title: DMPFHxSP3GS89_L002

description:
DM_PFHxS_P3_G
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: G


title: Ncor1/2_dKO_DEX3

status: Public on Feb 22 2024

type: SRA

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
nf-core/rnaseq V 3.5 pipeline for cutadapter, read alignment to mm10 using STAR aligner, read counts and quality control of results
Differential gene analysis was performed in R V4.1.3 using Deseq2 V1.34.0
Assembly: mm10
Supplementary files format and content: RNA_TPM.tsv: tab-separated TPM counts from nf-core/rnaseq
Supplementary files format and content: .csv: comma-separated output of Deseq2, differential expression tests (log2 fold change, p-value)

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries were geneated by Novogene for sequencing on the Illumina Platform

treatment_protocol: Mice were injected with 1 mg/kg Dexamethasone or Vehicle and sacrificed two hours later. Tissues were snap frozen and used later for RNAseq analysis.

tag: tissue

value: liver

tag: time

tag: Sex

value: Male

tag: genotype

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

tag: data collection_time

value: Day 5 post AAV

tag: treatment

value: DEX


title: lung.KO.7053282

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
Marc2_counts.txt
Marc2_TPM.txt

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

source_name: lung

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

value: lung


title: lung.WT.7070221

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFNAP1ES124_L002

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
DM_PFNA_P1_E
DM_PFNA_counts.filtered.+1.normFinal.txt

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

organism: Daphnia magna

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

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

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

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

value: whole body

value: GLTED-wt

value: PFNA (DTXSID8031863)

tag: conc.

tag: conc. units

value: ug/L

tag: conc code

value: E

tag: exposure duration

tag: age

tag: replicate plate_id


title: lung.WT.7018357

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFHxSP3ES91_L002

description:
DM_PFHxS_P3_E
DM_PFHxS_counts.filtered.+1.normFinal.txt

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

value: PFHxS (DTXSID3037709)


title: lung.WT.6980848

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_mut_28h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

organism: Caenorhabditis elegans

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

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

treatment_protocol: no treatment

tag: strain

tag: time (h)


title: DMPFHxSP3DS92_L002

description:
DM_PFHxS_P3_D
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: D


title: Ncor1/2_dKO_DEX2


title: ce_smallRNA_ebax_TC_mut_27h


title: DMPFHxSP3CS93_L002

description:
DM_PFHxS_P3_C
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: C


title: Ncor1/2_dKO_DEX1


title: lung.WT.6962451

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_mut_26h


title: lung.WT.6943256

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFHxSP3BS94_L002

description:
DM_PFHxS_P3_B
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: B


title: ce_smallRNA_ebax_TC_mut_25h


title: Ncor1/2_dKO_VEH3

value: VEH


title: Ncor1/2_dKO_VEH2


title: DMPFHxSP2HS81_L002

description:
DM_PFHxS_P2_H
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: H


title: lung.WT.6943255

description:
Marc2_counts.txt
Marc2_TPM.txt


title: liver.KO.7053282

description:
Marc2_counts.txt
Marc2_TPM.txt

value: liver


title: ce_smallRNA_ebax_TC_mut_24h


title: Ncor1/2_Cont_DEX3

value: Male

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


title: DMPFHxSP2GS82_L002

description:
DM_PFHxS_P2_G
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: G


title: liver.KO.7053281

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_mut_22h


title: Ncor1/2_Cont_DEX2

value: Day 5 post AAV

value: DEX


title: ce_smallRNA_ebax_TC_mut_23h


title: DMPFHxSP2FS83_L002

description:
DM_PFHxS_P2_F
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: whole body

value: F


title: DMPFHxSP2DS85_L002

description:
DM_PFHxS_P2_D
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: GLTED-wt


title: ce_smallRNA_ebax_TC_mut_20h


title: liver.KO.7053280

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_mut_21h


title: liver.KO.6999955

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor1/2_Cont_VEH3


title: DMPFHxSP2CS86_L002

description:
DM_PFHxS_P2_C
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: ug/L


title: ce_smallRNA_ebax_TC_mut_19h


title: ce_smallRNA_ebax_TC_mut_18h


title: liver.WT.7035605

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPFHxSP2BS87_L002

description:
DM_PFHxS_P2_B
DM_PFHxS_counts.filtered.+1.normFinal.txt


title: Ncor1/2_Cont_VEH2


title: liver.KO.7070224

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor1/2_dKO_VEH1

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


title: Ncor1/2_Cont_VEH1


title: DMPFHxSP2ES84_L002

description:
DM_PFHxS_P2_E
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: PFHxS (DTXSID3037709)

value: E


title: ce_smallRNA_ebax_TC_N2_31h

value: WT


title: Hdac3_day15_KO4

value: Hdac3 F/F +AAV-Cre

value: Day 15 post AAV


title: Ncor1/2_Cont_DEX1


title: liver.WT.7018357

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_N2_30h


title: DMPFHxSP1HS96_L002

description:
DM_PFHxS_P1_H
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: H


title: DMPFHxSP1GS74_L002

description:
DM_PFHxS_P1_G
DM_PFHxS_counts.filtered.+1.normFinal.txt


title: Hdac3_day15_KO3

value: liver


title: ce_smallRNA_ebax_TC_N2_29h


title: DMPFHxSP1FS75_L002

description:
DM_PFHxS_P1_F
DM_PFHxS_counts.filtered.+1.normFinal.txt


title: liver.WT.6962451

description:
Marc2_counts.txt
Marc2_TPM.txt


title: liver.WT.6943256

description:
Marc2_counts.txt
Marc2_TPM.txt


title: liver.WT.6980848

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Hdac3_day15_KO2

value: Male


title: Hdac3_day15_KO1


title: ce_smallRNA_ebax_TC_N2_28h


title: liver.WT.7070221

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_N2_27h


title: liver.WT.6943255

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Hdac3_day15_Cont4

value: Hdac3 F/F +AAV-eGFP


title: DMPFHxSP1CS78_L002

description:
DM_PFHxS_P1_C
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: C


title: ce_smallRNA_ebax_TC_N2_26h


title: DMPFHxSP1BS79_L002

description:
DM_PFHxS_P1_B
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: B


title: ce_smallRNA_ebax_TC_N2_25h


title: Hdac3_day15_Cont3


title: kidney.KO.7053282

description:
Marc2_counts.txt
Marc2_TPM.txt

source_name: kidney

value: kidney


title: Hdac3_day15_Cont2


title: DMPF4OPeAP3HS63_L002

description:
DM_PF4OPeA_P3_H
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to PF4OPeA

value: whole body

value: PF4OPeA (DTXSID70191136)


title: ce_smallRNA_ebax_TC_N2_24h


title: DMPFHxSP1ES76_L002

description:
DM_PFHxS_P1_E
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: GLTED-wt


title: DMPF4OPeAP3GS64_L002

description:
DM_PF4OPeA_P3_G
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: ug/L

value: G


title: Ncor2_day15_sKO3

value: Ncor2 F/F +AAV-Cre


title: kidney.KO.7053280

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_N2_23h


title: Hdac3_day15_Cont1


title: DMPF4OPeAP3FS65_L002

description:
DM_PF4OPeA_P3_F
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: F


title: kidney.KO.6999955

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor2_day15_sKO2


title: ce_smallRNA_ebax_TC_N2_22h

value: WT


title: kidney.WT.7070221

description:
Marc2_counts.txt
Marc2_TPM.txt


title: ce_smallRNA_ebax_TC_N2_21h


title: DMPFHxSP1DS77_L002

description:
DM_PFHxS_P1_D
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: PFHxS (DTXSID3037709)

value: D


title: DMPF4OPeAP3ES66_L002

description:
DM_PF4OPeA_P3_E
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: E


title: Ncor2_day15_sKO1

value: liver

value: Day 15 post AAV


title: DMPF4OPeAP3DS67_L002

description:
DM_PF4OPeA_P3_D
DM_PF4OPeA_counts.filtered.+1.normFinal.txt


title: kidney.KO.7070224

description:
Marc2_counts.txt
Marc2_TPM.txt


title: kidney.WT.7035605

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPF4OPeAP3CS68_L002

description:
DM_PF4OPeA_P3_C
DM_PF4OPeA_counts.filtered.+1.normFinal.txt


title: ce_smallRNA_ebax_TC_N2_19h


title: kidney.WT.7018357

description:
Marc2_counts.txt
Marc2_TPM.txt


title: kidney.KO.7053281

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor2_day15_Cont2

value: Male

value: Ncor2 F/F +AAV-eGFP


title: ce_smallRNA_ebax_TC_N2_18h


title: DMPF4OPeAP3BS69_L002

description:
DM_PF4OPeA_P3_B
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: B


title: Ncor2_day15_Cont1


title: DMPF4OPeAP3AS70_L002

description:
DM_PF4OPeA_P3_A
DM_PF4OPeA_counts.filtered.+1.normFinal.txt
DM_PFTP_counts.filtered.+1.normFinal.txt

value: A


title: kidney.WT.6980848

description:
Marc2_counts.txt
Marc2_TPM.txt

value: kidney


title: Ncor1_day15_sKO3

value: Ncor1 F/F +AAV-Cre


title: DMPF4OPeAP2HS55_L002

description:
DM_PF4OPeA_P2_H
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PF4OPeA (DTXSID70191136)

value: H


title: ce_smallRNA_ebax_TC_N2_20h


title: CD34+-derived proE/basoE cells, CTRL, input ctrl HDACi rep 4

city: Paris

first: David

last: Rombaut

address: 22 rue Méchain

country: France

institute: Institut Cochin

library_source: genomic

data_processing:
Reads were trimmed and filtered using fastp (v0.23.4) to remove low quality reads, low complexity sequences, as well as polyG tails. Reads were mapped to the human reference genome (GENCODE, GRCh37) with Bowtie2 (v2.3.5.1), using parameters --no-discordant and --no-mixed. Samblaster (v0.1.24) was used to remove duplicated reads, then Samtools (v1.10) to generate sorted (by coordinates) BAM files, with a cut-off for MAPQ score of 10.
Peaks were called for each replicate with the MACS algorithm (MACS3) in broad mode, with the input DNA as control as well as the same sample treated with RNH1, at q-value < 0.1. Resulting peaks were analysed by groups of biological replicates with MSPC (v5.5.0) with default cut-off.
To identify differentially expressed R-loops, we intersected the peaks from MACS3 calling with the 5.5 million of restriction fragments generated before S9.6 immunoprecipitation, using the resulting matrix as a reference frame for featureCounts (v2.0.0). Batch effect removal is necessary as samples has been sequenced at different times. Normalization and differential R-loop expression analysis between wild-type, mutant and control samples was performed with DESeq2, using at Benjamini-Hochberg (BH)- adjusted P-value < 0.05 and log2 (FC) > |1|.
Bedtools (v2.27.1) intersect was used for overlap analyses.
Assembly: GRCh37
Supplementary files format and content: Compressed bedGraph file. Considering exclusion of certain files, depending of the needed comparison (HDACi treatment, genotype), bedgraph are not normalized.
Library strategy: DRIP-seq

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
8x10^6 cells were harvested and processed for genomic DNA extraction by SDS/ Proteinase K treatment at 37°C followed by phenol-chloroform extraction and ethanol precipitation. 8 µg of genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI, and SspI. Then DNA pre-treated or not with RNase H1 (16UI/mL) overnight (New Engl Biolabs, Ipswitch, MA) was immunoprecipitated using S9.6 antibody overnight at 4°C.
For DRIP-seq, good quality DRIPed DNA samples (with and without RNase H1-treatment) were sonicated to get an average length 200-300 bp. Then samples were subjected to end-repair, dATP tailing, adaptor ligation and library indexing. Lastly, the libraries were cleaned up using AMPure beads, and amplified. After checking library quality on Agilent Bioanalyzer using Agilent High Sensitivity DNA 1000 kit, libraries were sequenced on Illumina NovaSeq instruments.

tag: cell line

tag: cell type

value: CD34+-derived proE/basoE

value: CTRL

value: HDACi

tag: sequencing batch


title: Ncor1_day15_sKO2

tag: tissue


title: kidney.WT.6962451

description:
Marc2_counts.txt
Marc2_TPM.txt


title: kidney.WT.6943256

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPF4OPeAP2GS56_L002

description:
DM_PF4OPeA_P2_G
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: ug/L

value: G


title: kidney.WT.6943255

description:
Marc2_counts.txt
Marc2_TPM.txt


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_NT 4


title: Ncor1_day15_sKO1

value: liver

tag: time


title: heart.KO.7070224

description:
Marc2_counts.txt
Marc2_TPM.txt

source_name: heart

value: heart


title: Ncor1_day15_Cont3

tag: Sex

value: Male

value: Ncor1 F/F +AAV-eGFP

value: Day 15 post AAV


title: DMPF4OPeAP2FS57_L002

description:
DM_PF4OPeA_P2_F
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

tag: genotype

value: F


title: CD34+-derived proE/basoE cells, CTRL, input ctrl rep 4

value: no


title: DMPF4OPeAP2ES58_L002

description:
DM_PF4OPeA_P2_E
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: E


title: Ncor2_day15_Cont3

value: Ncor2 F/F +AAV-eGFP

tag: data collection_time


title: CD34+-derived proE/basoE cells, CTRL, rep RH 4

tag: treatment

value: Rnase H1


title: Ncor1_day15_Cont2


title: DMPF4OPeAP2DS59_L002

description:
DM_PF4OPeA_P2_D
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: PF4OPeA (DTXSID70191136)

tag: conc.

value: D


title: heart.KO.7053282

description:
Marc2_counts.txt
Marc2_TPM.txt


title: heart.KO.7053281

description:
Marc2_counts.txt
Marc2_TPM.txt


title: CD34+-derived proE/basoE cells, CTRL, rep NT 4

value: CD34+-derived proE/basoE

value: CTRL


title: Ncor1_day15_Cont1


title: CD34+-derived proE/basoE cells, CTRL, input ctrl HDACi rep 3

value: HDACi


title: Ncor1/2_day15_dKO4

value: liver

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


title: DMPF4OPeAP2CS60_L002

description:
DM_PF4OPeA_P2_C
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

tag: conc. units

value: ug/L

value: C


title: heart.KO.7053280

description:
Marc2_counts.txt
Marc2_TPM.txt

value: heart


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_RH 4

value: HDACi + Rnase H1


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_RH 3


title: Ncor1/2_day15_dKO2

value: Male

value: Day 15 post AAV


title: heart.WT.7070221

description:
Marc2_counts.txt
Marc2_TPM.txt


title: DMPF4OPeAP2BS61_L002

description:
DM_PF4OPeA_P2_B
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

tag: conc code

value: B


title: Ncor1/2_day15_dKO3


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_NT 3


title: heart.KO.6999955

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor1/2_day15_dKO1


title: CD34+-derived proE/basoE cells, CTRL, input ctrl rep 3

value: no


title: DMPF4OPeAP1GS48_L002

description:
DM_PF4OPeA_P1_G
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: G

tag: exposure duration


title: heart.WT.7018357

description:
Marc2_counts.txt
Marc2_TPM.txt


title: Ncor1/2_day15_Cont4

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


title: DMPF4OPeAP2AS62_L002

description:
DM_PF4OPeA_P2_A
DM_PF4OPeA_counts.filtered.+1.normFinal.txt
DM_PFTP_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PF4OPeA (DTXSID70191136)

value: A

tag: age


title: CD34+-derived proE/basoE cells, CTRL, rep RH 3

value: CD34+-derived proE/basoE

value: CTRL

value: Rnase H1


title: CD34+-derived proE/basoE cells, CTRL, rep NT 3


title: DMPF4OPeAP1FS49_L002

description:
DM_PF4OPeA_P1_F
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: ug/L

value: F

tag: replicate plate_id


title: Ncor1/2_day15_Cont3

value: liver


title: DMPF4OPeAP1ES50_L002

description:
DM_PF4OPeA_P1_E
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: E


title: CD34+-derived proE/basoE cells, CTRL, input ctrl HDACi rep 2

value: HDACi


title: heart.WT.6980848

description:
Marc2_counts.txt
Marc2_TPM.txt

value: heart


title: heart.WT.6962451

description:
Marc2_counts.txt
Marc2_TPM.txt


title: heart.WT.6943256

description:
Marc2_counts.txt
Marc2_TPM.txt


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_RH 2

value: HDACi + Rnase H1


title: Ncor1/2_day15_Cont1

value: Male

value: Day 15 post AAV


title: DMPF4OPeAP1DS51_L002

description:
DM_PF4OPeA_P1_D
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: whole body

value: D


title: Ncor1/2_day15_Cont2

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


title: DMPF4OPeAP1CS52_L002

description:
DM_PF4OPeA_P1_C
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: PF4OPeA (DTXSID70191136)

value: C


title: DMPF4OPeAP1HS47_L002

description:
DM_PF4OPeA_P1_H
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: H


title: heart.WT.7035605

description:
Marc2_counts.txt
Marc2_TPM.txt


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_NT 2

value: CD34+-derived proE/basoE

value: CTRL


title: DMPF4OPeAP1BS53_L002

description:
DM_PF4OPeA_P1_B
DM_PF4OPeA_counts.filtered.+1.normFinal.txt

value: ug/L

value: B


title: Ncor1/2_day5_dKO2

value: liver

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

value: Day 5 post AAV


title: WAT.KO.6950227

description:
Marc1_counts.txt
Marc1_TPM.txt

source_name: WAT

value: WAT


title: Ncor1/2_day5_dKO3

value: Male


title: CD34+-derived proE/basoE cells, CTRL, rep RH 2

value: Rnase H1


title: WAT.KO.6950223

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMN-EtFOSA-MP3HS41_L002

description:
DM_N-EtFOSA-M_P3_H
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to N-EtFOSA-M

value: whole body

value: N-EtFOSA-M (DTXSID1032646)


title: DMPF4OPeAP1AS54_L002

description:
DM_PF4OPeA_P1_A
DM_PF4OPeA_counts.filtered.+1.normFinal.txt
DM_PFTP_counts.filtered.+1.normFinal.txt

value: A


title: Ncor1/2_day5_dKO1


title: CD34+-derived proE/basoE cells, CTRL, rep NT 2

value: no


title: WAT.KO.6950219

description:
Marc1_counts.txt
Marc1_TPM.txt


title: Ncor1/2_day5_Cont4

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


title: DMN-EtFOSA-MP3GS42_L002

description:
DM_N-EtFOSA-M_P3_G
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: G


title: CD34+-derived proE/basoE cells, CTRL, input ctrl HDACi rep 1

value: CD34+-derived proE/basoE

value: HDACi


title: WAT.KO.6950202

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMN-EtFOSA-MP3FS43_L002

description:
DM_N-EtFOSA-M_P3_F
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: F


title: Ncor1/2_day5_Cont3

value: liver


title: WAT.KO.6950187

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_RH 1

value: CTRL

value: HDACi + Rnase H1


title: Ncor1/2_day5_Cont2

value: Day 5 post AAV


title: DMN-EtFOSA-MP3ES44_L002

description:
DM_N-EtFOSA-M_P3_E
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: E


title: CD34+-derived proE/basoE cells, CTRL, rep HDACi_NT 1


title: WAT.KO.6927712

description:
Marc1_counts.txt
Marc1_TPM.txt

value: WAT


title: Ncor1/2_day5_Cont1

value: Male


title: heart.WT.6943255

description:
Marc2_counts.txt
Marc2_TPM.txt

value: heart


title: DMN-EtFOSA-MP3DS45_L002

description:
DM_N-EtFOSA-M_P3_D
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: whole body

value: N-EtFOSA-M (DTXSID1032646)

value: D


title: CD34+-derived proE/basoE cells, CTRL, input ctrl rep 1

value: no


title: CD34+-derived proE/basoE cells, CTRL, input ctrl rep 2


title: WAT.KO.6927706

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMN-EtFOSA-MP3CS46_L002

description:
DM_N-EtFOSA-M_P3_C
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: C


title: VIVO_B16F10-TDMa_sgNlrc5_Rep4

city: Sapporo

first: Koichi

middle: S.

last: Kobayashi

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Graduate school of medicine

country: Japan

institute: Hokkaido University

description: VIVO_DESeq2_log2_+1_normalized_count.csv

data_processing:
Quality of Fastq files were checked by FastQC (0.12.0).Sequence reads were directly mapped to GRCm39/mm39 using STAR (2.7.10a) and read counts were generated by --quantMode GeneCounts
Read counts normalization were perfromed by DESeq2 (1.36.0), log2(Normalized count + 1) were calculated by R.
Assembly: mm38
Supplementary files format and content: comma-separated values file which include log2(Normalized count + 1) values for each Sample

source_name: tumor

growth_protocol: B16F10-TDM and B16F10 TDMa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Sepasol (Nacalai). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: tumor

value: melanoma

value: sgNlrc5 sgRNA transduced


title: CD34+-derived proE/basoE cells, CTRL, rep RH 1

value: CD34+-derived proE/basoE

value: Rnase H1


title: WAT.KO.6913581

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMN-EtFOSA-MP3BS47_L002

description:
DM_N-EtFOSA-M_P3_B
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: B


title: WAT.WT.6950230

description:
Marc1_counts.txt
Marc1_TPM.txt


title: VIVO_B16F10-TDMa_sgNlrc5_Rep2


title: CD34+-derived proE/basoE cells, CTRL, rep NT 1

value: CTRL


title: DMN-EtFOSA-MP3AS48_L002

description:
DM_N-EtFOSA-M_P3_A
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: A


title: WAT.WT.6950224

description:
Marc1_counts.txt
Marc1_TPM.txt

value: WAT


title: VIVO_B16F10-TDMa_sgNlrc5_Rep1


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl HDACi rep 5

value: SF3B1 MUT

value: HDACi


title: WAT.WT.6950204

description:
Marc1_counts.txt
Marc1_TPM.txt


title: VIVO_B16F10-TDMa_sgScramble_Rep4

value: sgSramble sgRNA transduced


title: DMN-EtFOSA-MP2GS34_L002

description:
DM_N-EtFOSA-M_P2_G
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: whole body

value: N-EtFOSA-M (DTXSID1032646)

value: G


title: VIVO_B16F10-TDMa_sgScramble_Rep3


title: WAT.WT.6950200

description:
Marc1_counts.txt
Marc1_TPM.txt


title: WAT.WT.6950182

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl rep 5

value: no


title: DMN-EtFOSA-MP2FS35_L002

description:
DM_N-EtFOSA-M_P2_F
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: F


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_NT 5


title: WAT.WT.6950180

description:
Marc1_counts.txt
Marc1_TPM.txt


title: VIVO_B16F10-TDMa_sgNlrc5_Rep3

value: tumor

value: melanoma

value: sgNlrc5 sgRNA transduced


title: DMN-EtFOSA-MP2ES36_L002

description:
DM_N-EtFOSA-M_P2_E
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: E


title: VIVO_B16F10-TDMa_sgScramble_Rep2


title: VIVO_B16F10-TDMa_sgScramble_Rep1


title: DMN-EtFOSA-MP2DS37_L002

description:
DM_N-EtFOSA-M_P2_D
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: D


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep NT 5

value: CD34+-derived proE/basoE


title: B16F10-TDMa_sgNlrc5_Rep2

description: TDMa_DESeq2_log2_+1_normalized_count.csv

source_name: cell line

value: cell line


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep RH 5

value: SF3B1 MUT

value: Rnase H1


title: DMN-EtFOSA-MP2CS38_L002

description:
DM_N-EtFOSA-M_P2_C
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: C


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl HDACi rep 4

value: HDACi


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_RH 5

value: HDACi + Rnase H1


title: DMN-EtFOSA-MP2HS33_L002

description:
DM_N-EtFOSA-M_P2_H
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: whole body

value: N-EtFOSA-M (DTXSID1032646)

value: H


title: DMN-EtFOSA-MP2BS39_L002

description:
DM_N-EtFOSA-M_P2_B
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: B


title: B16F10-TDMa_sgScramble_Rep2

value: melanoma

value: sgSramble sgRNA transduced


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_RH 4


title: B16F10-TDMa_sgNlrc5_Rep1

value: sgNlrc5 sgRNA transduced


title: WAT.WT.6927708

description:
Marc1_counts.txt
Marc1_TPM.txt

value: WAT


title: DMN-EtFOSA-MP2AS40_L002

description:
DM_N-EtFOSA-M_P2_A
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: A


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_NT 4

value: CD34+-derived proE/basoE


title: lung.KO.6950227

description:
Marc1_counts.txt
Marc1_TPM.txt

value: lung


title: B16F10-TDMa_sgScramble_Rep1

value: cell line


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl rep 4

value: SF3B1 MUT

value: no


title: WAT.WT.6939296

description:
Marc1_counts.txt
Marc1_TPM.txt


title: B16F10-TDM_sgNlrc5_Rep2


title: lung.KO.6950219

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep RH 4

value: Rnase H1


title: B16F10-TDM_sgNlrc5_Rep1


title: DMN-EtFOSA-MP1FS27_L002

description:
DM_N-EtFOSA-M_P1_F
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: whole body

value: F


title: DMN-EtFOSA-MP1GS26_L002

description:
DM_N-EtFOSA-M_P1_G
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: N-EtFOSA-M (DTXSID1032646)

value: G


title: DMN-EtFOSA-MP1ES28_L002

description:
DM_N-EtFOSA-M_P1_E
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: E


title: WAT.WT.6927709

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl HDACi rep 3

value: HDACi


title: lung.KO.6950202

description:
Marc1_counts.txt
Marc1_TPM.txt


title: B16F10-TDM_sgScramble_Rep2

value: melanoma

value: sgSramble sgRNA transduced


title: B16F10-TDM_sgScramble_Rep1


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_RH 3

value: HDACi + Rnase H1


title: DMN-EtFOSA-MP1DS29_L002

description:
DM_N-EtFOSA-M_P1_D
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: D


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep HDACi_NT 3

value: CD34+-derived proE/basoE


title: DMN-EtFOSA-MP1CS30_L002

description:
DM_N-EtFOSA-M_P1_C
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: C


title: gWT,RNA-seq,rep3

city: Kunming

first: ying

last: cheng

state: Yunnan

address: University East Outer Ring South Road

department: lnstitute of Biomedical Research

country: China

institute: YunnanUniversity

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

source_name: brain

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

tag: strain

value: brain

value: microglia

value: 8 weeks

value: gWT


title: lung.KO.6927706

description:
Marc1_counts.txt
Marc1_TPM.txt

value: lung


title: gWT,RNA-seq,rep2


title: lung.KO.6950223

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMN-EtFOSA-MP1HS25_L002

description:
DM_N-EtFOSA-M_P1_H
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: whole body

value: N-EtFOSA-M (DTXSID1032646)

value: H


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, input ctrl rep 3

value: SF3B1 MUT

value: no


title: DMN-EtFOSA-MP1BS31_L002

description:
DM_N-EtFOSA-M_P1_B
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: B


title: lung.KO.6913581

description:
Marc1_counts.txt
Marc1_TPM.txt


title: gWT,RNA-seq,rep1


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep NT 4


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep RH 3

value: Rnase H1


title: gKO,RNA-seq,rep3

value: gKO


title: DMN-EtFOSA-MP1AS32_L002

description:
DM_N-EtFOSA-M_P1_A
DM_N-EtFOSA-M_counts.filtered.+1.normFinal.txt

value: ug/L

value: A


title: lung.WT.6950230

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP3HS17_L002

description:
DM_FHxSA_P3_H
DM_FHxSA_counts.filtered.+1.normFinal.txt

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

value: FHxSA (DTXSID50469320)


title: lung.KO.6950187

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, MDS SF3B1 MUT, rep NT 3

value: CD34+-derived proE/basoE


title: lung.WT.6950224

description:
Marc1_counts.txt
Marc1_TPM.txt


title: gKO,RNA-seq,rep2

value: brain

value: microglia


title: DMFHxSAP3GS18_L002

description:
DM_FHxSA_P3_G
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: G


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl HDACi rep 6

value: SF3B1 WT SRSF2 TET2 MUT

value: HDACi


title: lung.KO.6927712

description:
Marc1_counts.txt
Marc1_TPM.txt

value: lung


title: DMFHxSAP3FS19_L002

description:
DM_FHxSA_P3_F
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: F


title: gKO,RNA-seq,rep1

value: 8 weeks


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_RH 6

value: HDACi + Rnase H1


title: lung.WT.6950200

description:
Marc1_counts.txt
Marc1_TPM.txt


title: lung.WT.6950204

description:
Marc1_counts.txt
Marc1_TPM.txt


title: RNAseq_Testes_WT_Mcaf2_rep2

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California, Davis

data_processing:
Raw sequence reads were trimmed and filtered using trimmomatic v0.39.
Trimmed sequence reads were aligned to the mouse genome (GRCm38/mm10) using STAR version 2.5.4b with --outFilterMultimapNmax 1 options for unique alignments.
Aligned read counts for each gene were generated using featureCounts v2.0.1 based on the UCSC mouse refGene annotation.
The TPM normalization were performed on Microsoft excel softwere.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: Testis

extract_protocol:
Freshly collected tests from Mcaf2ctrl or Mcaf2KO mice were excised, detunicated, and washed with ice-cold 1x phosphate-buffered saline (PBS). Total RNA was purified from Mcaf2ctrl or Mcaf2-/- whole testis using an RNeasy micro kit (Qiagen) according to the manual provided. RNA quality and quantity were checked using, respectively, Bioanalyzer (Agilent) and Qubit (Life Technologies).
PolyA/stranded RNA-Seq library was performed using the Illumina TruSeq Stranded mRNA Library Prep kit (Product Number: 20020595) according to the manufacturer's instructions.

value: Testis

value: Male

value: Testicular cells

value: WT


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_NT 6


title: RNAseq_Testes_WT_Mcaf2_rep1


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl rep 6

value: no


title: DMFHxSAP3DS21_L002

description:
DM_FHxSA_P3_D
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: FHxSA (DTXSID50469320)

value: ug/L

value: D


title: lung.WT.6950182

description:
Marc1_counts.txt
Marc1_TPM.txt


title: RNAseq_Testes_KO_Mcaf2_rep2

value: Mcaf2 KO


title: lung.WT.6950180

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep RH 6

value: CD34+-derived proE/basoE

value: SF3B1 WT SRSF2 TET2 MUT

value: Rnase H1


title: DMFHxSAP3CS22_L002

description:
DM_FHxSA_P3_C
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: C


title: lung.WT.6939296

description:
Marc1_counts.txt
Marc1_TPM.txt

value: lung


title: RNAseq_Testes_KO_Mcaf2_rep1


title: lung.WT.6927709

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP3BS23_L002

description:
DM_FHxSA_P3_B
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: B


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep NT 6


title: lung.WT.6927708

description:
Marc1_counts.txt
Marc1_TPM.txt


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, input ctrl HDACi rep 5

value: SF3B1 WT TET2 RAS MUT

value: HDACi


title: cWT,scRNA-seq,rep2

library_source: transcriptomic single cell

data_processing:
Basic processing and visualization of the scRNA-seq data were performed with the Seurat package (Version 4.1.0) in R (Version 4.1.1).
To rule out outliers, we performed filtering on the two datasets obtained in the previous step.
Merge a dataset of 4 samples with the merge() function and normalize the data.
We then defined doublets/multiplets as any cluster that significantly expresses marker genes of more than one cell type, and these cell types are not associated
Assembly: mm10
Supplementary files format and content: tsv
Supplementary files format and content: mtx

extract_protocol:
The concentration of single-cell suspension was adjusted to 700–1200 cells/μL in ice-cold PBS containing 0.4% BSA . The Around 17,400 cells of each sample were then loaded into a Chromium Single Cell 3′ ' Chip (10x 10X Genomics) and processed following the manufacturer’s instructions.
he 10x 10X libraries were constructed using Chromium  Controller and Chromium Single Cell 3’Reagent Kits (v2 chemistry CG00052)

value: brain

value: 8 weeks

value: cWT


title: DMFHxSAP3AS24_L002

description:
DM_FHxSA_P3_A
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: A


title: DMFHxSAP2HS9_L002

description:
DM_FHxSA_P2_H
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: FHxSA (DTXSID50469320)

value: ug/L

value: H


title: cKO,scRNA-seq,rep2

value: Mir137 knockout


title: liver.KO.6950223

description:
Marc1_counts.txt
Marc1_TPM.txt

value: liver


title: liver.KO.6950227

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP3ES20_L002

description:
DM_FHxSA_P3_E
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: E


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, rep HDACi_RH 5

value: CD34+-derived proE/basoE

value: HDACi + Rnase H1


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, rep HDACi_NT 5


title: liver.KO.6950219

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,scRNA-seq,rep1


title: cWT,RNA-seq,rep2

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

value: male


title: cWT,RNA-seq,rep3


title: DMFHxSAP2FS11_L002

description:
DM_FHxSA_P2_F
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: F


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, input ctrl rep 5

value: SF3B1 WT TET2 RAS MUT

value: no


title: DMFHxSAP2DS13_L002

description:
DM_FHxSA_P2_D
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: D


title: DMFHxSAP2ES12_L002

description:
DM_FHxSA_P2_E
DM_FHxSA_counts.filtered.+1.normFinal.txt


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, rep RH 5

value: Rnase H1


title: CD34+-derived proE/basoE cells, CCUS SF3B1 WT, rep NT 5


title: cWT,RNA-seq,rep1

value: brain

value: 8 weeks

value: cWT


title: liver.KO.6950202

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP2CS14_L002

description:
DM_FHxSA_P2_C
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: FHxSA (DTXSID50469320)

value: ug/L

value: C


title: liver.KO.6950187

description:
Marc1_counts.txt
Marc1_TPM.txt

value: liver


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl HDACi rep 4

value: CD34+-derived proE/basoE

value: SF3B1 WT SRSF2 MUT

value: HDACi


title: cWT,scRNA-seq,rep1


title: cKO,RNA-seq,rep3

value: cKO

value: male


title: liver.KO.6927712

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,RNA-seq,rep2


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_RH 4

value: HDACi + Rnase H1


title: DMFHxSAP2BS15_L002

description:
DM_FHxSA_P2_B
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: B


title: liver.KO.6927706

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP2GS10_L002

description:
DM_FHxSA_P2_G
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: G


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_NT 4


title: DMFHxSAP2AS16_L002

description:
DM_FHxSA_P2_A
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: A


title: DMFHxSAP1HS1_L002

description:
DM_FHxSA_P1_H
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: H


title: liver.KO.6913581

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,RNA-seq,rep1

value: brain

value: 8 weeks


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl rep 4

value: no


title: cWT,Pu.1,rep3

data_processing:
The raw FASTQ files were aligned to the mouse reference genome (GRCm38/mm10) using bowtie2(Version 2.4.4).
Use MACS2(Version 2.2.7.1) software to find peaks.
Use chip-r(Version 1.2.0) to combine each identical biological sample into a single BED file.
Use bedtools(Version 2.30.0) to find KO-specific peaks and WT-specific peaks.
Use the HOMER(Version 4.11) software to find Peak's motif.
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
approximately 100,000 sorted primary microglias each genotype were harvested and washed with PBS and once with wash buffe in the CUT&Tag Assay Kit ( Vazyme, TD903).
The primary microglias are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. Genomic DNA regions of interest were isolated using  antibodies against  H3K27Ac (Active Motif, catalog number 39133，1:100)，H3K4me3 (Active Motif, catalog number39159,1:100), Poll (Active Motif, catalog number 39133，1:100), Poll ser5p (Active Motif, catalog number 39133，1:100), Pu.1 (Active Motif, catalog number39159,1:100), respectively. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation. DNA sequence is tagmented, with adapters (Vazyme, ,TD202) added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries.

value: cWT

tag: chip antibody

value: anti-Pu


title: cWT,Pu.1,rep2


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep RH 4

tag: cell line

value: Rnase H1


title: liver.WT.6950224

description:
Marc1_counts.txt
Marc1_TPM.txt

value: liver


title: DMFHxSAP1FS3_L002

description:
DM_FHxSA_P1_F
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: FHxSA (DTXSID50469320)

value: ug/L

value: F


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep NT 4

tag: cell type

value: CD34+-derived proE/basoE

value: SF3B1 WT SRSF2 MUT


title: liver.WT.6950204

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cWT,Pu.1,rep1


title: liver.WT.6950200

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP1DS5_L002

description:
DM_FHxSA_P1_D
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: D


title: liver.WT.6950182

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,Pu.1,rep3

value: cKO


title: cKO,Pu.1,rep2


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_RH 3

value: SF3B1 WT

value: HDACi + Rnase H1

tag: sequencing batch


title: DMFHxSAP1CS6_L002

description:
DM_FHxSA_P1_C
DM_FHxSA_counts.filtered.+1.normFinal.txt

tag: tissue

value: C


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep HDACi_NT 3

value: HDACi


title: liver.WT.6950230

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP1BS7_L002

description:
DM_FHxSA_P1_B
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: B


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl rep 3

value: no


title: liver.WT.6950180

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,Pu.1,rep1

value: brain

value: 8 weeks

value: anti-Pu


title: cWT,Pol II Ser5P,rep3

value: cWT

value: anti-Pol II Ser5P


title: DMFHxSAP1AS8_L002

description:
DM_FHxSA_P1_A
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: FHxSA (DTXSID50469320)

value: ug/L

value: A


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep RH 3

value: CD34+-derived proE/basoE

value: Rnase H1


title: liver.WT.6927709

description:
Marc1_counts.txt
Marc1_TPM.txt

value: liver


title: DMFHxSAP1GS2_L002

description:
DM_FHxSA_P1_G
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: whole body

value: G


title: cWT,Pol II Ser5P,rep2


title: DMFC8diolP3HS60_L002

description:
DM_FC8diol_P3_H
DM_FC8diol_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to FC8diol

value: FC8diol (DTXSID30396867)

value: H


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep NT 3

value: SF3B1 WT

value: no


title: liver.WT.6927708

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFHxSAP1ES4_L002

description:
DM_FHxSA_P1_E
DM_FHxSA_counts.filtered.+1.normFinal.txt

value: E


title: DMFC8diolP3GS61_L002

description:
DM_FC8diol_P3_G
DM_FC8diol_counts.filtered.+1.normFinal.txt


title: cWT,Pol II Ser5P,rep1

value: brain

value: 8 weeks


title: cKO,Pol II Ser5P,rep3

value: cKO

value: anti-Pol II Ser5P


title: CD34+-derived proE/basoE cells, MDS SF3B1 WT, input ctrl HDACi rep 3

value: HDACi


title: FTC133_NR1D1

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

data_processing:
FastQC/MultiQC, Trimmomatic v0.38, mapping with HISHAT2 v2.1.0, quantification using featureCounts v2.0.0
Assembly: GRCh38
Supplementary files format and content: a tab-delimited text file contains TPM values for paired samples

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. RNA QC: total >= 2 ug, concentration >= 50 ng/ul, RIN >= 6.8, OD260/OD230 >= 2.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NR1D1 overexpression


title: DMFC8diolP3ES63_L002

description:
DM_FC8diol_P3_E
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: ug/L


title: kidney.KO.6950223

description:
Marc1_counts.txt
Marc1_TPM.txt

value: kidney


title: FTC133_Vector

value: WT


title: DMFC8diolP3DS64_L002

description:
DM_FC8diol_P3_D
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: whole body

value: D


title: cKO,Pol II Ser5P,rep2


title: liver.WT.6939296

description:
Marc1_counts.txt
Marc1_TPM.txt

value: liver


title: kidney.KO.6950219

description:
Marc1_counts.txt
Marc1_TPM.txt


title: TPC1_NR1D1


title: TPC1_Vector


title: DMFC8diolP3CS65_L002

description:
DM_FC8diol_P3_C
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: FC8diol (DTXSID30396867)

value: C


title: cWT,Pol II,rep3

value: cWT

value: anti-Pol II


title: DMFC8diolP3AS66_L002

description:
DM_FC8diol_P3_A
DM_FC8diol_counts.filtered.+1.normFinal.txt
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt removed.txt

value: A


title: kidney.KO.6950202

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,Pol II Ser5P,rep1

value: brain

value: 8 weeks


title: kidney.KO.6950187

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cWT,Pol II,rep2


title: CAL62_siControl


title: CAL62_siNR1D1

value: NR1D1 knockdown


title: DMFC8diolP2HS52_L002

description:
DM_FC8diol_P2_H
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: H


title: cWT,Pol II,rep1


title: kidney.KO.6927706

description:
Marc1_counts.txt
Marc1_TPM.txt


title: kidney.KO.6950227

description:
Marc1_counts.txt
Marc1_TPM.txt


title: 8505C_siNR1D1


title: cKO,Pol II,rep3

value: cKO


title: DMFC8diolP2FS54_L002

description:
DM_FC8diol_P2_F
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: F


title: kidney.KO.6913581

description:
Marc1_counts.txt
Marc1_TPM.txt

value: kidney


title: 8505C_siControl

value: WT


title: cKO,Pol II,rep2


title: DMFC8diolP2ES55_L002

description:
DM_FC8diol_P2_E
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: E


title: cKO,Pol II,rep1


title: DMFC8diolP2DS56_L002

description:
DM_FC8diol_P2_D
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: FC8diol (DTXSID30396867)

value: D


title: kidney.WT.6950230

description:
Marc1_counts.txt
Marc1_TPM.txt


title: kidney.WT.6950224

description:
Marc1_counts.txt
Marc1_TPM.txt


title: LNCaP-CITED2 rep 1

city: New York

first: Juan

middle: M

last: Arriaga

state: NY

address: 1425 Madison Ave

department: Oncological Sciences, Urology

institute: Icahn School of Medicine at Mount Sinai

description:
Instrument model: Element AVITI
Sample 8

data_processing:
We use bases2fastq version 1.1.0.593880262  for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.44.0).
We test for differentially expressed genes using DESeq2,
Assembly: Ensembl v96, Human:GRCh38.p12
Supplementary files format and content: Kallisto generated raw read counts are provided

source_name: prostate cancer

extract_protocol:
MagMAX-96 total RNA isolation kit
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistr

value: prostate cancer

value: LNCaP

value: CITED2-human cDNA


title: kidney.WT.6950204

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFC8diolP2GS53_L002

description:
DM_FC8diol_P2_G
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: G


title: cWT,H3K4me3,rep3

value: brain

value: 8 weeks

value: cWT


title: DMFC8diolP2CS57_L002

description:
DM_FC8diol_P2_C
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: C


title: kidney.WT.6950200

description:
Marc1_counts.txt
Marc1_TPM.txt


title: LNCaP-CITED2 rep 2

description:
Instrument model: Element AVITI
Sample 9


title: cWT,H3K4me3,rep2


title: kidney.KO.6927712

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFC8diolP2AS59_L002

description:
DM_FC8diol_P2_A
DM_FC8diol_counts.filtered.+1.normFinal.txt
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt removed.txt

value: GLTED-wt

value: A


title: DMFC8diolP2BS58_L002

description:
DM_FC8diol_P2_B
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: B


title: LNCaP-Control rep 3

description:
Instrument model: Element AVITI
Sample 7

value: Empty vector


title: cKO,H3K4me3,rep3

value: cKO


title: LNCaP-Control rep 2

description:
Instrument model: Element AVITI
Sample 6


title: LNCaP-Control rep 1

description:
Instrument model: Element AVITI
Sample 5


title: DMFC8diolP1HS44_L002

description:
DM_FC8diol_P1_H
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: H


title: kidney.WT.6950182

description:
Marc1_counts.txt
Marc1_TPM.txt

value: kidney


title: cKO,H3K4me3,rep2


title: LNCaP-CITED2 rep 3

description:
Instrument model: Element AVITI
Sample 10

value: prostate cancer


title: 22Rv1-CITED2 rep 2

description:
Instrument model: Element AVITI
Sample 4

value: 22Rv1-CRISPRa clone 1


title: kidney.WT.6939296

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cKO,H3K4me3,rep1


title: DMFC8diolP1FS46_L002

description:
DM_FC8diol_P1_F
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: FC8diol (DTXSID30396867)

value: F


title: 22Rv1-CITED2 rep 1

description:
Instrument model: Element AVITI
Sample 3


title: kidney.WT.6927709

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cWT,H3K27ac,rep3

value: brain


title: 22Rv1-Control rep 2

description:
Instrument model: Element AVITI
Sample 2

value: sgControl


title: DMFC8diolP1ES47_L002

description:
DM_FC8diol_P1_E
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: E


title: cWT,H3K4me3,rep1

value: 8 weeks

value: cWT


title: kidney.WT.6927708

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cWT,H3K27ac,rep2


title: DMFC8diolP1CS49_L002

description:
DM_FC8diol_P1_C
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: C


title: cWT,H3K27ac,rep1


title: DMFC8diolP1DS48_L002

description:
DM_FC8diol_P1_D
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: D


title: kidney.WT.6950180

description:
Marc1_counts.txt
Marc1_TPM.txt


title: pbmc, brain fog, 5

city: Dublin

first: Chris

last: Greene

address: 123 St Stephen's Green

department: Physiology & Medical Physics

country: Ireland

institute: Royal College of Surgeons in Ireland

data_processing:
Raw FASTQ files were trimmed with CutAdapt (part of TrimGalore) and aligned to the Gencode GRCh38 Release 43 reference with STAR.
The resulting BAMs were sorted with STAR and indexed with Samtools.
Gene quantification was performed using RSEM’s rsem-calculate-expression tool. Count matrices produced by RSEM were processed with TxImport and the differential expression analysis was performed using DESeq2 v1.38.3 in R.
Assembly: GRCH38
Supplementary files format and content: tab-delimited count matrix

source_name: pbmc

extract_protocol:
RNA was extracted from 1-2 million cells using the E.Z.N.A total RNA kit. 10 ng of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA seq were prepared using SMART-Seq v4 Ultra Low Input RNA for Sequencing, Nextera XT DNA Library Preparation Kit

value: pbmc

value: female

tag: group

value: Long COVID brain fog


title: heart.KO.6950223

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: heart.KO.6950227

description:
Marc1_counts.txt
Marc1_TPM.txt


title: 22Rv1-Control rep 1

description:
Instrument model: Element AVITI
Sample 1


title: DMFC8diolP1GS45_L002

description:
DM_FC8diol_P1_G
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: G


title: pbmc, brain fog, 3

tag: Sex


title: cKO,H3K27ac,rep3

tag: genotype

value: cKO


title: heart.KO.6950219

description:
Marc1_counts.txt
Marc1_TPM.txt


title: pbmc, brain fog, 4


title: DMFC8diolP1BS50_L002

description:
DM_FC8diol_P1_B
DM_FC8diol_counts.filtered.+1.normFinal.txt

value: FC8diol (DTXSID30396867)

value: B


title: cKO,H3K27ac,rep2

value: brain


title: cKO,H3K27ac,rep1


title: DMFC8diolP1AS51_L002

description:
DM_FC8diol_P1_A
DM_FC8diol_counts.filtered.+1.normFinal.txt
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt removed.txt

value: A


title: heart.KO.6950202

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFC8DoDP3HS65_L002

description:
DM_FC8DoD_P3_H
DM_FC8DoD_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to FC8DoD

value: FC8DoD (DTXSID70381090)

value: H


title: pbmc, brain fog, 2


title: heart.KO.6950187

description:
Marc1_counts.txt
Marc1_TPM.txt


title: pbmc, long covid, 6

value: Long COVID


title: DMFC8DoDP3FS67_L002

description:
DM_FC8DoD_P3_F
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: F


title: cWT,ATAC-seq,rep3

data_processing:
The raw FASTQ files were aligned to the mouse reference genome (GRCm38/mm10) using bowtie2(Version 2.4.4).
For futher analysis, reads mapping to the mitochondrial genome and blacklisted regions were removed from the analysis.
Use MACS2(Version 2.2.7.1) software to find peaks.
Use chip-r(Version 1.2.0) to combine each identical biological sample into a single BED file.
Use the HOMER(Version 4.11) software to find Peak's motif.
Assembly: mm10
Supplementary files format and content: bed

extract_protocol: approximately 50,000 sorted primary microgliasmicroglia each genotype were harvested and washed once with PBS. Nuclei were extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix.

value: 8 weeks

value: cWT


title: DMFC8DoDP3GS66_L002

description:
DM_FC8DoD_P3_G
DM_FC8DoD_counts.filtered.+1.normFinal.txt


title: heart.KO.6927706

description:
Marc1_counts.txt
Marc1_TPM.txt


title: cWT,ATAC-seq,rep2


title: pbmc, long covid, 4

value: pbmc

value: female


title: heart.KO.6913581

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: pbmc, long covid, 5

value: male


title: pbmc, long covid, 2


title: DMFC8DoDP3ES68_L002

description:
DM_FC8DoD_P3_E
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: E


title: cKO,ATAC-seq,rep3

value: cKO


title: cWT,ATAC-seq,rep1

value: brain


title: DMFC8DoDP3DS69_L002

description:
DM_FC8DoD_P3_D
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: D


title: cKO,ATAC-seq,rep2


title: cKO,ATAC-seq,rep1


title: heart.WT.6950224

description:
Marc1_counts.txt
Marc1_TPM.txt


title: heart.WT.6950230

description:
Marc1_counts.txt
Marc1_TPM.txt


title: DMFC8DoDP3CS70_L002

description:
DM_FC8DoD_P3_C
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: FC8DoD (DTXSID70381090)

value: C


title: pbmc, brain fog, 1

value: Long COVID brain fog


title: heart.WT.6950204

description:
Marc1_counts.txt
Marc1_TPM.txt


title: Young_M2_SPTOM_09_16

city: Bronx

middle: Robert

last: Fooksman

address: 1300 Morris Park

department: Pathology

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were aligned to the mouse genome (mm39/GRCm39) using STAR aligner (v2.6.1b). Differential expression was computed using the DESeq2 (v 1.26.0).Alignment was done using STAR
Counts for individual genes were quantified using the RSEM program (v1.3.1)
immunoglobulin genes were removed
Differential expression was computed using the DESeq2 (v 1.26.0).
Assembly: mm10/GRCm38
Supplementary files format and content: immunoglobulin genes removed for total processing normalized counts
Supplementary files format and content: assembled BCR clones using mixcr analysis

source_name: Spleen

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing
Nextera XT DNA Library Preparation Kit

value: Spleen

value: primary FACS-purified cells

value: Bulk PC

value: BEC-YFP

value: 6-8 week old mouse, D90 post Tamoxifen


title: DMFC8DoDP3AS72_L002

description:
DM_FC8DoD_P3_A
DM_FC8DoD_counts.filtered.+1.normFinal.txt
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: A


title: DMFC8DoDP3BS71_L002

description:
DM_FC8DoD_P3_B
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: B


title: heart.WT.6950200

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: heart.KO.6927712

description:
Marc1_counts.txt
Marc1_TPM.txt


title: Young_M2_BMTOM_09_16

source_name: Bone marrow

value: Bone marrow


title: DMFC8DoDP2HS57_L002

description:
DM_FC8DoD_P2_H
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: H


title: pbmc, recovered, 5

value: pbmc

value: female

value: COVID convalescent


title: DMFC8DoDP2GS58_L002

description:
DM_FC8DoD_P2_G
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: FC8DoD (DTXSID70381090)

value: G


title: heart.WT.6950182

description:
Marc1_counts.txt
Marc1_TPM.txt


title: pbmc, long covid, 3

value: Long COVID


title: Young-F9-SPTOM-10-05

value: Spleen

value: primary FACS-purified cells

value: Bulk PC


title: pbmc, recovered, 4


title: Young-F9-SPYFP-10-05

value: LLPC

value: BEC-YFP

value: 6-8 week old mouse, D90 post Tamoxifen


title: heart.WT.6950180

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: DMFC8DoDP2FS59_L002

description:
DM_FC8DoD_P2_F
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: F


title: Young-F9-BMYFP-10-05

value: Bone marrow


title: DMFC8DoDP2DS61_L002

description:
DM_FC8DoD_P2_D
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: ug/L

value: D


title: pbmc, recovered, 3

value: pbmc

value: male

value: COVID convalescent


title: Young-F7-BMYFP-09-29


title: DMFC8DoDP2ES60_L002

description:
DM_FC8DoD_P2_E
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: FC8DoD (DTXSID70381090)

value: E


title: pbmc, recovered, 2

value: female


title: Young-F9-BMTOM-10-05

value: primary FACS-purified cells

value: Bulk PC


title: cb_smallRNA_TC_WT_33h

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.briggsae genome (WS225) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from MirgeneDB2 was used. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: WS225
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

organism: Caenorhabditis briggsae

growth_protocol: Synchronized L1's of WT C. briggsae were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 18h to 33h

extract_protocol:
We harvested worms from 18h to 33h in hourly interval. Worms were collected from paltes and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using conventional phenol extraction, as described previously (Hendriks et al., 2014). Total RNA was DNAse treated
Sequencing libraries were generated using Illumina TruSeq Small RNA Library Prep Kit according to the manufacturer’s instructions. Subsequently, library was sequenced on Illumina HiSeq2500, as 50 cycles single-end reads.

value: WT

tag: time (h)


title: heart.WT.6927709

description:
Marc1_counts.txt
Marc1_TPM.txt


title: pbmc, recovered, 1


title: cb_smallRNA_TC_WT_32h

tag: treatment


title: DMFC8DoDP2BS63_L002

description:
DM_FC8DoD_P2_B
DM_FC8DoD_counts.filtered.+1.normFinal.txt

tag: conc.

value: B


title: pbmc, unaffected, 7

value: Healthy


title: heart.WT.6939296

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: cb_smallRNA_TC_WT_31h


title: pbmc, long covid, 1

value: Long COVID


title: Young-F7-SPYFP-09-29

value: Spleen

value: LLPC

value: BEC-YFP

value: 6-8 week old mouse, D90 post Tamoxifen


title: DMFC8DoDP2CS62_L002

description:
DM_FC8DoD_P2_C
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

tag: conc. units

value: ug/L

value: C


title: pbmc, unaffected, 6

value: pbmc


title: Young-F2-SPTOM-09-17


title: cb_smallRNA_TC_WT_30h


title: Young-F2-SPYFP-09-17


title: DMFC8DoDP2AS64_L002

description:
DM_FC8DoD_P2_A
DM_FC8DoD_counts.filtered.+1.normFinal.txt
DM_PFHxS_counts.filtered.+1.normFinal.txt

value: FC8DoD (DTXSID70381090)

tag: conc code

value: A


title: Young-F2-BMTOM-09-17

value: Bone marrow

value: primary FACS-purified cells

value: Bulk PC


title: DMFC8DoDP1HS49_L002

description:
DM_FC8DoD_P1_H
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: H

tag: exposure duration


title: heart.WT.6927708

description:
Marc1_counts.txt
Marc1_TPM.txt

value: heart


title: pbmc, unaffected, 4

value: female

value: Healthy


title: pbmc, unaffected, 3


title: DMFC8DoDP1GS50_L002

description:
DM_FC8DoD_P1_G
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: G

tag: age


title: cb_smallRNA_TC_WT_29h

value: WT


title: Young-F2-BMYFP-09-17

value: LLPC

value: BEC-YFP

value: 6-8 week old mouse, D90 post Tamoxifen


title: DMFC8DoDP1FS51_L002

description:
DM_FC8DoD_P1_F
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: ug/L

value: F

tag: replicate plate_id


title: pbmc, unaffected, 2

value: pbmc

value: male


title: DMFC8DoDP1DS53_L002

description:
DM_FC8DoD_P1_D
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: FC8DoD (DTXSID70381090)

value: D


title: AsPC-1 7d6h rep2

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the R package DESeq2 with the likelihood ratio test option.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: Mice were housed in an animal facility with a 12-hour day/night light cycle, temperature maintained at 25°C and humidity at 60%. Mice were maintained under pathogen-free conditions, with food and water provided ad libitum.

extract_protocol:
Total RNA samples were extracted with RNA TRIzol Reagent (Magen) according to the manufacturer’s manual.
For RNA-sequencing, 1μg of total RNA was used for library construction. Sequencing libraries were generated using VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina®. The libraries were sequenced as 150bp paired-end reads using Illumina Novaseq6000 according to the manufacturer's instructions by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: H358 and AsPC-1 xenograft mouse model were MCB-22-294 (Bid, 30 mg/kg) treated, followed by harvest and RNA extraction at 1 hours and 6 hours after the last dose.

tag: strain

value: BALB/c nude

value: 6-8 weeks

value: Pancreatic Cancer

value: 30 mg/kg MCB-22-294 for 7d6h


title: cb_smallRNA_TC_WT_28h


title: Young-M7-SPTOM-09-16

value: Spleen

value: primary FACS-purified cells

value: Bulk PC


title: pbmc, unaffected, 5

value: female

value: Healthy


title: AsPC-1 7d6h rep1


title: pbmc, unaffected, 1


title: DMFC8DoDP1ES52_L002

description:
DM_FC8DoD_P1_E
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: E


title: R1_Bulk tumor MycOETrp53KO [WES]

city: Amsterdam

first: Masami

last: Ando-Kuri

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

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

source_name: liver

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

value: liver

value: Myc overexpression Trp53 knockout

tag: time

value: End-stage

tag: disease state

value: cancer


title: OLD-F12-SPYFP-09-17

tag: cell line

tag: cell type

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D90 post Tamoxifen


title: cb_smallRNA_TC_WT_26h

value: WT


title: OLD-F12-BMTOM-09-17

tag: tissue

value: Bone marrow


title: DMFC8DoDP1AS56_L002

description:
DM_FC8DoD_P1_A
DM_FC8DoD_counts.filtered.+1.normFinal.txt
DM_PFHxS_counts.filtered.+1.normFinal.txt

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

value: GLTED-wt

value: FC8DoD (DTXSID70381090)

value: ug/L

value: A


title: OLD-F12-SPTOM-09-17

value: Spleen

value: primary FACS-purified cells

value: Bulk PC


title: OLD-F12-BMYFP-09-17


title: OLD-F15-SPTOM-09-17


title: DMFC8DoDP1CS54_L002

description:
DM_FC8DoD_P1_C
DM_FC8DoD_counts.filtered.+1.normFinal.txt

value: whole body

value: C


title: AsPC-1 1d6h rep3

value: BALB/c nude

value: 6-8 weeks

value: Pancreatic Cancer

value: 30 mg/kg MCB-22-294 for 1d6h


title: cb_smallRNA_TC_WT_25h


title: AsPC-1 7d1h rep3

value: 30 mg/kg MCB-22-294 for 7d1h


title: cb_smallRNA_TC_WT_24h


title: AsPC-1 7d1h rep2


title: cb_smallRNA_TC_WT_23h


title: DMFC10diolP3GS82_L002

description:
DM_FC10diol_P3_G
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to FC10diol

value: FC10diol (DTXSID50369896)

value: G


title: cb_smallRNA_TC_WT_27h

value: WT


title: DMFC10diolP3ES84_L002

description:
DM_FC10diol_P3_E
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: E


title: Young-M7-BMTOM-09-16

value: Bone marrow

value: BEC-YFP

value: 6-8 week old mouse, D90 post Tamoxifen


title: AsPC-1 7d1h rep1


title: OLD-F15-BMYFP-09-17

value: primary FACS-purified cells

value: LLPC

value: 24 week old mouse, D90 post Tamoxifen


title: DMFC10diolP3STDS88_L002

description:
n/a
n/a

value: whole body

value: ug/L

value: STD


title: cb_smallRNA_TC_WT_18h


title: AsPC-1 1d1h rep3

value: BALB/c nude

value: 6-8 weeks

value: Pancreatic Cancer

value: 30 mg/kg MCB-22-294 for 1d1h


title: cb_smallRNA_TC_WT_22h


title: DMFC10diolP3HS81_L002

description:
DM_FC10diol_P3_H
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: FC10diol (DTXSID50369896)

value: H


title: cb_smallRNA_TC_WT_20h

value: WT


title: GR ChIP_GSK

city: CLEVELAND

first: Yuan

last: Gao

state: OH

address: 2109 Adelbert Rd., Wood Building Research Tower 300-7, Wood Building Research Tower 300-7

department: Pharmacology

institute: Case Western Reserve University

data_processing:
Raw reads from RNA-seq were mapped to reference genome mm10 using RNA STAR with default parameters. Read count tables were created using FeatureCounts with a custom GTF file containing protein coding genes only. Differentially expressed genes were analyzed using DESeq2 with two independent replicates using default parameters.
Raw reads from ChIP-seq were aligned to the reference genome hg38 using Bowtie2 with sensitive end-to-end setting. After removal of PCR duplication reads by SAMtools, peaks were identified using MACS2, with narrow peak option for TFs and broad peak option for H3K27Ac. Genome-wide read coverage was calculated by deepTools with a bin size of 50 bp.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: neutrophil

growth_protocol: Mouse neutrophils were isolated from the bone marrow of 8-week-old female BL/6 mice. Briefly, bone marrow was flushed from both femurs and tibias with 1x Hanks’ Balanced Salt Solution (HBSS) using a syringe with a 26G needle. After washing the bone marrow cells once with 1x HBSS, the cells were resuspended in ammonium-chloride-potassium (ACK) lysis buffer for 3 minutes on ice. The cells were then washed twice with 1x HBSS, resuspended in 2 ml of HBSS. Neutrophils were isolated by density gradient separation. The density gradient was made by layering 2 mL of bone marrow cells on top of 3 mL of 62% Percoll (#17-0891-02, GE Healthcare) on top of 3 mL of 81% Percoll in a 15 ml falcon tube, followed by centrifugation at 2,500 x g for 20 minutes at 4°C. Neutrophils were then taken from the middle interface, washed in HBSS, and resuspended in serum-free DMEM before use.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For ChIP_seq experiments, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
was constructed using the Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions.

value: neutrophil

value: bone marrow isolated neutrophils

value: treated with 10 uM GSK9027


title: AsPC-1 1d6h rep2

value: 30 mg/kg MCB-22-294 for 1d6h


title: AsPC-1 1d1h rep2


title: DMFC8DoDP1BS55_L002

description:
DM_FC8DoD_P1_B
DM_FC8DoD_counts.filtered.+1.normFinal.txt

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

value: GLTED-wt

value: FC8DoD (DTXSID70381090)

value: B


title: GR ChIP_Vehicle

value: vehicle(DMSO)


title: AsPC-1 1d6h rep1


title: OLD-F15-SPYFP-09-17

value: Spleen

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D90 post Tamoxifen


title: AsPC-1 1d1h rep1

value: BALB/c nude

value: 6-8 weeks

value: Pancreatic Cancer

value: 30 mg/kg MCB-22-294 for 1d1h


title: DMFC10diolP3DS85_L002

description:
DM_FC10diol_P3_D
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: FC10diol (DTXSID50369896)

value: ug/L

value: D


title: AsPC-1 rep3

value: vehicle


title: OLD-M3-SPTOM-09-15

value: Bulk PC


title: OLD-F15-BMTOM-09-17

value: Bone marrow


title: cb_smallRNA_TC_WT_19h

value: WT


title: Input_Vehicle

value: neutrophil

value: bone marrow isolated neutrophils

value: vehicle(DMSO)


title: cb_smallRNA_TC_WT_21h


title: OLD-M3-SPYFP-09-15

value: Spleen

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP


title: DMFC10diolP2ES77_L002

description:
DM_FC10diol_P2_E
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: E


title: DMFC10diolP2HS74_L002

description:
DM_FC10diol_P2_H
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: H


title: AsPC-1 rep2

value: BALB/c nude

value: 6-8 weeks

value: Pancreatic Cancer


title: OLD-M3-BMTOM-09-15

value: Bulk PC

value: 24 week old mouse, D90 post Tamoxifen


title: AsPC-1 rep1

value: vehicle


title: primary tumor_stress_d35_bio rep3

value: tumor

value: primary tumor

value: WT

value: stress


title: OLD-M2-SPYFP-09-15

value: Spleen

value: primary FACS-purified cells


title: DMFC10diolP3BS87_L002

description:
DM_FC10diol_P3_B
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: FC10diol (DTXSID50369896)

value: ug/L

value: B


title: DMFC10diolP2GS75_L002

description:
DM_FC10diol_P2_G
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: G


title: primary tumor_stress_d35_bio rep2


title: DMFC10diolP2DS78_L002

description:
DM_FC10diol_P2_D
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: D


title: H358 7d6h rep3

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 7d6h


title: OLD-M2-SPTOM-09-15

value: Bulk PC

value: BEC-YFP

value: 24 week old mouse, D90 post Tamoxifen


title: OLD-M3-BMYFP-09-15

value: Bone marrow

value: LLPC


title: primary tumor_control_bio rep3

value: tumor

value: primary tumor

value: WT

value: control


title: DMFC10diolP2CS79_L002

description:
DM_FC10diol_P2_C
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: FC10diol (DTXSID50369896)

value: ug/L

value: C


title: DMFC10diolP2BS80_L002

description:
DM_FC10diol_P2_B
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: GLTED-wt

value: B


title: H358 7d1h rep3

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 7d1h


title: primary tumor_control_bio rep1


title: H358 7d6h rep2

value: 30 mg/kg MCB-22-294 for 7d6h


title: DMFC10diolP1STDS73_L002

description:
n/a
n/a

value: STD


title: OLD-M2-BMYFP-09-15

value: Bone marrow

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D90 post Tamoxifen


title: D5-M1-SPTOM-09-29

value: Spleen

value: Bulk PC

value: 24 week old mouse, D5 post Tamoxifen


title: neutrophil_GSK_bio rep2

value: neutrophil

value: bone marrow isolated neutrophils

value: WT

value: treated with 10 uM GSK9027


title: DMFC10diolP1ES70_L002

description:
DM_FC10diol_P1_E
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: FC10diol (DTXSID50369896)

value: ug/L

value: E


title: D5-SPYFP-09-15


title: H358 7d6h rep1

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 7d6h


title: primary tumor_control_bio rep2

value: tumor

value: primary tumor

value: control


title: neutrophil_GSK_bio rep1


title: D5-BMTOM-09-15

value: Bone marrow

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D5 post Tamoxifen


title: neutrophil_Dex_bio rep2

value: neutrophil

value: bone marrow isolated neutrophils

value: WT

value: treated with 10 uM dexamethasone


title: DMFC10diolP1FS69_L002

description:
DM_FC10diol_P1_F
n/a
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: FC10diol (DTXSID50369896)

value: ug/L

value: F


title: neutrophil_Dex_bio rep1


title: D5-M1-BMYFP-09-29


title: H358 1d6h rep1

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 1d6h


title: H358 7d1h rep2

value: 30 mg/kg MCB-22-294 for 7d1h


title: D5-SPTOM-07-26

value: Spleen

value: primary FACS-purified cells

value: Bulk PC


title: DM8-2FTSP3GS66_L002

description:
DM_8-2FTS_P3_G
DM_8-2FTS_counts.filtered.+1.normFinal.txt

source_name: RNA-Seq of daphnia magna whole body after 24 h exposure to 8:2FTS

value: G


title: H358 1d1h rep3

value: 30 mg/kg MCB-22-294 for 1d1h


title: DM8-2FTSP3FS67_L002

description:
DM_8-2FTS_P3_F
DM_8-2FTS_counts.filtered.+1.normFinal.txt


title: neutrophil_stress_bio rep3

value: neutrophil

value: Ly6G+ cells enriched from lungs

value: WT

value: stress


title: DM8-2FTSP3ES68_L002

description:
DM_8-2FTS_P3_E
DM_8-2FTS_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: E


title: H358 7d1h rep1

value: BALB/c nude


title: D5-M1-SPYFP-09-29

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D5 post Tamoxifen


title: DMFC10diolP1DS71_L002

description:
DM_FC10diol_P1_D
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: FC10diol (DTXSID50369896)

value: ug/L

value: D


title: H358 1d6h rep3

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 1d6h


title: OLD-M2-BMTOM-09-15

value: Bone marrow

value: primary FACS-purified cells

value: Bulk PC

value: 24 week old mouse, D90 post Tamoxifen


title: primary tumor_stress_d35_bio rep1

value: tumor

value: primary tumor

value: WT

value: stress


title: neutrophil_stress_bio rep1

value: neutrophil

value: Ly6G+ cells enriched from lungs


title: DMFC10diolP1CS72_L002

description:
DM_FC10diol_P1_C
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: C


title: DMFC10diolP1HS67_L002

description:
DM_FC10diol_P1_H
DM_FC10diol_counts.filtered.+1.normFinal_QA_2687trt_removed.txt
DM_FC10diol_counts.filtered.+1.normFinal.txt

value: FC10diol (DTXSID50369896)

value: ug/L

value: H


title: H358 1d6h rep2

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: 30 mg/kg MCB-22-294 for 1d6h


title: DM8-2FTSP3HS65_L002

description:
DM_8-2FTS_P3_H
DM_8-2FTS_counts.filtered.+1.normFinal.txt


title: neutrophil_vehicle_bio rep2

value: bone marrow isolated neutrophils

value: vehicle(DMSO)


title: neutrophil_vehicle_bio rep1


title: D5-SPYFP-07-26

value: Spleen

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D5 post Tamoxifen


title: D5-BMTOM-07-26

value: Bone marrow

value: Bulk PC


title: D5-M1-BMTOM-09-29


title: H358 1d1h rep1

value: 30 mg/kg MCB-22-294 for 1d1h


title: neutrophil_stress_bio rep2

value: neutrophil

value: Ly6G+ cells enriched from lungs

value: WT

value: stress


title: neutrophil_control_bio rep1

value: control


title: D5-BMYFP-07-26


title: DM8-2FTSP3DS69_L002

description:
DM_8-2FTS_P3_D
DM_8-2FTS_counts.filtered.+1.normFinal.txt

value: whole body

value: GLTED-wt

value: ug/L

value: D


title: M14 3D CD20- replicate 3

city: Cardiff

first: Girish

middle: K

last: Patel

address: Maindy Road

country: United Kingdom

institute: Cardiff University

data_processing:
Trimmed and quality-checked reads were aligned to the GRCh38 human reference genome using HISAT2
normalised reads were generated using featureCounts (v1.5.0)
differentially expressed genes were then generated using the standard DESeq2 pipeline
Assembly: GRCh38/hg38
Supplementary files format and content: .txt data file normalised reads for each sample.

extract_protocol:
M14 cells were grown under non-adherent culture conditions to generate melanospheres. Melanospheres were mechanically dissociated, antibody labelled for CD20 and flow sorted to isolate CD20+ and CD20- populations. RNA was extracted from samples using an RNeasy mini kit as per manufacturers instructions. RNA was then quantified and quality assessed before being sent to Novogene (Cambridge, UK).
total RNA was extracted using Rneasy mini kit (QIAGEN).
RNA was sent to Novogene (Cambridge, UK). Libraries were generated using Illumina TruSeq RNA Library Prep Kit (v2) and were subsequently sequenced on a Illumina NovaSeq 6000


title: D5-SPTOM-09-01

value: Spleen


title: H358 rep3

value: BALB/c nude

value: 6-8 weeks

value: Non-Small Cell Lung Cancer

value: vehicle


title: DM8-2FTSP3CS70_L002

description:
DM_8-2FTS_P3_C
DM_8-2FTS_counts.filtered.+1.normFinal.txt

value: C


title: H358 rep2


title: H358 1d1h rep2


title: neutrophil_control_bio rep3


title: D5-SPYFP-09-01

value: primary FACS-purified cells

value: LLPC

value: BEC-YFP

value: 24 week old mouse, D5 post Tamoxifen


title: DM8-2FTSP3BS71_L002

description:
DM_8-2FTS_P3_B
DM_8-2FTS_counts.filtered.+1.normFinal.txt

value: B


title: D5-BMTOM-09-01

value: Bone marrow

value: Bulk PC


title: H358 rep1


title: DM8-2FTSP3AS72_L002

description:
DM_8-2FTS_P3_A
DM_8-2FTS_counts.filtered.+1.normFinal.txt
DM_PFTDoDA_counts.filtered.+1.normFinal.txt

value: whole body

value: A


title: neutrophil_control_bio rep2

value: neutrophil

value: Ly6G+ cells enriched from lungs

value: WT

value: control