title: SCR_Zn_RNA-seq_Rep2

status: Public on Oct 26 2024

city: Pittsburgh

first: David

last: Klein

state: PA

address: 4249 Fifth Ave

institute: University of Pittsburgh

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using STAR, with options --outFilterMismatchNoverReadLmax 0.02 and --outFilterMultimapNmax 1
Aligned reads were processed in deepTools by using the bamCoverage command to generate stranded bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: DESeq2 output files

source_name: Primary mouse myoblast cells

growth_protocol: Myoblasts were grown and differentiated on plates coated with 0.02% collagen (Advanced BioMatrix, Carlsbad, CA, USA). For the proliferation condition, the myoblasts were cultured in growth medium [1:1 v/v DMEM:F-12, 20% fetal bovine serum(FBS), and 25 ng/ml of basic fibroblast growth factor (FGF) for 48 h. To induce differentiation, the cells were allowed to reach 90% confluency and changed into differentiation medium (DMEM) containing 2% horse serum supplemented with insulin.

extract_protocol:
RNA was extracted from flash-frozen cell pellets with TRIzol per manufacturer's instructions.
RNA-seq; built with NEBNext Directional kit

treatment_protocol: Lipofectamine-mediated knockdowns of the indicated BAF complex subunits (or SCR control) were performed with addition of Cu, Zn, or no treatment as indicated.

value: Primary mouse myoblast cells

value: Myoblast


title: SCR_Zn_RNA-seq_Rep1

type: SRA

department: Biological Sciences

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: treatment


title: SCR_notreat_RNA-seq_Rep2


title: SCR_Cu_RNA-seq_Rep2


title: SCR_notreat_RNA-seq_Rep1


title: PG_HE_50dpf_1

status: Public on Oct 27 2024

city: Boston

first: Bo

last: Zhu

state: MA

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

description:
PG_HE_1
counts_raw.tab
counts_normalized.tab

data_processing:
Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2
Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads.
Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2
Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package.
Assembly: GRCz11
Supplementary files format and content: Raw read counts in a TAB delimited file
Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file

organism: Danio rerio

source_name: follicle

extract_protocol:
TRIzol reagent for RNA extraction
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: strain

value: AB

value: follicle

tag: developmental stage

value: primary growth

tag: age

tag: genotype

value: HE (cdkn1a +/-)


title: BRD9_Zn_RNA-seq_Rep1


title: SCR_Cu_RNA-seq_Rep1


title: BRD9_Zn_RNA-seq_Rep2


title: BRD9_notreat_RNA-seq_Rep1

value: Zn


title: BRD9_notreat_RNA-seq_Rep2


title: BRD9_Cu_RNA-seq_Rep2


title: BAF250_Zn_RNA-seq_Rep1


title: BAF250_Zn_RNA-seq_Rep2


title: BRD9_Cu_RNA-seq_Rep1


title: BAF250_notreat_RNA-seq_Rep1


title: BAF250_notreat_RNA-seq_Rep2


title: BAF250_Cu_RNA-seq_Rep2

value: Cu


title: BAF180_Zn_RNA-seq_Rep1


title: BAF180_Zn_RNA-seq_Rep2


title: BAF250_Cu_RNA-seq_Rep1


title: BAF180_notreat_RNA-seq_Rep1


title: BAF180_notreat_RNA-seq_Rep2


title: BAF180_Cu_RNA-seq_Rep2


title: Prol_rep3_no_treatment_MTF1_lib

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Reads trimmed to 25 bp
Reads aligned to mm10 using bowtie2 (options -q -N -X 1000 -I 50 --no-unal)
Aligned reads were deduplicated using Picard and quality-filtered using SAMtools (MAPQ ≥ 10)
Filtered reads were size-selected to separate factor-sized footprints (1-120 bp) using awk.
Size-selected reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 5 bp bins with normalization to 1X coverage and 20-bp smoothing.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Primary mouse myoblast

extract_protocol: Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodies or IgG control, followed by proteinA/proteinG-MNase. Cleavage of Mnase was initiated by Ca2+ addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

treatment_protocol: Proliferating myoblasts were treated with either Cu or no treatment.

value: Primary mouse myoblast


title: Prol_rep3_Cu_IgG_lib


title: Prol_rep3_Cu_MTF1_lib


title: Prol_rep3_no_treatment_IgG_lib


title: BAF180_Cu_RNA-seq_Rep1


title: Prol_rep2_no_treatment_MTF1_lib


title: Prol_rep2_Cu_MTF1_lib


title: Prol_rep1_no_treatment_MTF1_lib


title: Prol_rep2_Cu_IgG_lib


title: Prol_rep2_no_treatment_IgG_lib


title: Prol_rep1_Cu_MTF1_lib


title: Prol_rep1_Cu_IgG_lib


title: RT,replicate3,scATACseq

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

description: 10x Genmoics

data_processing:
Single-cell RNA-seq raw reads were aligned and assigned to Ensembl GRCh38 transcripts using the CellRanger v7.0.1 pipeline (10X Genomics Cloud analysis) with default parameters. Single-cell ATAC-seq raw reads were demultiplexed using CellRanger-ATAC mkfastq (Cell Ranger ATAC, version 2.1.0, 10× Genomics) and aligned to the GRCh38 reference genome and quantified using CellRanger-ATAC count function with default parameters.
Supplementary files format and content: hg38
Supplementary files format and content: Tab-sperated values files and matrix files

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
Human normal breast tissues were purchased from National Disease Research Interchange (NDRI, Philadelphia). Human primary breast tumor tissues were procured from Origene (OriGene Technologies Inc., Rockville, Maryland), and tamoxifen-treated recurrent breast tumor tissues were obtained from Ontario Tumor Bank. The use of human materials has been reviewed by MCW’s institutional review board.  Breast tissues (normal or tumor) were minced with scalpel to obtain 1-3 mm3 pieces into a sterile 35 mm culture dish. Then triturate the tissue in at least 1 ml culture medium (1:1 DMEM/F12 +10% FBS) with a widebore pipette tip to break the tissue into small pieces. Tissues and cells were centrifuged at 500×g at 4 °C for 5 min. Supernatant was discarded and the residual cells were added 5 mL medium, then added 250μL of 20× Collagenase II and incubated in 37°C, 5% CO2 for 60 min. Cells were strained with 40 μm cell strainer and the collected strained cell suspension was centrifuged at 500×g at 4°C for 5 min, supernatant was discarded. Cells were added 5 mL cold experimental medium, and centrifuged at 500×g at 4 °C for 5 min twice. Cells were resuspended in cold experimental medium and then quantified to count viable cells (85%-95% for tissues) using Trypan Blue. Single cells were subjective to live cell flow sorting using 7-AAD Viability Staining Solution.
For scRNA-seq, Samples were processed on a Sony SH800 Cell Sorter with a 100 mm sorting chip and GFP+/DRAQ5+ nuclei were collected into 1.5 ml centrifuge tubes containing 10 µl of the Pre-FACS buffer. We collected 10600, 15,300, and 15700 GFP+ nuclei from the two breast normal, three breast primary tumor, and three breast tam-treated recurrent tumor tissue samples, respectively. Using a Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics), GFP + nuclei were immediately loaded onto a Chromium Single Cell Processor (10X Genomics) for barcoding of RNA from single nuclei. Sequencing libraries were constructed according to the manufacturer’s instructions and resulting cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip as quality control and to determine cDNA concentrations. The samples were combined and run on an Illumina NextSeq HO 150 run. For scATAC-seq, Samples were processed on a Sony SH800 Cell Sorter with a 100 mm sorting chip and GFP+/DRAQ5+ nuclei were collected into 1.5 ml centrifuge tubes containing 10 µl of the Pre-FACS buffer. We collected 10600, 15,300, and 15700 GFP+ nuclei from the two breast normal, three breast primary tumor, and three breast tam-treated recurrent tumor tissue samples, respectively. Nuclei quality and quantity was evaluated using trypan blue on an Invitrogen Countess II device in duplicate, and a subset of nuclei was spun down in a fresh tube and resuspended in 10× sample dilution buffer. Nuclei were then used for single-cell ATAC-seq library construction using the Chromium Single Cell ATAC Solution v1.0 kit (10× Genomics) on a Chromium controller. Completed libraries were further quality checked for fragment size and distribution using an Agilent TapeStation prior to sequencing. Single-cell ATAC-seq samples were sequenced on a NextSeq HO 150 run (Illumina) instrument with 50 bp paired-end reads.
scRNA-seq and scATAC-seq

value: breast cancer


title: RT,replicate2,scATACseq

description: 10x Genmoics


title: NT,replicate1,scATACseq

description: 10x Genmoics


title: PT,replicate2,scATACseq

description: 10x Genmoics


title: PT,replicate1,scATACseq

description: 10x Genmoics


title: PT,replicate3,scATACseq

description: 10x Genmoics


title: RT,replicate2,scRNAseq

description: 10x Genmoics


title: NT,replicate2,scATACseq

description: 10x Genmoics


title: Prol_rep1_no_treatment_IgG_lib


title: PT,replicate2,scRNAseq

description: 10x Genmoics


title: PT,replicate3,scRNAseq

description: 10x Genmoics


title: NT,replicate2,scRNAseq

description: 10x Genmoics


title: PT,replicate1,scRNAseq

description: 10x Genmoics


title: NT,replicate1,scRNAseq

description: 10x Genmoics


title: Bl6_1L

city: New York

first: Sander

middle: M

last: Houten

state: NY

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.4.0g1)
gene-level read quantification via featureCounts v1.5.2
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing raw gene counts for each sample

molecule: polyA RNA

source_name: liver

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a read depth of approximately 51 million 100 nucleotide single-end reads per samples.

value: liver

tag: Sex

value: male

value: 14 weeks

value: WT

tag: diet

value: chow


title: DBA_2L


title: Bl6_2L


title: RT,replicate1,scATACseq

description: 10x Genmoics


title: gastroc.WT.WT.VL38.3

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.3.0e)
gene-level read quantification via featureCounts v1.4.4
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing raw gene counts for each sample

source_name: Gastrocnemius

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a read depth of approximately 70 million 100 nucleotide single-end reads per samples.

value: mixed (mostly C57BL/6N with some 129)

value: Acadl WT / Acadvl WT


title: DBA_1L


title: ESC_H3K4me3_exp1_cell5

city: Shanghai

first: Xiaodong

last: Zhao

address: 800 Dongchuan RD

country: China

institute: Shanghai Jiao Tong University

data_processing:
Sequenced reads were trimmed and filtered by cutadapt (v 2.10) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with default parameters.
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Bigwig files were generated from bam files using deeptools (v 3.3.0) bamCoverage, with parameter of "--binSize 1 --normalizeUsing BPM --skipNonCoveredRegions".
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage.

growth_protocol: Mouse embryonic stem cells were cultured in KnockOut DMEM supplemented with 15% (vol/vol) FBS, and human LIF at 37°C with 5% CO2.

extract_protocol:
Tn5 transposition was set up by incubation at 37°C for 50 min and 55°C for 10 min. After brief sonication, soluble chromatin was used for following ChIP experiments.DNA was reverse crosslinked and extracted by phenol/chloroform/isoamylalcohol.
Following single-cell 2cChIP protocol

value: embryo (blastocyst)


title: RT,replicate3,scRNAseq

description: 10x Genmoics


title: gastroc.WT.WT.VL38.2


title: gastroc.WT.WT.VL26.4


title: gastroc.WT.WT.VL26.3


title: gastroc.KO.WT.VL8.3

value: Acadl KO / Acadvl WT


title: T-ALL_7, H3K27ac

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
ChIP-seq reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using BWA-MEM (v0.7.17)
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.05
bigWig files were generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: bigwig files

source_name: bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: cell line

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)

tag: disease state

value: T-ALL


title: RT,replicate1,scRNAseq

description: 10x Genmoics


title: mouse, Tgfbr1 KO, soleus, rep 4

city: Amsterdam

first: Andi

last: Shi

address: De Boelelaan 1105

country: Netherlands

institute: vu

description:
bam/sol_ht139361_S98_R1_001.sorted.bam
sol_ht139361

data_processing:
Trimming: Cutadapt
Alignment: HISAT2 (version 1.33)
Quality check: FASTQC (version 0.11.9) , all sequences past Q value 30.
Count table: featureCounts (version 2.0.1)
Differentially expressed genes (DEGs): DESeq2 was used to analyse the DEGs on R2 platform (https://hgserver2.amc.nl/).
Assembly: GRCm38.p6, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/
Supplementary files format and content: countTable.txt

source_name: soleus

growth_protocol: Transgenic mice were cultured for 6 weeks.

extract_protocol:
Both left gastrocnemius medialis and soleus muscles were dissected and frozen in liquid nitrogen. PolyA tail RNA was collected from each whole muscle.
Muscles were homogenized by using TRIzol (Thermo Fisher Scientific). Ribopure Link (Thermo Fisher Scientific) and DNase I (Invitrogen) were used to isolate RNA. RNA purity was checked by 2200 TapeStation (Agilent Technologies), RIN values were all above 7.7. RNA concentration was measured by fluorometric quantification QbuitFluorometer (Life Technologies). Libraries were established following the protocol of Kappa-mRNA hyperprep kit (Roche Sequencing Solutions, Indianapolis, IN, USA).

treatment_protocol: Myofibre-specific knockout of Acvr1b and/or Tgfbr1 was performed on 6-week-old mice by injection of tamoxifen and animals were euthanized 3 months later.

value: soleus

value: Tgfbr1 KO


title: T-ALL_7, Input


title: mouse, Tgfbr1 KO, soleus, rep 3

description:
bam/sol_ht131982_S97_R1_001.sorted.bam
sol_ht131982


title: T-ALL_6, H3K27ac


title: gastroc.KO.WT.VL37.1


title: T-ALL_5, Input


title: T-ALL_4, Input


title: T-ALL_5, H3K27ac


title: mouse, Tgfbr1 KO, soleus, rep 1

description:
bam/sol_ht131227_S95_R1_001.sorted.bam
sol_ht131227


title: gastroc.KO.WT.VL32.1


title: gastroc.KO.WT.VL25.1


title: T-ALL_4, H3K27ac


title: mouse, control, soleus, rep 4

description:
bam/sol_hsa143216_S94_R1_001.sorted.bam
sol_hsa143216

value: control


title: T-ALL_3, Input


title: T-ALL_6, Input


title: T-ALL_2, Input


title: T-ALL_3, H3K27ac


title: gastroc.KO.Het.VL28.3

value: Acadl KO / Acadvl Het


title: mouse, control, soleus, rep 3

description:
bam/sol_hsa141559_S93_R1_001.sorted.bam
sol_hsa141559


title: mouse, control, soleus, rep 2

description:
bam/sol_hsa141555_S92_R1_001.sorted.bam
sol_hsa141555


title: gastroc.KO.Het.VL25.2


title: T-ALL_2, H3K27ac


title: WT-1

city: Yangzhou

first: Ling

last: Ling

address: 136 Jiangyang Road

department: Medical College

institute: Yangzhou university

data_processing:
First, Raw Reads were filtered and high quality sequences (Clean Reads) were obtained. All subsequent analyses were based on Clean Reads, which included reference genome comparison, gene expression analysis, differential analysis and enrichment analysis.
Assembly: This is a transcriptome data.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primary cell

extract_protocol:
Total RNA isolation was performed using TriZol Reagent.
After the library was qualified with Qubit3.0 and Agilent 2100, high-throughput sequencing platform was used for sequencing, and the sequencing strategy was PE150.

value: fetal livers from embryos at embryonic day 14.5

value: Embryonic hepatocyte

value: wide type

value: untreated


title: T-ALL_1, H3K27ac


title: mouse, Tgfbr1 KO, soleus, rep 2

description:
bam/sol_ht131231_S96_R1_001.sorted.bam
sol_ht131231


title: T-ALL_1, Input


title: gastroc.KO.Het.VL24.1

value: male

value: 14 weeks


title: mouse, Acvr1b and Tgfbr1 KO, soleus, rep 4

description:
bam/sol_hat166956_S90_R1_001.sorted.bam
sol_hat166956

value: Acvr1b and Tgfbr1 KO


title: mouse, control, soleus, rep 1

description:
bam/sol_hsa141261_S91_R1_001.sorted.bam
sol_hsa141261


title: J.gamma1, H3K27ac

source_name: cell line

value: cell line

value: T-ALL cells


title: gastroc.KO.Het.VL23.2

value: mixed (mostly C57BL/6N with some 129)

value: chow


title: J.gamma1, Input


title: gastroc.KO.Het.VL23.1


title: CD8+ T cells from patients with HPSCC, irradiated (2Gy), 24h, rep3

first: Jingyu

last: Ma

state: --- Select One ---

address: 83 Fenyang Road, Shanghai, China

institute: Eye & ENT Hospital, Fudan University

data_processing:
The samples were sequenced using a 2 × 150-bp paired-end configuration on Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., China) following the vendor's recommended protocol.
The raw sequence data were processed by fastp software (https://github.com/OpenGene/fastp) to remove the reads that contained adaptor contamination, low quality bases, and undetermined bases using default parameters. Quality control was performed using fastp.
The processed reads were mapped to the reference genome of Homo sapiens GRCh38 using HISAT2 (https://ccb.jhu.edu/software/hisat2), and the mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
The transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts and determine the expression level for mRNAs by calculating FPKM.
Assembly: GRCh38
Supplementary files format and content: gene_count_matrix for each sample

source_name: peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were extracted using Ficoll density gradient centrifugation. CD8+ T lymphocytes were isolated with EasySepTM human whole blood CD8 positive selection kit (STEMCELL) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara). The extracted RNA was assessed for quality by measuring the absorbance ranging from 1.8 to 2.1 using a NanoDrop 2000 Spectrophotometer (ThermoFisher), and RNA integrity was assessed by Bioanalyzer 2100 (Agilent).
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina following the manufacturer's instructions (New England Biolabs).

treatment_protocol: CD8+ T cells were untreated or irradiated at the dose of 2 Gy within an X-ray irradiator (RS2000, Rad Source, Georgia) in a dose equivalent time frame. Cells were harvested for RNA sequencing after 24 hours.Each group contained three independent samples.

value: peripheral blood

tag: individual

value: patients

value: CD8+ T cells

value: irradiated (2Gy)


title: CD8+ T cells from patients with HPSCC, irradiated (2Gy), 24h, rep2


title: mouse, Acvr1b and Tgfbr1 KO, soleus, rep 3

description:
bam/sol_hat166955_S89_R1_001.sorted.bam
sol_hat166955

value: soleus


title: CD8+ T cells from patients with HPSCC, irradiated (2Gy), 24h, rep1


title: CD8+ T cells from patients with HPSCC, untreated, 24h, rep3


title: gastroc.Het.WT.VL32.2

value: Acadl Het / Acadvl WT


title: CD8+ T cells from patients with HPSCC, untreated, 24h, rep2


title: CD8+ T cells from healthy individuals, irradiated (2Gy), 24h, rep2

value: healthy individuals


title: gastroc.Het.WT.VL31.1


title: mouse, Acvr1b and Tgfbr1 KO, soleus, rep 2

description:
bam/sol_hat166851_S88_R1_001.sorted.bam
sol_hat166851


title: CD8+ T cells from patients with HPSCC, untreated, 24h, rep1


title: mouse, Acvr1b and Tgfbr1 KO, soleus, rep 1

description:
bam/sol_hat166814_S87_R1_001.sorted.bam
sol_hat166814


title: CD8+ T cells from healthy individuals, untreated, 24h, rep3


title: CD8+ T cells from healthy individuals, irradiated (2Gy), 24h, rep3


title: CD8+ T cells from healthy individuals, untreated, 24h, rep1


title: mouse, Acvr1b KO, soleus, rep 2

description:
bam/sol_ha138856_S84_R1_001.sorted.bam
sol_ha138856

value: Acvr1b KO


title: CD8+ T cells from healthy individuals, irradiated (2Gy), 24h, rep1


title: gastroc.Het.WT.VL28.1


title: J.gamma1,ETS1,CUT&Tag,rep1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

tag: antibody

value: ETS1 (Proteintech, #66598-1-lg)


title: mouse, Acvr1b KO, soleus, rep 4

description:
bam/sol_ha140135_S86_R1_001.sorted.bam
sol_ha140135


title: gastroc.Het.WT.VL27.2


title: CD8+ T cells from healthy individuals, untreated, 24h, rep2

value: untreated


title: J.gamma1,RUNX1,CUT&Tag,rep1

value: RUNX1(Abcam, #Ab272456)


title: mouse, Acvr1b KO, soleus, rep 3

description:
bam/sol_ha139469_S85_R1_001.sorted.bam
sol_ha139469


title: gastroc.Het.KO.VL36.3

value: male

value: 14 weeks

value: Acadl Het / Acadvl KO


title: mouse, Tgfbr1 KO, gastrocnemius, rep 4

description:
bam/gm_ht139361_S82_R1_001.sorted.bam
gm_ht139361

source_name: gastrocnemius

value: gastrocnemius

value: Tgfbr1 KO


title: mouse, Acvr1b KO, soleus, rep 1

description:
bam/sol_ha131969_S83_R1_001.sorted.bam
sol_ha131969


title: gastroc.Het.KO.VL31.5

value: mixed (mostly C57BL/6N with some 129)

value: chow


title: J.gamma1,ETS1,CUT&Tag,rep2

value: cell line

value: T-ALL cells


title: J.gamma1,RUNX1,CUT&Tag,rep2


title: J.gamma1,IRF2BP2,CUT&Tag,rep1

value: IRF2BP2(Sigma, #HPA027815)


title: gastroc.Het.KO.VL30.1


title: J.gamma1,ERG,CUT&Tag,rep1

value: ERG(Proteintech, #14356-1-AP)


title: gastroc.Het.KO.VL25.3


title: J.gamma1,ERG,CUT&Tag,rep2


title: gastroc.Het.Het.VL30.2

value: Acadl Het / Acadvl Het


title: J.gamma1,IRF2BP2,CUT&Tag,rep2


title: mouse, Tgfbr1 KO, gastrocnemius, rep 1

description:
bam/gm_ht131227_S79_R1_001.sorted.bam
gm_ht131227


title: J.gamma1 shIRF2BP2_rep1

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: gastroc.Het.Het.VL27.1


title: mouse, Tgfbr1 KO, gastrocnemius, rep 3

description:
bam/gm_ht131982_S81_R1_001.sorted.bam
gm_ht131982


title: mouse, control, gastrocnemius, rep 3

description:
bam/gm_hsa141559_S77_R1_001.sorted.bam
gm_hsa141559

value: control


title: Liver.WT.WT.VL38.3

source_name: Liver

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a read depth of approximately 33 million 100 nucleotide single-end reads per samples.

value: Acadl WT / Acadvl WT


title: gastroc.Het.Het.VL8.1


title: J.gamma1 shIRF2BP2_rep2


title: mouse, control, gastrocnemius, rep 2

description:
bam/gm_hsa141555_S76_R1_001.sorted.bam
gm_hsa141555


title: mouse, control, gastrocnemius, rep 4

description:
bam/gm_hsa143216_S78_R1_001.sorted.bam
gm_hsa143216


title: J.gamma1 shNC_rep2

value: shNC


title: hPSC shSMARCA4 RNA-seq Rep#1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: Hs shSMARCA4 rp1

data_processing:
STAR --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1 --outSAMtype BAM Unsorted --twopassMode Basic --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeDir hg38_gencode_v32_starsolo/SAindex --sjdbGTFfile gencode.v32.annotation.gtf --runThreadN 24 --readFilesIn ${p1} ${p2} --outFileNamePrefix ${out} --outTmpDir ${out}
te_count -g hg38 -i ${out}Aligned.out.bam --o ${out}tecount.tsv -m genes_tes
Tag counts were GC normalised with EDASeq
Assembly: hg38
Supplementary files format and content: genes_ntc_expression.tsv.gz: TSV file containing ensembl gene number, gene symbol, and the mean of the normalised tag count for replicate samples
Supplementary files format and content: genes_ntc_expression_nonmerged.tsv.gz:  TSV file containing ensembl gene number, gene symbol, and the merged normalised tag count for replicate samples

growth_protocol: The cell line used in this study was hESCs H1 cell line. hESCs were grown in mTeSR1 (Stemcell technologies: 85850) on pre-coated Matrigel plates (Corning: 354277). The medium was replaced every day. Cells were passaged by single-cell digestion with Accutase (SIGMA: A6964) every 4-5 days.

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol and prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). RNA quality was tested using an Agilent 2100 and a minimum RIN score of 8.0 was required for sequencing. Samples were sequenced on an Illumina Novaseq 6000.
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

treatment_protocol: The shRNA virus was packaged using PMD2G, PsPAX2 and target plasmid co-transfected into 293T cells. After 36 hours virus was collected, and purified. Two days later puromycin was used to select transfected cells.

value: Human pluripotent stem cells

value: wildype

value: shRNA SMARCA4


title: J.gamma1,ELF1,CUT&Tag,rep2

value: ELF1 (Abcam, #AB64937)


title: Kidney, Kidney Stone, Day12, rep3

city: Wuhan

first: Fan

last: Cheng

state: China

address: Wuhan ,Hubei,China

institute: Department of Urology, Renmin Hospital of Wuhan University

data_processing:
This project uses the filtering software SOAPnuke (v1.5.2) developed by BGI independently for filtering. The filtered "Clean Reads" are saved in FASTQ format. Parameters: -l 15 -q 0.2 -n 0.05.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT, v2.0.4) is software for mapping RNA-seq reads. Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw fpkm for each sample

source_name: Kidney

growth_protocol: The mice were acclimatized in the animal house of our institution at a steady temperature of 22 ± 2°C and humidity of 40%–70% on a 12/12-h light-dark cycle and with free access to water and feed.

extract_protocol:
Total RNA was extracted from kidney tissues using TRIzol (Invitrogen, Carlsbad, CA, USA).
1) RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 2) End repair, add A and adaptor ligation; 3) PCR; 4) Circularization and make DNB.

treatment_protocol: Male C57BL/6 mice (weight 24-26 g, 6-8 weeks old) were treated with 120 mg/kg of glyoxylic acid (G10601, Sigma-Aldrich) intraperitoneal injection once a day for 12 days to construct the CaOx kidney stone model. The control mice were treated with equal volume of saline.

value: Kidney

value: WT

value: 120 mg/kg of glyoxylic acid intraperitoneal injection once a day for 12 days


title: J.gamma1 shNC_rep1


title: Kidney, Kidney Stone, Day12, rep2


title: gastroc.Het.Het.VL24.2

value: mixed (mostly C57BL/6N with some 129)

value: male

value: 14 weeks


title: hPSC shSMARCA4 RNA-seq Rep#2

description: Hs shSMARCA4 rp2

value: cell line


title: mouse, Tgfbr1 KO, gastrocnemius, rep 2

description:
bam/gm_ht131231_S80_R1_001.sorted.bam
gm_ht131231

value: gastrocnemius

value: Tgfbr1 KO


title: J.gamma1,ELF1,CUT&Tag,rep1

value: T-ALL cells


title: mouse, Acvr1b and Tgfbr1 KO, gastrocnemius, rep 4

description:
bam/gm_hat166956_S74_R1_001.sorted.bam
gm_hat166956

value: Acvr1b and Tgfbr1 KO


title: Kidney, Control, Day12, rep3

value: equal volume of saline


title: hPSC shMAFK RNA-seq Rep#2

description: Hs shMAFK rp2

value: shRNA MAFK


title: Liver.WT.WT.VL26.3

value: Acadl WT / Acadvl WT

value: chow


title: hPSC shMAFK RNA-seq Rep#1

description: Hs shMAFK rp1

value: Human pluripotent stem cells

value: wildype


title: hPSC shLUC RNA-seq Rep#2

description: Hs shLUC rp2

value: shRNA LUC


title: mouse, control, gastrocnemius, rep 1

description:
bam/gm_hsa141261_S75_R1_001.sorted.bam
gm_hsa141261

value: control


title: Kidney, Control, Day12, rep2

value: Kidney

value: WT


title: Liver.WT.WT.VL38.2

value: mixed (mostly C57BL/6N with some 129)

value: male


title: Kidney, Kidney Stone, Day12, rep1

value: 120 mg/kg of glyoxylic acid intraperitoneal injection once a day for 12 days


title: Liver.KO.WT.VL8.3

value: 14 weeks

value: Acadl KO / Acadvl WT


title: mouse, Acvr1b and Tgfbr1 KO, gastrocnemius, rep 2

description:
bam/gm_hat166851_S72_R1_001.sorted.bam
gm_hat166851

value: gastrocnemius


title: Liver.WT.WT.VL26.4


title: hPSC shKDM1A RNA-seq Rep#2

description: Hs shKDM1A rp2

value: cell line

value: shRNA KDM1A


title: mouse, Acvr1b and Tgfbr1 KO, gastrocnemius, rep 1

description:
bam/gm_hat166814_S71_R1_001.sorted.bam
gm_hat166814

value: Acvr1b and Tgfbr1 KO


title: mouse, Acvr1b and Tgfbr1 KO, gastrocnemius, rep 3

description:
bam/gm_hat166955_S73_R1_001.sorted.bam
gm_hat166955


title: Kidney, Control, Day12, rep1

value: equal volume of saline


title: Liver.KO.WT.VL37.1

value: chow


title: hPSC shKDM1A RNA-seq Rep#1

description: Hs shKDM1A rp1

value: Human pluripotent stem cells


title: hPSC shE2F6 RNA-seq Rep#2

description: Hs shE2F6 rp2

value: wildype

value: shRNA E2F6


title: Cgref1 KO, biol rep 3

city: Hong Kong

first: Pearl

last: Chan

address: 21 Sassoon Road, Lab Block, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: F

data_processing:
Clean reads were filtered from the raw data and mapped to the reference genome using HISAT.
Clean reads were then aligned to reference genes using Bowtie2.
Genes expression is quantified by the RSEM software.
Differential genes are screened using DEseq2.
Assembly: PE150
Supplementary files format and content: tab-delimited txt file includes Fragments Per Kilobase per Million mapped fragments (FKPM) counts for each sample
Supplementary files format and content: tab-delimited txt file includes transcripts per million (TPM) counts for each sample
Supplementary files format and content: tab-delimited txt file includes raw reads for each sample

extract_protocol:
Total RNA extraction was performed using RNAiso Plus (Takara). At least 200 ng of total RNA from each sample was sent for RNA-seq.
The protocol includes the following major steps: 1) mRNA enrichment 2) reverse-transcription 3) bubble adaptor ligation (patent-protected) 4) PCR amplification and 5) circular single-stranded DNA generation.

value: Liver

value: Hepatocytes

value: Cgref1 KO


title: mouse, Acvr1b KO, gastrocnemius, rep 4

description:
bam/gm_ha140135_S70_R1_001.sorted.bam
gm_ha140135

value: Acvr1b KO


title: hPSC shE2F6 RNA-seq Rep#1

description: Hs shE2F6 rp1


title: Wild Type, biol rep 3

description: C

value: Wild Type


title: mouse, Acvr1b KO, gastrocnemius, rep 1

description:
bam/gm_ha131969_S67_R1_001.sorted.bam
gm_ha131969


title: mouse, Acvr1b KO, gastrocnemius, rep 3

description:
bam/gm_ha139469_S69_R1_001.sorted.bam
gm_ha139469


title: Liver.KO.WT.VL25.1

value: mixed (mostly C57BL/6N with some 129)

value: male


title: Liver.KO.Het.VL28.3

value: 14 weeks

value: Acadl KO / Acadvl Het


title: mouse, Acvr1b KO, gastrocnemius, rep 2

description:
bam/gm_ha138856_S68_R1_001.sorted.bam
gm_ha138856

value: gastrocnemius


title: Liver.KO.Het.VL25.2


title: Wild Type, biol rep 1

description: A


title: hPSC shSMARCA4 HiC Rep#2

data_processing:
Reads were aligned using bowtie2
Hi-C matrices were generated using te_hic
Matrices were balanced usng ICE from the cooler package
TopDom (v0.3.2) was used to call TADs
Assembly: hg38
Supplementary files format and content: cooler ICE balanced matrices

extract_protocol:
The cell was digested into single cell with accutase. Cell was washed three times with DPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The chromatin was digested with HindIII restriction enzyme, the biotinylated dATP was ligated in to the overhang site which generated by HindIII digestion. After reversal of crosslinks, the genome DNA was purified and sheared, the fragment was select around 300-500bp, the point ligation junctions with biotinylated dATP were pulled down with streptavidin beads and prepped for Illumina sequencing.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: cell line

value: shRNA SMARCA4


title: Cgref1 KO, biol rep 2

description: E


title: Liver.KO.WT.VL32.1

value: Acadl KO / Acadvl WT


title: hPSC shSMARCA4 HiC Rep#1


title: Liver.KO.Het.VL24.1

value: chow


title: hPSC shLUC RNA-seq Rep#1

description: Hs shLUC rp1

value: Human pluripotent stem cells

value: shRNA LUC


title: Cgref1 KO, biol rep 1

description: D


title: hPSC shMAFK HiC Rep#2

value: wildype

value: shRNA MAFK


title: Wild Type, biol rep 2

description: B

value: Liver

value: Hepatocytes


title: Com_4

city: changsha

first: yating

last: dian

address: xiangya hospital

institute: Xiangya Hospital Central South University

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone and anti-PD-1
Com_4

data_processing:
Data quality was assessed using FastQC software (https://github.com/s-andrews/FastQC).
After obtaining the BAM file, paired-end clean reads were aligned to the GRCm38 reference genome (mm10) using HISAT2 (v.2.2.1) .
We further processed the sequencing alignments using SAMTools (v.1.9)  which facilitated sorting, indexing, and filtering for RNA-seq data preparation.
Assembly: mm10
Supplementary files format and content: Comma-Separated Values file include raw counts for each sample
Supplementary files format and content: Comma-Separated Values file include TPM for each sample

source_name: tumor

extract_protocol:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received intra-peritoneal injections of anti-PD-1 treatment or IgG control with or without propafenone
SMARTER mRNA-seq library Prep kit following manufacturer's protocols

value: tumor

value: melanoma cells

value: wild type

value: propafenone +anti-PD-1


title: Com_5

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone and anti-PD-1
Com_5


title: Liver.KO.Het.VL23.1

value: mixed (mostly C57BL/6N with some 129)

value: male

value: 14 weeks


title: intestinal epithelial-specific HIF-1α overexpression mice-3

city: Louisville

first: MING

last: SONG

state: KY

address: 505 S. Hancock St.

institute: University of Louisville

description:
CKRN220019544-1A
IECOE3_F_IL

data_processing:
Hisat2 v2.0.5
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome [Mus Musculus(GRCm38/mm10)]  using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file include counts and FPKM values for each sample

source_name: Ileum

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Ileum

value: intestinal epithelial-specific HIF-1alpha overexpression


title: intestinal epithelial-specific HIF-1α overexpression mice-2

description:
CKRN220019543-1A
IECOE2_M_IL


title: hPSC shMAFK HiC Rep#1

value: cell line


title: Com_3

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone and anti-PD-1
Com_3


title: intestinal epithelial-specific HIF-1α overexpression mice-1

description:
CKRN220019542-1A
IECOE1_M_IL


title: Liver.Het.WT.VL31.1

value: Acadl Het / Acadvl WT

value: chow


title: Com_2

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone and anti-PD-1
Com_2


title: Liver.Het.WT.VL32.2


title: Com_1

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone and anti-PD-1
Com_1


title: hPSC shLUC HiC Rep#2

value: Human pluripotent stem cells

value: shRNA LUC


title: Liver.Het.WT.VL28.1


title: flox control-2

description:
CKRN220019540-1A
FLOX2_M_IL

value: flox control


title: Liver.KO.Het.VL23.2

value: Acadl KO / Acadvl Het


title: Liver.Het.WT.VL27.2


title: flox control-3

description:
CKRN220019541-1A
FLOX3_F_IL


title: hPSC shLUC HiC Rep#1

value: wildype


title: PD-1_5

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received anti-PD-1
PD-1_5

value: tumor


title: hPSC shKDM1A HiC Rep#1

value: shRNA KDM1A


title: hPSC shKDM1A HiC Rep#2


title: PD-1_4

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received anti-PD-1
PD-1_4

value: melanoma cells

value: wild type


title: hPSC shE2F6 HiC Rep#2

value: shRNA E2F6


title: PD-1_3

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received anti-PD-1
PD-1_3


title: flox control-1

description:
CKRN220019539-1A
FLOX1_M_IL


title: Liver.Het.KO.VL36.3

value: mixed (mostly C57BL/6N with some 129)

value: male

value: Acadl Het / Acadvl KO


title: Liver.Het.KO.VL31.5

value: 14 weeks


title: PD-1_2

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received anti-PD-1
PD-1_2


title: hPSC shE2F6 HiC Rep#1

value: cell line


title: PD-1_1

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received anti-PD-1
PD-1_1


title: Wild type control, rep3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

source_name: CD3+ T cells isolated from spleen

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD3+ T cells isolated from spleen

value: CD3+ T cells

value: Wild type


title: Wild type control, rep2


title: Wild type control, rep1


title: Irf2bp2 KO, rep2

value: Irf2bp2 KO


title: WT_3

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
RSEM
Assembly: GRCh38

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq RNA Sample Prep Kit (Illumina)

value: WT


title: Irf2bp2 KO, rep1


title: PPF_5

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone
PPF_5

value: propafenone


title: WT_1


title: PPF_4

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone
PPF_4


title: WT_2


title: DCP1a/b_KO_3

value: DCP1a and DCP1b double knock out


title: Liver.Het.Het.VL8.1

value: Acadl Het / Acadvl Het

value: chow


title: PPF_3

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone
PPF_3

value: tumor

value: melanoma cells


title: Liver.Het.Het.VL30.2


title: Liver.Het.Het.VL27.1


title: DCP1a/b_KO_1


title: Liver.Het.KO.VL30.1


title: dTom_2-antibody capture

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

description:
3P 10x Chromium
dTom_2_MMT_barcodes.tsv.gz
dTom_2_MMT_features.tsv.gz
dTom_2_MMT_matrix.mtx.gz

library_source: other

data_processing:
alignment, filtering, counting barcodes, quantifying unique molecular identifiers (UMIs), and conducting antibody capture analysis to determine the gene transcript counts per cell was executed using the “count” function of Cell Ranger (v6.0.1; 10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files, comma-seperated values files and matrix files

molecule: protein

source_name: KPC LUAD tumor

growth_protocol: Lung tumorigenesis was initiated in cohorts of KPC mice as described (DuPage et al., 2009 Nat Protoc) by intratracheal infection with 1 x 105 lentiviral particles.

extract_protocol:
4 Con and 4 mA1 largest KPC tumors were dissected at 16 weeks pti, minced using a razor blade, and incubated at 37°C for 30 min in dissociation solution containing DNAse (1µg/ml, Sigma-Aldrich) and Collagenase IV (200 U/ml, Sigma-Aldrich), prior to filtering through Flowmi Cell Strainer (BAH136800040, Sigma-Aldrich), and dead cells removal (MACS dead cell removal kit, 130-090-101, Miltenyibiotec). Cell Hashtagging was performed using CD45 and MHC Class I TotalSeq-B antibodies (anti-mouse Hashtag 1_ACCCACCAGTAAGAC, 155831, and Hashtag 2_ GGTCGAGAGCATTCA, 155833, BioLegend) and multiplexed samples were submitted for 3P 10x Chromium sequencing
Library was prepared using 10x Single Cell 3 Prime V3 kit following the manufacturer's instructions

treatment_protocol: Largest KPC tumors were dissected at 16 weeks pti, minced using a razor blade, and incubated at 37°C for 30 min in dissociation solution containing DNAse (1µg/ml, Sigma-Aldrich) and Collagenase IV (200 U/ml, Sigma-Aldrich), prior to filtering through Flowmi Cell Strainer (BAH136800040, Sigma-Aldrich), and dead cells removal (MACS dead cell removal kit, 130-090-101, Miltenyibiotec).

value: KPC LUAD tumor

value: Con dRNA

tag: library type

value: ADT


title: PPF_1

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone
PPF_1

value: wild type


title: DCP1b_KO_3

value: DCP1b knock out


title: dTom_1-antibody capture

description:
3P 10x Chromium
dTom_1_MMT_barcodes.tsv.gz
dTom_1_MMT_features.tsv.gz
dTom_1_MMT_matrix.mtx.gz


title: Liver.Het.KO.VL25.3

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.3.0e)
gene-level read quantification via featureCounts v1.4.4
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing raw gene counts for each sample

value: mixed (mostly C57BL/6N with some 129)

value: male

value: 14 weeks

value: Acadl Het / Acadvl KO


title: Ctrl_5

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received IgG
Ctrl_5

value: IgG


title: Ctrl_4

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received IgG
Ctrl_4


title: dTom_1-GEX

library_source: transcriptomic single cell

value: mRNA


title: DCP1b_KO_2


title: Liver.Het.Het.VL24.2


title: d10_2-antibody capture

description:
3P 10x Chromium
d10_2_MMT_barcodes.tsv.gz
d10_2_MMT_features.tsv.gz
d10_2_MMT_matrix.mtx.gz

value: mA1 dRNA


title: PPF_2

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received propafenone
PPF_2

value: propafenone


title: DCP1a/b_KO_2

value: DCP1a and DCP1b double knock out


title: Test Group, biological rep 3

type: RNA

hyb_protocol: Labelled ss-cDNA samples were loaded onto a GeneChip Cartridge Array where they were hybridyzed to DNA probes. Washing and staining steps were performed on the GeneChip Fluidics Station 450.

scan_protocol: Cartridge was scanned on the GeneChip Scanner 3000.

data_processing: The Transcriptome Analysis Console Software was used for data analysis. Fold changes were significantly different when the P-value was smaller than 0.05.

label: biotin

source_name: Liver Tissue, AAV-CREB-H-ΔTC, 2 weeks post AAV induction

label_protocol: ss-cDNA was then fragmented and labelled with biotin.

growth_protocol: CREB-H KO mice of 8 weeks of age were housed with a daylight cycle from 7 am to 7 pm. Normal diet was provided.

extract_protocol: Total RNA was extracted from mouse liver tissues and converted into ss-cDNA through various synthetic reactions.

treatment_protocol: Animals received intraperitoneal injections (1x1011 genome copies) of liver targeting AAV. The test group received AAV-CREB-H- ΔTC. The control group received AAV-GFP. The sample size was n=3 per group. Mice were sacrificed two weeks after the injection. Liver tissues were extracted and processed for microarray analysis.

value: Liver

value: CREB-H KO, Allele Symbol (Jackson Laboratory):Creb3l3tm1.1Sad/J

value: 8 weeks old


title: d10_2-GEX

value: KPC LUAD tumor


title: Ctrl_2

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received IgG
Ctrl_2

value: tumor

value: melanoma cells


title: d10_1-antibody capture

description:
3P 10x Chromium
d10_1_MMT_barcodes.tsv.gz
d10_1_MMT_features.tsv.gz
d10_1_MMT_matrix.mtx.gz

value: ADT


title: DCP1a_KO_2

value: DCP1a knock out


title: Test Group, biological rep 2


title: Ctrl_1

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received IgG
Ctrl_1

value: wild type


title: DCP1a_KO_1


title: SC9_C2o3_S61

status: Public on Oct 25 2024

city: Paris

first: Michel

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

description: sequencing run 1

data_processing:
Sequences were demultiplexed using bcl2fastq v2.20.0 and trimmed to remove adapters and low quality end bases using cutadapt v2.9. After trimming, reads shorter than 20 bases were discarded. Reads were then aligned to the mm10 mouse reference genome using STAR (v2.7.9a) with default options (Dobin et al., 2013). Mapped reads were then quantitated using the RSEM pipeline (v1.3.3) with the --single-cell-prior option (2). Quality control and data filtering were performed separately for the two sequencing runs. In both runs, cells with more than 10 million reads or 20% of reads mapping to mitonchondrial genes or more than 1% of spike-ins reads were filtered out. Cells expressing fewer than 4800 genes in the sequencing run 1 or fewer than 4,000 genes in the sequencing run 2 were excluded from the downstream analyses. 170 cells out of the 184 sequenced cells (20x E3.25, 22x E3.75, 14x E4.0, 31x E2.75+16h ctl, 31x E2.75+16h LY, 28x E2.75+24h ctl, 24x E2.75+24h LY) were kept for downstream analyses. Reads were aligned to the mm10 genome and transcripts per million (TPM) computed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for 170 of 184 single-cell samples

source_name: Embryo

growth_protocol: Embryos were obtained from timed natural matings. Noon of the day when the vaginal plugs of mated females were identified was scored as E0.5. E2.75 were culture in KSOM for 16 and 24 hours.

extract_protocol:
mRNAs from single cell were extracted, reverse-transcribed from 3’UTR and amplified following the Tang et al, 2010 protocol.
cDNAs larger than 500 bp were recovered and purified after agarose electrophoreisis. Illumina librairies were then prepared using the Nextera XT DNA Library Prep Kit. The tagmented cDNAs were amplified using a unique combination of i5 and i7 indexes and purified using AMPure XP beads. Paired-end sequencing was performed on pooled librairies using a NextSeq 550 (Illumina).

treatment_protocol: Zona pellucida was removed from embryos prior to immunosurgery. E2.75 morulae embryos were cultured for 16 and 24 hours with vehicle (DMSO) or 10µM LY.

value: Embryo

tag: date


title: SC9_C2o2_S59

description: sequencing run 2


title: SC9_C2o1_S54

description: sequencing run 1


title: SC9_C1o3_S46

description: sequencing run 1


title: Control Group, biological rep 3

source_name: Liver Tissue, AAV-GFP, 2 weeks post AAV induction


title: Control Group, biological rep 2


title: SC9_C1o1_S51

description: sequencing run 2


title: SC9_C1o2_S55

description: sequencing run 1


title: SC8_C8o1_S92

description: sequencing run 2


title: SC8_C8o2_S25

description: sequencing run 1


title: SC8_C7o3_S17

description: sequencing run 1


title: SC8_C7o1_S47

description: sequencing run 1


title: SC8_C6o1_S41

description: sequencing run 2


title: DCP1b_KO_1

value: DCP1b knock out


title: SC8-C7o2_S9

description: sequencing run 1


title: DCP1a_KO_3


title: SC8_C5o4_S86

description: sequencing run 2


title: Ctrl_3

description:
Immunocompetent C57BL/6 mice implanted with B16F10 melanoma cells received IgG
Ctrl_3


title: SC8_C5o2_S84

description: sequencing run 2


title: Control Group, biological rep 1


title: SC8_C5o3_S33

description: sequencing run 2


title: SC8_C3o1_S17

description: sequencing run 2


title: d10_1-GEX


title: SC8_C3o2_S25

description: sequencing run 2


title: SC8_C3o3_S1

description: sequencing run 1


title: Test Group, biological rep 1


title: SC8_C4o1_S37

description: sequencing run 1


title: SC8_C5o1_S45

description: sequencing run 1


title: SC8_C2o1_S9

description: sequencing run 2


title: SC6_C5o3_S81

description: sequencing run 2


title: dTom_2-GEX

value: Con dRNA


title: SC6_C5o1_S63

description: sequencing run 1


title: SC6_C4o2_S22

description: sequencing run 2


title: SC6_C2o3_S38

description: sequencing run 2


title: SC6_C2o1_S60

description: sequencing run 1


title: SC6_C2o2_S30

description: sequencing run 2


title: SC6_C3o2_S73

description: sequencing run 2


title: SC5_C4o1_S12

description: sequencing run 1


title: SC5_C4o2_S75

description: sequencing run 2


title: SC6_C1o2_S56

description: sequencing run 1


title: SC5_C3o4_S72

description: sequencing run 2


title: SC5_C4o3_S20

description: sequencing run 1


title: SC5_C4o4_S28

description: sequencing run 1


title: SC5_C3o1_S8

description: sequencing run 2


title: SC5_C3o3_S69

description: sequencing run 1


title: SC5_C3o2_S48

description: sequencing run 1


title: SC5_C2o4_S64

description: sequencing run 2


title: SC5_C2o2_S62

description: sequencing run 1


title: SC8_C1o1_S1

description: sequencing run 2


title: SC5_C2o1_S67

description: sequencing run 2


title: SC8_C1o2_S95

description: sequencing run 2


title: SC6_C5o4_S89

description: sequencing run 2


title: SC3_T6o3_S12

description: sequencing run 2

value: LY


title: SC3_T6o1_S70

description: sequencing run 2


title: SC3_T6o2_S69

description: sequencing run 2


title: SC3_T5o2_S4

description: sequencing run 2


title: SC3_T4o2_S52

description: sequencing run 1


title: SC3_T5o1_S59

description: sequencing run 1


title: SC3_T6o1_S66

description: sequencing run 1


title: SC3_T2o2_S23

description: sequencing run 2


title: SC3_T4o1_S75

description: sequencing run 1


title: SC3_C4o1_S44

description: sequencing run 1

value: DMSO


title: SC3_T1o1_S61

description: sequencing run 2


title: SC3_C3o4_S53

description: sequencing run 2


title: SC3_C2o21_S91

description: sequencing run 2


title: SC3_C2o2_S62

description: sequencing run 2


title: SC3_C3o1_S68

description: sequencing run 1


title: SC3_C1o1_S83

description: sequencing run 2


title: SC3_C2o1_S36

description: sequencing run 1


title: SC16_T3o2_S4

description: sequencing run 1


title: SC16_T2o1_S43

description: sequencing run 2


title: SC16_T3o1_S86

description: sequencing run 1


title: SC5_C2o3_S45

description: sequencing run 2


title: SC16_T1o2_S35

description: sequencing run 2


title: SC16_T1o1_S72

description: sequencing run 1


title: SC16_C4o1_S27

description: sequencing run 2


title: SC16_T2o2_S79

description: sequencing run 1


title: SC16_C3o1_S58

description: sequencing run 1


title: SC16_C3o3_S19

description: sequencing run 2


title: SC16_C3o2_S65

description: sequencing run 1


title: SC16_C2o2_S51

description: sequencing run 1


title: SC16_C1o4_S38

description: sequencing run 1


title: SC16_C2o1_S43

description: sequencing run 1


title: SC16_C1o3_S35

description: sequencing run 1


title: SC16_C1o2_S27

description: sequencing run 1


title: SC15-2_T4o4_S15

description: sequencing run 2


title: SC16_C1o1_S37

description: sequencing run 2


title: SC15-2_T4o3_S54

description: sequencing run 2


title: SC15-2_T4o1_S11

description: sequencing run 2


title: SC15-2_T4o6_S19

description: sequencing run 1


title: SC15-2_T3o2_S11

description: sequencing run 1


title: SC15-2_C5o4_S85

description: sequencing run 1


title: SC15-2_C5o1_S3

description: sequencing run 2


title: SC15-2_T3o1_S3

description: sequencing run 1


title: SC15-2_T3o1_S96

description: sequencing run 2


title: SC15-2_C4o3_S32

description: sequencing run 1


title: SC15-2_T3o5_S30

description: sequencing run 1


title: SC15-2_C4o5_S22

description: sequencing run 1


title: SC15-2_C5o3_S78

description: sequencing run 1


title: SC15-2_C4o1_S64

description: sequencing run 1


title: SC15-2_C3o4_S29

description: sequencing run 2


title: SC15-2_C4o2_S71

description: sequencing run 1


title: SC15-2_C3o6_S46

description: sequencing run 2


title: SC15-2_C3o3_S21

description: sequencing run 2


title: SC15-2_C3o1_S57

description: sequencing run 1


title: SC15-1_T1o5_S50

description: sequencing run 1


title: SC15-1_T2o1_S90

description: sequencing run 2


title: SC15-1_T1o3_S42

description: sequencing run 1


title: SC15-1_T1o2_S14

description: sequencing run 1


title: SC15-1_C2o4_S74

description: sequencing run 2


title: SC15-1_C2o3_S34

description: sequencing run 1


title: SC15-2_T4o2_S88

description: sequencing run 2


title: SC15-1_C2o2_S66

description: sequencing run 2


title: SC15-1_C2o1_S6

description: sequencing run 1


title: SC15-1_C1o5_S26

description: sequencing run 1


title: SC15-1_C1o4_S58

description: sequencing run 2


title: SC15-1_C1o3_S90

description: sequencing run 1


title: SC15-1_C1o2_S50

description: sequencing run 2


title: SC14_T3o4_S18

description: sequencing run 1


title: SC14_T3o2_S2

description: sequencing run 1


title: SC14_T3o3_S10

description: sequencing run 1


title: SC14_T2o5_S77

description: sequencing run 1


title: SC14_T3o1_S84

description: sequencing run 1


title: SC14_T1o3_S70

description: sequencing run 1


title: SC14_T2o1_S13

description: sequencing run 2


title: SC14_T1o1_S34

description: sequencing run 2


title: SC14_T2o4_S88

description: sequencing run 1


title: SC14_C2o1_S26

description: sequencing run 2


title: SC14_T2o2_S42

description: sequencing run 2


title: SC15-1_T1o4_S8

description: sequencing run 1


title: SC14_C1o2_S81

description: sequencing run 1


title: SC14_C1o1_S18

description: sequencing run 2


title: SC13_C3o1_S56

description: sequencing run 2


title: SC15-1_T1o1_S82

description: sequencing run 2


title: SC13_C2o5_S48

description: sequencing run 2


title: SC13_C3o2_S10

description: sequencing run 2


title: SC13_C3o1_S67

description: sequencing run 1


title: SC13_C2o2_S83

description: sequencing run 1


title: SC13_C2o4_S80

description: sequencing run 2


title: SC13_C1o5_S7

description: sequencing run 2


title: SC13_C1o4_S24

description: sequencing run 1


title: SC13_C1o3_S76

description: sequencing run 1


title: SC13_C1o2_S94

description: sequencing run 2


title: SC13_C1o1_S2

description: sequencing run 2


title: SC12_T3o1_S76

description: sequencing run 2


title: SC12_T2o2_S68

description: sequencing run 2


title: SC14_T1o2_S5

description: sequencing run 2


title: SC12_T1o1_S79

description: sequencing run 2


title: SC13_C3o6_S74

description: sequencing run 1


title: SC12_T1o2_S87

description: sequencing run 2


title: SC12_C3o3_S40

description: sequencing run 2


title: SC12_C2o4_S63

description: sequencing run 2


title: SC12_C3o1_S60

description: sequencing run 2


title: SC12_C2o3_S55

description: sequencing run 2


title: SC12_C2o1_S47

description: sequencing run 2


title: SC12_C3o2_S71

description: sequencing run 2


title: SC12_C1o3_S39

description: sequencing run 2


title: SC12_C2o2_S16

description: sequencing run 1


title: SC12_C1o2_S24

description: sequencing run 2


title: SC11_T5o3_S29

description: sequencing run 1


title: SC11_T5o1_S44

description: sequencing run 2


title: SC12_C1o4_S32

description: sequencing run 2


title: SC11_T5o2_S52

description: sequencing run 2


title: SC11_T3o1_S28

description: sequencing run 2


title: SC12_C1o5_S40

description: sequencing run 1


title: SC11_T4o4_S21

description: sequencing run 1


title: SC11_T4o1_S16

description: sequencing run 2


title: SC11_T4o2_S31

description: sequencing run 1


title: SC12_T2o1_S39

description: sequencing run 1


title: SC11_T2o4_S23

description: sequencing run 1


title: SC11_T4o3_S36

description: sequencing run 2


title: SC11_T2o3_S20

description: sequencing run 2


title: SC12_C1o1_S31

description: sequencing run 2


title: SC11_T2o1_S78

description: sequencing run 2


title: SC11_C4o4_S13

description: sequencing run 1


title: SC11_T1o1_S15

description: sequencing run 1


title: SC11_T3o2_S14

description: sequencing run 2


title: SC11_C4o3_S7

description: sequencing run 1


title: SC11_C2o3_S85

description: sequencing run 2


title: SC11_C3o2_S93

description: sequencing run 2


title: SC11_C1o3_S89

description: sequencing run 1


title: SC11_C2o1_S87

description: sequencing run 1


title: SC11_C4o2_S5

description: sequencing run 1


title: SC11_C1o1_S82

description: sequencing run 1


title: SC11_C1o2_S73

description: sequencing run 1


title: SC11_C4o1_S6

description: sequencing run 2


title: SC10_C3o3_S65

description: sequencing run 2


title: SC11_C2o2_S77

description: sequencing run 2


title: SC10_C4o2_S33

description: sequencing run 1


title: SC10_C4o3_S41

description: sequencing run 1


title: G31

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

data_processing: Sequencing reads from each sample were mapped to medaka reference transcripts (Ensembl version 95) using HISAT2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software (http://cole-trapnell-lab.github.io/cufflinks/, University of Washington) was used to conduct differentially expressed gene (DEG) analysis on the raw count data.

organism: Oryzias latipes

source_name: Male Testis

growth_protocol: The medaka strain Hd-rR was used and maintained under standard conditions

extract_protocol:
Total RNA from each sample were extracted from each tissue sample using the Zymo Miniprep Plus Kit (Zymo Research, Irivine, CA) with DNase/digestion of RNA according to manufacturer’s instructions.
The RNA-seq library were prepared using NEBNext® Ultra II RNA Library Prep Kit for Illumina (E7775, NEB) according to manufacturer's instruction.

treatment_protocol: Adult medaka were exposed to 50 μg/L THC for 21 days. The exposure solutions were changed every 7 days. Each treatment contained 3 biological replicates.

value: Hd-rR

value: testis

tag: gender

value: Male

value: THC


title: G34

source_name: Female Ovary

tag: tissue

value: ovary

value: Female


title: G28


title: SC10_C5o2_S49

description: sequencing run 1


title: SC10_C1o1_S53

description: sequencing run 1


title: SC10_C3o1_S57

description: sequencing run 2


title: G25


title: G19


title: SC11_C1o4_S80

description: sequencing run 1


title: G16

value: Control


title: G13


title: G10


title: G7


title: G4


title: G22


title: B28

source_name: Female Brain

value: brain


title: B31

source_name: Male Brain


title: B22


title: B19


title: B13


title: B16


title: B7


title: sibling, replicate 2, snRNAseq

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

description: 10X Genomics

data_processing:
The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer (Illumina version 2.4.7) and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20.
The raw sequencing data was processed using cellranger v6.0, or demultiplexing, barcode processing, gene count processing. For alignment, we used Danio rerio Genome assembly GRCz11 v109 from Ensembl.
Furthere downstream processing was done using Seurat (v4) in R
Assembly: GRCz11 v109 Ensembl
Supplementary files format and content: barcodes, tab seprated values
Supplementary files format and content: feature counts, tab seprated values
Supplementary files format and content: matrix, matrix

molecule: nuclear RNA

source_name: heart

extract_protocol:
Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of ~50 hearts were collected within one hour in ice-cold Leibovitz's L-15 Medium (Thermo Fisher Scientific), supplemented with 10% fetal bovine serum (Sigma -Aldrich, F7524), centrifuged for 4 minutes at 300 g, snap frozen and preserved in liquid nitrogen. Two replicates, each consisting of four pools, were obtained for each experimental group (sibling, mutant). Single nuclei suspensions containing 3800-4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor (10 x Genomics, PN-1000494) following the samples Prep User Guide (10 x Genomics, CG000505, Rev A).
The Transposition, GEM generation & barcoding, reverse transcription, and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (10x Genomics, CG000338 Rev F) with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step, GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at -80° C. When samples were retrieved from storage, they were cleaned-up as stipulated in step 3.0 of the user guide. Thereafter, a pre-amplification step was performed with 6 PCR cycles, followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit (Agilent, DNF-473), respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM, asymmetric paired-end and dual indexed, using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles (Illumina, 20028319) on an Illumina NovaSeq 6000. The read set-up was as follows: read 1: 29 cycles, i7 index: 10 cycles, i5: 10 cycles and read 2: 89-91 cycles.
snRNA-seq

value: heart

value: wt sibling


title: B10


title: B4


title: spns_mutant, replicate 1, snRNAseq

description: 10X Genomics

value: spns mutant


title: B1


title: SC10_C2o3_S49

description: sequencing run 2


title: DME_Flag_knockin_rep2

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetative tissues, the plants were planted in greenhouses.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645) and sequenced using an Illumina Novaseq 6000 platform (paired-end 150 bp reads).

value: shoot


title: DME_Flag_knockin_rep1


title: sibling, replicate 1, snRNAseq

description: 10X Genomics


title: spns_mutant, replicate 2, snRNAseq

description: 10X Genomics


title: msi2msi3_20d_RNAseq_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown in a growth chamber for 20 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 20-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000, paired-end 150bp).

value: Arabidopsis seedlings

tag: time


title: dme-2_de_novo_shoot_rep3

city: Seoul

first: Seunga

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped to a custom reference genome for Ler using STAR (v2.7.10a) with “--pOverlapNbasesMin 12 --peOverlapMMp 0.1 --twopassMode Basic” options.
Raw counts were obtained from STAR (v2.7.10a) with "--quantMode GeneCounts" option.
RSEM (v1.3.1) was used to quantify transcript abundance to obtain TPM values.
Assembly: GCA_900660825
Supplementary files format and content: Tab-separated values file includes raw counts for each sample
Supplementary files format and content: Tab-separated values file includes TPM values for each sample

source_name: de novo shoot

extract_protocol:
Total RNA Qiagen RNeasy Kit (Qiagen)
TruSeq stranded mRNA Kit (Illumina)

value: de novo shoot

value: Ler dme-2/-


title: Col-0_20d_RNAseq_rep2

value: wild type


title: msi2msi3_20d_RNAseq_rep1


title: hag2msi2msi3_20d_RNAseq_rep3


title: Col-0_20d_RNAseq_rep3


title: hag2msi2msi3_20d_RNAseq_rep2


title: msi2msi3_20d_RNAseq_rep2


title: G1

tag: treatment


title: B34

tag: strain


title: B25


title: WT_de_novo_shoot_rep3

value: Ler WT


title: WT_de_novo_shoot_rep1


title: dme-2_de_novo_shoot_rep1


title: WT_de_novo_shoot_rep2


title: dme-2_callus_rep3

source_name: leaf explant-derived callus

value: leaf explant-derived callus


title: dme-2_callus_rep1


title: hag2msi2msi3_20d_RNAseq_rep1


title: dme-2_callus_rep2


title: WT_callus_rep1


title: Col-0_20d_RNAseq_rep1


title: hag2nasp_H4K12Ac_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with H4K12Ac antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: hag2-/- nasp-/-

value: Abcam, ab46983


title: Col-0_H4K12Ac_rep4


title: hag2nasp_H4K12Ac_rep1


title: nasp_H4K12Ac_rep1

tag: cell type

value: nasp-/-


title: nasp_H4K12Ac_rep2


title: Col-0_H4K12Ac_rep3


title: hag2msi2msi3_H4K12Ac_rep2


title: dme-2_de_novo_shoot_rep2


title: nasp_ATACseq_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
ATAC-enriched peaks were called uing MACS2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
The nuclei of 12-day-old Arabidopsis wild type and four mutants were extracted in a nuclear extraction buffer (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 0.3% [v/v] Triton X-100, and 0.1% cocktail, Roche) and resuspended in a nuclear purification buffer (20 mM MOPS pH 7.0, 90 mM KCl, 40 mM NaCl, 2 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.5 mM spermidine, 0.2 mM spermine, and 0.1% cocktail, Roche). The quality of the nuclei was determined under a microscope, followed by Tn5 fragmentation and DNA fragment purification.
Libraries were built for ATAC-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)


title: hag2msi2msi3_H4K12Ac_rep1


title: Col-0_H4K12Ac_rep2


title: hag2nasp_ATACseq_rep2


title: msi2msi3nasp_ATACseq_rep1


title: Col-0_H4K12Ac_rep1


title: hag2nasp_ATACseq_rep1


title: WT_callus_rep2


title: C-3

city: Lanzhou

first: Qiaozhen

last: Zhou

address: No.199 Donggang West Road

department: School/Hospital of Stomatology Lanzhou University

institute: Lanzhou University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) was used for image processing and base identification. The sequencing quality of reads after desarticulation was assessed by FastQC software (cutadapt was used to desarticulate 5‘and  3’ desarticulations). The reference genome was compared by Hisat2 software.
Transcription abundance estimation was performed using StringTie software with reference to official database annotation information. The FPKM at gene level and transcript level was calculated using the R software Ballgown, and the expression differences at gene level and transcript level were calculated respectively, and the genes were differentially expressed between the screened samples or between groups.
New gene/transcript predictions were made using StringTie to assemble, merge, and compare each sample separately with official annotation information, obtained by Ballgown calculation, and new transcripts were predicted using CPAT for encoding capacity.
Variable splicing event detection, difference calculation and mapping using rTMATS.
PCA analysis and correlation analysis based on gene expression level, and further data mining analysis such as clustering of differentially expressed genes, GO functional significance enrichment analysis, Pathway significance enrichment analysis, etc., are completed by custom programs (python/R/shell, etc.).
Assembly: mm10
Supplementary files format and content: processed data

organism: Rattus norvegicus

source_name: Dorsal tongue epithelium

extract_protocol:
Total RNA was extracted and RNA sequencing library was constructed.
The constructed libraries were provided with quality inspection by Aglent 2100, quantitative analysis by qPCR, and sequencing by Ilumina NovaSeq 6000 sequencer.

value: Dorsal tongue epithelium

tag: disease

value: non-periodontitis rat


title: T-1

value: chronic periodontitis rat


title: hag2msi2msi3_ATACseq_rep1

tag: genotype


title: T-3


title: WT_callus_rep3


title: C-2


title: Col-0_ATACseq_rep2


title: Col-0_ATACseq_rep3


title: C-1


title: Col-0_ATACseq_rep1


title: Col-0_ATACseq_rep4


title: T-2


title: hag2msi2msi3_ATACseq_rep2


title: BT408, scRNAseq

city: Montreal

first: Kevin

last: Petrecca

state: Quebec

address: 3801 Rue University

department: Neuro

country: Canada

institute: McGill

description: 10x Genomics

data_processing:
demultiplexing, barcode processing and gene counting was made with CellRanger v3.0.1 and normalization with Seurat v5
Assembly: GRCh38
Supplementary files format and content: Tab-separated format containing gene counts matrices

source_name: Brain, Right temporal

extract_protocol:
1. Weight empty 10cm dish (same that will be used tissue) ex: 18.42g 2. Weight tissue 18.69g 3. Wash tissue 2x with PBS+ antibiotics (PS) 4. Remove necrosis area and blood vessels with scalpels 5. Add 0.5mL digestion buffer and cut tissue in 2 or 3 in order to have ~ 1mm piece 6. Transfer tissue + digestion buffer in 15ml tube 7. Add 0.5ml of digestion buffer and inc 20min in 37C and invert tube few times every hour and Triturate with 1000ul pipette tip few time 8. Leave tissue to be digest o/n at 37C (or until tissue can be dissociate by pipetting ) 9. Centrifuge 1400 rpm for 10min 10. Remove supernatant 11. Add 9ml PBS + PS 12. Resuspend pellet using 5ml pipette 13. Add 21 ml percoll to ultracentrifugation tube, then add 9 ml of cells mix well by inverting tube 14. Centrifuge 15000 rpm 30min 4C (program #2) in Jack Antel’s lab 15. Remove debris from top of tube 16. Transfer cells (middle layer) to 50 ml tube and count cells 17. Filled up to 50ml with PBS+PS 18. Centrifuge 1400 rpm 10min 19. Count cells
Single-cell capture was done following the Single Cell 3’ Reagent Kits v2 User Guide (CG0052 10X Genomics) 1. Briefly, a single cell RNA library was generated using the GemCode Single-Cell Instrument (10X Genomics, Pleasanton, CA, USA) and Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (P/N 120236 P/N 120237 10x Genomics). The sequencing ready libraries were purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin-Elmer) and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824).

value: Brain, Right temporal

value: WT

value: Glioblastoma


title: BT419, scRNAseq

description: 10x Genomics

source_name: Brain, Left temporal

value: Brain, Left temporal


title: BT426, scRNAseq

description: 10x Genomics


title: BT402, scRNAseq

description: 10x Genomics

source_name: Brain, Right frontal, parietal

value: Brain, Right frontal, parietal


title: BT397, scRNAseq

description: 10x Genomics

source_name: Brain, Left frontal

value: Brain, Left frontal


title: msi2msi3nasp_ATACseq_rep2

value: Arabidopsis seedlings


title: nasp_ATACseq_rep1


title: BT407, scRNAseq

description: 10x Genomics

source_name: Brain, Right frontal, temporal

value: Brain, Right frontal, temporal


title: BT420, scRNAseq

description: 10x Genomics

source_name: Brain, Right temporal, insular

value: Brain, Right temporal, insular


title: BT389A, scRNAseq

description: 10x Genomics

source_name: Brain, Right parietal, temporal, occipital


title: BT409, scRNAseq

description: 10x Genomics

source_name: Brain, Right temporal, parietal, occipital


title: BT380, scRNAseq

description: 10x Genomics

source_name: Brain, Right frontal, insular

value: Brain, Right frontal, insular


title: BT396, scRNAseq

description: 10x Genomics

source_name: Brain, Left parietal

value: Brain, Left parietal


title: BT400, scRNAseq

description: 10x Genomics


title: BT389, scRNAseq

description: 10x Genomics

source_name: Brain, Left temporal, insular

value: Brain, Left temporal, insular


title: BT390, scRNAseq

description: 10x Genomics

source_name: Brain, Right temporal, occipital

value: Brain, Right temporal, occipital


title: BT377, scRNAseq

description: 10x Genomics


title: BT373, scRNAseq

description: 10x Genomics


title: BT374, scRNAseq

description: 10x Genomics


title: BT356, scRNAseq

description: 10x Genomics

source_name: Brain, Right Frontal

value: Brain, Right Frontal


title: BT363, scRNAseq

description: 10x Genomics


title: BT368, scRNAseq

description: 10x Genomics


title: D15_3

data_processing: Sequencing reads from each sample were mapped to human reference transcripts (GRCH38) using HISAT2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software (http://cole-trapnell-lab.github.io/cufflinks/, University of Washington) was used to conduct differentially expressed gene (DEG) analysis on the raw count data.

growth_protocol: Cell culture was conducted using immortalized human bronchial epithelial cells (BEAS-2B), which were obtained by ATCC in Manassas, Virginia. Cells were grown in LHC-9 (1x) media and maintained at 37° C in a humidified incubator with 5% CO 2 and 95% air in vented T-75 flasks (Corning).

extract_protocol:
After exposure cells were collected and RNA was extracted using the ZR Duet Kit
The RNA-seq library were prepared using NEBNext® Ultra II RNA Library Prep Kit for Illumina (E7775, NEB) according to manufacturer's instruction.

treatment_protocol: When cells were 95-100% confluent they were seeded in 24well plates and exposed to 800ng/ml - 1500ng/ml of Delta 9 Tetrahydrocannabinol and vehicle for 24hrs.

value: bronchial epithelial cells (BEAS-2B)

value: THC 1500 ng/ml


title: BT364, scRNAseq

description: 10x Genomics

source_name: Brain, Left parietal, occipital

value: Brain, Left parietal, occipital


title: D15_1


title: D12_3

value: THC 1200 ng/ml


title: D10_2

value: THC 1000 ng/ml


title: D8_3

source_name: T800 Rep 3

value: THC 800 ng/ml


title: D15_2


title: D12_2


title: D8_1

source_name: T800 Rep 1


title: D8_2

source_name: T800 Rep 2


title: D10_1


title: D12_1


title: V3

source_name: Vehicle Rep 3

value: Control


title: M3

source_name: Media Rep 3


title: M1

source_name: Media Rep 1


title: M2

source_name: Media Rep 2


title: V2

source_name: Vehicle Rep 2


title: VSMCs, Ctrl-3

city: Zhongshan

first: Jie

last: Sun

state: Guangdong

address: Sun Wendong Road No. 2

department: Department of Cardiology

institute: Zhongshan City People Hospital

data_processing:
The paired-end reads were collected from the Illumina HiSeq 4000 sequencer, and the quality score was set at Q30.
Following 3’ adaptor trimming and poor-quality read exclusion using Cutadapt software, the superior-quality trimmed reads were analyzed to identify lncRNAs. The high-quality reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, Cuffdiff software (v2.2.1, included in Cufflinks) was used to obtain fragments per kilobase of transcript per million mapped reads (FPKM) values to asses lncRNA expression profiles.
Fold changes and p-values were calculated based on FPKM values, and differentially expressed lncRNAs were identified
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: aorta

growth_protocol: Mouse aortic VSMCs were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Mouse aortic VSMCs were collected, and RNA was extracted using the TRIzol reagent. Ribosomal RNA (rRNA) was removed from the total RNA using a Ribo-Zero rRNA removal kit (Illumina, USA).
RNA libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina).

treatment_protocol: Mouse aortic VSMCs were transfected with Myocd knockdown adenoviruses and the negative control viruses for 48 h.

value: vascular smooth muscle cells

value: aorta

value: transfected with negative control ADV

value: control


title: VSMCs, Ctrl-2


title: VSMCs, ADV-3

value: transfected with Myocd knokdown ADV

value: Myocd knockdown


title: VSMCs, Ctrl-1


title: BT369, scRNAseq

description: 10x Genomics

source_name: Brain, Left Temporal

value: Brain, Left Temporal

value: WT

value: Glioblastoma


title: VSMCs, ADV-1


title: D10_3


title: Morula embryo, heat-exposed sperm fertilized, rep 21

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Small RNA: Adaptor sequences were trimmed using trimmomatic and sequenced reads were mapped to small RNAs using Bowtie 2 and totaled using Feature counts. Mapped reads were normalized to parts per million for subsequent analysis. mRNA: Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) with each sheet (tab) containing processed data for each cell type i.e. sperm and embryo

source_name: preimplantation embryo

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit
Sperm pellets were resuspended in lysis buffer supplemented with 33 mM DTT and 0.66 mg/mL Proteinase K and incubated at 60°C for 15 min. After incubation, an equal volume of water and TRIzol was added to each sample. The samples were transferred to phase lock tubes for phase separation and precipitation. Small RNA was purified using denaturing polyacrylamide gel electrophoresis. Single embryos were collected into 1 x TCL buffer with 1% beta-mercaptoethanol and stored at -80°C prior to sequencing. At time of sequencing embryos were further lysed in fresh lysis buffer and RNA was captured using RNA Clean XP beads.
For sperm samples - Illumina Tru-seq Small RNA Library Preparation Kit and single embryo samples - Nextera XT kit (Illumina)

treatment_protocol: Adult (8-12 wk old) male mice were randomly assigned to control sham or heat exposure group. Experimental animals were exposed to increased ambient temperature in an animal intensive care unit for 7 days, using a cycle of 35°C for 8 h and 25°C for 16 h. Sham control animals were housed in identical conditions in the intensive care unit set ata constant temperature of 21°C. Mice were sacrificed on the morning of Day 8 for collection of tissues.

value: preimplantation embryo

tag: developmental stage

value: Morula

value: heat-exposed sperm fertilized embryo


title: Morula embryo, heat-exposed sperm fertilized, rep 20


title: VSMCs, ADV-2


title: Morula embryo, heat-exposed sperm fertilized, rep 19


title: Morula embryo, heat-exposed sperm fertilized, rep 16


title: Morula embryo, heat-exposed sperm fertilized, rep 14


title: V1

source_name: Vehicle Rep 1

value: bronchial epithelial cells (BEAS-2B)


title: Morula embryo, heat-exposed sperm fertilized, rep 10


title: Morula embryo, heat-exposed sperm fertilized, rep 8


title: Morula embryo, heat-exposed sperm fertilized, rep 5


title: Morula embryo, heat-exposed sperm fertilized, rep 12


title: Morula embryo, heat-exposed sperm fertilized, rep 6


title: Morula embryo, heat-exposed sperm fertilized, rep 13


title: Morula embryo, heat-exposed sperm fertilized, rep 9


title: Morula embryo, heat-exposed sperm fertilized, rep 1


title: Morula embryo, heat-exposed sperm fertilized, rep 18


title: Morula embryo, heat-exposed sperm fertilized, rep 3


title: Morula embryo, control sperm fertilized, rep 22

value: control-sperm fertilized embryo


title: Morula embryo, control sperm fertilized, rep 21


title: Morula embryo, control sperm fertilized, rep 20


title: Morula embryo, heat-exposed sperm fertilized, rep 2


title: Morula embryo, control sperm fertilized, rep 19


title: Morula embryo, control sperm fertilized, rep 18


title: Morula embryo, control sperm fertilized, rep 17


title: Morula embryo, heat-exposed sperm fertilized, rep 17


title: Morula embryo, control sperm fertilized, rep 16


title: Morula embryo, control sperm fertilized, rep 13


title: Morula embryo, control sperm fertilized, rep 14


title: Morula embryo, heat-exposed sperm fertilized, rep 15


title: Morula embryo, heat-exposed sperm fertilized, rep 11


title: Morula embryo, control sperm fertilized, rep 12


title: Morula embryo, control sperm fertilized, rep 11


title: Morula embryo, heat-exposed sperm fertilized, rep 4


title: Morula embryo, heat-exposed sperm fertilized, rep 7


title: Morula embryo, control sperm fertilized, rep 6


title: Morula embryo, control sperm fertilized, rep 9


title: Morula embryo, control sperm fertilized, rep 10


title: Morula embryo, control sperm fertilized, rep 8


title: Morula embryo, control sperm fertilized, rep 2


title: Morula embryo, control sperm fertilized, rep 7


title: Morula embryo, control sperm fertilized, rep 4


title: 4-cell embryo, heat-exposed sperm fertilized, rep 17


title: 4-cell embryo, heat-exposed sperm fertilized, rep 13


title: 4-cell embryo, heat-exposed sperm fertilized, rep 16


title: 4-cell embryo, heat-exposed sperm fertilized, rep 12


title: 4-cell embryo, heat-exposed sperm fertilized, rep 15


title: 4-cell embryo, heat-exposed sperm fertilized, rep 18


title: 4-cell embryo, heat-exposed sperm fertilized, rep 11


title: Morula embryo, control sperm fertilized, rep 15


title: 4-cell embryo, heat-exposed sperm fertilized, rep 10


title: 4-cell embryo, heat-exposed sperm fertilized, rep 8


title: 4-cell embryo, heat-exposed sperm fertilized, rep 7


title: 4-cell embryo, heat-exposed sperm fertilized, rep 9


title: 4-cell embryo, heat-exposed sperm fertilized, rep 6


title: 4-cell embryo, control sperm fertilized, rep 16


title: 4-cell embryo, heat-exposed sperm fertilized, rep 5


title: Morula embryo, control sperm fertilized, rep 3


title: 4-cell embryo, heat-exposed sperm fertilized, rep 1


title: Morula embryo, control sperm fertilized, rep 5


title: 4-cell embryo, heat-exposed sperm fertilized, rep 3


title: 4-cell embryo, heat-exposed sperm fertilized, rep 2


title: 4-cell embryo, control sperm fertilized, rep 15


title: Morula embryo, control sperm fertilized, rep 1


title: 4-cell embryo, control sperm fertilized, rep 12


title: 4-cell embryo, control sperm fertilized, rep 9


title: 4-cell embryo, control sperm fertilized, rep 10


title: 4-cell embryo, control sperm fertilized, rep 8


title: 4-cell embryo, control sperm fertilized, rep 6


title: 4-cell embryo, control sperm fertilized, rep 3


title: 4-cell embryo, control sperm fertilized, rep 5


title: 4-cell embryo, control sperm fertilized, rep 4


title: 4-cell embryo, control sperm fertilized, rep 7


title: 4-cell embryo, heat-exposed sperm fertilized, rep 4


title: 4-cell embryo, control sperm fertilized, rep 2


title: cauda sperm, heat-exposed, rep 3

data_processing:
For each small RNA library, reads were mapped to rRNAs, miRbase, murine tRNAs, piRNA clusters, to Repeatmasker, and Refseq using Bowtie 2.
Small RNA: Adaptor sequences were trimmed using trimmomatic and sequenced reads were mapped to small RNAs using Bowtie 2 and totaled using Feature counts. Mapped reads were normalized to parts per million for subsequent analysis. mRNA: Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) with each sheet (tab) containing processed data for each cell type i.e. sperm and embryo

source_name: sperm

extract_protocol:
Total RNA was extracted from sperm samples and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Tru-seq Small RNA Library
Sperm pellets were resuspended in lysis buffer supplemented with 33 mM DTT and 0.66 mg/mL Proteinase K and incubated at 60°C for 15 min. After incubation, an equal volume of water and TRIzol was added to each sample. The samples were transferred to phase lock tubes for phase separation and precipitation. Small RNA was purified using denaturing polyacrylamide gel electrophoresis. Single embryos were collected into 1 x TCL buffer with 1% beta-mercaptoethanol and stored at -80°C prior to sequencing. At time of sequencing embryos were further lysed in fresh lysis buffer and RNA was captured using RNA Clean XP beads.
For sperm samples - Illumina Tru-seq Small RNA Library Preparation Kit and single embryo samples - Nextera XT kit (Illumina)

value: sperm

value: heat-exposed


title: cauda sperm, heat-exposed, rep 2


title: cauda sperm, sham, rep 2


title: cauda sperm, heat-exposed, rep 1


title: cauda sperm, sham, rep 3


title: 4-cell embryo, control sperm fertilized, rep 13


title: cauda sperm, sham, rep 1


title: ML336_EIDD1931_0uM_1_HTB7385_M21

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

description: TC-83 nsP2-4

data_processing:
Basecalling was done using Nanopore Guppy (ver. 5.1.12)
Sequencing reads were checked for read quality and de-multiplexed using 9 nt-long barcode sequence plus adjacent 10 nt primer sequence
Reads were aligned to Venezuelan equine encephalitis virus genome L01443.1 using Minimap2 (version 2.17-r941)
VCF for each sample was generated by SAMtools mpileup function using mapped BAM file.
Assembly: L01443.1
Supplementary files format and content: vcf format

organism: Venezuelan equine encephalitis virus (strain TC-83)

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.

value: 1uM ML336 + DMSO


title: 4-cell embryo, control sperm fertilized, rep 1


title: ML336_EIDD1931_0uM_1_HTB7386_A1

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7385_H14

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7385_F17

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7385_A7

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7385_C12

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_O6

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_O12

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7385_A3

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_O11

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_H2

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_J18

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_F3

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_A9

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_A15

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7379_A18

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7379_G4

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7378_O5

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7378_J9

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7378_O2

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7378_A5

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7378_A15

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_P23

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_H16

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_A6

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_A12

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_O17

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_O14

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_P11

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7379_K6

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_N19

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_E15

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7377_L13

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_L10

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_G17

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_G4

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_I20

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7379_A14

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_N10

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_K8

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_G12

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_E9

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_D3

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_C3

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_B15

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_K20

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_B11

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_O19

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_J20

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_A20

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_P11

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_O17

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_O15

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_O4

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_N16

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_M14

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_J10

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_I10

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_H7

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_D9

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7093_A5

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_L19

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_L14

description: TC-83 nsP2-4


title: 4-cell embryo, heat-exposed sperm fertilized, rep 14


title: EIDD1931_50uM_3_HTB7092_E4

description: TC-83 nsP2-4