title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 23

tag: strain

tag: age

tag: dev stage

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: collected by

tag: exposure duration

tag: measured conc

tag: extrapolated conc

tag: extrapolated conc_units

value: copper sulfate (DTXSID6034479)


title: UT-TERT cells PFBS treated3

status: Public on Oct 18 2024

type: SRA

city: Omaha

first: Kendra

last: Clark

state: Nebraska

address: 560 South 45th street

country: USA

institute: University of Nebraska Medical Center

library_source: transcriptomic

data_processing:
The nf-core pipeline trim the fastq files using cutadapt (Martin & Marcel 2011) and trimgalore to remove adapters, terminal unknown bases (Ns) and low-quality 3’ regions (Phred score < 30).
The trimmed fastq files were mapped to the hg38 Human reference genome using the nf-core v3.14.0 (Ewels et al., 2020) pipeline in Nextflow v23.10.1 (Di Tommaso et al., 2017) to perform the RNAseq analysis.
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: The text files give normalized expression abundance in Count, TPM and FPKM values for all the available genes.

molecule: total RNA

organism: Homo sapiens

source_name: UT-TERT

extract_protocol:
Total RNA was isolated from control and PFAS treated cells using the Zymo Direct-zol Microprep Kit
Libraries were prepped using 75 Universal Plus™ mRNA-Seq with NuQuant (Tecan Genomics, Morgan Hill, CA). Starting amount of RNA was 50 ng and procedure followed per manufacturers recommendations.

tag: cell line

value: UT-TERT

tag: treatment

value: PFAS -PFBS


title: Testis, wild type, mouse WT27, batch 2

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed using Dragen BCLConvert (v3.10.11).
RNA-seq read alignment and UMI counting was performed in R (v4.1.2). The scPipe package (v1.14.0) was employed to process the data. Multiplex RNA-seq FASTQ files had already been demultiplexed and contained the I1 index and UMI sequences in the read header, but headers were reformatted using awk for compatibility with scPipe.
Read alignment was performed using the RSubread package (v2.6.4). An index was built using the Ensembl Mus musculus GRCm39 top level genome file and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm39 v109 GFF3 genome annotation file. BAM files were processed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
Additional gene annotation was obtained using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed, grouping samples by genotype (WT or Ifne KO), also incorporating the sequencing batch. Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function. Sample weights were incorporated and donor was used as a blocking factor, as there were technical replicates of mice WT10, Ifne13 and Ifne16 across the two sequencing batches.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the eBayes function. Differentially expressed genes were determined using a false discovery rate (FDR)-adjusted p-value < 0.05.
Assembly: mm39
Supplementary files format and content: Comma-separated text fiile with UMI-corrected counts for every gene and every sample

organism: Mus musculus

source_name: Testis

growth_protocol: Sexually mature male mice aged between 8–12 weeks were used in these experiments. IFNε-/- mice on C57BL/6J background were maintained in standard specific pathogen-free (SPF) conditions. Age matched C57BL/6J (WT) mice were used as controls, since the colony was maintained as a homozygous only colony, and therefore obtaining littermate controls was not possible. WT mice were purchased from Monash Animal Services Animals and were acclimatised for one week. All animal experiments were approved by the Monash Medical Centre Animal Ethics Committee and the Monash Animal Research Platform Animal Ethics Committee, and were performed in strict accordance with the National Health and Medical Research Council Code of Practice for the Care and Use of Animals for Experimental Purposes.

extract_protocol:
Total cellular RNA was extracted from snap frozen testes, using the RNeasy mini kit (QIAGEN GmBH, Hilden, Germany) with on-column DNAse treatment, following manufacturer's instructions. Total RNA concentration was quantified by Qubit (Invitrogen) and quality checked by Bioanalyzer (Agilent) or capillary electrophoresis (BiOptic QSep100). RNA samples with an RNA integrity number ≥7.0 were used for RNA-seq analysis.
Libraries were generated using an in-house multiplex RNA-seq method (version 01/09/2021) and were prepared using 25 ng (batch 1) or 30 ng (batch 2) of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. Illumina P5 was added by tagmentation by Nextera transposase and PCR and Illumina P7 was added by PCR. The library was designed so that the forward read (R1) used the standard R1 primer to sequence the cDNA in the sense direction for transcript identification. The index read (I1) used the standard i7 primer to sequence directly into the sample index and then the 10 bp UMI. Sequencing (R1 up to 111 bp; I1 18 bp) was performed on a NextSeq 2000 (Illumina) P2 100 cycle run, as per the manufacturer’s instructions. On-board denaturing and clustering were done using 900 pM of library pool (Illumina Protocol 1000000109376 v3 Nov2020).

treatment_protocol: Adult wildtype mice (WT) and Ifne-/- mice lacking IFNe were culled using carbon dioxide overdose at the age of 8–12 weeks. Serum and reproductive tract organs were collected for analysis.

tag: tissue

value: Testis

tag: genotype

value: WT

value: PBS

tag: donor

tag: batch


title: Testis, wild type, mouse WT26, batch 2

tag: strain


title: UT-TERT cells genx treated2

value: PFAS -GENX


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 22

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

data_processing:
Base calling: Base calling was done by Illumina Real Time Analysis (v3.4.4)
Demultiplex: output was demultiplexed and converted to FastQ format with Bcl2fastq (v2.20.0, Illumina).
Indexing: The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al., 2022) was indexed with STAR (v2.7.10a, except for the estrone exposure, which used v2.7.9a) and concurrently had in-house gene annotations loaded. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 149.
Quality control and trimming: After performing quality control on the raw FastQ data using FastQC and MultiQC (v1.12), raw reads were trimmed using Trim Galore! (v0.6.6) to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp. Trim Galore! is a wrapper script that makes use of the publicly available adapter trimming tool Cutadapt (v4.0).
Mapping: Trimmed reads were then mapped to the indexed genome with STAR version 2.7 using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS.  Samtools (v1.15.1) was used to sort and index the alignment files.
Assign counts: HTSeq (v2.0.1) was used to assign counts to each gene with the following parameters: -f bam -r pos -s no. FastQC and MultiQC (v1.12) were used to assess quality control metrics of the processed reads.  Counts to each gene were parsed, and count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Filter counts: Raw counts were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al., 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out.
Count normalization and filtering: Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Multidimensional scaling (MDS) plots were generated to look for possible outliers. Individual samples separated from all remaining replicate samples within the same treatment group on either the first or second principal component by >2x the span of all other samples on the corresponding PC axis were considered strong outliers and removed. If multiple potential outlier samples were present on the same PCA, they were only removed if each outlier sample corresponded to a different treatment group, as such samples were unlikely to represent any reproducible dose-dependent effect.
Assembly: assembly GCA_016745375.1
Supplementary files format and content: *.txt file raw count matrix
Supplementary files format and content: *.txt file count matrix with all filtering, normalization and quality control filters applied. Header rows provide unique sample ID and expsoure concentrations. Starting at row 5, rows are genes and columns are normalized counts with a psuedo-count of 1 added, log2 transformed, and filtered.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Total RNA was isolated from each homogenate using MagMAX-96 Total RNA Isolation kits (AM1830, Thermo Fisher Scientific, MA, USA) following the manufacturer’s instructions.  All isolated RNA was quantified with spectrophotometry (Synergy HTX plate reader and a Take3 microvolume plate, BioTek, VT, USA) and 16 randomly chosen RNA samples per 96-well plate were analyzed with electrophoresis (4200 Tapestation, Agilent, CA, USA) to confirm quality of the RNA isolation procedure (RINe > 9).
Each cDNA library was prepared from 250 ng of total RNA using commercially available kits that select for mRNA (SENSE mRNA-Seq Library Prep kit, Lexogen, NH, USA) following the manufacturer’s instructions.  The quality and size distribution of libraries was determined using a 4200 TapeStation, and concentrations were measured with a fluorescence-based assay (Quant-iT PicoGreen dsDNA Assay, Thermo Fisher Scientific, MA, USA).

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units

value: bisphenol A (DTXSID7020182)


title: Testis, Ifne KO, mouse Ifne16, batch 2

value: Ifne KO


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 32

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: extrapolated conc


title: UT-TERT cells mix treated2

tag: cell line

value: UT-TERT

tag: treatment

value: PFAS -MIX


title: Testis, Ifne KO, mouse Ifne13, batch 2

tag: tissue

value: Testis

tag: genotype

tag: donor

tag: batch

tag: strain


title: Testis, wild type, mouse WT10, batch 2

value: WT

value: PBS


title: UT-TERT cells control treated3

value: CTL


title: Testis, Ifne KO, mouse Ifne16, batch 1


title: UT-TERT cells control treated2


title: Testis, Ifne KO, mouse Ifne13, batch 1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 19

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: measured conc_units

tag: nominal conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 20

value: larvae

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: nominal conc_units


title: UT-TERT cells control treated1

tag: cell line

tag: treatment


title: Testis, Ifne KO, mouse Ifne15, batch 1

tag: tissue

tag: genotype

value: Ifne KO

tag: donor

tag: batch

tag: strain


title: Testis, Ifne KO, mouse Ifne14, batch 1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 18

tag: age

tag: dev stage

value: whole body

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: extrapolated conc

value: bisphenol A (DTXSID7020182)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 17

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: extrapolated conc_units


title: Testis, wild type, mouse WT10, batch 1

tag: tissue

value: Testis

tag: genotype

tag: treatment

tag: donor

tag: batch

tag: strain


title: COPD11,scRNAseq

city: Hangzhou

first: Baihui

last: lv

state: Zhejiang

address: Yuhangtang Road, Hangzhou City, Zhejiang Province

country: China

institute: Zhejiang University

description: Microwell seq 2.0

library_source: transcriptomic single cell

data_processing:
Following the Microwell methods, fastq file with N8 sequence data was converted to a txt.gz file using a Python script and label it by sample number. Imported all sample matrices into Rstudio and created Seurat objects using the Seurat toolkit in R. Quality control excluded feature transcripts with profiles below 200, total transcript below 500 or above 7000, and those with mitochondrial sources exceeding 10% of the total. The data was normalized and scaled using NormalizeData and ScaleData. Unsupervised clustering was performed on Seurat objects with Principal components analysis (PCA), Uniform manifold approximation and projection (UMAP) was used for dimensionality reduction. Harmony toolkit was applied to correct batch effect clustering errors. Cell group identities were determined using published single-cell lung tissue articles and the Zhejiang University Human Single Cell Atlas (https://bis.zju.edu.cn/HCL/gallery.html).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

molecule: polyA RNA

source_name: lung

extract_protocol:
18 patients who had lung tissue resection for conditions like lung cancer and pulmonary nodules were selected. They were divided into two groups based on whether their FEV1/FVC was below 70%: 11 patients with COPD and 7 control patients. Lung tissues were originated from the dorsal or basal segments. A tissue farthest from the lesion was excised in a 1 cm3 volume. The tissue was digested with 50 mg/ml collagenase V, and red blood cells were lysed in a buffer at 4℃ for 5 minutes. The subsequent procedures involved single cell separation, RNA capture, reverse transcription, barcode removal, DNA synthesis with random primers, PCR amplification, length screening, DNA library construction using the Illumina assay kit, and final sequencing analysis with a microplate system
Constructing a gene library with the Microwell method. The cDNA library was fragmented using a custom transposase from Illumina's TruePrep Kit V2, following the manufacturer's instructions. We substituted the index 2 primer with the P5 primer to selectively amplify fragments with the transcript's 3' end, while other fragments formed self-loops. The library was purified with AMPure XP beads to remove primer dimers and large fragments.

value: lung


title: C47_WB

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

country: Japan

institute: KDDI research Inc

library_source: genomic

data_processing:
The raw data underwent quality filtering based on their sequence quality using FastQC (v0.11.7). After trimming with Trimmomatic (v0.38), the remaining reads were mapped using Methylpy (v1.4.2). TDF files were generated using igvtools.
Assembly: CanFam3.1
Supplementary files format and content: Methylation levels at base resolution in TDF format

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: whole blood

extract_protocol:
Genomic DNA was extracted from whole blood using the DNeasy Blood and Tissue Kit (QIAGEN, Germantown, MD, USA) following the manufacturer’s protocol.
The Bisulfite conversion process was performed using the Zymo Research EZ DNA Methylation Gold Kit. For library preparation, the ABclonal Scale Methyl-DNA Lib Prep Kit was utilized. The libraries were prepared and sequenced externally at Novogene.

value: whole blood

value: Poodle (Toy)


title: COPD10,scRNAseq

description: Microwell seq 2.0


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 16

value: GLTED-Duluth-wt

tag: age

tag: dev stage

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: measured conc_units

tag: nominal conc_units


title: C44_WB


title: C45_WB


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 21

value: 5-6 dpf

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: nominal conc

tag: extrapolated conc


title: C43_WB

tag: tissue

tag: genotype


title: C14_WB

value: Shiba


title: COPD09,scRNAseq

description: Microwell seq 2.0


title: C42_WB

value: Dachshund (Miniature)


title: C46_WB


title: UT-TERT cells genx treated1

tag: cell line

value: UT-TERT

tag: treatment

value: PFAS -GENX


title: COPD08,scRNAseq

description: Microwell seq 2.0


title: Testis, wild type, mouse WT11, batch 1

value: WT

value: PBS

tag: donor

tag: batch

tag: strain


title: C11_WB


title: C12_WB


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 14

tag: age

tag: dev stage

value: larvae

value: whole body

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: exposure duration

tag: measured conc

value: mg/L

tag: extrapolated conc_units


title: COPD06,scRNAseq

description: Microwell seq 2.0

value: lung


title: COPD07,scRNAseq

description: Microwell seq 2.0


title: COPD05,scRNAseq

description: Microwell seq 2.0


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 13

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

value: bisphenol A (DTXSID7020182)


title: C7_WB

tag: tissue

value: whole blood

tag: genotype

value: Shiba


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 15

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: extrapolated conc

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 11

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: exposure duration

tag: measured conc


title: C13_WB

value: Poodle (Toy)


title: C8_WB

value: Dachshund (Miniature)


title: C5_WB


title: COPD04,scRNAseq

description: Microwell seq 2.0


title: C6_WB


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 10

value: larvae

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: extrapolated conc_units


title: C4_WB

tag: tissue


title: COPD03,scRNAseq

description: Microwell seq 2.0


title: C3_WB

tag: genotype


title: control 3

city: CINCINNATI

first: Behrouz

last: Shamsaei

state: OH

institute: university of Cincinnati

data_processing:
Fastq file were aligned with STAR to human genome GRCh38 and GENCODE version 35 definition of genes were used for counts quantification.
Count table was created by combining output from STAR.
Quality control was accessed by fastqc and RNASeQC.
Differentiation analysis were performed with EdgeR.
Assembly: GRch38
Supplementary files format and content: tab delimted file includes raw counts for each samples, with additional columns for genes description (id, symbol, descrition, positions)

growth_protocol: 786-O were grown in DMEM/F12 media with 10% serum.

extract_protocol:
RNA was extracted using miRNA isoaltion kit (Ambion)
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB) following manufacturer's protcol

treatment_protocol: Serum was incubated with CuSO4 overnight at 4oC to bind Cu ions to proteins. This serum was used in the media to expose cells to high Cu conditions. For control condition, serum was treated identivally except for addiotn of Cu.

tag: cell line

tag: cell type

value: renal cell carcinoma

value: wild type

value: No Cu control


title: COPD02,scRNAseq

description: Microwell seq 2.0


title: control 2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 9

tag: strain

tag: age

tag: dev stage

value: whole body

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 8

value: not determined

value: -80 deg C

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: exposure duration

tag: measured conc

value: mg/L

tag: extrapolated conc

tag: treatment


title: C9_WB

tag: tissue

value: whole blood

tag: genotype


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 7

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

value: Great Lakes Toxicology & Ecology Division

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: C10_WB


title: COPD01,scRNAseq

description: Microwell seq 2.0

value: lung


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 12

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: collected by

tag: measured conc_units

value: copper sulfate (DTXSID6034479)


title: Chronic Cu treatment 2

tag: cell line

tag: cell type

value: renal cell carcinoma

value: 31 uM chronic Cu


title: Chronic Cu treatment 3

value: wild type

value: 32 uM chronic Cu


title: Chronic Cu treatment 1

value: 30 uM chronic Cu


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 6

value: larvae

value: whole body

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

tag: exposure duration

tag: measured conc

tag: nominal conc

tag: nominal conc_units


title: CTL05,scRNAseq

description: Microwell seq 2.0

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 5

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: extrapolated conc

tag: treatment


title: C2_WB

value: whole blood

tag: genotype

value: Poodle (Toy)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 4

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: HCT116 CMC-treated rep1

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

description: Discover the pseudouridylation of the mammalian transcriptome

data_processing:
Raw data gained from Illumina HiSeqX10 with 150 bp paired end reads
Cutadapt (v2.8) was used to remove the adaptors of the paired-end reads with the following parameters: -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15. The paired-end reads without adaptors were further merged using FLASH software (v1.2.11) with following parameters: -z -m 10 -M 135 -x 0.25, and fastx_collapser software was used to collapse the reads with the default parameters. These filtered reads were subsequently mapped to the human reference genome (hg38) and transcriptome with STAR software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --alignEndsProtrude 150 ConcordantPair --limitOutSJcollapsed 5000000 --readFilesCommand zcat.
To identify significantly enriched Ψ sites, we calculated the coverage of reads ending one nucleotide upstream at each position and reads reading through each position in all annotated transcripts. We reasoned that reads ending one nucleotide upstream at a candidate Ψ site should be significantly higher over the one nucleotide upstream and downstream and over the corresponding position in the matched input sample. Finally, we developed the computational tools to calculate the coverage of reads reading through the candidate Ψ sites (totalCov) and the coverage of reads ending one nucleotide upstream at the candidate Ψ sites (endCov), the one nucleotide upstream (upCov) and the one nucleotide downstream (downCov) in the edu-Ψ-seq and input data. Citeria are defined by high confidence rRNA Ψ sites, for HEK293 libraries, a positive signal had to meet the following criteria: (1) upFold=endCov/upCov≥3; (2) downFold=endCov/downCov≥2.5; (3) upFoldFC=upFold/ctrlUpFold≥1.5; (4) downFoldFC=downFold/ctrlDownFold≥1.5; (5)StopRate≥0.04；(6)stopRateFC=StopRate/ctrlStopRate=(endCov/totalCov)/(ctrlEndCov/ctrlTotalCov) =2. For HCT116 libraries, a positive signal had to meet the following criteria: (1) upFold=endCov/upCov≥1.5; (2) downFold=endCov/downCov≥1.5;(3)downFoldFC=downFold/ctrlDownFold≥1.5; (4) StopRate≥0.04; (5) stopRateFC=StopRate/ctrlStopRate=(endCov/totalCov)/(ctrlEndCov/ctrlTotalCov) =3. A candidate Ψ site was retained when it satisfies the above criteria in two replicate of the experiments. These stringent parameters allowed us to identify the highest-confidence candidate Ψ sites.
Genome_build: hg38
Supplementary_files_format_and_content: bed files include stop read information for each CMC-treatment and CMC-control group, e.g. treatStopRatio, ctrlStopRatio
Supplementary_files_format_and_content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (rpm).

source_name: Human colorectal carcinoma cells

growth_protocol: HEK293T and HCT116 cells were clutured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. 12 ug of polyA+ RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PolyadenylatedRNA (polyA+ RNA) was isolated from 300 μg of total RNA using oligo d(T)25 magnetic beads.20 μg of polyA+ RNA was fragmented into ~250 nt by using magnesium RNA fragmentation buffer at 94 ℃ for 5 min following by treated with 100 μl of 0.2 M CMC in BEU buffe at 37 ℃ for 20 min and Na2CO3 buffer at 37 °C for 6 h.

tag: treatment label

value: CMC-treated

tag: cell line

value: wild type


title: CTL04,scRNAseq

description: Microwell seq 2.0

value: lung


title: HCT116 CMC-treated rep2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 3

value: larvae

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: exposure duration

tag: measured conc

tag: nominal conc

tag: nominal conc_units


title: control 1

tag: cell type

value: renal cell carcinoma

tag: treatment

value: No Cu control


title: CTL07,scRNAseq

description: Microwell seq 2.0

tag: tissue


title: HCT116 CMC-treated+Terminator rep2

description:
Discover the pseudouridylation of the mammalian transcriptome
HCT116_mRNA_CMC_Lacz_BEU_Lacz_rep2_all.bed

value: CMC+,RA3+,AP5+,Terminator+,DA3+ ,XhoI

tag: genotype


title: HCT116 CMC-untreated rep2

value: CMC-untreated


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 2

tag: strain

tag: age

tag: dev stage

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 1

value: GLTED-Duluth-wt

tag: biomaterial provider

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: measured conc_units

value: mg/L

tag: extrapolated conc_units

value: copper sulfate (DTXSID6034479)


title: HCT116 CMC-untreated knock down DKC1 rep2

description:
Discover the pseudouridylation of the mammalian transcriptome
HCT116_mRNA_shDKC1_1_CMC_Lacz_BEU_Lacz_rep2_all.bed

tag: treatment

tag: treatment label

tag: cell line

value: KD DKC1


title: HCT116 CMC-treated+Terminator rep1

description:
Discover the pseudouridylation of the mammalian transcriptome
HCT116_mRNA_CMC_Lacz_BEU_Lacz_rep1_all.bed

value: CMC-treated

tag: genotype

value: wild type


title: HCT116 CMC-treated+Terminator knock down DKC1 rep1

description:
Discover the pseudouridylation of the mammalian transcriptome
HCT116_mRNA_shDKC1_1_CMC_Lacz_BEU_Lacz_rep1_all.bed


title: CTL02,scRNAseq

description: Microwell seq 2.0

tag: tissue

value: lung


title: CTL06,scRNAseq

description: Microwell seq 2.0


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 90

tag: strain

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: nominal conc

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: HCT116 CMC-untreated knock down DKC1 rep1

value: CMC-untreated


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 89

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

value: less than limit of quantification

tag: extrapolated conc


title: CTL01,scRNAseq

description: Microwell seq 2.0


title: AUTAB3

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
The raw paired-end fastq reads underwent filtering by fastp to eliminate adapters and low-quality bases.
The resulting clean reads were then aligned to the genome using HISAT2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing StringTie.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene_count values for each Sample

source_name: Breast; Mammary gland

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424)
High-quality RNA  was used for library construction and sequencing. Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12309ES, China) following manufacturer’s recommendations.

value: Breast; Mammary gland

tag: cell line

tag: cell type

value: epithelial cell

tag: treatment

value: AUTAB


title: HEK293T CMC-treated+Terminator rep2

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_AndTer_BEU_rep2_all.bed

source_name: Human embryonic kidney 293 cells

tag: treatment label

tag: genotype


title: HCT116 CMC-untreated rep1


title: AUTAB2

tag: tissue


title: AUTAB1


title: CTL03,scRNAseq

description: Microwell seq 2.0


title: HEK293T CMC-treated+Terminator rep1

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_AndTer_BEU_rep1_all.bed


title: HEK293T CMC-untreated rep2

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_BEU_rep2_all.bed
HEK293T_CMC_AndTer_BEU_rep2_all.bed


title: HCT116 CMC-treated+Terminator knock down DKC1 rep2

value: CMC+,RA3+,AP5+,Terminator+,DA3+ ,XhoI


title: HEK293T CMC-untreated rep1

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_BEU_rep1_all.bed
HEK293T_CMC_AndTer_BEU_rep1_all.bed


title: PEI3

value: PEI


title: HEK293T CMC-treated rep1

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_BEU_rep1_all.bed


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 88

tag: strain

value: GLTED-Duluth-wt

tag: age

tag: dev stage

value: -80 deg C

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc_units

value: mg/L

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 87

value: 5-6 dpf

value: larvae

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: Great Lakes Toxicology & Ecology Division

tag: measured conc

tag: nominal conc

tag: nominal conc_units


title: HEK293T CMC-treated rep2

description:
Discover the pseudouridylation of the mammalian transcriptome
HEK293T_CMC_BEU_rep2_all.bed

tag: treatment

tag: treatment label

value: CMC-treated

tag: cell line

tag: genotype

value: wild type


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 86

tag: strain

tag: age

tag: dev stage

tag: tissue

value: whole body

value: not determined

tag: birth location

tag: breeding method

value: less than limit of quantification

tag: extrapolated conc

value: 4-nonylphenol (DTXSID5033836)


title: Input_of_H3K27ac_SAHA_3

first: Min

last: Huang

address: 555, Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

data_processing:
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Genomic alignment (version from UCSC genome browser) was using bowtie2 (version: 2.4.2) to get uniquely mapping reads.
MACS2 (version 2.2.7) was employed to perform peak calling with the corresponding input sample serving as control, then using Hommer(version:4.11.1) to annotate.
Genome_build: hg19

source_name: Breast Cancer

extract_protocol:
ChIP assay was performed using SimpleChIP Plus Enzymatic Chromatin IP Kit (#9005, Cell Signaling Technology) according to the procedures provided by the manufacturer.
The ChIP-Seq libraries were constructed following the Illumina ChIP-Seq library generation protocol.

treatment_protocol: MDA-MB-468 cells were treated with SAHA (10 μM, 12 hr) alone or in combination with sonidegib (10 μM, pretreatment for 72 hr).

tag: chip antibody


title: Input_of_H3K27ac_SAHA_1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 85

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration

tag: measured conc_units

tag: extrapolated conc_units


title: H3K27ac_SAHA_2

value: H3K27ac (#39133, Active Motif)


title: Input_of_H3K27ac_SAHA_2


title: PEI2

value: Breast; Mammary gland

tag: cell line

tag: cell type

value: epithelial cell

tag: treatment

value: PEI


title: Atz2

value: Atz


title: Atz3


title: H3K27ac_SAHA_1


title: PEI1


title: H3K27ac_SAHA_3


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 84

tag: strain

value: GLTED-Duluth-wt

tag: age

tag: dev stage

value: -80 deg C

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: measured conc

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 83

value: 5-6 dpf

value: larvae

tag: tissue

tag: Sex

tag: store cond

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: extrapolated conc


title: Input_of_H3K27ac_SAHA+sonidedgib_2

tag: chip antibody


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 82

value: whole body

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc_units

tag: extrapolated conc_units


title: H3K27ac_SAHA+sonidedgib_3


title: Input_of_H3K27ac_SAHA+sonidedgib_3


title: Atz1

tag: cell line

tag: cell type

tag: treatment


title: H3K27ac_SAHA+sonidedgib_2


title: Input_of_H3K27ac_SAHA+sonidedgib_1


title: H3K27ac_SAHA+sonidedgib_1


title: Input_of_H3K27me3_sonidedgib_3


title: Ctrl2

value: Ctrl


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 80

tag: strain

tag: age

tag: dev stage

value: not determined

tag: biomaterial provider

tag: measured conc

tag: nominal conc

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: Input_of_H3K27me3_sonidedgib_1

tag: chip antibody


title: Ctrl1

tag: tissue

value: Breast; Mammary gland


title: H3K27me3_sonidedgib_3

value: H3K27me3 (#9733, Cell Signaling Technology)


title: Input_of_H3K27me3_sonidedgib_2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 78

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: birth location

tag: breeding method

value: less than limit of quantification

tag: extrapolated conc


title: H3K27me3_sonidedgib_1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 77

tag: collected by

tag: exposure duration

tag: measured conc_units

tag: extrapolated conc_units

tag: treatment


title: Input_of_H3K27me3_con_1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 76

tag: strain

tag: age

tag: dev stage

tag: biomaterial provider

tag: measured conc


title: Ctrl3

tag: tissue

tag: cell line

tag: cell type

value: epithelial cell


title: Input_of_H3K27me3_con_3

tag: chip antibody


title: Input_of_H3K27ac_con_3


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 75

value: GLTED-Duluth-wt

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

tag: birth location

tag: nominal conc

tag: nominal conc_units


title: iEC, NOTCH1 WT, control untreated, rep 2

city: Columbus

first: Vidu

last: Garg

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description:
iEC_WT_NG2
DEseq_results_N1_WT.csv

data_processing:
FASTQ files were trimmed to remove Illumina adaptor sequences and low-quality reads using TrimGalore! in “paired” mode
Paired, trimmed reads were then aligned against Homo sapiens assembly version GRCh38.p14, GENCODE 44 (http://Jul2023.archive.ensembl.org/Homo_sapiens/Info/Annotation), using the STAR alignment tool (v2.7.10b) with “--quantMode TranscriptomeSAM” option
The transcriptome-aligned BAM was used to collect gene-level and transcriptome-level count estimates using RSEM (v1.3.1)
The gene count estimates were used to identify differentially expressed genes using DESeq2 (v1.34.0)
Assembly: Homo sapiens assembly version GRCh38.p14
Supplementary files format and content: raw_counts.csv: CSV file containing raw counts for each sample
Supplementary files format and content: DEseq_results_N1_WT.csv : CSV file containing DESeq2 output of  iEC NOTCH1 +/-  untreated control vs iEC NOTCH1 WT untreated control
Supplementary files format and content: DEseq_results_H2O2_N1_WT.csv : CSV file containing DESeq2 output of  iEC NOTCH1+/- H2O2 treated vs iEC WT H2O2 treated.

source_name: iPSC

growth_protocol: NCHi014 (NOTCH1 WT and NOTCH1 +/-)  induced pluripotent stem cells were cultured in complete E8 media until 90% confluency after which media was switched to endothelial cell differentiation media according to previously published protocol (DOI: 10.1007/7651_2021_427)

extract_protocol:
RNA was harvested using total RNA purification kit (Norgen Biotek).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Following differentiation into endothelial cells (iEC), a subset of iEC were exposed to EGM-2 media containing 50 micromolar hydrogen peroxide while the control subset were exposed to untreated EGM-2 media. Media was refreshed everyday for 4 days after which the cells were lysed and total RNA was extracted from each group.

value: iPSC

value: induced pluripotent stem cells

tag: genotype

value: NOTCH1 WT

tag: treatment

value: Untreated control


title: iEC, NOTCH1 WT, control untreated, rep 1

description:
iEC_WT_NG1
DEseq_results_N1_WT.csv


title: iEC, NOTCH1 WT, control untreated, rep 3

description:
iEC_WT_NG3
DEseq_results_N1_WT.csv


title: Input_of_H3K27ac_con_2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 79

tag: strain

tag: age

value: 5-6 dpf

value: larvae

value: -80 deg C

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: iEC, NOTCH1 WT, H2O2 treated, rep 3

description:
iEC_WT_H2O23
DEseq_results_H2O2_N1_WT.csv

tag: tissue

tag: cell line

tag: cell type

value: 50 micromolar H2O2 for 4 days


title: Input_of_H3K27ac_con_1

tag: chip antibody


title: H3K27me3_con_2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 73

tag: dev stage

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: Great Lakes Toxicology & Ecology Division

tag: measured conc

value: mg/L


title: iEC, NOTCH1 WT, H2O2 treated, rep 1

description:
iEC_WT_H2O21
DEseq_results_H2O2_N1_WT.csv

tag: genotype

tag: treatment


title: H3K27me3_con_3

value: H3K27me3 (#9733, Cell Signaling Technology)


title: iEC, NOTCH1 WT, H2O2 treated, rep 2

description:
iEC_WT_H2O22
DEseq_results_H2O2_N1_WT.csv


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 74

tag: strain

value: GLTED-Duluth-wt

tag: age

tag: breeding method

tag: collected by

tag: exposure duration

value: less than limit of quantification

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: H3K27ac_con_3

tag: chip antibody

value: H3K27ac (#39133, Active Motif)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 72

tag: dev stage

tag: tissue

tag: Sex

tag: store cond

tag: extrapolated conc

tag: extrapolated conc_units


title: H3K27me3_sonidedgib_2


title: H3K27ac_con_2


title: Input_of_H3K27me3_con_2


title: iEC, NOTCH1+/-, control untreated, rep 3

description:
iEC_N1_NG3
DEseq_results_N1_WT.csv

value: iPSC

tag: cell line

tag: cell type

value: induced pluripotent stem cells

tag: genotype

value: NOTCH1 +/-

value: Untreated control


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 81

tag: strain

tag: age

value: 5-6 dpf

value: larvae

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: measured conc

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 71

tag: dev stage

value: whole body

value: not determined

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: H3K27ac_con_1

tag: chip antibody


title: E11.5_KDR+/PECAM1+_tdTomato-

city: Oxford

first: Oliver

middle: Andrew

last: Stone

state: Oxfordshire

address: IDRM, Old Road Campus, Roosevelt Drive

department: Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description: FACS sorted CD45-CD41-KDR+/CD31+ Pax3Cre;tdTomato-ve cells

data_processing:
CellRanger 5.0.0 for cell calling and mapping to mm10 with the tdtomato gene added
Seurat 4.0 for normalisation and clustering
FastMNN for batch correction
PAGA-initiated FA2 for visualisation
Assembly: mm10
Supplementary files format and content: integrated.rds is a Seurat Object that contains all 6 samples
Supplementary files format and content: integrated_paga.h5py is a Scanpy Object that contains the PAGA analysis for all 6 samples
Supplementary files format and content: lymphatic.rds is a Seurat Object that contains the re-clustering of the LEC, LEC_Prog, Vein and Angioblast subset from the integrated object
Supplementary files format and content: subset_dynamic.h5ad is a Scanpy Object that contains the RNA velocity and CellRank analyses for the lymphatic subset

source_name: Angioblasts and endothelial cells

extract_protocol:
Embryos were dissociated using 2 mg/ml Collagenase IV and 0.2 mg/ml Dnase I in 10% FBS/PBS, stained with surface antibodies against CD41, CD45, KDR and CD31, then FACS sorted.
scRNA-seq libraries were produced using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

tag: tissue

value: Angioblasts and endothelial cells


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 70

tag: strain

tag: Sex

tag: store cond

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: Great Lakes Toxicology & Ecology Division

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units


title: E10.5_KDR+/PECAM1+_tdTomato+

description: FACS sorted CD45-CD41-KDR+/CD31+ Pax3Cre;tdTomato+ve cells


title: E11.5_KDR+/PECAM1+_tdTomato+


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 69

value: GLTED-Duluth-wt

tag: age

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

value: 4-nonylphenol (DTXSID5033836)


title: E10.5_KDR+/PECAM1+_tdTomato-


title: iEC, NOTCH1+/-, control untreated, rep 1

description:
iEC_N1_NG1
DEseq_results_N1_WT.csv

value: iPSC

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: E9.5_KDR+_tdTomato-

description: FACS sorted CD45-CD41-KDR+ Pax3Cre;tdTomato-ve cells


title: H3K27me3_con_1

value: H3K27me3 (#9733, Cell Signaling Technology)


title: iEC, NOTCH1+/-, H2O2 treated, rep 2

description:
iEC_N1_H2O22
DEseq_results_H2O2_N1_WT.csv

value: induced pluripotent stem cells

value: NOTCH1 +/-

value: 50 micromolar H2O2 for 4 days


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 68

value: 5-6 dpf

tag: dev stage

value: larvae

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 67

tag: strain

tag: age

tag: tissue

tag: Sex

tag: store cond

value: -80 deg C

value: USA:Minnesota, Duluth

value: less than limit of quantification

tag: extrapolated conc

tag: extrapolated conc_units


title: follicular B cell, anti-Dll4,48h, rep3

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description:
FO_48_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Assembly: GRCm38/mm10 cDNA
Supplementary files format and content: DLL1_DLL4.all.rawTPM.txt: matrix file of transript per million (TPM) values from pseudoalignment (Kallisto).
Supplementary files format and content: DLL1_DLL4.all.normExp.txt: matrix file of normalized TPM values for analyses performed (voom, limma).

source_name: spleen

growth_protocol: C57BL6 mice were purchased from Jackson Laboratories and housed in the University of Pennsylvania ULAR facilities.

extract_protocol:
Pure cell populations were FACS-sorted into Trizol reagent supplemented with 0.5% 2-mercaptoethanol. Phenol-Chloroform RNA isolation and precipitation was performed with glycogen carrier according to manufacturer protocol.
cDNA was prepared using Takara Clonetech SMART-seq HT kit and Illumina Nextera XT kits according to SMART-seq HT kit protocol.

treatment_protocol: 8-12 week old mice were injected intraperitoneally with 5 mg/kg anti-Dll1 (hIgG1 clone: YW161.11, Genentech), anti-Dll4 (hIgG1 clone: OR-216987, Genentech), or isotype control (anti-GD, hIgG1 clone: 5237, Genentech) 12-48 hours before sacrifice.

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: anti-Dll4, 48h


title: iEC, NOTCH1+/-, H2O2 treated, rep 1

description:
iEC_N1_H2O21
DEseq_results_H2O2_N1_WT.csv

tag: cell line

tag: treatment


title: E9.5_KDR+_tdTomato+

description: FACS sorted CD45-CD41-KDR+ Pax3Cre;tdTomato+ve cells

value: Angioblasts and endothelial cells


title: follicular B cell, anti-Dll4,24h, rep3

description:
FO_24_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll4, 24h


title: follicular B cell, anti-Dll4,48h, rep1

description:
FO_48_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: follicular B cell, anti-Dll4,48h, rep4

description:
FO_48_DL4_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: follicular B cell, anti-Dll4,24h, rep1

description:
FO_24_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: HPMC with OV90 spheroid-3

city: Lund

first: Kaname

last: Uno

address: Medicon Village Building 404:B3

department: Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
RNA sequencing data were analyzed using GensSpring (version 14.9.1, Agilent), with low-expressed genes filtered by applying a 20% minimum percentile cutoff to minimize noise.
The output was further processed in R (V 4.2.3) with RStudio (V 2023.06.0+421) as an integrated development environment. Intensities were log2-transformed and median-centered to produce expression matrix.
For clustering, principal component analysis (PCA), differentially expressed genes (DEG) analysis, gene ontology (GO) analysis, and gene set enrichment analysis (GSEA) analysis, the following R packages were used: mixOmics package (V 6.22.0) (Rohart et al. 2017), Limma package (V 3.54.2) (Ritchie et al., 2015), and clusterProfiler package (V 4.6.2) (Wu et al., 2021).
Gene set enrichment analysis (GSEA) was performed using a desktop application (http://www.broadinstitute.org/gsea/index.jsp). Human transcript models were based on hg38 (NCBI).
RNA sequencing data were compared between two groups: (i) OV90 spheroids with and without mesothelial cells, and (ii) mesothelial spheroids with and without OV90 cells. Differential expression analysis was conducted using the limma package, and principal component analysis (PCA) was performed using the mixOmics package. Statistically significant RNA expression was defined as a p-value <0.05 and a fold change >2.0 in hetero-cellular spheroids compared to single-cell spheroids.
Assembly: Human transcript models were based on hg38 (NCBI)
Supplementary files format and content: excel file includes raw counts for each sample

source_name: omentum

growth_protocol: OV90 and primary human mesothelial cells (HPMC) were mainteined in RPMI1640 with 10% fetal bovine serum (FBS) and penicillin/streptomycin with humidified atomosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the ReliaPrep RNA Miniprep System (Promega). RNA samples were diluted in 30 µL of nuclease-free water (two extractions of 15 µL each). RNA concentrations were confirmed to be > 10 ng/µL for all samples.
DNA libraries were generated with the Nextera XT DNA Sample Preparation Kit.

treatment_protocol:
Spheroid formation for 72 hours to form spheroids in ultra-low attachement 96-well round-bottome plates. Three types of cell components were incubated ; (i) OV90-GFP only (2,000 cells/well), (ii) HPMC cells only (4,000 cells/well), (iii) a co-culture of OV90-GFP and HPMC cells (2,000 cells/well each).
Before analyzing, these spheroids were disaggregated with trypsin and collected by FACS. Comparative gene expression profile analysis of RNA-seq data for (i) OV90-GFP cells with or without interaction with HPMC, and (ii) HPMC cells with or without interaction with OV90-GFP.

value: omentum

value: primary mesothelial cell

value: Mesothelilal cell

value: WT

value: spheroid formation


title: follicular B cell, anti-Dll4,12h, rep2

description:
FO_12_DL4_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll4, 12h


title: follicular B cell, anti-Dll4,12h, rep1

description:
FO_12_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 65

value: GLTED-Duluth-wt

tag: dev stage

value: whole body

value: not determined

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

value: mg/L

value: 4-nonylphenol (DTXSID5033836)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 64

tag: strain

tag: age

value: 5-6 dpf

value: larvae

value: -80 deg C

value: USA:Minnesota, Duluth

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

value: less than limit of quantification

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: follicular B cell, anti-Dll1,48h, rep4

description:
FO_48_DL1_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: anti-Dll1, 48h


title: OV90 with HPMC spheroid-3

source_name: ovarian cancer

value: ovarian cancer

tag: cell line

value: Epithelial ovarian cancer

value: GFP-labbeled

tag: treatment

value: spheroid formation


title: follicular B cell, anti-Dll4,12h, rep3

description:
FO_12_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll4, 12h


title: HPMC only spheroid-3

value: omentum

value: primary mesothelial cell

value: Mesothelilal cell

value: WT


title: follicular B cell, anti-Dll1,48h, rep3

description:
FO_48_DL1_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: iEC, NOTCH1+/-, control untreated, rep 2

description:
iEC_N1_NG2
DEseq_results_N1_WT.csv

value: iPSC

value: induced pluripotent stem cells

value: NOTCH1 +/-

value: Untreated control


title: OV90 only spheroid-3


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 63

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: less than limit of quantification

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: follicular B cell, anti-Dll1, 24h, rep4

description:
FO_24_DL1_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: follicular B cell

value: anti-Dll1, 24h


title: follicular B cell, anti-Dll1,48h, rep1

description:
FO_48_DL1_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll1, 48h


title: follicular B cell, anti-Dll1, 24h, rep3

description:
FO_24_DL1_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 66

tag: strain

tag: age

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration


title: iEC, NOTCH1+/-, H2O2 treated, rep 3

description:
iEC_N1_H2O23
DEseq_results_H2O2_N1_WT.csv

tag: tissue

value: iPSC

tag: cell type

value: induced pluripotent stem cells

tag: genotype

value: NOTCH1 +/-

value: 50 micromolar H2O2 for 4 days


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 61

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: follicular B cell, anti-Dll1, 12h, rep2

description:
FO_12_DL1_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll1, 12h


title: HPMC with OV90 spheroid-2

value: omentum

tag: cell line

value: primary mesothelial cell

value: Mesothelilal cell

value: WT

value: spheroid formation


title: follicular B cell, anti-Dll1, 12h, rep4

description:
FO_12_DL1_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: follicular B cell


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 60

tag: strain

tag: Sex

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: follicular B cell, anti-Dll1, 12h, rep1

description:
FO_12_DL1_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue


title: follicular B cell, isotype control, rep4

description:
FO_48_Iso_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: cell type

value: isotype control, 48h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 59

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

value: larvae

value: whole body

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

value: copper sulfate (DTXSID6034479)


title: follicular B cell, isotype control, rep3

description:
FO_48_Iso_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: genotype

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 62

tag: strain

tag: dev stage

value: not determined

tag: measured conc

value: less than limit of quantification

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: OV90 with HPMC spheroid-2

value: ovarian cancer

tag: cell line

value: Epithelial ovarian cancer

value: GFP-labbeled

value: spheroid formation


title: follicular B cell, isotype control, rep2

description:
FO_48_Iso_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue

value: spleen

value: follicular B cell


title: HPMC only spheroid-2

value: omentum

value: primary mesothelial cell

tag: cell type

value: Mesothelilal cell

value: WT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 58

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: Sex

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: OV90 only spheroid-2

value: ovarian cancer

value: Epithelial ovarian cancer

tag: genotype

tag: treatment


title: follicular B cell, isotype control, rep1

description:
FO_48_Iso_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: isotype control, 48h


title: marginal zone B cell, anti-Dll4, 48h, rep4

description:
MZ_48_DL4_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: marginal zone B cell

value: anti-Dll4, 48h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 57

tag: strain

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

value: less than limit of quantification


title: marginal zone B cell, anti-Dll4, 48h, rep3

description:
MZ_48_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue

tag: cell type


title: HPMC with OV90 spheroid-1

value: omentum

tag: cell line

value: primary mesothelial cell

value: Mesothelilal cell

value: WT

value: spheroid formation


title: OV90 with HPMC spheroid-1

value: GFP-labbeled


title: marginal zone B cell, anti-Dll4, 48h, rep2

description:
MZ_48_DL4_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: marginal zone B cell, anti-Dll4, 24h, rep4

description:
MZ_24_DL4_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll4, 24h


title: marginal zone B cell, anti-Dll4, 48h, rep1

description:
MZ_48_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 56

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: Sex

tag: store cond

value: -80 deg C

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: measured conc

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: follicular B cell, anti-Dll1, 24h, rep1

description:
FO_24_DL1_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: follicular B cell

tag: genotype

tag: treatment

value: anti-Dll1, 24h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 55

tag: strain

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: Great Lakes Toxicology & Ecology Division

value: less than limit of quantification

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 53

tag: tissue

tag: birth location

tag: breeding method

tag: collected by

tag: exposure duration


title: marginal zone B cell, anti-Dll4, 24h, rep2

description:
MZ_24_DL4_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: cell type

value: marginal zone B cell

value: anti-Dll4, 24h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 54

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: Sex

tag: store cond

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: marginal zone B cell, anti-Dll4, 24h, rep1

description:
MZ_24_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: genotype

tag: treatment


title: marginal zone B cell, anti-Dll4, 24h, rep3

description:
MZ_24_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: marginal zone B cell, anti-Dll4, 12h, rep3

description:
MZ_12_DL4_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll4, 12h


title: MIP_nasal_swab_left_spia

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
Human Left nasal swab_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

data_processing:
quality control with FastQCv0.12.1
adapter removal with Cutadatv4.4 (bulk, SPE) and seqtkv1.2-r122 (MIP)
alignment with BWA-MEMv0.7.12-r1188
read extraction and filtering with bamtoolsv2.5.2 (MAPQ >30, NM<4)
count tables generated with SAMtoolsv0.7.17-r1188
Assembly: GCF_017329165.1 (Sa M2872), GCF_006094375.1 (Se ATCC 14990), GCF_002993865.1 (Sa USA300)
Supplementary files format and content: Supp_Table_06_Bulk_data_expdb.xlsx: table of bulk RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_05_Bulk_data_refdb.xlsx: table of bulk RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_08_MIP_data_expdb.xlsx: table of MIP RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_07_MIP_data_refdb.xlsx: table of MIP RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_10_SPE_data_expdb.xlsx: table of SPE RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_09_SPE_data_refdb.xlsx: table of SPE RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.

source_name: nasal swab

extract_protocol:
RNA was extracted using RNeasy 96 QIAcube HT kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions. Samples were eluted in nuclease-free water (Qiagen, Hilden, Germany) and frozen at -80°C until sequencing preparation.
The sequencing libraries were prepared with NEBNext rRNA Depletion Kit v2 (New England Biolabs, Ipswich, MA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following the manufacturer’s directions.

treatment_protocol: S. aureus and S. epidermidis were grown in TSB, TSB pH 4.8 or on reconstructed human epidermidis for bulk and targted RNA-seq with and without ribo-depletion and/or SPIA.

value: nasal swab

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 2

tag: treatment rrna

value: no ribo-depletion

tag: treatment spia

value: SPIA


title: MIP_nasal_swab_right_spia

description:
Human Right nasal swab_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

tag: tissue


title: OV90 only spheroid-1

value: ovarian cancer

tag: cell line

value: Epithelial ovarian cancer

value: GFP-labbeled

value: spheroid formation


title: marginal zone B cell, anti-Dll1, 48h, rep4

description:
MZ_48_DL1_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: anti-Dll1, 48h


title: marginal zone B cell, anti-Dll4, 12h, rep1

description:
MZ_12_DL4_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: marginal zone B cell, anti-Dll4, 12h, rep2

description:
MZ_12_DL4_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: marginal zone B cell, anti-Dll1, 48h, rep3

description:
MZ_48_DL1_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: MIP_nasal_swab_right_half_spia

description:
Human Right nasal swab_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: half SPIA


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 52

tag: strain

tag: dev stage

value: larvae

value: whole body

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

value: less than limit of quantification

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: HPMC only spheroid-1

value: omentum

value: primary mesothelial cell

tag: cell type

value: Mesothelilal cell

tag: genotype

value: WT

tag: treatment


title: MIP_nasal_swab_left_half_spia

description:
Human Left nasal swab_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: nasal swab

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 2

tag: treatment rrna

value: no ribo-depletion

tag: treatment spia


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 51

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

tag: Sex

tag: store cond

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: marginal zone B cell, anti-Dll1, 48h, rep1

description:
MZ_48_DL1_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

tag: cell type

value: marginal zone B cell

value: anti-Dll1, 48h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 50

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

value: less than limit of quantification

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: marginal zone B cell, anti-Dll1, 12h, rep4

description:
MZ_12_DL1_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue

tag: genotype

tag: treatment

value: anti-Dll1, 12h


title: MIP_human_DNA

description:
10ng Human blood gDNA (#5)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

source_name: blood

value: blood

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 1

tag: treatment rrna

value: no ribo-depletion

tag: treatment spia

value: no SPIA


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 49

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

tag: store cond

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: marginal zone B cell, anti-Dll1, 12h, rep3

description:
MZ_12_DL1_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

tag: cell type

value: marginal zone B cell


title: marginal zone B cell, anti-Dll1, 12h, rep2

description:
MZ_12_DL1_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 48

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 47

tag: strain

tag: age

tag: dev stage

tag: Sex

value: mg/L

tag: treatment

value: copper sulfate (DTXSID6034479)


title: marginal zone B cell, isotype control, rep3

description:
MZ_48_Iso_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: genotype

value: isotype control, 48h


title: marginal zone B cell, isotype control, rep4

description:
MZ_48_Iso_4
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: cell type


title: SPE_ICHT_DNA

description:
ICHT_24_3_Human Source_well H4
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

source_name: skin

tag: tissue

value: skin

tag: seqeuncing appraoch

value: Allegro (SPE)

tag: experimental batch

value: batch 1

tag: treatment rrna

value: no ribo-depletion

tag: treatment spia


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 46

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

value: 4-nonylphenol (DTXSID5033836)


title: marginal zone B cell, isotype control, rep1

description:
MZ_48_Iso_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: spleen

value: marginal zone B cell

tag: genotype

tag: treatment


title: U20S cells WT rep 3

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

data_processing:
ChromRNASeq adapters were trimmed using Cutadapt (version 4.4)  in paired end mode and the quality of the resulting fastq files were assessed using FastQC
The trimmed reads were then aligned to human hg19 reference genome using STAR aligner
Each alignment file was then split using Samtools into two alignment files containing positively stranded and negatively stranded reads
Strand specific coverage files containing CPM normalized read count per nucleotide position was generated for each alignment using deeptools bamCoverage
ComputeMatrix operation of deepTools was then performed on the strand separated bigwig files to calculate the CPM coverage in the 2.5kb flanking region of AsiSI site with bin size set at one
Assembly: hg19
Supplementary files format and content: bigwig containing CPM coverage at each nucleotide position (non-strand separated coverage)

source_name: Bone

extract_protocol:
RNA was extracted by Trizol/chloroform RNA extraction, and further cleaning (to get rid of DNA contamination) with Monarch® Total RNA Miniprep Kit (NEB,T2010S) by following manufacturer's protocol.
Sequencing libraries preparation was performed with the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) followed by paired-end sequencing on HiSeq6000 (Illumina).
library strategy: chrRNA-Seq

treatment_protocol: The wild-type U2OS orAsiSI-ER U2OS cells with proper RNAi reaching 50%-70% confluency in 15cm dish (~4-8 million cells) before starting of work. Following DSB induction, cells were washed and harvested by gently scrapping into 5mL PBS and pelleted by centrifuge (400g, 5min, 4°C). The cell pellets were lysed with 4 mL HLB+N buffer [10mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40], and underlaid with 1 mL HLB+NS buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10% sucrose] before spin at 400g for 5min (4°C) to collect the nuclear pellets. Cytoplasmic fragment was collected for western blot to confirm the successful breakage of cells. Next, nuclear pellets were lysed and resuspended in 125µLNUN1 buffer [20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, 50% glycerol], and chromatin was extracted by incubating in 1.2 mL NUN2 buffer [20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% NP-40, 1M urea] on ice for 15min with interval vortex in every 3-4 min. The chromatin samples were then collected by full speed spin at 4°C for 15min. To digest DNA and chromatin-associated proteins, 2µL/sample Proteinase K(20ug/uL)(NEB,P8107S) and 1µL/sample Turbo DNase in 1X Turbo DNase Buffer (100µL/sample)(Thermo fisher,AM2238) was added to digest chromatin pellets at37°Cwith 1000rpm shake until pellets were dissolved.

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: osteosarcoma

value: WT


title: S1pr1-/-, follicular B cell, anti-Notch2, 96h, rep4

description:
FO_s1pr1ko_96h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Assembly: GRCm38/mm10 cDNA
Supplementary files format and content: S1pr1.all.rawTPM.txt: matrix file of transript per million (TPM) values from pseudoalignment (Kallisto).
Supplementary files format and content: S1pr1.all.normExp.txt: matrix file of normalized TPM values for analyses performed (voom, limma).

growth_protocol: Mb1Cre (B6.C(Cg)-Cd79atm1(cre)Reth/EhobJ) and S1pr1Flox (B6.129S6(FVB)-S1pr1tm2.1Rlp/J) mice were bred and housed in the University of Pennsylvania ULAR facilities.

treatment_protocol: Mice were injected intraperitoneally with 5 mg/kg anti-Notch2 (mIgG2a clone: YW163.54.76, Genentech) or isotype control (anti-ragweed, mIgG2a clone: 10D9.W.STABLE, Genentech) antibody 48-96 hours before sacrifice.

value: follicular B cell

value: anti-Notch2, 96h


title: marginal zone B cell, isotype control, rep2

description:
MZ_48_Iso_2
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt


title: marginal zone B cell, anti-Dll1, 24h, rep3

description:
MZ_24_DL1_3
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

value: anti-Dll1, 24h