title: DMPFTrDAP3HS113_L002

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
DM_PFTrDA_P3_H
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

data_processing:
RNA sequencing was performed at the Michigan State University Research Technology Support Facility Genomics Core. Libraries were quality control checked and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000, and Invitrogen Collibri Library Quantification qPCR assays. Each pool (corresponding to ≈ 96 samples from assays with two PFAS) was loaded onto one lane of a NovaSeq S4 flow cell. Sequencing was performed in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit (target read depth of ≈28,000 MB/sample). Base calling was done by Illumina Real Time Analysis v3.4.4, and the output was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v2.20.0.
The Daphnia magna reference genome (assembly ASM2063170v1.1, RefSeq GCF_020631705.1) was indexed with STAR version 2.7.10a using the following sample specific parameters: --genomeSAindexNbases 12 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC and MultiQC version 1.12, raw reads were trimmed using Trim Galore! version 0.6.6, with the parameters --illumina --stringency 3 --quality 20 –e 0.1 --length 20 --paired, to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp.
Trimmed reads were then mapped with STAR version 2.7.10a to the indexed genome using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS. Samtools version 1.15.1 was used to sort and index the alignment files.
HTSeq version 2.0.1 was used to assign counts to each gene with the following parameters: -f bam -r pos -s no. FastQC and MultiQC version 1.12 were used to assess quality control metrics of the processed reads. Count data for treatment and plate-specific control samples for each PFAS were written to a single tab-delimited matrix file, where each column represented a sample and each row represented a gene.
Additional quality control and filter steps were applied to each count matrix using the R statistical computing software (R Core Team, 2022) prior to concentration response modeling. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al. 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out. Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors() which was used for counts per million mapped reads (CPM) normalization. The filtered CPM normalized count matrix was log2 transformed with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses; i.e., log2(CPM+1)).
Assembly: Daphnia magna reference genome (assembly ASM2063170v1.1, RefSeq GCF_020631705.1)
Supplementary files format and content: Count matrices provided as tab delimited text files. Top row = sample names. Second row = treatment concentration (ug/L); all subsequent rows provide filtered counts per million (CPM) log2 transformed with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses; i.e., log2(CPM+1), with each row corresponding to a separate transcript and each column corresponding to a sample. One count matrix file per chemical exposure experiment.

organism: Daphnia magna

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFTrDA

growth_protocol: Daphnia magna were obtained from an onsite culture unit at the U.S. EPA Great Lakes Toxicology and Ecology Division, Duluth, MN. For use in the assays, Daphnia magna were reared in mass culture in amended LSW and held at 20° C until they were 72 hours old. They were fed a diet of yeast-Cerophyll-trout chow and algae (USEPA 2016d) until ready for use in the assays. All procedures involving animals were approved by a local animal care and use committee.

extract_protocol:
RNA was extracted from pooled homogenates using Zymo Research Direct-zol-96 RNA kit (Zymo Research) protocol adapted to the Biomek i5 to yield 40 µl of RNA. Previously extracted control RNA was added to empty wells on the final RNA plate. Concentrations of RNA for each well were measured on a NanoDrop spectrophotometer (Thermo Scientific, NanoDrop Eight) and diluted if necessary.
RNA extracts (10 µl) were used to prepare cDNA libraries with the Lexogen Poly(A) RNA Selection Kit V1.5 (catalog #157; Lexogen GmbH, Austria) and Lexogen CORALL mRNA-Seq Library Prep Kit with UDIs (catalog #158-163) both adapted to the Biomek i5. Resulting cDNA library samples were evaluated on a 4200 TapeStation (Agilent Technologies, CA, USA) using the D1000 ScreenTape (Agilent) analysis protocol to assess cDNA quality. Samples were quantified using the Quant-iT Picogreen dsDNA assay kit (catalog # P11495; Thermo Fischer Scientific), diluted if necessary, and equal portions of each sample pooled for use in RNA sequencing by Michigan State University.

treatment_protocol: All assays were conducted in 96-well plate format using 1 ml volume deep-well plates (Catalog # 502162, NEST Scientific). Daphnia magna, one individual per well, were exposed to eight different concentrations of PFAS (two PFAS tested per plate) plus controls. Nominal PFAS concentrations ranged from 0.03 to 100 uM with 1/2 log spacing. Five replicate individuals were exposed to each treatment per plate, except control treatments (n=8). Uniform age (72 ± 6 h) Daphnia magna were manually loaded to each well of three replicate 96-well plates using a P1000 pipet with the end of the tip cut off to a one cm bore diameter. The volume in each well was reduced to a uniform volume of 50 µl using the Biomek i5 liquid handler. Assays were initiated by adding 550 µl of exposure solution from a dosing plate to the three replicate exposure plates for each assay. Immediately after dosing, each plate was covered with a silicone sealing mat (catalog #506065; NEST Scientific) and then placed in a 20°C incubator for 24 h. At test termination, each well was inspected and all mortalities (immobile with gentle prodding) were recorded and removed. Live daphnia were also examined for phenotypic abnormalities, although none were noted at sublethal concentrations. The Biomek i5 was then used to transfer 100 µl of exposure solution to an “exposure verification plate”, where the n=5 samples for each treatment concentration were subsequently pooled together into a total volume of 500 on a per-plate basis. The pooled exposure solution for each treatment was collected for quantitification of PFAS concentrations, with measured concentrations ultimately used for data analysis. The remaining volume of exposure medium in each well was replaced with 60 µl of Trizol (Zymo Research, CA, USA). A 2.3 mm stainless steel bead was added to each well, then the plate was homogenized at 30 Hz for two minutes using an Omni-Bead Ruptor bead mill. Homogenates of individual Daphnia magna from the same treatment group were pooled together, on a per plate basis  to generate one pooled sample per treatment, per plate. Only live daphnia were included in the homogenate pools.

value: whole body

value: GLTED-wt

value: PFTrDA (DTXSID90868151)

tag: conc.

tag: conc. units

value: ug/L

tag: conc code

value: H

tag: exposure duration

tag: replicate plate_id


title: DMPFTrDAP3GS114_L002

status: Public on Feb 22 2024

type: SRA

country: USA

description:
DM_PFTrDA_P3_G
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment

value: G

tag: age


title: DMPFTrDAP3FS115_L002

description:
DM_PFTrDA_P3_F
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: F


title: DMPFTrDAP3ES116_L002

description:
DM_PFTrDA_P3_E
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: E


title: DMPFTrDAP3CS118_L002

description:
DM_PFTrDA_P3_C
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: C


title: DMPFTrDAP3BS119_L002

description:
DM_PFTrDA_P3_B
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: B


title: DMPFTrDAP3DS117_L002

description:
DM_PFTrDA_P3_D
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: D


title: DMPFTrDAP2GS106_L002

description:
DM_PFTrDA_P2_G
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: DMPFTrDAP2HS105_L002

description:
DM_PFTrDA_P2_H
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: DMPFTrDAP2DS109_L002

description:
DM_PFTrDA_P2_D
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: DMPFTrDAP2FS107_L002

description:
DM_PFTrDA_P2_F
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: DMPFTrDAP2BS111_L002

description:
DM_PFTrDA_P2_B
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: Patient Normal_1, Non-cancerous fallopian tube/fimbria

city: Helsinki

first: Anna

last: Perkiö

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

library_source: transcriptomic single cell

data_processing:
Reads originating from poor-quality cells were excluded (quality control steps done and explained by Zhang et al., 2022, doi:10.1126/sciadv.abm1831 )
STAR 2.7.8a was used to perform alignment. Genome indices were generated based on the GRCh38.d1.vd1 reference genome and GENCODE v25 annotation. A maximum of two mismatches per read was allowed.
For the L1 expression matrix only: Reads mapping more than 1 percent or more to exons were excluded. In addition, reads mapping 90 percent or more to repeats were excluded. The annotations were derived from RepeatMasker (<http://www.repeatmasker.org>). The described steps were performed with Intersect from Pybedtools (v0.8.1), a wrapper of Bedtools
For the L1 expression matrix only: To extract reads aligned in 1kb downstream windows of L1s, Intersect was again used to only retain reads with a minimum overlap of 60 percent with the reference regions. The 1kb reference windows were based on the list from Deininger et al. (2017, doi:10.1093/nar/gkw1067), consisting of L1 loci with potentially functional promoters.
For the L1 expression matrix only: To exclude reads that mapped ambiguously to polyA regions, Pysam 0.16.0.1, a python wrapper of SAMtools, was used to exclude reads for which the A or T base composition was 60 percent or higher.
The expression of both L1s and the rest of the genome was quantified with UMI-tools 1.1.1. Before the alignment, cell barcodes and UMIs were extracted from the reads. Subsequently, the unfiltered reads were assigned straight to the genome (featureCounts from Subread v2.0.1), and the filtered reads were assigned to the L1 1kb downstream windows. Only reads that mapped uniquely and to the same strand as the reference were considered, deduplicated and counted per feature per cell.
For the gene expression matrix only: The genes with a total of less than 95 UMIs (from all samples combined) were excluded.
Assembly: GRCh38.d1.vd1, GENCODE v25
Supplementary files format and content: comma-separated files for gene expression (tumor samples) and L1 expression (all samples)

molecule: polyA RNA

organism: Homo sapiens

source_name: fallopian tube/fimbriae

extract_protocol:
The samples were incubated overnight in a mixture of collagenase and hyaluronidase to obtain single cell suspensions.
Standard Chromium Single Cell 3′ Reagent Kit v. 2.0 (10x Genomics)

value: fallopian tube/fimbriae

tag: cell line

value: clinical patient sample

tag: cell type

value: fallopian tube/fimbriae + microenvironment

value: no treatment


title: DMPFTrDAP3AS120_L002

description:
DM_PFTrDA_P3_A
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt
DM_PFNA_counts.filtered.+1.normFinal.txt
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: A


title: DMPFTrDAP2ES108_L002

description:
DM_PFTrDA_P2_E
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt


title: DMPFTrDAP2AS112_L002

description:
DM_PFTrDA_P2_A
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt
DM_PFNA_counts.filtered.+1.normFinal.txt


title: Patient Normal_2, Non-cancerous fallopian tube/fimbria


title: HGSOC Patient EOC540, pre-chemotherapy

source_name: High-grade serous ovarian cancer

value: High-grade serous ovarian cancer

value: tumor + microenvironment


title: normal sample 19 [480-3C]

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Reads whose first 25 nucleotides had sequencing scores less than 30 were discarded.
Reads with at least 18 nt after removing the 3'-adapters were kept.
The unique sequences of the remaining reads were obtained and aligned to the miRNA sequences using the BLAST algorithm with the options of ``-S 1 -m 8 -e 0.01".
The abundances of miRNAs were calculated.
Assembly: hg38
Supplementary files format and content: MS Excel file includes raw count and normal abundance (Reads Per Ten Million sequencing tag) of miRNAs for each sample.

source_name: lung

extract_protocol:
The total RNA of each sample was extracted using TRIZOL reagent.
The extracted small RNAs were enriched and purified, and then add 3' end adaptor by ligating the 5-adenylated and 3-blocked adaptor to the 3' end of the small RNA fragment. Next, add Unique molecular identifiers (UMI) labeled Primer, and then ligate 5' end adaptor.  The first strand with UMI labeled Primer was synthesized, then the second strand synthesis. Select the fragment. Take Library quantitative, pooling cyclization and Library QC.   Finally, the small RNA was sequenced on DNBSEQ.

value: lung

tag: gender

value: male

tag: sample type

value: non-malignant lung parenchymal tissue from lung adenocarcinoma patient

tag: tumor stage

tag: smoking status

value: smoker

tag: age at_diagnosis


title: DMPFTrDAP1HS97_L002

description:
DM_PFTrDA_P1_H
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: whole body

value: GLTED-wt

value: PFTrDA (DTXSID90868151)

value: ug/L

value: H


title: normal sample 17 [475-3C]

value: female

value: never smoker


title: DMPFTrDAP1FS99_L002

description:
DM_PFTrDA_P1_F
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: F


title: normal sample 18 [478-3C]


title: normal sample 16 [474-3C]


title: DMPFTrDAP1GS98_L002

description:
DM_PFTrDA_P1_G
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: G


title: DMPFTrDAP1ES100_L002

description:
DM_PFTrDA_P1_E
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: E


title: normal sample 15 [473-3C]


title: DMPFTrDAP1DS101_L002

description:
DM_PFTrDA_P1_D
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: D


title: DMPFTrDAP1BS103_L002

description:
DM_PFTrDA_P1_B
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: B


title: normal sample 14 [472-3C]


title: DMPFTrDAP1AS104_L002

description:
DM_PFTrDA_P1_A
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: A


title: DMPFTrDAP1CS102_L002

description:
DM_PFTrDA_P1_C
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: C


title: normal sample 12 [453-3C]

value: lung

value: male


title: normal sample 11 [433-3C]

value: non-malignant lung parenchymal tissue from lung adenocarcinoma patient

value: smoker


title: normal sample 13 [466-3C]


title: DMPFTPP3HS86_L002

description:
DM_PFTP_P3_H
DM_PFTP_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFTP

value: whole body

value: GLTED-wt

value: PFTP (DTXSID70379295)


title: DMPFTrDAP2CS110_L002

description:
DM_PFTrDA_P2_C
DM_PFTrDA_counts.filtered.+1.normFinal_5_concentrations.txt

value: PFTrDA (DTXSID90868151)

value: ug/L


title: DMPFTPP3FS88_L002

description:
DM_PFTP_P3_F
DM_PFTP_counts.filtered.+1.normFinal.txt


title: normal sample 9 [422-3C]

value: female

value: never smoker


title: normal sample 6 [416-3C]


title: normal sample 10 [426-3C]


title: DMPFTPP3ES89_L002

description:
DM_PFTP_P3_E
DM_PFTP_counts.filtered.+1.normFinal.txt


title: normal sample 8 [419-3C]


title: DMPFTPP3GS87_L002

description:
DM_PFTP_P3_G
DM_PFTP_counts.filtered.+1.normFinal.txt

value: G


title: normal sample 5 [414-3C]


title: normal sample 7 [417-3C]


title: DMPFTPP2GS79_L002

description:
DM_PFTP_P2_G
DM_PFTP_counts.filtered.+1.normFinal.txt


title: DMPFTPP3CS91_L002

description:
DM_PFTP_P3_C
DM_PFTP_counts.filtered.+1.normFinal.txt


title: normal sample 4 [412-3C]


title: DMPFTPP3BS92_L002

description:
DM_PFTP_P3_B
DM_PFTP_counts.filtered.+1.normFinal.txt


title: DMPFTPP2ES81_L002

description:
DM_PFTP_P2_E
DM_PFTP_counts.filtered.+1.normFinal.txt

value: E


title: DMPFTPP2HS78_L002

description:
DM_PFTP_P2_H
DM_PFTP_counts.filtered.+1.normFinal.txt

value: H


title: LUAD sample 19 [480-1C]

value: lung adenocarcinoma tumor


title: normal sample 2 [408-3C]

value: IIIA


title: DMPFTPP2FS80_L002

description:
DM_PFTP_P2_F
DM_PFTP_counts.filtered.+1.normFinal.txt

value: F


title: LUAD sample 18 [478-1C]

value: lung


title: DMPFTPP2CS83_L002

description:
DM_PFTP_P2_C
DM_PFTP_counts.filtered.+1.normFinal.txt

value: C


title: DMPFTPP2DS82_L002

description:
DM_PFTP_P2_D
DM_PFTP_counts.filtered.+1.normFinal.txt

value: D


title: DMPFTPP2BS84_L002

description:
DM_PFTP_P2_B
DM_PFTP_counts.filtered.+1.normFinal.txt

value: B


title: DMPFTPP1GS72_L002

description:
DM_PFTP_P1_G
DM_PFTP_counts.filtered.+1.normFinal.txt

value: whole body


title: DMPFTPP1HS71_L002

description:
DM_PFTP_P1_H
DM_PFTP_counts.filtered.+1.normFinal.txt

value: GLTED-wt


title: LUAD sample 16 [474-1C]


title: DMPFTPP3DS90_L002

description:
DM_PFTP_P3_D
DM_PFTP_counts.filtered.+1.normFinal.txt

value: PFTP (DTXSID70379295)


title: normal sample 3 [411-3C]

value: non-malignant lung parenchymal tissue from lung adenocarcinoma patient

value: IA a


title: LUAD sample 15 [473-1C]

value: female


title: normal sample 1 [383-3C]

value: IB

value: never smoker


title: LUAD sample 14 [472-1C]

value: male

value: smoker


title: LUAD sample 13 [466-1C]

value: lung adenocarcinoma tumor


title: DMPFTPP1DS74_L002

description:
DM_PFTP_P1_D
DM_PFTP_counts.filtered.+1.normFinal.txt

value: ug/L


title: LUAD sample 10 [426-1C]


title: LUAD sample 11 [433-1C]


title: DMPFTPP1CS75_L002

description:
DM_PFTP_P1_C
DM_PFTP_counts.filtered.+1.normFinal.txt


title: LUAD sample 17 [475-1C]


title: LUAD sample 12 [453-1C]


title: DMPFTPP1BS76_L002

description:
DM_PFTP_P1_B
DM_PFTP_counts.filtered.+1.normFinal.txt


title: LUAD sample 8 [419-1C]


title: DMPFTDoDAP3HS89_L002

description:
DM_PFTDoDA_P3_H
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFTDoDA

value: PFTDoDA (DTXSID70276659)

value: H


title: DMPFTDoDAP3STDS96_L002

description:
n/a
n/a

value: STD


title: LUAD sample 9 [422-1C]

value: lung


title: LUAD sample 7 [417-1C]


title: LUAD sample 6 [416-1C]


title: DMPFTDoDAP3FS91_L002

description:
DM_PFTDoDA_P3_F
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: F


title: DMPFTDoDAP3ES92_L002

description:
DM_PFTDoDA_P3_E
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: whole body

value: E


title: LUAD sample 5 [414-1C]


title: DMPFTDoDAP3GS90_L002

description:
DM_PFTDoDA_P3_G
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: G


title: DMPFTDoDAP3DS93_L002

description:
DM_PFTDoDA_P3_D
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: D


title: LUAD sample 4 [412-1C]


title: DMPFTDoDAP3CS94_L002

description:
DM_PFTDoDA_P3_C
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: C


title: LUAD sample 2 [408-1C]

value: IIIA


title: DMPFTDoDAP2STDS88_L002

description:
n/a
n/a


title: DMPFTDoDAP3BS95_L002

description:
DM_PFTDoDA_P3_B
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: B


title: DMPFTDoDAP2HS81_L002

description:
DM_PFTDoDA_P2_H
DM_PFTDoDA_counts.filtered.+1.normFinal.txt


title: LUAD sample 1 [383-1B]

value: female

value: IB

value: never smoker


title: LUAD sample 3 [411-1C]

value: lung adenocarcinoma tumor

value: IA a


title: GDKO, LPS [MGISEQ]

city: Beijing

first: Minmin

last: Luo

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

description: 10x Genomics

data_processing:
Demultiplexing was performed using MGI.Lite.BaseCall_1.2.0.99. Barcode processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1, with the "--include-introns" flag added, according to manufacturer's suggestion. For GDKO PBS, GDKO LPS, the digital expression matrix generated using default parameters contained large fraction of empty droplets. Therefore, fastq files from these two experiments were re-analyzed using the parameter --force-cells=8000 (GDKO PBS) and --force-cells=9000 (GDKO LPS), respectively.
Assembly: mm10
Supplementary files format and content: Preprocessed gene-by-cell matrix in the CellRanger h5 output format.
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

organism: Mus musculus

source_name: brain, motor cortex

extract_protocol:
For single cell dissociation, artificial cerebral spinal fluid (ACSF) was prepared using the “protective cutting” formula. Before the experiment, ACSF was bubbled with carbogen gas (95% O2 and 5% CO2) for ~30 mins. Mice were anesthetized and perfused transcardially with ACSF. The brain was quickly removed and submerged in carbogen bubbled ice-cold ACSF. 8 brain slices (200μm) were sectioned using vibratome and the motor cortex was micro-dissected. The dissected tissue pieces were then digested using the Papain dissociation system, supplemented with DNaseI. After 30 mins, the digestion was quenched by exchanging the solution with quenching (Q) buffer (ACSF with 1% FBS and 0.2% BSA) 3 times. The quenched solution was placed on ice for 5 mins and then proceeded to trituration. The tissue pieces were gently triturated through Pasteur pipettes with fire polished tip openings at 3 different diameters (600μm, 300μm, 150μm). The cell suspension was then centrifuged at 100g for 10 mins and resuspended in Q buffer for FACS sorting. Single cells were sorted (BD Aria III) using a 130μm nozzle and a sheath pressure of 10 psi. 15mL conical tube containing ~12mL collection (C) buffer (ACSF with 13.2mM trehalose, 2% FBS and 1% BSA) was used for collecting the target population.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, dissociated brain cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA. For each library, cDNA were amplified with polymerase chain reaction (PCR). The purified product were then converted to DNA nanoballs (MGIEasy Universal Library Conversion Kit) for sequencing with the MGISEQ-2000 or DNBSEQ-T7 model.

treatment_protocol: PBS or LPS (40mg/kg) were administered ~8 hours prior to single cell dissociation.

value: brain, motor cortex

value: Gsdmd-/-

value: LPS

tag: dose

tag: time

tag: Sex

value: Adult (6-8 weeks)


title: DMPFTPP1ES73_L002

description:
DM_PFTP_P1_E
DM_PFTP_counts.filtered.+1.normFinal.txt

value: whole body

value: PFTP (DTXSID70379295)

tag: conc.

tag: conc. units

value: ug/L

tag: conc code


title: DMPFTDoDAP2GS82_L002

description:
DM_PFTDoDA_P2_G
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

tag: tissue

value: GLTED-wt

value: PFTDoDA (DTXSID70276659)

value: G

tag: exposure duration

tag: replicate plate_id


title: WT, LPS [MGISEQ]

description: 10x Genomics

tag: genotype

value: wild type

tag: treatment

tag: age


title: DMPFTDoDAP2FS83_L002

description:
DM_PFTDoDA_P2_F
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: F


title: DMPFTDoDAP2DS85_L002

description:
DM_PFTDoDA_P2_D
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: D


title: DMPFTDoDAP2ES84_L002

description:
DM_PFTDoDA_P2_E
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: E


title: GDKO, PBS [MGISEQ]

description: 10x Genomics

value: PBS

value: female


title: DMPFTDoDAP2BS87_L002

description:
DM_PFTDoDA_P2_B
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: B


title: sorted CD8+ PD-1+ T cells 7 days after treatment with combination RT and anti-PDL1

city: atlanta

first: zach

last: Buchwald

state: ga

address: 1365 Clifton Rd NE Building C

institute: Winship Cancer Institute of Emory University

data_processing:
The Cell Ranger Single Cell Software Suite (version 5.0.1) by 10x Genomics was used to perform de-multiplexing, barcode processing, and single-cell 3’ gene counting.
Assembly: mm10-2020
Supplementary files format and content: tab-separated, matrix files

source_name: lymph node

extract_protocol:
Freshly collected CD8+ PD-1+ CD44+ cells from the tumor-draining LNs were flow sorted on a FACSAria (BD) flow cytometer. Individual mice samples were hashed (BioLegend) and pooled for sequencing
single cell 3' v2 protocol, 10x genomics

value: lymph node

tag: cell line

value: RT plus anti-PDL1


title: sorted CD8+ PD-1+ T cells 7 days after treatment with RT alone

value: RT


title: sorted CD8+ PD-1+ T cells; control

value: Untreated


title: DMPFTDoDAP1HS73_L002

description:
DM_PFTDoDA_P1_H
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: whole body

value: H


title: DMPFTDoDAP2CS86_L002

description:
DM_PFTDoDA_P2_C
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: ug/L

value: C


title: DMPFTDoDAP1STDS80_L002

description:
n/a
n/a

value: GLTED-wt

value: PFTDoDA (DTXSID70276659)

value: STD


title: DMPFTDoDAP1GS74_L002

description:
DM_PFTDoDA_P1_G
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: G


title: DMPFTDoDAP1FS75_L002

description:
DM_PFTDoDA_P1_F
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: F


title: cKO+Pu.1,inhibitor RNA-seq,rep1

first: ying

last: cheng

address: University East Outer Ring South Road

department: lnstitute of Biomedical Research

institute: YunnanUniversity

data_processing:
Using STAR(Version2.7.9a) , the raw FASTQ files were compared to the mouse reference genome(GRCm38/mm10).
Use RSEM(RNA-Seq by Expectation-Maximization Version 1.3.1) to quantify STAR's BAM files.
The DESeq2 (R)packet was used to perform differential gene expression analysis on the obtained count matrix.
Assembly: mm10
Supplementary files format and content: tsv

source_name: brain

extract_protocol:
Total RNA was extracted using a Direct-zol™ RNA Miniprep Kit (Zymo Research, cat R2051)
total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

value: brain

tag: breed

value: 6-8 weeks

value: cKO

value: Pu.1 inhibitor


title: cKO+Pu.1,inhibitor RNA-seq,rep3


title: cKO+Pu.1,inhibitor RNA-seq,rep2


title: DMPFTDoDAP1ES76_L002

description:
DM_PFTDoDA_P1_E
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: E


title: IR_Matn3_ko3

city: suzhou

first: Yong-Ming

last: Zhu

address: Renai Road Num 199

institute: soochow university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: peri-infarct area of the ischemic cerebral cortex

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Matn3 knockout

value: tMCAO (Ischemia for 60 min and reperfusion for 1 day）


title: DMPFTDoDAP1DS77_L002

description:
DM_PFTDoDA_P1_D
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: D


title: IR_Matn3_ko2

value: peri-infarct area of the ischemic cerebral cortex


title: DMPFTDoDAP1CS78_L002

description:
DM_PFTDoDA_P1_C
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: whole body


title: IR_Matn3_ko1


title: DMPFTDoDAP1BS79_L002

description:
DM_PFTDoDA_P1_B
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: ug/L

value: B


title: DMPFPeAP3HS171_L002

description:
DM_PFPeA_P3_H
DM_PFPeA_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFPeA

value: GLTED-wt

value: PFPeA (DTXSID6062599)

value: H


title: IR_WT3

value: WT


title: IR_WT2


title: WT, PBS [MGISEQ]

description: 10x Genomics

value: brain, motor cortex

value: wild type

value: PBS

value: female

value: Adult (6-8 weeks)


title: sorted CD8+ PD-1+ T cells 7 days after treatment with anti-PDL1 alone

value: lymph node


title: DMPFPeAP3GS172_L002

description:
DM_PFPeA_P3_G
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: G


title: DMPFPeAP3FS173_L002

description:
DM_PFPeA_P3_F
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: F


title: sham_WT3

source_name: cerebral cortex

value: cerebral cortex

value: Sham surgery


title: sham_WT2


title: DMPFPeAP3ES174_L002

description:
DM_PFPeA_P3_E
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: E


title: IR_WT1

value: peri-infarct area of the ischemic cerebral cortex

value: tMCAO (Ischemia for 60 min and reperfusion for 1 day）


title: DMPFPeAP3DS175_L002

description:
DM_PFPeA_P3_D
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PFPeA (DTXSID6062599)

value: ug/L

value: D


title: sham_WT1

value: WT


title: DMPFPeAP3BS176_L002

description:
DM_PFPeA_P3_B
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: B


title: NCOR1_ChIP_dKO_VEH_BioRep1

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

library_source: genomic

data_processing:
Trim-galore v0.6.4 was used to cut adapter reads
BWA MEM v0.7.17 with default settings was used to align the trimmed reads to mm10 reference genome
MarkDuplicates V2.23.1 was used to mark and exclude the duplicated reads from bam files
Homer V4.11 were used to make tag directories from bam files using makeTagDirectory command with default parameters
Homer V4.11 findPeaks command with parameter -style factor was used to call peaks
BEDTools v2.29.2 was used to generate bigwig files
Assembly: mm10
Supplementary files format and content: .peaks: peaks called by Homer
Supplementary files format and content: .bigWig: bigWig summary for visualization

molecule: genomic DNA

source_name: liver

extract_protocol:
For chromatin immunoprecipitation, livers were minced in PBS containing 1% formaldehyde and rotated end-over-end at room temperature for 20 minutes. Samples were then quenched with glycine, washed with PBS, and dounce homogenized in ChIP buffer (50 mM HEPES pH 7.4, 1.1% Triton X-100, 0.11% Sodium Deoxycholate, 1 mM EDTA, 155 mM NaCl, supplemented with protease and phosphatase inhibitors), and sonicated via probe sonication (Branson). Homogenates were subsequently subject to chromatin immunoprecipitation via overnight incubation with the following antibodies: NCOR1 (Generated in-house and previously described, raised in rabbit against amino acids 1944-2453), IgG (Cell Signaling 2729), GR (2 ug each of: Santa Cruz-393232, Thermo Fisher MA1510, Thermo Fisher PA1-511A). All antibodies have been previously validated in the literature for ChIP. ChIP conjugates were captured via Protein-A/G sepharose beads blocked with BSA, exhaustively washed, eluted, reverse crosslinked, and subject to protease digestion followed by DNA isolation.
ChIP libraries were generated using the NEBNext Ulta II DNA library Prep Kit (NEB). Library size and quality was assessed using DNA highsensitivity kits on an Agilent Tapestation and sequenced on a NOVAseqX Plus.

treatment_protocol: Mice were treated with Vehicle or Dexamethasone (1mg/kg) at ZT8 via IP injection. 2 hours later (ZT10), mice were sacrificed and livers were snap frozen for RNAseq and ChIPseq analysis.

value: liver

tag: time (zt)

value: MALE

value: CRE

value: VEH

tag: chip antibody

tag: library prep-size selection

value: Size Selection


title: DMPFPeAP2GS164_L002

description:
DM_PFPeA_P2_G
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: G


title: DMPFPeAP2HS163_L002

description:
DM_PFPeA_P2_H
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: H


title: NCOR1_ChIP_Cont_DEX_BioRep2

value: GFP

value: DEX


title: DMPFPeAP2FS165_L002

description:
DM_PFPeA_P2_F
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: F


title: NCOR1_ChIP_Cont_VEH_BioRep1


title: GR_ChIP_dKO_DEX_BioRep2

value: GR

value: No size selection


title: DMPFPeAP2DS167_L002

description:
DM_PFPeA_P2_D
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PFPeA (DTXSID6062599)

value: ug/L


title: DMPFPeAP2CS168_L002

description:
DM_PFPeA_P2_C
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: C


title: GR_ChIP_dKO_DEX_BioRep1

value: liver


title: DMPFPeAP1HS156_L002

description:
DM_PFPeA_P1_H
DM_PFPeA_counts.filtered.+1.normFinal.txt


title: DMPFPeAP1GS157_L002

description:
DM_PFPeA_P1_G
DM_PFPeA_counts.filtered.+1.normFinal.txt


title: GR_ChIP_dKO_VEH_BioRep2

value: MALE


title: GR_ChIP_dKO_VEH_BioRep1

value: CRE


title: GR_ChIP_Cont_DEX_BioRep2


title: DMPFPeAP1ES159_L002

description:
DM_PFPeA_P1_E
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: E


title: GR_ChIP_Cont_DEX_BioRep1


title: DMPFPeAP1FS158_L002

description:
DM_PFPeA_P1_F
DM_PFPeA_counts.filtered.+1.normFinal.txt


title: DMPFPeAP1CS160_L002

description:
DM_PFPeA_P1_C
DM_PFPeA_counts.filtered.+1.normFinal.txt


title: INPUT

value: VEH

value: INPUT

value: Size Selection


title: connected organoids

city: Meguro

first: Yoshiho

last: Ikeuchi

state: Tokyo

address: 4-6-1 Komaba

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

data_processing: The sequencing data were processed using Cell Ranger analysis pipeline v3 with default parameters. Reads were aligned to human reference genome (GRCh38). Cell Ranger output “filtered gene-barcoded” count matrix was loaded into Scanpy (Wolf et al., 2018) with other python packages (scanpy==1.8.1 anndata==0.7.6 umap==0.5.1 numpy==1.19.5 scipy==1.4.1 pandas==1.1.5 scikit-learn==0.22.2.post1 statsmodels==0.10.2 python-igraph==0.9.6 pynndescent==0.5.4) for downstream analysis. Poor-quality cells were excluded based on the following criterion: min_genes > 200 and min_cells < 3, mitochondrial gene percentage < 10%, and nFeatures <4000. Cells with percentage of hemoglobin reads > 5% were discarded. In total, 17,636 cells remained for subsequent analysis. Batch effect correction was performed.

source_name: cerebral organoids

extract_protocol: Single, fused, and connected organoid at 7 weeks of culture on PDMS-MEA chip were first extracted from PDMS device in warmed maintenance medium and centrifuged at 100 xg for 30 seconds. To get single-cell suspensions, the organoids were dissociated by AccuMax for 10-30 min at 37°C and then centrifuged 200 xg for 5 min. Then, the pelleted cells were re-suspended in DMEM containing 10% FBS to be subjected to 10x Genomics Chromium single-cell RNA-seq library preparation, according to the manufacturer’s protocol. Finally, the library was sequencing with 150-bp paired-end reads on DNBSEQ.

value: 7 weeks

tag: structure

value: connected

value: cerebral organoids


title: GR_ChIP_Cont_VEH_BioRep2

value: GFP


title: GR_ChIP_Cont_VEH_BioRep1

value: GR


title: fused organoids

value: fused


title: DMPFPBP3HS16_L002

description:
DM_PFPB_P3_H
DM_PFPB_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFPB

value: whole body

value: GLTED-wt

value: PFPB (DTXSID60663110)

value: H


title: DMPFPBP3DS17_L002

description:
DM_PFPB_P3_D
DM_PFPB_counts.filtered.+1.normFinal.txt

value: ug/L

value: D


title: DMPFPeAP2ES166_L002

description:
DM_PFPeA_P2_E
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: PFPeA (DTXSID6062599)


title: NCOR1_ChIP_Cont_DEX_BioRep1

value: liver

value: MALE

value: DEX


title: C57BL6 mouse aortic arch intima lesser curvature (18hr LPS)

city: Toronto

first: Corey

middle: A

last: Scipione

state: Ontario

address: 101 College Ave., TMDT 3-307 G,

department: Toronto General Hospital Research Institute

country: Canada

institute: University Health Network

data_processing:
Digital gene expression matrices were generated with the Cell Ranger Pipeline v3.1 and aligned to the mm10-2020-A reference transcriptome. The resulting digital gene expression matrix was filtered, normalized, and clustered using R 4.2.1 and Seurat 4.2.0. Features that were detected in less than 3 cells and cells with less than 200 features were excluded. We further filtered out cells with less than 500 transcripts, greater than 5000 features or a mitochondrial transcriptome of >25%. Normalization was performed using LogNormalize feature with a scale factor of 100000. PCA was performed on the top 2000 variable features that were identified using the “vst” selection method. The datasets were integrated using the Harmony algorithm based on the first 20 principal components. Cells were clustered using the Louvain algorithm based on the first 20 harmony dimensions with a resolution of 0.5. UMAP was used for non-linear reduction and two-dimensional data visualization.
Digital gene expression matrices were generated with the Cell Ranger Pipeline v3.1 and aligned to the mm10-2020-A reference transcriptome, for the 18hrLPS sample the number of GEMs analyzed was forced to 6000 cells.
Assembly: mm10-2020A
Supplementary files format and content: filtered feature matrix files

source_name: Aortic arch intima

extract_protocol:
Briefly, aortas were harvested from mice perfused with ice-cold PBS-/- supplemented with 1 μg/mL actinomycin D and 1% heparin. The ascending aorta was isolated and pinned en face in a dish with PBS-/- supplemented with 2 μg/mL actinomycin D. The dissection buffer was washed off, then the tissue was digested for 10 minutes at 37°C with a mixture of Collagenase D and DNAse I in PBS. Following digestion, aortas were washed twice; first with PBS + 2mM EDTA to inactivate the enzymes, followed by PBS alone to remove excess EDTA. Cells from the lesser curvature were gently dislodged and aspirated into PBS-/- (with 0.05% BSA to minimize cell loss and aggregation) with a P10 pipet tip.
Libraries where constructed as per the v3 ChromiumTM Single Cell 3’ Library Kit manufacturer's protocol.

treatment_protocol: For the 18hr LPS sample, mice were injected intravenously with 30 ug ultrapure LPS 18 hours prior to tissue harvest.

value: Aortic arch intima

value: 12-13 weeks

value: pooled male and female

tag: cell type

value: Intimal cells

value: C57Bl/6J wildtype

value: 30 ug ultrapure LPS (i.v.), 18 hours prior to harvest


title: single organoids

value: 7 weeks

value: single

value: cerebral organoids


title: DMPFPBP3CS18_L002

description:
DM_PFPB_P3_C
DM_PFPB_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PFPB (DTXSID60663110)

value: C


title: DMPFPBP3BS19_L002

description:
DM_PFPB_P3_B
DM_PFPB_counts.filtered.+1.normFinal.txt

value: ug/L

value: B


title: DMPFPeAP2BS169_L002

description:
DM_PFPeA_P2_B
DM_PFPeA_counts.filtered.+1.normFinal.txt

value: PFPeA (DTXSID6062599)


title: C57BL6 mouse aortic arch intima lesser curvature (untreated control-replicate)

tag: Sex


title: DMPFPBP2HS8_L002

description:
DM_PFPB_P2_H
DM_PFPB_counts.filtered.+1.normFinal.txt

tag: conc.

value: H


title: C57BL6 mouse aortic arch intima lesser curvature (untreated control)

value: Aortic arch intima


title: DMPFPBP2ES11_L002

description:
DM_PFPB_P2_E
DM_PFPB_counts.filtered.+1.normFinal.txt

tag: conc. units

value: E


title: DMPFPBP2FS10_L002

description:
DM_PFPB_P2_F
DM_PFPB_counts.filtered.+1.normFinal.txt

tag: conc code

value: F


title: DMPFPBP2GS9_L002

description:
DM_PFPB_P2_G
DM_PFPB_counts.filtered.+1.normFinal.txt

tag: tissue

value: G


title: ATAC-seq in MEFs in hypoxia, immortalized

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

description: ATAC-seq

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Supplementary files format and content: Called peaks with MACS2 q<0.05 in narrowPeak format
Supplementary files format and content: Normalized ATAC-seq signal in binary bigWig format
Assembly: GRCm38/mm10

source_name: MEFs

growth_protocol: Culture medium used was DMEM supplemented with 10% fetal bovine serum (FBS; Life Technologies), penicillin 40 μg/ml, and streptomycin 40 μg/ml (Merck).

extract_protocol:
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: MEFs were cultured under normoxic (20% O2) or hypoxic (3% O2) atmospheres with 5% CO2 at 37ºC. Hypoxia was achieved and maintained by flushing hypoxic gas mixture in CO2 incubators.

value: MEFs

tag: developmental stage

value: E13.5 embryos

tag: strain

value: Hypoxia 3percent oxygen

value: Immortalized


title: DMPFPeAP1BS161_L002

description:
DM_PFPeA_P1_B
DM_PFPeA_counts.filtered.+1.normFinal.txt

tag: genotype

tag: exposure duration

tag: replicate plate_id


title: ATAC-seq in MEFs in hypoxia, pass 1

description: ATAC-seq

tag: treatment

value: Pass 1


title: DMPFPBP2DS12_L002

description:
DM_PFPB_P2_D
DM_PFPB_counts.filtered.+1.normFinal.txt

value: whole body

value: D

tag: age


title: DMPFPBP2CS13_L002

description:
DM_PFPB_P2_C
DM_PFPB_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PFPB (DTXSID60663110)


title: DMPFPBP2BS14_L002

description:
DM_PFPB_P2_B
DM_PFPB_counts.filtered.+1.normFinal.txt

value: ug/L


title: ATAC-seq in MEFs in normoxia, senescent

description: ATAC-seq

value: Normoxia 20percent oxygen

value: Senescent


title: DMPFPBP1GS1_L002

description:
DM_PFPB_P1_G
DM_PFPB_counts.filtered.+1.normFinal.txt


title: DMPFPBP3AS20_L002

description:
DM_PFPB_P3_A
DM_PFPB_counts.filtered.+1.normFinal.txt

value: A


title: Glutamate_1

type: RNA

city: Fukui

first: Masaru

last: Takashima

address: 3-9-1 Bunkyo

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: RaGene-2_0-st.pgf
meta-probeset file: RaGene-2_0-st.mps

label: biotin

organism: Rattus norvegicus

source_name: Rat lense, 30mM galactose, 6days, 20mM Glutamate added, replicate1

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

value: Sprague Dawley

value: lens


title: Glutamate_2

source_name: Rat lense, 30mM galactose, 6days, 20mM Glutamate added, replicate2


title: Galactose_3

source_name: Rat lense, 30mM galactose, 6days, replicate3

value: 30mM galactose, 6days


title: Galactose_1

source_name: Rat lense, 30mM galactose, 6days, replicate1


title: DMPFPBP2AS15_L002

description:
DM_PFPB_P2_A
DM_PFPB_counts.filtered.+1.normFinal.txt


title: Galactose_2

source_name: Rat lense, 30mM galactose, 6days, replicate2


title: ce_smallRNA_ebax_LateTC_mut_42h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1's of N2 and HW3527 (ebax-1(tm2321) IV ) were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 25h to 42h

extract_protocol:
We harvested worms from 25h to 42h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using  Direct-zol™ RNA MicroPrep kit (Zymo Research; R2062) as per manufacturere's instructions. Total RNA was treated with DNAse on column
Sequencing libraries were generated using CleanTag Small RNA Library Preparation Kit according to the manufacturer’s instructions. The library pool was size selected on a gel (140-160 bp) to enrich for the small RNA fraction. Subsequently, library was sequenced on NextSeq500, as 76 cycles single-end reads.

treatment_protocol: no treatment

tag: time (h)


title: ATAC-seq in MEFs in normoxia, pass 1

description: ATAC-seq


title: DMPFOSP3ES20_L002

description:
DM_PFOS_P3_E
n/a
DM_PFOS_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFOS

value: PFOS (DTXSID8037706)

value: E


title: ce_smallRNA_ebax_LateTC_mut_40h


title: DMPFOSP3CS22_L002

description:
DM_PFOS_P3_C
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: C


title: WT-622-LPGP

city: Cardiff

first: Girish

middle: K

last: Patel

address: Maindy Road

country: United Kingdom

institute: Cardiff University

description: To determine whether HPV8 E6-driven Lrig1+ hair follicle junctional zone keratinocyte stem cellproliferation was sufficient to cause expansion into the overlying epidermis by lineage tracing we generated Lrig1CreERT2:R26RConfetti:HPV8-E6tg and Lrig1CreERT2:R26RConfetti:WT mice. Confetti labeled cells were isolated by flow-cytometry, enabling us to simultaneously identify Lrig1+cells by antibody labeling, such that we could isolate flow-sorted Lrig1+ confetti+ and their Lrig1-confetti+ progeny. Lrig1+ confetti+ and their Lrig1- confetti+ progeny from both HPV8-E6tg and WT mice were sequenced by RNA-seq and gene expression profiling analysis was performed on the dataset.

data_processing:
Trimmed and quality-checked reads were aligned to the GRCm39 mouse reference genome using HiSat2 (v2.0.5)
normalised reads were generated using featureCounts (v1.5.0)
differentially expressed genes were then generated using EdgeR (v3.22.5).
Assembly: GRCm39/mm39
Supplementary files format and content: .txt data file contains raw and normalised reads for each sample.

source_name: WT Lrig1+Confetti+.Mouse.RNA.Seq.Sample

extract_protocol:
total RNA was extracted using Rneasy micro kit (QIAGEN).
libraries were generated using Illumina TruSeq RNA Library Prep Kit (v2) and were subsequently sequenced on a NovaSeq 6000 PE150

value: skin tissue


title: WT-609-LNGP

source_name: WT Lrig1-Confetti+.Mouse.RNA.Seq.Sample


title: DMPFPBP1FS2_L002

description:
DM_PFPB_P1_F
DM_PFPB_counts.filtered.+1.normFinal.txt

value: F


title: DMPFPBP1CS5_L002

description:
DM_PFPB_P1_C
DM_PFPB_counts.filtered.+1.normFinal.txt


title: DMPFOSP3BS23_L002

description:
DM_PFOS_P3_B
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: B


title: WT-421-LPGP


title: WT-622-LNGP


title: WT-422-LPGP


title: ce_smallRNA_ebax_LateTC_mut_41h


title: ce_smallRNA_ebax_LateTC_mut_38h


title: DMPFPBP1DS4_L002

description:
DM_PFPB_P1_D
DM_PFPB_counts.filtered.+1.normFinal.txt

value: whole body


title: DMPFOSP3GS18_L002

description:
DM_PFOS_P3_G
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: G


title: DMPFPBP1ES3_L002

description:
DM_PFPB_P1_E
DM_PFPB_counts.filtered.+1.normFinal.txt

value: GLTED-wt


title: DMPFOSP3FS19_L002

description:
DM_PFOS_P3_F
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt


title: DMPFOSP2HS9_L002

description:
DM_PFOS_P2_H
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: H


title: WT-609-LPGP


title: ce_smallRNA_ebax_LateTC_mut_39h


title: WT-421-LNGP


title: DMPFOSP3DS21_L002

description:
DM_PFOS_P3_D
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: ug/L

value: D


title: DMPFOSP3HS17_L002

description:
DM_PFOS_P3_H
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt


title: DMPFOSP3AS24_L002

description:
DM_PFOS_P3_A
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt
DM_PFOA_counts.filtered.+1.normFinal.txt


title: DMPFPBP1BS6_L002

description:
DM_PFPB_P1_B
DM_PFPB_counts.filtered.+1.normFinal.txt

value: PFPB (DTXSID60663110)


title: Control-Day4

source_name: Rat lense, without galactose, 4 days

value: without galactose, 4 days


title: Nova-ST_MouseBrain_Rep5

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: Fresh frozen Nova-ST spatial transcriptome sequencing

data_processing:
Raw sequencing data was processed using bcl2fastq to generate fastq files
Nova-ST chip tiles were identified using a subset of data, and a witelist of barcodes was created from these tiles. Data was mapped and quantified against the mm10 using this whitelist and STARsolo
X/Y coordinates for barcodes with identified counts were normalised into a chip-based space and used alongside the expression data to create GEM files.
Assembly: mm10
Supplementary files format and content: tiff: H&E stained images
Supplementary files format and content: gem.txt.gz: GEM formatted expression matrix including normalized X/Y coordinates of each cluster
Supplementary files format and content: BC_Coords.pickle: Python pickled dictionaries containing barcodes, tile information and X/Y coordinates used for whitelist creation.
Library strategy: Spatial Transcriptomics (Nova-ST)

source_name: Brain

growth_protocol: Six to eight weeks old mice (C57BL/6J) used in the study were kept on a 14 h light, 10 h dark–light cycle from 7:00 to 21:00

extract_protocol:
Brains were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, brains were embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on the Nova-ST chips
Pepsin was used to permeabilise the sectioned tissue and Maxima Rtase for the reverse transcription. Samples were treated with endonuclease and then tissue was cleared with Proteinase K. Klenow Fragment was used for second strand synthesis and the resulting cDNA was amplified and prepared for sequencing by addition of indexes and Illumina flow cell attachment sites.

value: Brain


title: ce_smallRNA_ebax_LateTC_mut_37h


title: DMPFOSP2GS10_L002

description:
DM_PFOS_P2_G
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt


title: E6-661-LPGP


title: Nova-ST_MouseBrain_Rep4


title: DMPFOSP2FS11_L002

description:
DM_PFOS_P2_F
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt


title: Nova-ST_MouseBrain_Rep3


title: E6-626-LPGP


title: E6-526-LPGP


title: ce_smallRNA_ebax_LateTC_mut_35h


title: ce_smallRNA_ebax_LateTC_mut_33h


title: ce_smallRNA_ebax_LateTC_mut_34h


title: Nova-ST_MouseBrain_Rep2


title: E6-626-LNGP


title: DMPFOSP2CS14_L002

description:
DM_PFOS_P2_C
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt


title: DMPFOSP2ES12_L002

description:
DM_PFOS_P2_E
n/a
DM_PFOS_counts.filtered.+1.normFinal.txt


title: Nova-ST_MouseBrain_Rep1


title: ce_smallRNA_ebax_LateTC_mut_32h


title: E6-384-LNGP

description: To determine whether HPV8 E6-driven Lrig1+ hair follicle junctional zone keratinocyte stem cellproliferation was sufficient to cause expansion into the overlying epidermis by lineage tracing we generated Lrig1CreERT2:R26RConfetti:HPV8-E6tg and Lrig1CreERT2:R26RConfetti:WT mice. Confetti labeled cells were isolated by flow-cytometry, enabling us to simultaneously identify Lrig1+cells by antibody labeling, such that we could isolate flow-sorted Lrig1+ confetti+ and their Lrig1-confetti+ progeny. Lrig1+ confetti+ and their Lrig1- confetti+ progeny from both HPV8-E6tg and WT mice were sequenced by RNA-seq and gene expression profiling analysis was performed on the dataset.


title: MCF-10A cells, EGF, DMSO, 6h, biol rep 3

city: Stanford

first: Peter

last: Jackson

state: CA

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

data_processing:
Quality control: FastQC v0.11.3
Read alignment: Tophat v2.1.1 against GENCODE v25 gene model and GRCh38.p7 genome assembly (index built using Bowtie 2 v2.2.9)
Count tabulation: featureCounts (Subread v1.5.1) against GENCODE v25 gene model
Assembly: hg38 (GRCh38.p7)
Supplementary files format and content: *.feature_counts.txt: tab-delimited text files include gene counts for each gene in a sample

source_name: Cell line

growth_protocol: MCF-10A cells were maintained in DMEM/F12 supplemented with 5% horse serum, 20 ng/mL EGF, 10 µg/mL insulin, 0.5 µg/mL hydrocortisone, 100 ng/mL cholera toxin, 50 U/mL penicillin and 50 µg/mL streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Qiashredder and RNeasy Kit (Qiagen).
RNA libraries for RNA Seq were prepared using the KAPA Stranded mRNA-Seq Kit and mRNA capture beeds (Roche) according to manufacturer's instructions.

treatment_protocol:
MCF-10A cells were starved for 48 hours in serum-free DMEM/F12 and released into the cell cycle with 20 ng/ml EGF.
MCF-10A cells were treated for 3 or 6 hours with the indicated inhibitors C75 (30µM) targeting FASN, GSK2194069 (GSKi, 50µM) targeting FASN, CAY10566 (SCDi, 32µM), targeting SCD or DMSO (control).

value: Cell line

tag: cell line

value: Breast epithelial cell

value: WT

value: EGF 9h plus DMSO 6h


title: MCF-10A cells, EGF, SCDi, 6h, biol rep 3

value: EGF 9h plus SCDi 6h


title: DMPFOSP2BS15_L002

description:
DM_PFOS_P2_B
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: PFOS (DTXSID8037706)


title: MCF-10A cells, EGF, GSKi, 6h, biol rep 3

value: EGF 9h plus GSKi 6h


title: ce_smallRNA_ebax_LateTC_mut_31h


title: ce_smallRNA_ebax_LateTC_mut_30h


title: iWAT, 6-month-old, CE, snRNA-seq

first: Meng

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: 10x Genomics

data_processing:
Raw fastq data was mapped to mm10 genome using CellRanger version 7.0.0
Assembly: mm10
Supplementary files format and content: Tab-seperated values and matrix files from CellRanger

source_name: iWAT Adipose

extract_protocol:
Nuclei isolation from adipose tissue was performed according to a published protocol with slight modification (Van Hauwaert et al., 2021). Briefly, adipose tissues were minced in a petri dish containing 500 mL nuclei isolation buffer (NIB) that contains 250 mM sucrose (Solarbio, Cat. No. S8271), 10 mM HEPES (Solarbio, Cat. No. H8090), 1.5 mM MgCl2 (Sigma-Aldrich, Cat. No. M8266), 10 mM KCl (Sigma-Aldrich, Cat. No. P5405), 0.001% IGEPAL CA-630 (NP-40) (Sigma-Aldrich, Cat. No. I3021), 0.2 mM DTT (Sigma-Aldrich, Cat. No. D9779), and 1 U/μL RNase inhibitor (Solarbio, Cat. No. R8061) in DEPC-treated water. The samples were further homogenized using a 2 mL dounce homogenizer (Sigma-Aldrich, Cat. No. D8938), applying three strokes with the loose pestle. The homogenate was filtered through a 70 μm cell strainer (Falcon, Cat. No. 352350) and centrifuged at 500 g for 5 min at 4°C. The nuclear pellet was resuspended in 2 mL NIB and centrifuged at 300 g for 3 min at 4°C. Finally, the nuclear pellet was resuspended in 300 μL nuclei resuspension buffer that contains 2% BSA (Sigma-Aldrich, Cat. No. A1933), 1.5 mM MgCl2, 1 U/μL RNase inhibitor in PBS. All solutions were sterile filtered prior to use, and all procedures were performed on ice.
Nuclei suspensions were stained with 10 μg/mL 7-AAD (Invitrogen, Cat. No. A1310) and sorted on a BD Fusion Flow Cytometer (BD FACSMelody™4-Way Cell Sorter) with a 100 µm nozzle. Nuclei were counted using a Countstar Automated Cell Counter (Countstar Rigel S5) and approximately 20,000 nuclei per sample were loaded into the 10x Chromium system using the Single-Cell 3′ Reagent Kit v3.1 according to the manufacturer’s instructions (10X Genomics). GEM-Reverse Transcription was performed with a thermal cycler using the following program: 53℃ for 45 minutes, 85℃ for 5 minutes, and held at 4℃. After reverse transcription and cell barcoding, emulsions were lysed and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Scientific), followed by PCR amplification. The cDNA was then evaluated using an Agilent Bioanalyzer. Libraries were prepared according to the manufacturer’s instructions and purified for quality assessment.

value: iWAT Adipose

value: 16 weeks old

value: male

tag: diet

value: Normal Chow diet

value: Cold exposure (4degreeC for 3 days)


title: DMPFOSP2AS16_L002

first: Daniel

last: Villeneuve

address: 6201 Congdon Blvd

institute: US EPA

description:
DM_PFOS_P2_A
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt
DM_PFOA_counts.filtered.+1.normFinal.txt

data_processing:
RNA sequencing was performed at the Michigan State University Research Technology Support Facility Genomics Core. Libraries were quality control checked and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000, and Invitrogen Collibri Library Quantification qPCR assays. Each pool (corresponding to ≈ 96 samples from assays with two PFAS) was loaded onto one lane of a NovaSeq S4 flow cell. Sequencing was performed in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit (target read depth of ≈28,000 MB/sample). Base calling was done by Illumina Real Time Analysis v3.4.4, and the output was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v2.20.0.
The Daphnia magna reference genome (assembly ASM2063170v1.1, RefSeq GCF_020631705.1) was indexed with STAR version 2.7.10a using the following sample specific parameters: --genomeSAindexNbases 12 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC and MultiQC version 1.12, raw reads were trimmed using Trim Galore! version 0.6.6, with the parameters --illumina --stringency 3 --quality 20 –e 0.1 --length 20 --paired, to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp.
Trimmed reads were then mapped with STAR version 2.7.10a to the indexed genome using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS. Samtools version 1.15.1 was used to sort and index the alignment files.
HTSeq version 2.0.1 was used to assign counts to each gene with the following parameters: -f bam -r pos -s no. FastQC and MultiQC version 1.12 were used to assess quality control metrics of the processed reads. Count data for treatment and plate-specific control samples for each PFAS were written to a single tab-delimited matrix file, where each column represented a sample and each row represented a gene.
Additional quality control and filter steps were applied to each count matrix using the R statistical computing software (R Core Team, 2022) prior to concentration response modeling. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al. 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out. Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors() which was used for counts per million mapped reads (CPM) normalization. The filtered CPM normalized count matrix was log2 transformed with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses; i.e., log2(CPM+1)).
Assembly: Daphnia magna reference genome (assembly ASM2063170v1.1, RefSeq GCF_020631705.1)
Supplementary files format and content: Count matrices provided as tab delimited text files. Top row = sample names. Second row = treatment concentration (ug/L); all subsequent rows provide filtered counts per million (CPM) log2 transformed with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses; i.e., log2(CPM+1), with each row corresponding to a separate transcript and each column corresponding to a sample. One count matrix file per chemical exposure experiment.

extract_protocol:
RNA was extracted from pooled homogenates using Zymo Research Direct-zol-96 RNA kit (Zymo Research) protocol adapted to the Biomek i5 to yield 40 µl of RNA. Previously extracted control RNA was added to empty wells on the final RNA plate. Concentrations of RNA for each well were measured on a NanoDrop spectrophotometer (Thermo Scientific, NanoDrop Eight) and diluted if necessary.
RNA extracts (10 µl) were used to prepare cDNA libraries with the Lexogen Poly(A) RNA Selection Kit V1.5 (catalog #157; Lexogen GmbH, Austria) and Lexogen CORALL mRNA-Seq Library Prep Kit with UDIs (catalog #158-163) both adapted to the Biomek i5. Resulting cDNA library samples were evaluated on a 4200 TapeStation (Agilent Technologies, CA, USA) using the D1000 ScreenTape (Agilent) analysis protocol to assess cDNA quality. Samples were quantified using the Quant-iT Picogreen dsDNA assay kit (catalog # P11495; Thermo Fischer Scientific), diluted if necessary, and equal portions of each sample pooled for use in RNA sequencing by Michigan State University.

value: whole body

value: GLTED-wt

value: ug/L

value: A


title: DMPFOSP2DS13_L002

description:
DM_PFOS_P2_D
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: D


title: ce_smallRNA_ebax_LateTC_mut_36h


title: E6-526-LNGP

value: skin tissue


title: MCF-10A cells, EGF, C75, 6h, biol rep 3

value: Cell line

value: Breast epithelial cell

value: EGF 9h plus C75 6h


title: DMPFOSP1HS1_L002

description:
DM_PFOS_P1_H
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: H


title: ce_smallRNA_ebax_LateTC_mut_29h


title: iWAT, 6-month-old, RT, snRNA-seq

description: 10x Genomics

value: Room temperature (22degreeC)


title: Control-Day6

source_name: Rat lense, without galactose, 6 days

value: Sprague Dawley

value: lens

value: without galactose, 6 days


title: ce_smallRNA_ebax_LateTC_mut_28h


title: DMPFOSP1GS2_L002

description:
DM_PFOS_P1_G
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: PFOS (DTXSID8037706)

value: G


title: iBAT, 6-month-old, CE, snRNA-seq

description: 10x Genomics

source_name: iBAT Adipose

value: iBAT Adipose

value: 16 weeks old

value: male

value: Normal Chow diet

value: Cold exposure (4degreeC for 3 days)


title: ce_smallRNA_ebax_LateTC_mut_27h


title: DMPFOSP1FS3_L002

description:
DM_PFOS_P1_F
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: ug/L

value: F


title: lPRAT, 6-month-old, RT, snRNA-seq

description: 10x Genomics

source_name: lPRAT Adipose

value: lPRAT Adipose


title: ce_smallRNA_ebax_LateTC_mut_26h


title: MCF-10A cells, EGF, SCDi, 3h, biol rep 3

value: Cell line

value: Breast epithelial cell

value: WT

value: EGF 9h plus SCDi 3h


title: DMPFOSP1ES4_L002

description:
DM_PFOS_P1_E
n/a
DM_PFOS_counts.filtered.+1.normFinal.txt

value: E


title: MCF-10A cells, EGF, GSKi, 3h, biol rep 3

value: EGF 9h plus GSKi 3h


title: lPRAT, 2-month-old, RT, snRNA-seq

description: 10x Genomics

value: 8 weeks old

value: Room temperature (22degreeC)


title: MCF-10A cells, EGF, C75, 3h, biol rep 3

value: EGF 9h plus C75 3h


title: MCF-10A cells, EGF, DMSO, 3h, biol rep 3

value: EGF 9h plus DMSO 3h


title: ce_smallRNA_ebax_LateTC_mut_25h


title: MCF-10A cells, EGF, 9h, biol rep 3

value: Cell cycle release with EGF 9h


title: ce_smallRNA_ebax_LateTC_N2_42h


title: MCF-10A cells, starved, 0h, biol rep 3

value: Starvation control


title: mPRAT, 6-month-old, CE, snRNA-seq

description: 10x Genomics

source_name: mPRAT Adipose

value: mPRAT Adipose

value: 16 weeks old

value: male

value: Normal Chow diet

value: Cold exposure (4degreeC for 3 days)


title: DMPFOSP1CS6_L002

description:
DM_PFOS_P1_C
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PFOS (DTXSID8037706)

value: ug/L

value: C


title: DMPFOSP1DS5_L002

description:
DM_PFOS_P1_D
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: D


title: iBAT, 6-month-old, RT, snRNA-seq

description: 10x Genomics

extract_protocol:
Nuclei isolation from adipose tissue was performed according to a published protocol with slight modification (Van Hauwaert et al., 2021). Briefly, adipose tissues were minced in a petri dish containing 500 mL nuclei isolation buffer (NIB) that contains 250 mM sucrose (Solarbio, Cat. No. S8271), 10 mM HEPES (Solarbio, Cat. No. H8090), 1.5 mM MgCl2 (Sigma-Aldrich, Cat. No. M8266), 10 mM KCl (Sigma-Aldrich, Cat. No. P5405), 0.001% IGEPAL CA-630 (NP-40) (Sigma-Aldrich, Cat. No. I3021), 0.2 mM DTT (Sigma-Aldrich, Cat. No. D9779), and 1 U/μL RNase inhibitor (Solarbio, Cat. No. R8061) in DEPC-treated water. The samples were further homogenized using a 2 mL dounce homogenizer (Sigma-Aldrich, Cat. No. D8938), applying three strokes with the loose pestle. The homogenate was filtered through a 70 μm cell strainer (Falcon, Cat. No. 352350) and centrifuged at 500 g for 5 min at 4°C. The nuclear pellet was resuspended in 2 mL NIB and centrifuged at 300 g for 3 min at 4°C. Finally, the nuclear pellet was resuspended in 300 μL nuclei resuspension buffer that contains 2% BSA (Sigma-Aldrich, Cat. No. A1933), 1.5 mM MgCl2, 1 U/μL RNase inhibitor in PBS. All solutions were sterile filtered prior to use, and all procedures were performed on ice.
Nuclei suspensions were stained with 10 μg/mL 7-AAD (Invitrogen, Cat. No. A1310) and sorted on a BD Fusion Flow Cytometer (BD FACSMelody™4-Way Cell Sorter) with a 100 µm nozzle. Nuclei were counted using a Countstar Automated Cell Counter (Countstar Rigel S5) and approximately 20,000 nuclei per sample were loaded into the 10x Chromium system using the Single-Cell 3′ Reagent Kit v3.1 according to the manufacturer’s instructions (10X Genomics). GEM-Reverse Transcription was performed with a thermal cycler using the following program: 53℃ for 45 minutes, 85℃ for 5 minutes, and held at 4℃. After reverse transcription and cell barcoding, emulsions were lysed and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Scientific), followed by PCR amplification. The cDNA was then evaluated using an Agilent Bioanalyzer. Libraries were prepared according to the manufacturer’s instructions and purified for quality assessment.
snRNA-seq

value: iBAT Adipose


title: DMPFOSP1BS7_L002

description:
DM_PFOS_P1_B
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt

value: B


title: ce_smallRNA_ebax_LateTC_N2_41h

value: WT


title: mPRAT, 6-month-old, RT, snRNA-seq

description: 10x Genomics

value: Room temperature (22degreeC)


title: MCF-10A cells, EGF, SCDi, 6h, biol rep 2

value: Cell line

value: Breast epithelial cell

value: EGF 9h plus SCDi 6h


title: iBAT, 1-month-old, RT, snRNA-seq

description: 10x Genomics

value: 4 weeks old


title: DMPFOSP1AS8_L002

description:
DM_PFOS_P1_A
DM_PFOS_counts.filtered.+1.normFinal_QA_contaminated_910_trt_removed.txt
DM_PFOS_counts.filtered.+1.normFinal.txt
DM_PFOA_counts.filtered.+1.normFinal.txt

value: A


title: DMPFOAP3HS41_L002

description:
DM_PFOA_P3_H
DM_PFOA_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFOA

value: PFOA (DTXSID8031865)

value: H


title: ce_smallRNA_ebax_LateTC_N2_39h


title: MCF-10A cells, EGF, GSKi, 6h, biol rep 2

value: EGF 9h plus GSKi 6h


title: mPRAT, 2-month-old, RT, snRNA-seq

description: 10x Genomics

value: mPRAT Adipose

value: 8 weeks old

value: male

value: Normal Chow diet


title: DMPFOAP3GS42_L002

description:
DM_PFOA_P3_G
DM_PFOA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: ug/L

value: G


title: ce_smallRNA_ebax_LateTC_N2_38h

value: WT


title: ce_smallRNA_ebax_LateTC_N2_37h


title: DMPFOAP3FS43_L002

description:
DM_PFOA_P3_F
DM_PFOA_counts.filtered.+1.normFinal.txt

value: F


title: MCF-10A cells, EGF, SCDi, 3h, biol rep 2

value: Cell line

value: Breast epithelial cell

value: EGF 9h plus SCDi 3h


title: MCF-10A cells, EGF, C75, 6h, biol rep 2

value: EGF 9h plus C75 6h


title: mPRAT, 1-month-old, RT, snRNA-seq

description: 10x Genomics

value: 4 weeks old

value: Room temperature (22degreeC)


title: E14, RPB1, RNASEA, PGA, REP1,  CHIP

city: London

first: Alex

last: Hall Hickman

state: Please select

address: Flat A, 75 Dunsmure Road, Dunsmure Road

department: Cancer Institute

institute: University College London

data_processing:
Adapters trimmed with Trim Galore!
Reads were aligned using BWA
Diplicates marked with picard and reads filteredf for blacklisted regions, unmapped reads and duplicates using SAMtools
Bigwigs scaled to 1 million mapped reads using BEDTools
Assembly: GRCm38
Supplementary files format and content: bigwig

source_name: CELL LINE

growth_protocol: KO-DMEM (ThermoFisher, 10829018), 10% FBS, One Shot™ format, United States, validated for mouse ESC culture (ThermoFisher, A3160401), non-essential amino acids (ThermoFisher, 11140035), 2 mM L-glutamine (ThermoFisher, 25030–024), 50 μM 2-mercaptoethanol (ThermoFisher, 31350010), 100 U/mL penicillin-streptomycin (ThermoFisher, 15140–122), 1 mM sodium pyruvate (ThermoFisher, 11360039) and 1000 U/mL leukemia inhibitory factor (Stemgent, 03-0011-100). ESCs were plated and grown on 0.1% gelatin coated dishes.

extract_protocol:
Cells were fixed for 10 minutes in 1% formaldehyde. Cells were lysed and sonicated for 20 mins (replicate 1) or 40 minutes (replicate 2)
Replicate 1 was constructed using the kapa hyperplus kit and replicate 2 was constructed using the nebnext ultra ii dna library prep kit for illumina

value: CELL LINE

value: mESC

value: RNaseA PGA


title: ce_smallRNA_ebax_LateTC_N2_36h


title: MCF-10A cells, EGF, DMSO, 3h, biol rep 2

value: EGF 9h plus DMSO 3h


title: iBAT, 2-month-old, RT, snRNA-seq

description: 10x Genomics

value: iBAT Adipose

value: 8 weeks old

value: male

value: Normal Chow diet


title: E14, RPB1, RNASEA, REP1,  CHIP

value: RNaseA


title: DMPFOAP3DS45_L002

description:
DM_PFOA_P3_D
DM_PFOA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PFOA (DTXSID8031865)

value: ug/L

value: D


title: ce_smallRNA_ebax_LateTC_N2_40h

value: WT


title: MCF-10A cells, EGF, GSKi, 3h, biol rep 2

value: Cell line

value: Breast epithelial cell

value: EGF 9h plus GSKi 3h


title: ce_smallRNA_ebax_LateTC_N2_35h


title: MCF-10A cells, EGF, DMSO, 6h, biol rep 2

value: EGF 9h plus DMSO 6h


title: DMPFOAP3CS46_L002

description:
DM_PFOA_P3_C
DM_PFOA_counts.filtered.+1.normFinal.txt

value: C


title: E14, RPB1, REP1, CHIP

value: CELL LINE

value: mESC


title: ce_smallRNA_ebax_LateTC_N2_34h


title: E14, SUZ12, RNASEA, PGA, REP1,  CHIP

value: RNaseA PGA


title: MCF-10A cells, EGF, C75, 3h, biol rep 2

value: EGF 9h plus C75 3h


title: MCF-10A cells, EGF, 9h, biol rep 2

value: Cell cycle release with EGF 9h


title: DMPFOAP3BS47_L002

description:
DM_PFOA_P3_B
DM_PFOA_counts.filtered.+1.normFinal.txt

value: B


title: ce_smallRNA_ebax_LateTC_N2_33h


title: E14, SUZ12, REP1, CHIP


title: E14, SUZ12, RNASEA, REP1,  CHIP

value: RNaseA


title: ce_smallRNA_ebax_LateTC_N2_31h


title: DMPFOAP2GS34_L002

description:
DM_PFOA_P2_G
DM_PFOA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: G


title: ce_smallRNA_ebax_LateTC_N2_32h


title: MCF-10A cells, starved, 0h, biol rep 2

value: Starvation control


title: DMPFOAP3ES44_L002

description:
DM_PFOA_P3_E
DM_PFOA_counts.filtered.+1.normFinal.txt

value: PFOA (DTXSID8031865)

value: ug/L

value: E


title: E14, H3K27ME3, RNASEA, PGA, REP1,  CHIP


title: DMPFOAP2HS33_L002

description:
DM_PFOA_P2_H
DM_PFOA_counts.filtered.+1.normFinal.txt

value: H


title: DMPFOAP2FS35_L002

description:
DM_PFOA_P2_F
DM_PFOA_counts.filtered.+1.normFinal.txt

value: F


title: MCF-10A cells, EGF, SCDi, 6h, biol rep 1

value: Cell line

value: Breast epithelial cell

value: WT

value: EGF 9h plus SCDi 6h


title: E14, H3K27ME3, RNASEA, REP1,  CHIP

value: CELL LINE

value: mESC


title: MCF-10A cells, EGF, GSKi, 6h, biol rep 1

value: EGF 9h plus GSKi 6h


title: ce_smallRNA_ebax_LateTC_N2_29h


title: DMPFOAP2ES36_L002

description:
DM_PFOA_P2_E
DM_PFOA_counts.filtered.+1.normFinal.txt


title: ce_smallRNA_ebax_LateTC_N2_28h


title: MCF-10A cells, EGF, DMSO, 6h, biol rep 1

value: EGF 9h plus DMSO 6h


title: MCF-10A cells, EGF, C75, 6h, biol rep 1

value: EGF 9h plus C75 6h


title: E14, H3K27ME3, REP1, CHIP


title: DMPFOAP2CS38_L002

description:
DM_PFOA_P2_C
DM_PFOA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: C


title: E14, INPUT, REP1, CHIP


title: DMPFOAP2BS39_L002

description:
DM_PFOA_P2_B
DM_PFOA_counts.filtered.+1.normFinal.txt

value: PFOA (DTXSID8031865)

value: B


title: MCF-10A cells, EGF, SCDi, 3h, biol rep 1

value: EGF 9h plus SCDi 3h


title: DMPFOAP2DS37_L002

description:
DM_PFOA_P2_D
DM_PFOA_counts.filtered.+1.normFinal.txt

value: ug/L

value: D


title: E14, RPB1, RNASEA, PGA, REP2,  CHIP

value: RNaseA PGA


title: ce_smallRNA_ebax_LateTC_N2_30h


title: MCF-10A cells, EGF, DMSO, 3h, biol rep 1

value: Cell line

value: Breast epithelial cell

value: EGF 9h plus DMSO 3h


title: ce_smallRNA_ebax_LateTC_N2_26h

value: WT


title: E14, RPB1, RNASEA, REP2,  CHIP

value: CELL LINE

value: mESC

value: RNaseA


title: DMPFOAP1HS25_L002

description:
DM_PFOA_P1_H
DM_PFOA_counts.filtered.+1.normFinal.txt

value: H


title: ce_smallRNA_ebax_LateTC_N2_25h


title: ce_smallRNA_mir235seed_TC_mut_30h

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. To quantify both strands of the seed mutant of mir-235, we added a fasta file containing the sequences of the two additional miRNAs as an auxilliary file when performing the alignments. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100,auxiliaryFile="mir235SeedMutant.txt",)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

growth_protocol: Synchronized L1's of N2 and HW2643 (mir-235(xe181[seed_mutant]) I were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 18h to 30h

extract_protocol:
We harvested worms from 18h to 30h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using  Direct-zol™ RNA MicroPrep kit (Zymo Research; R2062) as per manufacturere's instructions. Total RNA was treated with DNAse on column
Sequencing libraries were generated using CleanTag Small RNA Library Preparation Kit according to the manufacturer’s instructions. The library pool was size selected on a gel (140-160 bp) to enrich for the small RNA fraction. Subsequently, library was sequenced on Illumina Next Seq500, as 51 cycles single-end reads.


title: E14, SUZ12, RNASEA, PGA, REP2,  CHIP


title: MCF-10A cells, EGF, GSKi, 3h, biol rep 1

value: EGF 9h plus GSKi 3h


title: MCF-10A cells, EGF, C75, 3h, biol rep 1

value: EGF 9h plus C75 3h


title: ce_smallRNA_mir235seed_TC_mut_29h


title: DMPFOAP1FS27_L002

description:
DM_PFOA_P1_F
DM_PFOA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: F


title: MCF-10A cells, EGF, 9h, biol rep 1

value: Cell cycle release with EGF 9h


title: E14, SUZ12, RNASEA, REP2,  CHIP


title: ce_smallRNA_mir235seed_TC_mut_28h


title: DMPFOAP1ES28_L002

description:
DM_PFOA_P1_E
DM_PFOA_counts.filtered.+1.normFinal.txt

value: PFOA (DTXSID8031865)

value: ug/L

value: E


title: MCF-10A cells, starved, 0h, biol rep 1

value: Cell line

value: Starvation control


title: ce_smallRNA_ebax_LateTC_N2_27h


title: E14, SUZ12, REP2, CHIP


title: DMPFOAP1DS29_L002

description:
DM_PFOA_P1_D
DM_PFOA_counts.filtered.+1.normFinal.txt

value: D


title: 3.11-44b

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

data_processing:
Fastq files were then aligned using STAR algorithm (version 2.7.6a)
quality control of the alignment realized with Picard tools (version 2.8.1)
Reads were then count using RSEM (v1.3.1)
the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0)
Assembly: Ensembl Homo sapiens GRCm38 reference, release 101
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: KGN

growth_protocol: KGN cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA extraction was performed 30 hours after transfection, following the TRI-reagent supplier’s instructions (MRC)
1 ug of high quality total RNA sample (RIN >8.8) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions.

value: KGN

value: Granulosa cell line

value: FOXL2 WT/C134W


title: ce_smallRNA_mir235seed_TC_mut_27h


title: ce_smallRNA_mir235seed_TC_mut_26h


title: DMPFOAP1CS30_L002

city: Duluth

description:
DM_PFOA_P1_C
DM_PFOA_counts.filtered.+1.normFinal.txt

value: C


title: DMPFOAP1BS31_L002

description:
DM_PFOA_P1_B
DM_PFOA_counts.filtered.+1.normFinal.txt

value: B


title: 44b


title: E14, RPB1, REP2, CHIP

value: CELL LINE

value: mESC


title: E14, H3K27ME3, RNASEA, REP2,  CHIP

value: RNaseA


title: E14, H3K27ME3, REP2, CHIP


title: 3.11


title: ce_smallRNA_mir235seed_TC_mut_25h


title: ce_smallRNA_mir235seed_TC_mut_24h


title: DMPFNAP3HS137_L002

description:
DM_PFNA_P3_H
DM_PFNA_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFNA

value: whole body

value: GLTED-wt

value: PFNA (DTXSID8031863)

value: H


title: 4.72-44a

value: FOXL2 WT/WT

value: CRISPR/Cas9 to reverted C134W mutation


title: DMPFOAP1GS26_L002

description:
DM_PFOA_P1_G
DM_PFOA_counts.filtered.+1.normFinal.txt

value: PFOA (DTXSID8031865)

value: ug/L

value: G


title: E14, INPUT, REP2, CHIP


title: DMPFNAP3FS139_L002

description:
DM_PFNA_P3_F
DM_PFNA_counts.filtered.+1.normFinal.txt

value: F


title: 4.72

value: KGN

value: Granulosa cell line


title: ce_smallRNA_mir235seed_TC_mut_22h


title: R2_Bulk tumor NrasG12VPtenKO [WES]

city: Amsterdam

first: Masami

last: Ando-Kuri

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

data_processing:
library strategy: WES
The paired-end reads were trimmed using SeqPurge and aligned with Burrows–Wheeler alignment (v.0.5.10) to GRCm38 (mm10). PCR duplicates were designated using rumidup (https://github.com/NKI-GCF/rumidup).
For basecall recalibration and variant calling, the BaseRecalibrator and Mutect2 functions from the genome analysis toolkit121 (GATK; v.4.2.6.0) and were applied, respectively.
SNPEff122 and SnpSift123, (v.5.1d), were used to annotate and select the somatic variants calls with TLOD greater or equal than 15 and filtered on the disruptive effects (conservative inframe deletion, disruptive inframe deletion, disruptive inframe insertion, frameshift variant, missense variant, start lost, stop gained, stop lost or stop retained variant).
Assembly: mm10
Supplementary files format and content: vcf.gz: These files are the compressed "Variant Call Format". It includes a header with metadata. The columns include: CHROM (CHROMOSOME NAME)  POS ( position of the variation)     ID (identifier of the variation)      REF (reference base at the position)    ALT  (alternative alleles at the position)    QUAL (quality score)    FILTER (flag indicating which of a given set of filters the variation has failed or PASS) INFO (description of the variation)   FORMAT ( list of fields for describing the samples) SAMPLE (values are given for the fields listed in FORMAT)

source_name: liver

extract_protocol:
For WES, macro-dissected HCC were weighted and equal amounts (~1mg each) from end-stage (n=3 each genotype) HCC-bearing mice and control liver (n=3). Following DNA extraction and fragmentation (200-300 bp), a maximum of 1 μg of sheared DNA was used for library preparation using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234) following manufacturer’s instructions.
With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 100bp sequencing on an Illumina Illumina Novaseq 6000, according to manufacturer’s instructions.

value: liver

value: NrasG12V overexpression Pten knockout

tag: time

value: End-stage

tag: disease state

value: cancer


title: 44a

tag: cell type


title: DMPFNAP3ES140_L002

description:
DM_PFNA_P3_E
DM_PFNA_counts.filtered.+1.normFinal.txt

tag: conc.

value: E


title: ce_smallRNA_mir235seed_TC_mut_21h


title: R1_Bulk tumor NrasG12VPtenKO [WES]


title: E14, H3K27ME3, RNASEA, PGA, REP2,  CHIP

value: CELL LINE

value: mESC

value: RNaseA PGA


title: ce_smallRNA_mir235seed_TC_mut_20h


title: R3_Bulk tumor NrasG12DPtenKO [WES]

value: NrasG12D overexpression Pten knockout


title: DMPFNAP3CS142_L002

description:
DM_PFNA_P3_C
DM_PFNA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PFNA (DTXSID8031863)

tag: conc. units

value: C


title: R2_Bulk tumor NrasG12DPtenKO [WES]


title: WAT.KO.7053281

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Marc2_counts.txt
Marc2_TPM.txt

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17.
Reads were decoded based on their barcodes and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio software (OmicSoft Corp. (Cary, NC) allowing two mismatches
Reads mapped to the exons of a gene were summed at the gene level.
Assembly: NCBI GRCm38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains TPM values for each sample

source_name: WAT

extract_protocol:
Total RNA was purified from tissues using MagMAX™-96 for Microarrays Total RNA Isolation kit (Life Technologies (Carlsbad, CA)), according to manufacturer’s specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above. Messenger RNA was purified from total RNA using Dynabeads mRNA purification kit (Invitrogen (Waltham, MA)).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using KAPA mRNA-Seq Library Preparation kit (Kapa Biosystems (Wilmington, MA)). After mRNA quality control analysis, RNA-seq libraries were prepared and long read sequencing (75bp, single end, 15M reads) was used for all samples. Sequencing was performed on Illumina HiSeq®2500 by a multiplexed single-read run with 33 cycles.

value: WAT


title: ce_smallRNA_mir235seed_TC_mut_23h


title: WAT.KO.7053282

description:
Marc2_counts.txt
Marc2_TPM.txt


title: WAT.KO.7070224

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_mut_19h


title: DMPFNAP2HS129_L002

description:
DM_PFNA_P2_H
DM_PFNA_counts.filtered.+1.normFinal.txt

value: ug/L

tag: conc code

value: H


title: ce_smallRNA_mir235seed_TC_mut_18h


title: DMPFNAP2GS130_L002

description:
DM_PFNA_P2_G
DM_PFNA_counts.filtered.+1.normFinal.txt

tag: tissue

value: G


title: DMPFNAP3BS143_L002

description:
DM_PFNA_P3_B
DM_PFNA_counts.filtered.+1.normFinal.txt

value: B


title: DMPFNAP3GS138_L002

description:
DM_PFNA_P3_G
DM_PFNA_counts.filtered.+1.normFinal.txt


title: WAT.KO.7053280

description:
Marc2_counts.txt
Marc2_TPM.txt


title: WAT.WT.7070221

description:
Marc2_counts.txt
Marc2_TPM.txt


title: R1_Bulk tumor NrasG12DPtenKO [WES]

value: liver


title: R3_Bulk tumor MycOEPtenKO [WES]

value: Myc overexpression Pten knockout

value: End-stage


title: R2_Bulk tumor MycOEPtenKO [WES]

value: cancer


title: ce_smallRNA_mir235seed_TC_N2_30h

value: WT


title: R3_Bulk tumor NrasG12VPtenKO [WES]

value: NrasG12V overexpression Pten knockout


title: ce_smallRNA_mir235seed_TC_N2_29h


title: DMPFNAP2FS131_L002

description:
DM_PFNA_P2_F
DM_PFNA_counts.filtered.+1.normFinal.txt

value: F


title: DMPFNAP3DS141_L002

description:
DM_PFNA_P3_D
DM_PFNA_counts.filtered.+1.normFinal.txt

value: D


title: WAT.WT.7035605

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_N2_28h


title: R1_Bulk tumor MycOEPtenKO [WES]


title: DMPFNAP2ES132_L002

description:
DM_PFNA_P2_E
DM_PFNA_counts.filtered.+1.normFinal.txt

value: whole body

value: E


title: ce_smallRNA_mir235seed_TC_N2_27h


title: R3_Bulk tumor MycOETrp53KO [WES]

value: Myc overexpression Trp53 knockout


title: WAT.WT.7018357

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFNAP2DS133_L002

description:
DM_PFNA_P2_D
DM_PFNA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PFNA (DTXSID8031863)


title: WAT.KO.6999955

description:
Marc2_counts.txt
Marc2_TPM.txt

value: WAT


title: R2_Bulk tumor MycOETrp53KO [WES]


title: DMPFNAP2CS134_L002

description:
DM_PFNA_P2_C
DM_PFNA_counts.filtered.+1.normFinal.txt

value: ug/L

value: C


title: ce_smallRNA_mir235seed_TC_N2_26h


title: WAT.WT.6980848

description:
Marc2_counts.txt
Marc2_TPM.txt


title: WAT.WT.6962451

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_N2_25h


title: ce_smallRNA_mir235seed_TC_N2_24h


title: WAT.WT.6943256

description:
Marc2_counts.txt
Marc2_TPM.txt


title: R2_Control_Liver [WES]

value: 15 weeks

value: normal


title: R3_Control_Liver [WES]

value: liver


title: DMPFNAP1GS122_L002

description:
DM_PFNA_P1_G
DM_PFNA_counts.filtered.+1.normFinal.txt

value: G


title: ce_smallRNA_mir235seed_TC_N2_23h


title: lung.KO.7070224

description:
Marc2_counts.txt
Marc2_TPM.txt

source_name: lung

value: lung


title: DMPFNAP1HS121_L002

description:
DM_PFNA_P1_H
DM_PFNA_counts.filtered.+1.normFinal.txt

value: H


title: ce_smallRNA_mir235seed_TC_N2_22h

value: WT


title: R1_Control_Liver [WES]


title: WAT.WT.6943255

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_N2_21h


title: Ncor1/2_ATAC_dKO3

data_processing:
raw data were preprocessed using nfcore/atacseq V1.2.2 with default parameters
Trim-galore V0.6.4 was used to remove the adapters
trimmed reads were mapped to mm10 using BWAMEM v0.7.17
Picard MarkDuplicates v2.23.1 was used to mark the duplicates reads
duplicated and multimapping reads were filtered using the Samtools v1.10
Homer V4.11 was used to make tag directories of filtered bam using makeTagDirectory command with default parameters
findPeaks command with parameter -style factor was used to call peaks
Assembly: mm10
Supplementary files format and content: .peaks: Homer peak files, tab-separated
Supplementary files format and content: .bigWig: BigWig format

source_name: liver-Hnf4a+ hepatocytes

extract_protocol:
HNF4a+ nuclei were FACS sorted from control and dKO livers
ATAC libraries were prepared via the Omni-ATAC protocol with AMPuree beads utilized for size selection

value: liver-Hnf4a+ hepatocytes

tag: Sex

value: Male

value: Ncor1/2 F/F +AAV-Cre

tag: data collection_time

value: Day 5 post AAV


title: DMPFNAP1FS123_L002

description:
DM_PFNA_P1_F
DM_PFNA_counts.filtered.+1.normFinal.txt

value: whole body

tag: genotype

value: F


title: ce_smallRNA_mir235seed_TC_N2_20h

tag: strain


title: lung.KO.7053281

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_N2_19h


title: Ncor1/2_ATAC_dKO2


title: lung.KO.7053280

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFNAP1DS125_L002

description:
DM_PFNA_P1_D
DM_PFNA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PFNA (DTXSID8031863)

value: D

tag: exposure duration

tag: replicate plate_id


title: DMPFNAP1CS126_L002

description:
DM_PFNA_P1_C
DM_PFNA_counts.filtered.+1.normFinal.txt

tag: treatment

value: ug/L

value: C

tag: age


title: Ncor1/2_ATAC_Cont3

value: Ncor1/2 F/F +AAV-eGFP


title: lung.KO.6999955

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_mir235seed_TC_N2_18h

tag: time (h)


title: DMPFNAP2BS135_L002

description:
DM_PFNA_P2_B
DM_PFNA_counts.filtered.+1.normFinal.txt

value: B


title: Ncor1/2_ATAC_dKO1


title: Ncor1/2_ATAC_Cont2


title: lung.WT.7035605

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor1/2_ATAC_Cont1


title: ce_smallRNA_ebax_TC_mut_30h

growth_protocol: Synchronized L1's of N2 and HW3527 (ebax-1(tm2321) IV ) were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 18h to 31h

extract_protocol:
We harvested worms from 18h to 31h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using  Direct-zol™ RNA MicroPrep kit (Zymo Research; R2062) as per manufacturere's instructions. Total RNA was treated with DNAse on column
Sequencing libraries were generated using CleanTag Small RNA Library Preparation Kit according to the manufacturer’s instructions. The library pool was size selected on a gel (140-160 bp) to enrich for the small RNA fraction. Subsequently, library was sequenced on NextSeq500, as 76 cycles single-end reads.


title: ce_smallRNA_ebax_TC_mut_31h


title: DMPFHxSP3FS90_L002

description:
DM_PFHxS_P3_F
DM_PFHxS_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PFHxS

value: PFHxS (DTXSID3037709)


title: DMPFNAP1BS127_L002

description:
DM_PFNA_P1_B
DM_PFNA_counts.filtered.+1.normFinal.txt


title: ce_smallRNA_ebax_TC_mut_29h