.
CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033–2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample)

treatment_protocol: not treated

value: blood


title: Patient AML050, blood, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35978_rep2


title: Organoid D60 D60_1O_03


title: Patient AML050, bonemarrow, time point 3, Batch 3

source_name: bonemarrow

value: bonemarrow


title: PFAS-6_replicate-4 [run64_s058]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM N-Ethylperfluorooctanesulfonamide (PFAS-6; CAS 4151-50-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Tropical 5D Wildtype


title: PFAS-13_replicate-4 [run64_s063]

value: 48 hours post fertilization


title: PFAS-14_replicate-4 [run64_s062]

description:
Total RNA isolated from zebrafish embryos treated with 20 µM 1H,1H,5H,5H-Perfluoro-1,5-pentanediol diacrylate (PFAS-14; CAS 678-95-5; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35978_rep1


title: Patient AML050, bonemarrow, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35983_rep2


title: Organoid D120 D120_04


title: PFAS-5_replicate-4 [run64_s057]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM Perfluoroheptanesulfonic acid (PFAS-5; CAS 375-92-8; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluoroheptanesulfonic acid (PFAS-5)


title: Patient AML048, blood, time point 2, Batch 3


title: Patient AML048, bonemarrow, time point 2, Batch 3


title: Patient AML047, blood, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35970_rep3


title: Patient AML047, blood, time point 1, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35970_rep2


title: Patient AML047, bonemarrow, time point 2, Batch 3


title: Patient AML050, blood, time point 3, Batch 3


title: PFAS-3_replicate-4 [run64_s056]

description:
Total RNA isolated from zebrafish embryos treated with 13.8 µM Potassium perfluorooctanesulfonate (PFAS-3; CAS 2795-39-3; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: 10 whole embryos


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35970_rep1


title: PFAS-1_replicate-4 [run64_s052]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM 9-Chloro-perfluorononanoic acid (PFAS-1; CAS 865-79-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML046, blood, time point 2, Batch 3


title: PFAS-10_replicate-4 [run64_s054]

description:
Total RNA isolated from zebrafish embryos treated with 8 µM Perfluorooctanesulfonamide (PFAS-10; CAS 754-91-6; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluorooctanesulfonamide (PFAS-10)


title: Patient AML046, bonemarrow, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35957_rep1


title: Patient AML042, blood, time point 3, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35941_rep3


title: Patient AML045, blood, time point 1, Batch 3


title: Patient AML045, bonemarrow, time point 1, Batch 3


title: Patient AML042, blood, time point 2, Batch 3


title: PFAS-2_replicate-3 [run64_s050]


title: Patient AML044, blood, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35957_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35957_rep3


title: Patient AML044, blood, time point 3, Batch 3


title: Control-A_replicate-5 [run64_s051]


title: Patient AML044, bonemarrow, time point 3, Batch 3


title: Patient AML041, bonemarrow, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35941_rep1


title: Patient AML041, blood, time point 1, Batch 3


title: Patient AML042, bonemarrow, time point 3, Batch 3


title: PFAS-11_replicate-4 [run64_s055]

description:
Total RNA isolated from zebrafish embryos treated with 28 µM Perfluorohexanesulfonamide (PFAS-11; CAS 41997-13-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: Perfluorohexanesulfonamide (PFAS-11)


title: PFAS-3_replicate-3 [run64_s047]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35939_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35941_rep2


title: PFAS-6_replicate-3 [run64_s049]


title: Patient AML040, blood, time point 2, Batch 3


title: Patient AML042, bonemarrow, time point 2, Batch 3


title: PFAS-5_replicate-3 [run64_s048]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35939_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35939_rep1


title: PFAS-4_replicate-3 [run64_s053]

description:
Total RNA isolated from zebrafish embryos treated with 50 µM Perfluoro-3,6,9-trioxatridecanoic acid (PFAS-4; CAS 330562-41-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-4_replicate-2 [run64_s044]


title: Patient AML037, blood, time point 1, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35921_rep3


title: Patient AML039, blood, time point 1, Batch 3


title: Patient AML037, bonemarrow, time point 3, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35921_rep2


title: Patient AML039, bonemarrow, time point 1, Batch 3


title: Patient AML037, blood, time point 3, Batch 3


title: Patient AML037, blood, time point 2, Batch 3


title: PFAS-10_replicate-3 [run64_s045]


title: Patient AML038, blood, time point 1, Batch 3


title: PFAS-11_replicate-3 [run64_s046]


title: Patient AML035, blood, time point 1, Batch 3


title: Patient AML035, bonemarrow, time point 1, Batch 3


title: Patient AML040, blood, time point 1, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35904_rep2


title: Patient AML036, blood, time point 3, Batch 3


title: PFAS-1_replicate-3 [run64_s043]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35904_rep1


title: Patient AML036, blood, time point 1, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35921_rep1


title: Patient AML036, bonemarrow, time point 3, Batch 3


title: Patient AML034, bonemarrow, time point 2, Batch 3


title: PFAS-12_replicate-3 [run64_s041]

description:
Total RNA isolated from zebrafish embryos treated with 100 µM 3H-Perfluoro-2,2,4,4-tetrahydroxypentane (PFAS-12; CAS 77953-71-0; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML034, blood, time point 3, Batch 3


title: Patient AML034, bonemarrow, time point 3, Batch 3


title: PFAS-9_replicate-3 [run64_s042]


title: Patient AML036, bonemarrow, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35893_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35904_rep3


title: PFAS-8_replicate-2 [run64_s039]

description:
Total RNA isolated from zebrafish embryos treated with 53 µM 1H,1H,11H,11H-Perfluorotetraethylene glycol (PFAS-8; CAS 330562-44-2; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-15_replicate-3 [run64_s038]


title: Patient AML034, blood, time point 2, Batch 3


title: Patient AML033, blood, time point 2, Batch 3


title: Patient AML032, blood, time point 3, Batch 3


title: Patient AML033, blood, time point 3, Batch 3


title: PFAS-13_replicate-3 [run64_s037]

description:
Total RNA isolated from zebrafish embryos treated with 25 µM 1H,1H,10H,10H-Perfluorodecane-1,10-diol (PFAS-13; CAS 754-96-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: PFAS-14_replicate-3 [run64_s036]


title: Patient AML033, bonemarrow, time point 2, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35893_rep2


title: Patient AML032, bonemarrow, time point 3, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35893_rep1


title: PFAS-7_replicate-3 [run64_s040]

description:
Total RNA isolated from zebrafish embryos treated with 39.7 µM 1-(Perfluorofluorooctyl)propane-2,3-diol (PFAS-7; CAS 94159-84-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML030, bonemarrow, time point 3, Batch 3


title: Patient AML022, bonemarrow, time point 1, Batch 3


title: Patient AML024, bonemarrow, time point 3, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35873_rep3


title: Control-A_replicate-4 [run64_s035]

description:
Total RNA isolated from zebrafish embryos treated with 1% DMSO (controls) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML030, blood, time point 3, Batch 3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35873_rep2


title: Patient AML034, blood, time point 1, Batch 2


title: Patient AML033, bonemarrow, time point 1, Batch 2


title: Patient AML032, blood, time point 1, Batch 2


title: Patient AML030, blood, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35869_rep3


title: PFAS-2_replicate-2 [run64_s032]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35873_rep1


title: Control-A_replicate-3 [run64_s033]


title: Patient AML028, blood, time point 3, Batch 2


title: Patient AML028, blood, time point 2, Batch 2


title: PFAS-6_replicate-2 [run64_s031]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35869_rep1


title: Patient AML028, blood, time point 1, Batch 2


title: PFAS-5_replicate-2 [run64_s030]


title: Patient AML028, bonemarrow, time point 3, Batch 2


title: Control-B_replicate-3 [run64_s034]


title: Patient AML033, blood, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35868_rep2


title: PFAS-3_replicate-2 [run64_s029]


title: Patient AML025, blood, time point 3, Batch 2


title: PFAS-10_replicate-2 [run64_s027]


title: Patient AML025, blood, time point 2, Batch 2


title: Patient AML027, blood, time point 1, Batch 2


title: Patient AML028, bonemarrow, time point 2, Batch 2


title: Patient AML024, blood, time point 3, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35868_rep1


title: Patient AML028, bonemarrow, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35844_rep3


title: Patient AML024, bonemarrow, time point 3, Batch 2


title: Patient AML023, blood, time point 2, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35844_rep2


title: PFAS-4_replicate-1 [run64_s026]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35869_rep2


title: PFAS-1_replicate-2 [run64_s025]


title: Patient AML023, bonemarrow, time point 3, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35844_rep1


title: Patient AML023, bonemarrow, time point 2, Batch 2


title: PFAS-9_replicate-2 [run64_s024]


title: Patient AML023, blood, time point 3, Batch 2


title: Patient AML022, blood, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35868_rep3


title: Patient AML021, blood, time point 2, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35838_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35838_rep3


title: Patient AML021, blood, time point 1, Batch 2


title: PFAS-12_replicate-2 [run64_s023]


title: Patient AML021, bonemarrow, time point 2, Batch 2


title: PFAS-11_replicate-2 [run64_s028]


title: PFAS-15_replicate-2 [run64_s021]

description:
Total RNA isolated from zebrafish embryos treated with 20 µM 1H,1H,6H,6H-Perfluorohexane-1,6-diol diacrylate (PFAS-15; CAS 2264-01-9; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B


title: Patient AML022, bonemarrow, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35823_rep3


title: PFAS-13_replicate-2 [run64_s020]


title: Patient AML021, bonemarrow, time point 3, Batch 2


title: Patient AML020, blood, time point 2, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35823_rep2


title: Patient AML020, blood, time point 3, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35838_rep1


title: Patient AML020, blood, time point 1, Batch 2


title: Patient AML020, bonemarrow, time point 3, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35798_rep3


title: PFAS-14_replicate-2 [run64_s019]


title: Patient AML021, bonemarrow, time point 1, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35798_rep2


title: Control-B_replicate-2 [run64_s017]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35823_rep1


title: Patient AML019, blood, time point 3, Batch 2


title: Patient AML019, bonemarrow, time point 2, Batch 2


title: PFAS-7_replicate-2 [run64_s022]


title: Patient AML018, bonemarrow, time point 3, Batch 2


title: Patient AML015, blood, time point 3, Batch 2


title: PFAS-2_replicate-1 [run64_s016]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35798_rep1


title: PFAS-6_replicate-1 [run64_s015]


title: brown adipocyte, ATAC-seq, repeat 1

city: Nanjing

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: brown adipose tissue

extract_protocol:
SVF cells were obtained from adipose tissue in the brown fat of male C57BL/6J mice at 3-4 weeks old. Type I collagenase (2mg/ml, Sigma, SCR103) was preconfigured using DMEM basic medium (Gibco, C11995500BT) containing 2% volume of FBS (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and stored in the dark after removal of bacteria by filtration using a 0.22 μM filter. The volume ratio of collagenase to adipose tissue was maintained at 2:1. Then the adipose pad was cut into pieces to 1mm³ and digested in 37℃ water bath for 1h, during which the tube was reversed and mixed every five minutes. The digested adipocytes were filtered (70 μm), then centrifuged at 1000 rpm for 10 min. After re-suspension with PBS, centrifuge at the same speed and time. DMEM/F-12 (Meilunbio, MA0214) containing 10% FBS (Gibco) and 1% penicillin-streptomycin was used to culture the primary SVF, and then the cells were implanted into the pore plate of appropriate size. The medium was changed 24 h later, and then every 48 h until the cells grew to contact inhibition state. The plate-fully-covered cells then subjected to differentiation. As for brown adipogenesis, culture medium was added insulin (5μg/ml, sigma, I3536), Dexamethasone (5μM, sigma, D4902), 3,3',5-Triiodo-L-thyronine (T3, 1nM, sigma, T2977), Rosiglitazone (1μM, sigma, R2408), Isobutyl methylxanthine (0.5mM, sigma, I5879). The above differentiation medium were changed 48 h later with medium only containing insulin, T3 and rosiglitazone, and renewed every 48 h. Cells were incubated at 37℃ in a suitable atmosphere containing 5% CO2. Native nuclei were purified from adipocytes，and washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
For ATAC seq, the Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer's manual. 50,000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen). ATAC Libraries were pooled to a final concentration of 10nM and sequenced paired-end using the Illumina NovaSeq 6000.

value: brown adipose tissue

value: SVF derived primary adipocyte

value: adipocyte

value: wild type C57

value: SVF cells isolated from brown adipose tissue were cultured in vitro and induced to differentiate into primary brown adipocyte. After 7 days, the cells were collected for cell library construction and sequencing


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35785_rep3


title: brown adipocyte, ATAC-seq, repeat 2


title: Patient AML014, blood, time point 2, Batch 2


title: Patient AML020, bonemarrow, time point 2, Batch 2


title: Control-A_replicate-2 [run64_s018]

value: untreated (Control-A)


title: PFAS-5_replicate-1 [run64_s014]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35785_rep2


title: Patient AML013, blood, time point 3, Batch 2


title: PFAS-3_replicate-1 [run64_s013]


title: Patient AML015, bonemarrow, time point 1, Batch 1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35785_rep1


title: Patient AML012, bonemarrow, time point 3, Batch 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35777_rep2


title: AD/KO microglia_rep1

city: Bangalore

first: Maneesha

middle: S

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur, Bangalore.

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Sequenced reads in FASTQ files were trimmed and filtered to remove adaptor sequences and low-quality bases (Q <20), respectively, using the FastQC tool, followed by a data quality check. Reads were aligned to the indexed UCSC mm10 mouse reference genome using HISAT 2. Quality control filtering and removal of PCR duplicates were performed using Samtools. SAM files were converted and sorted/indexed by coordinate to BAM files. FeatureCounts program of the Subread R package was used to calculate and summarize per-gene read counts as expression values. DESeq2 (v1.30.0) was utilized for differential gene expression (DEG) analysis. Principal Component Analysis (PCA) plots were generated using the plotPCA command in DEseq2.
Assembly: mm10
Supplementary files format and content: tab-limited text files containing raw read counts for each sample

source_name: 10-month-old mouse brain

extract_protocol:
RNA was extracted from microglial cells using the TRIzol method.
rRNA depletion was performed using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). cDNA libraries were constructed utilizing the NEBNext Ultra II Directional RNA Library Prep (stranded) kit (NEB).

value: 10-month-old mouse brain

value: CD11b+ microglia

value: APP/PS1+ asrij-/- (AD/KO)


title: Patient AML019, blood, time point 1, Batch 2

value: blood


title: AD/KO microglia_rep2


title: PFAS-11_replicate-1 [run64_s012]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35777_rep3


title: PFAS-10_replicate-1 [run64_s011]


title: Patient AML018, blood, time point 1, Batch 1


title: AD microglia_rep1

value: APP/PS1+ asrij+/+(AD)


title: PFAS-1_replicate-1 [run64_s010]

value: Tropical 5D Wildtype


title: MC38_tumor_HFD_anti-PD1_CD45pos_TCR

city: Nashville

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
cellranger
Assembly: mm10
Supplementary files format and content: h5, csv

source_name: Tumor

extract_protocol:
10X
10X Single Cell 5' PE
mRNA 5' capture

treatment_protocol: 8-week-old C57BL/6 male mice were fed ad libitum a 10% kcal from fat (low fat) diet or a 45% kcal fat (high fat) diet (Research Diets D12450H and D12451, respectively). Following 28 weeks of diet treatment mice were injected subcutaneously with 2x105 MC38 cells. Tumors were collected on Day 20 post injection and mechanically and enzymatically digested using miltenyi mouse tumor digestion kit following manufacturer’s instructions. CD45+ and CD45- cells were separated from tumor suspensions using CD45+ microbeads (miltenyi) and enriched for live cells using a dead cell removal kit (miltenyi). Three samples from each diet treatment group were resuspended in PBS + 0.4% FBS and pooled together in equal number of live cells prior to submitting to single cell sequencing. Cell viability for all samples were >95% via trypan blue prior to submission

value: Tumor


title: MC38_tumor_LFD_anti-PD1_CD45pos_TCR


title: AD microglia_rep2


title: PFAS-9_replicate-1 [run64_s009]

description:
Total RNA isolated from zebrafish embryos treated with 62 µM 2,2,3,3-Tetrafluoropropyl acrylate (PFAS-9; CAS 7383-71-3; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B

value: 48 hours post fertilization


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35777_rep1


title: Patient AML013, blood, time point 3, Batch 1


title: MC38_tumor_HFD_CD45pos_TCR


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35730_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35730_rep2


title: PFAS-12_replicate-1 [run64_s008]

value: 10 whole embryos


title: PFAS-8_replicate-1 [run64_s006]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35730_rep1


title: Patient AML014, bonemarrow, time point 2, Batch 1

value: bonemarrow


title: MC38_tumor_HFD_anti-PD1 CD45neg


title: PFAS-7_replicate-1 [run64_s007]


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35725_rep3


title: Patient AML013, blood, time point 1, Batch 1


title: Patient AML012, blood, time point 3, Batch 1


title: MC38_tumor_HFD_CD45neg


title: MC38_tumor_LFD_anti-PD1 CD45neg


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35725_rep1


title: Patient AML013, bonemarrow, time point 3, Batch 1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35725_rep2


title: Patient AML014, blood, time point 2, Batch 1


title: PFAS-15_replicate-1 [run64_s005]


title: PFAS-13_replicate-1 [run64_s004]


title: MC38_tumor_LFD_CD45pos_TCR


title: Patient AML012, bonemarrow, time point 3, Batch 1


title: MC38_tumor_LFD_CD45neg


title: PFAS-14_replicate-1 [run64_s003]


title: Patient AML010, blood, time point 2, Batch 1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35706_rep1


title: Control-B_replicate-1 [run64_s001]

value: untreated (Control-B)


title: Control-A_replicate-1 [run64_s002]


title: MC38_tumor_HFD_anti-PD1_CD45pos


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35706_rep3


title: Patient AML010, blood, time point 3, Batch 1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35706_rep2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35705_rep3


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35705_rep1


title: PVT-Second

city: Chengdu

first: Cheng

last: Zhou

state: Sichuan

address: No District, Chengdu, Sichuan Province. 37 Guoxue Lane, Wuhou

institute: West China Hospital of Sichuan University

data_processing:
The single cell suspension was loaded into Chromium microfluidic chips with 30 (v2 or v3, depends on project) chemistry and barcoded with a 10 Chromium Controller (10X Genomics).
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2 (v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions.
Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq) according to the manufacturer’s instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by a 10X Genomics Cell Ranger pipeline using the default parameters.
Assembly: mm8
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain-PVT area

extract_protocol:
Mice were anaesthetized with 2% isoflurane, and then the brains were rapidly removed. The brain was frozen using a freezing microtome (CM1850; Leica, Buffalo Grove, IL, USA) and then cut into slices (~300 μm). The PVT tissues were taken quickly and stored in liquid nitrogen.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: brain-PVT area

value: fresh tissue

value: all cells in the brain-PVT area

value: no treatment


title: ADAM24 KO

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the raw reads were trimmed by using Trim Galore (version 0.5.0_dev, Cutadapt version 1.15) with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10), and quantified by using Salmon5. The transcript-level quantification results were converted to the gene-level quantities with tximport R package.
DESeq2 R package was used to normalize the gene-level quantities and followed by differential expression analysis between selected samples with the same package.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: T cells

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and KO CD8+ T cells were sorted from the spleens of recipient mice 7 days after LM-OVA infection in the co-transfer model.

value: T cells

value: CD8+ T cells

value: KO

value: 15 days after LM-OVA infection


title: MC38_tumor_LFD_anti-PD1_CD45pos


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35681_rep3


title: Patient AML010, bonemarrow, time point 2, Batch 1


title: Patient AML008, blood, time point 2, Batch 1


title: Patient AML009, blood, time point 3, Batch 1


title: Patient AML008, bonemarrow, time point 2, Batch 1


title: PVT-First


title: Patient AML012, blood, time point 1, Batch 1


title: heterozygote embryo-2

city: HangZhou

first: LI

last: XU

state: Zhejiang Province

address: Binwen 7-3-1101,Binwen Road

department: School of Basic Medical Science

institute: Zhejiang Chinese Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: 12 days  embryo

label_protocol: total RNA from each sample was linearly amplified and labeled with Cy3-UTP.The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The animal housing facility is a barrier housing facility, and it is maintained in accordance with the national standards (Laboratory Animal-Requirements of Environment and Housing Facilities, GB 14925–2001).

extract_protocol: Total RNA of tumor tissue were isolated using Trizol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: embryo


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35705_rep2


title: wild type embryo-1


title: wild type embryo-2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35681_rep1


title: xal12 roots biol rep 3

city: Mexico City

first: Adriana

last: Garay Arroyo

state: Mexico City

address: C.U., Coyoacán

department: Ecología Funcional

country: Mexico

institute: Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM

data_processing:
For the differential transcript accumulation analysis, raw sequencing data were trimmed with Trimmomatic version 0.39 (Bolger et al., 2014) using the parameters ILLUMINACLIP: 2:30:10 LEADING:3 TRAILING:3 SLIDING WINDOW:4:15 MINLEN:50 HEADCROP:10. The quality of reads was evaluated with FastQC version 0.11.9 (Andrews, 2010) before and after the trimming process. Biological replicates were aligned to the Arabidopsis genome from TAIR10 (https://www.arabidopsis.org/) and the abundance of the transcripts was estimated using Subread version 2.0.1 (Liao et al., 2019). Raw count tables were used for differential transcript accumulation analysis using DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a padj <0.05 and log2 fold change > 1.5.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: Excel file includes RPKM values and raw counts for each sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown with 0.2X Murashige and Skoog (MS) salts (Murashige and Skoog, 1962) and 1% sucrose on vertical plates in climate chambers at 22°C with the photoperiods (110 mEm22 s21) established at 16 h of light followed by 8 h of dark as described by Tapia- Lopez et al. (2008).

extract_protocol:
Three biological replicates of around 60 plants each were prepared, and the total RNA of 8 dps (days post sowing) roots were extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, USA), including a DNaseI treatment step to remove any contaminating DNA. The RNA integrity and quantity was checked using a 2100 Bioanalyzer.
The libraries were constructed as indicated by the Illumina TruSeq Stranded mRNA Reference Guide for paired-end sequencing (2017).

value: Root

value: 8-day-old whole roots, excluding hypocotyls and cotyledons

value: XAL1 loss of function mutant

value: MS 0.2X