title: Mix7_21_R4_P7_H_pool2

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.422. The FASTQ files were were processed using the R-ODAF pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada). Briefly:
Reads were trimmed and filtered with fastp (--cut_front_window_size 1, --cut_front_mean_quality 3, --cut_tail_window_size 1, --cut_tail_mean_quality 3, --cut_right_window_size 4, --cut_right_mean_quality 15, --length_required 50). Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2). Quantification was performed in R using the qAlign function from the QuasR package.
Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2).
Quantification was performed in R using the qAlign function from the QuasR package.
Assembly: GTF file generated from probe sequences in Biospyder manifest file
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

growth_protocol: MCF-7 cells were maintained in complete media (phenol red DMEM + 10% FBS + 1% P/S) in 10 cm culture dishes at 37°C in a humidified atmosphere (5% CO2). Cells were depleted of estrogen for 96h in phenol red-free DMEM supplemented with CS 5% FBS + 1% P/S. 48h into the estrogen depletion cells were plated in 96-well plates prior to chemical exposure.

extract_protocol:
Cells were lysed and RNA was extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries using the TempO-Seq Human Whole Transcriptome 2.1 kit (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 [?] individual libraries were pooled to create a single pool for sequencing on the [instrument] (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.

treatment_protocol: After estrogen depletion, cells were exposed to chemicals (dissolved in DMSO, final DMSO concentration 0.1%) under serum free conditions (phenol red-free DMEM + 2% BSA + 1%) for 48h.

tag: cell line

tag: plate

tag: chemical

value: Mix 7

tag: dose


title: Mix7_10-5_R4_P7_H_pool2

status: Public on Jun 30 2025

type: SRA

state: Ontario

country: Canada

library_source: other

molecule: other

organism: Homo sapiens


title: PC_UH_R7_P7_H_pool2

value: No cells; Universal human positive control


title: PC_B_R7_P7_H_pool2

value: No cells; Brain positive control


title: genomic DNA from CD4+ T-cell_VAS110

type: genomic

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

hyb_protocol: Five hundred nanograms of each DNA sample was bisulfite-converted with the EZ DNA MethylationTM kit (Zymo Research, Irvine, CA, USA), following the manufacturer's instructions. Samples were hybridized onto an Infinium MethylationEPIC Bead Chip array

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
DNA methylation raw data (IDAT files) were processed using ShinyÉPICo, a graphical pipeline based on minfi and limma R packages.
Samples showing poor bisulfite conversion and those with gender discordance between prediction and demographic information were filtered out from further analyses. In addition, we used the 59 single nucleotide polymorphisms (SNPs) probes included in the array to check for sample duplication. One individual from each pair of duplicates was excluded.
Probes with a detection p-value < 0.01 were removed. To avoid technical and biological bias, we also excluded CpGs from X and Y chromosomes as well as those probes containing either a SNP at the CpG interrogation site or at the single base extension site. Probes were annotated using IlluminaHumanMethylationEPICmanifest v0.4.0
Raw methylation values were normalized using the Noob+Quantile method, and DNA methylation was measured as beta and M values.
To identify associations between DNA methylation levels and GCA disease state or clinical status along the genome, we applied a eBayes moderated t-test with trend and robust options enabled. We used a false discovery rate (FDR) to correct for multiple testing and those probes with a FDR < 0.05 were considered as differentially methylated positions (DMPs).
Sensitivity analyses were realized for each comparison to examine the contribution of all potential confounders (sex, age, slide, array and sample plate). Pearson correlation or Wilcoxon signed-rank test was applied depending on whether the variable of interest was continuous or categorical. Variables with a p-value < 0.05 were considered to significantly contribute to DNA methylation and were therefore included as covariates in the model.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: SAMPLE_12 genomic DNA from CD4+ T-cell_VAS110

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were first obtained from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). For subsequent CD14 T-cell  isolation, PBMCs were incubated with CD14-PE and CD15-FITC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes in the dark. Pure monocytes were next isolated by positive selection as CD14+CD15- cells using flow cytometry sorting and were pelleted and stored at -80ºC. Genomic DNA were extracted  the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. DNA were quantified with Nanodrop ND-2100 and Qubit® DNA assay kit (invitrogen).

tag: gender

value: F

tag: age

tag: classification


title: Mix7_2-62_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS107

source_name: SAMPLE_10 genomic DNA from CD4+ T-cell_VAS107


title: Mix7_1-31_R4_P7_H_pool2


title: Mix7_0-66_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS106

source_name: SAMPLE_9 genomic DNA from CD4+ T-cell_VAS106

value: M


title: genomic DNA from CD4+ T-cell_VAS104

source_name: SAMPLE_7 genomic DNA from CD4+ T-cell_VAS104


title: genomic DNA from CD4+ T-cell_VAS105

source_name: SAMPLE_8 genomic DNA from CD4+ T-cell_VAS105


title: BPB_10_R4_P7_H_pool2

value: Bisphenol B


title: BPB_50_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS15

source_name: SAMPLE_19 genomic DNA from CD4+ T-cell_VAS15


title: genomic DNA from CD4+ T-cell_VAS102

source_name: SAMPLE_5 genomic DNA from CD4+ T-cell_VAS102


title: genomic DNA from CD4+ T-cell_VAS103

source_name: SAMPLE_6 genomic DNA from CD4+ T-cell_VAS103


title: BPB_5_R4_P7_H_pool2


title: BPB_0-5_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS101

source_name: SAMPLE_4 genomic DNA from CD4+ T-cell_VAS101


title: genomic DNA from CD4+ T-cell_VAS10

source_name: SAMPLE_2 genomic DNA from CD4+ T-cell_VAS10


title: genomic DNA from CD4+ T-cell_VAS11

source_name: SAMPLE_11 genomic DNA from CD4+ T-cell_VAS11


title: Mix7_5-25_R4_P7_H_pool2


title: BPB_1_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS1

source_name: SAMPLE_1 genomic DNA from CD4+ T-cell_VAS1


title: BPB_0-1_R4_P7_H_pool2


title: BPB_0-001_R4_P7_H_pool2


title: 24BPS_50_R4_P7_H_pool2

value: 2,4'-Bisphenol S


title: 24BPS_1_R4_P7_H_pool2


title: 24BPS_0-5_R4_P7_H_pool2


title: 24BPS_0-1_R4_P7_H_pool2


title: Plasma_HAVD_rep8

type: RNA

city: Guangzhou

first: Hanjun

last: Zheng

address: Xinzao street, Panyu district, Guangzhou, Guangdong, China.

country: China

institute: Guangzhou Medical University

description: Gene expression in human blood

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Labeling kit according to manufacture's protocol.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
a)The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.
b)We use Median Normalization Method to obtain Normalized Data, Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.
c)After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

molecule: total RNA

source_name: Plasma extratced from human whole blood

label_protocol: Labeling operated following the miRCURY Array Power Labeling kit instructions (Cat #208032-A, Exiqon)

extract_protocol: Total RNA extracted using TRIzol LS following manufacturer's instructions

value: Male


title: 24BPS_0-01_R4_P7_H_pool2


title: Plasma_HAVD_rep7

description: Gene expression in human blood


title: BPZ_50_R4_P7_H_pool2

value: Bisphenol Z


title: Plasma_HAVD_rep4

description: Gene expression in human blood


title: Plasma_HAVD_rep2

description: Gene expression in human blood


title: 24BPS_0-001_R4_P7_H_pool2


title: BPZ_10_R4_P7_H_pool2


title: genomic DNA from CD4+ T-cell_VAS100

source_name: SAMPLE_3 genomic DNA from CD4+ T-cell_VAS100


title: BPZ_5_R4_P7_H_pool2


title: 24BPS_10_R4_P7_H_pool2


title: BPZ_1_R4_P7_H_pool2


title: BPB_0-01_R4_P7_H_pool2


title: Plasma_HAVD_rep5

description: Gene expression in human blood


title: BPZ_0-1_R4_P7_H_pool2


title: Plasma_HAVD_rep1

description: Gene expression in human blood


title: BPZ_0-5_R4_P7_H_pool2


title: 24BPS_5_R4_P7_H_pool2


title: Plasma_exposure_rep6

description: Gene expression in human blood


title: BPZ_0-01_R4_P7_H_pool2


title: Plasma_HAVD_rep6

description: Gene expression in human blood


title: Plasma_exposure_rep4

description: Gene expression in human blood


title: Plasma_exposure_rep5

description: Gene expression in human blood


title: Plasma_HAVD_rep3

description: Gene expression in human blood


title: BPB_10_R3_P7_H_pool2


title: Plasma_exposure_rep7

description: Gene expression in human blood


title: BPB_1_R3_P7_H_pool2


title: Plasma_control_rep8

description: Gene expression in human blood


title: Plasma_control_rep7

description: Gene expression in human blood


title: BPB_0-1_R3_P7_H_pool2


title: Plasma_exposure_rep8

description: Gene expression in human blood


title: Plasma_control_rep6

description: Gene expression in human blood


title: 24BPS_10_R3_P7_H_pool2


title: Plasma_control_rep5

description: Gene expression in human blood


title: Plasma_control_rep4

description: Gene expression in human blood


title: Plasma_control_rep2

description: Gene expression in human blood


title: Plasma_exposure_rep3

description: Gene expression in human blood


title: BPB_50_R3_P7_H_pool2


title: Plasma_control_rep1

description: Gene expression in human blood


title: Plasma_exposure_rep2

description: Gene expression in human blood


title: Plasma_exposure_rep1

description: Gene expression in human blood


title: U87 cells, control shRNA, Day 7 [gene]

city: Montpellier

first: Domenico

last: Maiorano

address: 141, rue de la cardonille

country: France

institute: CNRS

description: gene expression data from U87 cells expressing a control shRNA for 7 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  HuGene2.1 ST array strip (Affymetrix).  Strips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix microarrays were processed at the Microarray Core Facility of the Institute of Regenerative Medicine and Biotherapy, CHU-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/

label: biotin

molecule: polyA RNA

source_name: U87 cells shRNAcontrol day 7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in Dulbecco’s modified eagle’s medium (DMEM) supplemented with 10 % (v/v) fetal bovine serum, 2 mM glutamine and antibiotics in a humidified atmosphere of 5 % CO2 at 37 °C.

extract_protocol: Total RNA was isolated from U87 cells in which Rad18 was downregulated or not by siRNA using the RNeasy kit according to the manufacturer's instructions (Qiagen). Residual DNA was removed by DNAseI digestion.

treatment_protocol: For siRNA treatment, cells were transfected either with siRNA Rad18 or siRNA Luciferase (Ctrl) as a control as previously described (Kermi et al., Developmetal Cell 2015). Twenty-four hours after transfection, cells were trypsinized and seeded in 12 wells plates at a density of 104 cells/well. For shRNA treatment, cells were transduced with lentiviral particles expressing SMART vectors doxycyclin-inducible shRNA (Dharmacon).

tag: disease state

value: glioblastoma stage 4


title: U87 cells,  Rad18 siRNA, 72 hrs [gene]

description: gene expression data from U87 cells treated with a control siRNA for 72 hours

source_name: U87 cells siRNA Rad18 72 hours


title: BPZ_0-001_R4_P7_H_pool2


title: 24BPS_1_R3_P7_H_pool2


title: BPB_5_R3_P7_H_pool2


title: 24BPS_50_R3_P7_H_pool2


title: U87 cells,  control siRNA, 72 hrs [gene]

source_name: U87 cells control siRNA 72 hours


title: 24BPS_0-5_R3_P7_H_pool2


title: BPB_0-5_R3_P7_H_pool2


title: BPB_0-01_R3_P7_H_pool2


title: BPB_0-001_R3_P7_H_pool2


title: 24BPS_0-1_R3_P7_H_pool2


title: Plasma_control_rep3

description: Gene expression in human blood


title: 24BPS_0-01_R3_P7_H_pool2


title: 24BPS_5_R3_P7_H_pool2


title: aak(0) PD S1

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

institute: McGill University

description:
Library name: Sample 7
aak_PD_1

library_source: transcriptomic

data_processing:
Reference genome assembly and DESeq2. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference C. elegans genome version WBcel235 (gene annotation from Ensembl version 104) using STAR version 2.7.1a. Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries. DESeq2 version 1.30.1 was then used to normalize gene readcounts. Sample clustering based on normalized log readcounts produces the following hierarchy of samples
Assembly: WBcel235 (gene annotation from Ensembl version 104)
Supplementary files format and content: "daf2 vs aak FKPM.tsv" contains read counts, pairwise comparisons in 4 separate files for fold change calculations

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Bleach-synchronized worms were put onto large NGM plates and grown at 25 °C. Dauer animals were collected after 96 hours (i.e. Day 2 in dauer) and washed with M9, post-dauer animals collected after 192 hours. Animals were immediately subjected to Trizol RNA extraction after collection.

extract_protocol:
Standard Trizol RNA extraction was carried out, approximately 200 ul per 20 ul packed worms. Freeze-thawing with liquid nitrogen was carried out to separate RNA, followed by heavy centrifugation. Two rounds of chloform extraction were carried out (50 ul per 200 ul Trizol). Samples were washed with isopropanol followed by 70% EtoH, and air-dryed before dissolving in ultrapure water. Sample concentration was measured using Nanodrop, and run on agarose gels to verify integrity of RNA. RNA was stored at -80 °C for up to 3 days before being sent for sequencing. Minimum of 100 ng/ul RNA was sent for sequencing.
mRNA-Seq with PolyA selection, 150 cycles Paired-End (maximum 2x80nt), 400M fragments, using KAPA mRNA Hyper Prep Hyperprep library per manufacturer instructions

tag: tissue

value: Whole animal

tag: Sex

value: Hermaphrodite

tag: genotype

value: daf-2; aak(0)

tag: treatment

value: Trizol

tag: time

value: 192 hrs


title: aak(0) Dauer S1

description:
Library name: Sample 5
aak_Dauer_1


title: daf-2 Dauer S2

description:
Library name: Sample 2
daf-2_Dauer_2

value: 96 hrs


title: daf-2 PD S1

description:
Library name: Sample 3
daf-2_PD_1


title: P201_10_R4_P7_H_pool2


title: P201_50_R4_P7_H_pool2


title: U87  cells, shRad18, Day7 [gene]

description: gene expression data from U87 cells expressing a Rad18 shRNA for 7 days

source_name: U87  cells, shRad18, Day7


title: P201_5_R4_P7_H_pool2


title: P201_1_R4_P7_H_pool2


title: lipl-4Tg-H3-rep2

city: Houston

first: Qinghao

last: Zhang

email: qinghaoz@bcm.edu, qhzhang87@gmail.com

state: Texas

address: BCM N820, One Baylor Plaza

department: Huffington Center on Aging

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Illumina NextSeq 500 system was used for base-calling.
Raw reads of ChIP-seq were filtered using Trim Galore (version 0.4.5).
Reads were aligned to the C.elegans reference genome by Bowtie2 (version 2.1.0).
Samtools (version 1.7) was used to converse sequence alignment/map (sam) format to binary alignment/map (bam).
MACS2 algorithm (version 2.1.0) was used to call peaks for H3K79me2 and H3K79me3 by arguments "-t -c --broad -g --broad-cutoff 0.1 -B", where histone H3 ChIP-seq reads were set as controls for normalization and to offset differences derived from nucleosome occupancy.
Assembly: Ce11
Supplementary files format and content: bigWig, broadpeak.

source_name: whole hermaphrodite_day-1 adult

growth_protocol: Worms were grown on standard nematode growth medium (NGM) agar plates seeded with a pre-cultured common laboratory bacterial strain E. coli OP50 (straptomycin-resistant) at 20 °C

extract_protocol:
Age synchronized worms at day-1 adulthood were used for sample preparation. Samples were fixed in 1% formaldehyde/PBS solution for 10 min. Crosslinking was quenched by adding glycine solution to a final concentration of 125 mM. Chromatin was sonicated at 4 °C using a Branson 250 sonicator. The ChIP-seq formulated antibodies were anti-histone H3 (CST #4620), H3K79me2 (CST #5427), H3K79me3 (Abcam ab2621).
Sequencing libraries were constructed by NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads kit (NEB #E7103S) according to manufacturer’s instructions. Liberaries were pooled together and sequenced on the Illumina NextSeq 500 system.

value: whole hermaphrodite_day-1 adult

tag: antibody


title: P201_0-5_R4_P7_H_pool2


title: lipl-4Tg-H3-rep1


title: aak(0) PD S2

description:
Library name: Sample 8
aak_PD_2


title: lipl-4Tg-H3K79me3-vs-H3-rep2


title: aak(0) Dauer S2

description:
Library name: Sample 6
aak_Dauer_2


title: P201_0-001_R4_P7_H_pool2


title: lipl-4Tg-H3K79me3-vs-H3-rep1


title: lipl-4Tg-H3K79me2-vs-H3-rep2


title: NC_R13_P7_H_pool2

value: No cells; 1X Lysis buffer


title: lipl-4Tg-H3K79me2-vs-H3-rep1


title: N2-H3-rep2

value: wild type


title: NC_R14_P7_H_pool2


title: N2-H3-rep1


title: daf-2 PD S2

description:
Library name: Sample 4
daf-2_PD_2


title: DMSO_0-1_R44_P7_H_pool2

value: Dimethyl sulfoxide


title: 24BPS_0-001_R3_P7_H_pool2


title: DMSO_0-1_R43_P7_H_pool2


title: daf-2 Dauer S1

description:
Library name: Sample 1
daf-2_Dauer_1


title: N2-H3K79me2-vs-H3-rep2


title: DMSO_0-1_R41_P7_H_pool2


title: DMSO_0-1_R40_P7_H_pool2


title: N2-H3K79me3-vs-H3-rep1


title: N2-H3K79me2-vs-H3-rep1


title: DMSO_0-1_R42_P7_H_pool2


title: 24BPF_50_R4_P7_H_pool2

value: 2,4'-Bisphenol F


title: P201_0-1_R4_P7_H_pool2


title: DMSO_0-1_R39_P7_H_pool2


title: P201_0-01_R4_P7_H_pool2


title: HEK293T cells, ERVK3-1 knockout with gRNA 2and 4, biol rep 2

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: CT

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University - West Campus

description:
Library name: ERVK3-1_KO_2and4_2a
Column_name_in_processed_data_file: ERVK3-1_KO_2and4_2a

data_processing:
Raw reads were assessed with FastQC and adapter sequences were trimmed using cutadapt (v3.6).
Reads were aligned to the human genome (GRCh38) using STAR (v2.7.10a) in two-pass mode with parameters --outFilterMultimapNmax 100 and --winAnchorMultimapNmax 200.
Spike-in normalization was performed using Drosophila melanogaster total RNA and alignment to BDGP6.54.
Gene-level quantification was done using featureCounts (v2.0.8) with Ensembl GRCh38.109 annotation.
Transposable element expression was quantified using TEtranscripts (v2.2.3) with UCSC RepeatMasker annotations.
Locus-level ERV expression was quantified using the ERVmap annotation and featureCounts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for genes, transposable elements (TEs), and endogenous retroviruses (ERVs) for all samples.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO₂.

extract_protocol:
Total RNA was extracted using RNEasy Kit (Qiagen, Cat. No. 74104) and treated with Turbo DNase I (NEB Cat. No. M0303S) according to the manufacturer’s protocol.
Stranded RNA-seq libraries were prepared following rRNA depletion using biotinylated rRNA-specific probes and streptavidin bead capture.

tag: cell type

value: human embryonic kidney cells

value: ERVK3-1 Knockout


title: HEK293T cells, ERVK3-1 knockout with gRNA 2and 4, biol rep 3

description:
Library name: ERVK3-1_KO_2and4_3a
Column_name_in_processed_data_file: ERVK3-1_KO_2and4_3a


title: HEK293T cells, ERVK3-1 knockout with gRNA 2and 4, biol rep 1

description:
Library name: ERVK3-1_KO_2and4_1a
Column_name_in_processed_data_file: ERVK3-1_KO_2and4_1a


title: HEK293T cells, Cas9 control, biol rep 3

description:
Library name: Cas9_3a
Column_name_in_processed_data_file: Cas9_3a

value: Cas9 non-target control


title: 24BPF_5_R4_P7_H_pool2


title: HEK293T cells, WT, biol rep 3

description:
Library name: WT_3a
Column_name_in_processed_data_file: WT_3a

value: WT


title: HEK293T cells, Cas9 control, biol rep 1

description:
Library name: Cas9_1a
Column_name_in_processed_data_file: Cas9_1a


title: 24BPF_0-1_R4_P7_H_pool2


title: 24BPF_0-01_R4_P7_H_pool2


title: 24BPF_10_R4_P7_H_pool2


title: 24BPF_0-5_R4_P7_H_pool2


title: HEK293T cells, Cas9 control, biol rep 2

description:
Library name: Cas9_2a
Column_name_in_processed_data_file: Cas9_2a


title: 24BPF_1_R4_P7_H_pool2


title: HEK293T cells, WT, biol rep 2

description:
Library name: WT_2a
Column_name_in_processed_data_file: WT_2a


title: BPS_50_R4_P7_H_pool2

value: Bisphenol S


title: HEK293T cells, WT, biol rep 1

description:
Library name: WT_1a
Column_name_in_processed_data_file: WT_1a


title: 24BPF_0-001_R4_P7_H_pool2


title: N2-H3K79me3-vs-H3-rep2


title: BPS_5_R4_P7_H_pool2


title: BPS_10_R4_P7_H_pool2


title: LC71

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description: Library name: LC71

library_source: transcriptomic single cell

data_processing:
Sequenced reads were aligned to the human reference transcriptome (GRCh38) using the Cell Ranger (10x Genomics, v9.0.1) with default setting and generate gene-by-cell count matrices.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data

source_name: Lung

extract_protocol:
In brief, tissues were minced and enzymatically digested using a human tissue dissociation kit (Miltenyi Biotec Inc., Auburn, CA, USA, Cat# 130-095-929). The digested mixture was sequentially filtered and washed twice. Then, cells were cryopreserved in a solution of 10% DMSO and 90% fetal bovine serum at -80°C. For long-term storage, cells were placed in the vapor phase of a liquid nitrogen storage system.
All gene expression libraries were sequenced on the Illumina NovaSeq 6000 system using paired-end reads with dual indexing: 28 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, and 90 cycles for Read 2. A sequencing depth of approximately 20,000 read pairs per cell was targeted. In this study, we used only gene expression data.

value: Lung


title: LC63

description: Library name: LC63


title: BPS_1_R4_P7_H_pool2


title: LC52

description: Library name: LC52


title: LC57

description: Library name: LC57


title: BPS_0-5_R4_P7_H_pool2


title: LC38

description: Library name: LC38


title: BPS_0-1_R4_P7_H_pool2


title: BPS_0-01_R4_P7_H_pool2


title: BPS_0-001_R4_P7_H_pool2


title: LC115

description: Library name: LC115


title: BPAP_50_R4_P7_H_pool2

value: Bisphenol AP


title: LC221

description: Library name: LC221


title: BPAP_5_R4_P7_H_pool2


title: BPAP_0-5_R4_P7_H_pool2


title: BPAP_0-1_R4_P7_H_pool2


title: BPAP_1_R4_P7_H_pool2


title: BPAP_10_R4_P7_H_pool2


title: LC104

description: Library name: LC104


title: Patient 1, fibroblast-like synoviocytes, IL-1b, EZH2 (Input)

city: Caen

first: Catherine

last: Baugé

address: Esplanade de la paix

institute: Université de Caen Normandie

description: Library name: Patient1_IL-1b, IN

data_processing:
Quality control of sequencing reads was performed using FastQC. Reads were aligned to the reference genome (hg38) obtained from the UCSC genome browser using BWA. Samples were filtered for regions blacklisted by the ENCODE project. Multimapping reads and PCR duplicates were removed using samtools functionalities. Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using MACS2.
Assembly: hg38
Supplementary files format and content: peaks bed files

source_name: synovial membrane

growth_protocol: Dulbecco’s Modified Eagle Medium high glucose with glutamine and sodium pyruvate (DMEM, Dutscher, Bernolsheim, France), supplemented with 10% Fetal Bovine Serum (FBS, Dutscher) and penicillin-streptomycin (Lonza, Basel, Switzerland), then incubated at 37l’l°C in a humid atmosphere containing 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico sonication device (Diagenode)
Libraries were prepared using IP-Star® Compact Automated System (Diagenode) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).

treatment_protocol: IL-1b 1ng/mL 48h

value: synovial membrane

value: human fibroblast-like synoviocytes


title: Patient 2, fibroblast-like synoviocytes, IL-1b, EZH2 (ChIP)

description: Library name: Patient2_IL-1b, ChIP


title: Patient 2, fibroblast-like synoviocytes, Control, EZH2 (ChIP)

description: Library name: Patient2_control, ChIP

value: Control


title: Patient 1, fibroblast-like synoviocytes, Control, EZH2 (Input)

description: Library name: Patient1_control, IN


title: BPAP_0-001_R4_P7_H_pool2


title: Patient 2, fibroblast-like synoviocytes, IL-1b, EZH2 (Input)

description: Library name: Patient2_IL-1b, IN


title: DMSO_0-1_R38_P7_H_pool2


title: Patient 1, fibroblast-like synoviocytes, Control, EZH2 (ChIP)

description: Library name: Patient1_control, ChIP


title: BPAP_0-01_R4_P7_H_pool2


title: Patient 2, fibroblast-like synoviocytes, Control, EZH2 (Input)

description: Library name: Patient2_control, IN


title: DMSO_0-1_R37_P7_H_pool2


title: Patient 1, fibroblast-like synoviocytes, IL-1b, EZH2 (ChIP)

description: Library name: Patient1_IL-1b, ChIP


title: DMSO_0-1_R35_P7_H_pool2


title: DMSO_0-1_R36_P7_H_pool2


title: DMSO_0-1_R34_P7_H_pool2


title: PANC1-Drug resistance cell line-1

description: Library name: PR1530A

data_processing:
The raw sequence reads were aligned to the GRCh38 reference genome using STAR.
RSEM was used for transcript quantification based on the STAR alignment.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.


title: PANC1-Drug resistance cell line-2

description: Library name: PR1530B


title: PANC parent cell line-1

description: Library name: PANC1A


title: DMSO_0-1_R33_P7_H_pool2


title: PANC parent cell line-2

description: Library name: PANC1B


title: KPC parent cell line -2

description: Library name: KPCB

source_name: KPC

value: KPC


title: TMBPF_1_R4_P7_H_pool2

value: Tetramethyl bisphenol F


title: KPC parent cell line -1

description: Library name: KPCA


title: KPC Drug resistance cell line - 2

description: Library name: KPC5RB


title: TMBPF_0-1_R4_P7_H_pool2


title: PC_B_R6_P6_G_pool2

value: No cells; Brain positive control


title: PC_UH_R6_P6_G_pool2

value: No cells; Universal human positive control


title: KPC Drug resistance cell line - 1

description: Library name: KPC5RA


title: Mix7_21_R3_P6_G_pool2

value: Mix 7


title: 21E24_ESCI_5HT_48h_CTB

city: New Haven

first: Nolwenn

middle: Sue

last: Morris

address: 333 Cedar Street

department: OBGYN

institute: Yale University

description:
Library name: Sample 18
Column name in gene_count_matrix.csv: S_21E24_lex_2b_5HT

data_processing:
Flow Cell Preparation and Sequencing: Sample concentrations were normalized to 2.0 nM and loaded onto an Illumina NovaSeq (San Diego, CA) flow cell at a concentration that yields 35 million passing filter clusters per sample. Samples were sequenced using 100bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols. The 10bp unique dual index was read during additional sequencing reads that automatically follow the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the Yale Center for Genomic Analysis (New Haven, CT) high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.
Data Analysis and Storage: Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Base calls were transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis—sample de-multiplexing and alignment to the human genome—was performed using Illumina's CASAVA 1.8.2 software suite. The data were returned to the user if the sample error rate was less than 2% and the distribution of reads per sample in a lane was within reasonable tolerance. Data was retained on the cluster for at least 6 months, after which it was transferred to a tape backup system.
Following RNA sequencing, low quality reads were trimmed, and adaptor contamination were removed using Trim Galore (v0.5.0; Babraham Bioinformatics, Cambridge, UK). Trimmed reads were mapped to the human reference genome (mm10) using HISAT2 (v2.1.0) (22). Gene expression levels were quantified using StringTie (v1.3.3b) (23) with gene models (v27) from the GENCODE project (24). Differentially expressed genes were identified using DESeq2 (v 1.22.1) (25). Transcripts per million (TPM) were calculated as previously described (26), while adjusted p values were calculated with DESeq2 using the Benjamini and Hochberg method (27).
Volcano plots were created by plotting the log2FoldChange (x-axis), minus log10 p-values (y-axis) of all genes as reported by DESeq2.
Assembly: HG38
Supplementary files format and content: gene_count_matrix.csv: tab delimited text file includes raw counts for each sample

source_name: Placenta

growth_protocol: Cytotrophoblast were prepared from fresh human term placentas by trypsin digestion and Percoll gradient fractionation, with the addition of an anti-CD9 and CD45 magnetic bead purification step, as previously described (19,20). During the initial steps of the digestions and up to the magnetic purification step, 10% fetal bovine serum (FBS, Gemini Bio-Products, Broderick, CA, 100-106) diluted in DMEM/F12 (Gibco, ThermoFisher Scientific, Waltham, MA, 11330-032) with 4 mM L-glutamine, 1% penicillin/streptomycin was utilized. After the magnetic purification step, no FBS was added to the culture media, unless specifically noted. Cytotrophoblasts were then diluted to 1x106 cells per ml in DMEM/F12 with 4 mM L-glutamine, 1% penicillin/streptomycin and either: 1) pelleted immediately by centrifugation for a zero-time point; 2) cultured in two- or four-chamber Nunc™ Lab-Tek™ II Chamber Slide™ System slides (ThermoFisher Scientific) or six-wells plates (CELLSTAR® #657160 6-well cell culture plates) for 24-96 hours in humidified 5% CO2-95% air at 37˚C.

extract_protocol:
Cells were lysed in QIAzol, and RNA was isolated using the miRNeasy Mini Kit (Qiagen), also following the manufacturer's protocol. An on-column DNase digestion was performed.
RNA Seq Library Prep: Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351, Roche Diagnostics, Indianapolis, IN), rRNA was depleted starting from a normalized input of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA. Samples were then fragmented using heat and magnesium. 1st strand synthesis was performed using random priming. 2nd strand synthesis incorporated dUTPs into the 2nd strand cDNA. Adapters were then ligated, and the library was amplified. Strands marked with dUTPs were not amplified allowing for strand-specific sequencing. Indexed libraries that meet appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Library Quant Kit, Roche Diagnostics, 07960298001) and insert size distribution determined with an Agilent Bioanalyzer (Agilent TapeStation 4200). Samples with a yield of ≥0.5 ng/µl were used for sequencing.

treatment_protocol: Purified cytotrophoblasts were cultured in Nunc™ Lab-Tek™ II Chamber Slide™ System slides with or without serotonin hydrochloride, with or without cystamine, or with or without escitalopram oxalate.

value: Placenta

value: Purified trophoblast

value: 200uM Escitalopram + 3 uM 5HT


title: 12D24_ESCI_5HT_48h_SCTB

description:
Library name: Sample 17
Column name in gene_count_matrix.csv: S_12D24_lex_2b_5HT


title: 12D24_ESCI_48h_CTB

description:
Library name: Sample 14
Column name in gene_count_matrix.csv: S_12D24_lex

value: 200uM Escitalopram


title: 21E24_CYS_5HT_48h_CTB

description:
Library name: Sample 12
Column name in gene_count_matrix.csv: S_21E24_cys_2b_5HT

value: 10 mM Cystamine + 3uM 5HT


title: 27C24_ESCI_48h_CTB

description:
Library name: Sample 13
Column name in gene_count_matrix.csv: S_27C24_lex


title: 21E24_ESCI_48h_CTB

description:
Library name: Sample 15
Column name in gene_count_matrix.csv: S_21E24_lex


title: 27C24_ESCI_5HT_48h_CTB

description:
Library name: Sample 16
Column name in gene_count_matrix.csv: S_27C24_lex_2b_5HT


title: Mix7_2-62_R3_P6_G_pool2


title: Mix7_1-31_R3_P6_G_pool2


title: Mix7_10-5_R3_P6_G_pool2


title: P201_50_R3_P6_G_pool2


title: Mix7_0-66_R3_P6_G_pool2


title: 12D24_CYS_5HT_48h_CTB

description:
Library name: Sample 11
Column name in gene_count_matrix.csv: S_12D24_cys_2b_5HT


title: Mix7_5-25_R3_P6_G_pool2


title: 27C24_CYS_5HT_48h_CTB

description:
Library name: Sample 10
Column name in gene_count_matrix.csv: S_27C24_cys_2b_5HT


title: P201_10_R3_P6_G_pool2


title: 12D24_CYS_48h_CTB

description:
Library name: Sample 8
Column name in gene_count_matrix.csv: S_12D24_cys

value: 10 mM Cystamine


title: 21E24_CYS_48h_CTB

description:
Library name: Sample 9
Column name in gene_count_matrix.csv: S_21E24_cys


title: P201_1_R3_P6_G_pool2


title: 27C24_CYS_48h_CTB

description:
Library name: Sample 7
Column name in gene_count_matrix.csv: S_27C24_cys


title: P201_0-5_R3_P6_G_pool2


title: P201_5_R3_P6_G_pool2


title: 21E24_5HT_48h_CTB

description:
Library name: Sample 6
Column name in gene_count_matrix.csv: S_21E24_5HT

value: 3 uM 5HT


title: P201_0-1_R3_P6_G_pool2


title: 12D24_5HT_48h_CTB

description:
Library name: Sample 5
Column name in gene_count_matrix.csv: S_12D24_5HT


title: 27C24_5HT_48h_CTB

description:
Library name: Sample 4
Column name in gene_count_matrix.csv: S_27C24_5HT


title: P201_0-01_R3_P6_G_pool2


title: P201_0-001_R3_P6_G_pool2


title: 21E24_CTRL_48h_CTB

description:
Library name: Sample 3
Column name in gene_count_matrix.csv: S_21E24_Ctrl

value: CTRL


title: 24BPF_50_R3_P6_G_pool2

value: 2,4'-Bisphenol F


title: 24BPF_5_R3_P6_G_pool2


title: 24BPF_10_R3_P6_G_pool2


title: 12D24_CTRL_48h_CTB

description:
Library name: Sample 2
Column name in gene_count_matrix.csv: S_12D24_Ctrl


title: 24BPF_0-5_R3_P6_G_pool2


title: 27C24_CTRL_48h_CTB

description:
Library name: Sample 1
Column name in gene_count_matrix.csv: S_27C24_Ctrl


title: 24BPF_1_R3_P6_G_pool2


title: NLS-2

city: Hangzhou

first: zixin

last: wang

state: Zhejiang Province

address: No. 866, Yuhangtang Road, Xihu District

department: Institute of Immunology

institute: Zhejiang University School of Medicine

description: Library name: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

growth_protocol: Panc1 cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS, 10099141C, Gibco).

extract_protocol:
Total RNA was extracted using the  RNA Fast200 Cell/Tissue Total RNA Isolation Kit (Fastagen Cat, # 220011) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: TLR3 KO Panc1 cells were constructed using pCas91.1/gRNA Kit (V-solid, Cat# VK001-02). For plasmid transfection, TLR3 KO Panc1 cells were transfected with NLS-TLR3-Flag and NES-TLR3-Flag plasmid at a final concentration of 1 µg/100µl using X-treme GENE™ HP (06366236001, Sigma-Aldrich).

value: cancer cells

value: TLR3 KO with  NLS-TLR3 rescue


title: NES-1

description: Library name: Sample 3

value: TLR3 KO with  NES-TLR3 rescue


title: 24BPF_0-001_R3_P6_G_pool2


title: 24BPF_0-01_R3_P6_G_pool2


title: 24BPF_0-1_R3_P6_G_pool2


title: KO-2

description: Library name: Sample 2

value: TLR3 KO


title: BPZ_5_R3_P6_G_pool2

value: Bisphenol Z


title: BPZ_1_R3_P6_G_pool2


title: NES-2

description: Library name: Sample 4


title: NLS-1

description: Library name: Sample 5


title: BPZ_50_R3_P6_G_pool2


title: KO-1

description: Library name: Sample 1


title: PC3 10DPTR, biol rep 3, exp rep 2

city: Baltimore

first: Anna

last: Gonye

state: Maryland

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

description: Library name: Sample 53

data_processing:
Raw sequencing reads were demultiplexed and trimmed for adapter sequences using Cutdapt (v1.18; with parameter --minimum-length 40). Quality control of the raw reads was performed using FastQC (v0.12.1).
Reads were then aligned to the human genome reference using Bowtie2 (v2.3.5.1) with the following parameters: --no-unal --no-discordant --threads 14 -X 2000.
Duplicate reads were flagged with Picard.
Technical replicates were merged, and duplicated reads, mitochondrial reads, and low-quality alignments were removed using Samtools (v1.6).
Library complexity for each merged sample was determined via ATACseqQC (v1.29.0) in R (v4.4.1) and libraries were normalized based on the least-complex biological replicate through subsampling.
Peaks representing regions of accessible chromatin were called using Genrich (v0.6.2) in ATAC-seq mode (-j flag) with standard parameters; blacklisted hg38 genomic regions were excluded from analysis. To assess reproducibility, peak calling was performed on each biological replicate.
Assembly: GRCh38; patch release 14, NCBI accession GCA_000001405.29
Supplementary files format and content: narrowPeak

extract_protocol:
1x105 cells per sample were pelleted and washed twice in cold 1X PBS. Cells were lysed in cold lysis buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween 20, 0.1% NP40, 0.01% Digitonin, 1% BSA, 100 µM DTT] for 12 minutes on ice. Following lysis, cold wash buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween 20, 100 µM DTT] was added to each sample and nuclei were pelleted for 10 min at 500 xg at 4 °C. Three biological replicates of each group were prepared, with each containing experimental triplicate samples [Biological replicate sample was split into 3 experimental samples prior to tagmentation/library construction, so each experimental replicate was prepped and sequenced independently].
Transposition/tagmentation was carried out via a modified version of 10X Genomics’ ATAC protocol. Briefly, nuclei were resuspended Nuclei Buffer (10X Genomics, #2000207) prior to the addition of ATAC Buffer B (10X Genomics, #2000193) and ATAC Enzyme B (10X Genomics, 2000265). Following gentle mixing, transposition/tagmentation was carried out 37 °C for 1 hr. Tagmented samples were then underwent 14 cycles of PCR amplification with the NEBNext HiFidelity 2X PCR Master Mix (New England Biolabs, #M0541) and Nextera PCR primers. Libraries were purified with 1.2X Ampure XP Beads (Beckman Coulter, #A63881).

value: cisplatin, 10 days post-treatment removal


title: PC3 10DPTR, biol rep 3, exp rep 3

description: Library name: Sample 54


title: PC3 10DPTR, biol rep 3, exp rep 1

description: Library name: Sample 52


title: PC3 1DPTR, biol rep 3, exp rep 2

description: Library name: Sample 50

value: cisplatin, 1 day post-treatment removal


title: BPZ_0-1_R3_P6_G_pool2


title: BPZ_10_R3_P6_G_pool2


title: PC3 1DPTR, biol rep 3, exp rep 3

description: Library name: Sample 51


title: BPZ_0-01_R3_P6_G_pool2


title: PC3 control, biol rep 3, exp rep 3

description: Library name: Sample 48

value: control


title: PC3 1DPTR, biol rep 3, exp rep 1

description: Library name: Sample 49


title: BPZ_0-001_R3_P6_G_pool2


title: BPB_50_R2_P6_G_pool2

value: Bisphenol B


title: PC3 control, biol rep 3, exp rep 1

description: Library name: Sample 46


title: PC3 10DPTR, biol rep 2, exp rep 3

description: Library name: Sample 45


title: BPB_10_R2_P6_G_pool2


title: PC3 1DPTR, biol rep 2, exp rep 3

description: Library name: Sample 42


title: BPZ_0-5_R3_P6_G_pool2


title: PC3 1DPTR, biol rep 2, exp rep 2

description: Library name: Sample 41


title: BPB_5_R2_P6_G_pool2


title: BPB_0-1_R2_P6_G_pool2


title: BPB_0-5_R2_P6_G_pool2


title: PC3 10DPTR, biol rep 2, exp rep 2

description: Library name: Sample 44


title: BPB_0-01_R2_P6_G_pool2


title: 24BPS_50_R2_P6_G_pool2

value: 2,4'-Bisphenol S


title: PC3 control, biol rep 2, exp rep 3

description: Library name: Sample 39


title: 24BPS_10_R2_P6_G_pool2


title: PC3 1DPTR, biol rep 2, exp rep 1

description: Library name: Sample 40


title: BPB_1_R2_P6_G_pool2


title: BPB_0-001_R2_P6_G_pool2


title: PC3 control, biol rep 2, exp rep 2

description: Library name: Sample 38


title: 24BPS_5_R2_P6_G_pool2


title: PC3 control, biol rep 2, exp rep 1

description: Library name: Sample 37


title: PC3 10DPTR, biol rep 1, exp rep 2

description: Library name: Sample 35


title: PC3 10DPTR, biol rep 1, exp rep 3

description: Library name: Sample 36


title: 24BPS_1_R2_P6_G_pool2


title: 24BPS_0-5_R2_P6_G_pool2


title: PC3 1DPTR, biol rep 1, exp rep 3

description: Library name: Sample 33


title: PC3 10DPTR, biol rep 1, exp rep 1

description: Library name: Sample 34


title: 24BPS_0-1_R2_P6_G_pool2


title: PC3 control, biol rep 3, exp rep 2

description: Library name: Sample 47


title: 24BPS_0-01_R2_P6_G_pool2


title: PC3 1DPTR, biol rep 1, exp rep 2

description: Library name: Sample 32


title: 24BPS_0-001_R2_P6_G_pool2


title: P201_50_R2_P6_G_pool2


title: PC3 control, biol rep 1, exp rep 3

description: Library name: Sample 30


title: P201_10_R2_P6_G_pool2


title: PC3 control, biol rep 1, exp rep 2

description: Library name: Sample 29


title: P201_1_R2_P6_G_pool2


title: P201_5_R2_P6_G_pool2


title: PC3 control, biol rep 1, exp rep 1

description: Library name: Sample 28


title: MDA-MB-231 10DPTR, biol rep 3, exp rep 3

description: Library name: Sample 27


title: MDA-MB-231 1DPTR, biol rep 3, exp rep 3

description: Library name: Sample 24


title: MDA-MB-231 10DPTR, biol rep 3, exp rep 1

description: Library name: Sample 25


title: P201_0-5_R2_P6_G_pool2


title: P201_0-01_R2_P6_G_pool2


title: P201_0-1_R2_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 3, exp rep 2

description: Library name: Sample 26


title: NC_R12_P6_G_pool2

value: No cells; 1X Lysis buffer


title: MDA-MB-231 1DPTR, biol rep 3, exp rep 1

description: Library name: Sample 22


title: MDA-MB-231 1DPTR, biol rep 3, exp rep 2

description: Library name: Sample 23


title: P201_0-001_R2_P6_G_pool2


title: MDA-MB-231 control, biol rep 3, exp rep 3

description: Library name: Sample 21


title: MDA-MB-231 control, biol rep 3, exp rep 2

description: Library name: Sample 20


title: DMSO_0-1_R31_P6_G_pool2

value: Dimethyl sulfoxide


title: MDA-MB-231 control, biol rep 3, exp rep 1

description: Library name: Sample 19


title: DMSO_0-1_R30_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 2, exp rep 3

description: Library name: Sample 18


title: PC3 10DPTR, biol rep 2, exp rep 1

description: Library name: Sample 43


title: DMSO_0-1_R29_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 2, exp rep 2

description: Library name: Sample 17


title: DMSO_0-1_R28_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 2, exp rep 1

description: Library name: Sample 16


title: 24BPF_10_R2_P6_G_pool2


title: 24BPF_50_R2_P6_G_pool2


title: MDA-MB-231 1DPTR, biol rep 2, exp rep 1

description: Library name: Sample 13


title: MDA-MB-231 1DPTR, biol rep 2, exp rep 2

description: Library name: Sample 14


title: MDA-MB-231 1DPTR, biol rep 2, exp rep 3

description: Library name: Sample 15


title: 24BPF_0-1_R2_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 1, exp rep 3

description: Library name: Sample 9


title: NC_R11_P6_G_pool2


title: MDA-MB-231 control, biol rep 2, exp rep 3

description: Library name: Sample 12


title: 24BPF_5_R2_P6_G_pool2


title: 24BPF_1_R2_P6_G_pool2


title: 24BPF_0-001_R2_P6_G_pool2


title: MDA-MB-231 control, biol rep 2, exp rep 1

description: Library name: Sample 10


title: MDA-MB-231 10DPTR, biol rep 1, exp rep 2

description: Library name: Sample 8


title: 24BPF_0-01_R2_P6_G_pool2


title: DMSO_0-1_R32_P6_G_pool2


title: BPS_50_R3_P6_G_pool2

value: Bisphenol S


title: MDA-MB-231 control, biol rep 2, exp rep 2

description: Library name: Sample 11


title: MDA-MB-231 1DPTR, biol rep 1, exp rep 3

description: Library name: Sample 6


title: 24BPF_0-5_R2_P6_G_pool2


title: BPS_10_R3_P6_G_pool2


title: MDA-MB-231 1DPTR, biol rep 1, exp rep 2

description: Library name: Sample 5


title: BPS_5_R3_P6_G_pool2


title: BPS_1_R3_P6_G_pool2


title: DMSO_0-1_R27_P6_G_pool2


title: MDA-MB-231 control, biol rep 1, exp rep 3

description: Library name: Sample 3


title: MDA-MB-231 1DPTR, biol rep 1, exp rep 1

description: Library name: Sample 4


title: BPS_0-5_R3_P6_G_pool2


title: PC3 1DPTR, biol rep 1, exp rep 1

description: Library name: Sample 31


title: BPS_0-01_R3_P6_G_pool2


title: BPAP_10_R3_P6_G_pool2

value: Bisphenol AP


title: PDO8-DMSO

city: Nantes

first: jennifer

last: Derrien

address: 8 quai moncousu

institute: INSERM

description: Library name: PDO8-DMSO

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
The demultiplexing, barcode processing, and gene counting were performed using Cell Ranger software v.6.1.2.
Samples PDO3- DMSO-Taxol-Doxo were multiplexed using the 10X Genomics CellPlex kit were demultiplexed using the CellRanger multi configuration. 10X Genomics cell multiplexing oligos used for each individual sample were as follow: DMSO-CMO305; Taxol-CMO309; Doxo-CMO307
Assembly: GRCh38-3.0.0
Supplementary files format and content: The processed data files include tab-separated values (.tsv) files and matrix files (.mtx)

source_name: breast

growth_protocol: PDO culture was performed using a protocol adapted from Sachs and colleagues (Sachs et al., 2018). Briefly, cells were seeded in advanced DMEM/F12 (Thermo-Fisher) supplemented with glutamax, HEPES, 10% R-spondin 1, 10% noggin, 2% B-27, nicotinamide (10 mM), N-acetyl-L-cysteine (500 mM), primocin (100 µg/mL), Y-27632 (5µM), heregulin β1 (5 nM), FGF-7 (5 ng/mL), FGF-10 (5 ng/mL), A83-01 (0.5 µM), EGF (5 ng/mL), SB202190 (1 µM) containing 5% matrigel. 200,000 cells were seeded per well in 24-well ultralow attachment plates (Corning).

extract_protocol:
PDOs were dissociated with trypsin and dissociated cells were processed for library preparation.
Libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3’ v3 protocol (10x Genomics). Sequencing was performed on a NovaSeq 6000 platform as paired-end reads: 28 bp for Read 1 and 90 bp for Read 2 (GenoA, UMS Biocore, SFR Bonamy, Nantes).

treatment_protocol: PDOs were treated with DMSO, taxol (10 nM), doxorubicin 100 nM) for 24 or 48 hours.

value: breast


title: PDO8-Nao-3

description: Library name: PDO8-Nao-3


title: PDO3-Doxo

description: Library name: PDO3-Doxo


title: PDO3-Taxol

description: Library name: PDO3-Taxol


title: MDA-MB-231 control, biol rep 1, exp rep 1

description: Library name: Sample 1


title: PDO3-treatment-naive

description: Library name: PDO3-treatment-naive


title: BPAP_0-5_R3_P6_G_pool2


title: MDA-MB-231 10DPTR, biol rep 1, exp rep 1

description: Library name: Sample 7


title: BPS_0-001_R3_P6_G_pool2


title: BPAP_50_R3_P6_G_pool2


title: BPAP_0-01_R3_P6_G_pool2


title: Basal Tumor 77

city: Cambridge

first: Eric

middle: Scott

last: Lightcap

state: MA

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

description:
Library name: 30-609774425_77
77_001

data_processing:
QIAGEN OmicSoft Suite 12.3 (QIAGEN, Redwood City, CA) with default settings was used for raw FASTQ data quality control (QC), alignment to genome, aligned data QC, gene expression quantification, and differential expression analyses. Reads were aligned using OSA4 and gene expression quantification was performed by counting the mapped reads with an expectation-maximization algorithm to the Human.B38 (GRCh38) genome and annotations provided by the OmicsoftGenCode.V33 (GENCODE 33) gene model. Log2-transformed counts per million were used to perform multidimensional scaling (MDS) in R 4.2.2 with Glimma 2.8.0 for additional sample QC.
All samples passed raw and aligned data QC according to the following metrics: 40 < GC% < 60, overrepresented sequence < 25, duplication level 10+ < 50, N rate < 5%, Q30 base rate > 70, overall mapping rate > 50%, uniquely mapped rate > 40%, paired mapping rate > 40, exon rate > 30%, mitochondrial rate < 40%, and rRNA rate < 1%. One MDS outlier sample was removed from downstream analysis.
Differential expression analysis was performed in OmicSoft using DESeq2 1.30.1.   The model included Experiment Group without covariates, and all pairwise comparisons between groups were performed to test the effects of HC-7366 dosages against vehicle control and HC-7366 dosages against each other. The false discovery rate (FDR) method of Benjamini & Hochberg (1995) was used to adjust for multiple testing.
Assembly: Human B38 (GRCh38)
Supplementary files format and content: Expression.FPKM.xlsx

source_name: xenograft tumor tissue

growth_protocol: Animal specifics: 119 female NOD SCID mice. Age: 6 to 8 weeks. Body Weight: 16 to 23 g. Each mouse was inoculated subcutaneously on the right flank with MOLM-16 tumor cells (1 x 10^7) in 0.1 ml of RPMI 1640 medium without serum for tumor development. Groups and treatments were started when the mean tumor volume reached about 302 mm^3 for efficacy cohort and 302 mm^3 for PKPD cohort at Day 17 post inoculation. Based on the tumor volume and body weight, mice were assigned to respective groups such that the average starting tumor size is the same for each treatment group.

extract_protocol:
RNA was extracted from tumor (~10 mg) using the RNeasy plus mini kit (Qiagen) according to manufacturer’s instructions with the DNase treatment option.
RNA library preparation and sequencing were conducted at Azenta Life Sciences (South Plainfield, NJ, USA). RNA samples received were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 min at 94 °C. First-strand and second-strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

treatment_protocol: 19 mice (10 for efficacy, 9 for PK/PD measurement) were treated PO BID with the following treatments: Vehicle Control (5% (v/v) DMSO and 95% (v/v) Captisol (20% w/v) in PBS (pH 7.4)), HC-7366 (0.3, 1, 3, 10, or 30 mg/kg groups), or baseline tumor control (untreated, n=5 for PD). After 3 days of dosing on Day 4, 1 h post AM dose euthanized 9 animals and collected blood for PK.  After blood collection, removed tumors and prepared tissues 1/3 FFPE (multiwelled), 1/3 Frozen, and 1/3 RNA later.

value: xenograft tumor tissue

value: MOLM-16 (DSMZ, ACC 555)

value: acute myeloid leukemia (LAML)

value: Basal Tumor

tag: batch


title: BPAP_0-001_R3_P6_G_pool2


title: Basal Tumor 62

description:
Library name: 30-609774425_62
62_001


title: BPS_0-1_R3_P6_G_pool2


title: HC-7366 30 mg/kg 166

description:
Library name: 30-609774425_166
166_001


title: BPAP_5_R3_P6_G_pool2


title: PDO3-DMSO

description: Library name: PDO3-DMSO


title: BPAP_1_R3_P6_G_pool2


title: Basal Tumor 106

description:
Library name: 30-609774425_106
106_001


title: BPAP_0-1_R3_P6_G_pool2


title: Basal Tumor 69

description:
Library name: 30-609774425_69
69_001


title: HC-7366 30 mg/kg 154

description:
Library name: 30-609774425_154
154_001


title: Mix7_5-25_R2_P6_G_pool2

value: Mix 7


title: Mix7_21_R2_P6_G_pool2


title: MDA-MB-231 control, biol rep 1, exp rep 2

description: Library name: Sample 2


title: HC-7366 30 mg/kg 125

description:
Library name: 30-609774425_125
125_001


title: Mix7_1-31_R2_P6_G_pool2


title: HC-7366 30 mg/kg 121

description:
Library name: 30-609774425_121
121_001


title: Mix7_10-5_R2_P6_G_pool2


title: Basal Tumor 112

description:
Library name: 30-609774425_112
112_001


title: PC_B_R5_P5_F_pool2

value: No cells; Brain positive control


title: HC-7366 30 mg/kg 76

description:
Library name: 30-609774425_76
76_001


title: Mix7_0-66_R2_P6_G_pool2


title: HC-7366 30 mg/kg 190

description:
Library name: 30-609774425_190
190_001


title: DMSO_0-1_R26_P6_G_pool2


title: DMSO_0-1_R25_P6_G_pool2


title: HC-7366 30 mg/kg 50

description:
Library name: 30-609774425_50
50_001


title: Mix7_21_R1_P5_F_pool2


title: HC-7366 30 mg/kg 61

description:
Library name: 30-609774425_61
61_001


title: Mix7_10-5_R1_P5_F_pool2


title: HC-7366 10 mg/kg 174

description:
Library name: 30-609774425_174
174_001


title: HC-7366 10 mg/kg 183

description:
Library name: 30-609774425_183
183_001


title: HC-7366 10 mg/kg 152

description:
Library name: 30-609774425_152
152_001


title: Mix7_2-62_R2_P6_G_pool2


title: HC-7366 10 mg/kg 118

description:
Library name: 30-609774425_118
118_001


title: HC-7366 10 mg/kg 80

description:
Library name: 30-609774425_80
80_001


title: BPS_50_R2_P5_F_pool2


title: BPS_10_R2_P5_F_pool2


title: PC_UH_R5_P5_F_pool2

value: No cells; Universal human positive control


title: HC-7366 10 mg/kg 24

description:
Library name: 30-609774425_24
24_001


title: HC-7366 3 mg/kg 197

description:
Library name: 30-609774425_197
197_001


title: BPS_0-1_R2_P5_F_pool2


title: BPS_0-01_R2_P5_F_pool2


title: BPS_0-5_R2_P5_F_pool2


title: HC-7366 3 mg/kg 185

description:
Library name: 30-609774425_185
185_001


title: HC-7366 3 mg/kg 179

description:
Library name: 30-609774425_179
179_001


title: HC-7366 30 mg/kg 103

description:
Library name: 30-609774425_103
103_001


title: BPAP_50_R2_P5_F_pool2


title: HC-7366 3 mg/kg 164

description:
Library name: 30-609774425_164
164_001


title: Mix7_5-25_R1_P5_F_pool2


title: BPAP_10_R2_P5_F_pool2


title: Mix7_1-31_R1_P5_F_pool2


title: HC-7366 10 mg/kg 131

description:
Library name: 30-609774425_131
131_001


title: HC-7366 3 mg/kg 129

description:
Library name: 30-609774425_129
129_001


title: HC-7366 10 mg/kg 97

description:
Library name: 30-609774425_97
97_001


title: BPAP_5_R2_P5_F_pool2


title: HC-7366 10 mg/kg 63

description:
Library name: 30-609774425_63
63_001


title: HC-7366 3 mg/kg 176

description:
Library name: 30-609774425_176
176_001


title: BPS_5_R2_P5_F_pool2


title: BPS_0-001_R2_P5_F_pool2


title: BPAP_1_R2_P5_F_pool2


title: HC-7366 3 mg/kg 107

description:
Library name: 30-609774425_107
107_001


title: HC-7366 1 mg/kg 193

description:
Library name: 30-609774425_193
193_001


title: HC-7366 3 mg/kg 122

description:
Library name: 30-609774425_122
122_001


title: Mix7_2-62_R1_P5_F_pool2


title: HC-7366 3 mg/kg 119

description:
Library name: 30-609774425_119
119_001


title: BPAP_0-001_R2_P5_F_pool2


title: BPAP_0-01_R2_P5_F_pool2


title: Mix7_0-66_R1_P5_F_pool2


title: HC-7366 1 mg/kg 130

description:
Library name: 30-609774425_130
130_001


title: HC-7366 1 mg/kg 135

description:
Library name: 30-609774425_135
135_001


title: BPZ_50_R2_P5_F_pool2

value: Bisphenol Z


title: BPZ_5_R2_P5_F_pool2


title: HC-7366 1 mg/kg 55

description:
Library name: 30-609774425_55
55_001


title: BPS_1_R2_P5_F_pool2


title: BPZ_10_R2_P5_F_pool2


title: BPZ_0-5_R2_P5_F_pool2


title: HC-7366 1 mg/kg 52

description:
Library name: 30-609774425_52
52_001


title: HC-7366 1 mg/kg 25

description:
Library name: 30-609774425_25
25_001


title: HC-7366 1 mg/kg 48

description:
Library name: 30-609774425_48
48_001


title: BPZ_0-1_R2_P5_F_pool2


title: BPAP_0-1_R2_P5_F_pool2


title: BPZ_0-01_R2_P5_F_pool2


title: BPZ_1_R2_P5_F_pool2


title: HC-7366 0.3 mg/kg 198

description:
Library name: 30-609774425_198
198_001


title: HC-7366 0.3 mg/kg 187

description:
Library name: 30-609774425_187
187_001


title: HC-7366 1 mg/kg 162

description:
Library name: 30-609774425_162
162_001


title: HC-7366 1 mg/kg 30

description:
Library name: 30-609774425_30
30_001


title: BPAP_0-5_R2_P5_F_pool2


title: BPZ_0-001_R2_P5_F_pool2


title: HC-7366 0.3 mg/kg 182

description:
Library name: 30-609774425_182
182_001


title: BPB_50_R1_P5_F_pool2


title: BPB_1_R1_P5_F_pool2


title: BPB_5_R1_P5_F_pool2


title: BPB_0-5_R1_P5_F_pool2


title: Mesothelioma_TMA2_[MERFISH]

first: Ken

last: Chen

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

description: MERFISH

hyb_protocol: RNA transcript is assigned a unique binary barcode, read through sequential imaging rounds. MERFISH utilizes sequential imaging rounds with fluorescently labeled probes to read out unique barcodes assigned to each RNA transcript.

scan_protocol: MERFISH generates a series of images capturing the location of different RNA species in the sample.

data_processing: MERFISH pipeline was performed to generate cellpose_cell_by_gene, cellpose_metadata, and cellpose_detected_transcripts files.

source_name: Mesothelioma

growth_protocol: No growth protocol

extract_protocol: No extraction protocol

treatment_protocol: No treatment protocol

value: pleural mesothelioma


title: HC-7366 0.3 mg/kg 151

description:
Library name: 30-609774425_151
151_001


title: Lung_Adenocarcinoma_TMA2_[MERFISH]

description: MERFISH

source_name: Lung Adenocarcinoma

value: lung adenocarcinoma


title: Lung_Adenocarcinoma_TMA1_[MERFISH]

description: MERFISH


title: total, KMS11, plumKD, ctrl, rep1

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Reads were mapped to GRCh38 using STAR
Counts across GENCODE genes by featureCounts
Assembly: hg38
Supplementary files format and content: tsv, counts

source_name: Haematopoietic and Lymphoid

growth_protocol: Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).

extract_protocol:
phenol-chloroform extraction followed by DNAse treatment and rRNA depletion
NEBNext® UltraTM II Directional RNA Library Prep Kit

treatment_protocol: Cells were transduced with shRNA-PLUM targeting virus and selected with 0.1 µg/ml puromycin for 48h followed by recovery of 3 days. Following recovery, cells were harvested/seeded for RNA-seq, ChIP-seq and other functional assays.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: Female

value: control


title: BPB_0-01_R1_P5_F_pool2

data_processing:
The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.422. The FASTQ files were were processed using the R-ODAF pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada). Briefly:
Reads were trimmed and filtered with fastp (--cut_front_window_size 1, --cut_front_mean_quality 3, --cut_tail_window_size 1, --cut_tail_mean_quality 3, --cut_right_window_size 4, --cut_right_mean_quality 15, --length_required 50). Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2). Quantification was performed in R using the qAlign function from the QuasR package.
Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2).
Quantification was performed in R using the qAlign function from the QuasR package.
Assembly: GTF file generated from probe sequences in Biospyder manifest file
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

extract_protocol:
Cells were lysed and RNA was extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries using the TempO-Seq Human Whole Transcriptome 2.1 kit (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 [?] individual libraries were pooled to create a single pool for sequencing on the [instrument] (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.

value: Bisphenol B


title: HC-7366 0.3 mg/kg 157

description:
Library name: 30-609774425_157
157_001


title: BPB_0-1_R1_P5_F_pool2


title: BPB_0-001_R1_P5_F_pool2


title: HC-7366 0.3 mg/kg 108

description:
Library name: 30-609774425_108
108_001


title: 24BPS_10_R1_P5_F_pool2

value: 2,4'-Bisphenol S


title: HC-7366 0.3 mg/kg 96

description:
Library name: 30-609774425_96
96_001

value: xenograft tumor tissue


title: total, KMS11, plumKD, ctrl, rep3


title: 24BPS_50_R1_P5_F_pool2


title: HC-7366 0.3 mg/kg 78

description:
Library name: 30-609774425_78
78_001

value: MOLM-16 (DSMZ, ACC 555)


title: BPB_10_R1_P5_F_pool2


title: 24BPS_5_R1_P5_F_pool2


title: HC-7366 0.3 mg/kg 43

description:
Library name: 30-609774425_43
43_001

value: acute myeloid leukemia (LAML)


title: total, KMS11, plumKD, trgt, rep1

value: PLUM KD


title: 24BPS_0-5_R1_P5_F_pool2


title: 24BPS_0-1_R1_P5_F_pool2


title: total, KMS11, plumKD, trgt, rep2


title: 24BPS_0-01_R1_P5_F_pool2


title: 24BPS_1_R1_P5_F_pool2


title: Vehicle 186

description:
Library name: 30-609774425_186
186_001

value: Vehicle


title: P201_10_R1_P5_F_pool2


title: Vehicle 199

description:
Library name: 30-609774425_199
199_001


title: P201_50_R1_P5_F_pool2


title: 24BPS_0-001_R1_P5_F_pool2


title: total, KMS11, plumKD, trgt, rep3


title: P201_0-5_R1_P5_F_pool2


title: P2R+SA3

city: Chang Sha

first: Yang

last: Han

address: No. 498, Shaoshan South Road

institute: Central South University of Forestry&Technology

description: Library name: P2R+SA3

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to thereference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: Trametes hirsuta X-13 whole genome sequence (GCA_030411785.1)
Supplementary files format and content: The tab-delimited text include FPKM values for each Sample

organism: Aspergillus fumigatus

source_name: mycelium

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the  manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000  spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: mycelium


title: P2R+SA2

description: Library name: P2R+SA2


title: Vehicle 124

description:
Library name: 30-609774425_124
124_001


title: Vehicle 117

description:
Library name: 30-609774425_117
117_001


title: P201_5_R1_P5_F_pool2

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada


title: P201_0-1_R1_P5_F_pool2


title: P201_1_R1_P5_F_pool2


title: P2R+SA1

description: Library name: P2R+SA1


title: P201_0-01_R1_P5_F_pool2


title: total, KMS11, plumKD, ctrl, rep2


title: P201_0-001_R1_P5_F_pool2


title: SA3

description: Library name: SA3


title: Vehicle 75

description:
Library name: 30-609774425_75
75_001


title: NC_R10_P5_F_pool2

value: No cells; 1X Lysis buffer


title: NC_R9_P5_F_pool2


title: DMSO_0-1_R21_P5_F_pool2

value: Dimethyl sulfoxide


title: DMSO_0-1_R24_P5_F_pool2


title: DMSO_0-1_R22_P5_F_pool2


title: Vehicle 59

description:
Library name: 30-609774425_59
59_001


title: Vehicle 72

description:
Library name: 30-609774425_72
72_001


title: DMSO_0-1_R23_P5_F_pool2


title: Vehicle 37

description:
Library name: 30-609774425_37
37_001


title: SA2

description: Library name: SA2


title: P2R3

description: Library name: P2R3


title: SA1

description: Library name: SA1


title: DMSO_0-1_R19_P5_F_pool2


title: P2R2

description: Library name: P2R2


title: DMSO_0-1_R20_P5_F_pool2


title: 24BPF_10_R1_P5_F_pool2

value: 2,4'-Bisphenol F


title: D65 days, R403C, rep3

city: Nashville

first: Vivian

last: Gama

address: 465 21st Ave South

institute: Vanderbilt University

description: Library name: D65RCG3_423

data_processing:
Raw reads of fastq format were firstly processed through Novogene in-house perl scripts. Clean reads were obtained by removing reads containing adapter, poly-N and low-quality reads from raw data; Q20, Q30 and GC content of the clean data were calculated. All downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads mapped to each gene; FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis was performed using DESeq2 (1.20.0). Adjusted p-values were calculated using the Benjamini-Hochberg False Discovery Rate (FDR) method. Genes with an adjusted P-value<=0.05 found by DESeq2 were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented using clusterProfiler. GO terms with corrected P-value less than 0.05 were considered significantly enriched by differential expressed genes. clusterProfiler was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

growth_protocol: PGP1 DRP1 mutant iPSCs differentiated into cortical neurons using dual SMAD inhibition and switched to neural maintenance media for long term maturation

extract_protocol:
Cells were washed with PBS and scraped into 1000μl Trizol reagent. 200μl of chloroform was added, and the samples were incubated at room temperature for 5 minutes. The samples were centrifuged at 12,000 g, and the aqueous phase was collected. 500μl of isopropanol was added to precipitate RNA, and the sample was incubated for 25 minutes at room temperature, followed by centrifugation at 12,000 g for 10 minutes at 4°C. The RNA pellet was washed with 75% ethanol, semi-dried, and resuspended in 30μl of DEPC-treated water. After quantification and adjustment of the volume of all the samples to 1μg/μl, the samples were treated with DNAse (New England Biolabs #M0303). 10μl of this volume was used to generate cDNA using the manufacturer’s protocol (Thermo Fisher #4368814).
Novogene in-house protocol

value: cortical neurons


title: 24BPF_50_R1_P5_F_pool2


title: CK3

description: Library name: CK3


title: 24BPF_0-5_R1_P5_F_pool2


title: P2R1

description: Library name: P2R1


title: D65 days, R403C, rep2

description: Library name: D65RCD5_423


title: 24BPF_5_R1_P5_F_pool2


title: D65 days, R403C, rep1

description: Library name: D65RCG3_222


title: 24BPF_1_R1_P5_F_pool2


title: 24BPF_0-1_R1_P5_F_pool2


title: 24BPF_0-001_R1_P5_F_pool2


title: CK2

description: Library name: CK2


title: 24BPF_0-01_R1_P5_F_pool2


title: D65 days, R403C, rep4

description: Library name: D65RC_1123


title: BPS_50_R1_P5_F_pool2

value: Bisphenol S


title: D65 days, G32A, rep3

description: Library name: D65GAG5_423


title: CK1

description: Library name: CK1


title: BPS_10_R1_P5_F_pool2


title: SP_0.5_2

city: Guangzhou City

first: zhou

last: wei

address: No. 100, Outer Ring Road, Guangzhou University Town, Xiaoguwei Street, Panyu District

institute: Guangdong University of Technology

description: Library name: Sample 10

data_processing:
not collected
Assembly: Reference sequence using: Mus_musculus/Ensembl_release110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Mus musculus

source_name: Melanocytes

extract_protocol:
1.0μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library PrepKit following manufacturer's protocols

value: Melanocytes

value: Drug treatment


title: BPS_5_R1_P5_F_pool2

city: Ottawa


title: D65 days, G32A, rep2

description: Library name: D65GAF7_423


title: SP_0.5_1

description: Library name: Sample 9


title: BPS_1_R1_P5_F_pool2


title: SP_0.25_2

description: Library name: Sample 8


title: Vehicle 27

description:
Library name: 30-609774425_27
27_001


title: D65 days, G32A, rep1

description: Library name: D65GAF7_222


title: BPS_0-5_R1_P5_F_pool2


title: D65 days, G32A, rep4

description: Library name: D65GA_1123


title: BPS_0-01_R1_P5_F_pool2


title: BPS_0-001_R1_P5_F_pool2


title: BPS_0-1_R1_P5_F_pool2


title: D65 days, Control, rep2

description: Library name: D65Ctrl_423

value: Control


title: BPAP_50_R1_P5_F_pool2

value: Bisphenol AP


title: BPAP_10_R1_P5_F_pool2


title: D65 days, Control, rep1

description: Library name: D65Ctrl_222


title: SP_0.125_2

description: Library name: Sample 6


title: BPAP_1_R1_P5_F_pool2


title: SP_0.25_1

description: Library name: Sample 7


title: SP_0.125_1

description: Library name: Sample 5


title: BPAP_5_R1_P5_F_pool2


title: BPAP_0-1_R1_P5_F_pool2


title: BPAP_0-5_R1_P5_F_pool2


title: Ar_0.25_2

description: Library name: Sample 4


title: D65 days, Control, rep3

description: Library name: D65Ctrl_1123


title: D35 days, R403C, rep6

description: Library name: D35RCG3_323


title: BPAP_0-001_R1_P5_F_pool2


title: BPAP_0-01_R1_P5_F_pool2


title: Ar_0.25_1

description: Library name: Sample 3


title: BPZ_50_R1_P5_F_pool2

value: Bisphenol Z


title: D35 days, R403C, rep5

description: Library name: D35RCD5_323


title: CK-2

description: Library name: Sample 2

value: WT

value: missing


title: BPZ_5_R1_P5_F_pool2


title: CK-1

description: Library name: Sample 1


title: BPZ_1_R1_P5_F_pool2


title: BPZ_0-5_R1_P5_F_pool2


title: BPZ_0-1_R1_P5_F_pool2


title: D35 days, R403C, rep2

description: Library name: D35RCG3_222


title: BPZ_0-001_R1_P5_F_pool2


title: TMBPF_50_R4_P4_H_pool1

value: Tetramethyl bisphenol F


title: D35 days, G32A, rep5

description: Library name: D35GAF7_323


title: D35 days, R403C, rep1

description: Library name: D35RCD5_222


title: TMBPF_10_R4_P4_H_pool1


title: PC_UH_R4_P4_H_pool1

value: No cells; Universal human positive control


title: PC_B_R4_P4_H_pool1

value: No cells; Brain positive control


title: BPZ_10_R1_P5_F_pool2


title: Wild-type mouse kidney control WT2

city: Stony Brook

first: Karam

last: Aboudehen

state: NY

address: 101 Nicolls Rd, HSC T 15-112

department: Division of Nephrology & Hypertension

institute: Stony Brook University

description: Library name: WT2 in vivo

data_processing:
PCR and optical duplicates were removed from all fastq files with the bash Clumpify tool.
Sorted BAM alignment files were generated with STAR using default settings.
FeatureCounts was used for transcript quantification and annotation (gencode.vM36.chr_patch_hapl_scaff.annotation.gtf)
Count files for both the in vivo and in vitro experiments were subsequently loaded into R (libraries in use: tidyverse, DESeq2, biomaRt, dplyr, purrr) and DESeq2 was employed (design = ~ condition + genotype) for obtaining differential gene calls
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw counts

source_name: Kidney

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS and 1% Penstrep (Invitrogen).

extract_protocol:
Total RNA was extracted using the miRNeasy RNA purification kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: mIMCD3 cells were reverse transfected with ribonucleoprotein consisting of recombinant Cas9 (1uM) and two tracer/sgRNAs for Snhg5 using RNAi max transfection reagent (Invitrogen)

value: Kidney

tag: strain

value: Wild-type


title: Snhg5 null mouse kidney KO1

description: Library name: KO1 in vivo

value: Snhg5 knockout


title: Snhg5 null mouse kidney KO2

description: Library name: KO2 in vivo


title: Wild-type mouse kidney control WT1

description: Library name: WT1 in vivo


title: D35 days, R403C, rep4

description: Library name: D35RCG3_322

tag: cell line


title: E2_1_R4_P4_H_pool1

tag: plate


title: TMBPF_1_R4_P4_H_pool1

tag: chemical


title: TMBPF_5_R4_P4_H_pool1

tag: dose


title: Wild-type mIMCD3 cells control WT4

description: Library name: WT4 cultured

value: kidney epithelial cells


title: D35 days, G32A, rep3

description: Library name: D35GAF7_322


title: E2_0-1_R4_P4_H_pool1


title: D35 days, G32A, rep4

description: Library name: D35GAG5_323


title: Wild-type mIMCD3 cells control WT3

description: Library name: WT3 cultured


title: 44BPF_5_R4_P4_H_pool1

value: 4,4'-Bisphenol F


title: D35 days, G32A, rep2

description: Library name: D35GAG5_322

value: cortical neurons


title: 44BPF_50_R4_P4_H_pool1


title: D35 days, R403C, rep3

description: Library name: D35RCD5_322


title: BPZ_0-01_R1_P5_F_pool2


title: Wild-type mIMCD3 cells control WT2

description: Library name: WT2 cultured


title: 44BPF_10_R4_P4_H_pool1


title: 44BPF_1_R4_P4_H_pool1


title: D35 days, G32A, rep1

description: Library name: D35GAG5_222


title: 44BPF_0-5_R4_P4_H_pool1


title: D35 days, Control, rep3

description: Library name: D35Ctrl_323


title: 44BPF_0-01_R4_P4_H_pool1


title: D35 days, Control, rep2

description: Library name: D35Ctrl_322


title: Snhg5 null mIMCD3 cells KO2

description: Library name: KO2 cultured


title: Snhg5 null mIMCD3 cells KO1

description: Library name: KO1 cultured


title: 44BPF_0-1_R4_P4_H_pool1


title: BPC_10_R4_P4_H_pool1

value: Bisphenol C


title: BPC_50_R4_P4_H_pool1


title: Wild-type mIMCD3 cells control WT1

description: Library name: WT1 cultured


title: C264

city: Beijing

first: Yi

address: Beijing

institute: Peking University

description: Library name: Sample8

data_processing:
Illumina Casava1.7 software used for basecalling. Trim-galore v0.6.7 was used for adapter trimming and low-quality reads. Clean reads mapping was conducted by Hisat2 v2.2.1, and mm10 was used as mouse reference genome. Gene expression was quantified by featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: For RNA-Seq data, an Excel file contain count values for each gene of each sample.

source_name: Tumor

growth_protocol: Xenograft models were established on C57BL/6J mice with MC38 cells, treated with control or C26 (10 mg/kg) every other day for 2 weeks

extract_protocol:
The polyA mRNA isolation was performed using Oligo(dT) beads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor


title: Pulmonary cells, Nanoplastics 100 nm, 0.001 g/L C 3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: MC100_3

data_processing:
trimming and filtering was performed using Flexbar software (3.5.0)
Cleaned, good quality reads were mapped to the Mouse GRC39 assembly with STAR aligner (2.7.5c)
Htseq-count (1.99.2) was used for reads counting
Assembly: Mouse GRC39 annotation MM109
Supplementary files format and content: raw counts from Htseq-count

source_name: pulmonary fibroblast

extract_protocol:
3'mRNA-Seq
Library was prepared from 50 ng of total RNA with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Austria)

treatment_protocol: Treated and control cells were trypsinized, transferred to 1.5 mL Eppendorf-type tubes, and centrifuged at 500xg for 7 minutes. Obtained supernatants were instantly removed, and pelleted cells were snap-frozen at −80 °C pending RNA isolation. TRI Reagent™ Solution (ThermoFisher Scientific, USA) was used to purify total RNA according to a standard procedure. RNA was assessed for quality using the TapeStation 4150 System (Agilent, USA). RNA quantification was performed using the Qubit RNA BR assay (ThermoFisher Scientific, USA).

value: pulmonary fibroblast

value: Nanoplastics 100 nm, 0.001 g/L C 3


title: C263

last: Zhang

description: Library name: Sample7


title: BPC_0-5_R4_P4_H_pool1


title: BPC_1_R4_P4_H_pool1


title: BPC_0-1_R4_P4_H_pool1


title: D35 days, Control, rep1

description: Library name: D35Ctrl_222

value: Control


title: Pulmonary cells, Nanoplastics 100 nm, 0.001 g/L C 2

description: Library name: MC100_2

value: Nanoplastics 100 nm, 0.001 g/L C 2


title: 44BPF_0-001_R4_P4_H_pool1


title: C262

description: Library name: Sample6


title: Pulmonary cells, Nanoplastics 100 nm, 0.001 g/L C 1

description: Library name: MC100_1

value: Nanoplastics 100 nm, 0.001 g/L C 1


title: BPC_0-01_R4_P4_H_pool1


title: BPAF_10_R4_P4_H_pool1

value: Bisphenol AF


title: C261

description: Library name: Sample5


title: BPC_0-001_R4_P4_H_pool1


title: Pulmonary cells, Nanoplastics 100 nm, 0.01 g/L (B) 3

description: Library name: MB100_3

value: Nanoplastics 100 nm, 0.01 g/L (B) 3


title: C4

description: Library name: Sample4

value: Ctrl


title: Pulmonary cells, Nanoplastics 100 nm, 0.01 g/L (B) 2

description: Library name: MB100_2

value: Nanoplastics 100 nm, 0.01 g/L (B) 2


title: BPAF_50_R4_P4_H_pool1


title: BPAF_1_R4_P4_H_pool1


title: BPAF_5_R4_P4_H_pool1


title: C3

description: Library name: Sample3


title: BPC_5_R4_P4_H_pool1


title: BPAF_0-1_R4_P4_H_pool1


title: C2

description: Library name: Sample2


title: BPAF_0-01_R4_P4_H_pool1


title: Pulmonary cells, Nanoplastics 100 nm,  0.1 g/L (A) 3

description: Library name: MA100_3

value: Nanoplastics 100 nm,  0.1 g/L (A) 3


title: C1

description: Library name: Sample1


title: Pulmonary cells, Nanoplastics 100 nm,  0.1 g/L (A) 2

description: Library name: MA100_2

value: Nanoplastics 100 nm,  0.1 g/L (A) 2


title: BPAF_0-001_R4_P4_H_pool1


title: BPA_10_R4_P4_H_pool1

value: Bisphenol A


title: BPA_50_R4_P4_H_pool1


title: T1-balbc-WT4

first: Xin

last: Du

state: Zhejiang

address: No. 1, Banshandong Road

department: Breast Cancer Center

institute: The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)

description:
Library name: T1-balbc-WT4
10x Genomics

data_processing:
The fastq files were processed by cellranger-8.0.0 pipeline. using cellranger count function to generate the expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Tumor Homograft Models

extract_protocol:
Tumors were dissociated using Human Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer’s protocol.
According to the manufacturer’s instruction,Single cells were partitioned into droplets with gel beads in the Chromium Controller. After  the emulsions were formed,the single-cell libraries were constructed following the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3),The single-cell libraries were sequenced on Illumina novaseq xplus sequencing system (paired-end multiplexing run)

value: Tumor Homograft Models

value: Microenvironment cells

value: WT


title: BPA_5_R4_P4_H_pool1


title: BPA_0-5_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1 um, 0.001 g/L C 3

description: Library name: MC1_3

value: Microplastics 1 um, 0.001 g/L C 3


title: T1-balbc-WT3

description:
Library name: T1-balbc-WT3
10x Genomics


title: BPA_1_R4_P4_H_pool1


title: Pulmonary cells, Nanoplastics 100 nm,  0.1 g/L (A) 1

description: Library name: MA100_1

value: Nanoplastics 100 nm,  0.1 g/L (A) 1


title: BPA_0-1_R4_P4_H_pool1


title: BPAF_0-5_R4_P4_H_pool1


title: BPA_0-01_R4_P4_H_pool1


title: T1-balbc-WT1

description:
Library name: T1-balbc-WT1
10x Genomics


title: Pulmonary cells, Microplastics 1 um, 0.001 g/L C 2

description: Library name: MC1_2

value: pulmonary fibroblast

value: Microplastics 1 um, 0.001 g/L C 2


title: BPA_0-001_R4_P4_H_pool1


title: T1-balbc-Sh2

description:
Library name: T1-balbc-Sh2
10x Genomics


title: T1-balbc-Sh4

description:
Library name: T1-balbc-Sh4
10x Genomics


title: Mix6_10_R4_P4_H_pool1

value: Mix 6


title: Pulmonary cells, Nanoplastics 100 nm, 0.01 g/L (B) 1

description: Library name: MB100_1

value: Nanoplastics 100 nm, 0.01 g/L (B) 1


title: Pulmonary cells, Microplastics 1 um, 0.001 g/L C 1

description: Library name: MC1_1

value: Microplastics 1 um, 0.001 g/L C 1


title: Mix6_50_R4_P4_H_pool1


title: T1-balbc-Sh1

description:
Library name: T1-balbc-Sh1
10x Genomics


title: Mix6_0-5_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.01 g/L (B) 3

description: Library name: MB1_3

value: Microplastics 1um, 0.01 g/L (B) 3


title: Mix6_0-1_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.01 g/L (B) 2

description: Library name: MB1_2

value: Microplastics 1um, 0.01 g/L (B) 2


title: Mix6_0-01_R4_P4_H_pool1


title: EO771-c57-WT21

description:
Library name: EO771-c57-WT21
10x Genomics


title: Mix6_0-001_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.01 g/L (B) 1

description: Library name: MB1_1

value: Microplastics 1um, 0.01 g/L (B) 1


title: Mix5_50_R4_P4_H_pool1

value: Mix 5


title: Pulmonary cells, Microplastics 1um, 0.05 g/L (D) 3

description: Library name: MD1_3

value: Microplastics 1um, 0.05 g/L (D) 3


title: EO771-c57-WT20

description:
Library name: EO771-c57-WT20
10x Genomics


title: Mix5_10_R4_P4_H_pool1


title: EO771-c57-WT17

description:
Library name: EO771-c57-WT17
10x Genomics


title: Mix5_5_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.05 g/L (D) 2

description: Library name: MD1_2

value: Microplastics 1um, 0.05 g/L (D) 2


title: Mix6_5_R4_P4_H_pool1


title: Mix6_1_R4_P4_H_pool1


title: Mix5_0-5_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.05 g/L (D) 1

description: Library name: MD1_1

value: Microplastics 1um, 0.05 g/L (D) 1


title: EO771-c57-SH24

description:
Library name: EO771-c57-SH24
10x Genomics

value: Tumor Homograft Models


title: Mix5_0-01_R4_P4_H_pool1


title: EO771-c57-SH9

description:
Library name: EO771-c57-SH9
10x Genomics

value: Microenvironment cells


title: Pulmonary cells, Microplastics 1um, 0.1 g/L (A) 2

description: Library name: MA1_2

value: Microplastics 1um, 0.1 g/L (A) 2


title: EO771-c57-SH13

description:
Library name: EO771-c57-SH13
10x Genomics


title: Mix5_0-1_R4_P4_H_pool1


title: NC_R7_P4_H_pool1

value: No cells; 1X Lysis buffer


title: NC_R8_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.1 g/L (A) 3

description: Library name: MA1_3

value: Microplastics 1um, 0.1 g/L (A) 3


title: DMSO_0-1_R18_P4_H_pool1

value: Dimethyl sulfoxide


title: DMSO_0-1_R17_P4_H_pool1


title: H3K27ac_mg_GrnKO_rep2_input

city: South San Francisco

first: Leon

last: Tejwani

address: 161 Oyster Point Blv.

institute: Denali Therapeutics

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert reads aligning to a single genomic location into “tag directories” for subsequent analysis using the command makeTagDirectory (Heinz et al., 2010). To annotate raw and normalized H3K27ac signal around ATAC-seq peaks,  the annotatePeaks command was used with the parameters -raw for raw counts or default for normalized counts, along with -size 800 for the annotation region. DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal with > 2 fold-change and p-adj < 0.05. To identify motifs enriched in differential peak regions over background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. Background sequences were comprised of random GC-matched genomic sequences or experimental unchanged backgrounds as defined in the text.
Assembly: mm10
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.

source_name: Brain

extract_protocol:
Brain nuclei were isolated as previously described (Nott et al., 2019,2021), with initial homogenization and crosslinking performed with 1% formaldehyde in Dulbecco’s PBS for 10 minutes at room temperature. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099), and NEUN-AF488 (Millipore MAB 377X). Nuclei were stained with DAPI (BioLegend 422801) the next day then sorted with a BD Influx Cell Sorter. Nuclei were sorted as DAPI positive, singlets, PU.1+, OLIG2-, and NEUN-. Chromatin immunoprecipitation sequencing was performed as previously described (Heinz et al, 2010, Texari et al, 2021). For H3K27ac ChIP-seq, ~500,000 fixed nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Nuclei / chromatin was sheared by sonication using the PIXUL Multi-Sample Sonicator (Active Motif) in low bind 96 well plates following the manufacturer’s instructions. Samples were sonicated with the following settings: Pulse (N): 50, PRF [kHz]: 1.00, Process time: 60 min, Burst Rate [Hz]: 20.00. Samples were pulse spun to 600xg at 4°C in the 96-well plate, transferred to low-bind tubes, and chromatin recovered by retaining the supernatant following a spin at 21,000xg at 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. Two percent of the lysate was kept as ChIP input control. 10 μL of Dynabead Protein A and 10 μL of Protein G were added per sample, in addition to 2 μg of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) + 1x protease inhibitor cocktail, 3x with Wash Buffer III (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1 mM EDTA, 0.7% Sodium Deoxycholate) + 1x protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3x protease inhibitor cocktail, and 1x with IDTET (0.2% Tween-20, 10 mM Tris pH 8, 0.1 mM EDTA). Samples were finally resuspended in 25 μL TT buffer (10 mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation.
Sequencing libraries for H3K27ac ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB, E7645) reagents according to the manufacturer’s protocol on beads suspended in 25 μL TT (10 mM Tris/HCl pH 7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μL 10% SDS, 4.5 μL 5 M NaCl, 3 μL EDTA, 4 μL EGTA, 1 μL proteinase K (20 mg/ml), 16 μL water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (Cytiva GE45152105050250) in a 20% PEG8000 / 1.5M NaCl solution to final concentration of 12% PEG, then eluted with 25 μL TT. DNA contained in the eluate was then amplified for 12-14 cycles in 25 μL PCR reactions using NEBNext High-Fidelity Q5 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and paired-end sequenced using an Illumina NovaSeq instrument.

value: Brain

value: PU.1+ nuclei

value: GrnKO

tag: chip antibody


title: H3K27ac_mg_GrnKO_rep1_input


title: DMSO_0-1_R14_P4_H_pool1


title: DMSO_0-1_R16_P4_H_pool1


title: DMSO_0-1_R15_P4_H_pool1


title: Pulmonary cells, control, 2

description: Library name: CTR_2

value: pulmonary fibroblast

value: control


title: H3K27ac_mg_GrnKO_rep1

value: ActiveMotif #39685


title: Mix4_50_R4_P4_H_pool1

value: Mix 4


title: Pulmonary cells, control, 3

description: Library name: CTR_3


title: DMSO_0-1_R13_P4_H_pool1


title: Mix5_1_R4_P4_H_pool1

value: Mix 5


title: Mix4_10_R4_P4_H_pool1


title: Mix5_0-001_R4_P4_H_pool1


title: H3K27ac_mg_WT_rep2_input

value: WT


title: Mix4_5_R4_P4_H_pool1