title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 1687 ug/L, rep2

description:
T5Ad2
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 571 ug/L, rep1

status: Public on Aug 28 2024

type: SRA

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

country: USA

institute: US EPA

description:
T5Ae1
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt

library_source: transcriptomic

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).

tag: tissue

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: treatment

tag: repeat sample

value: No


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 1687 ug/L, rep4

description:
T5Ad4
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 1687 ug/L, rep1

description:
T5Ad1
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 6461 ug/L, rep4

description:
T5Ac4
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 6461 ug/L, rep2

description:
T5Ac2
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 6461 ug/L, rep1

description:
T5Ac1
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 6461 ug/L, rep5

description:
T5Ac5
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 6461 ug/L, rep3

description:
T5Ac3
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 52 ug/L, rep2

description:
T5Ag2
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 15875 ug/L, rep5

description:
T5Ab5
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 15875 ug/L, rep3

description:
T5Ab3
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 15875 ug/L, rep2

description:
T5Ab2
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 15875 ug/L, rep1

description:
T5Ab1
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 57325 ug/L, rep2

description:
T5Aa2
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 57325 ug/L, rep4

description:
T5Aa4
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 57325 ug/L, rep5

description:
T5Aa5
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 57325 ug/L, rep3

description:
T5Aa3
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 57325 ug/L, rep1

description:
T5Aa1
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 1687 ug/L, rep3

description:
T5Ad3
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 16 ug/L, rep5

description:
T4Ah5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 16 ug/L, rep3

description:
T4Ah3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 16 ug/L, rep4

description:
T4Ah4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 16 ug/L, rep2

description:
T4Ah2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 52 ug/L, rep5

description:
T4Ag6
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 16 ug/L, rep1

description:
T4Ah1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 52 ug/L, rep4

description:
T4Ag5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 52 ug/L, rep2

description:
T4Ag3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 52 ug/L, rep1

description:
T4Ag1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 160 ug/L, rep4

description:
T4Af5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 160 ug/L, rep3

description:
T4Af4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 160 ug/L, rep2

description:
T4Af2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 160 ug/L, rep5

description:
T4Af6
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-120hpf, 15875 ug/L, rep4

description:
T5Ab4
PFOA_T5_UMI_ZF_counts_matrix.txt
PFOA_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 571 ug/L, rep4

description:
T4Ae4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 571 ug/L, rep3

description:
T4Ae3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 571 ug/L, rep1

description:
T4Ae1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 160 ug/L, rep1

description:
T4Af1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 571 ug/L, rep5

description:
T4Ae5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 1687 ug/L, rep3

description:
T4Ad3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 1687 ug/L, rep4

description:
T4Ad4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep6

description:
T4Ac5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep5

description:
T4Ac4_rep
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt

value: Yes


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 1687 ug/L, rep2

description:
T4Ad2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 52 ug/L, rep3

description:
T4Ag4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep3

description:
T4Ac3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep1

description:
T4Ac1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 15875 ug/L, rep2

description:
T4Ab2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 15875 ug/L, rep3

description:
T4Ab3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 15875 ug/L, rep4

description:
T4Ab4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 571 ug/L, rep2

description:
T4Ae2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 57325 ug/L, rep5

description:
T4Aa5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep2

description:
T4Ac2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 57325 ug/L, rep4

description:
T4Aa4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 57325 ug/L, rep3

description:
T4Aa3
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 15875 ug/L, rep1

description:
T4Ab1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 57325 ug/L, rep1

description:
T4Aa1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 16 ug/L, rep5

description:
T3Ah5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 1687 ug/L, rep5

description:
T4Ad5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 16 ug/L, rep4

description:
T3Ah4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 16 ug/L, rep3

description:
T3Ah3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 1687 ug/L, rep1

description:
T4Ad1
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 16 ug/L, rep1

description:
T3Ah1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 57325 ug/L, rep2

description:
T4Aa2
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 6461 ug/L, rep4

description:
T4Ac4
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 52 ug/L, rep5

description:
T3Ag5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 52 ug/L, rep3

description:
T3Ag3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 52 ug/L, rep4

description:
T3Ag4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 160 ug/L, rep5

description:
T3Af5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 16 ug/L, rep2

description:
T3Ah2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-120hpf, 15875 ug/L, rep5

description:
T4Ab5
PFOA_T4_UMI_ZF_counts_matrix.txt
PFOA_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 52 ug/L, rep1

description:
T3Ag1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 160 ug/L, rep2

description:
T3Af2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 160 ug/L, rep3

description:
T3Af3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 160 ug/L, rep4

description:
T3Af4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 571 ug/L, rep4

description:
T3Ae4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 571 ug/L, rep2

description:
T3Ae2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 571 ug/L, rep1

description:
T3Ae1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 1687 ug/L, rep5

description:
T3Ad5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 571 ug/L, rep3

description:
T3Ae3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 1687 ug/L, rep4

description:
T3Ad4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 160 ug/L, rep1

description:
T3Af1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 1687 ug/L, rep3

description:
T3Ad3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 1687 ug/L, rep1

description:
T3Ad1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 52 ug/L, rep2

description:
T3Ag2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 6461 ug/L, rep2

description:
T3Ac2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 6461 ug/L, rep4

description:
T3Ac4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 6461 ug/L, rep5

description:
T3Ac5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 15875 ug/L, rep3

description:
T3Ab3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 15875 ug/L, rep5

description:
T3Ab5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 15875 ug/L, rep4

description:
T3Ab4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 6461 ug/L, rep3

description:
T3Ac3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 6461 ug/L, rep1

description:
T3Ac1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 15875 ug/L, rep1

description:
T3Ab1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 57325 ug/L, rep3

description:
T3Aa3
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 57325 ug/L, rep4

description:
T3Aa4
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 57325 ug/L, rep5

description:
T3Aa5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 57325 ug/L, rep2

description:
T3Aa2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 57325 ug/L, rep1

description:
T3Aa1
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 571 ug/L, rep5

description:
T3Ae5
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 16 ug/L, rep5

description:
T2Ah5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 16 ug/L, rep4

description:
T2Ah4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 16 ug/L, rep1

description:
T2Ah1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 16 ug/L, rep2

description:
T2Ah2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 1687 ug/L, rep2

description:
T3Ad2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep6

description:
T2Ag5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep5

description:
T2Ag4_rep
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep4

description:
T2Ag4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep2

description:
T2Ag2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 24-48hpf, 15875 ug/L, rep2

description:
T3Ab2
PFOA_T3_UMI_ZF_counts_matrix.txt
PFOA_T3_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48 hpf, 160 ug/L, rep5

description:
T2Af6
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 160 ug/L, rep1

description:
T2Af1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 160 ug/L, rep2

description:
T2Af2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep1

description:
T2Ag1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 160 ug/L, rep4

description:
T2Af4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 571 ug/L, rep4

description:
T2Ae4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 571 ug/L, rep3

description:
T2Ae3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 571 ug/L, rep1

description:
T2Ae1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 571 ug/L, rep5

description:
T2Ae5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 1687 ug/L, rep5

description:
T2Ad5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 571 ug/L, rep2

description:
T2Ae2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 1687 ug/L, rep4

description:
T2Ad4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 1687 ug/L, rep3

description:
T2Ad3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 1687 ug/L, rep1

description:
T2Ad1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 1687 ug/L, rep2

description:
T2Ad2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 6461 ug/L, rep3

description:
T2Ac3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 6461 ug/L, rep2

description:
T2Ac2
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 6461 ug/L, rep4

description:
T2Ac5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 52 ug/L, rep3

description:
T2Ag3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 6461 ug/L, rep1

description:
T2Ac1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 15875 ug/L, rep4

description:
T2Ab6
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48 hpf, 15875 ug/L, rep5

description:
T2Ab7
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 15875 ug/L, rep2

description:
T2Ab4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 15875 ug/L, rep1

description:
T2Ab1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 15875 ug/L, rep3

description:
T2Ab5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48 hpf, 160 ug/L, rep3

description:
T2Af3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48 hpf, 57325 ug/L, rep5

description:
T2Aa6
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 57325 ug/L, rep4

description:
T2Aa5
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 57325 ug/L, rep2

description:
T2Aa3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 57325 ug/L, rep3

description:
T2Aa4
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 16 ug/L, rep4

description:
T1Ah3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 57325 ug/L, rep1

description:
T2Aa1
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 16 ug/L, rep5

description:
T1Ah5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48 hpf, 6461 ug/L, rep5

description:
T2Ac6
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 52 ug/L, rep5

description:
T1Ag5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 16 ug/L, rep1

description:
T1Ah1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 52 ug/L, rep1

description:
T1Ag1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 16 ug/L, rep3

description:
T1Ah2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 160 ug/L, rep2

description:
T1Af2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 160 ug/L, rep4

description:
T1Af4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 160 ug/L, rep1

description:
T1Af1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep4

description:
T1Ae4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep5

description:
T1Ae5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 52 ug/L, rep3

description:
T1Ag3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 160 ug/L, rep3

description:
T1Af3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 160 ug/L, rep5

description:
T1Af5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep6

description:
T1Ae5_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep2

description:
T1Ae2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep1

description:
T1Ae1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-48hpf, 16 ug/L, rep3

description:
T2Ah3
PFOA_T2_UMI_ZF_counts_matrix.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep7

description:
T1Ad5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 571 ug/L, rep3

description:
T1Ae3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 16 ug/L, rep2

description:
T1Ah10
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep6

description:
T1Ad4_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep5

description:
T1Ad4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep2

description:
T1Ad2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 52 ug/L, rep4

description:
T1Ag4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep4

description:
T1Ad3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 52 ug/L, rep2

description:
T1Ag2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep3

description:
T1Ad2_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 1687 ug/L, rep1

description:
T1Ad1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 6461 ug/L, rep5

description:
T1Ac5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 6461 ug/L, rep2

description:
T1Ac2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 6461 ug/L, rep1

description:
T1Ac1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 6461 ug/L, rep3

description:
T1Ac3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep7

description:
T1Ab5_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep6

description:
T1Ab5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep5

description:
T1Ab4_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep3

description:
T1Ab3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep4

description:
T1Ab4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep1

description:
T1Ab1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 15875 ug/L, rep2

description:
T1Ab2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep7

description:
T1Aa5_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: znf_siRNA_B3

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Adapters and poorly sequenced reads were removed with TrimGalore.
Pre-processed reads were assessed with FASTQC.
Processed reads were aligned to the mouse reference (GRCm39) genome using STAR.
DeepTools bamCoverage was used to convert BAM alignments to BigWiG Format.
Genomic features were quantified with FeatureCounts.
DESeq2 was used for feature normalization and differential gene expression analysis.
Assembly: GRCm39
Supplementary files format and content: BigWig file of aligned reads

organism: Mus musculus

source_name: whole cell extract

extract_protocol: RNA library construction was conducted by Novogene. RNA library construction input was total RNAs with rRNA depletion. Standard Illumina adapters used.

value: whole cell extract

tag: cell line

value: znf siRNA B


title: znf_siRNA_B1


title: znf_siRNA_A3

value: znf siRNA A


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep5

description:
T1Aa4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: znf_siRNA_B2


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep4

description:
T1Aa3
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: znf_siRNA_A1


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 6461 ug/L, rep4

description:
T1Ac4
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: neg_control_siRNA_B3

value: negative control scrambled siRNA B


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep3

description:
T1Aa2
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep2

description:
T1Aa1_rep
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: znf_siRNA_A2


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep1

description:
T1Aa1
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep6

description:
T7Hh5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: neg_control_siRNA_B1


title: neg_control_siRNA_A2

value: negative control scrambled siRNA A


title: neg_control_siRNA_A1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep5

description:
T7Hh4_rep
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep4

description:
T7Hh4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep2

description:
T7Hh2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep3

description:
T7Hh3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: fmrp_siRNA_B1

value: fmrp siRNA B


title: fmrp_siRNA_B2


title: fmrp_siRNA_A3

value: fmrp siRNA A


title: fmrp_siRNA_A2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 15 ug/L, rep1

description:
T7Hh1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 49 ug/L, rep4

description:
T7Hg4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 49 ug/L, rep5

description:
T7Hg5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Normalcontrol，9

city: Hefei

first: Chengyu

last: Xia

address: 17 Lujiang Road, Hefei City, Anhui Province, China

country: China

institute: USTC

data_processing:
Magnetic beads with Oligo (dT) were used for enrichment and purification, Fragmentation Buffer was added to make the fragments into short fragments, and then cDNA was synthesized with the fragmented mRNA as a template. After the library was constructed, Qubit 3.0 was used for preliminary quantification. Subsequently, Agilent 2100 was used to detect the insert size of the library. After the insert size was in line with expectations, Q-PCR was performed using Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN. The effective concentration of the library was accurately quantified to ensure the quality of the library. Quality-qualified libraries were sequenced using the Illumina platform. The sequencing strategy was PE150.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: Superficialtemporalartery

extract_protocol: Total RNA was extracted from the STA tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. The integrity and concentration of RNA were detected using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, Calif., USA), enriched and purified with Oligo (dT) -bearing magnetic beads. RNA sequencing was performed by Anoroad (Beijing, China).

tag: Sex

value: Male

value: Superficialtemporalartery

tag: cell type

value: artery

tag: disease

value: normal


title: fmrp_siRNA_A1


title: Normalcontrol，7

value: Female


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 49 ug/L, rep1

description:
T7Hg1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: Normalcontrol，8


title: neg_control_siRNA_B2


title: Normalcontrol，3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 49 ug/L, rep2

description:
T7Hg2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: Normalcontrol，2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 191 ug/L, rep4

description:
T7Hf4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 191 ug/L, rep3

description:
T7Hf3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

value: No


title: fmrp_siRNA_B3


title: Normalcontrol，1


title: neg_control_siRNA_A3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 191 ug/L, rep2

description:
T7Hf2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Moyamoyadisease，20

value: moyamoya disease


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 578 ug/L, rep5

description:
T7He5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Moyamoyadisease，15


title: Moyamoyadisease，18


title: Moyamoyadisease，13


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 578 ug/L, rep3

description:
T7He3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Moyamoyadisease，14


title: Moyamoyadisease，12


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 191 ug/L, rep1

description:
T7Hf1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFOA (CAS 45285-51-6), 6-24hpf, 57325 ug/L, rep6

description:
T1Aa5
PFOA_T1_UMI_ZF_counts_matrix.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 578 ug/L, rep1

description:
T7He1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 578 ug/L, rep2

description:
T7He2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 1790 ug/L, rep4

description:
T7Hd4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 1790 ug/L, rep5

description:
T7Hd5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 1790 ug/L, rep1

description:
T7Hd1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 1790 ug/L, rep3

description:
T7Hd3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 7061 ug/L, rep5

description:
T7Hc5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 7061 ug/L, rep4

description:
T7Hc4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 1790 ug/L, rep2

description:
T7Hd2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 578 ug/L, rep4

description:
T7He4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 7061 ug/L, rep3

description:
T7Hc3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 7061 ug/L, rep1

description:
T7Hc1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 23251 ug/L, rep5

description:
T7Hb5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 49 ug/L, rep3

description:
T7Hg3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 23251 ug/L, rep3

description:
T7Hb3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 23251 ug/L, rep2

description:
T7Hb2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 23251 ug/L, rep4

description:
T7Hb4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 23251 ug/L, rep1

description:
T7Hb1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Cycle 2 and dose 2 for patient 4 [SC12]

type: RNA

city: Chicago

first: Anna

last: Di Rienzo

state: IL

department: Human Genetics

institute: University of Chicago

hyb_protocol: Total RNA was reverse transcribed into cDNA, labeled, hybridized to Illumina HumanHT-12 v4 Expression BeadChips and scanned at the Functional Genomics Facility at the University of Chicago

scan_protocol: standard protocol

data_processing: Low-level microarray analysis was performed using the Bioconductor software package LUMI in R

label: not provided

source_name: Whole blood (PaxGene)

label_protocol: not provided

extract_protocol: Blood was drawn into PaxGene RNA tubes and extracted using the PaxGene RNA isolation protocol

treatment_protocol: Blood samples were drawn from each patient (between 8–10 am) at baseline (i.e. before any therapy was administered), 24h after initial treatment with placebo/nab-paclitaxel, and then 24h after initial treatment with mifepristone/nab-paclitaxel.

tag: patient id

tag: nab-paclitaxel treatment

value: Yes

tag: mifepristone treatment

tag: date of collection

tag: rna concentration

tag: rin

tag: nab-paclitaxel concentration

tag: cortisol levels

tag: white blood cell count


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 7061 ug/L, rep2

description:
T7Hc2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

tag: tissue

tag: strain

tag: age

tag: developmental stage

tag: biological replicate

tag: time code


title: Cycle 1 and dose 2 for patient 3 [SC8]

tag: treatment


title: AML 3

city: New York

first: Jacob

middle: Lowell

last: Glass

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
TrimGalore!
STAR
HTSeq
Assembly: hg19
Supplementary files format and content: Count file, comma-separated values (CSV)

source_name: Bone marrow

extract_protocol:
TruSeq stranded total (Ribodepletion)
SMART-Seq v4 + KAPA Hyper (SMARTer)

value: Bone marrow

tag: diagnosis

value: AML


title: Baseline sample patient 4 [SC10]

tag: patient id

value: Baseline


title: Cycle 1 and dose 2 for patient 4 [SC11]

tag: nab-paclitaxel treatment


title: Cycle 2 and dose 2 for patient 3 [SC9]

tag: mifepristone treatment


title: AML 4


title: Baseline sample patient 2 [SC4]

tag: date of collection


title: Baseline sample patient 3 [SC7]

tag: rna concentration


title: Cycle 1 and dose 2 for patient 2 [SC5]

tag: rin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep4

description:
T7Ha3
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

tag: dose (ug/l)

tag: repeat sample


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep6

description:
T7Ha5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: Baseline sample patient 1 [SC1]

tag: cortisol levels

tag: white blood cell count


title: Cycle 2 and dose 2 for patient 2 [SC6]

tag: nab-paclitaxel concentration


title: Cycle 1 and dose 2 for patient 1 [SC2]


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep3

description:
T7Ha2
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

tag: tissue

tag: strain

tag: age


title: Cycle 2 and dose 2 for patient 1 [SC3]


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep5

description:
T7Ha4
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt

tag: developmental stage

tag: biological replicate

tag: time code


title: AML-MP 4, myeloid subset

tag: diagnosis

value: AML-MP

tag: subset

value: myeloid subset


title: AML 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep6

description:
T6Hh5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt

tag: treatment


title: AML-MP 2, myeloid subset


title: AML-MP 4, T subset

value: T subset


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep1

description:
T7Ha1
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: AML 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep1

description:
T6Hh1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 191 ug/L, rep5

description:
T7Hf5
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: MPAL 3, T subset

value: MPAL


title: AML-MP 3, T subset


title: AML-MP 1, T subset


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep5

description:
T6Hh4_rep
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: AML-MP 3, myeloid subset


title: MPAL 4, T subset


title: AML-MP 2, T subset


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep4

description:
T6Hh4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep2

description:
T6Hg2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep4

description:
T6Hg4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep3

description:
T6Hh3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep6

description:
T6Hg5_rep
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 15 ug/L, rep2

description:
T6Hh2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: AML-MP 1, myeloid subset


title: MPAL 1, myeloid subset


title: MPAL 3, myeloid subset


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 96-120hpf, 65395 ug/L, rep2

description:
T7Ha1_rep
PFHxS_T7_UMI_ZF_counts_matrix.txt
PFHxS_T7_ZF_counts.filtered.+1.normFinal.txt


title: MPAL 2, T subset


title: 200553C_TM

city: Guangzhou

first: zhou

last: feng

state: None Selected

address: 600# Tianhe Road, Guangzhou, Guangdong P.R, China

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcoded processing,gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: nomal(buttock)

extract_protocol:
4 mm punch biopsies were obtained from healthy whole skin specimens from the forearm and buttock region. Immediately after resection of subject, samples were kept in MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008) for no longer than 1 h before their enzymatical and mechanical dissociation with the Whole Skin Dissociation kit for human material (Miltenyi Biotec, cat. no. 130-101-540) and the Gentle MACS dissociator (Miltenyi Biotec), following the manufacturer’s instructions. Cell suspensions were then filtered through 70 µm cell strainers (Falcon) and depleted of cell debris and dead cells with the Dead Cell Removal Kit (Miltenyi Biotec, cat. no. 130-090-101).
Raw sequencing data was processed with Cell Ranger, version 3.1.0, from 10X Genomics.

value: nomal(buttock)

tag: cell line

value: skin cells

tag: cell type


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 191 ug/L, rep2

description:
T6Hf2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: 200553C_AM

description: 10X genomics

source_name: photoaging(Arm) skin

value: photoaging(Arm) skin


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep5

description:
T6Hg5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 578 ug/L, rep4

description:
T6He4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 578 ug/L, rep3

description:
T6He3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 578 ug/L, rep2

description:
T6He2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 191 ug/L, rep4

description:
T6Hf4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 191 ug/L, rep3

description:
T6Hf3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep1

description:
T6Hg1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 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

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.

value: U2OS Dmr-PERK

tag: genotype

value: WT

value: Dim 3 nM

tag: time


title: MPAL 1, T subset


title: Sorafenib-resistant huh7 cell lines-Ctrl

type: genomic

city: Xiamen

first: Chunli

last: Mo

state: fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: School of Life Sciences, Xiamen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850KEPIC Beadchip using standard Illumina protocol

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

data_processing: champ  pipeline

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: sorafenib-resistant huh7 cells were cultured in DMEM/High Glucose medium supplemented with 10% FBS.Cells were maintained at a density of 30 to 90% confluency.

extract_protocol: genomic DNA was extracted and purified from cell samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: sorafenib-resistant huh7 cell lines were infected with Ctrl and shTET1 virus,after 48h,added 1000X puro to cell culture daily, 1 week later,DNA were harvested.

value: control

value: Sorafenib-resistant huh7


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 191 ug/L, rep5

description:
T6Hf5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type

value: embryo

tag: dose (ug/l)

tag: repeat sample

value: No


title: MPAL 4, myeloid subset

value: Bone marrow


title: VIL230724JM, DP22, 7935

city: Portland

first: Joshua

middle: M

last: Moreau

state: OR

address: 2720 S Moody Ave.

department: Department of Dermatology

institute: Oregon Health & Science University

description: Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to hg38 genome to gene expression count using Space Rangers's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's defalut settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifiying spots
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Lesional skin punch biopsies were formalin-fixed and paraffin-embedded. Five-micron sections were placed on glass slides prior to hematoxylin-eosin staining and imaging with a Zeiss Axioscan 7 slider scanner.
Spatial transcriptome sequencing libraries was prepared with the Visium V2 Spatial Gene Expression kit (10X Genomics).

tag: individual

value: Skin

value: Untreated


title: MPAL 2, myeloid subset

value: myeloid subset


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 191 ug/L, rep1

description:
T6Hf1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 1790 ug/L, rep3

description:
T6Hd3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: VIL230724JM, DP23, 726

description: Spatial transcriptome sequencing

value: ustekinumab


title: Sorafenib-resistant huh7 cell lines-shTET1-2

source_name: Sorafenib-resistant huh7 cell lines-shTET12


title: Sorafenib-resistant huh7 cell lines-shTET1-1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 1790 ug/L, rep1

description:
T6Hd1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: VIL230724JM, DP22, 06924

description: Spatial transcriptome sequencing


title: DmrPERK, Dim 3 nM, 24h, replicate 3


title: VIL230724JM, DP23, 1206

description: Spatial transcriptome sequencing


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 7061 ug/L, rep5

description:
T6Hc5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 8h, replicate 1


title: DmrPERK, Dim 3 nM, 4h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 7061 ug/L, rep2

description:
T6Hc2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 578 ug/L, rep5

description:
T6He5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 578 ug/L, rep1

description:
T6He1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 24h, replicate 1


title: DmrPERK, Dim 3 nM, 16h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 1790 ug/L, rep5

description:
T6Hd5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 1790 ug/L, rep4

description:
T6Hd4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 2h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 23251 ug/L, rep5

description:
T6Hb5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 23251 ug/L, rep4

description:
T6Hb4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 23251 ug/L, rep2

description:
T6Hb2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 1h, replicate 3


title: DmrPERK, Dim 3 nM, 16h, replicate 2


title: DmrPERK, Dim 3 nM, 16h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 23251 ug/L, rep1

description:
T6Hb1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 1790 ug/L, rep2

description:
T6Hd2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 8h, replicate 3


title: DmrPERK, UT 2, 0h, replicate 3

value: NT


title: DmrPERK, Dim 3 nM, 8h, replicate 2


title: DmrPERK, UT 2, 0h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 49 ug/L, rep3

description:
T6Hg3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 7061 ug/L, rep4

description:
T6Hc4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 4h, replicate 1


title: DmrPERK, Dim 3 nM, 4h, replicate 3


title: DmrPERK, Dim 3 nM, 2h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 15 ug/L, rep5

description:
T5Hh5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 2h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 7061 ug/L, rep1

description:
T6Hc1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 7061 ug/L, rep3

description:
T6Hc3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 1h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 15 ug/L, rep3

description:
T5Hh3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 65395 ug/L, rep4

description:
T6Ha4
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 15 ug/L, rep2

description:
T5Hh2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 23251 ug/L, rep3

description:
T6Hb3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


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

value: Dim .195 nM


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 65395 ug/L, rep2

description:
T6Ha2
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 65395 ug/L, rep3

description:
T6Ha3
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 15 ug/L, rep1

description:
T5Hh1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim 3 nM, 1h, replicate 2


title: DmrPERK, UT 2, 0h, replicate 1


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 49 ug/L, rep4

description:
T5Hg4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 65395 ug/L, rep1

description:
T6Ha1
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 15 ug/L, rep4

description:
T5Hh4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 49 ug/L, rep3

description:
T5Hg3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 49 ug/L, rep2

description:
T5Hg2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


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


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 48-120hpf, 65395 ug/L, rep5

description:
T6Ha5
PFHxS_T6_UMI_ZF_counts_matrix.txt
PFHxS_T6_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep6

description:
T5Hf5_rep
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt

value: Yes


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

value: U2OS Dmr-PERK


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

value: WT


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep3

description:
T5Hf3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .195 nM, 1h, replicate 3


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep4

description:
T5Hf4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep2

description:
T5Hf2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 49 ug/L, rep1

description:
T5Hg1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 578 ug/L, rep4

description:
T5He4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 24h, replicate 2

value: Dim .01 nM


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep5

description:
T5Hf5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 24h, replicate 3


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


title: DmrPERK, Dim .01 nM, 24h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 49 ug/L, rep5

description:
T5Hg5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 191 ug/L, rep1

description:
T5Hf1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 578 ug/L, rep3

description:
T5He3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 578 ug/L, rep2

description:
T5He2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 16h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 1790 ug/L, rep3

description:
T5Hd3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 578 ug/L, rep1

description:
T5He1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 1790 ug/L, rep2

description:
T5Hd2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 1790 ug/L, rep1

description:
T5Hd1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 7061 ug/L, rep5

description:
T5Hc5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 16h, replicate 2


title: DmrPERK, Dim .01 nM, 8h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 1790 ug/L, rep5

description:
T5Hd5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 1790 ug/L, rep4

description:
T5Hd4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 4h, replicate 3


title: DmrPERK, Dim .01 nM, 4h, replicate 2


title: DmrPERK, Dim .01 nM, 8h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 7061 ug/L, rep4

description:
T5Hc4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 4h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 578 ug/L, rep5

description:
T5He5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 16h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 7061 ug/L, rep3

description:
T5Hc3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 23251 ug/L, rep5

description:
T5Hb5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 23251 ug/L, rep4

description:
T5Hb4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 1h, replicate 2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 23251 ug/L, rep3

description:
T5Hb3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 23251 ug/L, rep2

description:
T5Hb2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 0h, replicate 3


title: DmrPERK, Dim .01 nM, 1h, replicate 3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 23251 ug/L, rep1

description:
T5Hb1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 7061 ug/L, rep2

description:
T5Hc2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, UT, 0h, replicate 2


title: DmrPERK, Dim .01 nM, 2h, replicate 3


title: DmrPERK, Dim .01 nM, 2h, replicate 2


title: DmrPERK, Dim .01 nM, 1h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 65395 ug/L, rep5

description:
T5Ha5
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 65395 ug/L, rep2

description:
T5Ha2
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: DmrPERK, Dim .01 nM, 8h, replicate 2


title: DmrPERK, UT, 0h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 15 ug/L, rep5

description:
T4Hh6
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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

value: Tg 100 nM


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


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 65395 ug/L, rep4

description:
T5Ha4
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 7061 ug/L, rep1

description:
T5Hc1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 15 ug/L, rep2

description:
T4Hh3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 15 ug/L, rep1

description:
T4Hh1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 15 ug/L, rep4

description:
T4Hh5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 15 ug/L, rep3

description:
T4Hh4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 49 ug/L, rep4

description:
T4Hg5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 49 ug/L, rep2

description:
T4Hg3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 49 ug/L, rep3

description:
T4Hg4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 65395 ug/L, rep3

description:
T5Ha3
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-120hpf, 65395 ug/L, rep1

description:
T5Ha1
PFHxS_T5_UMI_ZF_counts_matrix.txt
PFHxS_T5_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 49 ug/L, rep1

description:
T4Hg1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 191 ug/L, rep3

description:
T4Hf4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 191 ug/L, rep4

description:
T4Hf5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 191 ug/L, rep5

description:
T4Hf6
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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

value: Arsenite .05 mM


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 191 ug/L, rep2

description:
T4Hf2
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 191 ug/L, rep1

description:
T4Hf1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 578 ug/L, rep4

description:
T4He4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt

value: embryo


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 578 ug/L, rep5

description:
T4He5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt

value: No


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


title: DmrPERK, Dim .01 nM, 2h, replicate 1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 578 ug/L, rep3

description:
T4He3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 578 ug/L, rep2

description:
T4He2
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 578 ug/L, rep1

description:
T4He1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 1790 ug/L, rep5

description:
T4Hd5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 1790 ug/L, rep4

description:
T4Hd4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 1790 ug/L, rep3

description:
T4Hd3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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


title: Tumor derived-ILC1_3

first: XiqQiong

last: Wang

state: Anhui

address: School of Life Sciences, No. 443 Huangshan Road

institute: University Of Science And Technology Of China

data_processing:
Fastp (version 0.23.4,-f 15 -F 15) was used for filtering and evaluating the quality of sequenced data.
Clean RNA-seq reads were aligned to the reference genome using HISAT2(version 2.1.0), And uniquely mapped reads were used for further analysis.
Then we use FeatureCounts(version 2.0.1) to calculate Raw Counts of genes
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: MC38 tumors tissues

growth_protocol: MC38 Colon Carcinoma cells (from C57BL/6 mice) were cultured at 37 °C under 5% CO2 in DMEM medium (BI) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (BI). All of the cell lines have been tested for mycoplasma contamination.

extract_protocol:
Total RNA from cells was extracted using TRIzol reagent (Takara) according to the manufacturer's instructions. Specifically, the samples were homogenized with TRIzol reagent, chloroform was added, and the homogenate was separated into a clear upper aqueous layer containing RNA, an interphase layer, and a pink lower organic layer containing DNA and protein. The RNA was precipitated out of the upper aqueous layer with isopropanol. Then,total RNA was used for the construction of sequencing libraries.
The mRNA was purified using Oligo(dT)-attached magnetic beads. cDNA was then generated by using random hexamer-primed reverse transcription. Then cDNA fragment was amplified by PCR and the product was purified with Ampure XP Beads and then dissolved in EB solution. Products were quality controlled on the Agilent Technologies 2100 bioanalyzer. The double-stranded PCR product from the previous step was heat denatured and looped through the spliced oligonucleotide sequence to obtain the final library. The single strand circle DNA (ssCir DNA) was formatted into a final library. The final library was amplified with phi29 into a DNA nanoball (DNB) with more than 300 copies of a molecule, DNBs were loaded into patterned nanoarrays and single end 50 bases reads were generated on the BGIseq500 platform (BGI, Shenzhen, China).

treatment_protocol: In the subcutaneous injection model, 1 × 106 MC38 cells were injected subcutaneously into wild-type C57/BL6 mice.

value: MC38 tumors tissues


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 1790 ug/L, rep2

description:
T4Hd2
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 1790 ug/L, rep1

description:
T4Hd1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep4

description:
T4Hc3_rep
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: Tumor derived-ILC1_1


title: Tumor derived-ILC1_2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep5

description:
T4Hc4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep6

description:
T4Hc5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep1

description:
T4Hc1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep2

description:
T4Hc2
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 23251 ug/L, rep5

description:
T4Hb7
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: Tumor derived-NK_1

value: NK


title: Tumor derived-NK_2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 23251 ug/L, rep2

description:
T4Hb4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 23251 ug/L, rep1

description:
T4Hb3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 65395 ug/L, rep5

description:
T4Ha5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 7061 ug/L, rep3

description:
T4Hc3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: Tumor derived-NK_3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 65395 ug/L, rep3

description:
T4Ha3
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 65395 ug/L, rep4

description:
T4Ha4
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 65395 ug/L, rep1

description:
T4Ha1
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 65395 ug/L, rep2

description:
T4Ha2
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 15 ug/L, rep4

description:
T3Hh4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


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


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 6-120hpf, 23251 ug/L, rep4

description:
T4Hb6
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 15 ug/L, rep5

description:
T3Hh5
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), 6-120hpf, 23251 ug/L, rep3

description:
T4Hb5
PFHxS_T4_UMI_ZF_counts_matrix.txt
PFHxS_T4_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 15 ug/L, rep3

description:
T3Hh3
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, 15 ug/L, rep2

description:
T3Hh2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+24h_rep1

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

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)

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)

value: Forelimb bud

value: WT Swiss Albino

value: DMSO

tag: timepoint of_treatment

tag: timepoint of_dissection


title: RNA_FL_timecourse_E10.5+C59+24h_rep2

tag: tissue


title: RNA_FL_timecourse_E10.5+C59+24h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 49 ug/L, rep5

description:
T3Hg5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: strain

tag: age


title: RNA_FL_timecourse_E10.5+C59+24h_rep3


title: RNA_FL_timecourse_E10.5+C59+18h_rep3


title: RNA_FL_timecourse_E10.5+DMSO+24h_rep3


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 15 ug/L, rep1

description:
T3Hh1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: developmental stage

tag: biological replicate


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 49 ug/L, rep3

description:
T3Hg3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt

tag: time code


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 49 ug/L, rep4

description:
T3Hg4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+C59+18h_rep2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 49 ug/L, rep1

description:
T3Hg1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+24h_rep2


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


title: RNA_FL_timecourse_E10.5+C59+18h_rep1


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 191 ug/L, rep4

description:
T3Hf4
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, 49 ug/L, rep2

description:
T3Hg2
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+18h_rep3


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 191 ug/L, rep2

description:
T3Hf2
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, rep3

description:
T3Hf3
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+18h_rep2


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 578 ug/L, rep5

description:
T3He5
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


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


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 191 ug/L, rep1

description:
T3Hf1
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


title: RNA_FL_timecourse_E10.5+DMSO+18h_rep1


title: whole body zebrafish embyro, PFHxS (CAS 355-46-4), 24-48hpf, 578 ug/L, rep4

description:
T3He4
PFHxS_T3_UMI_ZF_counts_matrix.txt
PFHxS_T3_ZF_counts.filtered.+1.normFinal.txt


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


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