title: HUVEC, 240 min TNFa

description: 10x Genomics

data_processing:
Extraction of UMIs, genome mapping, exon quantification in genes and intron quantification in transcripts were conducted using the nf-core rnaseq pipeline v3.9.0 (www.nf-co.re/rnaseq) in Nextflow v22.10.6.
Assembly: GRCh38-2020-A
Supplementary files format and content: single cell intronic UMI count matrix of transcripts, single cell exonic UMI count matrix of genes

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared on 384-well plates with the SMART-seq 2.5 protocol as described previously (DR Ghasemi et al. 2024, Nat Commun; doi: 10.1038/s41467-023-44117-x).


title: HUVEC, 0 min TNFa, replicate 3

status: Public on Jan 01 2025

type: SRA

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger software v7.1.0 (support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell count matrix of features

molecule: total RNA

organism: Homo sapiens

source_name: Umbilical vein endothelial cells

growth_protocol: HUVECs from pooled donors (Lonza, cat. #00191027, lot #18TL232828) were cultured in endothelial basal medium (EBM-2) with supplements (Lonza, cat. #CC-3162). Low passage number cells were seeded in 18-well slides (Ibidi) and starved for 20-24 h in EBM + 0.5% FBS prior to treatment.

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared according to the Chromium Next GEM Single Cell 5' (dual index) protocol v2 from 10x Genomics (Pleasanton, USA).

treatment_protocol: HUVECs were treated with 10 ng/mL human TNFα (PeproTech, cat. #300-01A) for 0, 30 and 240 min.

tag: cell type

value: Umbilical vein endothelial cells

tag: treatment

value: TNFa

tag: time point

value: 0 min


title: HUVEC, 240 min TNFa, replicate 2

description: 10x Genomics

value: 240 min


title: HUVEC, 30 min TNFa

description: 10x Genomics

molecule: nuclear RNA

value: 30 min


title: Mix 100 μM, rep 1

city: Daejeon

first: Soontag

last: Jung

address: 141 Gajeong-ro, Yuseong-gu

department: Developmental and reproductive toxicology

country: South Korea

institute: Korea Institute of Toxicology

library_source: transcriptomic

data_processing:
Raw reads underwent adapter and low-quality sequence removal using Trimmomatic v0.38, followed by quality checks with FastQC before and after trimming.
Trimmed reads were aligned to the GRCh38 reference genome using HISAT2 v2.1.0.
Mapped reads were then assembled individually for each gene using StringTie v2.1.3b.
Assembled read counts were normalized using the trimmed mean of M-values method via the EdgeR v4.0.9 within R v4.3.2.
Assembly: GRCh38
Supplementary files format and content: Comma separated value file includes raw count for each sample

source_name: Rencell VM

growth_protocol: ReNcell VM (Merck Millipore, Darmstadt, Germany), an immortalized human neural progenitor cell line, was employed as a substitute for primary human neural progenitor cells. Before ReNcell VM seeding, all tissue culture plastic ware was coated with DMEM/F-12 supplemented with GlutaMAX™ (Gibco) and 20 μg/mL laminin (Gibco) at 37 °C for 4 h. ReNcell VM were maintained in growth medium consisting of ReNcell® NSC Maintenance Media (Merck Millipore) supplemented with 20 ng/mL epidermal growth factor (EGF, Merck Millipore), 20 ng/mL basic fibroblast growth factor (bFGF, Merck Millipore), and 1% penicillin/streptomycin (Thermo Fisher Scientific, Waltham, MA). Cells were cultured in a humidified incubator at 37 °C with 5% CO2, and the growth medium was changed every two days. Neurospheres were prepared using round bottom ultra-low attachment 384-well spheroid microplates (ULA plate, Corning, Tewksbury, MA). Briefly, ReNcell VM cells that reached confluency were detached with Accutase (Innovative Cell Technologies, San Diego, CA) and seeded on ULA plates at 8000 cells/well in 40 μL of growth medium. Neurospheres were cultured in a humidified incubator at 37 °C with 5% CO2 for 4 days without replacing the medium.

extract_protocol:
Total RNA was extracted by pooling six neurospheres using the Maxwell® RSC simplyRNA Cells Kit (Promega, Madison, WI) following the manufacturer's instructions.
cDNA libraries for RNA-seq were prepared using SureSelect RNA Direct Human Library Preparation kit following manufacturer's protocols.

treatment_protocol: Neurospheres were transferred to a laminin-coated 48-well plate and then cultured in differentiation medium containing N-2 Supplement (Gibco) in DMEM/F-12 supplemented with GlutaMAX™ (Gibco), treated with test substances at concentrations ranging from 0.3 to 100 μM. . The neurospheres were cultured for 6   days, with the differentiation medium and test substances replaced every 2 days.

tag: cell line

value: Rencell VM

value: Neurosphere

value: Mix 100 uM


title: HUVEC, 0 min TNFa

description: 10x Genomics


title: HUVEC, 30 min TNFa, replicate 1

description: 10x Genomics


title: HUVEC, 30 min TNFa, replicate 2

description: 10x Genomics


title: NMF-044, Control group

city: Columbia

first: Bettina

last: Mittendorfer

state: MO

address: 1030 Hitt St, 3rd floor

department: Nutrition and Exercise Physiology

country: USA

institute: University of Missouri - Columbia

data_processing:
The raw data is demultiplexed by bcl-convert1, cleaned, and trimmed by quality using Fastp2; only high-quality reads were used for downstream analysis. Adapter sequences are removed, and bases with an average PHRED quality of <20 are removed. Finally, reads shorter than 36bp (i.e., clipped reads) are discarded. QC metrics are compiled and summarized with MultiQC3. All workflows are custom-built with Nextflow4 to allow complete reproducibility.
STAR5was used to map clean reads to the reference genome and then quantify the mapped reads.
Assembly: Ensembl (GRCh38.p14)
Supplementary files format and content: Raw count for all samples
Supplementary files format and content: RPKM count for all samples

source_name: skeletal muscle

extract_protocol:
RNA samples were extract with QIAzol lysis reagent and a RNeasy Fibrous Tissue mini kit (#74704Qiagen, Valencia, CA) in combination with TRIzol/Choloroform (#15-596-018, Invitrogen, Waltham, MA)
libraries were prepared by using a TruSeq Stranded mRNA kit (#20020594, Illumina, San Diego, CA) with total RNA and cDNA fragments generated on an Illumina NovaSeq-PE-100 6000

tag: tissue

value: skeletal muscle

value: tissue

value: striated muscle

tag: genotype

value: wild type


title: HUVEC, 240 min TNFa, replicate 1

description: 10x Genomics


title: HUVEC, 0 min TNFa, replicate 1

description: 10x Genomics


title: HUVEC, 0 min TNFa, replicate 2

description: 10x Genomics


title: HUVEC, 0 min TNFa, replicate 3 [snATAC-seq]

description: 10x Genomics, TurboATAC protocol

library_source: genomic

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file
Library strategy: snATAC-seq

molecule: genomic DNA

extract_protocol:
For harvesting, cells were treated with trypsin and resuspended in EBM + 0.5% FBS. After centrifugation, the cell pellet was resuspended in PBS/BSA.
Libraries were prepared using our improved TurboATAC protocol that provides an increased Tn5 integration efficiency (I Seufert et al. 2023, Front Epigenet Epigenom; doi: 10.3389/freae.2023.1245879) with the Chromium Next GEM Single Cell ATAC kit v2 from 10x Genomics (Pleasanton, USA).


title: NMF-039, Prediabetes group


title: NMF-050, Prediabetes group


title: NMF-040, Control group


title: NMF-042, Prediabetes group


title: NMF-031, Prediabetes group


title: NMF-028, Control group


title: NMF-038, Control group


title: NMF-024, Control group


title: NMF-027, Prediabetes group


title: NMF-025, Prediabetes group


title: NMF-022, Control group


title: NMF-020, Control group


title: NMF-019, Prediabete group


title: NMF-014, Control group


title: NMF-008, Control group


title: NMF-007, Prediabetes group


title: NMF-002, Prediabetes group


title: NMF-006, Control group


title: OA, Patient6

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were aligned to the hg38 reference genome using Bowtie2 short read aligner using default settings.
Peaks were called using MACS2 with the –nomodel option on.
bigWig files were generated using the bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: bigWig of merged replicates per MSC donor treatment or hip cartilage patient disease state

source_name: cartilage

growth_protocol: Human bone marrow mesenchymal stem cells (MSC) cultured in Mesenchymal Stem Cell Growth Medium (Lonza) supplemented with 5ng/ml fibroblast growth factor-2 in a humid atmosphere of 5% CO2/95% air at 37°C. Human articular chondrocytes (HACs) were enzymatically digested out of hip articular cartilage with1mg/mL hyaluronidase in PBS for 15 minutes, then 2.5mg/mL trypsin in PBS for 30 minutes, then with 2mg/mL collagenase in DMEM +10% FBS and antibiotics overnight at 37°C.

extract_protocol:
MSCs were enzymatically digested out of Day14 cartilage discs with 1mg/mL hyaluronidase in PBS for 15 minutes, then 2.5mg/mL trypsin in PBS for 30 minutes, then with 2mg/mL collagenase in chondrogenic differentiation medium for 1-1.5hrs at 37°C. HACs were enzymatically digested out of hip articular cartilage with 1mg/mL hyaluronidase in PBS for 15 minutes, then 2.5mg/mL trypsin in PBS for 30 minutes, then with 2mg/mL collagenase in DMEM +10% FBS and antibiotics overnight at 37°C
Nuclei were isolated by lysis of 50,000 cells using ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifugation at 500g for 10 minutes at 4oC. Following isolation, the nuclei were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase TDE1 (Nextera Tn5 Transposase, Illumina, Cambridge, UK) in a total volume of 50 μL  and incubated for 30 minutes at 37oC. All samples were subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Manchester, UK), eluting in 10μl of Elution Buffer
Transposed DNA (10ul) was PCR amplified using the NEB Next High-Fidelity PCR Master Mix and primer Ad1_noMX in combination with barcoded primers. The number of cycles in the thermocycler was optimised on a per sample basis to avoid amplification to saturation. Samples were cleaned up with Ampure XP beads and quantitified on an Agilent 4200 TapeStation

treatment_protocol:
Chondrogenic differentiation of MSCs was induced with high glucose DMEM containing 100 µg/ml sodium pyruvate, 10 ng/ml TGF-β3, 100 nM dexamethasone, 1x ITS-1 premix, 40 µg/ml proline, and 25 µg/ml ascorbate-2-phosphate in 6.5mm diameter, 0.4-µm pore size polycarbonate Transwell filters.
Media were replaced every 2/3 days for a duration of 14 days.

value: cartilage

value: chondrocytes

tag: disease state

value: osteoarthritis

tag: Sex

value: Female

tag: age


title: OA, Patient7

value: Male


title: NMF-005, Control group


title: OA, Patient4


title: OA, Patient3


title: OA, Patient2


title: OA, Patient1


title: OA, Patient5


title: NMF-030, Control group


title: NOF, Patient8

value: control


title: NMF-023, Control group


title: NOF, Patient9


title: NOF, Patient7


title: NOF, Patient6


title: NOF, Patient3


title: MSC 8A, Day14, Replicate2

source_name: mesenchymal stem cells

value: mesenchymal stem cells

tag: time

value: female

value: chondrogenic differentiation


title: MSC 8A, Day14, Replicate1


title: NOF, Patient5


title: NOF, Patient4


title: MSC 8A, Day0, Replicate2


title: NOF, Patient2


title: NMF-012, Control group


title: NMF-018, Prediabetes group


title: NOF, Patient1


title: MSC 2454E, Day14, Replicate2


title: MSC 2454E, Day14, Replicate3


title: MSC 8A, Day0, Replicate1


title: MSC 2454E, Day14, Replicate1


title: MSC 2454E, Day0, Replicate1


title: MSC 2454E, Day0, Replicate2


title: 33NKT_AML

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: In vitro

extract_protocol:
T cells collected from in vitro culture both before (sequenced with 5' GEX and scTCR) and after repeated tumor challenges (sequenced with 3' GEX) were subjected to scRNA-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: After tumor challenge

value: T cells

value: In vitro


title: MSC 2454E, Day0, Replicate3


title: 33T_AML

description: 10x Genomics


title: 33NKT

description: 10x Genomics

value: Before tumor challenge


title: SHSY5Y cells, Thapsigargin, rep 1

city: Kolkata

first: Saikat

last: Chakrabarti

state: West Bengal

address: CN-6, Sector V

country: India

institute: CSIR-IICB

data_processing:
Adaptor trimming and QC filtering of raw files (Qscore > 30).
Filtered reads were aligned to GRCh38 with STAR alignment tool.
Read count was generated by HTSeq
Assembly: GRCh38
Supplementary files format and content: Comma separated values file includes normalized counts for each samples

source_name: SHSY5Y cells

extract_protocol:
RNA was extracted from the samples using TRIzol LS reagent (Invitrogen). Ethanol precipitation was done before shipment.
RNA libraries for RNA-seq were prepared using Truseq RNA library prep kit using manufacturer's protocol.

value: SHSY5Y cells

value: Neuroblastoma cells

value: WT

value: Thapsigargin


title: 33T

description: 10x Genomics


title: SHSY5Y cells, DMSO, rep 2

value: DMSO


title: SHSY5Y cells, DMSO, rep 1


title: SHSY5Y cells, DMSO, rep 3


title: SHSY5Y cells, Thapsigargin, rep 3


title: SHSY5Y cells, Thapsigargin, rep 2


title: D6, scGlycosylation-seq

city: Haikou

first: wanyi

last: feng

state: Hainan

address: No.58 Renmin Avenue

country: China

institute: hainan university

data_processing:
Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads using Cutadapt v3.7.
scRNA-Seq library analysis: R2 reads were aligned against the GRCh38 transcriptome using STAR v2.6.1b. Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
scGlycosylation seq library analysis: The 15bp tag sequence was extracted from the R2 reads according to the position, and compared with the known glycosylation tag sequence. Tag sequence with a Hamming distance less than 2 was considered as a valid tag. The number of tag UMI contained in each cell barcode is counted to generate a single cell glycosylation UMI expression matrix.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: clone10 induced pluripotent stem cell

extract_protocol:
In hematopoietic induction in vitro, samples of D0, D2, D4, D6, D8, D10 are dissociated into single-cell solution. Briefly, cells from different time point samples were dissociated with 1 ml/well of Accutase at 37°C for 8 min. Cells were washed and resuspended with differentiation medium (IMDM, 5 ng/ml BMP4, 10 ng/ml VEGF, 2 U/ml EPO (MCE), 20 ng/ml SCF (MCE), 15 μM NAC (Sigma-Aldrich), and 1 μM minocycline hydrochloride (Selleck)). The collection of cells was performed using the Dead Cell Removal Kit (Miltenyi). For labeling experiments, transfer the prepared single cells to the labeling culture medium and keep the cell culture away from light. After incubation, discard supernatant and resuspend cell pellet in an appropriate volume of PBS. Glycosylation sites on the cell surface were labeled with fucose residues carrying a tag containing a PCR handle, known sequence, and polyA sequence, and glycosylation sites on the cell surface were labeled with fucose residues carrying a tag containing a PCR handle, known sequence, and polyA sequence.
Single-cell suspensions with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: clone10 induced pluripotent stem cell

value: Hematopoiesis induction in vitro for 6 days


title: D8, scGlycosylation-seq

value: Hematopoiesis induction in vitro for 8 days


title: D10, scGlycosylation-seq

value: Hematopoiesis induction in vitro for 10 days


title: D4, scGlycosylation-seq

value: Hematopoiesis induction in vitro for 4 days


title: D8, scDynamic RNA-seq


title: D0, scGlycosylation-seq

value: Hematopoiesis induction in vitro for 0 days


title: D10, scDynamic RNA-seq


title: D2, scDynamic RNA-seq

value: Hematopoiesis induction in vitro for 2 days


title: D2, scGlycosylation-seq


title: D4, scDynamic RNA-seq


title: D6, scRNA-seq


title: D0, scDynamic RNA-seq


title: D10, scRNA-seq


title: D4, scRNA-seq


title: D2, scRNA-seq


title: D8, scRNA-seq


title: D0, scRNA-seq


title: HIO day 28

city: Cincinnati

first: Michael

last: Helmrath

address: 3333 Burnet Avenue

institute: Cincinnati Children’s Hospital Medical Center

data_processing:
Raw count matrices were processed using Seurat v4.3.0.1. Cells from each sample were processed separately. First, cells were filtered on the basis of the number of detected genes and the fraction of mitochondrial genes. The gene expression values from each sample were normalized using the SCTransform 27 function from the Seurat package with the parameters method set to "glmGamPoi" and vars.to.regress set to "percent.mt". Next, samples were integrated following Seurat’s guidelines. 3000 genes were selected using the SelectIntegrationFeatures function before prepping the integration using the PrepSCTIntegration function. Integration anchors were defined using the FindIntegrationAnchors function before IntegrateData was used to integrate all datasets, with the normalization.method parameter set to "SCT".
Assembly: hg38
Supplementary files format and content: tab-delimited text files and matrix files

source_name: intestine

growth_protocol: Human esophageal, gastric, intesinal, and colonic organoids were cultured in Matrigel overlaid with intestinal growth medium (Advanced DMEM/F-12, N2, B27, 15 mM HEPES, 2 mM L-glutamine, penicillin-streptomycin) supplemented with 100 ng/mL EGF.

extract_protocol:
organoids were recovered from the Matrigel using Cell Recovery Solution and transferred in 15mL tubes. Then, organoids were washed using dPBS and dissociated with 500mL of trypsin-EDTA at 37°C. Full dissociation was achieved by manual dissociation using a micropipette. Trypsin-EDTA was inhibited by the addition of 4.5mL of DMEM/F12 supplemented with 10% FBS. Solutions were filtered using a 40µm cell strainer and centrifuged at 300g for 5min. Supernatant was removed and replaced by DMEM/F12 supplemented with Y-27632. Cells were counted and viability assessed using Trypan blue exclusion dye.
scRNA-seq libraries were prepared using the 10x Genomics Chromium platform using version 3.1 chemistry. Sequencing was performed using a NovaSeq 6000 (Illumina) machine and Raw scRNA-Seq data was processed using CellRanger (v2.0.0 10x Genomics)

treatment_protocol: For human intestinal (HIO) and colonic (HCO) organoids generation, H1 human embryonic stem cells were first differentiated into definitive endoderm (DE) by treatment with 100 ng/mL of activin A in DE induction media [RPM1 1640, 1× NEAA and 0.2-2% dialyzed fetal calf serum (dFCS)] for three days. DE was then treated with hindgut induction medium composed of 100 ng/mL FGF4 and 3 μM Chiron 99021 in RPMI 1640, 1x NEAA, and 2% dFCS for four days to induce the formation of mid-hindgut spheroids. For human esophageal (HEO) and gastric (HGO) organoids generation, H1 cells were treated with 100 ng/mL activin A and 50 ng/mL BMP4 (R&D systems) for one day and 100 ng/mL activin A for the two following days. To generate HGOs, DE was then treated with 500 ng/mL of FGF4, 200 ng/mL of NOG, and 2 mM of CHIR for 3 days. 2 mM of RA was added on the third day of FGF4/NOG/CHIR treatment. Foregut spheroids were then collected and plated in Growth Factor Reduced Matrigel at a density of approximately 40 spheroids per 50 µL Matrigel drops. Spheroids were cultured in organoid growth medium supplemented with 100 ng/mL EGF plus 200 ng/mL NOG, and 2 mM RA for 3 days. To generate HEOs, DE was treated with 500 ng/mL of FGF4, 200 ng/mL of NOG, and 500 ng/mL of Wnt3a for 2 days. On the third day, Wnt3a was replaced with 2 mM RA. Foregut spheroids were then collected and plated in Growth Factor Reduced Matrigel at a density of approximately 40 spheroids per 50 µL Matrigel drops. Spheroids were cultured in organoid growth medium supplemented with 100 ng/mL EGF plus 200 ng/mL NOG and 50 ng/mL FGF10 (R&D systems) for 3 days.

value: intestine

value: Human embryonic stem

tag: organoid

value: HIO

value: day 28


title: HCO day 18

source_name: Colon

value: Colon

value: HCO

value: day 18


title: HIO day 18


title: HGO day 28

source_name: stomach

value: stomach

value: HGO


title: HEO day 18

source_name: esophagus

value: esophagus

value: HEO


title: HGO day 18


title: HEO day 28


title: R663H + verapamil rep3

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg

department: Chemical Engineering

institute: University of California Santa Barbara

data_processing:
The resulting raw FASTQ files were trimmed using the default settings of TrimGalore in paired end mode. Afterwards, STAR (STAR aligner version 2.7.8a) was used to map and quantify gene expression levels using the human genome assembly GRCh37 (hg19). DESeq2 with adaptive shrinkage was used for normalization and differential gene expression calling. A shrunken absolute log fold change cutoff of 1 and adjusted p-value cutoff of 0.05 was used for differential gene expression calling. For visualization and clustering, variance stabilizing transformation was performed. The removeBatchEffect function in the LIMMA package was used to remove batch effects observed between two successive rounds of sequencing. David Bioinformatics Resources was used for gene ontology analysis.
Assembly: hg19
Supplementary files format and content: STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options:
Supplementary files format and content: column 1: gene ID
Supplementary files format and content: column 2: counts for unstranded RNA-seq
Supplementary files format and content: column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)
Supplementary files format and content: column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Supplementary files format and content: Novogene utilized an unstranded RNA-seq library construction.

molecule: polyA RNA

source_name: D60 hiPSC-CM

growth_protocol: hiPSC-CM and hiPSC-CF differentiation: Directed cardiac differentiation was achieved using the WNT modulating protocol previously described (Lian, X. et al. 2012). Upon D12 of cardiac differentiation, hiPSC-CMs were purified by glucose starvation (RPMI(-Glucose) + B27 supplement) as previously described (Sharma, A. et al, 2015). hiPSC-CMs were further maintained in RPMI + B27 supplement with media changes every 48hrs. Directed cardiac fibroblast differentiation was achieved using the previously described protocol (Whitehead, A. J., Hocker, J. D., Ren, B. & Engler, A. J., 2022). Upon D32 of cardiac fibroblast differentiation, hiPSC-CFs were passaged and maintained in Promocell Fibroblast Growth Medium 3 with media changes every 48 hrs. hiPSC CFs were passaged with Accutase® when cultures reached 80% confluence.

extract_protocol:
RNA extraction and purification was performed using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions.
Total RNA was sent to Novogene (Beijing, China) for library construction and 150 base pair pair-end sequencing. Novogene utilized the NEB Next Ultra II kit (Poly A) for library construction.

treatment_protocol: At day 59, hiPSC-CM were cultured with verapamil (100 nM) or levosimendan (300 nM) or no drug for 24 hours prior to cell isolation for RNA-seq at Day 60.

value: D60 hiPSC-CM

value: MYH7- R663H patient derived hiPSC line

value: 24 hr verapamil (100 nM)


title: R663H + verapamil rep2


title: R663H + verapamil rep1


title: R663H Control rep3


title: D6, scDynamic RNA-seq

value: clone10 induced pluripotent stem cell

value: Hematopoiesis induction in vitro for 6 days


title: R663H Control rep1


title: R663H Control rep2


title: WT + levosimendan rep3

tag: biomaterial provider

value: 24 hr levosimendan (300 nM)


title: WT + levosimendan rep2


title: 8 postnatal day 7 nontransgenic pituitary glands

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

data_processing:
FastQC was used to analyze read quality
Bowtie2 was used to align reads to the mm39 Genome assembly
Genes were annotated using Cufflinks and FPKM was converted to TPM using TPMconverter
Assembly: Genome Reference Consortium Mouse Build 39
Supplementary files format and content: Tab delimited txt files for the all FPKM isoform reads is provided for each data set

organism: Mus musculus

source_name: pituitary

extract_protocol:
Pitutary glands were extracted and dispersed using collagenase.  Dispersed cells were FACS sorted and the GFP positive fraction was collected for RNA extraction using the QIAGEN Rneasy MicroRNA kit.
250ng of RNA was used as input to extract cDNA using a ribo-depeletion method to capture both mRNA and lncRNA

value: pituitary

value: all pituitary cells

value: nontransgenic


title: 5 postnatal day 7 Tshbcre-YFP pituitary glands pooled, FACS sorted

value: sorted Tshbcre positive

value: Tshbcre-YFP


title: WT Control Rep3


title: One adult pitutary gland

value: adult


title: 7 adult Lhbcre-YFP pituitary glands pooled, FACS sorted

value: sorted Lhbcre positive

value: Lhbcre-YFP


title: WT Control Rep2


title: WT Control Rep1


title: HCO day 28

value: Colon

value: Human embryonic stem

value: HCO

value: day 28


title: 12 adult Ghcre-YFP pituitary glands pooled, FACS sorted

value: sorted Ghcre positive

value: Ghcre-YFP


title: 42 adult Tshbcre-YFP pituitary glands pooled, FACS sorted


title: OT10_1550

city: Lausanne

first: Isaac

last: Crespo

state: Vaud

address: Bugnon 25A

department: Oncology

country: Switzerland

institute: Ludwig Cancer Research,UNIL

data_processing:
The scRNA-Seq reads were aligned to the mm10-2020-A reference genome and quantified using cellranger count (10X Genomics, version 5.0.1). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
To filter out low-quality transcriptomes, total ribosomal and mitochondrial count filters were applied, with maximum accepted percentage counts coming from ribosomal and mitochondrial genes of 60% and 10%, respectively. In addition, the acceptable number of detected genes per cell ranges between 250 and 6000.
After the filtering, data was normalized using the “LogNormalize” function from the “Seurat v3.0.2” package, which normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor of 10,000 and log-transforms the result.
Assembly: mm10-2020-A
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in tab-separated format

growth_protocol: Naïve CD8+OT1 T cells were activated in vitro on day 0 with anti-CD3/anti-CD28 coated beads and expanded in presence of IL-2, IL-2v or IL-15 (5 and/or 50 IU/mL) up to 10 days. Next, cells at different time points of in vitro culture (before expansion, day 0 and after 3, 5, 7, and 10 days) were processed for scRNAseq analysis.

extract_protocol: For scRNA-seq of CD8+OT1 TILs, live CD44+CD45.1+CD8+T cells were sorted using a BD FACSAria™ III (BD Bioscences).

value: T cell

value: anti CD3/CD28 beads + Interleukin-16 , 50 IU/mL


title: dh1f cells, post-OSKM MRG15 knock-out replica #3

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

data_processing:
STAR was used to align Fastq files to the latest human reference transcriptome
Salmon was used for quantification
Tximport and DEseq2 used for normalisation of counts
Assembly: GRCh38
Supplementary files format and content: XLSX files of all sample counts

extract_protocol:
Zymo Research RNA Extraction Kit
TruSeq Stranded mRNA

value: MRG15 knockout

tag: sgrna

value: sgRNA MRG15

value: post-OSKM


title: dh1f cells, post-OSKM MRG15 knock-out replica #2


title: OT10_1505

value: anti CD3/CD28 beads + Interleukin-15 , 5 IU/mL


title: dh1f cells, post-OSKM Non targeting replica #2

value: Wildtype

value: sgRNA control


title: OT10_bg05

value: anti CD3/CD28 beads + mutant IL-2bg , 5 IU/mL


title: dh1f cells, pre-OSKM MRG15 knock-out replica #3

value: pre-OSKM


title: OT10_205

value: anti CD3/CD28 beads + wild type Interleukin-2 , 5 IU/mL


title: OT10_250

value: anti CD3/CD28 beads + wild type Interleukin-3 , 50 IU/mL


title: dh1f cells, pre-OSKM MRG15 knock-out replica #2


title: WT + levosimendan rep1

value: D60 hiPSC-CM

value: 24 hr levosimendan (300 nM)


title: dh1f cells, pre-OSKM MRG15 knock-out replica #1


title: OT5_1550


title: OT5_1505


title: dh1f cells, pre-OSKM Non targeting replica #2


title: OT10_bg50

value: anti CD3/CD28 beads + mutant IL-2bg , 50 IU/mL


title: dh1f cells, pre-OSKM Non targeting replica #1


title: HFF cells, shTASOR, HCMV, 48h, rep2

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

institute: institute of Virology, University Medical Center Freiburg

data_processing:
Sequence reads were mapping to hg38 by STAR
Assembly: hg38
Supplementary files format and content: counts file were generated by featurecounts

source_name: HFF

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq with rRNA depletion as indicated

value: HFF

value: HFF cells

value: TASOR knockdown

value: HCMV


title: HFF cells, shTASOR, HCMV, 48h, rep1


title: OT5_205

value: T cell


title: OT5_noC

value: anti CD3/CD28 beads + no exogeneous cytokine


title: dh1f cells, post-OSKM MRG15 knock-out replica #1

value: MRG15 knockout

value: sgRNA MRG15

value: post-OSKM


title: OT5_250


title: HFF cells, shTASOR, mock, 48h, rep1

value: mock


title: OT3_1505

value: anti CD3/CD28 beads + Interleukin-15 , 5 IU/mL


title: OT3_bg50


title: HFF cells, shPPHLN1, HCMV, 48h, rep2

value: PPHLN1 knockdown


title: dh1f cells, post-OSKM Non targeting replica #1

value: Wildtype

value: sgRNA control


title: HFF cells, shPPHLN1, HCMV, 48h, rep1


title: HFF cells, shPPHLN1, mock, 48h, rep2


title: OT3_bg05

value: anti CD3/CD28 beads + mutant IL-2bg , 5 IU/mL


title: HFF cells, shPPHLN1, mock, 48h, rep1


title: OT5_bg50


title: OT3_noC


title: HFF cells, shMPP8, HCMV, 48h, rep2

value: MPP8 knockdown


title: OT3_205

value: anti CD3/CD28 beads + wild type Interleukin-2 , 5 IU/mL


title: HFF cells, shMPP8, mock, 48h, rep2

value: HFF


title: dh1f cells, pre-OSKM Non targeting replica #3

value: pre-OSKM


title: HFF cells, shTASOR, mock, 48h, rep2

value: HFF cells

value: TASOR knockdown


title: OT5_bg05

value: T cell


title: HFF cells, shMPP8, HCMV, 48h, rep1

value: HCMV


title: OT0

value: no treatment


title: HFF cells, shMPP8, mock, 48h, rep1


title: HFF cells, shKAP1, HCMV, 48h, rep1

value: KAP1 knockdown


title: OT3_1550

value: anti CD3/CD28 beads + Interleukin-16 , 50 IU/mL


title: HFF cells, shKAP1, HCMV, 48h, rep2


title: dh1f cells, post-OSKM Non targeting replica #3

value: post-OSKM


title: HFF cells, shKAP1, mock, 48h, rep2

value: mock


title: HFF cells, shKAP1, mock, 48h, rep1


title: HFF cells, shCK, HCMV, 48h, rep2

value: shRNA CK


title: TLR3Injured-1

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (mm10) (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using WS220 as the reference genome sequence. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff2. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: trachea - Bronchoalveolar Lavage

growth_protocol: Klebsiella Pneumoniae, strain 43816, serotype 2, was cultured overnight in tryticase soy broth with re-inoculation the following morning into fresh medium to bring the bacteria into a logarithmic growth phase. Optical density was measured at 600nm and serial dilutions were then made to reach a concentration of 500 CFU of bacteria per 30ul.

extract_protocol:
Macrophages were isolated from the BAL fluid and total RNA was extracted from Macrophages using Qiagen Rneasy Mini Kit.
Paired end 50. TruSeq mRNA.

treatment_protocol: Mice were inoculated with bacterial suspension or saline via deep hypopharyngeal injection under isoflurane anaesthesia.

value: Macrophages

value: following pneumonia


title: TLR3control-2


title: TLR3control-4


title: TLR3Injured-4


title: TLR3Injured-2


title: TLR3Injured-3


title: TLR3control-3


title: HFF cells, shCK, mock, 48h, rep2


title: TLR3control-1


title: OT3_250

value: anti CD3/CD28 beads + wild type Interleukin-3 , 50 IU/mL


title: WTInjured-2

value: WT


title: HFF cells, shCK, HCMV, 48h, rep1


title: WTInjured-4


title: HFF cells, shCK, mock, 48h, rep1


title: RiboWo

city: hangzhou

first: Wenlong

last: Ding

state: zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: Life Sciences Institute

institute: Zhejiang University

library_source: other

data_processing:
*library strategy: Ribo-seq
The raw reads were cleaned and subjected to genome mapping with TopHat2 (2.0.12)
Quantification of the mapped results at the gene level was performed using HTSeq (0.9.1).
Assembly: GRCh37/hg19
Supplementary files format and content: xls file including raw counts for each sample
Supplementary files format and content: xls file including RPKM normalizated counts for each sample

molecule: other

growth_protocol: Human embryonic kidney HEK293T cells (ATCC) were cultured in an exponential growth as a monolayer in Dulbecco’s Modified Eagle Medium (DMEM, Gibco), supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco); cell lines were maintained in a humidified atmosphere containing 5% of CO2 at 37℃ and passaged every 2-3 days up to 20 passages.

extract_protocol: The following library construction and sequencing was performed using Novogene (Beijing, China) use SE50 sequencing for 30 M raw reads

treatment_protocol: HEK293T cells were plated in 15 cm dishes and co-transfected with pCMV-Nes--chPylRSIPYE (TetRS)TetRS-12*(U6-CM15CGA) with or without pEGFP-mCherry-T2A-EGFP-151TCG in the presence of TetBu. The two samples were named as RiboW and RiboWo. After 30 h of expression, cells were incubated with fresh medium containing 0.1mg mL-1 CHX for 1 min, washed three times with 5 mL PBS containing 0.1 mg mL-1 CHX, gently collected with a scraper.

value: Human embryonic kidney

value: HEK293T cells were plated in 15 cm dishes and co-transfected with pCMV-Nes--chPylRSIPYE (TetRS)TetRS-12*(U6-CM15CGA) with without pEGFP-mCherry-T2A-EGFP-151TCG in the presence of TetBu.


title: WTInjured-3


title: RiboW

value: HEK293T cells were plated in 15 cm dishes and co-transfected with pCMV-Nes--chPylRSIPYE (TetRS)TetRS-12*(U6-CM15CGA) with  pEGFP-mCherry-T2A-EGFP-151TCG in the presence of TetBu.


title: RTS-Rep

data_processing:
Raw reads were trimmed with fastp to remove adapter sequences and then aligned to the reference human genome GRCh37/hg19 with STAR (v2.4.2a)
Gene expression abundance was estimated by RSEM (v1.3.3) based on the uniquely mapped reads.
Assembly: GRCh37/hg19
Supplementary files format and content: xls file including raw counts for each sample
Supplementary files format and content: xls file including TMM normalizated counts for each sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)
The Illumina TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation.

treatment_protocol: HEK293T cells were plated in 10 cm dishes. Three groups were setted. Sample-1 was HEK293T cells transfected with TCG recoding system plasmid pCMV-Nes-chPylRSIPYE (TetRS)-12*(U6-CM15CGA). Sample-2 was HEK293T cells co-transfected with TCG recoding system plasmid  pCMV-Nes-chPylRSIPYE (TetRS)-12*(U6-CM15CGA) and EGFP-151TCG reporter plasmid pEGFP-mCherry-T2A-EGFP-151TCG. Sample-3 was HEK293T cells transfected with blank palsmid vector. After 5h transfection, the medium was replaced with fresh medium containing 0.2 mM TetBu. After transfection(24h), cells were washed, trypsinized and centrifuged to collect the cell pellets, and then subjected to RNA-Seq.

value: Cells were transfetced with TCG recoding system and EGFP-151TCG reporter, and then added 0.2 mM TetBu to keep culturing 24h.


title: WTcontrol-4


title: Vec

value: Cells were transfetced with plasmid of TCG recoding system and added 0.2 mM TetBu to keep culturing 24h.


title: WTcontrol-3


title: WTInjured-1


title: RTS

value: Cells were transfetced with blank plasmid vector and added 0.2 mM TetBu to keep culturing 24h.


title: WTcontrol-2


title: HGC-27 cells, OE_3

city: Nanjing

first: Yunru

last: Gu

address: Guangzhou Road 300

institute: The First Affiliated hospital of Nanjing Medical University

data_processing:
HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: hg38
Supplementary files format and content: an excel file include fpkm and count values of each sample

source_name: cell line

growth_protocol: HGC-27 gastric cancer cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen), and RNA concentration and quality were assessed by NanoDrop (Thermo Fisher). The RNA integrity was determined by Bioanalyzer 2100 (Agilent, CA, USA) and confirmed by electrophoresis with denaturing agarose gel. Total RNA >1 ug was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The Vector and CBX4-overexpressing plasmids were designed and synthesized from GENECHEM (Shanghai, China). The transfection were conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) according to the manufactuer's protocols.

value: cell line

value: Gastric cancer cells

value: CBX4 overexpression


title: HGC-27 cells, OE_2


title: HGC-27 cells, OE_1


title: WTcontrol-1


title: NRVMs, Ad-Klf2, PE-3

city: ShenZhen

first: Juan

last: Huang

address: Langshan Road

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences

description:
Library name: Ad-Klf2-PE-3
Klf2_oe_rawcount.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore.
Trimmed sequence reads were mapped to mratbn7.2 using STAR.
Read count extraction was performed using featureCounts
Assembly: mratbn7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigwig, narrowPeak

organism: Rattus norvegicus

source_name: NRVMs

growth_protocol: NRVMs were maintained in DMEM medium containing 1% Insulin-Transferrin-Selenium (ITSS-10201, OriCell, China) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (R1050, ZYMO RESEARCH, USA). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations.

treatment_protocol: The cardiac hypertrophy model was established by treating with 100 µM PE (HY-B0769, MedChemExpress, USA) for 36 hours in NRVMs.To investigate whether KLF2  deficiency aggravates cardiac hypertrophy, NRVMs were infected with siNeg or siKlf2 for 12 hours and subsequently treated with or without PE for 36 hours; To explore whetherKLF2 overexpression attenuates cardiac hypertrophy, NRVMs were treated with or without PE for 12 hours and subsequently infected with Ad-GFP or Ad-Klf2 for another 24 hours.

value: NRVMs

value: neonatal rat ventricular myocytes

value: KLF2 overexpression

value: 100 µM PE treatment

tag: batch

value: 36 hours


title: HGC-27 cells, CTRL_1


title: HGC-27 cells, CTRL_3


title: NRVMs, Ad-Klf2, PE-2

description:
Library name: Ad-Klf2-PE-2
Klf2_oe_rawcount.txt


title: HGC-27 cells, CTRL_2


title: NRVMs, Ad-Klf2, PE-1

description:
Library name: Ad-Klf2-PE-1
Klf2_oe_rawcount.txt


title: OA15-A

city: hefei

first: youguang

last: pu

state: 安徽

address: NO 96，Jinzhai Road

institute: University of Science and Technology of Chin

data_processing:
ATAC-seq data preprocessing was performed as previously described. Raw ATAC-seq reads were trimmed and filtered for quality using Trim Galore! v.0.4.5 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) powered by CutAdapt v.1.16 (https://doi-org.proxy.library.cornell. edu/10.14806/ej.17.1.200) and FastQC v.0.11.7 (http://www.bioinformatics.babra- ham.ac.uk/projects/fastqc/). Paired end reads were aligned to the hg19 genome using Bowtie2 v.2.3.4.1 in very sensitive local mode (-q –local –very-sensitive-local –no-discordant –no-mixed –dovetail -I 10 X 20), and paired reads that mappedreSeArCH. Letterto different chromosomes or that mapped too far away were discarded. Unpaired reads, discordant reads, reads with mapQ <20, or SAM flags 0x4 and 0x400, as well as reads marked as optical or PCR duplicates using picard MarkDuplicates v.2.18.3-SNAPSHOT and reads overlapping the ENCODE hg19 functional genomics regions blacklist (at mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed to improve the quality of the retained fragments. To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to centre the reads on the transposase-binding event. Overall mapping statistics confirmed high-quality ATAC-seq data, with a high alignment rate (over 76.8% in all samples) and high coverage (over 30 million aligned read pairs per sample) across experiments (Supplementary Table 13). As an additional quality control metric, we confirmed that all ATAC-seq libraries dis- played the expected insert size distribution computed from aligned read pairs, with nucleosome-free, mono-nucleosomal, and di-nucleosomal modes (see Extended Data Fig. 8a for representative plots)
We then pooled the shifted reads by sample and identified peaks using MACS2 with a threshold of FDR-corrected P < 0.01 using the Benjamini–Hochberg procedure for multiple- hypothesis correction. As called peaks may be caused by noise in the assay and not reflect true chromatin accessibility, we calculated an irreproducible discovery rate (IDR) for all pairs of replicates across a cell type. Given two ranked lists of events from replicate experiments, in this case peak calls ranked by P value, IDR estimates a threshold at which events are no longer reproducible. Using this measure, we excluded peaks that were not reproducible (IDR <0.005) in at least one pair of replicates for at least one cell type or time point. Reproducible peaks from each cell type were combined to create a genome-wide atlas of accessible chromatin regions. Reproducible peaks from different samples were merged if they overlapped by more than 75%. This produced an atlas of ~182,800 reproducible peaks of median width 586 bp. The numbers of reproducible peaks per time point and organoid line are provided in Supplementary Table 14. Track diagrams at specific loci visually confirm that replicate ATAC-seq experiments show reproducible accessible sites
The RefSeq transcript annotations of the hg19 human genome were used to define the genomic location of transcription units. For genes with multiple gene models, the longest transcription unit was used for the gene locus definition. ATAC-seq peaks located in the body of the transcription unit, together with the 2-kb regions upstream of the transcription start site and downstream of the 3′ end, were assigned to the gene. If a peak was found in the overlap of the transcription units of two genes, one of the genes was chosen arbitrarily. Intergenic peaks were assigned to the gene with a transcription start site or 3′ end that was closest to the peak. In this way, each peak was unambiguously assigned to one gene. Peaks were annotated as promoter peaks if they were within 2 kb of a transcription start site. Non-promoter peaks were annotated as intergenic, intronic or exonic according to the relevant RefSeq transcript annotation. The atlas-wide distribution of promoter, intergenic or exonic peak assignment was consistent with high-quality ATAC-seq datasets (Extended Data Fig. 9), with 31.6% of peaks at promoters and the rest nearly equally divided between intergenic and intronic regions, with a small fraction annotated as exonic
Assembly: hg19
Supplementary files format and content: peak files

source_name: breast cancer

extract_protocol: Freshly sorted cells carrying breast cancer samples were treated with trypsin to obtain 50,000 cells (counted by using trypan blue exclusion) for ATAC-seq. After a wash step in cold cell wash buffer (CWB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2), outer membranes were disrupted in lysis buffer (CWB + 0.1% NP40) on ice for 2 minutes. The lysis reaction was stopped with the addition of 1 ml CWB. After a centrifugation step at 1,500g for 10 minutes, pelleted nuclei were used for the next step. In a 50-μl final volume, tagmentation was performed for 30 minutes at 37℃ using the Nextera DNA library prep kit (Illumina FC-121-1030). After adding SDS to a final concentration of 0.2%, DNA was purified on AMPure XP beads (Beckman Coulter A63881) using a 2:1 ratio (v/v) of beads:tagmented DNA. Freshly eluted DNA was barcoded and amplified in 110-μl PCR volume (NEB Next Q5 Hot Start HiFi PCR, M0543L) to generate a library with the following PCR program: 65℃, 5 minutes; 98℃, 30 seconds; 11 cycles of (98℃, 10 seconds ramping to 65℃, 30 seconds), 4℃ hold. Quality control of the libraries was performed with a Bioanalyzer 2200 (Agilent Technologies, D1000 screentapes and reagents, 5067-5582) to assess size range of amplified DNA fragments and with Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher P11496) to quantify the DNA fragments generated. ATAC libraries were then pooled at equimolar concentration and were sequenced multiplexed on the Illumina HiSeq with 50-bp paired-ends.

value: breast cancer

value: female

tag: subtype classification

tag: tumor grade

value: IDC


title: NRVMs, Ad-GFP, PE-3

description:
Library name: Ad-GFP-PE-3
Klf2_oe_rawcount.txt

value: Control


title: OA13-P

source_name: paracancerous tissue

value: paracancerous tissue


title: NRVMs, Ad-GFP, PE-2

description:
Library name: Ad-GFP-PE-2
Klf2_oe_rawcount.txt


title: NRVMs, Ad-GFP, PE-1

description:
Library name: Ad-GFP-PE-1
Klf2_oe_rawcount.txt


title: NRVMs, Ad-Klf2-2

description:
Library name: Ad-Klf2-2
Klf2_oe_rawcount.txt

value: 0 hour


title: NRVMs, Ad-Klf2-3

description:
Library name: Ad-Klf2-3
Klf2_oe_rawcount.txt


title: OA10-A


title: NRVMs, Ad-Klf2-1

description:
Library name: Ad-Klf2-1
Klf2_oe_rawcount.txt


title: OA9-P


title: OA13-A


title: OA10-P


title: NRVMs, Ad-GFP-2

description:
Library name: Ad-GFP-2
Klf2_oe_rawcount.txt


title: OA9-A


title: NRVMs, Ad-GFP-3

description:
Library name: Ad-GFP-3
Klf2_oe_rawcount.txt


title: OA7-A


title: NRVMs, Ad-GFP-1

description:
Library name: Ad-GFP-1
Klf2_oe_rawcount.txt


title: OA6-P


title: NRVMs, siKlf2, PE-2

description:
Library name: siKlf2-PE-2
Klf2_kd_rawcount.txt

value: Klf2 Knockdown


title: OA15-P


title: OA5-P


title: NRVMs, siNegative control, PE-1

description:
Library name: siNeg-PE-1
Klf2_kd_rawcount.txt

value: Negative control


title: NRVMs, siKlf2, PE-1

description:
Library name: siKlf2-PE-1
Klf2_kd_rawcount.txt


title: OA5-A

value: DCIS


title: OA6-A


title: OA4-A

value: ILC


title: OA3-P


title: NRVMs, siNegative control-2

description:
Library name: siNeg-2
Klf2_kd_rawcount.txt


title: OA3-A


title: PSTT_Control_001

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >17.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarry 8x60K Ver. 3.0 (G4858A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded.  After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: PSTT_001, control tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy (QIAGEN) according to the manufacturer's instructions.

tag: tissue/cell type

value: 6-week gestational whole villus tissues


title: OA1-P


title: 1411H

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
Demultiplexing was done with bcl2fastq v2.20.0.422. Analysis was performed using ‘nf-core/smrnaseq v2.2.0‘, against the human reference genome GRCh38. The statistical QC was performed using the FastQC tool. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), generating the mean quality scores of all sequences, sequence duplication levels and the count of unique / duplicate reads. Counts per million were calculated by the TMM normalization method in the edgeR package.
Assembly: GRCh38
Supplementary files format and content: Excel data, showing expression intensities of each analyzed microRNA. Values are averaged from 2x paired-end sequening runs performed for each sample.

source_name: non-seminoma germ cell tumor cell line, intermediate embryonal carcinoma / yolk-sac tumor

growth_protocol: Cell lines were grown in DMEM (1X) GlutaMAX-I, + Pyruvat, + 4,5g/l D-Glucose (1411H, 2102EP, NTD1) or RPMI (GCT72, NCCIT) plus supplementation of 10 % FBS, 1 % P/S (10,000 U), 1 % L-Glutamin (200 mM).

extract_protocol:
Total RNA was isolated by the TRIzol reagent according to the manual (Qiagen, Hilden, Germany). RNA concentrations and purities were measured by the Nanodrop 2000 photo-spectrometer (260 / 280 nm; 260 / 230 nm) and RIN numbers were detemrined by Fragment Analyzer measurememt.
200 ng of total RNA were used for library preparation and microRNA sequencing (microRNAseq). Library preparation (NEXTFLEX Small RNA-Seq Kit v4‘ (Revvity, Hamburg, Germany)) and microRNAseq (NovaSeq6000 SP 2 x 50 bp) has been carried out at the ‘Competence Centre for Genomic Analysis’ (Kiel, Germany).


title: Female F30000x, BioRep 5

city: Montreal

first: Zixuan

last: Li

state: Quebec

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

data_processing:
Novogene RNA-seq Data Analysis
Quality control analysis processed first through in-house perl scripts
HiSat2 v2.0.5 was used to build the reference genome and align the paired-end reads
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene
Assembly: rn_6
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Adrenal gland

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

treatment_protocol: Adult Sprague Dawley rats were exposed to 3 doses of organopshosphate esters

value: Adrenal gland


title: Female F30000x, BioRep 4


title: NT2D1

source_name: non-seminoma germ cell tumor cell line, embryonal carcinoma


title: Female F30000x, BioRep 3


title: Female F30000x, BioRep 2


title: NCCIT

description: NCCIT

value: non-seminoma germ cell tumor cell line, embryonal carcinoma


title: Female F30000x, BioRep 1


title: 2102EP

description: microRNA sequencing of 2102EP


title: PSTT_Tumor_002

source_name: PSTT_002, tumor

value: placental site trophoblastic tumor (PSTT)


title: Female F1000x, BioRep 5


title: NRVMs, siNegative control, PE-2

description:
Library name: siNeg-PE-2
Klf2_kd_rawcount.txt

value: NRVMs

tag: cell type

value: neonatal rat ventricular myocytes


title: NRVMs, siKlf2-2

description:
Library name: siKlf2-2
Klf2_kd_rawcount.txt

tag: treatment

value: 100 µM PE treatment


title: Female F1000x, BioRep 4


title: NRVMs, siKlf2-1

description:
Library name: siKlf2-1
Klf2_kd_rawcount.txt


title: Female F1000x, BioRep 3


title: Female F1000x, BioRep 1


title: OA4-P


title: 293T cells, dox, 12h, rep1

value: cell line

value: HEK 293T cells

value: dox


title: 293T cells, dox, 12h, rep2


title: Female F1000x, BioRep 2


title: OA1-A

value: breast cancer

value: female

value: IDC


title: 293T cells, mock, 12h, rep1

value: mock


title: Female F30x, BioRep 5


title: Case15（MHD WITH HEART FAILURE）

city: Nanchong Sichuan

first: Wenwu

last: Tang

state: Sichuan province

address: Shunqing District Zhongcheng Street Fujiang Road No.234 North Sichuan Hospital Shunqing Campus

institute: North sichuan medical college

data_processing:
After the inferior-quality reads were deleted, the cleanreads were aligned into the human genomic reference (GRCh38_gencode_v33) by HISATI.
Assembly: GRCh38_gencode_v33
Supplementary files format and content: htseqcount_result.txt

source_name: blood

growth_protocol: no

extract_protocol:
Peripheral blood mononuclear cell (PBMC) samples of 15 dialysis patients without heart failure (Normal) and 15 dialysis patients with heart failure (Case) human were collected for mRNA transcriptome sequencing. RNA was isolated and purified from the total samples using TRlzol (invitrogen, CA,USA) according to the manufacturer's protocol. NanoDrop ND-1000 (Wilminton, DE, USA) was used to control the total RNA sender bulk and cleanliness.
The fragmented RNA was synthesized into cDNA by reverse transcriptase, and the cDNA was amplified and purified. Building the library and prepared for sequencing on the illumina Novaseq 6000 sequencing platform.

treatment_protocol: no

value: blood

tag: condition

value: Case

value: no


title: Case14（MHD WITH HEART FAILURE）

value: Peripheral blood mononuclear cell (PBMC)


title: Female F30x, BioRep 3

value: Adrenal gland


title: Female F30x, BioRep 2


title: Case13（MHD WITH HEART FAILURE）


title: Case12（MHD WITH HEART FAILURE）


title: GCT72

description: microRNA sequencing of GCT72

source_name: non-seminoma germ cell tumor cell line, yolk-sac tumor


title: Case10（MHD WITH HEART FAILURE）


title: Female Control, Biorep 5

value: Control


title: Female Control, Biorep 4


title: H3 2

city: 青岛

first: 佳岷

last: 李

address: 山东省青岛市崂山区松岭路238号中国海洋大学

institute: 中国海洋大学

data_processing:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion)　following the manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis．
The libraries   were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were   sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X   Ten) and 125bp/150bp paired-end reads were generated.
Assembly: NCBI_ASM14940v2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Thalassiosira pseudonana

extract_protocol:
RNA was harvested using mirVana miRNA ISOlation Kit. 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols

tag: cell line

value: Thalassiosira pseudonana cells

value: WT

value: 30PSU culture


title: Female Control, Biorep 3

tag: tissue


title: 293T cells, mock, 12h, rep2

tag: genotype


title: Case9（MHD WITH HEART FAILURE）


title: H3 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Female Control, Biorep 2


title: Female Control, Biorep 1


title: Case8（MHD WITH HEART FAILURE）


title: Male M30000x, BioRep 5


title: M3 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学

value: 9PSU culture


title: Male M30000x, BioRep 4


title: Case7（MHD WITH HEART FAILURE）


title: Female F30x, BioRep 4


title: M3 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Male M30000x, BioRep 3


title: L3 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学

value: 3PSU culture


title: Case11（MHD WITH HEART FAILURE）


title: Female F30x, BioRep 1


title: Male M30000x, BioRep 2


title: Male M1000x, BioRep 3


title: Case5（MHD WITH HEART FAILURE）


title: Male M1000x, BioRep 2


title: Male M1000x, BioRep 5


title: Male M1000x, BioRep 4


title: Case4（MHD WITH HEART FAILURE）


title: L3 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Male M1000x, BioRep 1


title: Case3（MHD WITH HEART FAILURE）


title: H2 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Case6（MHD WITH HEART FAILURE）


title: Male M30x, BioRep 5


title: Male M30x, BioRep 4


title: H2 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Case2（MHD WITH HEART FAILURE）


title: Male M30x, BioRep 3


title: Male M30x, BioRep 2


title: M2 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Male M30x, BioRep 1


title: M2 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Case1（MHD WITH HEART FAILURE）


title: Male Control, Biorep 5


title: Normal15（MHD WITHOUT HEART FAILURE）

value: Normal


title: Male M30000x, BioRep 1


title: Male Control, Biorep 4


title: L2 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Male Control, Biorep 3


title: Normal14（MHD WITHOUT HEART FAILURE）


title: L2 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Normal13（MHD WITHOUT HEART FAILURE）


title: Male Control, Biorep 1


title: WTCHG_809568_73235299, Kidney, NoOp

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

institute: UCB

data_processing:
Reads were trimmed of adapter sequence using bbduk
Reads were quantified using Salmon with rn6
Quantifications were summarised to the Length Scaled TPM metric via tximport
Modelling was perfomed using Limma with voom transformed counts
Assembly: rn6
Supplementary files format and content: Gunzip Compressed tsv. Voom transformed normalised counts
Supplementary files format and content: Gunzip Compressed tsv. Raw Counts

source_name: Kidney

growth_protocol: Samples are from Kidney

extract_protocol:
RNA was depleted of ribosomal RNA using NEBNext rRNA Depletion Kit.
Strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB).
Paired End Illumina RNA Sequencing

treatment_protocol: Healthy or SNx Kidney

value: Kidney

value: NoOp


title: H1 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Normal12（MHD WITHOUT HEART FAILURE）


title: WTCHG_809568_73225298, Kidney, SNx

value: SNx


title: H1 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: Normal11（MHD WITHOUT HEART FAILURE）


title: WTCHG_809568_73175293, Kidney, NoOp


title: WTCHG_809568_73165292, Kidney, SNx


title: M1 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: WTCHG_809568_73155291, Kidney, SNx


title: Normal10（MHD WITHOUT HEART FAILURE）


title: 72875263, Kidney, SNx


title: Normal9（MHD WITHOUT HEART FAILURE）


title: L1 2

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: 72845260, Kidney, SNx


title: 72805256, Kidney, SNx


title: Normal8（MHD WITHOUT HEART FAILURE）


title: L1 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学


title: 72765252, Kidney, SNx


title: Male Control, Biorep 2


title: Normal7（MHD WITHOUT HEART FAILURE）


title: 72745250, Kidney, SNx


title: 72145286, Kidney, NoOp


title: whole juvenile shrimp 0.67 g/L rep5 [W_C4Rep5]

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

institute: University of Saskatchewan

description:
JoinedFiles_KallistoCounts.csv
0.67_vs_0.xlsx

data_processing:
Raw files were trimmed using Trimmomatic v0.38
Trimmed fastq files were pseudoaligned to a de novo assembled transcriptome (MysidAssembledTranscriptome.fasta.gz) using Kallisto
Only features with at least 5 counts per million in at least 3 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |log2FC| ≥ 1
Assembly: de novo reference transcriptome
Supplementary files format and content: fasta.gz - assembled reference transcriptome
Supplementary files format and content: tabular - raw counts of each sample
Supplementary files format and content: csv - raw counts of all samples joined together
Supplementary files format and content: xlsx - differential expression results using DESeq2

organism: Americamysis bahia

source_name: whole body tissue

growth_protocol: Juvenile mysids were exposed to one of two types of TWP leachates (created with 25 ppt filtered seawater) within an environmental chamber set to a 16-hr light: 8-hr dark photoperiod between 540-1080 lux, at 25 °C ± 1 °C. Every 12 hrs, the mysids were fed with < 24 hr old Artemia nauplii at a rate of 5-8 nauplii per mysid.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Juvenile mysids were exposed (waterborne) to "weathered" and "un-weathered" TWP leachates for 96 hours. Weathered leachates were at concentrations of 2.68, 1.34, and 0.67 g/L. Un-weathered TWP leachates were at concentrations of 1.08, 0.54, and 0.27 g/L.

tag: exposure compound

value: Weathered TWP leachate

tag: treatment/measured concentration

value: 0.67 g/L TWP leachate


title: WTCHG_809568_73215297, Kidney, NoOp


title: Normal6（MHD WITHOUT HEART FAILURE）

value: blood


title: whole juvenile shrimp 0.67 g/L rep4 [W_C4Rep4]

tag: age


title: 72115283, Kidney, NoOp


title: Normal5（MHD WITHOUT HEART FAILURE）


title: 72105282, Kidney, NoOp


title: Normal4（MHD WITHOUT HEART FAILURE）


title: 72075279, Kidney, SNx


title: whole juvenile shrimp 0.67 g/L rep3 [W_C4Rep3]


title: 72055277, Kidney, SNx


title: 72045276, Kidney, SNx


title: whole juvenile shrimp 0.67 g/L rep2 [W_C4Rep2]


title: 72825258, Kidney, SNx


title: Normal3（MHD WITHOUT HEART FAILURE）


title: whole juvenile shrimp 0.67 g/L rep1 [W_C4Rep1]


title: Normal2（MHD WITHOUT HEART FAILURE）


title: M1 1

address: 山东省青岛市崂山区松岭路238号中国海洋大学

tag: time


title: whole juvenile shrimp 1.34 g/L rep5 [W_C3Rep5]

description:
JoinedFiles_KallistoCounts.csv
1.34_vs_0.xlsx

value: 1.34 g/L TWP leachate


title: CRBM_H59

city: Coralville

first: Hui

last: Wang

state: IA

address: 2501 Crosspark Rd

institute: University of Iowa

data_processing:
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC rn6 rat reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC Rattus Norvegicus (rn6) reference genome
Assembly: Rn6
Supplementary files format and content: CSV file includes raw counts for each sample

source_name: cerebellum

growth_protocol: Sixty male juvenile Sprague-Dawley rats (n=15 for each exposure group, 21 days of age, 52±8 g) were ordered in 4 cohorts 3 weeks apart from Envigo (Indianapolis, IN, USA).  Rats were housed in polypropylene, fiber-covered cages in an AAALAC-accredited animal facility at 20-26 °C and 55% relative humidity with a 12 h light:dark cycle. Food (sterile Teklad 5% stock diet, Harlan, Madison, Wisconsin, USA) and water via an automated watering system were available ad libitum. After 7 days of acclimation, rats in each cohort were randomly assigned to four groups (sham, low (1%), medium (5%), or high (10%); 3 or 4 rats in each exposure group) using a random number generator (https://www.random.org/) and grafted with implants (1.3 ± 0.1 mg/g body weight) containing 0, 1, 5 or 10% of 4-OH-PCB52 on the back of the subcutaneous cavity on PND 28.

extract_protocol:
Tissue punches collected from brain regions of interest were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples.
mRNA enrichment: poly (A) capture or rRNA removal

treatment_protocol: Animals were exposed to sham (0%), low (1%), medium (5%), or high (10%) 4-OH-PCB52 containing implants subcutaneously for 28 days

value: cerebellum

tag: Sex

value: Male

tag: strain

value: Sprague-Dawley

value: high


title: Normal1（MHD WITHOUT HEART FAILURE）

value: Peripheral blood mononuclear cell (PBMC)

value: no


title: CRBM_H58


title: whole juvenile shrimp 1.34 g/L rep4 [W_C3Rep4]


title: CRBM_M57

value: medium


title: 72015273, Kidney, SNx


title: 72135285, Kidney, NoOp


title: 72125284, Kidney, NoOp


title: 71945266, Kidney, SNx


title: VCaP16, input, BRD4, p300

city: Boston

first: Steven

middle: P

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

data_processing:
CHromatin enrIchment ProceSsor (CHIPS) an analysis pipelinewas used to analyze ChIP-seq reads. Fastq files were aligned to hg19 reference genome using bwa mem aligner (0.7.15-r1140) with default parameters
MACS2 (2.2.7.1) or HOMER (v3.12 ) was used to call peaks
MACS2 (2.2.7.1) and bedGraphToBigWig (v 4) were used to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigwig files contain aweraged genome-wide signal data betweeen replicates, bed files contain intersected genomic regions between replicates, narrowPeak.bed files contain genomic regions for each sample,

source_name: Prostate

growth_protocol: VCaP cells were cultured in DMEM (10% FBS), enzalutamide-resistant VCaP (VCaP16) cells were cultured in DMEM (10% FBS) with 16uM enzalutamide. LNCaP95 cells were cultured in RPMI (10% FBS).

extract_protocol:
Cells were crosslinked with fresh 1% methanol-free formaldehyde (FA) for 10 minutes. This step was carried out for immunoprecipitation (IP) of histone modification marks (H3K27Ac, H3K4me1), ARfl, FOXA1, BRD4, and p300. Double fixation: For IP of ARv7, cells were first crosslinked in 2 mM fresh disuccinimidyl glutarate for 35 minutes, followed by 1% FA for an additional 10 minutes. The samples were sonicated using the Covaris E220 in sarkosyl lysis buffer.
ChIP-seq libraries for ARv7, ARfl and H3K27Ac ChIP DNA were generated using the ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer’s instructions and standard 8 bp Illumina primers. Libraries were pooled and sequenced on the Illumina NextSeq 500 platform at the Molecular Biology Core Facility (DFCI). ChIP-seq libraries for H3K4me1, FOXA1 were prepared using Accel-NGS 2S Plus DNA Libraries Kit with Unique Dual Indexing (Swift Biosciences, cat# 29096/290384) according to the manufacturer’s instructions. ChIP-seq libraries for H3K27Ac, BRD4 and p300 were generated using SimpleChIP ChIP-seq Multiplex Oligos for Illumina with Dual Index Primers (Cell Signaling Technology, cat# 47538) according to the manufacturer’s instructions. Libraries were pooled and sequenced using a NovaSeq 6000 Sequencing System.

treatment_protocol: VCaP, VCaP16 or LNCaP95 cells were grown to 70-80% confluence.

value: Prostate

value: ENZ-resistant VCaP

value: prostate cancer

value: WT

value: Input gDNA


title: whole juvenile shrimp 1.34 g/L rep3 [W_C3Rep3]


title: CRBM_M54


title: CRBM_L53

value: low


title: CRBM_L51


title: VCaP16, input, H3K27Ac


title: CRBM_S48

value: sham


title: whole juvenile shrimp 1.34 g/L rep2 [W_C3Rep2]

value: Weathered TWP leachate


title: VCaP16 DMSO, p300, IP rep 3

value: p300 (Cell Signaling, 57625S)


title: CRBM_H44


title: CRBM_M41


title: VCaP16 DMSO, p300, IP rep 2


title: 72035275, Kidney, SNx

value: Kidney

value: SNx


title: whole juvenile shrimp 1.34 g/L rep1 [W_C3Rep1]

value: 1.34 g/L TWP leachate


title: CRBM_H43

value: cerebellum

value: Male

value: Sprague-Dawley


title: whole juvenile shrimp 2.68 g/L rep5 [W_C2Rep5]

description:
JoinedFiles_KallistoCounts.csv
2.68_vs_0.xlsx

value: 2.68 g/L TWP leachate


title: CRBM_L37


title: VCaP16 DMSO, p300, IP rep 1


title: whole juvenile shrimp 2.68 g/L rep4 [W_C2Rep4]


title: CRBM_M40

value: medium


title: VCaP16 ARCC-32, p300, IP rep 3

value: Prostate


title: CRBM_L35


title: CRBM_S34


title: CRBM_S32


title: VCaP16 ARCC-32, p300, IP rep 2

value: ENZ-resistant VCaP


title: CRBM_S18


title: CRBM_S17


title: whole juvenile shrimp 2.68 g/L rep2 [W_C2Rep2]


title: VCaP16 ARCC-32, p300, IP rep 1

value: prostate cancer


title: whole juvenile shrimp 2.68 g/L rep3 [W_C2Rep3]


title: CRBM_H28

value: high


title: whole juvenile shrimp  2.68 g/L rep1 [W_C2Rep1]


title: CRBM_H27


title: CRBM_M26


title: whole juvenile shrimp 0.27 g/L rep5 [UW_C4Rep5]

description:
JoinedFiles_KallistoCounts.csv
0.27_vs_0.xlsx

value: Un-weathered TWP leachate

value: 0.27 g/L TWP leachate


title: VCaP16 DMSO, BRD4, IP rep 2

value: WT

value: BRD4 (Diagenode, C15410337)


title: CRBM_M24


title: CRBM_L22

value: low


title: VCaP16 DMSO, BRD4, IP rep 1


title: whole juvenile shrimp 0.27 g/L rep3 [UW_C4Rep3]


title: CRBM_H14


title: whole juvenile shrimp 0.27 g/L rep4 [UW_C4Rep4]


title: CRBM_H13


title: whole juvenile shrimp 0.27 g/L rep1 [UW_C4Rep1]


title: VCaP16 ARCC-32, BRD4, IP rep 2


title: VCaP16 ARCC-32, BRD4, IP rep 3


title: CRBM_L7


title: CRBM_M8


title: CRBM_M10


title: VCaP16 ARCC-32, BRD4, IP rep 1


title: CRBM_L6


title: whole juvenile shrimp 0.54 g/L rep5 [UW_C3Rep5]

description:
JoinedFiles_KallistoCounts.csv
0.54_vs_0.xlsx

value: 0.54 g/L TWP leachate


title: whole juvenile shrimp 0.27 g/L rep2 [UW_C4Rep2]


title: VCaP16 DMSO, H3K27Ac, IP rep 3

value: H3K27Ac (Diagenode, C15410196)


title: STN_H59

source_name: striatum

value: striatum


title: CRBM_S3

value: cerebellum

value: sham


title: CRBM_S1

value: Male

value: Sprague-Dawley


title: whole juvenile shrimp 0.54 g/L rep4 [UW_C3Rep4]


title: VCaP16 DMSO, BRD4, IP rep 3


title: STN_H58


title: STN_M57

value: medium


title: CRBM_L20


title: STN_L53


title: STN_M54


title: whole juvenile shrimp 0.54 g/L rep2 [UW_C3Rep2]


title: STN_S49


title: VCaP16 ARCC-32, H3K27Ac, IP rep 3

value: Prostate


title: STN_L51


title: NRVMs, siNegative control-1

description:
Library name: siNeg-1
Klf2_kd_rawcount.txt

value: NRVMs

value: neonatal rat ventricular myocytes

value: Negative control

value: 100 µM PE treatment

value: 0 hour


title: whole juvenile shrimp 0.54 g/L rep1 [UW_C3Rep1]

value: Un-weathered TWP leachate


title: whole juvenile shrimp 0.54 g/L rep3 [UW_C3Rep3]


title: STN_H44

value: high


title: STN_S48


title: whole juvenile shrimp 1.08 g/L rep5 [UW_C2Rep5]

description:
JoinedFiles_KallistoCounts.csv
1.08_vs_0.xlsx

value: 1.08 g/L TWP leachate


title: VCaP16 DMSO, H3K27Ac, IP rep 1

value: ENZ-resistant VCaP

value: prostate cancer

value: WT


title: VCaP16 ARCC-32, H3K27Ac, IP rep 2

value: H3K27Ac (Diagenode, C15410196)


title: VCaP16 ARCC-32, H3K27Ac, IP rep 1


title: STN_H43

value: striatum


title: STN_M40

value: Male


title: whole juvenile shrimp 1.08 g/L rep4 [UW_C2Rep4]


title: VCaP16 DMSO, H3K27Ac, IP rep 2


title: STN_S34

value: Sprague-Dawley

value: sham


title: STN_L37

value: low


title: STN_S18


title: LNCaP95 Dex, ARv7, IP rep2

value: Prostate


title: whole juvenile shrimp 1.08 g/L rep2 [UW_C2Rep2]


title: STN_S17


title: whole juvenile shrimp 1.08 g/L rep1 [UW_C2Rep1]


title: STN_H28


title: LNCaP95 DHT, ARv7, IP rep2


title: STN_H27


title: whole juvenile shrimp 0 g/L rep5 [ControlRep5]

value: 25 ppt seawater

value: 0 g/L TWP leachate


title: STN_M26

value: medium


title: LNCaP95 DHT, ARv7, IP rep1


title: whole juvenile shrimp 0 g/L rep4 [ControlRep4]


title: LNCaP95, Input

value: Input gDNA


title: STN_M41


title: STN_M24


title: LNCaP95 DMSO, ARv7, IP rep2


title: STN_L20


title: STN_L22


title: whole juvenile shrimp 1.08 g/L rep3 [UW_C2Rep3]

value: Un-weathered TWP leachate


title: STN_H13

value: high


title: STN_H14


title: VCaP16, H3K4me1, IP rep 2

value: H3K4me1 (Abcam, ab8895)


title: STN_S32


title: STN_M8


title: STN_M10


title: LNCaP95 DMSO, ARv7, IP rep1


title: whole juvenile shrimp 0 g/L rep1 [ControlRep1]


title: STN_L7


title: LNCaP95 Dex, ARv7, IP rep1


title: VCaP16, H3K4me1, IP rep 1

value: ENZ-resistant VCaP


title: STN_S3


title: Fibroblasts, UUO, rep3

city: Shanghai

first: Yulu

address: No.180 Fenglin Road,Xuhui District

institute: Zhongshan Hospital, Fudan University

description: Library name: U3

data_processing:
Raw sequecing data were processed using FastQC v0.11.7 to generate FASTQ files.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.36, dicarding reads left with <36 nt.
Trimmed sequence reads were mapped to GrCM38/mm10 using BSMAP v 2.7.3.
Methylation levels at individual sites were calculated using BSMAP v 2.7.3
DMRs (differentially methylated regions) analysis using metilene v0.2-8 software.
Assembly: mm10
Supplementary files format and content: bedGraph, average beta values for each sample

source_name: kidney

extract_protocol:
Genomic DNA was extracted from FACS-sorted fibroblasts using TIANamp Micro DNA Kit (TIANGEN) .
Genomic DNA was subjected to RRBS library preparation using the Acegen Rapid Library Prep Kit(Acegen) and then bisulfite-treated using EZ DNA Methylation Gold Kit (Zymo Research). After bisulfite treatment, DNA  was amplified with 12 cycles of PCR. Post amplification libraries were size selected at 100-350bp in length using a dual-SPRI® protocol.

value: kidney

value: renal fibroblasts

value: UUO


title: VCaP, H3K4me1, IP rep 2

value: VCaP

value: prostate cancer

value: WT


title: myd88-/-_3, 5 dpf

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

country: Netherlands

institute: Leiden University

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HM7YFDSXY_104255-001-046R_GATTGGAG-CGAGAGAA_L002

data_processing:
RNAseq reads of tirap mutant and myd88 mutant and their corresponding wild type controls were aligned and mapped to the zebrafish genome GRCz11 using Salmon v1.2.1
Differential gene expression was analyzed by using DESeq2 v1.24.0. Statistical significance was determined by a padj value of ≤ 0.05 by utilizing apeglm.
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: excel files include RPKM, Total counts,  TPM, and CPM values for each sample
Supplementary files format and content: excel files include fold change values and padj values of tirap mutant and myd88 mutant compared with their corresponding wild type controls

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from all groups  groups (n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: myd88 mutant

value: whole embryos

value: 5 days post fertilization


title: Fibroblasts, UUO, rep2

description: Library name: U2


title: myd88-/-_2, 5 dpf

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HY2YTDSXY_104255-001-024R_CGTCTTGT-TTGCGAGA_L003


title: VCaP, H3K4me1, IP rep 1

value: Prostate


title: myd88-/-_1, 5 dpf

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HM7YFDSXY_104255-001-022R_TGATACGC-CAACGAGT_L002


title: whole juvenile shrimp 0 g/L rep3 [ControlRep3]

value: 25 ppt seawater

value: 0 g/L TWP leachate


title: myd88+/+_1, 5 dpf

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HM7YFDSXY_104255-001-019_TGGAAGCA-GTACTCTC_L002

value: wild type


title: tirap-/-_3, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HM7YFDSXY_104255-001-048_CCACAACA-TGTGGTAC_L002

value: tirap mutant


title: Fibroblasts, UUO, rep1

description: Library name: U1


title: myd88+/+_2, 5 dpf

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HY2YTDSXY_104255-001-020_CAATAGCC-TGCGTAGA_L003


title: Fibroblasts, Sham, rep3

description: Library name: S3

value: Sham


title: myd88+/+_3, 5 dpf

description:
150 nucleotides
Myd88_vs_WT_padjvalue
Myd88_Expression_Browser
HM7YFDSXY_104255-001-021_CTCGAACA-GGAATTGC_L002


title: whole juvenile shrimp 0 g/L rep2 [ControlRep2]


title: VCaP16

data_processing:
The analysis of WES data followed the established Genome Analysis Toolkit (GATK 4.1.9.0) Best Practices Workflows. The raw reads were aligned to the hg38 reference genome using the Burrows-Wheeler Aligner (BWA) version 0.7.8. The identification of candidate somatic variants was carried out using the Mutect2 function from GATK version 4.1.9.0. Identified somatic variants were annotated using Funcotator, which is a part of GATK 4.1.9.0. ANNOVAR (ANNOtate VARiation) tool was utilized for the interpretation and prioritization of the filtered somatic variants. To assess copy ratio alterations, we employed a suite of functions from GATK 4.1.9.0, including PreprocessIntervals, CollectReadCounts, DenoiseReadCounts, and PlotDenoisedCopyRatios, which also allowed for visualization of the data.
Assembly: hg38
Supplementary files format and content: Comma separated values file
Library strategy: WES

growth_protocol: VCaP cells were cultured in DMEM (10% FBS), enzalutamide-resistant VCaP (VCaP16) cells were cultured  in DMEM (10% FBS) with 16uM enzalutamide.

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen)
DNA library preparation (Agilent v6)

value: enzalutamide-resistant VCaP

value: 16uM ENZ


title: VCaP, DMSO

value: DMSO


title: VCaP16, ARD_3, ChIP paied

description:
Cuff_Gene_Counts_VCaP16_ARD_DMSO_ChIPpaired.csv
VCaP16_ARD_vs_DMSO_ChIPpaired.deseq.csv

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
cufflinks v2.2.1 was used to generate FPKM values
Assembly: hg19
Supplementary files format and content: comma-separated values file includes FPKM vaues for each sample
Supplementary files format and content: comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values)

growth_protocol: VCaP cells (ATCC, Manassas, VA) were maintained in DMEM with 10% fetal bovine serum (FBS), VCaP16 cells (enzalutamide-resistant VCaP) were maintained in DMEM with 10% fetal bovine serum (FBS) with 16uM enzalutamide.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Transcriptome library construction (with Novogene)

treatment_protocol: VCaP cells in DMSO (VCaP_DMSO), VCaP treated with 10uM enzalutamide for 96 hrs (VCaP-E), enzalutamide-resistant VCaP16 cells in 16uM enzalutamide (VCaP16). VCaP16 in DMSO and treated with AR degrader (ARD) - 500nM ARCC-32 for 36 or 24hrs. VCaP16 cells treated with AR variant 7 siRNA (siV7), with AR Exon1 siRNA (siEx1), with AR Exon7 siRNA (siEx7), with FOXA1 siRNA (siFOXA1), with NFIB and NFIX siRNA (siNFIBX) and with non-targeted control siRNA (siNTC_AR, siNTC_FOXA1, siNTC_NFIBX).

value: ENZ-resistant VCaP

value: 16uM enzalutamide + 500nM ARCC-32 24hrs


title: Fibroblasts, Sham, rep1

description: Library name: S1

value: kidney

value: renal fibroblasts


title: VCaP16, ARD_2, ChIP paied

value: prostate cancer

value: WT


title: tirap-/-_2, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HM7YFDSXY_104255-001-030_GATCTTGC-TGCTCATG_L002

value: whole embryos


title: tirap+/+_2, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HYJ7LDSXY_104255-001-026_TTACGTGC-CAAGGTCT_L001

value: 5 days post fertilization


title: tirap+/+_3, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HM7YFDSXY_104255-001-027_AGCTAAGC-GTAACGAC_L002


title: Fibroblasts, Sham, rep2

description: Library name: S2


title: tirap-/-_1, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HM7YFDSXY_104255-001-029_CAACTCCA-ACGGATTC_L002


title: VCaP16, ARD_1, ChIP paied

value: Prostate


title: STN_S1

value: striatum

value: Male

value: Sprague-Dawley

value: sham


title: NK cells treated with VPA

city: Changchun

first: Xiumin

last: Shi

state: Jilin

address: No.1 Xinmin Street

department: Department of Hematology

institute: The First Hospital of Jilin University

description: Library name: S2

data_processing:
Seqtk was used to filter data
RNA-Seq reads were aligned to the UCSC hg19 genome using TopHat software.
Gene counts were normalized to the values of fragments per kilobase of exon model per million mapped reads (FPKM)
Cuffdiff was used to calculate the differentially expressed RNAs when the fold-change was > 2 and p < 0.05 with an unpaired two-sided t test.
Assembly: hg19
Supplementary files format and content: lncRNA FPKMs

source_name: nk cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll gradient density centrifugation and cultured in AlyS505 NK-EX containing 10% autologous serum plus 600 IU/mL interleukin-2.

extract_protocol:
Total RNA was extracted from human cultured NK cells treated (2mM for 24h) and untreated with VPA. The indexed libraries were prepared using Illumina TruSeq RNA Library Preparation Kit v2. Paired-end sequencing in triplicate was performed by Shanghai Biotechnology Corporation.
The indexed libraries were prepared using Illumina TruSeq RNA Library Preparation Kit v2.

treatment_protocol: Activated NK cells were treated (2mM for 24h) and untreated with VPA.

value: nk cell


title: tirap+/+_1, 5 dpf

description:
150 nucleotides
Tirap_vs_WT_padjvalue
Tirap_Expression_Browser
HY2YTDSXY_104255-001-025R_CGTATCTC-GTACCTTG_L004

value: wild type


title: Anopheles-Olfactory, 12am, Read 1, rep 3

city: PUNE

first: Tanwee

last: Das De

state: MAHARASHTRA

address: Dr. Homi Bhaba Road, Pashan

department: Department of Biology

institute: Indian Institute of Science Education and Research

data_processing:
The raw reads were demultiplexed and converted to FASTQ format using bcl2fastq software
Sequence reads were trimmed for adaptor sequence and low quality sequence using FastQC tool using default parameter
After quality checking and adaptor trimming the sample specific reads were aligned to the reference genome of An. culicifacies (VectorBase-54-AculicifaciesA-37-Genome) and Ae. aegypti (VectorBase-54-AaegyptiLVP-AGWG-Genome) respectively by using STAR-alignment tool
The transcriptome data of An. culicifacies showed 70-80% alignment rate whereas, Ae. aegypti data showed ~90% alignment
Read counts are calculated by htseq count tool
Assembly: AaegL5.0 &   AculA1.7
Supplementary files format and content: Tab delimited text file includes raw counts of Aedes samples
Supplementary files format and content: Tab delimited text file includes raw counts of Anopheles samples

organism: Anopheles culicifacies

source_name: Olfactory

growth_protocol: Both Aedes and Anopheles mosquitoes were maintained at 80% relative humidity and 27 ± 2°C temperature under 12hr/12hr LD cycle

extract_protocol:
Total RNA was extracted from the clean olfactory and brain tissues by standard trizol method
cDNA library were prepared using NEBNext® UltraII RNA library preparation kit (Cat No. E7775S) by following the manufacturer protocol.
For multiplexing of the samples NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (Cat No. E6440S) were used.

treatment_protocol: To understand the molecular rhythm of the olfactory and the brain system, complete olfactory tissue including antennae, maxillary palp, proboscis and labium, and the brain were dissected from 5-6-day old adult females’ mosquitoes (same cohort) at four different zeitgeber times 6am, 12pm, 6pm and 12am.

value: Olfactory

value: Circadian Cycle


title: NK cells without VPA

description: Library name: S0


title: VCaP16, DMSO_3, ChIP paied

value: ENZ-resistant VCaP

value: 16uM enzalutamide + DMSO


title: Anopheles-Olfactory, 6pm, Read 1, rep 3


title: Control vector  total RNA rep 3

city: Chicago

first: Marcelo

middle: G.

last: Bonini

state: IL

address: 303 E. Superior St. Suite 7-123

department: Feinberg School of Medicine

institute: Northwestern University

description: Library name: HW-11

data_processing:
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).  Trimmed reads were aligned to the Human genome (hg38) using STAR (Dobin et al, 2013).  Read counts for each gene were calculated using htseq-count (Anders et al, 2015) in conjunction with a gene annotation file for hg38 obtained from Ensembl
Assembly: hg38
Supplementary files format and content: htseq count files

extract_protocol:
Total RNA was harvested using Trizol kit (Ambion).  250 ng of total RNA was used for the construction of sequencing libraries. Polysomal RNA was harvested using AllPrep RNA/Protein kit (Qiagen). 1000 ng polysomal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA-Seq Library Prep kit.

treatment_protocol: Briefly, the cells need to be treated with 10 ug/ml cyclohexamide for 20 mins before collection, then cells were treated with hypotonic lysis buffer containing cyclohexamide.  Polysomal fractionation was performed using 10-50% sucrose gradients and polysomal fractions were pooled and RNA was extracted. Total RNA was extracted, in parallel, from the same cells that did not go through a polysome isolation process.

value: myeloid lineage cells


title: Control vector polysomal RNA rep 2

description: Library name: HW-6


title: Control vector  total RNA rep 2

description: Library name: HW-10


title: VCaP16, DMSO_2, ChIP paied


title: Anopheles-Olfactory, 6am, Read 1, rep 3


title: VCaP16, DMSO_1, ChIP paied


title: Anopheles-Olfactory, 12am, Read 1, rep 2


title: Triad1 shRNA + Gcn1 shRNA total RNA rep 2

description: Library name: HW-16

value: Triad1 and GCN1 double knockdown


title: Control vector polysomal RNA rep 1

description: Library name: HW-2


title: Triad1 shRNA + Gcn1 shRNA total RNA rep 3

description: Library name: HW-17


title: VCaP16, siNTC_NFIBX_1

description:
Cuff_Gene_Counts_VCaP16siNFIBX_siNTC.csv
VC16siNFIBXvsCTR.deseq.csv

value: prostate cancer

value: 16uM enzalutamide + non-targeted siRNA


title: Triad1 shRNA + Gcn1 shRNA total RNA rep 1

description: Library name: HW-15


title: Control vector  total RNA rep 1

description: Library name: HW-9

value: WT


title: VCaP16, siNTC_NFIBX_2


title: Anopheles-Olfactory, 6pm, Read 1, rep 2


title: Triad1 shRNA total RNA rep 2

description: Library name: HW-13

value: Triad1 knockdown


title: Anopheles-Olfactory, 12pm, Read 1, rep 2


title: VCaP16, siNFIBX_2

value: Prostate

value: 16uM enzalutamide + NFIB and NFIX siRNA


title: Triad1 shRNA total RNA rep 1

description: Library name: HW-12


title: Anopheles-Olfactory, 6am, Read 1, rep 2


title: Triad1 shRNA total RNA rep 3

description: Library name: HW-14


title: VCaP16, siNFIBX_1


title: Triad1 shRNA polysomal RNA rep 2

description: Library name: HW-8


title: Triad1 shRNA polysomal RNA rep 1

description: Library name: HW-4


title: Anopheles-Olfactory, 12pm, Read 1, rep 3


title: Anopheles-Olfactory, 12am, Read 1, rep 1


title: 100n dTag Cut&Run rep2

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The cleaned reads were aligned to mouse mm10 genome via bowtie2.
The bam files were sorted by samtools. Duplicates were marked and removed by Picard, and then, MACS2 was used to call significant peaks with parameters “-f BAMPE --keep-dup all -g mm -q 0.05 --broad --max-gap 200”.
For IGV visualization of the signals, the read coverage was normalized by reads per kilobase per million (RPKM) via bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

source_name: 2i+LIF ESC

extract_protocol:
Cells were treated homemade pAG-MNase and antibody, then digested DNA was enriched.
NEBNext Ultra II DNA Library Prep Kit for llumina was used for library contrucation following manufacture’s protocol.

value: 2i+LIF ESC

value: mESC

value: Brg1 dTag knock in

value: 24h, 100n mol/L  dTag


title: 100n dTag Cut&Run rep1


title: Anopheles-Olfactory, 6pm, Read 1, rep 1


title: Triad1 shRNA polysomal RNA rep 4

description: Library name: HW-20


title: 10n dTag Cut&Run rep2

value: 24h, 10n mol/L  dTag


title: Anopheles-Olfactory, 12pm, Read 1, rep 1

value: Olfactory


title: VCaP16, siFOXA1_2

description:
Cuff_Gene_Counts_VCaP16siFOXA1_siNTC.csv
VCaP16siFOXA1_vs_siNTC.deseq.csv

value: 16uM enzalutamide + FOXA1 siRNA