title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 45

tag: strain

tag: age

tag: dev stage

value: whole body

tag: Sex

value: not determined

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: collected by

value: less than limit of quantification

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: U20S cells WT rep 1

status: Public on Oct 18 2024

type: SRA

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

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)

molecule: total RNA

organism: Homo sapiens

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

tag: genotype

value: WT

tag: treatment


title: S1pr1-/-, follicular B cell, anti-Notch2, 96h, rep2

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

country: USA

institute: University of Pennsylvania

description:
FO_s1pr1ko_96h_02
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).

molecule: polyA RNA

organism: Mus musculus

source_name: spleen

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.

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: 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: spleen

value: follicular B cell

value: anti-Notch2, 96h


title: U20S cells WT rep 2


title: marginal zone B cell, anti-Dll1, 24h, rep1

description:
MZ_24_DL1_1
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).

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

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: marginal zone B cell

value: anti-Dll1, 24h


title: S1pr1-/-, follicular B cell, anti-Notch2, 96h, rep1

description:
FO_s1pr1ko_96h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: control, follicular B cell, anti-Notch2, 96h, rep2

description:
FO_mb1cre_96h_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: MIP_SE_DNA_1ng_human_10ng

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
1ng SE + 10ng Human gDNA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

library_source: genomic

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.

molecule: genomic DNA

source_name: skin + bacterial culture

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: skin + bacterial culture

tag: strain se

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 44

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).

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

value: larvae

value: whole body

value: not determined

tag: store cond

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

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

value: 4-nonylphenol (DTXSID5033836)


title: control, follicular B cell, anti-Notch2, 96h, rep1

description:
FO_mb1cre_96h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

tag: treatment

value: anti-Notch2, 96h


title: control, follicular B cell, anti-Notch2, 96h, rep3

description:
FO_mb1cre_96h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: S2-D ccRCC stage-III tissue

city: CINCINNATI

first: Behrouz

last: Shamsaei

state: OH

institute: university of Cincinnati

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequencing were aligned to homo sapiens genome to extract gene expression count using Space Ranger default setting
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_position_list.csv: list of spatial barcodes and coordinates specifying spots
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue imgage
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Library strategy: Spatial transcriptomics

source_name: formalin-fixed paraffin-embedded (FFPE) tissue

extract_protocol:
FFPE ccRCC tissue were cut following 10x genomics protocol.
Spatial transcriptomics sequencing libraries were prepared with 10x Genomics Visium spatial gene expression slides

value: clear Cell Renal Cell Carcinoma

tag: Stage

value: III

value: renal cell carcinoma

tag: bmi

tag: smoking status

value: never smoker


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 42

tag: strain

tag: age

tag: dev stage

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).

tag: collected by

value: Great Lakes Toxicology & Ecology Division

value: less than limit of quantification

value: mg/L

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 43

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

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


title: marginal zone B cell, anti-Dll1, 12h, rep1

description:
MZ_12_DL1_1
DLL1_DLL4.all.rawTPM.txt
DLL1_DLL4.all.normExp.txt

tag: tissue

tag: cell type

value: marginal zone B cell

tag: genotype

tag: treatment

value: anti-Dll1, 12h


title: S2-C ccRCC stage-III tissue

tag: Stage

tag: age

tag: bmi

tag: smoking status

value: current smoker


title: S1pr1-/-, follicular B cell, anti-Notch2, 48h, rep3

description:
FO_s1pr1ko_48h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: spleen

value: follicular B cell

value: anti-Notch2, 48h


title: S1pr1-/-, follicular B cell, anti-Notch2, 48h, rep4

description:
FO_s1pr1ko_48h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 41

tag: strain

tag: dev stage

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

value: USA:Minnesota, Duluth

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

tag: collected by

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: control, follicular B cell, anti-Notch2, 48h, rep3

description:
FO_mb1cre_48h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue


title: control, follicular B cell, anti-Notch2, 48h, rep4

description:
FO_mb1cre_48h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: cell type


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 40

tag: geo loc_name

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).

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


title: S1pr1-/-, follicular B cell, anti-Notch2, 48h, rep1

description:
FO_s1pr1ko_48h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: genotype

tag: treatment


title: S2-B ccRCC stage-III tissue

value: clear Cell Renal Cell Carcinoma

tag: Stage

value: III

value: renal cell carcinoma

tag: age

tag: bmi

tag: smoking status

value: former smoker


title: control, follicular B cell, anti-Notch2, 48h, rep1

description:
FO_mb1cre_48h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 39

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

tag: store cond

tag: collection date

tag: collected by

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: S1pr1-/-, follicular B cell, isotype control, rep4

description:
FO_s1pr1ko_iso_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue

value: spleen

tag: cell type

value: follicular B cell

value: isotype control, 48h


title: U20S cells siCtrl +4OHT rep2

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)
Library strategy: chrRNA-Seq

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).

value: Bone

tag: cell line

value: osteosarcoma

tag: genotype

value: AsiSI

value: siCtrl +4OHT


title: S1-D ccRCC stage-III tissue

tag: Stage

value: never smoker


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 38

tag: age

value: not determined

value: -80 deg C

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: exposure duration

tag: measured conc

value: less than limit of quantification

tag: measured conc_units

tag: nominal conc

tag: treatment

value: 4-nonylphenol (DTXSID5033836)


title: U20S cells siCtrl +4OHT rep3


title: S1pr1-/-, follicular B cell, isotype control, rep1

description:
FO_s1pr1ko_iso_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: S1-B ccRCC stage-III tissue

value: clear Cell Renal Cell Carcinoma

value: III

value: renal cell carcinoma

tag: bmi

tag: smoking status

value: former smoker


title: S1pr1-/-, follicular B cell, isotype control, rep2

description:
FO_s1pr1ko_iso_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue

value: spleen

value: follicular B cell

value: isotype control, 48h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 37

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

tag: store cond

tag: collection date

tag: collected by

value: Great Lakes Toxicology & Ecology Division

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: control, follicular B cell, isotype control, rep 2

description:
FO_mb1cre_iso_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: cell type

tag: genotype


title: U20S cells siINTS6 +4OHT rep3

value: Bone

tag: cell line

value: osteosarcoma

value: AsiSI

value: siINTS6 + 4OHT


title: control, follicular B cell, isotype control, rep 3

description:
FO_mb1cre_iso_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: control, follicular B cell, isotype control, rep 1

description:
FO_mb1cre_iso_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 36

tag: age

value: not determined

value: -80 deg C

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: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

value: 4-nonylphenol (DTXSID5033836)


title: control, follicular B cell, isotype control, rep 4

description:
FO_mb1cre_iso_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue

value: spleen

value: follicular B cell

tag: treatment

value: isotype control, 48h


title: U20S cells siCtrl +4OHT rep1

value: siCtrl +4OHT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 35

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

tag: store cond

tag: collection date

tag: collected by

tag: nominal conc_units


title: control, follicular B cell, anti-Notch2, 48h, rep2

description:
FO_mb1cre_48h_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: cell type

tag: genotype

value: anti-Notch2, 48h


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

description:
MZ_s1pr1ko_96h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: marginal zone B cell

value: anti-Notch2, 96h


title: S1pr1-/-, marginal zone B cell, anti-Notch2, 96h, rep2

description:
MZ_s1pr1ko_96h_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 34

tag: age

value: not determined

tag: geo loc_name

tag: biomaterial provider

tag: birth location

value: Great Lakes Toxicology & Ecology Division

value: less than limit of quantification

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units


title: S1pr1-/-, follicular B cell, isotype control, rep3

description:
FO_s1pr1ko_iso_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue


title: S1pr1-/-, marginal zone B cell, anti-Notch2, 96h, rep1

description:
MZ_s1pr1ko_96h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: treatment


title: control, marginal zone B cell, anti-Notch2, 96h, rep3

description:
MZ_mb1cre_96h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: control, marginal zone B cell, anti-Notch2, 96h, rep2

description:
MZ_mb1cre_96h_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: U20S cells siINTS6 +4OHT rep1

value: Bone

tag: cell line

value: osteosarcoma

value: AsiSI

value: siINTS6 + 4OHT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 33

tag: strain

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: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

value: 4-nonylphenol (DTXSID5033836)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 32

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

tag: Sex

tag: store cond

tag: collection date

tag: collected by

tag: nominal conc_units


title: S1pr1-/-, marginal zone B cell, anti-Notch2, 48h, rep4

description:
MZ_s1pr1ko_48h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: spleen

tag: cell type

value: marginal zone B cell

tag: genotype

value: anti-Notch2, 48h


title: control, marginal zone B cell, anti-Notch2, 96h, rep1

description:
MZ_mb1cre_96h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue

value: anti-Notch2, 96h


title: S1pr1-/-, marginal zone B cell, anti-Notch2, 48h, rep3

description:
MZ_s1pr1ko_48h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: treatment


title: control, marginal zone B cell, anti-Notch2, 48h, rep4

description:
MZ_mb1cre_48h_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 31

tag: age

value: not determined

tag: geo loc_name

tag: biomaterial provider

tag: birth location

value: Great Lakes Toxicology & Ecology Division

value: less than limit of quantification

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units


title: H9_iNK_NKG2A_KO rep2

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

description: raw gene count and TPM

data_processing:
Real-Time Analysis (RTA) v3.4.4 software was used for base calling and Illumina BCL
Convert v3.9.3 to convert base call (BCL) files into FASTQ files
Subread package (release 2.0.6) was used for allignment
featureCounts was used for gene counts
Assembly: human hg38 genome
Supplementary files format and content: csv  featureCount output
Supplementary files format and content: csv TPM+1

source_name: Embronic stem cell

growth_protocol: NK medium

extract_protocol:
triZol
KAPA mRNA HyperPrep kit

value: Embronic stem cell

tag: cell line

value: H9 NK NKG2A-KO clone D

value: hPSC derived NK cells

value: cell line

tag: library label_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 29

tag: strain

tag: dev stage

tag: Sex

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: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

value: 4-nonylphenol (DTXSID5033836)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 30

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

tag: tissue

value: whole body

tag: store cond

tag: collection date

tag: collected by

tag: nominal conc_units

tag: treatment


title: PBMC_iNK_NKG2A_KO rep2

description: raw gene count and TPM

source_name: PBMC

value: PBMC

value: PBiPS-NK NKG2A-KO clone B

tag: cell type

tag: genotype


title: H9-iNK

description: raw gene count and TPM

tag: cell line

value: H9 NK

value: wild type

tag: library label_name


title: S1pr1-/-, marginal zone B cell, anti-Notch2, 48h, rep1

description:
MZ_s1pr1ko_48h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: spleen

value: marginal zone B cell

value: anti-Notch2, 48h


title: S1pr1-/-, marginal zone B cell, isotype control, rep4

description:
MZ_s1pr1ko_iso_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: isotype control, 48h


title: control, marginal zone B cell, anti-Notch2, 48h, rep3

description:
MZ_mb1cre_48h_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: control, marginal zone B cell, anti-Notch2, 48h, rep2

description:
MZ_mb1cre_48h_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: H9_iNK_NKG2A_KO rep1

description: raw gene count and TPM

value: Embronic stem cell

value: H9 NK NKG2A-KO clone B

value: hPSC derived NK cells

value: cell line


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 28

tag: strain

tag: age

tag: dev stage

value: not determined

value: -80 deg C

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

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: S1pr1-/-, marginal zone B cell, isotype control, rep3

description:
MZ_s1pr1ko_iso_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: tissue


title: U20S cells siINTS6 +4OHT rep2

value: Bone

value: osteosarcoma

value: AsiSI

value: siINTS6 + 4OHT


title: PBMC_iNK

description: raw gene count and TPM

value: PBMC

value: PBiPS-NK

value: wild type


title: PBMC_iNK_NKG2A_KO rep1

description: raw gene count and TPM

value: PBiPS-NK NKG2A-KO clone A

value: hPSC derived NK cells


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 26

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: S1pr1-/-, marginal zone B cell, isotype control, rep1

description:
MZ_s1pr1ko_iso_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: spleen

tag: cell type

value: marginal zone B cell

tag: genotype

tag: treatment

value: isotype control, 48h


title: IMR90 rep1

description: raw gene count and TPM

source_name: fibroblast

value: fibroblast

tag: cell line

value: IMR90 FBiPS-NK

value: cell line

tag: library label_name


title: control, marginal zone B cell, isotype control, rep 4

description:
MZ_mb1cre_iso_04
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: PBMC rep3

description: raw gene count and TPM

value: PBMC

value: PB-NK

value: Primary NK cells


title: control, marginal zone B cell, anti-Notch2, 48h, rep1

description:
MZ_mb1cre_48h_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: anti-Notch2, 48h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 25

tag: strain

tag: age

tag: dev stage

value: -80 deg C

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

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

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: PBMC rep2

description: raw gene count and TPM

tag: tissue

value: wild type


title: plasma, 9982, day 11

city: Grugliasco

first: Eugenio

last: Martignani

state: TO

address: Largo Braccini 2

department: Veterinary Science

country: Italy

institute: University of Torino

data_processing:
• Base calling and demultiplexing. Processing raw data for both format conversion and de-multiplexing by Bcl2Fastq1 2.20 version of the Illumina pipeline. • The sRNAbench tool, a sRNAtoolbox2,3 tool, which gives expression profiling of small RNAs, prediction of novel microRNAs, analysis of isomiRs, genome mapping and read length statistics. ---- Mapping parameters and Annotations ---- Number of allowed mismatches: 0 (mm=0) Alignment type: seed alignment (alignType=n) Length of the seed: 20 (seed=20) Used genome assembly bowtie1 index: Oar_rambouillet_v1_0_mp Minimum number of reads: 2 Minimum read length: 15 No maximum read length: ---- ANNOTATIONS ---- Used miRNAs reference species from miRBase v22 Used miRNAs for species: oar Used ncRNA annotations: libs=Oar_rambouillet_v1_0_RNAcentral (RNAcentral database 20.0) libs=Oar_rambouillet_v1_0_ncRNA (ncRNA from Ensembl release 104 (51 for Metazoan)) libs=Oar_rambouillet_v1_0_cdna (cDNA from Ensembl release 104 (51 for Metazoan))
Assembly: miRBase v22, oar species
Supplementary files format and content: txt formatted file containing sequence, annotation, read counts and normalized read counts

organism: Ovis aries

source_name: Blood plasma

extract_protocol:
Samples were extracted from 500ul plasma with Maxwell® RSC miRNA Plasma and Serum Kit, with a Maxwell RSC. Both instrument and reagents were from Promega Corporation
QIAseq miRNA library kit (QIAGEN, Hilden, Germany) has been used for library preparation following the manufacturer’s instructions. Libraries were prepared for sequencing and sequenced on single-end 150 bp mode

value: Blood plasma

tag: time

value: day 11

tag: breed

value: Frabosana-Roaschina

tag: Sex

value: female


title: plasma, 6150, day 11


title: PBMC rep1

description: raw gene count and TPM

tag: cell type


title: control, marginal zone B cell, isotype control, rep 2

description:
MZ_mb1cre_iso_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: spleen

value: marginal zone B cell

tag: genotype

value: isotype control, 48h


title: control, marginal zone B cell, isotype control, rep 1

description:
MZ_mb1cre_iso_01
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

tag: treatment


title: plasma, 6149, day 11


title: LOAD35 BA9+BA20+H;HD1 BA9+BA20+H PM086

city: New York

first: John

last: Tuddenham

state: NY

institute: Columbia University

description:
LOAD35 BA9+BA20+H;HD1 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

library_source: transcriptomic single cell

data_processing:
Fastq files were run through 10x Genomics Cellranger v3.1.0.
Assembly: hg38.91
Supplementary files format and content: Counts tables for all barcodes, filtered by CellRanger, in standard hdf5 output from CellRanger. For samples with cell hashing, HTO count library is also included.

extract_protocol:
CD45+ cells were isolated from autopsy tissue or surgical resections using a cold mechanical dissociation protocol, as described in our publication. (Tuddenham, Taga, Haage, et al. 2022)
10x Genomics Chromium 3' v2 and v3 chemistry

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (5,6,7,8,9,10)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 27

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

value: not determined

tag: store cond

tag: collection date

tag: breeding method

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: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 23

tag: strain

tag: age

tag: dev stage

tag: tissue

value: -80 deg C

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

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

tag: nominal conc_units

value: 4-nonylphenol (DTXSID5033836)


title: plasma, 0012, day 11

value: Blood plasma

tag: time

value: day 11

tag: breed

value: Frabosana-Roaschina

tag: Sex

value: female


title: Myc-/-, follicular B cell, anti-Notch2, rep5

description:
FO.Flox.N2.5
NotchMyc.all.rawTPM.txt
NotchMyc.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: NotchMyc.all.rawTPM.txt: matrix file of transript per million (TPM) values from pseudoalignment (Kallisto).
Supplementary files format and content: NotchMyc.all.normExp.txt: matrix file of normalized TPM values for analyses performed (voom, limma).

growth_protocol: hCD20Tam-Cre and MycFlox  mice were bred and housed in the University of Pennsylvania ULAR facilities.

treatment_protocol: Mice were fed tamoxifen in their diet for 4 weeks prior to being 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 24 hours before sacrifice.

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

tag: treatment

value: tamoxifen, 4wk,anti-Notch2, 24h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 21

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

tag: store cond

tag: collection date

tag: breeding method

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: extrapolated conc


title: LOAD34 BA9+AWS PM085

description:
LOAD34 BA9+AWS
polyA RNA, HTO
F libraries are HTO

tag: tissue

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (6,10)


title: Myc-/-, follicular B cell, anti-Notch2, rep4

description:
FO.Flox.N2.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: S1pr1-/-, marginal zone B cell, isotype control, rep2

description:
MZ_s1pr1ko_iso_02
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt

value: marginal zone B cell

value: isotype control, 48h


title: plasma, 5944, day 11


title: LOAD33 BA9+BA20+H PM084

description:
LOAD33 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

value: TotalSeq-B anti-human Hashtag Antibody (8,9,10)


title: plasma, 9986, day 11


title: plasma, 9986, day 2

value: day 2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 20

tag: strain

tag: age

tag: dev stage

value: not determined

value: -80 deg C

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

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_units

value: 4-nonylphenol (DTXSID5033836)


title: Myc-/-, follicular B cell, anti-Notch2, rep3

description:
FO.Flox.N2.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

tag: treatment

value: tamoxifen, 4wk,anti-Notch2, 24h


title: control, marginal zone B cell, isotype control, rep 3

description:
MZ_mb1cre_iso_03
S1pr1.all.rawTPM.txt
S1pr1.all.normExp.txt


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 19

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

tag: Sex

tag: store cond

tag: collection date

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: plasma, 9982, day 2

tag: tissue

value: Blood plasma

tag: time

value: day 2

tag: breed

value: Frabosana-Roaschina

value: female


title: Myc-/-, follicular B cell, anti-Notch2, rep1

description:
FO.Flox.N2.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


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

tag: strain

tag: age

tag: dev stage

value: not determined

value: -80 deg C

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: nominal conc

tag: extrapolated conc

value: copper sulfate (DTXSID6034479)


title: LOAD31 BA9+BA20+H PM082

description:
LOAD31 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (8,9,10)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 22

tag: Sex

tag: store cond

tag: collection date

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_units

tag: treatment

value: 4-nonylphenol (DTXSID5033836)


title: Myc-/-, follicular B cell, isotype control, rep6

description:
FO.Flox.Iso.6
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: tissue

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: tamoxifen, 4wk, isotype control, 24h


title: plasma, 6149, day 2

value: Blood plasma

tag: time

tag: breed


title: ALS9 BA9+BA4+SC PM080

description:
ALS9 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

value: TotalSeq-B anti-human Hashtag Antibody (6,9,10)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 17

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: LOAD28 BA9+BA20+H PM078

description:
LOAD28 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: antibodies


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 18

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

value: USA:Minnesota, Duluth

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

tag: birth location

tag: collected by

tag: nominal conc

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 16

tag: strain

tag: age

tag: dev stage

tag: tissue

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

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 15

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

tag: exposure duration

tag: measured conc

value: mg/L

value: 4-nonylphenol (DTXSID5033836)


title: LOAD27 BA9+H PM076

description:
LOAD27 BA9+H
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8)


title: plasma, 5944, day 2

tag: time

value: day 2

tag: breed

value: Frabosana-Roaschina

tag: Sex

value: female


title: Myc-/-, follicular B cell, isotype control, rep4

description:
FO.Flox.Iso.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: tamoxifen, 4wk, isotype control, 24h


title: LOAD32 BA9+BA20+H PM083

description:
LOAD32 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

value: TotalSeq-B anti-human Hashtag Antibody (8,9,10)


title: control, follicular B cell, anti-Notch2, rep4

description:
FO.Cre.N2.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: tamoxifen, 4wk,anti-Notch2, 24h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 14

value: GLTED-Duluth-wt

value: 5-6 dpf

value: larvae

value: whole body

value: not determined

tag: store cond

tag: collection date

tag: birth location

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: plasma, 0012, day 2

tag: tissue

value: Blood plasma


title: LOAD26 GM PM075

description:
LOAD26 GM
polyA RNA


title: ALS/FTD2 BA9+BA4+SC; DLBD-PD5 BA9+SN PM077

description:
ALS/FTD2 BA9+BA4+SC; DLBD-PD5 BA9+SN
polyA RNA, HTO
F libraries are HTO

value: TotalSeq-B anti-human Hashtag Antibody (6,7,8,9,10)


title: Myc-/-, follicular B cell, isotype control, rep1

description:
FO.Flox.Iso.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 13

tag: strain

tag: age

tag: dev stage

value: -80 deg C

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: 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

value: copper sulfate (DTXSID6034479)


title: MIP_SA_DNA_10ng

description:
SA (10ng – 100ng) low input 10ng
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

organism: Staphylococcus aureus

source_name: bacterial culture

value: bacterial culture

tag: strain se

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

tag: treatment media

value: TSB


title: plasma, 6150, day 2

tag: time

value: day 2

tag: breed

value: Frabosana-Roaschina

tag: Sex

value: female


title: CNTRL1 BA9+BA4+H+SN PM073

description:
CNTRL1 BA9+BA4+H+SN
polyA RNA, HTO
F libraries are HTO

tag: tissue

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (6,7,8,9)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 12

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

tag: collection date

tag: birth location

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment

value: 4-nonylphenol (DTXSID5033836)


title: control, follicular B cell, anti-Notch2, rep2

description:
FO.Cre.N2.2
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: tamoxifen, 4wk,anti-Notch2, 24h


title: control, follicular B cell, anti-Notch2, rep3

description:
FO.Cre.N2.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: tissue


title: Myc-/-, follicular B cell, isotype control, rep5

description:
FO.Flox.Iso.5
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: tamoxifen, 4wk, isotype control, 24h


title: ALS8 BA9+BA4+SC PM069

description:
ALS8 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: MIP_SA_100ng

description:
SA (100ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: bacterial culture

tag: strain se

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

tag: treatment media

value: TSB


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 11

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: Sex

tag: store cond

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: exposure duration

tag: measured conc

value: less than limit of quantification

value: mg/L


title: MIP_SA_DNA_1ng

description:
SA (1ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

tag: tissue

tag: strain se

tag: seqeuncing appraoch

tag: experimental batch


title: control, follicular B cell, isotype control, rep4

description:
FO.Cre.Iso.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

tag: treatment


title: MIP_RHE_SA_10ng

description:
RHE_staph a_H_L_SA_E04 (10ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

source_name: RHE + bacterial culture

value: RHE + bacterial culture

tag: treatment rrna

tag: treatment spia

value: SPIA


title: DLBD-PD4 BA9+SN PM068

description:
DLBD-PD4 BA9+SN
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 10

tag: strain

tag: age

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: LOAD21 BA9+BA20+H PM067

description:
LOAD21 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: tissue

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: MIP_SA_DNA_50ng

description:
SA (50ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 1

value: no ribo-depletion

value: no SPIA

tag: treatment media

value: TSB


title: EOAD2 BA9+BA20+H PM066

description:
EOAD2 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: antibodies


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 9

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

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: 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: exposure duration

tag: measured conc

value: less than limit of quantification

value: mg/L

tag: treatment


title: control, follicular B cell, isotype control, rep2

description:
FO.Cre.Iso.2
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: tamoxifen, 4wk, isotype control, 24h


title: control, follicular B cell, isotype control, rep3

description:
FO.Cre.Iso.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 8

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: MIP_SA_10ng

description:
SA (10ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 1

tag: treatment rrna

value: no ribo-depletion

tag: treatment spia

value: SPIA

tag: treatment media

value: TSB


title: LOAD20 BA9+BA20+H PM065

description:
LOAD20 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: tissue

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 7

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: Sex

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: 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: exposure duration

tag: measured conc

value: less than limit of quantification

tag: treatment


title: SPE_SA_DNA_50ng

description:
SA (50ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

tag: strain se

tag: seqeuncing appraoch

value: Allegro (SPE)

tag: experimental batch

value: no SPIA


title: control, follicular B cell, isotype control, rep1

description:
FO.Cre.Iso.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: follicular B cell

tag: genotype

value: tamoxifen, 4wk, isotype control, 24h


title: SPE_SA_DNA_1ng

description:
SA (1ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

tag: tissue

value: bacterial culture

value: batch 1

tag: treatment rrna

tag: treatment spia

tag: treatment media


title: MS2 BA9+TH+Lesion+AWS PM064

description:
MS2 BA9+TH+Lesion+AWS
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9,10)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 6

tag: strain

tag: age

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: 4-nonylphenol (DTXSID5033836)


title: SPE_SA_DNA_10ng

description:
SA (10ng – 100ng) low input 10ng
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

tag: tissue

tag: strain se

tag: seqeuncing appraoch

tag: experimental batch

tag: treatment rrna

value: no ribo-depletion

value: TSB


title: SPE_SA_100ng

description:
SA (100ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

tag: treatment spia

tag: treatment media


title: control, follicular B cell, anti-Notch2, rep1

description:
FO.Cre.N2.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: cell type

tag: genotype

tag: treatment

value: tamoxifen, 4wk,anti-Notch2, 24h


title: Myc-/-, marginal zone B cell, anti-Notch2, rep5

description:
MZ.Flox.N2.5
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: marginal zone B cell


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 5

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

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

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: exposure duration

tag: measured conc

value: less than limit of quantification


title: ALS/FTD1 BA9+BA4+SC PM063

description:
ALS/FTD1 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

tag: tissue

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: Myc-/-, marginal zone B cell, anti-Notch2, rep4

description:
MZ.Flox.N2.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type


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

value: larvae

value: whole body

value: not determined

tag: biomaterial provider

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: ALS7 BA9+BA4+SC PM062

description:
ALS7 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO


title: Myc-/-, marginal zone B cell, anti-Notch2, rep3

description:
MZ.Flox.N2.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: genotype

tag: treatment


title: SPE_RHE_SA_spia

description:
RHE_staph a_H_L_SA_E04 (10ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: RHE + bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: Allegro (SPE)

tag: experimental batch

value: batch 1

tag: treatment rrna

tag: treatment spia

value: SPIA


title: EOAD1 BA9+BA20+H PM061

description:
EOAD1 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO


title: SPE_SA_spia

description:
SA (10ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: bacterial culture

value: no ribo-depletion

tag: treatment media

value: TSB


title: LOAD2 BA9+BA20+H PM060

description:
LOAD2 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: tissue


title: RNAseq_SA_10ng

description:
S.Aureus SA (10ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: bulk RNA-Seq

value: ribo-depletion


title: Myc-/-, marginal zone B cell, isotype control, rep6

description:
MZ.Flox.Iso.6
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: marginal zone B cell

value: tamoxifen, 4wk, isotype control, 24h


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 3

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

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

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: exposure duration

tag: measured conc

value: less than limit of quantification

value: mg/L

value: 4-nonylphenol (DTXSID5033836)


title: ALS6 BA9+BA4+SC PM058

description:
ALS6 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: MIP_SE_DNA_1ng

description:
SE (1ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

organism: Staphylococcus epidermidis

value: bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 1

tag: treatment rrna

value: no SPIA


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 1

tag: strain

value: larvae

tag: tissue

value: whole body

value: not determined

tag: biomaterial provider

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment

value: copper sulfate (DTXSID6034479)


title: HSC_APBR3_3

city: Chuncheon-si

first: Yong-Hyun

last: Han

state: Kangwondo

address: 307-ho, College of Pharmacy, 1, Kangwondaehak-gil

department: College of Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Hepatic stellate cell

growth_protocol: Primary hepatic stellate cells were incubated with vehicle- or APB-R3 for 24 hours.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: Vehicle or 150ug/kg of APB-R3 was incubated in hepatic stellate cells for 24 hours.

tag: cell type

value: Hepatic stellate cell

tag: genotype

value: Wild-type, male


title: Myc-/-, marginal zone B cell, isotype control, rep4

description:
MZ.Flox.Iso.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

value: marginal zone B cell

value: tamoxifen, 4wk, isotype control, 24h


title: HSC_APBR3_2


title: MS1 TH PM057

description:
MS1 TH
polyA RNA

source_name: AWS

value: AWS


title: MIP_SE_DNA_50ng

description:
SE (50ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: no ribo-depletion

tag: treatment spia

tag: treatment media

value: TSB


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to 4-nonylphenol, sample 2

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

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

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: exposure duration

tag: measured conc

value: mg/L

value: 4-nonylphenol (DTXSID5033836)


title: Myc-/-, marginal zone B cell, isotype control, rep1

description:
MZ.Flox.Iso.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

tag: tissue


title: RNAseq_SA_100ng

description:
S.Aureus SA (100ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: bulk RNA-Seq

tag: experimental batch

value: batch 1

tag: treatment rrna

value: ribo-depletion

value: no SPIA


title: MS1 GM PM056

description:
MS1 GM
polyA RNA

source_name: TH

value: TH


title: Myc-/-, marginal zone B cell, isotype control, rep5

description:
MZ.Flox.Iso.5
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

tag: cell type

value: marginal zone B cell

tag: genotype

tag: treatment

value: tamoxifen, 4wk, isotype control, 24h


title: HSC_APBR3_1

value: Hepatic stellate cell

value: Wild-type, male


title: control, marginal zone B cell, anti-Notch2, rep4

description:
MZ.Cre.N2.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: tamoxifen, 4wk,anti-Notch2, 24h


title: HSC_Ctrl_3

value: Vehicle


title: MIP_SE_50ng

value: Molecular Loop (MIP)

value: no ribo-depletion

tag: treatment spia

tag: treatment media

value: TSB


title: MIP_SE_DNA_10ng

description:
SE (10ng – 100ng) low input 10ng
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: control, marginal zone B cell, anti-Notch2, rep3

description:
MZ.Cre.N2.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: DLBD-PD3 SN PM054

description:
DLBD-PD3 SN
polyA RNA

source_name: SN

value: SN


title: Myc-/-, marginal zone B cell, anti-Notch2, rep1

description:
MZ.Flox.N2.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: control, marginal zone B cell, anti-Notch2, rep2

description:
MZ.Cre.N2.2
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: MS1 AWS PM055

description:
MS1 AWS
polyA RNA


title: MIP_SE_50pg

description:
Low Template Control (SE RNA 50pg)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: bacterial culture

value: SPIA


title: HSC_Ctrl_2


title: DLBD-PD3 GM PM053

description:
DLBD-PD3 GM
polyA RNA


title: LOAD1 BA9+BA20+H PM059

description:
LOAD1 BA9+BA20+H
polyA RNA, HTO
F libraries are HTO

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: HSC_Ctrl_1


title: MIP_RHE_SE_10ng

description:
RHE_S. epi 1-32_G04 (10ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: RHE + bacterial culture

value: batch 1


title: ALS5 SC PM052

description:
ALS5 SC
polyA RNA

source_name: SC

value: SC


title: MIP_SE_10ng

description:
SE (10ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: ALS5 GM PM051

description:
ALS5 GM
polyA RNA


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 48hr

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

institute: Yonsei University

data_processing:
Experimental Method(RNA QC/Library construction/sequencing) The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA). Namely, mRNA molecules were purified and fragmented from 1μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×151bp) using Illumina NovaSeq6000 (Illumina, CA, USA).
Transcriptome data analysis Filtering The quality of the reads was checked using FastQC (v0.12.1), which helped in understanding the basic quality metrics, including sequence quality scores, GC content, N content, length distribution, and duplication levels. Adapter sequences and the ends of the reads with a Phred quality score of less than 15 were trimmed, and simultaneously, reads shorter than 36 bp were removed using Trimmomatic (v0.39).
Sequence alignment Filtered reads were mapped to the reference genome of the species using the Bowtie aligner (v1.2.3).
Gene expression estimation Read count values were obtained using Subread (v2.0.3).
Differential Expressed gene (DEG) analysis Based on the estimated read counts from the previous step, normalization factors were calculated using the iterative DESeq2 (v1.40.2) method. Q-values were calculated from the p-values using the p.adjust function of the R package with default parameter settings. Differentially expressed genes (DEGs) were identified based on a q-value threshold of less than 0.05 to correct for errors caused by multiple testing.
Gene Ontology (GO) analysis The GO database provides a set of hierarchical controlled vocabulary classified into three categories: Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). For the functional characterization of the DEGs, a GO-based trend test was carried out using the R package called clusterProfiler (v4.8.3) through the Wallenius non-central hypergeometric distribution. Genes with P-values < 0.05 following the test were regarded as statistically significant.
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text file includes ReadCount values for each Sample

source_name: epithelial cells, mesenchymal cells

extract_protocol:
Primary tumor cells and cancer-associated fibroblasts were isolated from ameloblastoma patients. Normal fibroblasts were isolated from normal tissue adjacent tumors. Primary tumor cells were subjected to tumoroid culture in Matrigel. After tumoroid formation (7d), normal fibroblasts or cancer-associated fibroblasts were used to establish the stroma-rich tumoroid. Dexamethasone (100nM) was used for the synchronization of circadian rhythm in stroma-rich tumoroids. Matrigel was washed out with ice cold advanced DMEM,and the stroma-rich tumoroids were collected at the time-point of 0h, 8h, 16h, 24h, 32h, 40h, 48h after synchronization.The total RNA was extracted with TRIzol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: epithelial cells, mesenchymal cells

tag: disease state

value: cancer-associated fibroblast

value: Dexamethasone 100nM

tag: time

value: 48h after synchronization


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 40hr

value: 40h after synchronization


title: SPE_SE_DNA_1ng

description:
SE (1ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: Allegro (SPE)

value: no SPIA


title: control, marginal zone B cell, isotype control, rep3

description:
MZ.Cre.Iso.3
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: spleen

value: marginal zone B cell

value: tamoxifen, 4wk, isotype control, 24h


title: ALS3 SC PM048

description:
ALS3 SC
polyA RNA


title: control, marginal zone B cell, isotype control, rep2

description:
MZ.Cre.Iso.2
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: SPE_SE_DNA_10ng

description:
SE (10ng – 100ng) low input 10ng
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: no ribo-depletion

value: TSB


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 24hr

value: 24h after synchronization


title: SPE_SE_DNA_50ng

description:
SE (50ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: bacterial culture


title: SPE_SE_50ng


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 16hr

value: 16h after synchronization


title: ALS3 GM PM045

description:
ALS3 GM
polyA RNA


title: control, marginal zone B cell, isotype control, rep1

description:
MZ.Cre.Iso.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt


title: ALS3 GM PM046

description:
ALS3 GM
polyA RNA

source_name: FN

value: FN


title: rupture_nohCG_rep14

city: Somerville

first: Daniela

middle: Dolores

last: Russo

state: Massachusetts

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

description:
Smart-seq2
Rupture_Unrupture_H10

data_processing:
Raw sequencing data were demultiplexed and aligned to the GRCm38 genome using publicly available scripts on Terra (github.com/broadinstitute/TAG-public)
Cells expressing less than 500 genes were excluded from further analysis and genes were filtered to contain only those that were protein coding.
To filter for high-quality cells for each category, we utilized the AddModuleScore function in Seurat v4 (Hao et al., 2021) for scoring marker gene expression modules established from published datasets (Wang et al., 2020, Tharp et al., 2020, Zhang et al., 2018, Pangas et al., 2006) (Supplementary Table 1). Oocytes that scored highly for somatic cell gene expression (>2 standard deviations above the mean somatic cell module score) were removed. Similarly, somatic cells that scored highly for oocyte gene expression were also excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated counts and tpm files

source_name: Cumulus-oocyte complex

extract_protocol:
Mouse secondary follicles were isolated from the ovaries of 14-16 day-old CD-1 female mice enzymatically using L15 media (Thermo Fisher Scientific, Waltham, MA) with 1% penicillin-streptomycin (Thermo Fisher Scientific), 25 μg/ml liberase (Sigma-Aldrich, St. Louis, MO), and 200 μg/mlDNase I (Qiagen, Hilden, Germany). Ovary pieces were manually dispersed using a P1000 pipette to release follicles. Follicles with intact morphology were encapsulated in an alginate hydrogel (Sigma-Aldrich) for the preservation of the 3D structure of follicles throughout folliculogenesis. Follicles were cultured for 8 days, then antral follicles were removed, washed, and transferred to maturation media with or without human chorionic gonadotropin (Sigma-Aldrich for 12 hours to allow for ovulation and follicle rupture.
Bulk RNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using Maxima RT (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).

value: Cumulus-oocyte complex

tag: group


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 8hr

value: epithelial cells, mesenchymal cells

value: 8h after synchronization


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 0hr

value: cancer-associated fibroblast

value: Dexamethasone 100nM

value: 0h after synchronization


title: SPE_SE_spia_50ng

description:
Low Template Control (SE RNA 50pg)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: Allegro (SPE)

value: batch 1

value: SPIA


title: ALS2 SC PM043

description:
ALS2 SC
polyA RNA


title: rupture_nohCG_rep13

description:
Smart-seq2
Rupture_Unrupture_H09


title: SPE_RHE_SE_spia

description:
RHE_S. epi 1-32_G04 (10ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: RHE + bacterial culture


title: control, marginal zone B cell, anti-Notch2, rep1

description:
MZ.Cre.N2.1
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

source_name: spleen

value: spleen

value: marginal zone B cell

value: tamoxifen, 4wk,anti-Notch2, 24h


title: rupture_nohCG_rep12

description:
Smart-seq2
Rupture_Unrupture_H08


title: ALS2 FN PM042

description:
ALS2 FN
polyA RNA


title: control, marginal zone B cell, isotype control, rep4

description:
MZ.Cre.Iso.4
NotchMyc.all.rawTPM.txt
NotchMyc.all.normExp.txt

value: tamoxifen, 4wk, isotype control, 24h


title: stroma-rich AM tumoroid (cancer-associated fibroblast), 32hr

value: 32h after synchronization


title: ALS3 FN PM047

description:
ALS3 FN
polyA RNA


title: SPE_SE_spia

description:
SE (10ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: bacterial culture

value: no ribo-depletion

value: TSB


title: stroma-rich AM tumoroid (normal fibroblast), 48hr

value: epithelial cells, mesenchymal cells

value: normal fibroblast

value: 48h after synchronization


title: rupture_nohCG_rep11

description:
Smart-seq2
Rupture_Unrupture_H06

value: Cumulus-oocyte complex


title: stroma-rich AM tumoroid (normal fibroblast), 40hr

value: Dexamethasone 100nM

value: 40h after synchronization


title: RNAseq_SE_10ng

description:
S.Epidermidis SE (10ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: bulk RNA-Seq

value: batch 1

value: ribo-depletion


title: rupture_nohCG_rep10

description:
Smart-seq2
Rupture_Unrupture_H05


title: ALS2 GM PM040

description:
ALS2 GM
polyA RNA

value: FN


title: RNAseq_SE_100ng

description:
S.Epidermidis SE (100ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: no SPIA


title: stroma-rich AM tumoroid (normal fibroblast), 32hr


title: stroma-rich AM tumoroid (normal fibroblast), 24hr

value: 24h after synchronization


title: rupture_nohCG_rep9

description:
Smart-seq2
Rupture_Unrupture_H04


title: ALS1 SC PM039

description:
ALS1 SC
polyA RNA

value: SC


title: rupture_nohCG_rep8

description:
Smart-seq2
Rupture_Unrupture_H03


title: ALS1 FN PM038

description:
ALS1 FN
polyA RNA


title: Sorted MC38 tumor cells from high-fat-diet-fed mouse 5

city: San Mateo

first: Sreya

last: Bagchi

address: 1202 S Claremont Street

institute: Stanford University

data_processing:
Sequence reads were trimmed for adaptor sequences/low-quality sequences using Cutadapt v1.15 and quality was evaluated using FastQC v0.11.5.
Trimmed sequence reads were mapped to GrCM38/mm10 using bwa v0.7.12 and filtered for MAPQ < 5.
Read count extraction performed using DESeq2 v1.24.0 in R.
Assembly: mm10
Supplementary files format and content: Comma-delimited text file includes raw counts for each sample.

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini  kit (QIAGEN). >200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit following the manufacturer's protocol.

value: Tumor

tag: cell line

value: Tumor cell (CD45-negative)

value: High-fat-diet-fed


title: rupture_nohCG_rep7

description:
Smart-seq2
Rupture_Unrupture_H02


title: Sorted MC38 tumor cells from high-fat-diet-fed mouse 4


title: Sorted MC38 tumor cells from high-fat-diet-fed mouse 3


title: rupture_nohCG_rep6

description:
Smart-seq2
Rupture_Unrupture_H01


title: stroma-rich AM tumoroid (normal fibroblast), 8hr

value: 8h after synchronization


title: ALS1 GM PM036

description:
ALS1 GM
polyA RNA


title: Sorted MC38 tumor cells from high-fat-diet-fed mouse 2


title: Sorted tumor-associated macrophages from control-diet-fed mouse 2

extract_protocol:
RNA was harvested using Rneasy mini  kit (QIAGEN). >200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prepartion kit following the manufacturer's protocol.

value: Tumor model is MC38

value: Control-diet-fed


title: stroma-rich AM tumoroid (normal fibroblast), 0hr

value: epithelial cells, mesenchymal cells

value: normal fibroblast

value: 0h after synchronization


title: rupture_nohCG_rep5

description:
Smart-seq2
Rupture_Unrupture_G10

value: Cumulus-oocyte complex


title: ALS2 GM PM041

description:
ALS2 GM
polyA RNA


title: FTD1 GM PM030

description:
FTD1 GM
polyA RNA


title: FTD1 H PM031

description:
FTD1 H
polyA RNA

source_name: H

value: H


title: Sorted tumor-associated macrophages from control-diet-fed mouse 1


title: Sorted MC38 tumor cells from control-diet-fed mouse 5


title: rupture_nohCG_rep4

description:
Smart-seq2
Rupture_Unrupture_G09


title: Sorted MC38 tumor cells from high-fat-diet-fed mouse 1


title: PSP3 GM PM029

description:
PSP3 GM
polyA RNA


title: rupture_nohCG_rep3

description:
Smart-seq2
Rupture_Unrupture_G08


title: Sorted tumor-associated macrophages from high-fat-diet-fed mouse 2


title: Sorted MC38 tumor cells from control-diet-fed mouse 4


title: PSP2 SN PM027

description:
PSP2 SN
polyA RNA


title: Sorted tumor-associated macrophages from high-fat-diet-fed mouse 1


title: Sorted MC38 tumor cells from control-diet-fed mouse 3


title: stroma-rich AM tumoroid (normal fibroblast), 16hr

value: Dexamethasone 100nM

value: 16h after synchronization


title: rupture_nohCG_rep2

description:
Smart-seq2
Rupture_Unrupture_G07


title: unrupture_nohCG_rep15

description:
Smart-seq2
Rupture_Unrupture_G05


title: ALS1 GM PM037

description:
ALS1 GM
polyA RNA


title: rupture_nohCG_rep1

description:
Smart-seq2
Rupture_Unrupture_G06


title: LOAD15 SN PM025

description:
LOAD15 SN
polyA RNA

value: SN


title: PSP2 H PM026

description:
PSP2 H
polyA RNA