title: BMDMs form Sept2C111A mice treated with TNF-α, sample3

city: Nanjing

first: Hao

last: Zhang

address: Longmian Street

institute: Nanjing Medical University

description: BMDMs treated with TNF-α

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: BMDMs

extract_protocol:
Transfer aortic samples to corresponding grinding tube. Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min. Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube.Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. For BMDMs, add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells). Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃). Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: BMDMs

value: TNF-alpha


title: KO_6_dLN

status: Public on Nov 03 2024

type: SRA

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

country: USA

institute: Brigham and Women's Hospital

library_source: genomic

data_processing:
The BCL files were demultiplexed using bcl2fastq (v2.20.0.422)
ENCODE ATAC-seq pipeline (v1.5.4) was used for read alignment, filtering, peak calling, and quality control. Briefly, reads trimmed by cutadapt were aligned to the mm10 genome with Bowtie2, then filtered for duplicates using Picard MarkDuplicates.
After removing the mitochondrial reads, peaks were called using MACS2 with p-value threshold 0.01, smoothing window size 73, and IDR threshold 0.05.
The top 100,000 most significant peaks from each replicate were merged into a set of union peaks using bedtools merge (v2.26.0).
Read counts per peak were computed using featureCounts function in the R package Rsubread (v2.6.4). Peaks wider than 250 bp were selected for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigwig files of processed ATAC-seq read

molecule: genomic DNA

organism: Mus musculus

source_name: 2D2 Th17cells

growth_protocol: EX VIVO SAMPLES HARVESTED FROM DRAINING CERVIVAL LYMPH NODES

extract_protocol:
Provide samples in well labeled individual eppendorf tubes of, ideally, ~5000-6000 cells each (frozen in BamBanker solution). Wash/lyse/purify during transposition using Buenrostro ATAC protocol.
Modified protocol adapted for low yield bulk ATAC from Buenrostro J, et al. (current protocols in molecular biology, 2015)
Samples received, lysed and transposed using adapted bulk ATAC protocol. Cleaned using Qiagen MinElute spin columns. QC for amplification using KAPA quant. Libraries barcoded for sequencing using Nextera i5 and i7 primers. Pooled at 4nM and sequenced in house using Illumina Next-seq 75cycle high throughput kit. R1- 38cycles, R2- 38, i1- 8, i2- 0. All QCs done by qubit/KAPA/qPCR

tag: cell type

value: 2D2 Th17cells

tag: genotype

value: 2D2 dlck-Cre+Tcf7 fl/fl IL17aGFP+


title: BMDMs form Sept2C111A mice treated with TNF-α, sample4

country: China

description: BMDMs treated with TNF-α

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: KO_2_dLN RNA

data_processing:
Bulk RNA-seq data were preprocessed on Google Cloud via Terra.Bio. The BCL files were converted to FASTQ format using bcl2fastq (v2.20.0.422)
The fastq files were aligned to mouse genome mm10 using STAR version 2.7.5a.
Picard MarkDuplicates was used to identify the duplicate reads.
RNA-SeQC 2 was used for assessing sequencing depth and mapping quality.
Raw counts and TPMs were computed using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each sample

extract_protocol:
Samples provided in a 96 well plate preserved in 5-10 uL of lysis buffer (1000-5000 cells per well). RNA-SPRI used for RNA isolation and purification.
Modified protocol adapted for low yield non-nuclei samples from Picelli S, et al. (Nat Protocols, 2014)
Samples received, RNA extracted and libraries made following adapted bulk RNA-seq protocol. Libraries barcoded for sequencing using Nextera i5 and i7 primers. Pooled at 4nM and sequenced in house using Illumina Next-seq 75cycle high throughput kit. R1- 38cycles, R2- 38, i1- 8, i2- 8. All QCs done by qubit/bioA.


title: BMDMs form Sept2C111A mice treated with TNF-α, sample1

description: BMDMs treated with TNF-α


title: KO_1_dLN


title: KO_5_dLN


title: WT_7_dLN

value: 2D2 dlck-Cre- Tcf7fl/fl IL17aGFP+


title: KO_4_dLN


title: KO_3_dLN


title: blastocyst_dmso_2

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

country: United Kingdom

institute: Loke Centre for Trophoblast Research

description:
DMSO_SOP5502A169
blastocyst_counts.tsv
blastocyst_tpm.tsv

data_processing:
Technical replicate fastq files were merged and preprocessed using the nf-core/rnaseq pipeline 3.10.1 with Nextflow 22.10.1 (Ewels et al 2020). Briefly, reads were trimmed for adaptors and quality using Trimgalore 0.6.7 and cutadapt 3.4. Trimmed reads were pseudoaligned to GRCh38 with salmon 1.9.0 and used to generate estimated raw abundances and TPM normalized reads.
Resulting gene expression matrices were integrated and normalized to generate log-counts using Bioconductor tools (Amezquita 2019)
Assembly: GRCh38
Supplementary files format and content: blastocyst_counts.tsv raw estimated abundances from Salmon
Supplementary files format and content: blastocyst_tpm.tsv tpm normalized counts

organism: Homo sapiens

source_name: Blastocyst

growth_protocol: Human blastocysts were thawed using the Blast thaw kit (Origio; Cat# 10542010A) and cultured in GLOBAL culture medium (LifeGLOBAL; Cat# LGGG-20) with HAS protein supplement (LifeGLOBAL; Cat# LGPS-605) for 2h. Inhibitor or DMSO were applied in equilibrated GLOBAL culture medium with HAS protein supplementation for 20 – 24h.

extract_protocol:
Each blastocyst was briefly washed through PBS- (Gibco, 15140-122) and collected in 5 uL 10X Reaction buffer, containing 3.75 uL Lysis Buffer and 0.25 uL RNAse Inhibitor, provided in the the TAKARA SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Cat# v634890), and snap-frozen to -80˚C.
cDNA was generated using the TAKARA SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Cat# v634890). Retrosynthesis was performed using the provided Smart-seq V4 oligonucleotide primer and 3' Smart-seq CDS Primer II A. The samples were amplified over 18 or 21 PCR cycles and purified up with SPRI Beads (Beckman Coulter Cat#B23318). Preparation of the cDNA library was performed using Nextera_XT 15031942 (Illumina, Cat #FC-131-1096) and followed by paired-end 100 bp NovaSeq 600 sequencing.

treatment_protocol: Human blastocysts were treated with 100 uM A8301 or volume-matched DMSO in pre-equilibrated GLOBAL medium with HAS supplement, for 24h.

tag: tissue

value: Blastocyst

tag: batch

value: DMSO


title: BMDMs form Sept2C111A mice treated with TNF-α, sample2

description: BMDMs treated with TNF-α


title: WT_6_dLN


title: seq113-rat7A4-9m-hESgraft.rds

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

library_source: transcriptomic single cell

data_processing:
Basecalling using bcl2fastq 2.19
Cell Ranger pipeline (10x Genomics, Cellranger count v3) with default parameters  and a combined GrCh38/Rnor6 reference genome
Seurat (v 4.1.1 and R version 4.2.1) was applied to the scRNA-data for downstream analysis of matrix files.
Assembly: GrCH38/Rnor6

source_name: Nigral graft of dopamine progenitors in nude rat

growth_protocol: RC17 hESCs (Roslin Cells) were cultured at 37 °C and 5% CO2 and used for all transplantation experiments. Regional patterning of hESCs toward a ventral midbrain (VM) fate was performed via dual SMAD inhibition to induce neuralization, GSK3 inhibitor-mediated caudalization, and SHH-mediated ventralization. VM progentior cells were transplanted into the nigral brain region of of athymic nude rats. Lesion of the nigrostriatal pathway in rats was induced by unilateral injection of 6-hydroxydopamine into the right medial forebrain bundle (MFB).

extract_protocol:
Grafted VM patterned hESCs cells were dissected from rat nigra and transferred to a glass douncer containing 1 ml of nuclei lysis buffer (consisted of sucrose, CaCl2, MgAc, EDTA, Tril-HCl, DTT, Triton X-100, RNase inhibitor and RNase-free water) on ice. Tissue was completely minced and homogenized to nuclei suspension by sample grinding with Dounce homogenizers with 10 strokes with loose pestle and then 10 strokes with tight pestle. The nuclei suspension was filtered by loading through a 35-µm-diameter filter and followed by centrifuging for 10 min at 900g and 4 °C.
According to 10X protocols.

tag: culture condition

value: 9 months in vivo


title: WT_5_dLN


title: KO_2_dLN


title: blastocyst_dmso_1

description:
DMSO_SOP5502A1
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: BMDMs form wild-type mice treated with TNF-α, sample4

description: BMDMs treated with TNF-α


title: blastocyst_A8301_3

description:
A8301_SOP5502A173
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: WT_3_dLN


title: seq113-rat7A2-9m-hESgraft.rds

value: Nigral graft of dopamine progenitors in nude rat


title: WT_2_dLN


title: WT_1_dLN


title: MSC, IFN‐γ, 48 hours, rep3

city: Seoul

first: Seong-Who

last: Kim

address: 88, Olympic-ro 43-gil

country: South Korea

institute: University of Ulsan

data_processing:
RNA-seq was performed by Illumina HiSeq 2500 sequencer. Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastx_trimmer, then mapped to hg19 using Tophat.
Read count exraction and normalization were performed using EdgeR.
Assembly: hg19 (UCSC)
Supplementary files format and content: tab-delimited text files include normalized read count values for each sample.

source_name: Umbilical cord

growth_protocol: Cells were grown in α MEM (Gibco 11900024) supplemented with 10% FBS (Gibco 26140079) and 1% penicillin & streptomycin (Gibco 15140122).

extract_protocol:
Total RNA extraction were performed by TRIzol® (Invitrogen) as manufacturer's instruction.
Library was constructed using Clontech SMARTer Stranded RNA-Seq Kit as manufacturer's instruction by ebiogen (Seoul, Korea).

treatment_protocol: Cells were treated with 25 ng/ml of IFN‐γ for 7 hours or 48 hours.

value: Umbilical cord

value: mesenchymal stem cell

value: 25 ng/ml of IFN‐gamma

tag: time point

value: 48 hours


title: MSC, IFN‐γ, 48 hours, rep2


title: seq113-rat3C-9m-hESgraft.rds


title: seq113-rat4-9m-hESgraft.rds


title: BMDMs form wild-type mice treated with TNF-α, sample2

description: BMDMs treated with TNF-α


title: MSC, IFN‐γ, 7 hours, rep2

value: 7 hours


title: MSC, IFN‐γ, 7 hours, rep1


title: MSC, IFN‐γ, 48 hours, rep1


title: seq113-rat3B-9m-hESgraft.rds


title: MSC, untreated, rep3

value: Phosphate-buffered saline


title: seq113-rat3A-9m-hESgraft.rds


title: MSC, untreated, rep2


title: MSC, IFN‐γ, 7 hours, rep3


title: BMDMs form wild-type mice treated with TNF-α, sample3

description: BMDMs treated with TNF-α


title: seq103-rat8C-12m-hESgraft12months.rds

value: 12 months in vivo


title: BMDMs form wild-type mice treated with TNF-α, sample1

description: BMDMs treated with TNF-α


title: MSC, untreated, rep1


title: aortas from Apoe-/- mice that received  Apoe-/-Sept2C111A bone marrow, sample2

description: Mice infused with Ang II

source_name: aorta

value: aorta

value: Ang II infusion


title: seq113-rat7A1-9m-hESgraft.rds


title: Rad21het_rep1

city: Dunedin

first: Jisha

last: Antony

state: Otago

address: 58 Hanover Street

department: Pathology

country: New Zealand

institute: University of Otago

description: 10x genomics

data_processing:
Fastq files were aligned to the Danio Rerio GRCz11 genome (NCBI:GCA_000002035.4) using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98.
Assembly: Danio Rerio genome GRCz11
Supplementary files format and content: Tab seperated barcodes, features and matrix files

organism: Danio rerio

source_name: Whole kidney marrow

extract_protocol:
Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS-5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS-0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system.
Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 (10x Genomics).

value: Whole kidney marrow


title: aortas from Apoe-/- mice that received Apoe-/- bone marrow, sample3

description: Mice infused with Ang II


title: seq103-rat8B-12m-hESgraft12months.rds


title: WT_rep2

description: 10x genomics

value: wild type


title: WT_rep1

description: 10x genomics


title: Control Rep1

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
Raw sequencing data was subjected to quality control using FastQC.
After quality control, Cutadapt was employed to remove low-quality bases and adaptor contaminations. The quality of the resulting clean data was examined again using FastQC software.
Hisat2 was utilized to align the clean data to the mouse reference genome mm10, obtained from the Illumina iGenomes database. Following data mapping, SAM files and BAM files were manipulated using samtools.
The number of reads aligned to gene features was counted using HTSeq-count from the HTSeq package. Differentially expressed genes were identified by edgeR, using a cutoff of |log(fold change)| > 1 and a p-value < 0.01.
GSEA analysis was performed using GSEA software with standard gene sets from the MSigDB database.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

source_name: Tumor

growth_protocol: Cell line authentication and mycoplasma contamination testing were performed before all experiments. RIL-175 cells were maintained in Dulbecco's modified medium (DMEM) with 20% fetal bovine serum (FBS) with pyruvic acid and 1% penicillin/streptomycin.

extract_protocol:
Tumors were collected from mice treated with control IgG, anti-PD1 antibody alone, anti-CXCR4 antibody alone, and anti-PD1 antibody in combination with anti-CXCR4 antibody. Total RNA was extracted from the freshly isolated tumor tissues using Qiagen RNeasy Mini Kit (Cat. 74104).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from [200ng] of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7.

treatment_protocol: Treatments were administered intraperitoneally every three days for 21 days at 10 mg/kg (anti-PD1 antibody, anti-CXCR4 antibody, and immunoglobulin G [IgG] control) in survival studies. For the time-match study, all the mice with orthotopic grafted models were sacrificed on day 8.

value: Tumor

tag: cell line

value: RIL-175 (p53/Hras mutant)

value: hepatocellular carcinoma

value: p53/Hras mutant

value: Control


title: Rad21het_rep2

description: 10x genomics


title: C. elegans CDK-2gutminus RNA-seq 3

city: Stanford

first: Alexander

last: Lessenger

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description:
hermaphrodite
LowPloidyC

data_processing:
Alignment: the WS284 C. elegans and P. pacificus genomes were concatenated, then fragments were aligned using STAR aligner with default parameters. Only uniquely mapped reads were kept.
Counts: Aligned fragments were counted for each gene with featureCounts in R without multimappers
Assembly: WS284
Supplementary files format and content: tab-separated text (.tsv) file with raw counts for each gene

organism:
Caenorhabditis elegans
Pristionchus pacificus

source_name: anterior intestine

growth_protocol: Worms were age synchronized by egg laying and grown at 20ºC. C. elegans were dissected at 72 hrs post egg lay and P. pacificus at 96.

extract_protocol:
Dissected intestines of control or CDK-2gut(-) C. elegans intestines and P. pacificus intestines were flash frozen in liquid nitrogen then thawed directly into trizol. Lysates were pooled, and an equal amount of P. pacificus lysate was added to each control and CDK-2gut(-) C. elegans lysate as a biological spike-in. Total RNA was extracted using the Zymo Direct-zol microprep kit.
Libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB). Pooled libraries were sequenced with paired end sequencing on a Novoseq 6000 by Novogene.

value: anterior intestine

value: CDK-2gutminus:cdk-2::ZF::GFP, asp-1p::vhhGFP4::zif-1;  zif-1(gk117)

tag: developmental stage

value: adult


title: seq103-rat8A-12m-hESgraft12months.rds

value: Nigral graft of dopamine progenitors in nude rat


title: aortas from Apoe-/- mice that received Apoe-/- bone marrow, sample2

description: Mice infused with Ang II


title: aortas from Apoe-/- mice that received  Apoe-/-Sept2C111A bone marrow, sample1

description: Mice infused with Ang II


title: Heart, miR-187, rep 2

city: shanghai

first: tan

last: zizheng

address: songhu road

institute: Fudan university

data_processing:
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases. The clean reads obtained were then aligned to the mm10 mouse genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie. Differentially expressed genes (DEGs) were identified by Deseq2 (for sample with replications) with a cut-off value of log2 |fold change| >1 and p-adjust < 0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules based on gene ontology (GO) and KEGG pathway categories. Terms with pvalue<0.05 were considered significant. Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: mm10
Supplementary files format and content: Excel files includes FPKM for each Sample.
Supplementary files format and content: allgenes_sample_FPKM.xls

organism: Mus

source_name: Heart

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12310ES, China) following manufacturer’s recommendations. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

value: Heart


title: Heart, miR-187, rep 2

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <30 bp) and low quality reads using Fastp (v0.20.0), an ultra-fast all-in-one FASTQ preprocessor. Then FastQC is employed to ensure high reads quality and to process data quality control. The clean reads were mapped to the mm10 mouse genome using the Bowtie2 (v2.2.6) software and saved with format of bam by SAMtools (v1.10), bigwig and bedgraph by deepTools(v3.3.2) ,which also used for peaks count normalization and visualization. Peaks detection was performed using the MACS2 (v2.2.7.1) peaks finding algorithm with 0.01 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package . Differentially peaks were identified by DiffBind (for sample with replications) or MAnorm2 (for sample with no replication) with a cut-off value of log2|fold-change|>1 and p-value <0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant peaks, the potential peaks in identified modules based on gene ontology (GO) and KEGG pathway categories. HOMER(v4.11) was utilized to Motif prediction of peaks.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
Extract DNA using the ATAC seq library preparation kit (APExBIO) extraction kit
ATAC-seq libraries of cells were prepared as the manufacturer’s protocol (Cat. No. K1157, APExBIO). 50,000 cells of samples were lysed in 50 μL ice ATAC Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.5 μL 10% NP40, 0.5 μL 10% Tween 20, and 0.5 μL 2% Digitonin for 3 min. Lysates were spun at 1000 rpm for 10 min to obtain the pellet nuclei. The nuclei were then incubated with the transposase enzyme and tagmentation buffer at 37 °C for 30 min. The fragmented DNA was then purified using MinElute Reaction Cleanup Kit (Cat No. 28204, QIAGEN) in a final volume of 10 μL. ATAC-Seq Libraries were prepared following the Buenrostro protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/). The DNA libraries were amplified for 10 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 2×150 as the sequencing mode.


title: C. elegans CDK-2gutminus RNA-seq 2

description:
hermaphrodite
LowPloidyB


title: seq103-rat7C-12m-hESgraft12months.rds


title: C. elegans CDK-2gutminus RNA-seq 1

description:
hermaphrodite
LowPloidyA


title: Heart, miR-187, rep 1


title: seq069-rat6-12m-Seq069-3-hESgraft-12m-rat6.rds


title: Heart, WT, rep 1


title: Heart, WT, rep 2


title: seq103-rat7B-12m-hESgraft12months.rds


title: C. elegans Control RNA-seq 3

description:
hermaphrodite
ControlC

value: control:cdk-2::ZF::GFP; zif-1(gk117)


title: Heart, miR-187, rep 1


title: Sample_8

type: RNA

city: Philadelphia

first: Carson

last: Poltorack

state: PA

address: 421 Curie Blvd, Rm 445

institute: University of Pennsylvania Perelman School of Medicine

hyb_protocol: According to the provided barcode-transcript dictionary from 10x Genomics, barcode-complementary oligos were sequentially added to the slide and removed following imaging. All hybridization was performed onboard the Xenium analyzer.

scan_protocol: Barcode spatial localization was read out using sequential ISH and imaging.

data_processing: Cells were segmented by nuclear expansion and mRNA spots were identified and decoded onboard the Xenium instrument, yielding the expected output bundle.

label: Xenium human breast cell typing

source_name: Primary pancreatic ductal adenocarcinoma

label_protocol: Tissue was incubated with barcoded Xenium probes overnight. Probes were ligated and barcode regions amplified using Rolling Circle Amplification.

growth_protocol: Samples were prepared as indicated in the commercial 10x Genomics protocol and in Janesick et al (2023) PMID: 38114474. Post-surgical FFPE-embedded tumors were acquired from CHTN mid-atlantic division and stored at room temperature for between 1-10 years. 5 um sections were prepared under RNAse free conditions on Xenium slides.

extract_protocol: not provided


title: C. elegans Control RNA-seq 2

description:
hermaphrodite
ControlB


title: Heart, WT, rep 1


title: Sample_7

value: Primary pancreatic ductal adenocarcinoma


title: C. elegans Control RNA-seq 1

description:
hermaphrodite
ControlA


title: seq069-rat6-12m-Seq069-2-hESgraft-12m-rat6.rds

value: 12 months in vivo


title: seq103-rat7A-12m-hESgraft12months.rds


title: C. elegans, CDK-2gutminus, 4

description:
hermaphrodite
LP4_EL

data_processing:
Alignment: Fragments were aligned to the WBPS18 C. elegans genome using bowtie2 with default settings. Only properly matched, concordant reads were kept with `samtools view -b -f 0x2`
Defining the TSS: BigWig files were created from the 50 bp midpoints of each unique fragment using a custom python script. Metagene profiles surrounding the transcription start site (TSS) of genes identified as highly experessed in the intestine in our RNA-seq data set (Lessenger et al., 2024) were created using a custom R script using the genomation package in R. From these profiles, we defined the TSS peaks to be -200 to +100 bp surrounding the TSS.
Count and FPKM coverage: Using a custom python script, we counted the number of 50 bp midpoints that mapped to each TSS, gene body, and the fragments per kilobase million (FPKM) on gene bodies for each gene.
Control sample C3 was excluded from subsequent analysis in the manuscript due to the lack of a bimodal distrubition of FPKM values, indicating poor enrichment of Pol II covered fragments.
Assembly: WBPS18
Supplementary files format and content: Bigwig file for 50bp midpoints
Supplementary files format and content: tab-separated text (.tsv) files with counts (TSS and gene body) and FPKM (gene body) for each gene

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans expressing vit-5p::vhhGFP4 single copy transgene and endogenous AMA-1::GFP were age synchronized by L1 arrest, then grown at 15ºC on NGM-peptone plates with NA22 E. coli until adulthood

extract_protocol:
Adults were flash frozen in liquid nigtrogen, ground with mortor and pestle in liquid nitrogen, and thawed directly into 1.1% formaldehyde, cross-linked for 7 minutes at room temperature. Samples were lysed on a Fast Prep (3 cycles of 30 s at 5.5 M/s). Lysate was sonicated with a Branson 250 Sonifier. Chromatin was immunoprecipitated with the SV5-Pk1 antibody (BioRad).
Libraries were prepared from eluted DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Libraries were pooled and sequenced with paired end sequencing on a Novoseq 6000 by Novogene

treatment_protocol: Experimental Strain (CDK-2gut(-)): cdk-2::ZF, asp-1p::zif-1 I; zif-1(gk117) III. Control strain: cdk-2::ZF I; zif-1(gk117) III.

value: CDK-2gutminus:cdk-2::ZF, asp-1p::zif-1; vit-5p::vhhGFP4::3x-V5; zif-1(gk117)

tag: chip antibody

value: SV5-Pk1, Bio-Rad

value: whole organism


title: ExC_Foxi1MO-st10

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

country: Germany

institute: University Freiburg Medical Center

description:
Foxi1MO_noMT_(narrow_Peaks).bed
Foxi1MO_Bedgraph_Control.bedgraph
Foxi1MO_Bedgraph_Treatment.bedgraph
Foxi1MOnoMT.bigwig

data_processing:
Sequenced files were trimmed using Trim Galore v0.6.7 (automatic detection)
Reads were aligned to the Xenopus laevis 9.2 genome using BWA-MEM v0.7.17
Fragments within the mitochondrial genome were removed with Samtools v1.21
Peak calling was performed with the callpeak function of MACS2 v2.2.7.1
Differential peak detection was perfomed with the bdgdiff function of MACS2 v2.2.7.1
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: NarrowPeaks files and Bedgraph Treatment and Control files were generated in Macs2.
Supplementary files format and content: Bigwig files were generated in ucsc-wigtobigwig.

organism: Xenopus laevis

source_name: epidermis, animal cap explant, st10

growth_protocol: Animal caps were excised in 1X MBS at stage 9 and transferred to 0.5X MBS until collection at stage 10

extract_protocol:
Caps were transferred from MBS plates into a 1.5 mL low-bind microcentrifuge tube (Eppendorf, cat. No. 0030108051) containing 1 mL of ice-cold 1X PBS. Samples were spun at 500 g at 4 ºC in the centrifuge for five minutes before removing the PBS and repeating the wash step with fresh ice-cold 1X PBS. 50 µL of ice-cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (w/v) Igepal CA-630) and pipetted to break up samples. Samples were centrifuged at 500 g for 10 min at 4 ºC and pellets were resuspended in 25 µL TD Buffer, 2.5 µL TDE1 Enzyme and 22.5 µL Nuclease-Free water (Illumina, cat. No 20034198). Samples were pelleted to mix and incubated on a ThermoMixer at 37 ºC, 700 rpm for 30 min. Following incubation, the samples were cleaned with MinElute Reaction Cleanup Kit (Qiagen, cat. No. 28204), following manufacturer instructions and eluted into 11 µL Buffer EB.
Libraries were prepared with the ATAC-seq Kit (Active Motif, cat. No. 53150)

treatment_protocol: Embryos were either uninjected or injected bilaterally at stage 2 with 3 pmol Foxi1 MO in the animal pole

value: epidermis, animal cap explant, st10

value: wt

value: 3pmol Foxi1 MO


title: Sample_6


title: seq069-rat6-12m-Seq069-1-hESgraft-12m-rat6.rds


title: Sample_5


title: C. elegans, control, 4

description:
hermaphrodite
C4_EL


title: aortas from Apoe-/- mice that received Apoe-/- bone marrow, sample1

description: Mice infused with Ang II

value: aorta

value: Ang II infusion


title: seq069-rat5-12m-Seq069-1-hESgraft-12m-rat5.rds


title: Heart, WT, rep 2


title: seq069-rat11-12m-Seq069-1-hESgraft-12m-rat11-AF17.rds


title: aortas from Apoe-/- mice that received  Apoe-/-Sept2C111A bone marrow, sample3

description: Mice infused with Ang II


title: ExC_UC-st10

description:
UC_noMT_(narrow_Peaks).bed
UC_Bedgraph_Control.bedgraph
UC_Bedgraph_Treatment.bedgraph
UCnoMT.bigwig

value: Uninjected


title: Sample_3


title: seq069-rat10-12m-Seq069-2-hESgraft-12m-rat10.rds


title: Sample_2


title: C. elegans, CDK-2gutminus, 3

description:
hermaphrodite
LP3_EL


title: seq069-rat10-12m-Seq069-1-hESgraft-12m-rat10.rds


title: ExB_UC-st10


title: ExA_UC-st10


title: Sample_1


title: C. elegans, control, 1

description:
hermaphrodite
C1_EL


title: seq067-rat2-12m-Seq067-hES-GFP-12m-rat2AF018.rds


title: C. elegans, control, 2

description:
hermaphrodite
C2_EL


title: WC_unstimulated + WC_stimulated

status: Public on Nov 02 2024

city: Hong Kong

first: Weixin

last: Chen

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Barcodes for demultiplexing were provided. The demultiplexing, barcoded processing, gene counting and aggredation were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-flex-multi-frp).
Assembly: hg38
Supplementary files format and content: count matrix, barcodes and genes from Cell Rangerv7.2.0

molecule: nuclear RNA

source_name: PBMCs, well-controlled T2D patients, unstimulated cells + PBMCs, well-controlled T2D patients, cells stimulated by anti-CD3 and anti-CD28 antibodies for 48hours

extract_protocol:
Sorted alive PBMCs from different samples were fixed by 10X Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (1000414) according to the manufacturer's instructions.
Library was performed according to the manufacturer's instructions (10X Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples, CG000527)

tag: sample type

value: multiplexed

tag: sample

value: peripheral blood

tag: disease state

value: well-controlled T2D

value: PBMCs

value: unstimulated cells + cells stimulated by anti-CD3 and anti-CD28 antibodies for 48hours


title: PC_unstimulated + PC_stimulated

source_name: PBMCs, poor-controlled T2D patients, unstimulated cells + PBMCs, poor-controlled T2D patients, cells stimulated by anti-CD3 and anti-CD28 antibodies for 48hours

value: poor-controlled T2D


title: HC_unstimulated + HC_stimulated

source_name: PBMCs, healthy donor, unstimulated cells + PBMCs, healthy donor, cells stimulated by anti-CD3 and anti-CD28 antibodies for 48hours

value: healthy donor


title: ExB_Foxi1MO-st10


title: polII-E14-16h-Spt6KD-rep2

city: Wuhan

first: Shaobo

last: Liang

state: Hubei Sheng

address: BaYi Road, LUOJIA HILL

institute: Wuhan University

data_processing:
Reads trimmed by trim_galore were mapped to genome using bowtie2 (Cut&Tag and ChIP) or STAR (RNA-seq)
Redundant reads were deduplicated by picard
Peaks determintion was performed through Macs2 callpeak command. Deeptools bamCoverage converted BAM files into bigwig files
IDR was used to combine peaks of different replicates
FeatureCounts counted the read number on  gene level for each sample
Assembly: dm6, Ecoli
Supplementary files format and content: Cut&Tag and ChIP-seq bigwig file and narrowPeak file
Supplementary files format and content: gene read count for RNA-seq

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
cut&tag：Cells were immobilized on coA beads, antibodies were bound in antibody buffer  (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA),  and activate Tn5-PA transposase activity in tagmentation buffer  (10 mM MgCl2, 20 mM HEPES at pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin) , and cells were lysed to extract library fragments by add  1.5 μl 0.5 M EDTA, 0.5 μl 10% SDS and 1 μl 20 mg/mL proteinase K (sigma).
pol2 chip-seq：Cells were fixed with 1% paraformaldehyde for 10 min, and the chromosomes were fragmented using an ultrasonic crusher after lysis of the cells.
RNA-seq: RNA was extracted using trizol. 200 ng of total RNA was used to construct sequencing libraries.
cut&tag: 1×Agencourt AMPure XP beads (Beckman Coulter, A63881) were used to purify the tagementated DNA and eluted in 10 μl 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1× Q5 polymerase reaction buffer, incubated at 65 °C for 30 minutes and stopped by incubation at 80 °C for 20 minutes. The universal i5 primer, barcoded i7 primer and Phanta EVO Super-Fidelity DNA Polymerase (Vazyme, P503) were added to amplify the R-loop CUT&Tag library. The libraries were size-selected with 0.56-0.85* Sera-Mag carboxylate-modified magnetic beads and eluted in 20 ul RNase-free water.
pol2 chip-seq:  5ng DNA was used for dsDNA library construction according to manufacturer’s instructions (Rapid Plus DNA Lib Prep Kit for Illumina V2, ABclonal, RK20255).   The library was amplified for 13 cycles on the thermocycler.
RNA-seq: RNA libraries for Rna-Seq was prepared using MGIEasy RNA library Prep kit following manufacturer‘s protocols.

value: embryo

tag: time

value: Anti-RNA polymerase II  CTD repeat YSPTSPS (phospho S5) antibody(Abcam,#ab5408)


title: polII-E14-16h-Ctrl-rep2

value: Ctrl


title: Sample_4

value: Primary pancreatic ductal adenocarcinoma


title: ExA_Foxi1MO-st10

value: epidermis, animal cap explant, st10


title: polII-E14-16h-Ctrl-rep1


title: Rloop-E14-16h-Ctrl-rep2

data_processing:
Reads trimmed by trim_galore were mapped to genome using bowtie2 (Cut&Tag and ChIP) or STAR (RNA-seq)
Redundant reads were deduplicated by picard
Peaks determintion was performed through Macs2 callpeak command. Deeptools bamCoverage converted BAM files into bigwig files
IDR was used to combine peaks of different replicates
FeatureCounts counted the read number on  gene level for each sample
Assembly: dm6, Ecoli
Supplementary files format and content: Cut&Tag and ChIP-seq bigwig file and narrowPeak file
Supplementary files format and content: gene read count for RNA-seq
Library strategy: Cut&Tag


title: C. elegans, control, 3

description:
hermaphrodite
C3_EL

value: SV5-Pk1, Bio-Rad

value: adult

value: whole organism


title: polII-E14-16h-Spt6KD-rep1


title: Rloop-E14-16h-Spt6KD-rep1


title: Rloop-E14-16h-Ctrl-rep1


title: C. elegans, CDK-2gutminus, 1

description:
hermaphrodite
LP1_EL

value: CDK-2gutminus:cdk-2::ZF, asp-1p::zif-1; vit-5p::vhhGFP4::3x-V5; zif-1(gk117)


title: better prognosis  rep4

city: Beijing

first: Haizhen

last: Du

state: Beijing

address: No.52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital and Institute

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer after quality filtering. Firstly, Q30 was used to perform quality control. After 3’ adaptor-trimming and low quality reads trimming by cutadapt software (v1.9.2), based on these high quality reads, CloudSeq used different softwares to analyse mRNAs.The high quality reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl gtf gene annotation file with hisat2 software (v2.04). Then, cuffdiff software (part of cufflinks, v2.2.1) was used to get the  fragments per kilobase of exon per million fragments mapped (FPRM) as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentiallymRNA were identified. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Assembly: UCSC hg19
Supplementary files format and content: The fragments per kilobase of exon per million fragments mapped (FPRM) as the expression profiles of mRNA were included.

source_name: Human bile

extract_protocol:
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Human bile

tag: prognosis

value: better


title: Rloop-E14-16h-Spt6KD-rep2


title: Rloop-L3-stages-rep2

source_name: larva

value: larva


title: dismal prognosis rep4

value: dismal


title: Rloop-E20-22h-stages-rep2


title: better prognosis  rep2


title: Rloop-E20-22h-stages-rep1


title: Rloop-L3-stages-rep1


title: Rloop-E8-10h-stages-rep2


title: dismal prognosis rep1


title: better prognosis  rep1


title: Rloop-E8-10h-stages-rep1


title: Rloop-E2-4h-stages-rep2


title: iPSC OL, Sox6, CUT&RUN

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Low-quality reads and adapters were trimmed with Trimmomatic
The data were aligned to the mouse genome (mm10) using Bowtie2
Peak calling was performed using MACS2 and cluster plots and tracks were generated using deepTools
Assembly: mm10
Supplementary files format and content: BigWig and narrowPeaks (excluding igG input)
Library strategy: CUT&RUN

source_name: iPSC

extract_protocol:
Cells were fixed with in .1% formaldehyde, nuclei was extracted, antibody were bound, chromatin was pAG-mNase and CaCl2 digested
CUT&RUN libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Libraries were amplifed using 14 cycles.

value: iPSC

value: OL


title: iPSC OL, Input


title: Rloop-0DMF-E14-16h-rep2


title: Rloop-E2-4h-stages-rep1


title: iPSC OPC, Input

value: OPC


title: Rloop-0DMF-E14-16h-rep1


title: iPSC OPC, Sox6, CUT&RUN


title: BALC-7d-5

city: Anseong-si

first: Jun-Mo

address: 4726 Seodong-daero, Daedeok-myeon

institute: Chung-Ang University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Gene counting was performed using pig reference genomes and pig-virus combined reference genomes, respectively, according to the presence or absence of PRRSV infection.
After processing with the Cell Ranger, the information of three PRRSV strains was added to the features and matrix files (for aggregation).
Assembly: Ensembl Sscrofa11.1.106 (one pig reference genome) & Ensembl Sscrofa11.1.106 with each PRRSV strain (JB15-N-M8-GN; MZ287322.1, JA142; AY424271.1, JB15-N-PJ10-GN; MZ287321.1) (three pig-virus combined reference genomes)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: BALF cell

extract_protocol:
After euthanasia, the lungs were aseptically extracted with clamping the tracheal tube, and gross lesions were measured. The left mainstream bronchus was clamped, and tissue samples were collected from the clamped left lung lobes for RNA extraction and histopathological examinations. The right lung was lavaged with 15 mL of sterile PBS, containing 100 μg/mL ampicillin (USB Corporation Cleveland, OH, USA) and Anti-Anti, to retrieve the first lavage fluid. The second lavage was subsequently conducted with 75mL of PBS to collect the second lavage fluid. The collected lavage fluid was centrifuged at 1000 × g in room temperature for 10 min to separate the bronchoalveolar lavage fluid (BALF) and cells (BALF cells). The resulting supernatant or BALF from the first lavage were used for quantifying the protein levels of cytokine/chemokine. The cell pellet or BALF cells from both the first and second lavage were merged and used for flowcytometry, quantification of mRNA expression levels, and single cell RNA sequencing. The BALF cells were washed three times with PBS after red blood cell (RBC) lysis. The tissues and BALF as well as BALF cells were collected in tubes, snap-frozen using liquid nitrogen and stored immediately at -80°C for further analysis.
For scRNA-seq library construction, BALF cells were washed with cold Ca2+ and Mg2+ free 0.04 % BSA/PBS at 300 g for 5 min at 4°C. Samples were gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS, and then counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems, Anyang, Gyeonggi-do, Republic of Korea) using acridine orange and propidium iodide staining. ScRNA-seq libraries were constructed with the Chromium Single Cell 3’ v3.1 assay (10x Genomics, Pleasanton, CA, USA) using 36 BALF cells. According to the protocol, libraries were prepared using the 10x Chromium Controller and Next Gem Single cell 3’ Reagent v3.1 kits. Briefly, the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip to generate single-cell Gel Bead-in-emulsion (GEM). Poly-adenylated mRNA from single cells were uniquely barcoded and reverse-transcribed within GEM. After barcoded full-length cDNA was generated from mRNA through GEM-RT incubation, the barcoded cDNA molecules were amplified with PCR. For 3’ Gene Expression Library construction, the enriched cDNA was sequentially subjected to the enzymatic fragmentation, end-repair, A-tailing, adaptor ligation and index PCR. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Then, the libraries were sequenced using NovaSeq 6000 System (Illumina, Inc., San Diego, CA, USA), and 150 bp paired-end reads were generated. The sequencing depth of 3’ Gene Expression Library was about 20,000 read pairs per cell.

value: BALF cell

tag: disease

value: Negative

tag: days post_infection_(dpi)

tag: breed

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: BALC-7d-6

description: 10x Genomics

tag: cell type


title: better prognosis  rep3


title: 10% DMF-E10-14h-with-RNaseA

value: embryo

tag: treatment

value: 10%DMF+RNase A


title: IMR90, siCTCF, replicate 1

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

data_processing:
Paired-end RNA-seq reads were mapped to human reference genome build hg38 using STAR ver. 2.7.3a with default parameters, uniquely mapped gene counts quantified using HTSeq ver. 0.12.4, and normalizes using the RUVs module of the RUVseq package ver. 1.30.0.
Differentially expressed genes were defined via the DEseq2 ver. 1.36.0 package using its default Wald test and deemed as DEGs when they had a Padj <0.05 and absolute log2FC >0.6.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including the raw counts

growth_protocol: Proliferating primary lung fibroblasts (IMR90) isolates (I79 and I83, passage 5; Coriell) were grown in MEM (M4655, Sigma-Aldrich) supplemented with 1x non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
IMR90 were washed with 1x PBS and harvested directly in Trizol (Invitrogen, 15596018). RNA was isolated from this lysate by using the Direct-zol RNA MiniPrep Kit (Zymo Research, R2052:1074069) including an on-column DNase I treatment step according to the manufacturer’s instructions.
The library was constructed with the TruSeq kit (Illumina) before paired-end sequencing on a NovaSeq6000 platform (Illumina)

treatment_protocol: Senescence was induced after treating the cells for up to 6 days with 10μM inflachromene (ICM; Cayman Chemicals)

value: primary lung fibroblasts

tag: genotype

value: CTCF knockdown

value: ICM inducing senescence


title: 5% DMF-E10-14h-without-RNaseA

tag: tissue


title: IMR90, ICM, replicate 4

value: WT


title: dismal prognosis rep2


title: dismal prognosis rep3


title: 10% DMF-E10-14h-without-RNaseA


title: 5% DMF-E10-14h-with-RNaseA

value: 5%DMF+RNase A


title: IMR90, siCTCF, replicate 2


title: IMR90, ICM, replicate 3


title: BALC-7d-36

description: 10x Genomics

value: PRRSV infection (JB15-N-PJ10-GN strain)


title: BALC-7d-34

description: 10x Genomics


title: BALC-7d-35

description: 10x Genomics


title: siMettl4_oxLDL_1

first: Hong

last: Jiang

address: Longmian Road No.101

institute: Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: HMDM

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: HMDM


title: siMettl4_oxLDL_2


title: siMettl4_oxLDL_3


title: siNC_oxLDL_2

value: siNC


title: 2.5% DMF-E10-14h-with-RNaseA

value: 2.5%DMF+RNase A


title: BALC-7d-30

description: 10x Genomics

value: PRRSV infection (JB15-N-M8-GN strain)


title: 0% DMF-E10-14h-without-Rnase


title: CD4T_P18

city: Guangzhou

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

data_processing:
Data analysis was performed by R (v.4.2.1) software and limma (v.3.54.2) software packages.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes rwa counts for each sample

extract_protocol:
Total RNA was extracted using Trizol rent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).

tag: group

value: Resistant


title: CD4T_P17


title: BALC-7d-4

description: 10x Genomics


title: BALC-7d-29

description: 10x Genomics


title: 0% DMF-E10-14h-with-Rnase

value: 0%DMF+RNase A


title: CD4T_P16


title: CD4T_P15


title: CD4T_P14


title: CD4T_P12


title: CD4T_P13


title: BALC-7d-28

description: 10x Genomics

value: BALF cell


title: BALC-7d-18

description: 10x Genomics

value: PRRSV infection (JA142 strain)


title: S2-cell-without-RNaseA

source_name: S2 cells

value: S2 cells

value: germ cells


title: siNC_oxLDL_3

city: Nanjing


title: S2-cell-with-RNaseA

value: 10%DMF+RNase A


title: 2.5% DMF-E10-14h-without-RNaseA

value: embryo


title: BALC-7d-17

description: 10x Genomics

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: AGS_circ_hnRNPU

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of circ-hnRNPU

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: AGS stably transfected with circ-hnRNPU

growth_protocol: Human gastric cancer cell lines MKN-45 and AGS were grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The circ-hnRNPU expression or empty vector was transfected into cancer cells, and stable cell lines were screened by administration of puromycin.

value: gastric cancer

value: AGS

tag: passage


title: CD4T_P10


title: CD4T_P11


title: CD4T_P9

value: Sensitive


title: CD4T_P8


title: AGS_mock empty vector

description: Gene expression after stable transfection of empty vector

source_name: AGS stably transfected with empty vector

tag: cell line


title: BALC-7d-16

description: 10x Genomics


title: BALC-3d-33

description: 10x Genomics

value: PRRSV infection (JB15-N-PJ10-GN strain)


title: MKN45_circ_hnRNPU

source_name: MKN45 stably transfected with circ-hnRNPU


title: CD4T_P7


title: siNC_oxLDL_1

value: HMDM


title: CD4T_P6


title: MKN45_mock empty vector

source_name: MKN45 stably transfected with empty vector


title: BALC-3d-32

description: 10x Genomics


title: mouse liver input gw2

city: Wenzhou

first: yushu

last: Hou

state: Zhejiang

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Remove low quality reads and adapters. Software: fastp (0.20.1)
Map the reads of each sample to reference genome. Software: bowtie2 (2.4.2)
Peak calling. Software: Macs2 (2.2.7.1)
Peak annotation : Chipseeker
Motif: HOMER (4.11.1)
Assembly: GRCm38.p6
Supplementary files format and content: GW4064_IP-vs-GW4064_Input.peak.xls.

source_name: liver

extract_protocol:
The sample was fixed in 1% formaldehyde for Cross-Linking of DNA and Protein,after which 0.125M glycine was added and the mixture was sat to terminate the crosslinking reaction. Extract chromatin from samples by adding Lysis Buffer.Then, samples was sonicated to fragment chromatin DNA. The 10% lysis sonicated chromatin was stored and named “input”, and 90% was used in immunoprecipitation reactions with antibody and named “IP”.
The sequencing libraries of input and IP were generated by NEBNext® UltraTM DNA Library Prep Kit for Illumina.An A-base was added to the fragmented DNA ends and adapter was ligated.After purification with beads, products are amplified with PCR for 8-10 cycles. The library products corresponding to 100-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: liver


title: CD4T_P5


title: BALC-3d-31

description: 10x Genomics


title: Homozygous 5 Tumoroids Passage 5

city: Boston

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the Cellranger 6.1.2 (10x Genomics) to align the raw sequencing reads (fastq files) from TH-MYCN tumors to a modified mouse reference genome GRCm38. The modification was made to account for the MYCN-amplified mice. Specifically, the MYCN chromosome was appended to the genome reference file (fasta format). This step introduces an additional human MYCN gene to the reference, named “mycn__MYCN”.
Assembly: GRCm38 (modified)
Supplementary files format and content: count matrix in csv

source_name: Tumoroid culture

extract_protocol:
10X Genomics Single cell 3' gene expression V2 and V3
Single cells from TH-MYCN tumor and ex vivo cell culture  samples subjected to RBC ACK lysis were surface stained with anti-TER119-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/TER119-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

value: neuroblastoma

tag: sample id

value: Homozygous 5 Tumoroids Passage 5

value: Homozygous

tag: Sex

value: Female


title: mouse liver Chip gw1


title: CD4T_P4


title: BALC-3d-27

last: Kim

description: 10x Genomics

value: BALF cell

value: PRRSV infection (JB15-N-M8-GN strain)


title: CD4T_P3


title: BALC-3d-26

description: 10x Genomics


title: BALC-3d-3

description: 10x Genomics

value: Negative


title: CD4T_P2


title: Muscle GFP+, Sod1KO

city: Ann Arbor

first: Susan

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

data_processing:
Base calling, alignment, filtering, barcode counting, and UMI counting: CellRanger v7.1.0 (10X Genomics) was used to process raw data. The CellRanger count command was run with default parameters with the exception of the --expect-cells parameter which was set at 10000.
Data filtering and quality control process: Data filtering and quality control process: Barcodes, features, and count matrices were uploaded into Seurat (v4.30) using the ReadMtx() function. We filtered out cells with fewer than 200 UMIs and those with over 10% mitochondrial genes. Ambient RNA was removed using decontX with default settings. After consolidating Seurat objects from all samples into one, we normalized and scaled this merged object. Dimensional reduction was then executed using RunUMAP and FindNeighbors. Cells were annotated manually using upregulated markers distinctive to each cluster.
Assembly: mm10
Supplementary files format and content: Cell barcodes in tab-separated values format for each sample
Supplementary files format and content: Features ID  in tab-separated values format for each sample
Supplementary files format and content: Count matrix file in mtx format for each sample

source_name: skeletal muscle

extract_protocol:
For tissue collection, mice were anesthetized with 3% isoflurane, then euthanized by cervical dislocation, bilateral pneumothorax, and removal of the heart. Hind limb muscles (TA and GTN) of control and experimental mice were quickly harvested using sterile surgical tools and placed in separate plastic petri dishes containing cold phosphate-buffered saline (PBS). Using surgical scissors, muscle tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution (2.5 U/mL Dispase II and 0.2% [~1000 U/mL] Collagenase Type II, 1 mg/mL of hyaluronidase in Dulbecco’s modified Eagle medium [DMEM] per mouse). Samples were incubated on a rocker placed in a 37 ̊C incubator for 60 min with manual pipetting the solution up and down to break up tissue every 30 min using an FBS-coated 10 mL serological pipette. Once the digestion was completed, 20 mL of F12 media containing 20% heat inactivated FBS was added into each sample to inactivate enzyme activity. The solution was then filtered through a 70 mm cell strainer into a new 50 mL conical tube and centrifuged again at 300g for 5 min. Live cells were sorted from the suspension via addition of 1 μg of propidium iodide (PI) stain into each experimental sample and all samples were filtered through 70 mm cell strainers before the FACS. Cell sorting was done using a BD FACS Aria III Cell Sorter (BD Biosciences, San Jose, CA). GFP+ PI- and GFP- PI- cells were sorted into 0.02% BSA PBS solution for immediate processing.
RNA libraries for RNA Seq were prepared using GEM Single Cell 3' HT Reagent Kits v3 kits from 10X Genomics according to the manufacturer’s protocols.

value: skeletal muscle

value: S100GFPtg Sod1-/-

tag: age

value: 2 months


title: Homozygous 4 Tumoroids Passage 5

value: Homozygous 4 Tumoroids Passage 5


title: Muscle GFP-, Sod1KO


title: mouse liver input gw1


title: Homozygous 5 Tumoroids Passage 0

value: Homozygous 5 Tumoroids Passage 0


title: BALC-3d-25

description: 10x Genomics

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: mouse liver Chip gw2


title: Muscle GFP-, WT


title: BALC-3d-2

description: 10x Genomics


title: Homozygous 5

source_name: Tumor

value: Homozygous 5


title: Homozygous 4 Tumoroids Passage 0

value: Homozygous 4 Tumoroids Passage 0


title: Homozygous 4

value: Homozygous 4


title: CD4T_P1

value: Sensitive


title: Muscle GFP+, WT


title: naïve CD4+ T cells, poorly-controlled T2D patient_2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimed reads were mapped to UCSC human genome GRCh38/hg38 using STAR.
Gene counts were quantified by featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited csv files include raw count and TPM values for each donor.

source_name: peripheral blood

extract_protocol:
High-quality total RNA was extracted using RNeasy Mini Kit (Qiagen).
poly A enriched RNA-seq

value: peripheral blood

value: primary cells

value: Naive CD4+ T cells


title: BALC-3d-15

description: 10x Genomics

value: PRRSV infection (JA142 strain)


title: naïve CD4+ T cells, poorly-controlled T2D patient_1


title: BALC-3d-14

description: 10x Genomics

value: BALF cell


title: Homozygous 3

value: neuroblastoma

value: Homozygous 3

value: Homozygous

value: Female


title: Homozygous 2

value: Homozygous 2

value: Male


title: naïve CD4+ T cells, well-controlled T2D patient_3


title: BALC-3d-13

description: 10x Genomics


title: naïve CD4+ T cells, well-controlled T2D patient_2


title: Hemizygous 5

value: Hemizygous 5

value: Hemizygous


title: BALC-3d-1

description: 10x Genomics

value: Negative

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: Homozygous 1

value: Homozygous 1


title: Hemizygous 4

value: Hemizygous 4


title: 1694

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: primary pancreatic cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: primary pancreatic cancer


title: BALC-21d-23

description: 10x Genomics


title: 1963


title: naïve CD4+ T cells, healthy donor_1

value: peripheral blood

value: primary cells


title: 1972


title: Hemizygous 3

value: Hemizygous 3


title: BALC-21d-24

description: 10x Genomics

value: BALF cell

value: PRRSV infection (JA142 strain)


title: BEAS-2B cell line, Mn, 24 hr

city: Bhopal

first: Deepa

last: Gandhi

address: Saket Nagar

country: India

institute: AIIMS Bhopal

description: MicroRNA, treated_Mn_24hr

data_processing:
The obtained paired end reads were analysed using Oasis 2.0 (https://oasis.ims.bio/index.php) automated smallrna analysis pipeline with default optimal parameters. Following which, the feature counts v1.4.6 tool was sequentially implemented to derive the absolute mirna read counts per condition. The resultant read counts of Control_24hr vs. Mn_treated_24hr were directly compared. Based on differential read counts, the probable upregulated and downregulated mirna were determined (minimal cutoff of 10 read counts difference was implemented between Control_24hr vs. Mn_treated_24hr).
Assembly: hg38 human genome reference
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes differential counts for each miRNA

source_name: Lung; Bronchus

growth_protocol: BEAS-2B cells were maintained in a 1:1 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM) and HAM’S F-12 nutrient mixture (DMEM:F12) and supplemented with 10% FBS, and 1% antibiotic and antimycotic solution. They were cultured in a humidified chamber at 37°C with 5% CO2

extract_protocol: Total miRNA isolated by using miRNeasy kit.

treatment_protocol: BEAS-2B cells were treated with either vehicle or manganese for 24 h and collected for total miRNA isolation.

value: Lung; Bronchus

value: Lung epithelial cells

value: Wild type


title: Hemizygous 2

value: neuroblastoma

value: Hemizygous 2

value: Female


title: BALC-21d-12

description: 10x Genomics


title: BALC-21d-22

description: 10x Genomics


title: BEAS-2B cell line, ctrl, 24 hr

description: MicroRNA, Control_24hr


title: 1680


title: 1626


title: Hemizygous 1

value: Hemizygous 1

value: Hemizygous

value: Male


title: 1581


title: RNAseq-L1-Spt6KD-rep3

value: larva

tag: chip antibody


title: BALC-21d-11

description: 10x Genomics

value: Negative

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: 1542

value: primary pancreatic cancer


title: RNAseq-L1-Spt6KD-rep2


title: BALC-21d-10

description: 10x Genomics


title: RNA_hMEC1.3

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
Removed adaptor with cutadapt and kept only 10-40-mers
Mapped the reads on the organism's transcriptome - Bowtie (parameters: -v 2 -y -a -m 1 --best --strata -p 18)
Kept only the mapped reads - samtools (parameters: -F 4 -f 0,16 -h)
Assembly: hg38
Supplementary files format and content: txt files with the count of reads detected for each CDS

source_name: hMEC

growth_protocol: hMEC cell lines were cultured in DMEM F12 media (Gibco, 21331020) supplemented with 10% fetal bovine serum (Capricorn Scientific, FBS-12A), 1% penicillin-streptomycin, 1X GlutaMax, 0.01µg/mL hEGF, 0.5µg/mL hydrocortisone and 280mU/mL insulin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).  RNA depleted for rRNA was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

value: hMEC

value: WT


title: naïve CD4+ T cells, healthy donor_2

value: peripheral blood

value: primary cells

value: Naive CD4+ T cells


title: 1460


title: 1420


title: RNA_hMEC1.2


title: RNAseq-L1-Spt6KD-rep1

source_name: larva


title: RNAseq-L1-Ctrl-rep3

value: Ctrl


title: RNA_mZEB1.3


title: RNA_hMEC1.1


title: BALC-14d-8

description: 10x Genomics

value: BALF cell


title: BALC-14d-7

description: 10x Genomics


title: BALC-14d-9

description: 10x Genomics


title: RNA_mZEB1.2


title: 1388


title: RNAseq-L1-Ctrl-rep2


title: RNA_mZEB1.1


title: BALC-14d-21

description: 10x Genomics

value: PRRSV infection (JA142 strain)


title: BALC-14d-20

description: 10x Genomics


title: 1194


title: RNAseq-E14-16h-Spt6KD-rep3

source_name: embryo

value: embryo


title: 1216


title: RNAseq-E14-16h-Spt6KD-rep2


title: Ribo_hMEC1.3


title: 1093


title: Ribo_hMEC1.2


title: RNAseq-E14-16h-Spt6KD-rep1


title: 1051


title: 7A_2

city: Lianyungang

first: wenhao

last: cheng

state: Jiangsu

address: 59 Cangwu Road, Haizhou District

department: College of Pharmacy

institute: Jiangsu Ocean University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample

source_name: Colon Cancer

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without 7A for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Colon Cancer

value: Human Colon Cancer Cell


title: 944


title: 7A_1


title: 896


title: RNAseq-E14-16h-Ctrl-rep3

data_processing:
Reads trimmed by trim_galore were mapped to genome using bowtie2 (Cut&Tag and ChIP) or STAR (RNA-seq)
Redundant reads were deduplicated by picard
Peaks determintion was performed through Macs2 callpeak command. Deeptools bamCoverage converted BAM files into bigwig files
IDR was used to combine peaks of different replicates
FeatureCounts counted the read number on  gene level for each sample
Assembly: dm6, Ecoli
Supplementary files format and content: Cut&Tag and ChIP-seq bigwig file and narrowPeak file
Supplementary files format and content: gene read count for RNA-seq


title: Ribo_hMEC1.1


title: RNAseq-L1-Ctrl-rep1


title: RNAseq-E14-16h-Ctrl-rep2


title: Ribo_mZEB1.3


title: DMSO_1

description: DMSO

value: DMSO


title: 1149


title: DMSO_2

description: DMSO


title: Ribo_mZEB1.2


title: 829


title: Notch2 ChIP-seq rep1

status: Public on Nov 01 2024

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Notch2 ChIP-seq

data_processing:
fastq files were obtained from CCHMC DNA core.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with the following configurations: -S -m 1 --best
sam files were converted to bam files using samtools.
Reads were sorted and duplicates were removed using samtools.
MACS and HOMER were used as peak callers.
Genome_build: mm9
Supplementary_files_format_and_content: tdf files were generated using igvtools
Supplementary_files_format_and_content: peaks.bed files were generated using MACS and HOMER as peak callers

source_name: embryonic kidney

extract_protocol: Sequencing libraries were generated using NEBNext ChIP-seq library prep master mix set for Illumina.

value: mouse embryonic kidney

tag: Stage

value: Notch2 (Cell Signaling Technology)


title: Notch2 ChIP-seq rep2

description: Notch2 ChIP-seq


title: input

description: input

value: input DNA


title: 385


title: BALC-14d-19

description: 10x Genomics

source_name: BALF cell

value: Commercial breed (Landrace x Yorkshire x Duroc)


title: RNAseq-E14-16h-Ctrl-rep1

extract_protocol:
cut&tag：Cells were immobilized on coA beads, antibodies were bound in antibody buffer  (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA),  and activate Tn5-PA transposase activity in tagmentation buffer  (10 mM MgCl2, 20 mM HEPES at pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin) , and cells were lysed to extract library fragments by add  1.5 μl 0.5 M EDTA, 0.5 μl 10% SDS and 1 μl 20 mg/mL proteinase K (sigma).
pol2 chip-seq：Cells were fixed with 1% paraformaldehyde for 10 min, and the chromosomes were fragmented using an ultrasonic crusher after lysis of the cells.
RNA-seq: RNA was extracted using trizol. 200 ng of total RNA was used to construct sequencing libraries.
cut&tag: 1×Agencourt AMPure XP beads (Beckman Coulter, A63881) were used to purify the tagementated DNA and eluted in 10 μl 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1× Q5 polymerase reaction buffer, incubated at 65 °C for 30 minutes and stopped by incubation at 80 °C for 20 minutes. The universal i5 primer, barcoded i7 primer and Phanta EVO Super-Fidelity DNA Polymerase (Vazyme, P503) were added to amplify the R-loop CUT&Tag library. The libraries were size-selected with 0.56-0.85* Sera-Mag carboxylate-modified magnetic beads and eluted in 20 ul RNase-free water.
pol2 chip-seq:  5ng DNA was used for dsDNA library construction according to manufacturer’s instructions (Rapid Plus DNA Lib Prep Kit for Illumina V2, ABclonal, RK20255).   The library was amplified for 13 cycles on the thermocycler.
RNA-seq: RNA libraries for Rna-Seq was prepared using MGIEasy RNA library Prep kit following manufacturer‘s protocols.

tag: time


title: Ribo_mZEB1.1


title: iCAR, 2-Propylnonanoic acid_50uM, Rep4, P18 [PGD204-P18]

city: Mason

first: Yuqing

last: Shan

address: 8700 mason montgomery road

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P18

hyb_protocol: PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.

scan_protocol: Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

label: biotin

source_name: iCell Cardiomyocytes²

label_protocol: mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.

growth_protocol: MCF7, A549 and HepG2 cells were grown in phenol red free DMEM, supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin. The iCardiomyocyte cells were grown in a proprietary maintenance medium (FujiFilm Cellular Dynamics, Inc.) for 168 h before chemical treatment. All cells were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Cells were lysed with cell lysis buffer (100 µL per well), and stored at -80⁰C

treatment_protocol: Cells were treated with compounds for 6h at 37oC in an atmosphere of 5% CO2

value: Cardiomyocytes


title: iCAR, Valproic acid_50uM, Rep4, P14 [PGD204-P14]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P14


title: iCAR, 2-Ethylhexanoic acid_10uM, Rep3, P21 [PGD204-P21]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P21


title: iCAR, 2-Methylnonanoic acid_100uM, Rep4, P20 [PGD204-P20]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P20


title: iCAR, 2-Hexyldecanoic acid_5uM, Rep4, P04 [PGD204-P04]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P04


title: iCAR, 2-Ethylbutanoic acid_50uM, Rep4, P24 [PGD204-P24]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P24


title: 102

value: primary pancreatic cancer


title: input (high salt) control

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: input control

data_processing: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. More details as described in Jin et al., 2008

source_name: input-high

growth_protocol: Growth protocol as described in Jin et al., 2008

extract_protocol: Extract protocol as described in Jin et al., 2008

treatment_protocol: Treatment protocol as described in Jin et al., 2008

value: HeLa


title: iCAR, 2-Ethyl-1-hexanol_500uM, Rep3, P11 [PGD204-P11]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P11


title: iCAR, 2-Ethylbutanoic acid_5uM, Rep2, O20 [PGD204-O20]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O20


title: iCAR, DMSO, Rep3, P15 [PGD204-P15]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P15


title: iCAR, Di-n-pentylacetic acid_100uM, Rep2, O08 [PGD204-O08]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O08


title: iCAR, Valproic acid_5uM, Rep1, O17 [PGD204-O17]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O17


title: iCAR, 2-Methylnonanoic acid_1000uM, Rep1, O01 [PGD204-O01]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O01


title: iCAR, 2-Ethyl-1-hexanol_50uM, Rep4, P10 [PGD204-P10]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P10


title: iCAR, DMSO, Rep4, P16 [PGD204-P16]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-P16


title: iCAR, 2-Ethyl-1-hexanol_5uM, Rep4, N18 [PGD204-N18]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N18


title: iCAR, 2-Ethylbutanoic acid_5uM, Rep3, N21 [PGD204-N21]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N21


title: iCAR, Di-n-pentylacetic acid_1000uM, Rep4, N06 [PGD204-N06]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N06


title: iCAR, 2-Propylnonanoic acid_5uM, Rep4, N14 [PGD204-N14]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N14


title: iCAR, 2-Ethylbutanoic acid_500uM, Rep3, N23 [PGD204-N23]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N23


title: iCAR, 2-Ethyl-1-hexanol_50uM, Rep3, N01 [PGD204-N01]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N01


title: iCAR, DMSO, Rep4, N08 [PGD204-N08]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N08


title: iCAR, DMSO, Rep2, O16 [PGD204-O16]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O16


title: iCAR, DMSO, Rep1, O15 [PGD204-O15]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-O15


title: iCAR, DMSO, Rep3, N07 [PGD204-N07]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N07


title: iCAR, 2-Hexyldecanoic acid_500uM, Rep3, N15 [PGD204-N15]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N15


title: iCAR, 2-Propylnonanoic acid_500uM, Rep3, N09 [PGD204-N09]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-N09


title: iCAR, 2-Ethylhexanoic acid_100uM, Rep1, M15 [PGD204-M15]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M15


title: iCAR, 2-Ethyl-1-hexanol_5uM, Rep2, M12 [PGD204-M12]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M12


title: iCAR, DMSO, Rep2, M08 [PGD204-M08]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M08


title: iCAR, 2-Ethylhexanoic acid_1000uM, Rep2, M24 [PGD204-M24]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M24


title: iCAR, 2-Hexyldecanoic acid_5uM, Rep1, M13 [PGD204-M13]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M13


title: iCAR, 2-Hexyldecanoic acid_50uM, Rep2, M06 [PGD204-M06]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M06


title: iCAR, Valproic acid_50uM, Rep3, L23 [PGD204-L23]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L23


title: iCAR, 2-Methylnonanoic acid_100uM, Rep2, M14 [PGD204-M14]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M14


title: iCAR, DMSO, Rep1, M07 [PGD204-M07]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M07


title: iCAR, DMSO, Rep4, L02 [PGD204-L02]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L02


title: iCAR, Valproic acid_500uM, Rep3, L15 [PGD204-L15]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L15


title: iCAR, Di-n-pentylacetic acid_100uM, Rep1, M03 [PGD204-M03]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-M03


title: iCAR, Di-n-pentylacetic acid_10uM, Rep4, L04 [PGD204-L04]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L04


title: iCAR, DMSO, Rep3, L01 [PGD204-L01]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L01


title: iCAR, 2-Ethylbutanoic acid_5uM, Rep4, L14 [PGD204-L14]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L14


title: iCAR, DMSO, Rep4, L18 [PGD204-L18]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L18


title: iCAR, 2-Ethyl-1-hexanol_500uM, Rep2, K20 [PGD204-K20]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-K20


title: iCAR, 2-Ethyl-1-hexanol_500uM, Rep4, L08 [PGD204-L08]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-L08


title: iCAR, 2-Ethylbutanoic acid_500uM, Rep1, K23 [PGD204-K23]

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: all 9 chemicals were tested at 3 doses and 4 reps except octanoic acid which had 3 replicates.
PGD204-K23