title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 578 ug/L, rep3

description:
T3He3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+12h_rep2

status: Public on Aug 28 2024

type: SRA

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

library_source: transcriptomic

data_processing:
Low quality bases and Truseq adapters were removed with cutadapt v1.16 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15)
Reads were mapped on mm10 with STAR version 2.7.0e using ENCODE parameters using custom gtf https://doi.org/10.5281/zenodo.7510406, counts and coverage were computed at the same time.
FPKM values were computed with cufflinks version 2.2.1 (--max-bundle-length 10000000 --multi-read-correct --library-type "fr-unstranded" -b /home/ldelisle/genomes/fasta/mm10.fa  --no-effective-length-correction -M MTmouse.gtf -G custom.gtf)
Average coverage between replicates was computed with bigwigAverage from deepTools version 3.5.5
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified_timecourse.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts_subset_timecourse.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample, genes on chrX, Y, M were removed)

molecule: polyA RNA

organism: Mus musculus

source_name: Forelimb bud

extract_protocol:
Limb buds were dissected in ice-cold PBS, washed in PBS, transferred to RNAlater (Invitrogen), and stored overnight at -20°C. The next day, samples were transferred to -80°C for long-term storage. RNA isolation was performed with the RNeasy Kit (Qiagen) following manufacture instructions. After performing QC on a Fragment Analyzer (Advanced Analytical Technologies, Inc.), RNA was stored at -80 until shipping to Novogene.
Library constructions and sequencing were performed at Novogene.
Standard Illumina mRNA-libraries (by polyA-enrichment) were made and after successful QC sequenced. Libraries were sequenced as PE150 on a NovaSeq6000 (by Novogene)

tag: tissue

value: Forelimb bud

tag: genotype

value: WT Swiss Albino

tag: treatment

tag: timepoint of_treatment

tag: timepoint of_dissection


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 1790 ug/L, rep5

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

country: USA

institute: US EPA

description:
T3Hd9
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt

data_processing:
Library pools were quality-checked and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core.
Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit.
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
The zebrafish reference genome (GRCz11; RefSeq GCF_000002035.6) was indexed with STAR v2.7.10a. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 12 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC v0.11.9 and MultiQC v1.14, unique molecular indices were extracted from raw read 1 via fastp v0.23.2. Raw reads were additionally processed by fastp to perform PCR deduplication, read quality and length filtering (to retain reads >= 15 bp, with phred quality >=Q15, number of N bases =< 5, and <= 40% of unqualified bases), trimming of polyG tails, and trimming of Illumina adapters. The following command was used to perform all of the raw read processing steps: fastp -i [read1] -I [read2] -o Trimmed/[read1_trimmed] -O Trimmed/[read2_trimmed] --umi --umi_loc=read1 --umi_len=12 --dedup --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT .
Trimmed reads were then mapped and counted with STAR v2.7.10a to the indexed genome using the following sample specific parameters: --outSAMattributes NH HI AS NM MD --genomeDir [genome_index_build] --readFilesIn Trimmed/[read1_trimmed] Trimmed/[read2_trimmed] --outFileNamePrefix [sampleID]_ --readFilesCommand zcat --quantMode GeneCounts TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMheaderHD @HD VN:1.4 SO:sorted --outFilterType BySJout .
FastQC v0.11.9 and MultiQC v1.14 were used to assess the qualtiy control metrics of the processed reads.
Counts to each gene were parsed, and raw count data for each exposure condition (i.e., each chemical/control treatment by time code combination) written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Quality control screening and filter steps were applied to each raw count matrix (except for the transcription positive control and standard RNA pool matrices) using the R statistical computing software. Samples were first screened to see if any exhibited total counts < 2 million, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s 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(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Principal Component Analysis (PCA) plots were generated to look for possible outliers.
Assembly: GRCz11 (RefSeq GCF_000002035.6; NCBI Annotation Release 106)

molecule: total RNA

organism: Danio rerio

source_name: whole body zebrafish embyro

growth_protocol: Adult zebrafish (AB wild type strain) were housed in an onsite culture facility at the US Environmental Protection Agency (USEPA) laboratory in Duluth, MN. The fish were raised in a flow-through system with control UV-treated, filtered Lake Superior water (LSW) at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8-hour light/dark photoperiod cycle. Fish were housed in 5.5-gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp (Artemia) nauplii twice daily. The night prior, breeding zebrafish in groups of four males x six females were separated into breeding tanks containing a plastic screened spawning basket. The next morning, approximately two hours after the lights turned on, embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hours post fertilization (hpf), zebrafish embryos were screened under a stereo microscope, and only similarly staged embryos were sorted out for chemical exposure. All dead, malformed, and unfertilized eggs were discarded.

extract_protocol:
At the end of each PFAS, DMSO control, and Chlorpyrifos exposure period, zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol, then frozen. RNA was isolated with Ambion MagMAX-96 Total RNA Isolation kit.
Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA-Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina-compatible Lexogen CORALL RNA-Seq libraries were then prepared for RNA sequencing.

treatment_protocol: Zebrafish (Danio rerio) embryos were exposed to eight concentrations of three different per- or polyfluoroalkyl substances (PFAS), perfluorooctanesulfonic acid (PFOS; DTXSID3031864); perfluorooctanoic acid (PFOA; DTXSID8031865); and perfluorohexane sulfonate (PFHxS; DTXSID90892476) in concentration-response (0-100 uM, half-log dilutions). Embryos were exposed to each of the three PFAS over seven distinct exposure periods (6 hours post fertilization [hpf]-120 hpf; 6 hpf-48 hpf; 6 hpf-24 hpf; 24 hpf – 120 hpf; 48 hpf-120 hpf; and 96 hpf-120 hpf). Zebrafish were also exposed to 0.33% DMSO (vehicle control) and 1uM chlorpyrifos (transcription positive control).

value: whole body zebrafish embyro

tag: strain

value: AB wild type

tag: age

tag: developmental stage

value: embryo

tag: biological replicate

tag: time code

tag: dose (ug/l)

tag: repeat sample

value: No


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 1790 ug/L, rep4

description:
T3Hd8
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+12h_rep3


title: RNA_FL_timecourse_E10.5+C59+12h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 1790 ug/L, rep3

description:
T3Hd7
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 578 ug/L, rep2

description:
T3He2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 191 ug/L, rep5

description:
T3Hf5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 1790 ug/L, rep2

description:
T3Hd6
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 1790 ug/L, rep1

description:
T3Hd10
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 24h, replicate 2

city: South San Francisco

first: Carmela

last: Sidrauski

state: California

address: 1170 Veterans Blvd

institute: Calico Life Sciences

data_processing:
RNA-seq analysis was executed and visualized using an in-house, web-based platform, consisting of the following steps. Sequencing quality control was performed using FastQC (v0.11.5).
Transcript expression was then quantified using Salmon (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing transcript-per-million (TPM) estimates, using the Ensembl human GRCh38 transcriptome.
Assembly: Ensembl human GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Homo sapiens

source_name: U2OS Dmr-PERK

growth_protocol: U2OS cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma) and 1X antibiotic-antimycotic solution (Gibco). Cells were housed in an incubator at 37°C, 5% CO2, 20% O2 and passaged every 2-3 days with trypsin.

extract_protocol:
RNA was extracted using the MagMAX mirVana Total RNA Isolation Kit in 96-well plate format and processed on the KingFisher Flex Magnetic Particle Processor using the A27828_FLEX_Tissue_Cells protocol.
RNA-seq libraries were prepared using the NEBNextUltra II Directional RNA Library Prep Kit for Illumina with 1000 ng of input material. Samples were pooled for sequencing on the NovaSeq instrument.

treatment_protocol: Cells were seeded at 2.5x105 cells/mL in 24-well plates one day prior to treatment. Treatments added to wells at indicated time points prior to sample collection. Each condition and time point were measured in triplicate.

tag: cell line

value: U2OS Dmr-PERK

value: WT

value: UT

tag: time


title: DmrPERK, UT, 24h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 7061 ug/L, rep5

description:
T3Hc5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+12h_rep2

value: DMSO


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 7061 ug/L, rep4

description:
T3Hc4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+12h_rep3


title: DmrPERK, UT, 24h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 7061 ug/L, rep2

description:
T3Hc2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+12h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 7061 ug/L, rep1

description:
T3Hc1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 16h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 578 ug/L, rep1

description:
T3He1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 7061 ug/L, rep3

description:
T3Hc3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .195 nM, 2h, replicate 1

value: Dim .195 nM


title: RNA_FL_timecourse_E10.5+C59+6h_rep3

value: E10.5 + 6hours


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 23251 ug/L, rep5

description:
T3Hb5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 16h, replicate 2


title: RNA_FL_timecourse_E10.5+C59+6h_rep2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 23251 ug/L, rep4

description:
T3Hb4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 23251 ug/L, rep2

description:
T3Hb2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+6h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 23251 ug/L, rep1

description:
T3Hb1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 8h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 65395 ug/L, rep5

description:
T3Ha5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 65395 ug/L, rep4

description:
T3Ha4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 65395 ug/L, rep3

description:
T3Ha3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 8h, replicate 1


title: DmrPERK, UT, 8h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 65395 ug/L, rep2

description:
T3Ha2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 65395 ug/L, rep1

description:
T3Ha1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+6h_rep1


title: DmrPERK, UT, 4h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 15 ug/L, rep4

description:
T2Hh5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+1h_rep2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 15 ug/L, rep3

description:
T2Hh3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+1h_rep3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 15 ug/L, rep1

description:
T2Hh1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 15 ug/L, rep2

description:
T2Hh2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 16h, replicate 1


title: DmrPERK, UT, 4h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 49 ug/L, rep4

description:
T2Hg4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 0h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 23251 ug/L, rep3

description:
T3Hb3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 4h, replicate 1


title: RNA_FL_timecourse_E10.5+DMSO+6h_rep3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 49 ug/L, rep5

description:
T2Hg5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+1h_rep3


title: RNA_FL_timecourse_E10.5+DMSO+1h_rep2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 49 ug/L, rep2

description:
T2Hg2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+6h_rep2


title: DmrPERK, UT, 0h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 15 ug/L, rep5

description:
T2Hh6
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 191 ug/L, rep5

description:
T2Hf5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+1h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 191 ug/L, rep4

description:
T2Hf4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 49 ug/L, rep1

description:
T2Hg1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 24h, replicate 3

value: Tg 100 nM


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 191 ug/L, rep2

description:
T2Hf2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+1h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 191 ug/L, rep3

description:
T2Hf3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 191 ug/L, rep1

description:
T2Hf1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 24h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 578 ug/L, rep5

description:
T2He5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: AR 16S rRNA-seq 6

city: Harbin

first: Yanan

last: Jiang

state: Heilongjiang Province

address: Health Road Street

country: China

institute: Harbin medical university

description: Alcohol+Riboflavin

data_processing:
*library strategy: 16S rRNA-seq
Usearch sofeware is used to get the OTU data of 16S RNA-seq data.
FASTP ( 0.18.0) is used to get the clean reads to be analysis（eads quality score ≥ 20, basic group ≤50%）
FLASH（1.2.11） is used to get  the high quality Tags.
UPARSE(9.2.64) is used to deal with the clean tags into the OTUs.
Assembly: None
Supplementary files format and content: Processed data file.txt

source_name: stool

growth_protocol: C57BL/6 mouse

extract_protocol: The 16S rRNA sequencing (16S rRNA-seq) was detected by Gene Denovo company, China. Microbial DNA was extracted from stool samples using the HiPure Stool DNA Kits (Magen, China) according to the manufacturer’s instructions.A novaseq 6000 (Illumina, USA) was used for sequencing under PE250 model and got the 16S rRNA-seq date.

treatment_protocol: stool sample

value: stool

value: Alcohol+Riboflavin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 578 ug/L, rep4

description:
T2He4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: AR 16S rRNA-seq 5

description: Alcohol+Riboflavin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 49 ug/L, rep3

description:
T2Hg3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 16h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 578 ug/L, rep2

description:
T2He2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 24h, replicate 1


title: DmrPERK, UT, 0h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 578 ug/L, rep1

description:
T2He1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 1790 ug/L, rep5

description:
T2Hd5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: AR 16S rRNA-seq 4

description: Alcohol+Riboflavin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 578 ug/L, rep3

description:
T2He3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 16h, replicate 2


title: AR 16S rRNA-seq 3

description: Alcohol+Riboflavin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 1790 ug/L, rep4

description:
T2Hd4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 16h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 1790 ug/L, rep2

description:
T2Hd2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 1790 ug/L, rep1

description:
T2Hd1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep6

description:
T2Hc5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: AR 16S rRNA-seq 1

description: Alcohol+Riboflavin


title: AR 16S rRNA-seq 2

description: Alcohol+Riboflavin


title: Alcohol 16S rRNA-seq 6

description: Alcohol

value: Alcohol


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 1790 ug/L, rep3

description:
T2Hd3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep5

description:
T2Hc4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 8h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep4

description:
T2Hc3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep3

description:
T2Hc2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Alcohol 16S rRNA-seq 5

description: Alcohol


title: Alcohol 16S rRNA-seq 4

description: Alcohol


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep2

description:
T2Hc1_rep
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt

value: Yes


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 7061 ug/L, rep1

description:
T2Hc1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 23251 ug/L, rep4

description:
T2Hb4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 4h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 23251 ug/L, rep5

description:
T2Hb5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 4h, replicate 2


title: Parental, Thapsigargin 100 nM, 4h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 23251 ug/L, rep1

description:
T2Hb1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 23251 ug/L, rep2

description:
T2Hb2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Alcohol 16S rRNA-seq 2

description: Alcohol


title: Alcohol 16S rRNA-seq 1

description: Alcohol


title: Parental, Thapsigargin 100 nM, 2h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 65395 ug/L, rep5

description:
T2Ha5
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 65395 ug/L, rep4

description:
T2Ha4
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Control 16S rRNA-seq 6

description: Control

value: Control


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 65395 ug/L, rep3

description:
T2Ha3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 2h, replicate 2


title: Parental, Thapsigargin 100 nM, 8h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 65395 ug/L, rep2

description:
T2Ha2
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Thapsigargin 100 nM, 8h, replicate 3


title: Control 16S rRNA-seq 5

description: Control


title: Parental, Thapsigargin 100 nM, 2h, replicate 1


title: Control 16S rRNA-seq 4

description: Control


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 65395 ug/L, rep1

description:
T2Ha1
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Alcohol 16S rRNA-seq 3

description: Alcohol


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 15 ug/L, rep5

description:
T1Hh5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-48hpf, 23251 ug/L, rep3

description:
T2Hb3
PFHxS_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt


title: Control 16S rRNA-seq 3

description: Control


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 15 ug/L, rep4

description:
T1Hh4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 15 ug/L, rep3

description:
T1Hh3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 15 ug/L, rep2

description:
T1Hh2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 24h, replicate 3

value: Arsenite .05 mM


title: Parental, Arsenite .05mM, 24h, replicate 2


title: Control 16S rRNA-seq 2

description: Control


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 15 ug/L, rep1

description:
T1Hh1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 49 ug/L, rep4

description:
T1Hg4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 49 ug/L, rep3

description:
T1Hg3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: Parental, Arsenite .05mM, 16h, replicate 3


title: Parental, Arsenite .05mM, 24h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 49 ug/L, rep1

description:
T1Hg1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt

value: No


title: AR3

description: Alcohol + Riboflavin(AR) 3

data_processing:
FastQC v0.11.8 checked the quality of sequence data.
Cutadapt (v1.15) deal with the Reads data which score is lower than Q20.
HISAT2 v2.0.5 is used to compared the clean reads with Control genes.
HTSeq(0.9.1) is used to analysis the Read Count value.
DESeq software（1.20.0）is used to analysis the differential expression genes between two groups with the condition(|log2FoldChange| > 1 ，P value<0.05).

source_name: liver

extract_protocol: The RNA sequencing (RNA-seq) was detected by Shanghai Outdo Biotech company, China. Mouse liver tissue RNA was extract by Trizol Reagent (Invitrogen Life Technologies, USA). NovaSeq 6000(Illumina, USA) was used for sequencing of the cDNA library under PE150 model.

value: liver


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 191 ug/L, rep5

description:
T1Hf5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 16h, replicate 2

value: WT


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 191 ug/L, rep4

description:
T1Hf4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 191 ug/L, rep3

description:
T1Hf3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: AR2

description: Alcohol + Riboflavin(AR) 2


title: Parental, Arsenite .05mM, 16h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 191 ug/L, rep1

description:
T1Hf1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 191 ug/L, rep2

description:
T1Hf2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Alcohol 3

description: Alcohol 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 578 ug/L, rep5

description:
T1He5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 49 ug/L, rep5

description:
T1Hg5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Alcohol 1

description: Alcohol 1


title: Parental, Arsenite .05mM, 8h, replicate 3


title: Alcohol 2

description: Alcohol 2


title: Control 16S rRNA-seq 1

description: Control


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 578 ug/L, rep4

description:
T1He4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 578 ug/L, rep2

description:
T1He2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 578 ug/L, rep1

description:
T1He1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 4h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 578 ug/L, rep3

description:
T1He3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 8h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 49 ug/L, rep2

description:
T1Hg2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 1790 ug/L, rep5

description:
T1Hd5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 8h, replicate 1


title: C3

description: Control 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 1790 ug/L, rep3

description:
T1Hd3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: AR1

description: Alcohol + Riboflavin(AR) 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 1790 ug/L, rep2

description:
T1Hd2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 4h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 1790 ug/L, rep4

description:
T1Hd4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: C1

description: Control 1


title: C2

description: Control 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 1790 ug/L, rep1

description:
T1Hd1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 2h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 7061 ug/L, rep5

description:
T1Hc5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 7061 ug/L, rep4

description:
T1Hc4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 2h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 7061 ug/L, rep3

description:
T1Hc3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 2h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 7061 ug/L, rep2

description:
T1Hc2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 7061 ug/L, rep1

description:
T1Hc1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 23251 ug/L, rep5

description:
T1Hb5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Arsenite .05mM, 4h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 23251 ug/L, rep4

description:
T1Hb4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 24h, replicate 3


title: Tg_NMN_B39

city: Philadelphia

first: Joseph

last: Baur

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
DESeq2
Assembly: GRCm39
Supplementary files format and content: Excel File, deglists

source_name: heart

extract_protocol:
Qiagen RNEAsy Kits were used to extract RNA
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: mice were given treated water (500mg/kg) which was changed biweekly at the same time as doxycycline chow for 16-20 weeks

value: heart

value: transgenic shFxn

value: NMN


title: Tg_NMN_B36


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 23251 ug/L, rep2

description:
T1Hb2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 24h, replicate 2

value: Dim .195 nM


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 23251 ug/L, rep3

description:
T1Hb3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NMN_B35


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 65395 ug/L, rep5

description:
T1Ha5
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 24h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 65395 ug/L, rep4

description:
T1Ha4
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 65395 ug/L, rep3

description:
T1Ha3
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 16h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 65395 ug/L, rep2

description:
T1Ha2
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 65395 ug/L, rep1

description:
T1Ha1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_B28

value: NR


title: Tg_NMN_B40


title: Parental, Dim .195 nM, 16h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep17

description:
T7VBh8
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl


title: Tg_NR_B27


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep16

description:
T7VBg7
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 16h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep14

description:
T7VBe5
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 8h, replicate 3


title: Tg_NMN_B37


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep15

description:
T7VBf6
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_B26


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-24hpf, 23251 ug/L, rep1

description:
T1Hb1
PFHxS_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 8h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep13

description:
T7VBd4
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep12

description:
T7VBc3
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_B24


title: Tg_B23


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep10

description:
T7VBa1
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 8h, replicate 1


title: Tg_NR_B31


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep8

description:
T7VAg7
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep9

description:
T7VAh8
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep7

description:
T7VAf6
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Tg_B16


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep6

description:
T7VAe5_rep
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 4h, replicate 2


title: Parental, Dim .195 nM, 4h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep5

description:
T7VAe5
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep4

description:
T7VAd4
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: WT_B9

value: WT C57BL6J


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep3

description:
T7VAc3
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Tg_B15


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep16

description:
T6VBh8
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 2h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep1

description:
T7VAa1
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep2

description:
T7VAb2
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep14

description:
T6VBf6
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: WT_B7


title: Tg_B20


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep15

description:
T6VBg7
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 2h, replicate 2


title: Parental, UT, 24h, replicate 3

value: UT


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep13

description:
T6VBe5
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: WT_B5


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep12

description:
T6VBd4
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 2h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep11

description:
T6VBc3
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: WT_B8


title: WT_B4


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep10

description:
T6VBb2
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, Dim .195 nM, 4h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep9

description:
T6VBa1
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NMN_F_A44


title: Parental, UT, 24h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep8

description:
T6VAh8
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep7

description:
T6VAg7
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep6

description:
T6VAf6
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 16h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep5

description:
T6VAe5
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 16h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep3

description:
T6VAc3
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_F_A38


title: Parental, UT, 16h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep1

description:
T6VAa1
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep2

description:
T6VAb2
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 24h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep16

description:
T5VBh8
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Tg_F_A35


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep14

description:
T5VBf6
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 8h, replicate 2


title: WT_F_A32


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep13

description:
T5VBe5
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Tg_F_A34


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep15

description:
T5VBg7
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep12

description:
T5VBd4
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 8h, replicate 1


title: Tg_NMN_F_A43


title: Parental, UT, 4h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep11

description:
T5VBc3
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep10

description:
T5VBb2
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: WT_F_A30


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep9

description:
T5VBa1
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep8

description:
T5VAh8
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_F_A39


title: whole body zebrafish embyro, VehicleControl, 48-120hpf, rep4

description:
T6VAd4
Ctrl_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt
PFOA_T6_ZF_counts.filtered.+1.normFinal.txt
PFOS_T6_ZF_counts.filtered.+1.normFinal.txt


title: WT_F_A31


title: Parental, UT, 4h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep7

description:
T5VAg7
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: Parental, UT, 4h, replicate 1


title: WT_F_A29


title: Parental, UT, 8h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep6

description:
T5VAf6
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: WT_F_A28


title: Parental, UT, 0h, replicate 3


title: U937+ 10ug Fentanyl - replicate 2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

description:
miJTB736
countsTable.tab

data_processing:
Fastq files for downstream data analysis were automatically generated with Illumina BaseSpace Sequence Hub. Standard bioinformatic analysis was performed with BaseSpace app RNA-Seq Alignment v2.0.2 followed by RNA-Seq Differential Expression app version 1.0.1.
bcl files were demultiplexed and converted to fastq files using bcl2fastq
adaptes were trimmed and trimmed reads of length between 16 and 30 nucleotides were kept
fastq seqences were aligned to hg19 using bowtie
differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: tab-delimited file representing raw counts with miRNAs in rows and samples in columns

source_name: Peripheral blood

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% heat inactivated FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA of fentanyl-treated and untreated U937 cells was isolated using the commercially available miRNA Isolation Kit (miVana; Applied Biosystems; Carlsbad, CA) according to the manufacturer's protocol. A NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific; Waltham, MA) was used to determine total RNA concentration and purity. A 2100 Bioanalyzer (Agilent; Santa Clara, CA) and agarose electrophoresis were used to assess RNA integrity.
NEBNext small RNA sample library preparation kit (NEB; Ipswich, MA) was used to prepare the library with a modified approach for precise miRNA library size selection that allowed the kit to process low input and low-quality RNA with higher library recovery and miRNA read alignment. After 15 cycles of PCR with 100 ng total RNA as input, the libraries with unique indices were pooled, column cleaned, and combined with a custom-designed DNA ladder containing 135 and 146 base pairs (bp) purified PCR amplicon. This size range corresponds to a 16-27 nt insert miRNA library that covers all miRNAs. Agarose gel electrophoresis and gel excision were carried out. The library pool ranging from 135 to 146 bp, including the DNA marker, was gel purified and quantified using the NEBNext Library Quant kit (NEB) in the QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific; Waltham, MA). The first round of sequencing was performed using an Illumina Nextseq 550 sequencer to generate a few million reads to measure the relative concentration of each library. For the final data analysis, the capacity of each library was adjusted to generate the predicted number of equal reads from each sample.

treatment_protocol: Cells were treated with 10ug of fentanyl for 24 hours

value: Peripheral blood

tag: cell type

value: Macrophage cell line

value: Wild type

value: 10ug Fentanyl


title: U937+ 10ug Fentanyl - replicate 1

description:
miJTB734
countsTable.tab


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep5

description:
T5VAd4
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type


title: U937 No drug control - replicate 2

description:
miJTB735
countsTable.tab

value: No drug control


title: Parental, UT, 0h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep4

description:
T5VAc3
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt

value: embryo

value: No


title: WT_A26

value: heart


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep3

description:
T5VAb2
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: WT_A24


title: ATF4KO, DmrPERK, Dim .195, 24h, replicate 3

growth_protocol: U2OS cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma) and 1X antibiotic-antimycotic solution (Gibco) supplemented with 1X NEAA (Sigma) and 55nM beta mercaptoethanol (Gibco) for at least 24 hours prior to experimentation. Cells were housed in an incubator at 37°C, 5% CO2, 20% O2 and passaged every 2-3 days with trypsin.

value: U2OS Dmr-PERK


title: Parental, UT, 0h, replicate 1

value: WT


title: siS6K2_sgS6K1_rep3

first: David

middle: R.

last: Plas

address: 3125 Eden Ave.

department: Department of Cancer Biology

description: Sample 21

data_processing:
Fastq files for downstream data analysis were automatically generated via Illumina BaseSpace Sequence Hub after sequencing.
Alignment to reference genome hg19 was performed via the BaseSpace app RNA-Seq Alignment v1.1.1, using STAR.
To identify differentially expressed genes, standard bioinformatic was performed via Cufflinks Assembly & DE v2.1.0
Genome_build: Homo Sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts for each gene and sample
Supplementary_files_format_and_content: Gene-level differential expression (Cuffdiff output). Tests differences in the summed FPKM of transcripts sharing each gene_id

source_name: Glioblastoma

growth_protocol: LN229 cells were obtained from the American Type Culture Collection (ATCC). These cell lines were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS (Gibco), Penstrep and L-Glutamine.

extract_protocol:
RNA was extracted from the transfected LN229 cell line using TRIzol (Thermo fisher, Australia; cat 15596026) according to the manufacturer’s instructions. RNA samples were treated with 2 Units/μL of rDNase I enzyme for 10× DNase I Buffer and incubated at 37 °C for 30 min. The reaction was inactivated by adding DNase Inactivation Reagent.
Directional poly A RNA-sequencing was carried out by the Genomics, Epigenomics and Sequencing Core at the University of Cincinnati using standard protocols as established previously (PMID: 31120332 and 31420676). Briefly, total RNA was analyzed to check the quality with the help of Bioanalyzer (Agilent, Santa Clara, CA). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used to isolate poly A RNA meant for library preparation. RNA used was 1 µg of good quality as input. Next step was to enrich the polyA RNA with SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Library preparation was performed by NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) under PCR cycle number of 8. Once the library QC and quantification was done with real-time qPCR (NEBNext Library Quant Kit, New England BioLabs), individually numbered libraries were sequenced by NextSeq 550 sequencer (Illumina, San Diego, CA). Sequencing setting was kept as single read 1x85 bp.

treatment_protocol: sgNT, sgS6K1 ex5 and sgS6K2 ex9 LN229 cells were plated in 6-well plate at a density of 100,000 cells per plate in DMEM containing 10% FBS, Penstrep and L-Glutamine for 24 hours. After incubation for 24 hours, cells were transfected with 30nM siRNAs targeting NT, S6K1, S6K2 in OptiMEM and serum free media (DMEM) using Lipofectamine 3000 reagent for 72 hours. After 72 hours of transfection, cells were subjected to RNA isolation.

value: Brain; Right frontal parieto-occipital cortex

tag: disease

value: Glioblastoma

tag: morphology

value: epithelial

tag: si rna

value: siS6K2 and sgS6K1


title: U937 No drug control - replicate 1

description:
miJTB733
countsTable.tab

tag: tissue

tag: genotype


title: WT_A23

value: WT C57BL6J

tag: treatment


title: Tg_NMN_F_A20

value: transgenic shFxn

value: NMN


title: ATF4KO, DmrPERK, Dim .195, 24h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 24-120hpf, rep1

description:
T5VAa1
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl


title: whole body zebrafish embyro, VehicleControl, 24-120 hpf, rep2

description:
T5VAa5
Ctrl_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt
PFOS_T5_ZF_counts.filtered.+1.normFinal.txt


title: ATF4KO, DmrPERK, Dim .195, 24h, replicate 1


title: WT_A22


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep16

description:
T4VBh8
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: siS6K2_sgNon-Targeting_rep3

description: Sample 18

value: siS6K2 and sgNT


title: ATF4KO, DmrPERK, Dim .195, 16h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep15

description:
T4VBg7
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: ATF4KO, DmrPERK, Dim .195, 16h, replicate 2


title: Tg_NR_F_A16

value: NR


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep14

description:
T4VBf6
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: siS6K2_sgNon-Targeting_rep2

description: Sample 17


title: siS6K2_sgNon-Targeting_rep1

description: Sample 16


title: Tg_NMN_F_A18


title: ATF4KO, DmrPERK, Dim .195, 16h, replicate 1


title: ATF4KO, DmrPERK, Dim .195, 8h, replicate 3


title: siS6K1_sgS6K2_rep2

description: Sample 14

value: siS6K1 and sgS6K2


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep12

description:
T4VBd4
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: embryo

value: No


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep13

description:
T4VBe5
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: Tg_NR_F_A15

value: heart


title: siS6K2_sgS6K1_rep2

description: Sample 20


title: ATF4KO, DmrPERK, Dim .195, 8h, replicate 2

value: U2OS Dmr-PERK


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep11

description:
T4VBc3
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: siS6K1_sgS6K2_rep1

description: Sample 13

value: Brain; Right frontal parieto-occipital cortex


title: siS6K1_sgS6K2_rep3

description: Sample 15

value: Glioblastoma


title: Tg_F_A12


title: ATF4KO, DmrPERK, Dim .195, 8h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep10

description:
T4VBb2
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: Tg_F_A11


title: Tg_NMN_F_A19


title: siS6K1_sgNon-Targeting_rep3

description: Sample 12

value: epithelial

value: siS6K1 and sgNT


title: siS6K2_sgS6K1_rep1

description: Sample 19

value: siS6K2 and sgS6K1


title: ATF4KO, DmrPERK, Dim .195, 4h, replicate 3


title: Tg_F_A10

value: transgenic shFxn


title: siS6K1_sgNon-Targeting_rep2

description: Sample 11


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep8

description:
T4VAh8
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: ATF4KO, DmrPERK, Dim .195, 4h, replicate 2


title: Tg_NMN_A8

value: NMN


title: whole body zebrafish embyro, VehicleControl, 96-120hpf, rep11

description:
T7VBb2
Ctrl_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt
PFOA_T7_ZF_counts.filtered.+1.normFinal.txt
PFOS_T7_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep9

description:
T4VBa1
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: ATF4KO, DmrPERK, Dim .195, 4h, replicate 1


title: siNon-Targeting_sgS6K2_rep3

description: Sample 9

value: siNT and sgS6K2


title: ATF4KO, DmrPERK, Dim .195, 2h, replicate 3


title: ATF4KO, DmrPERK, Dim .195, 2h, replicate 2


title: Tg_NR_A6


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep5

description:
T4VAe5
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: ATF4KO, DmrPERK, Dim .195, 2h, replicate 1


title: Tg_NR_A4

value: NR


title: Tg_NR_A5


title: siNon-Targeting_sgS6K1_rep3

description: Sample 6

value: siNT and sgS6K1


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep3

description:
T4VAc3
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep4

description:
T4VAd4
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: siNon-Targeting_sgS6K1_rep2

description: Sample 5


title: ATF4KO, DmrPERK, NT, 0h, replicate 3

value: NT


title: ATF4KO, DmrPERK, NT, 0h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep7

description:
T4VAg7
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt

value: No


title: ATF4KO, DmrPERK, NT, 0h, replicate 1

value: U2OS Dmr-PERK


title: siNon-Targeting_sgS6K1_rep1

description: Sample 4

value: Brain; Right frontal parieto-occipital cortex


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep1

description:
T4VAa1
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: RNA-seq, SP140 IFNAR KO, untreated, rep 3

city: Berkeley

first: Russell

last: Vance

state: CA

address: Life Sciences Addition, University of California, Berkeley

institute: University of California, Berkeley

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=r k=23 mink=11 hdist=1 qtrim=r trimq=10 tpe tbo' and mapped to mm10 using hisat2 v2.1.0 with options ‘--no-softclip -k 100 | samtools view -q 10 -Sb - | samtools sort’.
Differentially expressed genes were called using DESeq2 v1.38.3 with design '~batch+genotype+treatment+genotype:treatment'. For the CRISPR KO differential expression analysis, normalized count data is derived from DESeq2 comparisons between: 1) SP140-KO & IFNAR-KO treated with DMXAA (3 replicates) vs IFNAR-KO treated with DMXAA (3 replicates); and 2) SP140-KO & IFNAR-KO untreated (3 replicates) vs IFNAR-KO untreated (3 replicates). Genes with zero counts across all samples were removed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including DESeq2 raw and normalized counts

source_name: bone marrow derived macrophage

extract_protocol:
Total RNA was isolated with the Omega Biotek Total RNA II kit, and DNAse-treated with TURBO DNAse (ThermoFisher Scientific, AM2238) according to manufacturer instructions.
RNA was polyA selected, and libraries were prepared with  KAPA HyperPrep reagents (Roche) after heat fragmentation. Libraries were subsequently size selected between 450-500 bp.

value: bone marrow derived macrophage

value: UT


title: Tg_A1

value: heart


title: Tg_NMN_A7


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep2

description:
T4VAb2
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: WT, DmrPERK, Dim .195, 24h, replicate 3

value: WT


title: whole body zebrafish embyro, VehicleControl, 6-120hpf, rep6

description:
T4VAf6
Ctrl_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt
PFOS_T4_ZF_counts.filtered.+1.normFinal.txt


title: siNon-Targeting_sgS6K2_rep2

description: Sample 8

value: Glioblastoma

value: epithelial


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep16

description:
T3VBh8
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl


title: WT, DmrPERK, Dim .195, 24h, replicate 2


title: siNon-Targeting_sgNon-Targeting_rep2

description: Sample 2

value: siNT and sgNT


title: RNA-seq, SP140 IFNAR KO, untreated, rep 2


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep15

description:
T3VBg7
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: siNon-Targeting_sgS6K2_rep1

description: Sample 7

value: siNT and sgS6K2


title: RNA-seq, SP140 IFNAR KO, untreated, rep 1


title: Tg_A2

value: transgenic shFxn


title: siNon-Targeting_sgNon-Targeting_rep1

description: Sample 1


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep14

description:
T3VBf6
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: RNA-seq, IFNAR KO, untreated, rep 3

value: IFNAR KO


title: 10T, DNMT3A-W330R-Ubmutant, H2AK119Ub, Cut&Run, R2

city: New York City

first: Kristjan

middle: H.

last: Gretarsson

state: New York

institute: Columbia University

library_source: genomic

data_processing:
Alignment was performed using Bowtie2 v.2.2.5, with multi-aligned, duplicates, and blacklist regions removed
Bigwigs were generated using Deeptools v.3.5.1
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: Cut&Run

molecule: genomic DNA

growth_protocol:
10T cells: Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS)
QKO mESC: mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol

extract_protocol:
CUT&RUN reaction: 500K cells were dispensed to individual wells of a 96-well plate, immobilized onto Concanavalin-A beads, and incubated overnight (4°C) with 0.5 µg of antibody. pAG-MNase was added and activated (2 hours @ 4°C) and CUT&RUN enriched DNA purified using Serapure beads.
Recovered DNA was quantified using PicoGreen and reactions were normalized to 5ng DNA (or entirety of the reaction if <5ng DNA was recovered) before preparing sequencing libraries (CUTANA CUT&RUN Library Prep kit; EpiCypher #14-1001)

value: mouse mesenchymal stem cell

tag: antibody


title: WT, DmrPERK, Dim .195, 16h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep13

description:
T3VBe5
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: strain

value: embryo

value: No


title: siS6K1_sgNon-Targeting_rep1

description: Sample 10

value: Brain; Right frontal parieto-occipital cortex

value: siS6K1 and sgNT


title: RNA-seq, IFNAR KO, untreated, rep 2

value: bone marrow derived macrophage

value: UT


title: RNA-seq, IFNAR KO, untreated, rep 1


title: 10T, DNMT3A-W330R-Ubmutant, H3K4me3, Cut&Run, R2

value: H3K4me3, EpiCypher #13-0041


title: WT, DmrPERK, Dim .195, 16h, replicate 1

value: U2OS Dmr-PERK

value: WT


title: WT, DmrPERK, Dim .195, 24h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep11

description:
T3VBb2
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: age

value: VehicleControl


title: siNon-Targeting_sgNon-Targeting_rep3

description: Sample 3

value: Glioblastoma

value: epithelial

value: siNT and sgNT


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep12

description:
T3VBc3
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

tag: developmental stage


title: WT, DmrPERK, Dim .195, 16h, replicate 2


title: RNA-seq, SP140 IFNAR KO, DMXAA treated, rep 3

value: 100 ug/mL DMXAA, 4 hous


title: WT, DmrPERK, Dim .195, 8h, replicate 3


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep10

description:
T3VBa4
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type

tag: biological replicate


title: 10T, DNMT3A-W330R-R181E, H2AK119Ub, Cut&Run, R2

value: mouse mesenchymal stem cell


title: WT, DmrPERK, Dim .195, 8h, replicate 2


title: RNA-seq, SP140 IFNAR KO, DMXAA treated, rep 2


title: RNA-seq, SP140 IFNAR KO, DMXAA treated, rep 1


title: 10T, DNMT3A-W330R-R181E, H3K27me3, Cut&Run, R2

value: H3K27me3, EpiCypher #13-0055


title: 10T, DNMT3A-W330R-Ubmutant, IgG, Cut&Run, R2

value: IgG, EpiCypher #13-0042


title: WT, DmrPERK, Dim .195, 8h, replicate 1


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep8

description:
T3VAh8
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: embryo

tag: time code

value: No


title: RNA-seq, IFNAR KO, DMXAA treated, rep 3

value: bone marrow derived macrophage

value: IFNAR KO


title: 10T, DNMT3A-W330R-R181E, H3K4me3, Cut&Run, R2

value: H3K4me3, EpiCypher #13-0041


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep7

description:
T3VAg7
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: dose (ug/l)


title: RNA-seq, IFNAR KO, DMXAA treated, rep 2


title: 10T, DNMT3A-W330R-R181E, IgG, Cut&Run, R2


title: WT, DmrPERK, Dim .195, 4h, replicate 3

value: U2OS Dmr-PERK


title: RNA-seq, IFNAR KO, DMXAA treated, rep 1


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep6

description:
T3VAf6
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: repeat sample


title: WT, DmrPERK, Dim .195, 4h, replicate 1

tag: cell line

value: WT


title: 10T, DNMT3A-W330R-Ubmutant, H3K27me3, Cut&Run, R2


title: WT, DmrPERK, Dim .195, 2h, replicate 3

tag: time


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep5

description:
T3VAe5
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep9

description:
T3VBa1
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt


title: 10T, DNMT3A-W330R, H3K4me3, Cut&Run, R2

tag: cell type


title: 10T, DNMT3A-W330R, H3K27me3, Cut&Run, R2


title: 10T, DNMT3A-W330R, H2AK119Ub, Cut&Run, R2


title: 10T, DNMT3A-W330R, IgG, Cut&Run, R2


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep4

description:
T3VAd4
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt


title: WT, DmrPERK, Dim .195, 2h, replicate 2


title: mESC TKO, DNMT3A1-Ubmutant, Emseq, R2

data_processing:
Raw reads were filtered with trim galore (--paired) and aligned to the mouse genome (GRCm39) using Bismark with the functions bismark and bismark_methylation_extractor(--no_overlap --ignore 3 --ignore_r2 2 --ignore_3prime 2 --ignore_3prime_r2 2) to generate bismark CpG coverage files
Assembly: GRCm39
Supplementary files format and content: bismark CpG coverage file
Library strategy: EnzymaticMethyl-seq

source_name: mESC QKO

growth_protocol: QKO or TKO mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol

extract_protocol:
Genomic DNA was purified using the NEB Monarch Genomic DNA Extraction kit and 10 ng sheared to an average fragment size of ~300 bp for enzymatic conversion. Prior to sonication, fully 5mC methylated pUC19 (0.01 ng) and fully unmethylated lambda DNA (0.02 ng) were spiked into each reaction to monitor conversion efficiency.
After nine cycles of PCR, library quality and quantification were assessed on the Agilent Tapestation 4200. Libraries were sequenced on an Illumina NovaSeq 6000 to generate 100-bp paired-end reads.

value: mESC QKO

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-Ubmutant


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep3

description:
T3VAc3
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: mESC TKO, DNMT3A1-R181E, Emseq, R2

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-R181E


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep2

description:
T3VAb2
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: mESC TKO, DNMT3A1-W330R, Emseq, R2

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-W330R


title: mESC TKO, DNMT3A1-WT, Emseq, R2

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-WT


title: WT, DmrPERK, NT, 0h, replicate 3

value: NT


title: WT, DmrPERK, Dim .195, 4h, replicate 2


title: 10T, DNMT3A-WT, H2AK119Ub, Cut&Run, R2

value: mouse mesenchymal stem cell


title: whole body zebrafish embyro, VehicleControl, 24-48hpf, rep1

description:
T3VAa1
Ctrl_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt
PFOS_T3_ZF_counts.filtered.+1.normFinal.txt

value: embryo

value: No


title: mESC TKO, DNMT3A1-R181E, Emseq, R1


title: WT, DmrPERK, NT, 0h, replicate 2


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep23

description:
T2VBh8
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: mESC TKO, DNMT3A1-Ubmutant, Emseq, R1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep22

description:
T2VBg7
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: 10T, DNMT3A-WT, H3K27me3, Cut&Run, R2

value: H3K27me3, EpiCypher #13-0055


title: mESC TKO, DNMT3A1-W330R, Emseq, R1


title: 10T, DNMT3A-WT, H3K4me3, Cut&Run, R2

value: H3K4me3, EpiCypher #13-0041


title: F

city: Guangzhou

first: Haolin

last: Yang

address: The Third Affiliated Hospital of Guangzhou University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNAs. miRBase20.0 was used as the reference, and the modified software mirdeep2 and sRNA-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The software miREvo and mirdeep2 were integrated to predict novel miRNAs.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Gene Ontology (GO) enrichment analysis was used on the target gene candidates of differentially expressed miRNAs.We used KOBAS (Maoet al., 2005) software to test the statistical enrichment of the target gene candidates in KEGG pathways.
Assembly: Homo Sapiens(GRCh38/hg38)

source_name: bone

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: bone

tag: disease state

value: orthopedic surgery patients

tag: Sex

value: Male


title: WT, DmrPERK, Dim .195, 2h, replicate 1

value: U2OS Dmr-PERK

value: WT


title: mESC TKO, DNMT3A1-WT, Emseq, R1

value: mESC QKO

value: Mouse Embryonic Stem cell


title: IgG CUT&RUN, WT cells

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the mm10 assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome were removed. Peak calling was performed using complete and size subsetted alignment files with MACS2 v2.1.1 with paired-end options ‘--format BAMPE --pvalue 0.01 --SPMR -B --call-summits’. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Assembly: mm10
Supplementary files format and content: signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format
Library strategy: CUT&RUN

extract_protocol:
Sp140–/– BMMs were retrovirally transduced with HA-SP140 or SP140, and stimulated for 8 hours with 100 mg/mL DMXAA. Half a million cells were input into CUT&RUN in biological triplicates using the Epicypher CUTANATM ChIC/CUT&RUN kit (Epicypher, 14-1048), using 0.5 mg of rabbit anti-HA monoclonal antibody (Cell Signaling Technologies, C29F4) with E. coli genomic DNA spike-in. Non-transduced B6 BMMs (0.5 e6) were also put into CUT&RUN with 0.5 mg of rabbit isotype control IgG (Epicypher, 13-0042), with a single biological replicate. CUT&RUN was carried out according to kit instructions.
Libraries were prepared using the Epicypher CUTANATM CUT&RUN library prep kit (Epicypher, 14-1001) according to kit instructions

value: bone marrow derived macrophage

value: 100 ug/mL DMXAA, 8 hrs


title: 10T, DNMT3A-W330R-Ubmutant, H3K4me3, Cut&Run, R1


title: 10T, DNMT3A-W330R-Ubmutant, H3K27me3, Cut&Run, R1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep21

description:
T2VBf9
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type

value: VehicleControl


title: D

institute: Guangzhou University of Chinese Medicine


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep19

description:
T2VBe8
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep18

description:
T2VBe5
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: C

value: Female


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep17

description:
T2VBd4
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: anti HA CUT&RUN, untagged SP140, replicate 1


title: anti HA CUT&RUN, untagged SP140, replicate 2


title: anti HA CUT&RUN, untagged SP140, replicate 3


title: WT, DmrPERK, NT, 0h, replicate 1

value: NT


title: 10T, DNMT3A-W330R-Ubmutant, IgG, Cut&Run, R1

value: mouse mesenchymal stem cell

value: IgG, EpiCypher #13-0042


title: E

value: bone


title: 10T, DNMT3A-WT, IgG, Cut&Run, R2


title: B

value: orthopedic surgery patients


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep20

description:
T2VBf6
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: No


title: 10T, DNMT3A-W330R-R181E, H2AK119Ub, Cut&Run, R1


title: A

value: Male


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep15

description:
T2VBc3
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: anti HA CUT&RUN, HA-SP140, replicate 3

value: SP140 KO + HA-SP140


title: 10T, DNMT3A-W330R-Ubmutant, H2AK119Ub, Cut&Run, R1


title: anti HA CUT&RUN, HA-SP140, replicate 2


title: 10T, DNMT3A-W330R-R181E, H3K27me3, Cut&Run, R1

value: H3K27me3, EpiCypher #13-0055


title: 10T, DNMT3A-W330R-R181E, IgG, Cut&Run, R1


title: H929 con3-bio rep 1

city: Xuzhou

first: Yao

last: Yao

state: Jiangsu

address: #84 Huaihai west RD

institute: Associate professor, Xuzhou Medical University

data_processing:
fastp, Version 0.19.5; HISAT2, Version 2.1.0; StringTie, Version 2.1.0; RSEM, Version 1.3.3.
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.  RSEM was used to quantify  gene  abundances.
Assembly: GRCh38.p13
Supplementary files format and content: txt file includes raw counts data of each sample
Supplementary files format and content: txt file includes TPM data of each sample

growth_protocol: H929 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37℃ and 5% CO2.

extract_protocol:
Cells were harvested and total RNA was extracted using TRIzol Reagent. Only 1μg RNA with high quality was used to construct sequencing library.
Paired-end  RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer in accordance with the manufacturer’s protocol.

treatment_protocol: H929 cells were treated with 1μM Mi-2 or DMSO for 24 hours.

value: multiple myeloma cells

value: WT

value: DMSO treatment for 24 hours


title: CAR-T_pre_KO

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

data_processing:
Using next-generation sequencing with high-throughput sequencing technology (https://jp.illumina.com/content/dam/illumina-marketing/apac/japan/documents/pdf/2012_illumina_techsupport_session1.pdf), we obtained the nucleotide sequences of library-prepared samples.
The quality of the raw paired-end sequence reads was assessed with FastQC and Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads for mapping were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0)
Assembly: hg38
Supplementary files format and content: The raw read counts were normalized with transcripts per million (TPM).

source_name: PBMC

extract_protocol:
On day 12, the CD8α+ and CAR+ cells sorted by a cell sorter (Sony) were used as an RNA sequencing of pre-sample. Regarding post-samples, T cells were subjected to the repeated stimulation assay in 6-well plates, transferring T cells to freshly seeded cancer cells (A549) every 48-72 hours. Cultured T cells were sorted after chronic stimulation using cell sorter (Sony) to obtain a pure population of HER2 CAR positive CD8α+ T cells from the co-cultures with target cancer cells. Total RNA from pre and post-CAR T cells was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530) following manufacture's protocol

value: PBMC

value: CD8+ T cell


title: corpus callosum, double knockout, biol rep4

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files containing counts and DESeq results

source_name: corpus callosum

extract_protocol:
Animals were sacrificed 21 days after the first tamoxifen injection and corpus callosum was dissected. RNA was prepared using Trizol (Invitrogen). Following Dnase treatment samples were cleaned up using the RNeasy Mini Kit (Quiagen).
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.

treatment_protocol: Oligodendroglial knockout of Sox-genes was induced by  injection of 10mg/ml tamoxifen for five consecutive days starting at postnatal day 60.

value: corpus callosum

value: Sox8fl/fl Sox10fl/fl Plp1::CreERT2/+

value: tamoxifen injection


title: 10T, DNMT3A-W330R-R181E, H3K4me3, Cut&Run, R1

value: H3K4me3, EpiCypher #13-0041


title: Tg_NR_F_A14

value: heart

value: transgenic shFxn

value: NR


title: anti HA CUT&RUN, HA-SP140, replicate 1

value: bone marrow derived macrophage

value: 100 ug/mL DMXAA, 8 hrs


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep16

description:
T2VBd1
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type

value: embryo

value: VehicleControl

value: No


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep12

description:
T2VBa1_rep
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: Yes


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep13

description:
T2VBb2
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: corpus callosum, double knockout, biol rep3


title: 10T, DNMT3A-W330R, H2AK119Ub, Cut&Run, R1

value: mouse mesenchymal stem cell


title: CAR-T_pre_WT

value: PBMC

value: CD8+ T cell


title: H929 con2-bio rep 1

value: multiple myeloma cells

value: WT

value: DMSO treatment for 24 hours


title: H929 treat3-bio rep 1

value: 1μM Mi-2 treatment for 24 hours


title: corpus callosum, double knockout, biol rep1

value: corpus callosum

value: Sox8fl/fl Sox10fl/fl Plp1::CreERT2/+

value: tamoxifen injection


title: 10T, DNMT3A-W330R, IgG, Cut&Run, R1

value: IgG, EpiCypher #13-0042


title: 10T, DNMT3A-W330R, H3K27me3, Cut&Run, R1

value: H3K27me3, EpiCypher #13-0055


title: H929 con1-bio rep 1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep11

description:
T2VBa1
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep14

description:
T2VBb6
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: embryo

value: VehicleControl


title: corpus callosum, double knockout, biol rep2


title: 10T, DNMT3A-W330R, H3K4me3, Cut&Run, R1

value: H3K4me3, EpiCypher #13-0041


title: 10T, DNMT3A-WT, H2AK119Ub, Cut&Run, R1

value: mouse mesenchymal stem cell


title: H929 treat1-bio rep 1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep9

description:
T2VAg7
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: No


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep10

description:
T2VAh8
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: corpus callosum, Sox10 knockout, biol rep3

value: Sox10fl/fl Plp1::CreERT2/+


title: 10T, DNMT3A-WT, H3K27me3, Cut&Run, R1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep8

description:
T2VAf6_rep
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: Yes


title: corpus callosum, Sox10 knockout, biol rep2


title: IdU-treated, replicate 2

city: San Francisco

first: Binyamin

last: Zuckerman

institute: UCSF

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to hg38 reference genome and further processed using 10x Cell Ranger (7.0.1). Intronic reads were excluded.
Seurat was used to filter for high-quality homogeneous cell population using the following filters: 3000 < detected genes < 5000, 8000 < UMI counts < 15000, and <10% reads mapping to mitochondrial genes per cell. The resulting count matrix was then further filtered by the BASiCS_Filter function function from the BASiCS R package with default parameters, which limited the analysis to genes with sufficient sequencing coverage for reliable noise quantification.
The output count matrix consisted of 5988 and 5786 cells for DMSO samples and 5148 and 4701 cells for IdU samples across 1107 genes. This output was then used to run 5 normalization pipelines according to their protocols: SCTransform, scran, Linnorm, BASiCS, and SCnorm.
BASiCS was run with default parameters and recommended settings (N=20000, Thin=20 and Burn=10000) using the horizontal integration strategy (no-spikes). The other packages were run with default parameters.
Assembly: hg38
Supplementary files format and content: tsv files and matrix files
Supplementary files format and content: Jurkat_scRNAseq_processed_data.csv contains summary statistics of the data as analyzed by above-mentioned methods. For each sample, we calculated separately for each biological replicate the mean, CV2, and Fano values per gene and then averaged the values of both replicates for further analysis.

source_name: Jurkat T Lymphocytes

growth_protocol: Jurkat T Lymphocytes were cultured in RPMI-1640 medium (supplemented with L-glutamine, 10% fetal bovine serum, and 1% penicillin-streptomycin), at 37°C, 5% CO2, in humidified conditions.

extract_protocol:
Two biological replicates (4 samples) of single-cell suspensions were loaded on a Chromium X instrument using a Chromium Next GEM Single Cell 3' HT Kit v3.1 (10x Genomics)
Libraries were constructed following manufacturer's protocol.

treatment_protocol: Cells were treated with either DMSO or 20 uM IdU (I7125, Millipore Sigma) for 48h.

value: Jurkat T Lymphocytes

value: IdU


title: corpus callosum, Sox10 knockout, biol rep1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep6

description:
T2VAe5
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: 10T, DNMT3A-WT, IgG, Cut&Run, R1


title: 10T, DNMT3A-WT, H3K4me3, Cut&Run, R1


title: DMSO-treated, replicate 2

description: 10x Genomics

value: DMSO


title: H929 treat2-bio rep 1

value: multiple myeloma cells

value: WT

value: 1μM Mi-2 treatment for 24 hours


title: IdU-treated, replicate 1

description: 10x Genomics


title: QKO, H2AK119Ub, Cut&Run, R2

value: mESC QKO

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO + DNMT3A-WT


title: DMSO-treated, replicate 1

description: 10x Genomics


title: corpus callosum, Sox8 knockout, biol rep3

value: corpus callosum

value: Sox8fl/fl Plp1::CreERT2/+

value: tamoxifen injection


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep4

description:
T2VAc3
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type

value: embryo

value: VehicleControl


title: corpus callosum, Sox8 knockout, biol rep4


title: corpus callosum, Sox10 knockout, biol rep4

value: Sox10fl/fl Plp1::CreERT2/+