title: E14.5 Female PGC RNAseq Tet1-WT1

city: Philadelphia

first: Rexxi

middle: Diptya

last: Prasasya

state: PA

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: WT PGC F1

data_processing:
Quality of raw reads were assessed using FastQC
Raw reads were quality-trimmed Using Trim Galore (v0.6.7)
Reads were aligned to GRCm39 (mm10) using STAR (v2.7.10b) with default parameters and a maximum fragment size of 2000bp
Properly paired primary alignments were retained for downstream analysis using Samtools (v1.9)
Count matrices were generated using featureCounts 2.0.3 against RefSeq gene annotation
Assembly: mm10
Supplementary files format and content: Text file of summary count

source_name: Primordial germ cell

extract_protocol:
Total RNA was extrated using Quick RNA Microprep Kit by Zymo Research from 5000 cells
mRNA library was generated using Oligo d(T)25 RNA Magnetic Isolation Module followed by UltraII RNA Library Prep Kit (NEB) following manufacturer's protocol

value: Primordial germ cell

tag: Sex

value: Female

value: WT


title: HepaPlate02_F03

status: Public on Feb 26 2024

type: SRA

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples

molecule: total RNA

organism: Homo sapiens

source_name: Blank

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

tag: cell line

value: Blank

tag: cell type

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

tag: treatment

value: AFFF-6 (FireStopper)


title: E14.5 Female PGC RNAseq Tet1-WT3

description: WT PGC F3

organism: Mus musculus

tag: tissue

tag: genotype


title: E14.5 Female PGC RNAseq Tet1-WT2

description: WT PGC F2


title: E14.5 Female PGC RNAseq Tet1-V3

description: V PGC F3


title: E14.5 Female PGC RNAseq Tet1-V2

description: V PGC F2


title: HepaPlate02_E12

value: AFFF-3 (Phos-Check)


title: HepaPlate02_F11

value: 4:2 Fluorotelomer alcohol


title: E14.5 Female PGC RNAseq Tet1-V1

description: V PGC F1


title: HepaPlate02_E09

value: AFFF-5 (Solberg 6%)


title: HepaPlate02_E10


title: E14.5 Female PGC RNAseq Tet1-KO2

description: KO PGC F2

value: KO Tet1-/-


title: HepaPlate02_E08

value: 8:2 Fluorotelomer alcohol


title: HepaPlate02_F08


title: E14.5 Female PGC RNAseq Tet1-KO1

description: KO PGC F1


title: WT leaf bio bio rep 1

city: Auckland

first: Joanna

last: Putterill

state: Auckland

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

data_processing:
The quality of the sequenced raw reads (FASTQ files) was assessed and the trimming of the reads was done using Fastp (version 0.21) (Chen et al., 2018). Reads were trimmed from the 3′ end where quality dropped below a PHRED score of 20 and any remaining reads under 36 bp in length were also excluded.
The trimmed reads were mapped to the Mt4.0v2 transcriptome (Young et al., 2011; Tang et al., 2014) using Salmon (v0.8.2) (Patro et al., 2017). The resulting count tables, in which abundance is measured as Transcripts per Million (TPM), were then imported into R (R Core Team, 2018) using the tximport package (v1.12.0) (Soneson et al., 2015). Normalisation and differential expression analysis visualization were performed using DESeq2 (v1.24.0) (Love et al., 2014). Differentially expressed transcripts were filtered-out using a cut-off of adjusted p-value ≤ 0.05 and log2fold-change ≥ 1 or ≤-1.
Assembly: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary files format and content: Excel file including raw counts for each sample
Supplementary files format and content: excel file including normalised counts for each sample

organism: Medicago truncatula

source_name: leaf

growth_protocol: Medicago seeds were first scarified in between two pieces of sandpaper, sterilized in chlorine solution  for 5-10 minutes and germinated overnight at 15°C in the dark. Germinated seeds were placed on moist filter paper and stored at 4°C in the dark for 3 weeks. Germinated seeds with or without vernalisation were planted in seed raising mix (Daltons Limited, NZ) and placed on sub-irrigated rockwool mats. Seedlings were transplanted after 11-14 days to 2L pots of soil mix consisting of potting mix,  vermiculite and number 2 sand. Plants were grown in controlled rooms in long day (LD, 16 hours light/8 hours dark) or short day (SD, 8 hours light/16 hours dark) photoperiods at 22°C.

extract_protocol:
Fully expanded trifoliate leaves (leaf) or shoot apices (apex) (15-100 mg), were harvested from plants grown under VLD conditions at Zeitgeber time 4 (4 h after dawn). Tissues were snap frozen with metal beads and homogenised using a Geno/Grinder (New Jersey, USA) into powder in liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) following the manufacturer’s protocol. The quantity and quality of RNA were checked by Bioanalyzer 2100 (Agilent Technologies, USA).
The RNA of Mtsoc1a mutant and wild type R108 were constructed into 12 strand-specific mRNA libraries with polyA enrichment and were subjected to Illuminia NovaSeq 6000 paired-end 150 bp sequencing by Novogene. The RNA of triple Mtsoc1-4 mutant were constructed into three strand-specific mRNA libraries with polyA enrichment and sequenced on Illumina platform NovaSeq 6000, paired-end 150 bp by Novogene (Hong Kong).

treatment_protocol: Fully expanded trifoliate leaves (leaf) or shoot apices (apex) were harvested from 15 day old Mtsoc1a and WT. Two trifoliate leaves, one leaf taken from each of two plants, were pooled to make up one biological replicate; with three biological replicates harvested for each genotype. For the RNA-seq on the Mtsoc1-4 mutant, the upper portion of three primary stems with their shoot apex, from three plants, were pooled to make up one biological replicate, with three biological replicates harvested for each genotype.

value: leaf

tag: developmental stage

value: 15 days old

tag: genetic modification

value: wild type


title: HepaPlate02_E06

value: Perfluoroundecanoic acid


title: E14.5 Female PGC RNAseq Tet1-HxD2

description: HxD PGC F2


title: E14.5 Female PGC RNAseq Tet1-HxD1

description: HxD PGC F1


title: HepaPlate02_E05

value: AFFF-2 (Chemguard 6%)


title: HepaPlate02_D12


title: HepaPlate02_E03


title: HepaPlate02_E02

value: 8:2 Fluorotelomer sulfonic acid


title: E14.5 Male PGC RNAseq Tet1-WT3

data_processing:
Quality of raw reads were assessed using FastQC
Raw reads were quality-trimmed Using Trim Galore (v0.6.7)
Reads were aligned to GRCm39 (mm10) using STAR (v2.7.10b) with default parameters and a maximum fragment size of 2000bp
Properly paired primary alignments were retained for downstream analysis using Samtools (v1.9)
Count matrices were generated using featureCounts 2.0.3 against RefSeq gene annotation
Assembly: mm10

source_name: WT PGC3


title: E14.5 Male PGC RNAseq Tet1-WT2

source_name: WT PGC2


title: E14.5 Male PGC RNAseq Tet1-WT4

source_name: WT PGC4


title: E14.5 Female PGC RNAseq Tet1-KO3

description: KO PGC F3

value: Primordial germ cell


title: E14.5 Male PGC RNAseq Tet1-WT1

source_name: WT PGC1


title: E14.5 Male PGC RNAseq Tet1-V3

source_name: V PGC3

value: V


title: HepaPlate02_D09


title: HepaPlate02_L02

value: Perfluorononanoic acid


title: E14.5 Male PGC RNAseq Tet1-V2

source_name: V PGC2


title: E14.5 Male PGC RNAseq Tet1-KO3

source_name: KO PGC3

value: KO


title: E14.5 Male PGC RNAseq Tet1-V1

source_name: V PGC1


title: HepaPlate02_E07

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Sodium perfluorodecanesulfonate


title: E14.5 Male PGC RNAseq Tet1-KO2

source_name: KO PGC2


title: HepaPlate02_D07


title: HepaPlate02_D06


title: E14.5 Female PGC RNAseq Tet1-HxD3

description: HxD PGC F3

value: Female


title: E14.5 Male PGC RNAseq Tet1-KO1

source_name: KO PGC1


title: E14.5 Male PGC RNAseq Tet1-HxD3

source_name: HxD PGC3

value: HxD


title: E14.5 Male PGC RNAseq Tet1-HxD2

source_name: HxD PGC2


title: HepaPlate02_D04

value: AFFF-1 (Foamtec 3%)


title: HepaPlate02_D10


title: E14.5 Male PGC RNAseq Tet1-HxD1

source_name: HxD PGC1


title: HepaPlate01_M21

value: DMSO


title: HepaPlate01_M22


title: HepaPlate02_D03

value: AFFF-6 (FireStopper)


title: HepaPlate01_M20


title: HepaPlate01_M19


title: HepaPlate02_D02


title: HepaPlate01_M17


title: HepaPlate02_D08

value: 8:2 Fluorotelomer alcohol


title: HepaPlate01_M16


title: HepaPlate01_M18


title: HepaPlate01_M09


title: HepaPlate02_E11

value: 4:2 Fluorotelomer alcohol


title: HepaPlate02_D05


title: HepaPlate01_M03


title: HepaPlate01_M04


title: HepaPlate01_M05


title: HepaPlate01_M06


title: HepaPlate01_M08


title: sc_matched_708_709_713, GEX

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
scRNA-seq of matching samples
sc_matched_708_709_713_barcodes.tsv.gz
sc_matched_708_709_713_features.tsv.gz
sc_matched_708_709_713_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Spatial: Raw sequencing data were processed using the 10x Genomics Space Ranger v2.0.0 mkfastq pipeline to generate FASTQ files.
Sequences were aligned to the mm10 transcriptome and gene expression counts were obtained using SpaceRanger count.
scRNA-seq: Data were run through Cell Ranger v7.0.0 and demultiplexing of the hashtag oligo (HTO) data was performed using Bioconductor package demuxmix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg:  aligned image of microscope and CytAssist images
Supplementary files format and content: cytassist_image.tiff: corresponding CytAssist image

source_name: Spleen

extract_protocol:
OCT: Fresh frozen tissue was embedded in OCT and sectioned at 10µm on a cryostat. All blocks had a RIN score >8.0. FFPE: 40μm (8 x 5μm sections) each from mouse spleen. The RNA was extracted using the Qiagen FFPE extraction kit and the DV200 assessed on the TapeStation. All blocks had a DV200 >50%.
Spatial: Libraries were prepared with 10x Genomics Visium Spatial Gene Expression slides and reagent kit according to manufacturer's instructions.
scRNA-seq: 10x scRNA-seq with the large BioLegend panel of antibody derived tags (ADTs)
Spatial Transcriptomics and scRNA-seq

value: Spleen

value: WT

tag: disease state

value: malaria infection


title: sc_matched_708_709_713, HTO

description:
HTO of matching samples
sc_matched_708_709_713_barcodes.tsv.gz
sc_matched_708_709_713_features.tsv.gz
sc_matched_708_709_713_matrix.mtx.gz

data_processing:
Spatial: Raw sequencing data were processed using the 10x Genomics Space Ranger v2.0.0 mkfastq pipeline to generate FASTQ files.
Sequences were aligned to the mm10 transcriptome and gene expression counts were obtained using SpaceRanger count.
scRNA-seq: Data were run through Cell Ranger v7.0.0 and demultiplexing of the hashtag oligo (HTO) data was performed using Bioconductor package demuxmix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg:  aligned image of microscope and CytAssist images
Supplementary files format and content: cytassist_image.tiff: corresponding CytAssist image
Library strategy: HTO


title: HepaPlate01_L23

value: Perfluoroheptanoic acid


title: HepaPlate01_L22


title: FFPE_CytAssist_WT_713, ST

description: Formalin-fixed paraffin-embedded (FFPE) with CytAssist spatial transcriptome sequencing

data_processing:
Spatial: Raw sequencing data were processed using the 10x Genomics Space Ranger v2.0.0 mkfastq pipeline to generate FASTQ files.
Sequences were aligned to the mm10 transcriptome and gene expression counts were obtained using SpaceRanger count.
scRNA-seq: Data were run through Cell Ranger v7.0.0 and demultiplexing of the hashtag oligo (HTO) data was performed using Bioconductor package demuxmix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg:  aligned image of microscope and CytAssist images
Supplementary files format and content: cytassist_image.tiff: corresponding CytAssist image
Library strategy: Spatial Transcriptomics


title: HepaPlate01_L19


title: HepaPlate01_L21

value: 3:3 Fluorotelomer carboxylic acid


title: FFPE_CytAssist_WT_709, ST


title: HepaPlate01_L20

value: Ammonium perfluorooctanoate


title: HepaPlate01_L18

value: Perfluoro(4-methoxybutanoic) acid


title: FFPE_2_WT_713, ST

description: Formalin-fixed paraffin-embedded (FFPE) spatial transcriptome sequencing


title: Mtsoc1a single mutant leaf bio rep 1

value: leaf

value: 15 days old

value: SOC1a Tnt1 mutation


title: OCT_CytAssist_WT_713, ST

description: Fresh Frozen with CytAssist spatial transcriptome sequencing


title: OCT_CytAssist_WT_709, ST


title: HepaPlate01_M07

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: FFPE_2_WT_709, ST


title: HepaPlate01_L17

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: HepaPlate01_L16

value: Perfluorooctanamidine


title: FFPE_2_WT_708, ST


title: HepaPlate01_L12


title: HepaPlate01_L14

value: Nonafluoropentanamide


title: sc_matched_708_709_713, ADT

description:
ADT of matching samples
sc_matched_708_709_713_barcodes.tsv.gz
sc_matched_708_709_713_features.tsv.gz
sc_matched_708_709_713_matrix.mtx.gz

data_processing:
Spatial: Raw sequencing data were processed using the 10x Genomics Space Ranger v2.0.0 mkfastq pipeline to generate FASTQ files.
Sequences were aligned to the mm10 transcriptome and gene expression counts were obtained using SpaceRanger count.
scRNA-seq: Data were run through Cell Ranger v7.0.0 and demultiplexing of the hashtag oligo (HTO) data was performed using Bioconductor package demuxmix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg:  aligned image of microscope and CytAssist images
Supplementary files format and content: cytassist_image.tiff: corresponding CytAssist image
Library strategy: ADT


title: OCT_KOvsCTRL_KO_168, ST

description: Fresh Frozen spatial transcriptome sequencing

value: T-bet KO


title: HepaPlate01_L15

value: Perfluorohexanesulfonamide


title: HepaPlate01_L13

value: Perfluorononanoic acid


title: OCT_KOvsCTRL_CTRL_174, ST

value: Spleen

value: CTRL


title: OCT_KOvsCTRL_CTRL_173, ST

value: malaria infection


title: HepaPlate02_E04

value: AFFF-1 (Foamtec 3%)


title: HepaPlate01_L09

value: Ammonium perfluorooctanoate


title: HepaPlate01_L07

value: Perfluoro(4-methoxybutanoic) acid


title: OCT_KOvsCTRL_KO_167, ST


title: HepaPlate01_L08


title: OCT_WT_708, ST

value: WT


title: OCT_WT_545, ST


title: OCT_WT_544, ST


title: FFPE_2_WT_710, ST


title: HepaPlate02_D11

value: 4:2 Fluorotelomer alcohol


title: HepaPlate01_L04


title: FFPE_1_WT_460, ST


title: FFPE_1_WT_463, ST


title: OCT_pilot_KO_167, ST


title: HepaPlate01_L10

value: 3:3 Fluorotelomer carboxylic acid


title: HepaPlate01_K23

value: Blank

value: Perfluoroheptanoic acid


title: HepaPlate01_L02

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: OCT_pilot_WT_545, ST


title: OCT_WT_709, ST


title: OCT_pilot_CTRL_172, ST


title: OCT_pilot_WT_543, ST


title: HepaPlate01_L11


title: HepaPlate01_K21


title: PCSK9DY-WD_4

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Aorta

extract_protocol:
RNA-sequencing analysis was performed in the descending aorta. Aortic tissue was isolated, trimmed from fat and snap frozen in nitrogen. Total RNA was isolated with the RNA Mini Kit from Bio& SELL (Nuremberg, Germany) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
500 µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture's protocol (Vazyme). Sequencing was performed on NextSeq2000 instrument (Illumina) with 1x72 bp single end setup.

value: Aorta

value: diet:Western diet (WD)


title: PCSK9DY-WD_3


title: HepaPlate01_K20

source_name: Blank


title: PCSK9DY-WD_2


title: HepaPlate01_L06

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: HepaPlate01_K19


title: PCSK9DY-WD_1


title: HepaPlate01_K18


title: HepaPlate01_L05

value: Perfluorooctanamidine


title: FFPE_1_WT_462, ST


title: HepaPlate01_K16


title: chow_2


title: HepaPlate01_K15

value: Perfluorohexanesulfonamide


title: chow_1


title: HepaPlate01_L03

value: Nonafluoropentanamide


title: HepaPlate01_K14


title: HepaPlate01_K22


title: CD45.1 1DER T cells day 3 mediatinal lymph node replicate 2

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

description: 10X Genomics

data_processing:
initial quality check, adapter trimming and quantification using CellRanger to obtain gene level abundances using mm10 (UCSC) as reference
Post quantification we used Seurat v.4.3.0, an R package for downstream analysis, filtered count matrix of scRNA-seq were used as input, which were then normalized using the NormalizeData function in Seurat
for the CITE-seq data, the input was a concatenated matrix of log-transformed normalized gene expression data/gene activity score matrix and log-transformed ADTs matrix
The top 2,000 most variable genes were selected from scRNA-seq usingFindVariableFeatureswithvstas method. PCA was then performed on the merged matrix of scRNA-seq data. For all the datasets, 30 principal components (PCs) were used for joint visualization with UMAP (functionRunUMAP). Initially, the 12 clusters identified by PCA followed by UMAP in scRNA-seq data were annotated using ImmGen data and SingleR, R package
Assembly: mm10
Supplementary files format and content: features.tsv
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: matrix.mtx

source_name: lymph node

extract_protocol:
The mediastinal draining lymph node was dissociated in 5 ml of PBS+1%BSA and passed through 40um filters. For scRNA-seq with CITE-seq, cells were counted and blocked using TruStain FcX PLUS (anti-mouse CD16/32) antibody followed by 1DER CD45.1+ T cell labeling using TotalSeq™-B0178 anti-mouse CD45.1 Antibody (110755). The cells from whole lymph node were loaded as per the manufacture’s protocol (10x Genomic, CG000149) with a targeted cell recovery of 10,000 cells.
NextGEM 3PrimeV3.1 chemistry and associated feature barcode libraries (Total-seq B)

treatment_protocol: naïve 1DERYFP CD4+ T cells (CD45.1+) were transferred into CD45.2+ recipients and were immunized with 25 µg of HDM intranasally daily for 3 days.

value: lymph node

value: House dust mite intranasal


title: CD45.1 1DER T cells day 3 mediatinal lymph node replicate 1

description: 10X Genomics


title: HepaPlate01_K13

value: Perfluorononanoic acid


title: HepaPlate01_K12


title: Day 3 Mediastinal lymph node replicate 2

description: 10X Genomics


title: Day 3 Mediastinal lymph node replicate 1

description: 10X Genomics


title: HepaPlate01_K11


title: D17-21.Biopsy_219

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description: Post-injury Day:4Wound Zone:Edge

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized
Assembly: CanFam3.1
Supplementary files format and content: ExpectedCounts.txt.gz: Text file, mapping read counts
Supplementary files format and content: MedianNorm_TPMs.txt.gz: text file, normalized TPM values

organism: Canis lupus

source_name: Muscle

extract_protocol:
Total RNAs were isolated from tissues using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
One hundred nanograms of total RNA was used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol (Hou, Z. et al. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Sci Rep 5, 9570 (2015).)

value: Muscle

value: all cell types in muscle

value: No treatment (default healing)


title: genomic DNA from WT sperm 8

type: genomic

description:
Bisulfite treated
WT-1569

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Mouse285 Methylation BeadChip 12v1-0 using standard Illumina Protocol

scan_protocol: Illumina iScan System

data_processing:
SeSAMe R Package
Beta values of individual probe for each individual sample. Probes that did not pass SeSAMe quality control pOOBAH approach is maksed with NA

label: Cy5 and Cy3

molecule: genomic DNA

source_name: WT sperm

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using standard Phenol:Chloform extraction

value: WT

value: sperm


title: HepaPlate01_K10

value: Blank

value: 3:3 Fluorotelomer carboxylic acid


title: chow_4


title: D17-21.Biopsy_218

description: Post-injury Day:4Wound Zone:Intermediate


title: HepaPlate01_K09

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Ammonium perfluorooctanoate


title: HepaPlate01_K08


title: chow_3

value: Aorta


title: HepaPlate01_K17

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: genomic DNA from WT sperm 6

description:
Bisulfite treated
WT-1406


title: genomic DNA from WT sperm 4

description:
Bisulfite treated
WT-779


title: HepaPlate01_K06


title: D17-21.Biopsy_217

description: Post-injury Day:4Wound Zone:Center


title: HepaPlate01_K07

value: Perfluoro(4-methoxybutanoic) acid


title: D17-21.Biopsy_216

description: Post-injury Day:2Wound Zone:Edge


title: D17-21.Biopsy_215

description: Post-injury Day:2Wound Zone:Intermediate


title: genomic DNA from WT sperm 3

description:
Bisulfite treated
WT-586


title: genomic DNA from WT sperm 2

description:
Bisulfite treated
WT-557


title: genomic DNA from WT sperm 1

description:
Bisulfite treated
WT-4


title: HepaPlate01_K05

value: Perfluorooctanamidine


title: genomic DNA from Tet1-V sperm 10

description:
Bisulfite treated
V-1366

source_name: V sperm

value: V


title: genomic DNA from Tet1-V sperm 9

description:
Bisulfite treated
V-3753


title: genomic DNA from Tet1-V sperm 8

description:
Bisulfite treated
V-780


title: D17-21.Biopsy_214

description: Post-injury Day:2Wound Zone:Center


title: HepaPlate01_K04

value: Perfluorohexanesulfonamide


title: genomic DNA from Tet1-V sperm 6

description:
Bisulfite treated
V-1499


title: HepaPlate01_K03

value: Nonafluoropentanamide


title: genomic DNA from Tet1-V sperm 5

description:
Bisulfite treated
V-1407


title: genomic DNA from Tet1-V sperm 7

description:
Bisulfite treated
V-1521


title: D17-20.Biopsy_98

description: Post-injury Day:42Wound Zone:Edge


title: genomic DNA from WT sperm 5

description:
Bisulfite treated
WT-1360


title: HepaPlate01_K02

value: Perfluorononanoic acid


title: genomic DNA from Tet1-V sperm 3

description:
Bisulfite treated
V-ep3


title: genomic DNA from WT sperm 7

description:
Bisulfite treated
WT-1522


title: genomic DNA from Tet1-V sperm 4

description:
Bisulfite treated
V-1363


title: HepaPlate01_J23

value: Perfluoroheptanoic acid


title: D17-20.Biopsy_129

description: Post-injury Day:42Wound Zone:Edge

value: Muscle

value: all cell types in muscle


title: genomic DNA from Tet1-V sperm 1

description:
Bisulfite treated
V-685


title: genomic DNA from Tet1-KO sperm 9

description:
Bisulfite treated
KO-5715

source_name: KO sperm

value: KO


title: D17-20.Biopsy_127

description: Post-injury Day:42Wound Zone:Intermediate

value: No treatment (default healing)


title: HepaPlate01_J22

value: Blank


title: D17-20.Biopsy_128

description: Post-injury Day:42Wound Zone:Edge


title: genomic DNA from Tet1-KO sperm 10

description:
Bisulfite treated
KO-notag

value: sperm


title: HepaPlate01_J21

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 3:3 Fluorotelomer carboxylic acid


title: genomic DNA from Tet1-KO sperm 7

description:
Bisulfite treated
KO-1901


title: genomic DNA from Tet1-KO sperm 8

description:
Bisulfite treated
KO-3325


title: HepaPlate01_J20

value: Ammonium perfluorooctanoate


title: genomic DNA from Tet1-KO sperm 6

description:
Bisulfite treated
KO-1547


title: genomic DNA from Tet1-KO sperm 5

description:
Bisulfite treated
KO-1248


title: D17-20.Biopsy_125

description: Post-injury Day:42Wound Zone:Center


title: HepaPlate01_J19


title: D17-20.Biopsy_99

description: Post-injury Day:42Wound Zone:Edge


title: genomic DNA from Tet1-KO sperm 3

description:
Bisulfite treated
KO-ep4


title: genomic DNA from Tet1-KO sperm 4

description:
Bisulfite treated
KO_REP


title: D17-20.Biopsy_124

description: Post-injury Day:14Wound Zone:Edge


title: D17-20.Biopsy_123

description: Post-injury Day:14Wound Zone:Intermediate


title: genomic DNA from Tet1-KO sperm 2

description:
Bisulfite treated
KO-5333


title: HepaPlate01_J18


title: genomic DNA from Tet1-KO sperm 1

description:
Bisulfite treated
KO-5058


title: D17-20.Biopsy_103

description: Post-injury Day:14Wound Zone:Center


title: HepaPlate01_J17

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: genomic DNA from Tet1-HxD sperm 7

description:
Bisulfite treated
HxD-1450

source_name: HxD sperm

value: HxD


title: HepaPlate01_J16

value: Perfluorooctanamidine


title: D17-20.Biopsy_102

description: Post-injury Day:7Wound Zone:Edge


title: HepaPlate01_J15


title: genomic DNA from Tet1-HxD sperm 5

description:
Bisulfite treated
HxD-1447


title: HepaPlate01_J14


title: genomic DNA from Tet1-HxD sperm 2

description:
Bisulfite treated
HxD-254


title: D17-20.Biopsy_126


title: genomic DNA from Tet1-HxD sperm 1

description:
Bisulfite treated
HxD-102


title: HepaPlate01_J13


title: D17-20.Biopsy_100

description: Post-injury Day:7Wound Zone:Center


title: Vehicle12

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

data_processing:
ERCC analysis was performed with the ERCC analysis plugin in the Torrent. Spiked samples had an R2 above 0.9.
Ion Torrent derived reads were  aligned to the rattus norvegicus genome (rn6) using STAR 2.5.3a in the in the Partek Flow servers (Partek, Inc., St. Louis, MO).
Gene read counts were generated from Binary Alignment Map (BAM) files and annotated to the genome using Ensembl (version 104; Partek, Inc.).
Reads from FASTQ files produced by the Ion Torrent System were trimmed from both ends until all samples’ collective average Phred quality score was > 25. Reads shorter than 25 base pairs (bps) were also excluded.
Gene  with the total number of counts lower than 5 per sample was excluded from the analysis
DESeq2 was utilized to obtain a list of DEGs. A threshold p-value lower than 0.05 was used as a cut-off to statistically filter genes
Assembly: Ensembl (version 104; Partek, Inc.).
Supplementary files format and content: Comma-separated values (.csv) files that contain the normalized counts for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: DG region of the hippocampus

extract_protocol:
Rats were briefly anesthetized with isoflurane (Patterson Veterinary, Greenly, CO) and swiftly decapitated. The brains were then rapidly removed, and the hippocampi were dissected according to previously described methods (Lein 2004; Zeier 2011). The hippocampal regions DG was separated, placed in the tubes, and flash-frozen in liquid nitrogen. All samples were stored in at -80°C until processed. RNA was isolated from subregions of a hippocampus from a single hemisphere of each animal. RNA Isolation was performed according to methods previously described (Ianov 2016; Barter 2019). Briefly, RNA was isolated using the RNeasy Lipid Tissue Mini kit (Qiagen, catalog number 74804). Total RNA was treated with DNase using the RNase-Free DNase Set (Qiagen, catalog number 79254). Concentration of total RNA was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher catalog number ND-2000) and the RNA integrity number (RIN) was quantified using the Agilent 2200 Tapestation system with High Sensitivity RNA Screen Tape (Agilent Technologies, Santa Clara, CA). Mean RNA integrity across all samples was 9.05 (SEM ± 0.02) with values ranging from 8.2 to 9.3. Poly-A-selection for mRNA was performed using 250 ng of isolated total RNA in the Dynabeads mRNA DIRECT Micro kit (Thermo Fisher, catalog number 61021). External RNA Controls Consortium (ERCC) RNA Spike-In Control Mixes were included in all isolated mRNA samples (Thermo Fisher, catalog number 4456740).
Library preparation was performed using the Ion Total RNA-seq Kit v2 (Thermo Fisher, catalog number 4475936). Ion Xpress barcodes (Thermo Fisher, catalog number 4475485) were included with libraries for multiplex sequencing. In summary, isolated mRNA was fragmented with RNase III then ligated to the Ion Adapter Mix v2. RNA samples were then reverse transcribed. cDNA from each biological replicate was uniquely barcoded and amplified with 16 PCR cycles. Library concentration from each sample was quantified using the Qubit dsDNA HS Assay (Thermo Fisher, catalog number Q32851). DNA fragment size distribution was subsequently evaluated using High Sensitivity D1000 ScreenTape in the 2200 Tapestation system (Agilent Technologies, Santa Clara, CA).  Templates were prepared using the Ion Chef system (Thermo Fisher, catalog number 4484177) and sequencing was performed using the Ion Proton system (Thermo Fisher, catalog number 4476610) or Ion GeneStudio S5 system (Thermo Fisher, catalog number A38194).

tag: strain

value: F344 strain

value: Vehicle

tag: age

value: Young rats (6 months)

value: male


title: D15-20.Biopsy_93

description: Post-injury Day:7Wound Zone:Edge


title: D17-20.Biopsy_101

description: Post-injury Day:7Wound Zone:Intermediate


title: genomic DNA from Tet1-V sperm 2

description:
Bisulfite treated
V-774

value: V


title: Vehicle10


title: Vehicle11


title: Vehicle9


title: HepaPlate01_J12

value: Perfluoroheptanoic acid


title: D15-20.Biopsy_92

description: Post-injury Day:7Wound Zone:Edge

value: Muscle

value: all cell types in muscle


title: genomic DNA from Tet1-HxD sperm 8

description:
Bisulfite treated
HxD-1568


title: HepaPlate01_J11


title: Vehicle5


title: D15-20.Biopsy_91

description: Post-injury Day:7Wound Zone:Edge

value: No treatment (default healing)


title: genomic DNA from Tet1-HxD sperm 6

description:
Bisulfite treated
HxD-1449


title: Vehicle6


title: D15-20.Biopsy_90

description: Post-injury Day:7Wound Zone:Edge


title: genomic DNA from Tet1-HxD sperm 4

description:
Bisulfite treated
HxD-581


title: HepaPlate01_J10

value: Blank


title: genomic DNA from Tet1-HxD sperm 3

description:
Bisulfite treated
HxD-541

value: sperm


title: Vehicle3


title: Vehicle4


title: HepaPlate01_J09

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: Vehicle2


title: D15-20.Biopsy_89


title: HepaPlate01_J08


title: Vehicle1


title: DA12

value: Dox + ABT-263


title: D15-20.Biopsy_88


title: DA11


title: DA6


title: DA5


title: HepaPlate01_J06


title: D15-20.Biopsy_87


title: HepaPlate01_J07

value: Perfluoro(4-methoxybutanoic) acid


title: D15-20.Biopsy_86


title: DA3


title: DA2


title: D15-20.Biopsy_85

description: Post-injury Day:7Wound Zone:Center


title: HepaPlate01_J05


title: DA1


title: D13

value: Dox


title: DA4


title: HepaPlate01_J04

value: Perfluorohexanesulfonamide


title: D10


title: D14


title: HepaPlate01_J03

value: Nonafluoropentanamide


title: D7

value: F344 strain


title: D5


title: HepaPlate01_J02

value: Perfluorononanoic acid


title: D9

value: Young rats (6 months)


title: D15-20.Biopsy_82

description: Post-injury Day:3Wound Zone:Center


title: D15-20.Biopsy_83

description: Post-injury Day:3Wound Zone:Intermediate


title: D15-20.Biopsy_84

description: Post-injury Day:3Wound Zone:Edge


title: D2

value: male


title: D14-20.Biopsy_77

description: Post-injury Day:4Wound Zone:Edge


title: HepaPlate01_I23

value: Perfluorobutanesulfonic acid


title: D1


title: HepaPlate01_I22

value: Perfluorodecanoic acid


title: D14-20.Biopsy_76

description: Post-injury Day:4Wound Zone:Edge

value: Muscle


title: human CD34+ cells, surface expression

city: Bethesda

first: Daisuke

last: Araki

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

description: 10x Genomics

library_source: other

data_processing:
Illumina sequencer’s base call files (BCLs) were demultiplexed, for each flow cell directory, into FASTQ files using Cellranger mkfastq with default parameters except "include-introns" option set to "false" (v 7.1.0) in NIH Helix/Biowulf High Performance Computation (HPC) system.
FASTQ files were then processed using Cellranger Antibody Capture count with default parameters in NIH Helix/Biowulf HPC system.
Internally, the software relies on STAR for aligning reads to a pre-build filtered human reference genome relying on GRCh38, while genes are quantified using ENSEMBL genes as gene model.
The output of Cellranger is a filtered gene-barcode matrix containing the UMI counts for each gene.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: CD34+ cells

extract_protocol:
Mobilized peripheral blood human CD34+ cells from a healthy volunteer were stained with Total seq B CITE-seq antibodies, and subsequently prepared for CITE-seq library preparation.
3’ v3.1 GEX libraries were constructed according to 10x Genomics protocol. 3’ v3.1 GEX and ADT libraries were pooled in a 2:1 ratio and sequenced with an Illumina NovaSeq S1 flow cell. Target sequencing depth for the GEX libraries was 20,000 read pairs per cell and 5,000 read pairs per cell for the ADT libraries.

value: CD34+ cells

value: Hematopoietic stem and progenitor cells

tag: antibodies/tags

value: The following TotalSeqB antibodies:anti-CD34, anti-CD38, anti-CD90, anti-CD45RA, anti-CD49f, anti-CD135, anti-CD10, anti-CD45, anti-CD117, anti-CD133, anti-CD184, anti-CD201, anti-CD33, anti-CD110, hashtag1


title: human CD34+ cells, gene expression

description: 10x Genomics


title: HepaPlate01_I19

value: Blank

value: 6:2 Fluorotelomer sulfonic acid


title: D14-20.Biopsy_72

value: all cell types in muscle

value: No treatment (default healing)


title: HepaPlate01_I21

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorotetradecanoic acid


title: D14-20.Biopsy_75

description: Post-injury Day:4Wound Zone:Edge


title: CUTL1 KD 2% input

first: Stanley

last: Adoro

address: Center Dr

department: CCR

institute: NCI

library_source: genomic

data_processing:
Alignment bowtie  2-2.5.1
Remove duplicates sambamba  0.8.2
Peak calling MACS version 2.2.7.1 format BAMPE
Assembly: hg38
Supplementary files format and content: MAC2 peak calls,  format: MACS2 peaks.xls

growth_protocol: complete RPMI + 20% FBS

extract_protocol:
Cells were fixed, lysed, and sonicated using the CST Simple CHIP Plus Kit. 10ug of DNA was incubated with 4ug of each antibody (BRD4, Pol II, H3K27ac) over night, and then incubated with the protein G beads for 2 hours. After washing and elution, DNA was isolated with kit provided in the CST Simple CHIP Plus kit.
NEB NextUltra DNA Library Preparation kit

treatment_protocol: CUTLL1 cells were transduced with lentivirus containing pLKO CT/KD shRNA. After 48 hours, cells were treated with 1ug/ml puromycin for 3 days.

value: T-ALL

value: t(7;9)(q34;q34) translocation

value: CHMP5 shRNA


title: late-inflammation,replicate1,scRNAseq

city: Shanghai

first: Caiwen

last: Xiao

state: -- Select State/Province --

address: Zhizaoju Road

country: China

institute: Shanghai Ninth People's Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 40%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
; MT% < 40%;
; Cell Gene Number < Median Gene Number * 2;
; Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38_Ensembl104
Supplementary files format and content: Single cell matrix files

source_name: Lacrimal sac

extract_protocol:
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Lacrimal sac

value: dacryocystorhinostomy


title: D14-20.Biopsy_73


title: early-inflammation,replicate2,scRNAseq


title: HepaPlate01_I18

value: AFFF-7 (Tridol 6%)


title: CUTLL1 CT 2% input

value: CT shRNA


title: D14-20.Biopsy_71

value: Muscle


title: CUTLL1 H3K27ac KD


title: HepaPlate01_I17

value: Perfluoro-3-methoxypropanoic acid


title: late-inflammation,replicate3,scRNAseq


title: HepaPlate01_I20

value: Perfluorooctanamide


title: D14-20.Biopsy_74

description: Post-injury Day:4Wound Zone:Edge


title: late-inflammation,replicate2,scRNAseq


title: CUTLL1 BRD4 KD


title: early-inflammation,replicate1,scRNAseq


title: D14-20.Biopsy_70


title: CUTLL1 H3K27ac CT


title: CUTLL1 Pol II KD


title: HepaPlate01_I15

value: Dodecafluoroheptanol


title: CUTLL1 Pol II CT


title: HepaPlate01_I16

value: Blank

value: Perfluorotridecanoic acid


title: D14-20.Biopsy_69

description: Post-injury Day:4Wound Zone:Center

value: all cell types in muscle


title: CUTLL1 BRD4 CT


title: HepaPlate01_I14

value: AFFF-4 (FireAde 6%)


title: PHLPP1_S118P, scRNA cell surface protein barcode

city: La Jolla

first: Samuel

last: Myers

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Element Aviti was used for sequencing but is not currently available as an option in GEO/SRA; Illumina NovaSeq 6000 was chosen to avoid flags

data_processing:
Cellranger count v7.1.0 count and aggr were used to aggregate reads across multiple sequencing lanes, and in the case of GEX, multiple flowcells, into a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
Cellranger count v7.1.0 was used to generate a cloupe file which was used for quantifying ADTs and HTOs as well as GEX differential expression analyses
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: Cellranger output files: barcodes.tsv
Supplementary files format and content: Cellranger output files: features.tsv
Supplementary files format and content: Cellranger output files: matrix.mtx
Supplementary files format and content: feature_reference.csv - contains names and sequences of all CITE seq antibodies and barcodes in the Human Universal Panel

source_name: Jurkat E6.1

growth_protocol: RPMI plus GlutaMAX + 10%HI FBS; 37C; 5% CO2

extract_protocol:
After activation and antibody staining, cells were washed in cold 0.04% BSA in PBS -/-. Single cells were encapsulated in Gel-Beads-in-Emulsion (GEMs) using the 10X Chromium X with a Chromium Next GEM Single Cell 5' HT Kit. https://cdn.10xgenomics.com/image/upload/v1673041195/support-documents/CG000424_ChromiumNextGEMSingleCell5_HTv2_CellSurfaceProtein_UserGuide_RevD.pdf
Library prep was performed according to the manufacturer's protocol (CG000424 Rev D) 10X Genomics 5’ HT v2 with Feature Barcode Technology for Cell Surface Proteins.

treatment_protocol: Cells were incubated and activated with α-CD3/CD28 agonist antibodies at  1 ug/mL. Cells were activated for 0 and six hours. Cells were stained with BioLegend TotalSeq-C Human Universal Cocktail and anti-human hashtag antibodies according to NYCG CITEseq protocols [http://cite-seq.com/]

value: Jurkat E6.1

value: Jurkat cells

value: mixed sample, baseline + 6 hours post T cell activation + 24 hours post T cell activation

tag: library type

value: CSP (HTO+ADT)

tag: adt

value: TotalSeq-C Human Universal Cocktail, V1.0

tag: hto

value: TotalSeq™_C0251 anti_human Hashtag 1 Antibody ,TotalSeq™_C0252 anti_human Hashtag 2 Antibody, TotalSeq™_C0253 anti_human Hashtag 3 Antibody


title: PHLPP1_S118P, scRNA gene expression

value: mRNA


title: D14-20.Biopsy_68

description: Post-injury Day:1Wound Zone:Edge

value: No treatment (default healing)


title: HepaPlate01_I13

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanoic acid


title: MAPK1_Y187C, scRNA cell surface protein barcode


title: D14-20.Biopsy_66

description: Post-injury Day:1Wound Zone:Center

value: Muscle


title: HEK3, scRNA gene expression


title: LCP2splice, scRNA cell surface protein barcode


title: HepaPlate01_I12

value: Perfluorobutanesulfonic acid


title: D13-20.Biopsy_60

description: Post-injury Day:4Wound Zone:Edge


title: LCP2splice, scRNA gene expression


title: FAM120A, scRNA gene expression


title: D14-20.Biopsy_67

description: Post-injury Day:1Wound Zone:Intermediate


title: HepaPlate01_I09

value: Perfluorooctanamide


title: HepaPlate01_I08

value: Blank

value: 6:2 Fluorotelomer sulfonic acid


title: D13-20.Biopsy_59

description: Post-injury Day:4Wound Zone:Edge

value: all cell types in muscle


title: FAM120A, scRNA cell surface protein barcode


title: HEK3, scRNA cell surface protein barcode


title: HepaPlate01_I10

value: Perfluorotetradecanoic acid


title: MKN45 cells, IP-si1-2

city: Hangzhou

first: Ning

last: Ding

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University School of Medicine

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
HISAT2 software (http://daehwankimlab.github.io/hisat2) were used to align reads the reference Homo sapiens (Version: hg38).
MACS2 software (https://github.com/macs3-project/MACS/)were used to peakcalling for each IP and Input samples, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). HOMER (http://homer.ucsd.edu/homer/motif) were used for called peaks annotation and de novo motif finding followed by localization of the motif with respect to peak summit.
Then FeatureCounts (https://subread.sourceforge.net/featureCounts.html) was used to perform expression level for all mRNAs from input libraries by calculating counts.
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package Deseq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: hg38
Supplementary files format and content: bw

extract_protocol:
polyadenylated RNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, UK) and then fragmented into ~ 150 nt fragments using magnesium RNA fragmentation buffer (New England Biolabs).  Fragmented polyadenylated RNA (5%) was used as the input sample, and the remaining samples were conducted to m6A-RIP.
Library construction was performed using the NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module and NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.
m6A-RIP seq

value: human gastric cancer

value: transfected with IGF2BP1-siRNA1

tag: rip antibody

value: m6A (Synaptic Systems, Cat. No. 202003)


title: HepaPlate01_I11

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples

value: Perfluorodecanoic acid


title: HepaPlate01_I07

value: AFFF-7 (Tridol 6%)


title: MKN45 cells, IP-si1-1


title: D13-20.Biopsy_61

description: Post-injury Day:4Wound Zone:Edge


title: D13-20.Biopsy_58

description: Post-injury Day:4Wound Zone:Edge


title: MKN45 cells, IP-si3-2

value: transfected with IGF2BP1-siRNA2


title: MKN45 cells, IP-NC-1

value: transfected with scramble siRNA


title: MKN45 cells, IP-si3-1


title: D13-20.Biopsy_57

value: No treatment (default healing)


title: MKN45 cells, Input-si3-2


title: MAPK1_Y187C, scRNA gene expression

value: Jurkat E6.1

value: Jurkat cells

value: mixed sample, baseline + 6 hours post T cell activation + 24 hours post T cell activation

value: mRNA

value: TotalSeq-C Human Universal Cocktail, V1.0

value: TotalSeq™_C0251 anti_human Hashtag 1 Antibody ,TotalSeq™_C0252 anti_human Hashtag 2 Antibody, TotalSeq™_C0253 anti_human Hashtag 3 Antibody


title: HepaPlate01_I05

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorotridecanoic acid


title: D13-20.Biopsy_56

value: Muscle

value: all cell types in muscle


title: MKN45 cells, Input-si3-1

value: human gastric cancer


title: HepaPlate01_I04

value: Dodecafluoroheptanol


title: MKN45 cells, IP-NC-2

value: m6A (Synaptic Systems, Cat. No. 202003)


title: D13-20.Biopsy_54


title: MKN45 cells, Input-si1-2

value: transfected with IGF2BP1-siRNA1


title: MKN45 cells, Input-NC-2

value: transfected with scramble siRNA


title: MKN45 cells, Input-si1-1


title: D13-20.Biopsy_53

description: Post-injury Day:4Wound Zone:Center

value: No treatment (default healing)


title: MKN45 cells, Input-NC-1


title: HepaPlate01_I03

value: AFFF-4 (FireAde 6%)


title: HCT-116 cells, DAC30_EM_2

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description:
2x150 bp
DAC30_IP_rep2
All_samples_mergeCG_output.bed
DAC30.combined.8.betas.bw

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
EM-seq reads were aligned to human genome build hg38, duplicate marked (samblaster), and sorted (samtools) using the ‘biscuitBlaster’ pipeline from BISCUIT (v0.3.16) (https://huishenlab.github.io/biscuit/). Cytosine retention and callable SNP mutations were computed with ‘biscuit pileup’ and output into a VCF file. Cytosine beta values and coverage were extracted with ‘biscuit vcf2bed’ and CpG methylation status was merged with ‘biscuit mergecg’.
Integrated siQ-ChIP-seq and EM-seq analysis was conducted with deeptools (v3.2.0) (148) by constructing matrices with ‘computeMatrix’ across queried genomic coordinates with the respective bigwig data and visualizing the summarized integration with ‘plotProfile’ and ‘plotHeatmap’.
Assembly: hg38
Supplementary files format and content: tab delimited bed file of Biscuit output for determining b-values
Supplementary files format and content: bigwig file
Library strategy: Enzymatic-Methyl(EM)-seq

growth_protocol: HCT116 colon cancer cell lines was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol:
Cells exposed to drugs for 72 hours were fixed in buffer (1% formaldehyde, 50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min at room temp with shaking and then quenched with 125 mM glycine 5 min at room temp. Cells were scraped into cold PBS, washed 2X with cold PBS, flash frozen in liquid N2, and stored at -80°C until use. Thawed pellets were lysed in LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche protease inhibitor cocktail) for 20 min with rotation at 4°C and cleared by centrifugation at 300 x g for 5 min at 4°C. Supernatant with intact nuclei was set aside. Cell pellets were lysed again in 4x LB1 (LB1 with 2% NP-40 and 1% Triton X-100) for 20 min. Intact nuclei from this and the saved supernatant were collected by centrifugation at 1,700 x g for 5 min at 4°C, resuspended and washed in LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 min with rotation at 4°C, and collected again by centrifugation at 1,700 x g for 5 min at 4°C. Nuclei were gently rinsed 2x with LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) without disturbing the pellet. Nuclei were resuspended in 1 mL LB3 and transferred to a 1 ml milliTUBE (Covaris). Chromatin was sheared to a range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 450 µg of chromatin was brought to 500 µL in LB3 and 500 µL of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added. Prepared chromatin was pre-cleared by incubation with 20 µL of pre-washed Dynabeads Protein G magnetic beads (Invitrogen, 10004D) for 3 hours at 4°C with rotation. After bead removal, 10% input (100 µL) of pre-cleared chromatin was removed and set aside. Pre-cleared chromatin was immunoprecipitated with 5 µL of H3K27me3 antibody (Cell Signaling 9733) overnight at 4°C with constant rotation. Protein G magnetic beads (35 µL/IP) were blocked in buffer containing PBS, 0.5% BSA, and 20 µg Herring Sperm DNA (Sigma, D7290) with rotation at 4°C overnight. Blocked beads were washed 3X with PBS and 0.5% BSA and 2X with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours with rotation at 4°C. Bead-immuno-chromatin complexes were then washed 3X for 5 min with rotation at 4°C with WB1, 3X with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2X with WB1, and 1X with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were incubated in 50 µl of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) at 65°C for 15 min in 50 µL volume to elute immuno-chromatin complexes. The elution step was repeated, and eluates combined. Eluents and input were incubated overnight at 65°C with constant shaking to reverse crosslinks, followed by incubation at 37°C for 1 hour with DNase-free RNase A, then at 37°C for 2 hours with 10 µL of Proteinase K (20 mg/mL stock). DNA was isolated with a 1.5x ratio of KAPA Pure Beads (KAPA Biosystems KK8000) to DNA volume.
Libraries were prepared by the Van Andel Institute Genomics Core from an input of 41 ng to 51 ng of ChIP DNA using the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, Cat. #E7120L). Denaturation method used was 0.1 N sodium hydroxide, according to the protocol, and 8 cycles of PCR amplification were performed. Quality and quantity of the finished libraries were assessed using a combination of Agilent High Sensitivity DNA chip (Agilent Technologies, Inc., Cat. # 5067-4626) and QuantiFluor® dsDNA System (Promega Corp., Cat. # E2670). 150 bp paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S4, 300 bp sequencing kit (Illumina Inc., San Diego, CA, USA), with 10% PhiX to a minimum read depth of 100M read pairs per library. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: 5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 72 hours.

value: colorectal carcinoma

tag: passages

value: 4-5 passages

value: 5'aza-2'deoxycytidine (30 nM)

tag: time

value: 3 days

tag: chip antibody

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)


title: D13-20.Biopsy_55

tag: cell line

tag: cell type


title: HCT-116 cells, DAC30_EM_1

description:
2x150 bp
DAC30_IP_rep1
All_samples_mergeCG_output.bed
DAC30.combined.8.betas.bw

tag: treatment


title: D13-20.Biopsy_51

tag: tissue


title: HCT-116 cells, DAC300_EM_1

description:
2x150 bp
DAC300_IP_rep1
All_samples_mergeCG_output.bed
DAC300.combined.8.betas.bw

value: 5'aza-2'deoxycytidine (300 nM)


title: HepaPlate01_H23

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorobutanesulfonic acid


title: HCT-116 cells, Veh_EM_2

description:
2x150 bp
Veh_IP_rep2
All_samples_mergeCG_output.bed
Veh.combined.8.betas.bw

value: DMSO


title: HCT-116 cells, Combo_INPUT

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).
siQ-ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.5.0) and quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) and were deduplicated using removeDups from samblaster (v.0.1.24) (144). Aligned BAM files were used for quality control analysis with “deeptools” (v3.2.0) ‘plotFingerprint’ and ‘plotPCA’ functions. Aligned SAM files were then processed for pair-end reads with high mapping quality (MAQ >= 20), correct pair orientation (Sam Flags = 99, 163), and fragment length as described for siQ-ChIP (https://github.com/BradleyDickson/siQ-ChIP). Param.in files were prepared for each sample with all required parameters and measurements required for siQ-ChIP normalization. IP tracks (with H3K27me3 efficiency values) and comparative responses between drug treatments (relative to Vehicle) were generated with execution of getsiq.sh (version: February 2021) with the EXPlayout file
To determine the change in H3K27me3 distributions between inhibitor-treated samples and vehicle-treated samples, each inhibitor-treated biological replicate (e.g. DAC301) was individually compared to the two vehicle-treated biological replicates (e.g. DAC301vsVeh1, DAC301vsVeh2), and the average log2 fold-change in response (area of peak in inhibitor-treatment/area of peak in vehicle treatment) was calculated. Next, conserved peaks between inhibitor-treated biological duplicates were determined by calculating the proximity of replicate 1 peaks to replicate 2 peaks (e.g. DAC301, DAC302) using the ‘closest’ command from “bedtools” (v2.25.0). Peaks were considered conserved among biological replicates if the peaks overlapped or were within 200 bp of each other. Finally, the average log2 fold-change in response was calculated for the peaks conserved between the two inhibitor-treated biological replicates. Peaks were considered significant if the log2 fold-change in response was > 1.0 (increase in H3K27me3) or < -1.0 (decrease in H3K27me3).
Assembly: hg38
Supplementary files format and content: bigwig files for H3K27me3 efficiency values across genomic coordinates for each sample
Supplementary files format and content: tab delimited file of response calculations for each drug-treatment relative to Vehicle

extract_protocol:
Cells exposed to drugs for 72 hours were fixed in buffer (1% formaldehyde, 50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min at room temp with shaking and then quenched with 125 mM glycine 5 min at room temp. Cells were scraped into cold PBS, washed 2X with cold PBS, flash frozen in liquid N2, and stored at -80°C until use. Thawed pellets were lysed in LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche protease inhibitor cocktail) for 20 min with rotation at 4°C and cleared by centrifugation at 300 x g for 5 min at 4°C. Supernatant with intact nuclei was set aside. Cell pellets were lysed again in 4x LB1 (LB1 with 2% NP-40 and 1% Triton X-100) for 20 min. Intact nuclei from this and the saved supernatant were collected by centrifugation at 1,700 x g for 5 min at 4°C, resuspended and washed in LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 min with rotation at 4°C, and collected again by centrifugation at 1,700 x g for 5 min at 4°C. Nuclei were gently rinsed 2x with LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) without disturbing the pellet. Nuclei were resuspended in 1 mL LB3 and transferred to a 1 ml milliTUBE (Covaris). Chromatin was sheared to a range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 450 µg of chromatin was brought to 500 µL in LB3 and 500 µL of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added. Prepared chromatin was pre-cleared by incubation with 20 µL of pre-washed Dynabeads Protein G magnetic beads (Invitrogen, 10004D) for 3 hours at 4°C with rotation. After bead removal, 10% input (100 µL) of pre-cleared chromatin was removed and set aside. Pre-cleared chromatin was immunoprecipitated with 5 µL of H3K27me3 antibody (Cell Signaling 9733) overnight at 4°C with constant rotation. Protein G magnetic beads (35 µL/IP) were blocked in buffer containing PBS, 0.5% BSA, and 20 µg Herring Sperm DNA (Sigma, D7290) with rotation at 4°C overnight. Blocked beads were washed 3X with PBS and 0.5% BSA and 2X with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours with rotation at 4°C. Bead-immuno-chromatin complexes were then washed 3X for 5 min with rotation at 4°C with WB1, 3X with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2X with WB1, and 1X with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were incubated in 50 µl of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) at 65°C for 15 min in 50 µL volume to elute immuno-chromatin complexes. The elution step was repeated, and eluates combined. Eluents and input were incubated overnight at 65°C with constant shaking to reverse crosslinks, followed by incubation at 37°C for 1 hour with DNase-free RNase A, then at 37°C for 2 hours with 10 µL of Proteinase K (20 mg/mL stock). DNA was isolated with a 1.5x ratio of KAPA Pure Beads (KAPA Biosystems KK8000) to DNA volume.
Immunoprecipitated fragments and saved inputs were quantified with a Qubit dsDNA High Sensitivity Assay kit (Invitrogen Q32851), and 10 ng of purified DNA for each IP and input sample were used for library preparation with the KAPA Hyper Prep Kit (Kapa Biosystems KR0961). TAZ and Combo treatments required two IPs per biological replicate to attain enough material for library preparation, and this doubling has been accounted for in the parameters for siQ-ChIP (88,89) for these samples. Library preparation including fragment end-repair, A-tail extension, and adapter ligation was conducted per the manufacturer’s instructions (KAPA). Adapter-ligated fragments were amplified with 11 cycles following the recommended thermocycler program, and DNA was purified with two rounds of purification using KAPA Pure Beads (KK8000). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 75 bp, paired end sequencing was performed on an Illumina NextSeq 500 sequencer using a 150 bp HO sequencing kit (v2) (Illumina Inc., San Diego, CA, USA) or 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit to a minimum read depth of 50M read pairs per IP library and 100M read pairs per Input library.

treatment_protocol: 5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 72 hours. Tazemetostat (TAZ or EPZ6438, Selleck Chemicals S7128 and Cayman Chemical 16174) was dissolved in DMSO and sotred at -20C. Cells were treated for 72 hours.

value: 5'aza-2'deoxycytidine (30 nM) & EPZ-6438 (1 uM)

tag: sequence length

value: 2 x 50bp


title: D13-20.Biopsy_52

description: Post-injury Day:2Wound Zone:Edge

value: Muscle

value: all cell types in muscle


title: HepaPlate01_H22

value: Perfluorodecanoic acid


title: D13-20.Biopsy_50

description: Post-injury Day:2Wound Zone:Center

value: No treatment (default healing)


title: HCT-116 cells, TAZ_INPUT


title: HCT-116 cells, DAC300_INPUT


title: HepaPlate01_H21

value: Perfluorotetradecanoic acid


title: HepaPlate01_I06

value: Perfluoro-3-methoxypropanoic acid


title: HCT-116 cells, DAC300_EM_2

description:
2x150 bp
DAC300_IP_rep2
All_samples_mergeCG_output.bed
DAC300.combined.8.betas.bw

value: colorectal carcinoma

value: 4-5 passages


title: HCT-116 cells, Combo_H3K27me3_1

description:
Combo_IP_rep1
EPZDAC_conserved_peaks_Log2FC_all_regions.bed

value: 3 days


title: HepaPlate01_I02

value: Perfluorooctanoic acid


title: D12-20.Biopsy_45

description: Post-injury Day:2Wound Zone:Edge


title: HCT-116 cells, Veh_EM_1

description:
2x150 bp
Veh_IP_rep1
All_samples_mergeCG_output.bed
Veh.combined.8.betas.bw

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)


title: D12-20.Biopsy_44

description: Post-injury Day:2Wound Zone:Edge


title: HCT-116 cells, TAZ_H3K27me3_2

description:
TAZ_IP_rep2
EPZ_conserved_peaks_Log2FC_all_regions.bed


title: HCT-116 cells, TAZ_H3K27me3_1

description:
TAZ_IP_rep1
EPZ_conserved_peaks_Log2FC_all_regions.bed


title: HepaPlate01_H20

value: Blank

value: Perfluorooctanamide


title: HCT-116 cells, DAC300_H3K27me3_1

description:
DAC300_IP_rep1
DAC300_conserved_peaks_Log2FC_all_regions.bed

value: 5'aza-2'deoxycytidine (300 nM)


title: HepaPlate01_H17

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: Combo_RNA_D6_rep2

description:
Combo_D6_rep2
All_samples_raw_counts.txt
Combo_D6_logFC_FDR_to_Vehicle.txt
Combo_D6_vs_Veh_DESeq2_TE_only_output.txt

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).
Raw 50 bp paired-end reads were trimmed with TrimGalore!(http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by quality control analysis withFastQC. Trimmed reads were aligned to GRCh38.p12 and indexed to GENCODE v29 viaSTAR (v2.5.3a)aligner with flags ‘-twopassMode Basic\ -quantMode GeneCounts’ for feature counting.
ReadsPerGene output count files were constructed into a raw read count matrix in R. Low count genes were filtered (1 count in at least one sample) prior toedgeR (v3.36.0)count normalization and differential expression analysis with voomWithQualityWeights and quasi-likelihood fit set to robust. Principal component analysis was calculated using‘prcomp’ in the R stats package on the normalized expression matrix. Differential expression analysis was conducted with voomWithQualityWeights and a quasi-likelihood fit set to robust. Each dataset was treated separately for differential expression analysis (i.e. Day 3 acute treatment, Day 6 prolonged treatment, and CsA treatments), and all inhibitor treatments were compared to their respective Vehicle samples. Genes were considered differentially expressed if |Log2FC| > 1 and FDR < 0.01.
TE analysis of total RNA-seq datasets was conducted with SQuIRE (v0.9.9.92) (https://github.com/wyang17/SQuIRE) (156). TEs were aligned to hg38, counted, and analyzed for differential expression relative to the Vehicle-treated samples using ‘Map’, ‘Count’, and ‘Call’ commands, respectively. TEs were considered differentially expressed if |Log2FC| > 1 and adjusted p-value < 0.01.
Assembly: hg38
Supplementary files format and content: tab delimited file with raw counts for non-repetitive transcripts for each sample (matched by provided library name)
Supplementary files format and content: tab delimited file with logFC and FDR values for non-repetitive transcripts for each drug-treated sample relative to matching experiment's Vehicle
Supplementary files format and content: tab delimited file with logFC and FDR values for repetitive TE transcripts for each drug-treated sample relative to matching experiment's Vehicle

extract_protocol:
TRIzol Reagent (Invitrogen 15596026) was added directly to adhered cells, collected, and stored at -80°C. After thawing, total RNA was extracted following the manufacturer’s protocol, and RNA was resuspended in DEPC Nuclease-Free water.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA).  Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 50M raw paired-reads per transcriptome.

treatment_protocol: 5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 3 days or 6 days (treated twice). Tazemetostat (TAZ or EPZ6438, Selleck Chemicals S7128 and Cayman Chemical 16174) was dissolved in DMSO and sotred at -20C. Cells were treated for 3 days or 6 days (treated twice).

value: 5-6 passages

value: 5'aza-2'deoxycytidine (30 nM) & EPZ-6438 (1 uM)

value: 6 days

tag: batch


title: D12-20.Biopsy_43

description: Post-injury Day:2Wound Zone:Edge

value: Muscle

value: all cell types in muscle


title: HepaPlate01_H18

value: AFFF-7 (Tridol 6%)


title: Combo_RNA_D6_rep1

description:
Combo_D6_rep1
All_samples_raw_counts.txt
Combo_D6_logFC_FDR_to_Vehicle.txt
Combo_D6_vs_Veh_DESeq2_TE_only_output.txt


title: Combo_RNA_D6_rep3

description:
Combo_D6_rep3
All_samples_raw_counts.txt
Combo_D6_logFC_FDR_to_Vehicle.txt
Combo_D6_vs_Veh_DESeq2_TE_only_output.txt


title: HCT-116 cells, DAC300_H3K27me3_2

description:
DAC300_IP_rep2
DAC300_conserved_peaks_Log2FC_all_regions.bed

value: 2 x 50bp


title: D12-20.Biopsy_41

description: Post-injury Day:2Wound Zone:Intermediate

value: No treatment (default healing)


title: TAZ_RNA_D6_rep2

description:
TAZ_D6_rep2
All_samples_raw_counts.txt
TAZ_D6_logFC_FDR_to_Vehicle.txt
TAZ_D6_vs_Veh_DESeq2_TE_only_output.txt

value: colorectal carcinoma


title: TAZ_RNA_D6_rep3

description:
TAZ_D6_rep3
All_samples_raw_counts.txt
TAZ_D6_logFC_FDR_to_Vehicle.txt
TAZ_D6_vs_Veh_DESeq2_TE_only_output.txt


title: D12-20.Biopsy_42

description: Post-injury Day:2Wound Zone:Edge


title: TAZ_RNA_D6_rep1

description:
TAZ_D6_rep1
All_samples_raw_counts.txt
TAZ_D6_logFC_FDR_to_Vehicle.txt
TAZ_D6_vs_Veh_DESeq2_TE_only_output.txt


title: DAC30_RNA_D6_rep3

description:
DAC30_D6_rep3
All_samples_raw_counts.txt
DAC30_D6_logFC_FDR_to_Vehicle.txt
DAC30_D6_vs_Veh_DESeq2_TE_only_output.txt

value: 5'aza-2'deoxycytidine (30 nM)


title: HepaPlate01_H15

value: Dodecafluoroheptanol


title: D12-20.Biopsy_40


title: D12-20.Biopsy_39


title: DAC30_RNA_D6_rep2

description:
DAC30_D6_rep2
All_samples_raw_counts.txt
DAC30_D6_logFC_FDR_to_Vehicle.txt
DAC30_D6_vs_Veh_DESeq2_TE_only_output.txt


title: HCT-116 cells, Combo_H3K27me3_2

description:
Combo_IP_rep2
EPZDAC_conserved_peaks_Log2FC_all_regions.bed

value: 4-5 passages

value: 3 days


title: HepaPlate01_H19

value: Blank

value: 6:2 Fluorotelomer sulfonic acid


title: HepaPlate01_H14

value: AFFF-4 (FireAde 6%)


title: DAC30_RNA_D6_rep1

description:
DAC30_D6_rep1
All_samples_raw_counts.txt
DAC30_D6_logFC_FDR_to_Vehicle.txt
DAC30_D6_vs_Veh_DESeq2_TE_only_output.txt


title: HepaPlate01_H13

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanoic acid


title: D12-20.Biopsy_38


title: Veh_RNA_D6_rep3

description:
Veh_D6_rep3
All_samples_raw_counts.txt
none
none

value: 5-6 passages

value: DMSO


title: Veh_RNA_D6_rep2

description:
Veh_D6_rep2
All_samples_raw_counts.txt
none
none

value: 6 days


title: Veh_RNA_D6_rep1

description:
Veh_D6_rep1
All_samples_raw_counts.txt
none
none


title: D12-20.Biopsy_37

description: Post-injury Day:2Wound Zone:Center

value: Muscle

value: all cell types in muscle


title: HepaPlate01_H16

value: Perfluorotridecanoic acid


title: D12-20.Biopsy_36

description: Post-injury Day:1Wound Zone:Edge

value: No treatment (default healing)


title: CsA_Combo_RNA_D3_rep2

description:
CsA_Combo_D3_rep2
All_samples_raw_counts.txt
CsA_Combo_D3_logFC_FDR_to_Vehicle.txt
CsA_Combo_D3_vs_Veh_DESeq2_TE_only_output.txt

value: colorectal carcinoma

value: Cyclosporin A (5 uM) & 5'aza-2'deoxycytidine (30 nM) & EPZ-6438 (1 uM)


title: CsA_Combo_RNA_D3_rep1

description:
CsA_Combo_D3_rep1
All_samples_raw_counts.txt
CsA_Combo_D3_logFC_FDR_to_Vehicle.txt
CsA_Combo_D3_vs_Veh_DESeq2_TE_only_output.txt


title: HepaPlate01_H12

value: Perfluorobutanesulfonic acid


title: HepaPlate01_H11

value: Perfluorodecanoic acid


title: CsA_RNA_D3_rep3

description:
CsA_D3_rep3
All_samples_raw_counts.txt
CsA_D3_logFC_FDR_to_Vehicle.txt
CsA_D3_vs_Veh_DESeq2_TE_only_output.txt

value: 4-5 passages

value: Cyclosporin A (5 uM)

value: 3 days


title: D12-20.Biopsy_34

description: Post-injury Day:1Wound Zone:Center


title: CsA_RNA_D3_rep1

description:
CsA_D3_rep1
All_samples_raw_counts.txt
CsA_D3_logFC_FDR_to_Vehicle.txt
CsA_D3_vs_Veh_DESeq2_TE_only_output.txt


title: CsA_RNA_D3_rep2

description:
CsA_D3_rep2
All_samples_raw_counts.txt
CsA_D3_logFC_FDR_to_Vehicle.txt
CsA_D3_vs_Veh_DESeq2_TE_only_output.txt


title: Veh_RNA_D3_B2_rep2

description:
Veh_D3_B2_rep2
All_samples_raw_counts.txt
none
none


title: HepaPlate01_H09

value: Blank

value: Perfluorooctanamide


title: D12-20.Biopsy_35

description: Post-injury Day:1Wound Zone:Intermediate


title: HepaPlate01_H10

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorotetradecanoic acid


title: Veh_RNA_D3_B2_rep3

description:
Veh_D3_B2_rep3
All_samples_raw_counts.txt
none
none

value: DMSO


title: HepaPlate01_H08

value: 6:2 Fluorotelomer sulfonic acid


title: D11-20.Biopsy_28

description: Post-injury Day:3Wound Zone:Edge

value: Muscle


title: D11-20.Biopsy_29

description: Post-injury Day:3Wound Zone:Edge

value: all cell types in muscle


title: Veh_RNA_D3_B2_rep1

description:
Veh_D3_B2_rep1
All_samples_raw_counts.txt
none
none


title: Combo_RNA_D3_rep3

description:
Combo_D3_rep3
All_samples_raw_counts.txt
Combo_D3_logFC_FDR_to_Vehicle.txt
Combo_D3_vs_Veh_DESeq2_TE_only_output.txt

value: 5'aza-2'deoxycytidine (30 nM) & EPZ-6438 (1 uM)


title: HepaPlate01_H07

value: AFFF-7 (Tridol 6%)


title: D11-20.Biopsy_27

description: Post-injury Day:3Wound Zone:Intermediate

value: No treatment (default healing)


title: CsA_Combo_RNA_D3_rep3

description:
CsA_Combo_D3_rep3
All_samples_raw_counts.txt
CsA_Combo_D3_logFC_FDR_to_Vehicle.txt
CsA_Combo_D3_vs_Veh_DESeq2_TE_only_output.txt

value: colorectal carcinoma

value: Cyclosporin A (5 uM) & 5'aza-2'deoxycytidine (30 nM) & EPZ-6438 (1 uM)


title: Mock_RNAseq,15min, rep1

city: Cork

first: Martina

last: Yordonova

address: Western road

department: School of Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

data_processing:
These reads have being processed. This includes removal of the adapter sequence with Cutadapt. The multiplexed reads were then binned into individual samples based on the on the barcode. Next the 7 nucleotide UMI were used to remove duplicate sequences. Finally reads that mapped to rRNA or tRNA with Bowtie (version 1.2.3) were discarded.
Reads were mapped to the genomes of L. Lactis subsp. cremoris NZ9000 (accession number NC_017949.1) and SK1 (AF011378.1) with Bowtie, using -m 1 parameter.
Supplementary files format and content: tab-delimited text files include raw mapped reads to each gene for each Sample

organism: Lactococcus lactis

source_name: bacteria

growth_protocol: Two hundred millilitres of M17 broth supplemented with 5 g/litre glucose and 10 mM CaCl2 were inoculated with overnight culture to OD600nm of ~0.05 and incubated at 30°C with-out agitation to an OD600nm of 0.4-0.43.

extract_protocol:
Cells were pelleted by centrifugation; pellets were frozen and pulverized in Retsch Mixer Mill 400. 25 AU of lysate were supplemented with 5 mM CaCl2 and digested with 1500 U of Micrococcal nuclease (Roche) at 25°C for 1 hour with agitation at 1400 rpm.
Following end repair, pre-adenylated linkers bearing unique molecular identifiers (UMIs) and sample barcodes were ligated to footprints. rRNA removal was done with Ribo-Zero Magnetic kit for Gram-positive bacteria (Epicentre) according to the manufacturer’s protocol. Single-stranded cDNA was circularized and then amplified by 4 rounds of PCR. Deep sequencing was performed with the Illumina HiSEQ4000.
Other:Ribo-seq

treatment_protocol: To achieve a multiplicity of infection (MOI) of ~10, 12 millilitres of phage sk1 in SM buffer (100 mM NaCl, 50 mM Tris HCl, 10 mM MgSO4) with a titre of 5x1010 per mL were added to the two test samples. The same volume of SM buffer alone was added to the two mock samples at the same time. At 2-, 5-, and 15-min post infection, to stall translating ribosomes, chloramphenicol (100 µg/mL) was added for 2 min prior harvesting.

value: bacteria

tag: library prep

value: RNA-seq

value: 15 minutes

value: mock


title: Combo_RNA_D3_rep2

description:
Combo_D3_rep2
All_samples_raw_counts.txt
Combo_D3_logFC_FDR_to_Vehicle.txt
Combo_D3_vs_Veh_DESeq2_TE_only_output.txt

value: 4-5 passages

value: 3 days


title: HepaPlate01_H06

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluoro-3-methoxypropanoic acid


title: D11-20.Biopsy_25


title: HepaPlate01_H05

value: Perfluorotridecanoic acid


title: Combo_RNA_D3_rep1

description:
Combo_D3_rep1
All_samples_raw_counts.txt
Combo_D3_logFC_FDR_to_Vehicle.txt
Combo_D3_vs_Veh_DESeq2_TE_only_output.txt


title: Mock_RNAseq,2min, rep2

value: 2 minutes


title: D11-20.Biopsy_24

value: Muscle

value: all cell types in muscle


title: D11-20.Biopsy_23


title: HepaPlate01_H03

value: AFFF-4 (FireAde 6%)


title: TAZ_RNA_D3_rep2

description:
TAZ_D3_rep2
All_samples_raw_counts.txt
TAZ_D3_logFC_FDR_to_Vehicle.txt
TAZ_D3_vs_Veh_DESeq2_TE_only_output.txt


title: D11-20.Biopsy_22

description: Post-injury Day:3Wound Zone:Center

value: No treatment (default healing)


title: Phage riboseq, 15min, rep2

value: Ribo-seq

value: sk1 phage infected


title: Phage riboseq, 5min, rep2

value: bacteria

value: 5 minutes


title: D11-20.Biopsy_21

description: Post-injury Day:1Wound Zone:Edge


title: Phage riboseq, 2min, rep2


title: DAC30_RNA_D3_rep2

description:
DAC30_D3_rep2
All_samples_raw_counts.txt
DAC30_D3_logFC_FDR_to_Vehicle.txt
DAC30_D3_vs_Veh_DESeq2_TE_only_output.txt

value: colorectal carcinoma

value: 5'aza-2'deoxycytidine (30 nM)


title: D11-20.Biopsy_20


title: Mock_Rendseq, 15min, rep1

value: Rend-seq

value: 15 minutes

value: mock


title: HepaPlate01_G22

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorodecanoic acid


title: TAZ_RNA_D3_rep3

description:
TAZ_D3_rep3
All_samples_raw_counts.txt
TAZ_D3_logFC_FDR_to_Vehicle.txt
TAZ_D3_vs_Veh_DESeq2_TE_only_output.txt

value: 4-5 passages

value: 3 days


title: HepaPlate01_H04

value: Dodecafluoroheptanol


title: Phage riboseq, 15min, rep1


title: DAC30_RNA_D3_rep3

description:
DAC30_D3_rep3
All_samples_raw_counts.txt
DAC30_D3_logFC_FDR_to_Vehicle.txt
DAC30_D3_vs_Veh_DESeq2_TE_only_output.txt


title: DAC30_RNA_D3_rep1

description:
DAC30_D3_rep1
All_samples_raw_counts.txt
DAC30_D3_logFC_FDR_to_Vehicle.txt
DAC30_D3_vs_Veh_DESeq2_TE_only_output.txt


title: Veh_RNA_D3_B1_rep3

description:
Veh_D3_B1_rep3
All_samples_raw_counts.txt
none
none

value: DMSO


title: HepaPlate01_G23

value: Perfluorobutanesulfonic acid


title: HepaPlate01_G21

value: Perfluorotetradecanoic acid


title: HepaPlate01_G20

value: Perfluorooctanamide


title: Phage riboseq, 5min, rep1

value: bacteria

value: Ribo-seq

value: sk1 phage infected


title: dystrophin-deficient hiPSC-CM DMB02 line, differentiation run 2

city: Krakow

first: Jacek

last: Stepniewski

address: Gronostajowa 7

department: Department of Medical Biotechnology

country: Poland

institute: Jagiellonian University

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
DMD_2.2

data_processing:
Torrent Suite™ Software v5.12.1
The readings were aligned to hg19 AmpliSeq Transcriptome ERCC v1 reference database and counted by the Torrent Coverage Analysis Plugin program
The obtained results of gene expression were normalized and differential analysis was performed with the DESeq2 package available in the R software version 3.3.3.
Differential expression analysis and Gene Set Enrichment Analysis (GSEA) were performed in R (v.4.1.2) using DESeq2 (v.1.34.0) and clusterProfiler (v.4.2.2), respectively.
Batch effects estimation and correction were performed using sva (v.3.42.0) and limma (v.3.50.1) R libraries.
Assembly: hg19

growth_protocol: hiPSC-CM were maintained in RPMI medium supplemented with B-27 in humidified atmosphere at 37℃ and with 5% CO2

extract_protocol:
Total RNA was isolated accordingly to Chomczynski and Sacchi method using Fenozol.
RNA libraries for a total of eight samples were prepared using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

treatment_protocol: To investigate the effect of the lack of dystrophin on hiPSC-CM we established two isogenic hiPSC lines by deletion of DMD exon 50 in control (unaffected) cells.

value: hiPSC-derived cardiomyocytes

tag: genotype

value: mutation in DMD gene

tag: Sex

value: M


title: Mock_Rendseq, 2min, rep2

value: Rend-seq

value: 2 minutes

value: mock


title: D11-20.Biopsy_19

description: Post-injury Day:1Wound Zone:Center

value: Muscle

value: all cell types in muscle

value: No treatment (default healing)


title: HepaPlate01_H02

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanoic acid


title: HepaPlate01_G19

value: 6:2 Fluorotelomer sulfonic acid


title: TAZ_RNA_D3_rep1

description:
TAZ_D3_rep1
All_samples_raw_counts.txt
TAZ_D3_logFC_FDR_to_Vehicle.txt
TAZ_D3_vs_Veh_DESeq2_TE_only_output.txt

value: colorectal carcinoma

value: 4-5 passages

value: 3 days


title: Veh_RNA_D3_B1_rep2

description:
Veh_D3_B1_rep2
All_samples_raw_counts.txt
none
none

value: DMSO


title: Mock riboseq, 15min, rep2

value: bacteria

value: Ribo-seq

value: 15 minutes


title: Phage riboseq, 2min, rep1

value: sk1 phage infected


title: Veh_RNA_D3_B1_rep1

description:
Veh_D3_B1_rep1
All_samples_raw_counts.txt
none
none


title: dystrophin-deficient hiPSC-CM DMB02 line, differentiation run 1

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
DMD_2.1

value: hiPSC-derived cardiomyocytes

value: mutation in DMD gene

value: M


title: HepaPlate01_G18

value: AFFF-7 (Tridol 6%)


title: dystrophin-deficient hiPSC-CM DMB01 line, differentiation run 1

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
DMD_1.1


title: Hep3B cells, PUS1, with  doxycycline

city: Guangzhou

first: Yan-Xia

last: Hu

state: Guangdong

address: 600 Tianhe Road, Tianhe District

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

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v1.16).
rRNA contamination was filtered by Bowtie2 (v2.3.3.1).
Reads duplicates were collapsed using fastq2collapse.pl from CTK, and aligned to Ensembl-hg19 using BWA.aln.
C-to-U editing was acquired by joinWrapper.py and calculated by CIMS.pl.
C-to-U sites were further filtered, and only the sites with editing ratios > 0.05 were retained
Editing sites that were exclusively found in PUS1-APOBEC1 expressing cells were subject to further analysis.
mRNA transcripts with editing sites that were previously known to have pseudouridine modification (https://rna.sysu.edu.cn/rmbase/index.php) were considered as putative PUS1 target mRNAs.
Assembly: hg19
Supplementary files format and content: xlsx files include C to U editing sites identified by STAMP.

source_name: hepatocellular carcinoma

growth_protocol: Hep3B cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS), 1× MEM Non-Essential Amino Acids Solution (NEAA), 1mM Sodium Pyruvate and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V6 RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: EGFP-APOBEC1 and PUS1-APOBEC1 fusion protein was induced by treatment of Hep3B cells with 1μg/mL doxycycline (Dox).

value: hepatocellular carcinoma

value: Hep3B cells

value: hepatocellular carcinoma cells

value: PUS1-APOBEC1 overexpression

value: doxycycline treatment


title: HepaPlate01_G17

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluoro-3-methoxypropanoic acid


title: Mock riboseq, 2min, rep2

value: 2 minutes

value: mock


title: control hiPSC-CM DMB02 line, differentiation run 2

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
CTRL_2.2

value: control


title: Hep3B cells, PUS1 control, without  doxycycline

value: WT


title: HepaPlate01_G16

value: Perfluorotridecanoic acid


title: Hep3B cells, EGFP, with  doxycycline

value: EGFP-APOBEC1 overexpression


title: dystrophin-deficient hiPSC-CM DMB01 line, differentiation run 2

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
DMD_1.2

value: hiPSC-derived cardiomyocytes

value: mutation in DMD gene


title: control hiPSC-CM DMB01 line, differentiation run 2

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
CTRL_1.2

value: M


title: Hep3B cells, EGFP control, without  doxycycline

value: hepatocellular carcinoma


title: Mock riboseq, 15min, rep1

value: bacteria

value: Ribo-seq

value: 15 minutes


title: control hiPSC-CM DMB02 line, differentiation run 1

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
CTRL_2.1


title: Ovarian cancer, NACT, Post (R210197)

city: Lyon

first: Olivia

last: Le Saux

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a)
Gene expression was quantified using Salmon (v1.0.0) and the annotation of known genes from gencode v29
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file included counts values for each Sample

source_name: Ovary

extract_protocol:
Total RNA from FFPE tissues was extracted using 2 to 5 10-μm FFPE sections from pre- and post-treatment samples with FormaPure RNA kit (Beckman Coulter). RNA concentration and absorbances were analyzed with NanoDrop spectrophotometer (Thermo Fisher Scientific), and quality profiles assessed on Tapestation (Agilent Technologies).
Libraries were prepared with the TruSeq RNA Exome kit (Illumina)

value: Ovary

value: Ovarian cancer

value: NACT, Post


title: HepaPlate01_G13

first: Ivan

last: Rusyn

address: 4458 TAMU

institute: Texas A&M University

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanoic acid


title: HepaPlate01_G14

value: AFFF-4 (FireAde 6%)


title: HepaPlate01_G15

value: Dodecafluoroheptanol


title: Ovarian cancer, NACT, Pre (R210196)

value: NACT, Pre


title: KO2_agonist-p

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
The clean reads were aligned to Mus musculus genome (mm10) by bowtie2 with default parameter, and uniquely mapping reads were summarized by featureCounts (from Subread package)
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by DESeq2 with a cut-off threshold of 1.5-fold change and FDR adjusted p-value 0.05.
Assembly: mm10
Supplementary files format and content: txt file included FPKM values

source_name: thymus

growth_protocol: For in vitro samples: sorted WT and KO CD4+CD8+ DP thymocytes in vitro cultured in complete RPMI1640 culture medium, and stimulated with a-CD3(8μg/ml)+a-CD28(8μg/ml) for 24h, then sorted DN cells. For in vivo samples: sorted CD4-CD8-CD5+TCRb+ thymocytes (agonist-p) from Bcl6-wt and Bcl6-cko mice.

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol (Invitrogen, cat#15596018) according to the manufacturer’s protocol.
RNA-seq library was constructed for deep sequencing by BGI Genomics (in vivo) or Novogene (in vitro).

value: thymus

value: Bcl6fl/fl Cd4cre


title: control hiPSC-CM DMB01 line, differentiation run 1

description:
bc_matrix.xls
rpm_bc_matrix.xls
bc_summary.xls
CTRL_1.1

value: hiPSC-derived cardiomyocytes

value: control


title: Mock riboseq, 2min, rep1

value: 2 minutes

value: mock


title: Mock riboseq, 5min, rep2

value: bacteria

value: Ribo-seq

value: 5 minutes


title: Ovarian cancer, NACT+P, Post (R210195)

value: Ovary

value: Ovarian cancer

value: NACT+P, Post


title: Akt1s1-KO-3dpp-16

first: Huayu

last: Qi

address: 190 Kaiyuan Boulevard, Science City, huangpu District

department: Center for Cell Lineage and Development

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Library 16

data_processing:
Over 100 million raw reads obtained were pre-processed with trim-galore for trimming Illumina adaptor sequences.  Processed reads were quantified using Kallisto in pseudoalignment mode to an index of transcripts from mouse genome build to generate count and TPM (Transcripts Per Million).  Differentially expressed genes were identified with the DESeq2 package using raw counts.
Assembly: mm10
Supplementary files format and content: Text file with TPM

source_name: Testis

extract_protocol:
OCT4-GFP positive spermatogonia were isolated from mice using FACS following enzyme digestion of testes.  Each sample contained about 1-2 X 10-4 cells.  Total RNAs were extracted from OCT4-GFP+ cells using ToTal RNA extraction kit (Tiangen, DP419).  RNA yield and purity were evaluated using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific, Waltham, MA).  Quality and integrity were determined by RBA 6000 Nano kit with a Bioanalyzer 2100 (Agilent Technology, Santa Clara, CA).
cDNA libraries were prepared using Vazyme VAHTS mRNA-seq V3 Library Prep kit for Illumina (Vazyme, NR611).

treatment_protocol: Testis digested with collagenase, DNaseI and Trypsin before FACS

value: Testis

value: Primary spermatogonia

value: Pou5f1-Gfp;Akt1s1 null


title: KO1_agonist-p


title: Akt1s1-KO-3dpp-18

description: Library 18


title: WT2_agonist-p


title: HepaPlate01_G11

city: College Station

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorodecanoic acid


title: Ovarian cancer, NACT+P, Pre (R210194)

value: NACT+P, Pre


title: HepaPlate01_G10

value: Perfluorotetradecanoic acid


title: Og2-3dpp-15

description: Library 15


title: WT1_agonist-p

value: thymus


title: Ovarian cancer, NACT+P, Post (R210193)


title: HepaPlate01_G09

value: Perfluorooctanamide


title: Og2-3dpp-14

description: Library 14


title: Mock riboseq, 5min, rep1

value: mock


title: HepaPlate01_G12

value: Perfluorobutanesulfonic acid


title: Ovarian cancer, NACT+P, Pre (R210192)