title: dsIsPDIA6_Rep3

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

data_processing:
RNA-seq raw data were trimmed and aligned to the tick genome using HISAT2.
The aligned reads were then quantified and normalized by dividing the gene counts by the total number of reads followed by the addition of a small offset (0.0001).
The counts generated from three biological replicates each treatment were processed by DESeq2.
Assembly: IscaW1
Supplementary files format and content: tab-delimited text files include baseMean for each gene

organism: Ixodes scapularis

source_name: Gut

extract_protocol:
Tick gut was dissected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gut

tag: genotype

value: needle injected with IsPDIA6


title: Caco-2/15-Z2flag Postconfluent cells IP H2A.Z Exp2

status: Public on Oct 14 2024

type: SRA

city: TOULOUSE

first: Didier

last: Trouche

address: Université Toulouse III Paul Sabatier - Bât 4R4, 118 route de Narbonne

country: France

institute: Centre for Integrative Biology (CBI) of Toulouse MCD

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg38 human genome using BWA and processed (sorting, PCR duplicates, minimum quality of 25 and indexing).
BigWig were obtained using Deeptools with exactScaling parameters and CPM normalization
Peaks were called uing MACS with the significance cut-off q-value <=0.001
Assembly: hg38 human genome
Supplementary files format and content: narrowPeak,bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: Intestinal epithelium

growth_protocol: Samples were prepared in duplicates from subconfluent (Sc) or 7 days post-confluent (Pc) populations of Caco-2/15 cells expressing flagged version of H2A.Z.1 or H2A.Z.2 isoform.

extract_protocol: For ChIP-seq experiments, Caco-2/15 cells expressing Flag-H2AZ.1 and Flag-H2AZ.2, 100 mg of chromatin supplemented with 10 ng of Spike-in chromatin (Active Motif) were used per ChIP experiment. For each reaction, 4 µg of Flag M2 antibody (Sigma) and 1 µg of Spike-in antibody (Active Motif), were used. About 10 ng of immunoprecipated DNA (quantified with quantiFluor dsDNA system, Promega) were obtained at each time, and samples were submitted to EMBL-GeneCore Heidelberg for sequencing, that was performed by Illumina’s NextSeq 500 technology (single-end, 85 bp reads). The quality of each raw sequencing file was verified with FastQC.

tag: tissue

value: Intestinal epithelium

tag: cell line

value: Caco-2/15 cells

tag: cell type

value: colon cancer cells

value: heterozygous H2AFV-Flag

tag: treatment

value: 7-days postconfluence

tag: chip antibody

value: anti-H2A.Z (Active Motif #39113)


title: RNAseq_auxin_2h_rep1

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

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

library_source: transcriptomic

data_processing:
Adaptor sequences were removed using Trim Galore and reads shorter than 20 nucleotides were discarded. Reads were then mapped to mouse (mm10) genome with STAR-RSEM pipeline using ENSEMBL version 79 gene annotation as reference.
Differential gene expression was determined using DESeq2. Genes with log2(fold change) > 1.5 and q value < 0.05 were considered significantly different.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include normalized count values from DESeq2.

molecule: total RNA

organism: Mus musculus

growth_protocol: mESCs were cultured on gelatin-coated plates in DMEM high-glucose media supplemented with 15% FBS, 1 × GlutaMAX, 1 × nonessential amino acids, 1 × sodium pyruvate, 0.1 mM 2-mercaptoethanol, 3 μM CHIR99021，1 μM PD0325901 and 1,000 U/mL leukemia inhibitory factor (LIF).

extract_protocol:
Total RNAs were extracted with RNA Purification Kit PLUS (EZBioscience). mRNA was purified and used for the construction of sequencing libraries.
RNA sequencing libraries were constructed by using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01/02) according to the manufacturer’s instructions.

treatment_protocol: To induce DDX10 degradation, indole-3-acetic acid (IAA) was added to the medium at a final concentration of 500 μM.

value: embryonic stem cells

value: Ddx10-AID, Tir1

value: auxin-induced degradation of DDX10 2 h


title: CD4_Perturb-CITE-seq_CSP_07

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

country: USA

institute: UCSF Gladstone Institutes

data_processing:
Fastqs for each 10X well were concatenated across lanes and flow cells.
Alignment of perturb-seq data and count aggregation for the gene expression, CRISPR guide, and Antibody Derived Tag (ADT) libraries was performed with cellranger54 count (v7.1.0) using the default settings and –expect-cells=45000 –chemistry=SC5P-R2.
Gene expression fastqs were aligned to “refdata-gex-GRCh38- 2020-A” human transcriptome reference acquired from 10x Genomics. Guide sequences were aligned to a custom reference file using the pattern TAGCTCTTAAAC(BC) while ADTs were aligned to the TotalSeq-C-Human-Universal-Cocktail-399905-Antibody-reference-UMI-counting.csv provided by Biolegend, also including the hashtag oligo (HTO) sequences which were used to distinguish each cell type and stimulation condition.
Counts for each respective library were aggregated across wells with cellranger aggr using the default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes provided from cellranger after aggregation sourced from filtered_feature_bc_matrix
Supplementary files format and content: features provided from cellranger after aggregation sourced from filtered_feature_bc_matrix
Supplementary files format and content: Matrix provided from cellranger after aggregation sourced from filtered_feature_bc_matrix
Supplementary files format and content: sgrna calls per cell output from cellranger
Library strategy: Perturb-CITE-seq

source_name: Lymphocyte

growth_protocol: CD4+ regulatory and effector T cells were isolated from fresh Peripheral Blood Leukopaks (STEMCELL Technologies, #70500) from healthy human donors, after institutional review board–approved informed written consent (STEMCELL Technologies). The contents of the Leukopaks were washed twice with a 1X volume of EasySep buffer (DPBS, 2% fetal Bovine Serum (FBS), 1mM pH 8.0 EDTA) using centrifugation. The washed cells were resuspended at 200E6 cells/mL in EasySep buffer and isolated with the EasySep™ Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, #18063), according to the manufacturer’s protocol. Following isolation with the kit, Tregs were stained Alexa Fluor® 647 anti-human CD25 Antibody (Biolegend, #302618), PE anti-Human CD127 (Beckon Dickinson, #557938), and Pacific Blue™ anti-human CD4 Antibody (Biolegend, #344620) and isolated using FACS to ensure a pure population without contaminating effector cells. After sorting pure CD4+CD127lowCD25+ Regulatory T Cells, the cells were seeded at 1x106 cells/mL in XVIVO-15 (Lonza, #02-053Q) supplemented with 55 uM 2-mercaptoethanol, 4 mM N-acetyl L-cysteine, and 200 U/mL IL-2 (Amerisource Bergen, #10101641). Teffs were seeded at 1x106 cells/mL in RPMI-1640 supplemented with 10% FCS, 2 mM L-Glutamine (Fisher Scientific #25030081), 10 mM HEPES (Sigma, #H0887-100ML), 1X MEM Non-essential Amino Acids (Fisher, #11140050), 1 mM Sodium Pyruvate (Fisher Scientific #11360070), 100 U/mL Penicillin-Streptomycin (Sigma, #P4333-100ML), and 50 U/mL IL-2 (Amerisource Bergen, #10101641). Both cell subsets were then stimulated with ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990) at 25 uL/mL for Tregs and 6.25 uL/mL for Teff. Following activation and electroporation, cells were split 1:2 every 48 hours to maintain an approximate density of 1x106 cells/mL and supplemented with respective doses of IL-2.

extract_protocol:
On the 10th day after initial isolation, the samples were collected for 10X single cell sequencing. First, cells from each donor within the same stimulation and cell type condition were pooled at equal concentrations. Sorting was performed to isolate live GFP+ cells from each condition. Sorted cells were processed according to the Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening and Cell Surface Protein guide User Guide, CG000513. In brief, sorted cells were pelleted and washed once with Cell Staining Buffer (Biolegend, #420201). Next, the samples were blocked with Human TruStain FcX™ Fc Blocking reagent (Biolegend, #422302). Meanwhile, TotalSeq™-C Human Universal Cocktail V1.0 (Biolegend, #399905) was prepared using Cell Staining Buffer (Biolegend, #420201) and TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661) were added to aliquots of the cocktail. HTOs were added to label the following populations: Treg Resting-1, Treg Stimulated- 2, Teff Resting-3, Teff Stimulated- 4. After blocking, cells were stained with TotalSeq-C cocktail including one Hashtag per cell and stimulation condition. After staining, the cells were washed three times in Cell Staining Buffer. The samples were then resuspended in PBS with 1% BSA (Gibco) for final counting. The resulting samples were pooled across conditions and approximately 65,000 cells per well were loaded into 8 wells of a Chromium Next GEM Chip N Single Cell Kit (10X Genomics, #1000375) for GEM generation.
The samples were prepared for sequencing using the Chromium Next GEM Single Cell 5' HT Kit v2 (#1000374), 5' Feature Barcode Kit, (#1000256), and 5' CRISPR Kit (#1000451) according to the manufacturer’s protocol. GEM generation and library preparation was performed by the Gladstone Genomics Core. The resulting libraries were sequenced using a NovaSeqX Series 10B flowcell (Illumina, #20085595) at the UCSF CAT.

treatment_protocol: 24 hours after stimulation of isolated human Tregs and Teffs from 2 donors, the cells were transduced with Zim3-dCas9 lentivirus at 3% v/v. The following day, Perturb-seq guide library lentivirus was added at 0.75% v/v (MOI 0.3). 48 hours after transduction with Zim3-dCas9, 10 mg/ml blasticidin (Gibco, #A1113903) was added to each sample to select for dCas9+ cells. Blasticidin was replenished every 48 hours until the cells were processed for sequencing. 8 days after initial isolation and stimulation of cells, half of the Treg and Teff culture was restimulated with ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990).

value: Lymphocyte

value: CD4+ T cells

tag: adt

tag: hto

tag: kit

value: 5' Feature Barcode Kit, (#1000256)

tag: library type

value: CSP

tag: lane


title: dsIsPDIA6_Rep2


title: dsIsPDIA6_Rep1


title: dsGFP_Rep3

value: GFP (control)

value: needle injected with dsGFP


title: CD4_Perturb-CITE-seq_CSP_06

value: TotalSeq™-C Human Universal Cocktail V1.0 (Biolegend, #399905)

value: TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661)


title: RNAseq_untreated_rep1

value: auxin-induced degradation of DDX10 0 h


title: Caco-2/15-Z2flag Postconfluent cells IP Flag Exp2

value: Intestinal epithelium

value: Caco-2/15 cells

value: anti-Flag M2 (Sigma #F3165)


title: CD4_Perturb-CITE-seq_CSP_05


title: WTT_3

city: Taipei

first: Yijuang

last: Chern

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
Sequencing data and FASTQ reads were generated using an inhouse Welgene ’Biotech pipeline according to Illumina’s base calling program bcl2fastq v2.20.
The expression levels of mRNA were normalized in fragments per kilobase of transcript per million mapped reads (FPKM) by Welgene Biotech Co. (Welgene).
The selection criteria for DE mRNAs were FC > 1.25 and p < 0.05.
We next categorized the DEGs by their enriched cell type based on the Brain RNA-seq database (DOI: 10.1523/JNEUROSCI.1860-14.2014).
HISAT2
Genome_build: GRCm38
Supplementary_files_format_and_content: mRNA_Gene_Count.xlsx: Excel file includes mRNA gene counts for all Samples.
Supplementary_files_format_and_content: mRNA_Gene_FPKM.xlsx: Excel file includes FPKM values for all Samples.
Supplementary_files_format_and_content: R6_2C_vs_R6_2T_neuron-enriched_differentially_expressed_mRNA.txt: Tab-delimited text file includes FPKM values for R6/2C vs. R6/2T neuron-enriched differentially expressed mRNAs.

source_name: Striatum

growth_protocol: R6/2 mice (B6CBA-Tg(HDexon1)62Gpb/3J) were obtained from Jackson Laboratory (Bar Harbor, ME, USA) and mated with female control mice (B6CBAFI/J). Mice were housed at the Institute of Biomedical Sciences (IBMS) Animal Care Facility (Academia Sinica, Taipei, Taiwan) under a standard 12 hr light/dark cycle. Animal experiments were performed under approved protocols by the Academia Sinica Institutional Animal Care and Utilization Committee (Taipei, Taiwan).

extract_protocol:
RNA was extracted by TRIzol reagent or miRNeasy mini kit (Qiagen). DNase digestion was performed by the DNA-free™ Kit (Life Technologies, Carlsbad, CA, USA) or the RNase-free DNase set (Qiagen) following the manufacturer’s instructions. The concentration and purity of RNA were measured at 260, 280 and 230 nm by a NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA).
Library construction was carried out by TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA) followed by AMPure XP beads (Beckman Coulter, Brea, CA, USA) size selection.

treatment_protocol: For the bilateral intrastriatal delivery of AAV expressing control or TRAX shRNA, mice were anesthetized with ketamine/xylazine HCl (87.56 and 7.5 ug/kg, respectively, via an intraperitoneal injection) and injected with the indicated AAV (2 µl per injection spot, 2.5*10^9 vector genome/µl) with a 10 ml syringe (Hamilton, Reno, NV, USA) at a rate of 0.5 ul/min. The AAV was injected at the desired position: AP+0.5, L±2, DV-2.5 and -3.5 mm relative to bregma and the dura surface. Then the mouse brains were removed from the mice directly for dissection of striatum.

tag: strain

value: WT

tag: shRNA

value: shTRAX

value: Striatum

tag: age

value: 10.5 weeks


title: Caco-2/15-Z1flag Subconfluent cells IP H2A.Z Exp2

value: colon cancer cells

value: heterozygous H2AFZ-Flag

value: Subconfluence

value: anti-H2A.Z (Active Motif #39113)


title: Caco-2/15-Z1flag Subconfluent cells IP Flag Exp2


title: dsGFP_Rep2

value: Gut


title: WTT_1


title: CD4_Perturb-CITE-seq_CSP_03

value: Lymphocyte

value: CD4+ T cells

value: 5' Feature Barcode Kit, (#1000256)

value: CSP


title: dsGFP_Rep1

value: GFP (control)

value: needle injected with dsGFP


title: WTT_2


title: brain, Sham01

city: Changchun

first: Daoyu

last: Zhang

address: Xinzhu street 1977

institute: Jilin University

data_processing:
We used STAR (https://github.com/alexdobin/STAR/archive/2.7.3a.tar.gz) to compare transcriptome data and cuffLinks (http://cole-trapnell-lab.github.io/cufflinks/) for quantitative splicing.
Assembly: hg38
Supplementary files format and content: the processed data files include TPM value for each sample

organism: Rattus norvegicus

source_name: rat brain

extract_protocol:
Total RNA was extracted with a kit(Qiagen),Concentration ≥30ng/μl, total amount ≥0.8μg, RIN≥5.8
Smart-Seq2 method was used to amplify each sample according to the manufacturer’s instructions.

treatment_protocol: Rats were randomly divided into three groups. Sham group: rats received surgery without MCAO; MCAO group (IR group): rats were subjected to MCAO; MCAO+NMN group (IR+NMN group): rats were subjected to MCAO and injected with 100 mg/kg NMN (Selleck, USA) in saline.

value: rat brain

tag: group

value: control

value: PBS


title: RNAseq_untreated_rep2

value: embryonic stem cells

value: Ddx10-AID, Tir1

value: auxin-induced degradation of DDX10 0 h


title: CD4_Perturb-CITE-seq_CSP_02

value: TotalSeq™-C Human Universal Cocktail V1.0 (Biolegend, #399905)

value: TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661)


title: mixed blood stages, N67C, rep 5

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

data_processing:
Trim with Cutadapt v4.7
Map with STAR. v2.7.10b
Generate counts with RSEM v1.3.3
Differential expression with DESeq2
Assembly: P. yoelii yoelii N67C, PRJNA694977
Supplementary files format and content: raw counts matrix for all genes

organism: Plasmodium yoelii yoelii

source_name: Mixed blood stages

growth_protocol: Blood samples (200 ml) with approximately 30 ~ 40% parasitemia containing similar proportions of blood-stage parasites (ring, trophozoite, and schizont) were collected on day 4 after IP injection of mice with 1 × 106 iRBCs.

extract_protocol:
iRBCs after NWF filter treatment were placed in RNA-later, and total RNAs were extracted using the Direct-zol™ RNA MiniPrep (Zymo Research) following the manufacturer's protocol
Five hundred nanograms of the total RNA was used to prepare the sequencing library using Illumina TruSeq Stranded mRNA library prep kits.

treatment_protocol: Briefly, iRBCs in 1 ml of 1.5 % sodium citrate/0.9% sodium chloride buffer were centrifuged at 500g for 5 min, resuspended in 1 ml PBS, and passed through two consecutive NWF filters (Zhixing Bio, Bengbu, China) to remove white blood cells

value: Mixed blood stages


title: Caco-2/15-Z1flag Postconfluent cells IP H2A.Z Exp2

value: Intestinal epithelium

value: Caco-2/15 cells

value: colon cancer cells

value: heterozygous H2AFZ-Flag

value: 7-days postconfluence

value: anti-H2A.Z (Active Motif #39113)


title: mixed blood stages, N67C, rep 4


title: WTC_3

value: WT

value: Control

value: Striatum

value: 10.5 weeks


title: Caco-2/15-Z1flag Postconfluent cells IP Flag Exp2

value: anti-Flag M2 (Sigma #F3165)


title: CD4_Perturb-CITE-seq_CSP_01

value: Lymphocyte

value: CD4+ T cells

value: 5' Feature Barcode Kit, (#1000256)

value: CSP


title: Caco-2/15-Z2flag Subconfluent cells IP H2A.Z Exp1

value: heterozygous H2AFV-Flag

value: Subconfluence


title: CD4_Perturb-CITE-seq_CRISPR_08

value: TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661)

value: CRISPR


title: mixed blood stages, N67C, rep 3

value: Mixed blood stages


title: WTC_1


title: CD4_Perturb-CITE-seq_CRISPR_07


title: Caco-2/15-Z2flag Subconfluent cells IP Flag Exp1

value: Intestinal epithelium

value: Caco-2/15 cells

value: colon cancer cells


title: Caco-2/15-Z2flag Postconfluent cells IP H2A.Z Exp1

value: 7-days postconfluence

value: anti-H2A.Z (Active Motif #39113)


title: CD4_Perturb-CITE-seq_CSP_04

value: TotalSeq™-C Human Universal Cocktail V1.0 (Biolegend, #399905)


title: R6_2T_3

value: shTRAX

value: Striatum

value: 10.5 weeks


title: mixed blood stages, N67C, rep 2


title: R6_2T_2


title: CD4_Perturb-CITE-seq_CRISPR_05

value: Lymphocyte

value: CD4+ T cells


title: mixed blood stages, N67, rep 4


title: CD4_Perturb-CITE-seq_CRISPR_06


title: Control,ATAC,rep2

city: Shanghai

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

description:
Control.bowtie2_aln.sorted.bigwig
Control_peaks.narrowPeak
ATAC_peak_counts.xlsx

data_processing:
Raw fastq files were filtered and trimmed with fastp (v 0.22.0)
The filtered reads were aligned to the GRCm38 reference genome with Bowtie2(2.5.0)
Peak calling was performed using MACS2 (2.2.7.1) with the following parameters: --nomodel -s 1 --shift 75 --extsize 150 -q 0.01  -f BAMPE.
For track visualization, bigwig files were generated using deeptools(v 3.5.1) subcommand bamCoverage and normalized using FPKM.
Reads fall in peak regions were counted with bedtools(v 2.30.0).
Assembly: GRCm38
Supplementary files format and content: bigwig files for track visulization
Supplementary files format and content: NarrowPeak file
Supplementary files format and content: Read counts fall in peak regions

source_name: HT

growth_protocol: Tumor cells were cultured in RPMI-1640 supplemented with 10% Fetal bovine serum (Wisent) and 1x Penicillin-Streptomycin.

extract_protocol:
1x10^4 cells were used as for nucleus isolation and Tn5 tagmention. Tagmented DNA was amplified by PCR using the Illumina sequencing adapters as primers.
ATAC-Seq library were generated using Vazyme Hyperactive ATAC-Seq Library Prep Kit for Illumina following manufacturer's instruction.

value: HT

value: Pancreatic cancer cells

value: sgControl


title: R6_2C_3

value: Control


title: R6_2C_2


title: R6_2T_1


title: CD4_Perturb-CITE-seq_CRISPR_03

value: TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661)

value: CRISPR


title: Caco-2/15-Z2flag Postconfluent cells IP Flag Exp1

value: Intestinal epithelium

value: heterozygous H2AFV-Flag

value: anti-Flag M2 (Sigma #F3165)


title: mixed blood stages, N67C, rep 1

value: Mixed blood stages


title: Caco-2/15-Z1flag Subconfluent cells IP Flag Exp1

value: Caco-2/15 cells

value: colon cancer cells

value: heterozygous H2AFZ-Flag

value: Subconfluence


title: Caco-2/15-Z1flag Subconfluent cells IP H2A.Z Exp1

value: anti-H2A.Z (Active Motif #39113)


title: mixed blood stages, N67, rep 5


title: CD4_Perturb-CITE-seq_CRISPR_04

value: Lymphocyte


title: mixed blood stages, N67, rep 3


title: mixed blood stages, N67, rep 2


title: R6_2C_1

value: Striatum

value: 10.5 weeks


title: mixed blood stages, N67, rep 1


title: Caco-2/15-Z1flag Postconfluent cells IP Flag Exp1

value: 7-days postconfluence


title: CD4_Perturb-CITE-seq_CRISPR_01

value: CD4+ T cells


title: H9C2_M1-null rep2

status: Public on Oct 13 2024

city: Guangzhou

first: Tailai

last: Du

state: Guangdong

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

institute: Sun Yat-sen University

description:
Cas2b
H9C2-M1-null-RNA_raw_counts

data_processing:
For RNA-seq data analysis, the sequencing data was filtered with cutadapt. The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) or rat genome (Rattus_norvegicus.Rnor_6.0) using STAR or HISAT2, respectively. Expression level of gene was calculated by featureCounts and StringTie, respectively. The raw counts were then analyzed using DESeq2.
For Ribo-seq data analysis, the Ribo-seq raw data underwent adapter trimming and low-quality sequence filtering using cutadapt, followed by rRNA sequence removal using bowtie. Subsequently, the clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using STAR. Then ORF analysis and ORF counts analysis were conducted using RiboCode.
For TRAC-seq data analysis, following adapter trimming and quality filtering, the clean sequencing data were initially aligned to the tRNA sequences using Bowtie2. Subsequently, read counts for each tRNA were calculated using the method described in (Cozen et al., 2015).
Assembly: Mus_musculus.GRCm38; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: txt;raw counts

growth_protocol: H9C2 cardiomyocytes were cultured in DMEM high-glucose medium (Gibco) containing 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNAs were isolated using Trizol Reagent from H9C2 cardiomyocytes and tissue samples. Small RNAs (<200 nt) were initially purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
RNA libraries were constructed following the protocols provided by Illumina and MGISEQ. For Ribo-seq, libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina NovaSeq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: A line of genome-edited H9C2 cardiomyocytes was generated by CRISPR-Cas9, introducing a frameshift mutation to abolish the translation of Mettl1 protein. H9C2 cardiomyocytes with normal expression of Mettl1 were used as control.

value: Sprague-Dawley


title: H9C2_M1-null rep3

description:
Cas2c
H9C2-M1-null-RNA_raw_counts


title: SG2

first: lianyu

last: lin

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

description: Treatment with heat stress, Biological Replicate 2

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the Luffa aegyptiaca reference genome using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on the Luffa aegyptiaca reference genome annotations was determined using stringtie (v2.0) with the default parameter settings.
FPKM were calculated for representing the expression of each gene.
Assembly: Luffa aegyptiaca reference genome
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

organism: Luffa aegyptiaca

source_name: tissue

extract_protocol:
Total RNA was extracted from selected tissues using a plant-specific RNA extraction kit, ensuring minimal degradation and contamination. We then performed quality assessment of the isolated RNA with a bioanalyzer to confirm integrity and purity.
Following DNase treatment to eliminate any genomic DNA contamination, we synthesized cDNA using a high-fidelity reverse transcriptase and carried out second-strand synthesis to obtain double-stranded cDNA. The cDNA was processed through end repair, A-tailing, and adapter ligation to prepare it for size selection.
We selected cDNA fragments of an optimal size range and amplified them using PCR to create a library suitable for next-generation sequencing. The library was quantified and validated for quality and size distribution before being sequenced on an Illumina platform.

value: tissue


title: SG1

description: Treatment with heat stress, Biological Replicate 1


title: WTC_2

value: WT

value: Control


title: SG-CK1

description: Control sample, Biological Replicate 1


title: CD4_Perturb-CITE-seq_CRISPR_02

value: TotalSeq™-C0251 anti-human Hashtag Antibodies 1-4 (Biolegend, #394661)

value: CRISPR


title: Caco-2/15-Z1flag Postconfluent cells IP H2A.Z Exp1

value: Intestinal epithelium


title: SG-CK2

description: Control sample, Biological Replicate 2


title: H9C2_WT rep1

description:
Ctrl1
H9C2-M1-null-RNA_raw_counts


title: H9C2_WT rep2

description:
Ctrl2
H9C2-M1-null-RNA_raw_counts


title: VM04831590133R

first: Bingxue

state: China Mainland (PRC)

address: Guangzhou 510700

institute: Vision MedicalsCo., Ltd.

description: counts.txt for all RNA-Seq samples

data_processing:
Fastp removed low-quality, duplicate, <50 bp reads, and adapter contamination. Human sequences were excluded by mapping to the hg38 human genome using BWA, while ribosomal RNA was removed with SortMERNA v4.3.721
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes raw per-gene counts for each sample.

source_name: BALF

extract_protocol:
RNA extraction was carried out using a Direct-zol RNA Miniprep Kit (Zymo Research, USA), followed by the manufacturer's instructions
Library preparation was done using 10 μL of purified RNA with the Ovation Trio RNA-Seq Library Preparation Kit

value: BALF

value: nonARDS


title: 20220226MCX022R

description: counts.txt for all RNA-Seq samples


title: VM04831590195R

description: counts.txt for all RNA-Seq samples


title: 20220125MCX016R

description: counts.txt for all RNA-Seq samples


title: VM04831590147R

description: counts.txt for all RNA-Seq samples


title: H9C2_WT rep3

description:
Ctrl3
H9C2-M1-null-RNA_raw_counts


title: VM04831590292R

description: counts.txt for all RNA-Seq samples


title: H9C2_M1-null rep1

description:
Cas2a
H9C2-M1-null-RNA_raw_counts


title: 20220224MCX009R

description: counts.txt for all RNA-Seq samples


title: 20220115MCX010R

description: counts.txt for all RNA-Seq samples


title: 20220215MCX018R

description: counts.txt for all RNA-Seq samples


title: 220406MCX00012R

description: counts.txt for all RNA-Seq samples


title: 20220210MCX017R

description: counts.txt for all RNA-Seq samples


title: 20220118MCX016R

description: counts.txt for all RNA-Seq samples


title: 20211221MCX010R

description: counts.txt for all RNA-Seq samples


title: 20211218MCX005R

description: counts.txt for all RNA-Seq samples


title: 20211130MCX014R

description: counts.txt for all RNA-Seq samples


title: 20220112MCX018R

description: counts.txt for all RNA-Seq samples


title: 20211230MCX012R

description: counts.txt for all RNA-Seq samples


title: 20211224MCX012R

description: counts.txt for all RNA-Seq samples


title: 20211208MCX015R

description: counts.txt for all RNA-Seq samples


title: 20211117MCX015R

description: counts.txt for all RNA-Seq samples


title: 20211119MCX007R

description: counts.txt for all RNA-Seq samples


title: 20211125MCX009R

description: counts.txt for all RNA-Seq samples


title: 20211112MCX014R

description: counts.txt for all RNA-Seq samples


title: VM04831380050R

description: counts.txt for all RNA-Seq samples


title: 20211022MCX013R

description: counts.txt for all RNA-Seq samples


title: 20210923MCX014R

description: counts.txt for all RNA-Seq samples


title: 20210915MCX009R

description: counts.txt for all RNA-Seq samples


title: 20210907MCX019R

description: counts.txt for all RNA-Seq samples


title: 20211229MCX017R

description: counts.txt for all RNA-Seq samples


title: 20210915MCX007R

description: counts.txt for all RNA-Seq samples


title: Soya-2_S11_L001

city: Mysore

first: Gopinath

last: Meenakshisundaram

state: Karnataka

address: Cheluvamba Mansion

department: Molecular Nutrition

country: India

institute: Central Food Technological Research Institute

data_processing:
Processing small RNA seq data involves quality control, adapter removal, alignment to a reference, annotation, and quantification. Differential expression analysis identifies changes, and miRNA tools uncover known and novel miRNAs. Normalization corrects biases, and visualization aids exploration. Functional analysis offers biological insights, validated by methods like qRT-PCR. Integration with other omics data and a comprehensive report conclude the process.
Assembly: not applicable
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel files include normalised values for each Sample

organism: Glycine max

source_name: exosome-like nanovesicle (ENV)

extract_protocol:
ENVs were isolated from soy bean, ginger, amla and turmeric using a cost effective Polyethylene glycol- based (PEG) precipitation method developed in our lab (Kalarikkal et al., Scientific Reports, 2020). In brief, edible portion of plants were ground in phosphate buffered saline (PBS) using a kitchen mixer. In the case of Soybeans, they were soaked in PBS for overnight prior to grinding. Aqueous extracts were subjected to three rounds of centrifugation at 1200g for 20 min (remove cells/nuclei), 3000g for 20 min and 10,000g for 45 min (remove fibers and insoluble contents). This is known as S10 extract (crude extracellular extract). To purify ENVs, S10 extract was subjected precipitation with 10% PEG-6000, overnight followed by centrifugation at 10000g for 30 min. ENV pellets are suspended in sterile water and stored at -80 in aliqouts. ENVs were quantified by measuring the lipids by vanillin assay. Total RNA was isolated from two independent batches of ENVs (5mg lipid equivalent) for each plant by TRI RNA extraction reagent (Sigma Aldrich) as per manufacturers protocol.
1 μg of total RNA was subjected to library preparation

value: exosome-like nanovesicle (ENV)


title: 20210904MCX008R

description: counts.txt for all RNA-Seq samples


title: Soya-1_S1_L001


title: LLC LeptoM, Floating, R2

city: New York

first: Xinran

last: Tong

state: NY

address: 417 E 68th St

department: HOPP

institute: MSKCC

data_processing:
FASTQ files are mapped to the target genome using the STAR aligner that maps to map reads twice.
We then compute the expression count matrix from the mapped reads using HTSeq.
The raw count matrix generated by HTSeq are then be processed by DESeq.
Assembly: UCSC MM10
Supplementary files format and content: raw counts for each sample

source_name: Leptomeningeal metastasis

growth_protocol: LLC LeptoM was maintained in DMEM high glucose, 4T1 LeptoM was maintained in RPMI media. Both were supplemented with 10% fetal bovine serum, penicillin/streptavidin, Glutamax media in humidified chamber with 5% CO2 at 37C

extract_protocol:
RNA was isolated with Qiagen RNeasy Micro Kit.
RNA libraries were prepared using SMARTER mRNA-seq Library Prep Kit.

treatment_protocol: 20,000 LLC LeptoM mCherry cells were injected into the leptomeningeal space through cisternal magna, 25,000 LLC LeptoM mCherry cells were injected into lung parenchyma. 5,000 4T1 LeptoM mCherry cells were injected into the leptomeningeal space through cisternal magna, 50,000 4T1 LeptoM mCherry cells were injected into mammary fat pad. Tumor cells were harvested 2 weeks post injection by enzyme cocktail and flow sorted for downstream.

value: Leptomeningeal metastasis

value: LLC LeptoM

value: Mouse lung cancer derived leptomeningeal metastatic cells


title: 20210820MCX015R

description: counts.txt for all RNA-Seq samples


title: 20210813MCX011R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM, Floating, R1


title: 20210810MCX012R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM, Adherent, R1


title: 20210902MCX005R

description: counts.txt for all RNA-Seq samples


title: 20210726MCX012R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM, Lung, R2

source_name: Lung

value: Lung


title: LLC LeptoM, Adherent, R2


title: LLC LeptoM, Adherent, R3


title: 20210719MCX005R

description: counts.txt for all RNA-Seq samples


title: 20210716MCX019R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM, Lung, R1


title: 20210709MCX011R

description: counts.txt for all RNA-Seq samples


title: PA_HEART_7

city: Tallahassee

first: Evan

last: Lloyd

state: FL

address: 107 Chieftain Way

institute: Florida State University

data_processing:
sequences were trimmed to remove adapter sequences and low-quality reads (>10% missing bases)
sequences were mapped to Astyanax mexicanus reference genome (version 2.0, GenBank Accession Number: GCA_000372685.2) using the splice-aware mapper STAR  to generate raw counts.
Assembly: GCA_000372685.2
Supplementary files format and content: .csv files include raw counts for each sample

organism: Astyanax mexicanus

source_name: heart

extract_protocol:
To extract RNA, 1 ml of TRIzol was added to each sample. Samples were homogenized, and then 200μl chloroform was added to each tube, followed by vigorous shaking. Samples were incubated on ice for 15 min, then phase separated by centrifuging at 12,000 g for 15 min at 4°C. The resulting aqueous phase of the liquid was transferred to a fresh 1.5 ml tube, and then RNA was precipitated out by mixing with 0.5 ml isopropanol. Samples were incubated on ice for 10 min, then centrifuged at 12,000 g for 10 min at 4°C. The supernatant was removed by pouring and lightly shaking the tube, then the resulting pellet was washed by the addition of 1 ml 70% EtOH while vigorously flicking the tube. The samples were then centrifuged at 7500 g for 10 min at 4°C. The supernatant was removed by pouring and lightly shaking the tube, and the samples were air dried upside down for 10 min. Finally, the pellet was redissolved in 100ul of RNAse-free H 2 O.
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: heart

value: Cave morph

value: aged (7-8 years)


title: PA_HEART_8


title: 20210924MCX011R

description: counts.txt for all RNA-Seq samples


title: 20210705MCX013R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM, Floating, R3


title: PA_HEART_6


title: PA_HEART_5


title: PA_HEART_4

value: young (~1 year)


title: PA_HEART_2


title: 20210625MCX010R

description: counts.txt for all RNA-Seq samples


title: PA_HEART_3


title: LLC LeptoM, Lung, R3


title: 20210617MCX008R

description: counts.txt for all RNA-Seq samples


title: 20210622MCX005R

description: counts.txt for all RNA-Seq samples


title: 20210612MCX012R

description: counts.txt for all RNA-Seq samples


title: SF_HEART_8

value: Surface morph


title: 20210619MCX013R

description: counts.txt for all RNA-Seq samples


title: 20210609MCX005R

description: counts.txt for all RNA-Seq samples


title: 20210601MCX013R

description: counts.txt for all RNA-Seq samples


title: 20210601MCX009R

description: counts.txt for all RNA-Seq samples


title: 20210420MCX005R

description: counts.txt for all RNA-Seq samples


title: SF_HEART_4


title: SF_HEART_6


title: 20210409MCX016R

description: counts.txt for all RNA-Seq samples


title: SF_HEART_7


title: SF_HEART_2


title: 20210401MCX008R

description: counts.txt for all RNA-Seq samples


title: 20210318MCX014R

description: counts.txt for all RNA-Seq samples


title: 20210703MCX010R

description: counts.txt for all RNA-Seq samples


title: SF_HEART_1


title: PA_GUT_8

source_name: gut

value: gut


title: 20210313MCX003R

description: counts.txt for all RNA-Seq samples


title: PA_HEART_1


title: 20210227MCX003R

description: counts.txt for all RNA-Seq samples


title: 2234031591673R

description: counts.txt for all RNA-Seq samples


title: PA_GUT_6


title: PA_GUT_7


title: PA_GUT_3


title: PA_GUT_4


title: 20210514MCX011R

description: counts.txt for all RNA-Seq samples


title: 2234031381410R

description: counts.txt for all RNA-Seq samples


title: PA_GUT_5


title: SF_HEART_5


title: PA_GUT_1


title: 2234031591734R

description: counts.txt for all RNA-Seq samples


title: 2234031381199R

description: counts.txt for all RNA-Seq samples


title: 2234031043417R

description: counts.txt for all RNA-Seq samples


title: 2234031380246R

description: counts.txt for all RNA-Seq samples


title: SF_GUT_6


title: 2180931075839R

description: counts.txt for all RNA-Seq samples


title: SF_HEART_3


title: SF_GUT_4


title: 2234031042878R

description: counts.txt for all RNA-Seq samples


title: SF_GUT_7


title: 2126131075965R

description: counts.txt for all RNA-Seq samples


title: 2126131074609R

description: counts.txt for all RNA-Seq samples


title: SF_GUT_3


title: 2126131074517R

description: counts.txt for all RNA-Seq samples


title: SF_GUT_5


title: 2098331074676R

description: counts.txt for all RNA-Seq samples


title: SF_GUT_1


title: PA_GUT_2


title: SF_GUT_2


title: 2098331072139R

description: counts.txt for all RNA-Seq samples


title: 2078131076230R

description: counts.txt for all RNA-Seq samples


title: 2067931070548R

description: counts.txt for all RNA-Seq samples


title: PA_MUSCLE_6

source_name: muscle

value: muscle


title: PA_MUSCLE_5


title: PA_MUSCLE_8


title: PA_MUSCLE_4


title: VM04831590272R

description: counts.txt for all RNA-Seq samples

value: ARDS


title: PA_MUSCLE_2


title: VM04831590220R

description: counts.txt for all RNA-Seq samples


title: PA_MUSCLE_3


title: VM04831590231R

description: counts.txt for all RNA-Seq samples


title: VM04831590208R

description: counts.txt for all RNA-Seq samples


title: 2067931071859R

description: counts.txt for all RNA-Seq samples


title: VM04831590265R

description: counts.txt for all RNA-Seq samples


title: SF_MUSCLE_8


title: SF_MUSCLE_6


title: VM04831590171R

description: counts.txt for all RNA-Seq samples


title: VM04831590191R

description: counts.txt for all RNA-Seq samples


title: SF_MUSCLE_5


title: SF_MUSCLE_4


title: VM04831590149R

description: counts.txt for all RNA-Seq samples


title: 2067931072207R

description: counts.txt for all RNA-Seq samples


title: SF_MUSCLE_3


title: SF_MUSCLE_2


title: VM04831590120R

description: counts.txt for all RNA-Seq samples


title: VM04831590116R

description: counts.txt for all RNA-Seq samples


title: PA_MUSCLE_7


title: VM04831590255R

description: counts.txt for all RNA-Seq samples


title: VM04831590100R

description: counts.txt for all RNA-Seq samples


title: PA_LIVER_8

source_name: liver

value: liver


title: VM04831590065R

description: counts.txt for all RNA-Seq samples


title: PA_MUSCLE_1


title: PA_LIVER_7


title: VM04831590048R

description: counts.txt for all RNA-Seq samples


title: PA_LIVER_6


title: SF_MUSCLE_7


title: VM04831590040R

description: counts.txt for all RNA-Seq samples


title: VM04831590006R

description: counts.txt for all RNA-Seq samples


title: PA_LIVER_1


title: VM04831380176R

description: counts.txt for all RNA-Seq samples


title: PA_LIVER_3


title: PA_LIVER_5


title: VM04831590003R

description: counts.txt for all RNA-Seq samples


title: PA_LIVER_4


title: PA_LIVER_2


title: SF_LIVER_7


title: VM04831380111R

description: counts.txt for all RNA-Seq samples


title: VM04831380135R

description: counts.txt for all RNA-Seq samples


title: SF_LIVER_8


title: VM04831380100R

description: counts.txt for all RNA-Seq samples


title: VM04831380054R

description: counts.txt for all RNA-Seq samples


title: SF_LIVER_4


title: VM04831380096R

description: counts.txt for all RNA-Seq samples


title: SF_LIVER_6


title: SF_LIVER_3


title: VM04831590014R

description: counts.txt for all RNA-Seq samples


title: VM04831380002R

description: counts.txt for all RNA-Seq samples


title: 2234031591987R

description: counts.txt for all RNA-Seq samples


title: SF_LIVER_5


title: SF_MUSCLE_1


title: SF_LIVER_1


title: 2234031591758R

description: counts.txt for all RNA-Seq samples


title: VM04831380031R

description: counts.txt for all RNA-Seq samples


title: PA_BRAIN_7

source_name: brain

value: brain


title: 2234031591888R

description: counts.txt for all RNA-Seq samples

value: BALF


title: 2234031590416R

description: counts.txt for all RNA-Seq samples


title: PA_BRAIN_8


title: PA_BRAIN_3


title: PA_BRAIN_6


title: VM04831380001R

description: counts.txt for all RNA-Seq samples


title: SF_LIVER_2


title: PA_BRAIN_4


title: 2234031591239R

description: counts.txt for all RNA-Seq samples


title: PA_BRAIN_2


title: 2234031590133R

description: counts.txt for all RNA-Seq samples


title: 2234031590578R

description: counts.txt for all RNA-Seq samples


title: 2234031381984R

description: counts.txt for all RNA-Seq samples


title: SF_BRAIN_8


title: 2234031381977R

description: counts.txt for all RNA-Seq samples


title: 2234031382189R

description: counts.txt for all RNA-Seq samples


title: SF_BRAIN_6


title: 2234031381496R

description: counts.txt for all RNA-Seq samples


title: SF_BRAIN_4


title: SF_BRAIN_5


title: 2234031381182R

description: counts.txt for all RNA-Seq samples


title: SF_BRAIN_2


title: 2234031381434R

description: counts.txt for all RNA-Seq samples


title: 2234031381090R

description: counts.txt for all RNA-Seq samples


title: 2234031381175R

description: counts.txt for all RNA-Seq samples


title: SF_BRAIN_1


title: SF_BRAIN_3


title: 2234031043684R

description: counts.txt for all RNA-Seq samples


title: 2234031380239R

description: counts.txt for all RNA-Seq samples


title: PA_X_2

data_processing:
sequences were trimmed to remove adapter sequences and low-quality reads (>10% missing bases)
sequences were mapped to Astyanax mexicanus reference genome (version 2.0, GenBank Accession Number: GCA_000372685.2) using the splice-aware mapper STAR  to generate raw counts.
Assembly: GCA_000372685.2
Supplementary files format and content: .csv file includes raw counts for each sample

source_name: Whole body

treatment_protocol: fish were treated with exposure to 60 seconds UV-B radiation, or a white light control. 90 minutes after treatment, fish were pooled in groups of 4 and RNA was extracted.

value: Whole body

value: Pachon cave morph

value: 60 seconds UV-B


title: PA_X_1


title: PA_X_4


title: PA_CTRL_4

value: White light control


title: 2234031043387R

description: counts.txt for all RNA-Seq samples


title: 2234031043202R

description: counts.txt for all RNA-Seq samples


title: PA_CTRL_3


title: 2234031042632R

description: counts.txt for all RNA-Seq samples


title: PA_CTRL_2


title: 2234031042625R

description: counts.txt for all RNA-Seq samples


title: SF_X_4


title: 2180931075891R

description: counts.txt for all RNA-Seq samples


title: 2180931075761R

description: counts.txt for all RNA-Seq samples


title: PA_BRAIN_1


title: SF_X_2


title: 2234031380376R

description: counts.txt for all RNA-Seq samples


title: 2180931075310R

description: counts.txt for all RNA-Seq samples


title: SF_X_3


title: 2180931075020R

description: counts.txt for all RNA-Seq samples


title: SF_CTRL_2


title: SF_X_1


title: SF_CTRL_4


title: SF_CTRL_3


title: 2180931073859R

description: counts.txt for all RNA-Seq samples


title: SF_CTRL_1


title: 2180931072982R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 11 wph, biol rep 3

city: Kobe

first: Chika

last: Takahashi

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

country: Japan

institute: RIKEN

data_processing:
The quality check of raw sequencing data was performed using FastQC v0.11.8.
The raw data were processed using Trim-galore v0.6.4.
The processed reads were mapped to N. furzeri reference genome Nfu_20140520 using HISAT2 2.1.0.
The mapped reads were counted using featurecounts v.1.5.3.
Assembly: Nfu_20140520
Supplementary files format and content: tab-delimited text file including raw counts for each Sample
Supplementary files format and content: tab-delimited text file including TPM values for each Sample

organism: Nothobranchius furzeri

source_name: ovary of single-housed males at 11 wph

extract_protocol:
Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific), and subjected to DNase treatment with a TURBO DNA-free kit　(Invitrogen #AM1907) according to the manufacturer’s instructions.
For whole juvenile fish and livers, the libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490), NEBNext Ultra II Directional RNA Library Prep Kit (E7760), NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440). For ovaries and testes, the libraries were prepared using TruSeq stranded mRNA Library (Illumina, CA, USA).

value: ovary of single-housed males at 11 wph


title: ovary, single, male, 11 wph, biol rep 2


title: 2180931072470R

description: counts.txt for all RNA-Seq samples


title: 2126131075644R

description: counts.txt for all RNA-Seq samples


title: 2126131075897R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 8 wph, biol rep 3

source_name: ovary of single-housed males at 8 wph

value: ovary of single-housed males at 8 wph


title: 2126131074982R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 11 wph, biol rep 1


title: SF_BRAIN_7


title: ovary, single, male, 8 wph, biol rep 2


title: 2126131074869R

description: counts.txt for all RNA-Seq samples


title: 2180931075303R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 8 wph, biol rep 1


title: 2126131073794R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 5 wph, biol rep 2

source_name: ovary of single-housed males at 5 wph

value: ovary of single-housed males at 5 wph


title: 2126131073602R

description: counts.txt for all RNA-Seq samples


title: 2126131073633R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 5 wph, biol rep 1


title: 2126131072582R

description: counts.txt for all RNA-Seq samples


title: 2126131072544R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 3 wph, biol rep 3

source_name: ovary of single-housed males at 3 wph

value: ovary of single-housed males at 3 wph


title: ovary, group, male, 11 wph, biol rep 3

source_name: ovary of group-housed males at 11 wph

value: ovary of group-housed males at 11 wph


title: 2126131075941R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 3 wph, biol rep 2


title: ovary, single, male, 5 wph, biol rep 3


title: 2126131072360R

description: counts.txt for all RNA-Seq samples


title: ovary, single, male, 3 wph, biol rep 1


title: 2126131072353R

description: counts.txt for all RNA-Seq samples


title: ovary, group, male, 11 wph, biol rep 1


title: ovary, group, male, 11 wph, biol rep 2


title: 2126131070786R

description: counts.txt for all RNA-Seq samples


title: ovary, group, male, 10 wph, biol rep 3

source_name: ovary of group-housed males at 10 wph

value: ovary of group-housed males at 10 wph


title: 2117831077953R

description: counts.txt for all RNA-Seq samples


title: ovary, group, male, 10 wph, biol rep 2


title: 2117831074051R

description: counts.txt for all RNA-Seq samples


title: 2117831074044R

description: counts.txt for all RNA-Seq samples


title: ovary, group, male, 8 wph, biol rep 3

source_name: ovary of group-housed males at 8 wph

value: ovary of group-housed males at 8 wph


title: 2117831073597R

description: counts.txt for all RNA-Seq samples

source_name: BALF


title: ovary, group, male, 8 wph, biol rep 2


title: ovary, group, male, 8 wph, biol rep 1


title: 2117831072330R

description: counts.txt for all RNA-Seq samples


title: 2117831071494R

description: counts.txt for all RNA-Seq samples


title: 2126131072377R

description: counts.txt for all RNA-Seq samples


title: ovary, group, male, 5 wph, biol rep 3

source_name: ovary of group-housed males at 5 wph

value: ovary of group-housed males at 5 wph


title: ovary, group, male, 5 wph, biol rep 1


title: ovary, group, male, 5 wph, biol rep 2


title: 2098331079992R

description: counts.txt for all RNA-Seq samples


title: 2098331077714R

description: counts.txt for all RNA-Seq samples


title: 2126131070687R

description: counts.txt for all RNA-Seq samples


title: 2098331076601R

description: counts.txt for all RNA-Seq samples


title: 2098331079718R

description: counts.txt for all RNA-Seq samples


title: testis, single, male, 8 wph, biol rep 3

source_name: testis of single-housed males at 8 wph

value: testis of single-housed males at 8 wph


title: testis, single, male, 11 wph, biol rep 1

source_name: testis of single-housed males at 11 wph

value: testis of single-housed males at 11 wph


title: 2098331078681R

description: counts.txt for all RNA-Seq samples

value: ARDS


title: testis, single, male, 11 wph, biol rep 2


title: ovary, group, male, 10 wph, biol rep 1


title: 2098331075291R

description: counts.txt for all RNA-Seq samples


title: testis, single, male, 8 wph, biol rep 2


title: testis, single, male, 8 wph, biol rep 1


title: testis, single, male, 5 wph, biol rep 3

source_name: testis of single-housed males at 5 wph

value: testis of single-housed males at 5 wph


title: 2098331073211R

description: counts.txt for all RNA-Seq samples

value: BALF


title: 2117831073528R

description: counts.txt for all RNA-Seq samples


title: 2098331074980R

description: counts.txt for all RNA-Seq samples


title: testis, single, male, 5 wph, biol rep 2


title: 2098331072931R

description: counts.txt for all RNA-Seq samples


title: testis, single, male, 3 wph, biol rep 2

source_name: testis of single-housed males at 3 wph

value: testis of single-housed males at 3 wph


title: testis, single, male, 3 wph, biol rep 1


title: 2098331071439R

description: counts.txt for all RNA-Seq samples


title: testis, single, male, 11 wph, biol rep 3


title: 2098331071484R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 11 wph, biol rep 3

source_name: testis of group-housed males at 11 wph

value: testis of group-housed males at 11 wph


title: testis, group, male, 11 wph, biol rep 2


title: 2078131075080R

description: counts.txt for all RNA-Seq samples


title: 2098331071248R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 11 wph, biol rep 1


title: testis, group, male, 10 wph, biol rep 3

source_name: testis of group-housed males at 10 wph

value: testis of group-housed males at 10 wph


title: 2078131073314R

description: counts.txt for all RNA-Seq samples


title: 2078131073345R

description: counts.txt for all RNA-Seq samples


title: 2098331074997R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 10 wph, biol rep 1


title: 2098331074706R

description: counts.txt for all RNA-Seq samples


title: 2078131073215R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 10 wph, biol rep 2


title: testis, group, male, 8 wph, biol rep 3

source_name: testis of group-housed males at 8 wph

value: testis of group-housed males at 8 wph


title: testis, single, male, 5 wph, biol rep 1


title: 2078131073239R

description: counts.txt for all RNA-Seq samples


title: 2078131073055R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 8 wph, biol rep 2


title: 2078131073000R

description: counts.txt for all RNA-Seq samples


title: testis, group, male, 8 wph, biol rep 1


title: 2078131072980R

description: counts.txt for all RNA-Seq samples


title: BBN-NUMB_KO shLuc rep1

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

data_processing:
Sequenced raw reads were processed with NF-CORE RNASeq pipeline, using the human GRCh38 and mouse GRCm39 as reference genomes. Transcript abundances were quantified using the Salmon pseudo-aligner.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text file containing Salmon gene-level quantification for each sample, including feature length, effective length, TPM, and number of reads.

source_name: urothelial bladder cancer

extract_protocol:
Total RNA was extracted with QIAzol™ Reagent and then purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Gold kit according to the manufacturer’s protocol

value: urothelial bladder cancer

value: shLuc


title: BBN-NUMB_KO shCyr61/Ctgf rep1


title: BBN-NUMB_KO ROCKi rep2

value: ROCKi


title: testis, group, male, 5 wph, biol rep 3

source_name: testis of group-housed males at 5 wph

value: testis of group-housed males at 5 wph


title: testis, group, male, 5 wph, biol rep 2


title: 2078131072881R

description: counts.txt for all RNA-Seq samples


title: 2078131072959R

description: counts.txt for all RNA-Seq samples


title: BBN-NUMB_KO ROCKi rep1


title: 2078131072850R

description: counts.txt for all RNA-Seq samples


title: BBN-NUMB_KO Vehicle_ROCKi rep1

value: vehicle


title: testis, group, male, 5 wph, biol rep 1


title: MBO-NUMB_KO Verteporfin rep1

source_name: mouse bladder organoids

value: mouse bladder organoids

value: Verteporfin


title: liver, single, male, 14 wph, biol rep 10

source_name: liver of single-housed males at 14 wph

value: liver of single-housed males at 14 wph


title: MBO-NUMB_KO Vehicle rep1


title: 2078131072799R

description: counts.txt for all RNA-Seq samples


title: MBO-NUMB_KO ROCKi rep1


title: liver, single, male, 14 wph, biol rep 9


title: MBO-NUMB_KO rep6


title: 2078131072720R

description: counts.txt for all RNA-Seq samples


title: MBO-NUMB_KO rep4


title: 2078131072560R

description: counts.txt for all RNA-Seq samples


title: MBO-NUMB_KO rep5


title: liver, single, male, 14 wph, biol rep 8


title: MBO-NUMB_KO rep1


title: MBO-NUMB_KO rep3


title: liver, single, male, 14 wph, biol rep 7


title: BBN-NUMB_KO Vehicle_ROCKi rep2


title: MBO-NUMB_WT rep6


title: liver, single, male, 14 wph, biol rep 6


title: MBO-NUMB_WT rep5


title: 2078131072539R

description: counts.txt for all RNA-Seq samples


title: liver, single, male, 14 wph, biol rep 5


title: 2078131072522R

description: counts.txt for all RNA-Seq samples


title: 2078131072386R

description: counts.txt for all RNA-Seq samples


title: MBO-NUMB_WT rep2


title: 2078131072379R

description: counts.txt for all RNA-Seq samples


title: MBO-NUMB_WT rep4


title: MBO-NUMB_WT rep3


title: CX01, WT, rep1, scRNAseq

city: Boston

first: Danilo

last: Pellin

state: MA

address: 300 Longwood Ave

institute: Boston Childrens Hospital

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (v4.0). First, the cellranger mkfastq command was used to demultiplex the raw BCL files into FASTQ files. Next, the cellranger count command was used to align reads to the reference genome, generate feature-barcode matrices, and assign reads to individual cells using the cell barcodes and UMIs.
Assembly: mm10
Supplementary files format and content: Tab-separated files and matrix files

molecule: polyA RNA

source_name: CNS

extract_protocol:
GFP+ and GFP- cells were sorted from the Lin- pool isolated from Cx3cr1-/+ mice using the BD FACSAria II high speed cell sorter. Collected cells were freshly transplanted IV into busulfan (4 doses 25mg/kg) conditioned CD45.1 recipients at a 1:1 donor/recipient ratio.
The single-cell RNA-seq library was prepared using the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit (v3.1). Briefly, a single-cell suspension was loaded onto the Chromium Controller to encapsulate individual cells in Gel Bead-in-Emulsions (GEMs), where reverse transcription of mRNA occurred. Each cell was labeled with a unique cell barcode, and transcripts were tagged with Unique Molecular Identifiers (UMIs). After cDNA amplification, libraries were constructed by fragmentation, adapter ligation, and indexing. The final libraries were sequenced on an Illumina platform to generate paired-end reads.

value: CNS

value: Microglia-like cell


title: CX01, Het, rep1, scRNAseq

description: 10X Genomics


title: 2078131072133R

description: counts.txt for all RNA-Seq samples

value: ARDS


title: 4T1 LeptoM ATAC, Floating, R2

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files scaled by the size factors from DESeq2 normalization of the raw counts matrix.
Assembly: UCSC MM10
Supplementary files format and content: normalized bigwigs

source_name: Leptomeningeal metastasis

extract_protocol:
OMNI-ATAC protocol and ATAC-seq library preparation was performed as described in (Corces et al, 2017) without any modification.
Libraries were prepared for sequencing using standard Illumina protocols

value: Leptomeningeal metastasis

value: 4T1 LeptoM

value: Mouse breast cancer derived leptomeningeal metastatic cells

value: WT


title: 2078131072225R

description: counts.txt for all RNA-Seq samples

value: BALF


title: MBO-NUMB_KO rep2


title: 4T1 LeptoM ATAC, Floating, R3


title: 4T1 LeptoM ATAC, Floating, R1


title: liver, single, male, 14 wph, biol rep 2


title: liver, single, male, 14 wph, biol rep 3


title: liver, single, male, 14 wph, biol rep 1


title: 4T1 LeptoM ATAC, Adherent, R3


title: 2078131072126R

description: counts.txt for all RNA-Seq samples


title: 4T1 LeptoM ATAC, Adherent, R2


title: liver, group, male, 14 wph, biol rep 9

source_name: liver of group-housed males at 14 wph

value: liver of group-housed males at 14 wph


title: 4T1 LeptoM ATAC, Adherent, R1


title: liver, group, male, 14 wph, biol rep 8


title: 2078131072089R

description: counts.txt for all RNA-Seq samples


title: 4T1 LeptoM ATAC, MFP, R1

source_name: MFP

value: MFP


title: 4T1 LeptoM ATAC, MFP, R2


title: 2078131071945R

description: counts.txt for all RNA-Seq samples

source_name: BALF


title: liver, single, male, 14 wph, biol rep 4


title: MBO-NUMB_WT rep1


title: LLC LeptoM ATAC, Floating, R3

value: LLC LeptoM

value: Mouse lung cancer derived leptomeningeal metastatic cells


title: LLC LeptoM ATAC, Floating, R1


title: LLC LeptoM ATAC, Adherent, R3


title: 2078131071938R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM ATAC, Floating, R2


title: liver, group, male, 14 wph, biol rep 7


title: LLC LeptoM ATAC, Adherent, R2


title: 2078131071662R

description: counts.txt for all RNA-Seq samples


title: LLC LeptoM ATAC, Adherent, R1


title: LLC LeptoM ATAC, Lung, R3

source_name: Lung

value: Lung


title: LLC LeptoM ATAC, Lung, R2


title: liver, group, male, 14 wph, biol rep 5


title: 2078131071495R

description: counts.txt for all RNA-Seq samples


title: 2078131071471R

description: counts.txt for all RNA-Seq samples


title: RXRTKO_RA-R2

source_name: in vitro

growth_protocol: LLC LeptoM was maintained in DMEM high glucose supplemented with 10% fetal bovine serum, penicillin/streptavidin, Glutamax media in humidified chamber with 5% CO2 at 37C

extract_protocol:
RNA was isolated with Qiagen RNeasy Mini Kit.
RNA libraries were prepared using SMARTER mRNA-seq Library Prep Kit.

treatment_protocol: 20,000 LLC LeptoM vector control, Nr1h2/3 DKO and RXRα/β/γ were seeded into 6 well plate with DMEM complete media and treated with DMSO or 1μM 9 cis-RA one day after seeding. After treatment for 48hrs, cells were harvested with RNA lysis buffer and further processing for sequencing.

value: in vitro

value: RXRa/b/g triple knockout (TKO)

value: 1μM 9 cis-RA


title: liver, group, male, 14 wph, biol rep 3


title: RXRTKO_RA-R1


title: liver, group, male, 14 wph, biol rep 2


title: RXRTKO_RA-R3


title: 2078131071440R

description: counts.txt for all RNA-Seq samples


title: RXRTKO_DMSO-R3

value: DMSO


title: RXRTKO_DMSO-R2


title: LXRDKO_RA-R3

value: Nr1h2/3 double knockout (DKO)


title: RXRTKO_DMSO-R1


title: liver, group, male, 14 wph, biol rep 6


title: 2078131071709R

description: counts.txt for all RNA-Seq samples


title: LXRDKO_RA-R1


title: liver, single, male, 7 wph, biol rep 10

source_name: liver of single-housed males at 7 wph

value: liver of single-housed males at 7 wph


title: 2078131071327R

description: counts.txt for all RNA-Seq samples

value: ARDS


title: liver, single, male, 7 wph, biol rep 9


title: 2078131070436R

description: counts.txt for all RNA-Seq samples


title: LXRDKO_RA-R2


title: liver, group, male, 14 wph, biol rep 4


title: LXRDKO_DMSO-R3


title: LLC LeptoM ATAC, Lung, R1


title: liver, single, male, 7 wph, biol rep 8


title: LXRDKO_DMSO-R2


title: liver, single, male, 7 wph, biol rep 7


title: 2078131070320R

description: counts.txt for all RNA-Seq samples


title: 2078131070085R

description: counts.txt for all RNA-Seq samples


title: ctrl_RA-R1

value: vector control


title: ctrl_RA-R3


title: liver, group, male, 14 wph, biol rep 1


title: liver, single, male, 7 wph, biol rep 6


title: 2078131070016R

description: counts.txt for all RNA-Seq samples


title: ctrl_DMSO-R3


title: 2078131071389R

description: counts.txt for all RNA-Seq samples


title: ctrl_DMSO-R1


title: 2067931074041R

description: counts.txt for all RNA-Seq samples


title: liver, single, male, 7 wph, biol rep 5


title: 4T1 LeptoM, Floating, R3

value: Leptomeningeal metastasis

value: 4T1 LeptoM


title: 4T1 LeptoM, Floating, R2

value: Mouse breast cancer derived leptomeningeal metastatic cells

value: WT


title: liver, single, male, 7 wph, biol rep 4


title: 2067931073587R

description: counts.txt for all RNA-Seq samples

value: BALF


title: 2067931073792R

description: counts.txt for all RNA-Seq samples


title: 4T1 LeptoM, Adherent, R1


title: ctrl_DMSO-R2


title: liver, single, male, 7 wph, biol rep 2


title: 4T1 LeptoM, Adherent, R2


title: 4T1 LeptoM, MFP, R3

value: MFP


title: liver, single, male, 7 wph, biol rep 3


title: 4T1 LeptoM, Adherent, R3


title: 2067931071880R

description: counts.txt for all RNA-Seq samples


title: 4T1 LeptoM, MFP, R1


title: LXRDKO_DMSO-R1

value: LLC LeptoM


title: 4T1 LeptoM, MFP, R2


title: 2067931071743R

description: counts.txt for all RNA-Seq samples


title: liver, group, male, 7 wph, biol rep 10

source_name: liver of group-housed males at 7 wph

value: liver of group-housed males at 7 wph


title: liver, single, male, 7 wph, biol rep 1


title: oocytes from knock-out mice-6month-sample3

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-ko6m-3

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA), And R
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters.
Trimmed reads were mapped to the reference genome mus musculus mm10 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using mm10 assembly and GENCODE Genes- release M25.
Assembly: mm10
Supplementary files format and content: txt file with deseq2 normalised values for each sample

source_name: Ovary

extract_protocol:
RNA is extracted by RLT and ethanol precipitation
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014) and  miRNA sequencing was performed as per the Hagemann et al 2018 protocol

value: Ovary

value: oocytes


title: liver, group, male, 7 wph, biol rep 9


title: oocytes from knock-out mice-6month-sample2

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-ko6m-2


title: oocytes from knock-out mice-6month-sample1

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-ko6m-1


title: 4T1 LeptoM, Floating, R1


title: oocytes from wild type mice-6month-sample11

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-11


title: liver, group, male, 7 wph, biol rep 8


title: liver, group, male, 7 wph, biol rep 7


title: oocytes from wild type mice-6month-sample10

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-10


title: oocytes from wild type mice-6month-sample9

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-9


title: 2067931072429R

description: counts.txt for all RNA-Seq samples


title: oocytes from wild type mice-6month-sample8

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-8


title: oocytes from knock-out mice-6month-sample4

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-ko6m-4


title: liver, group, male, 7 wph, biol rep 6


title: oocytes from wild type mice-6month-sample7

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-7


title: oocytes from wild type mice-6month-sample6

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-6


title: liver, group, male, 7 wph, biol rep 5


title: oocytes from wild type mice-6month-sample3

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-3


title: liver, group, male, 7 wph, biol rep 4


title: oocytes from wild type mice-6month-sample5

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-5


title: Hepatoblastoma, LCM-5, Fetal, rep2

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were aligned to the human reference genome with STAR and read counts were obtained using featureCounts (Subread).
Assembly: GRCh38 3.0.0
Supplementary files format and content: Comma-separated values file of non-normalized raw read counts from all samples

source_name: Liver

extract_protocol:
Fresh sections of formalin-fixed paraffin-embedded tumor blocks were cut on a microtome at 7 micron thickness and mounted on glass slides with polyethylene naphthalate membranes and stored in a nitrogen chamber. In preparation for laser capture microdissection, slides were immersed sequentially for 20 seconds each in xylenes (three times), 100% ethanol (three times), 95% ethanol (two times), 70% ethanol (two times), water, hematoxylin, water, bluing reagent, water, 70% ethanol (two times), 95% ethanol (two times), 100% ethanol (three times), and xylenes (three times). Immediately after staining, cells were dissected on an ArcturusXT LCM System using the ultraviolet (UV) laser to cut the sample and the infrared laser to adhere it to a CapSure HS LCM Cap. Roughly 500 cells were captured by area, based on density estimates by cell counting on small areas. After LCM, the cap was sealed in a 0.5 mL tube and stored at −80°C until library preparation.
The Smart-3SEQ protocol is available here: https://genome.cshlp.org/content/suppl/2019/10/24/gr.234807.118.DC1/Supplemental_File_2.pdf. Sequencing libraries were prepared using the Smart-3SEQ protocol for FFPE tissue on an Arcturus LCM HS cap, with the pre-SPRI pooling option and a single batch for all samples. Libraries were characterized immediately and stored at −20°C until sequencing.
Sequencing was performed on the pooled library using the NextSeq 500/550 High Output V2 kit with 75 cycles (read 1: 76 cycles, index 1: 2bp, index 2: 8bp)

value: Liver

tag: Sex

value: F

value: Treated

tag: disease state

value: Hepatoblastoma


title: Hepatoblastoma, LCM-4, Embryonal, rep2

value: M


title: 2067931070982R

description: counts.txt for all RNA-Seq samples

tag: genotype

value: ARDS


title: oocytes from wild type mice-6month-sample1

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-1

tag: tissue


title: liver, group, male, 7 wph, biol rep 3


title: Hepatoblastoma, LCM-5, Embryonal, rep2


title: Hepatoblastoma, LCM-5, Normal (Midlobular), rep2

value: Non-tumor


title: Hepatoblastoma, LCM-5, Mesenchymal (Osteoid), rep2


title: liver, group, male, 7 wph, biol rep 2


title: Hepatoblastoma, LCM-4, Normal (Midlobular), rep2


title: oocytes from wild type mice-6month-sample2

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-2


title: oocytes from knock-out mice-week7-sample11

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-11


title: liver, group, male, 7 wph, biol rep 1


title: Hepatoblastoma, LCM-4, Fetal, rep2


title: oocytes from knock-out mice-week7-sample9

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-9


title: oocytes from knock-out mice-week7-sample10

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-10


title: Hepatoblastoma, LCM-3. Mesenchymal (Osteoid), rep2


title: oocytes from knock-out mice-week7-sample8

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-8


title: oocytes from wild type mice-6month-sample4

description:
oocyte_6month_raw_counts.txt
oocyte_6month_deseq2_normalised.txt
o-wt6m-4


title: oocytes from knock-out mice-week7-sample6

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-6


title: Hepatoblastoma, LCM-3, Embryonal, rep2


title: oocytes from knock-out mice-week7-sample7

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-7


title: whole body, sinlge, female, 21 dph, biol rep 3

source_name: whole body of single-housed females at 21 dph


title: oocytes from knock-out mice-week7-sample5

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-5


title: whole body, sinlge, female, 21 dph, biol rep 4

value: whole body of single-housed females at 21 dph


title: oocytes from knock-out mice-week7-sample3

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-3


title: Hepatoblastoma, LCM-3. Fetal, rep2


title: whole body, sinlge, female, 21 dph, biol rep 1


title: oocytes from knock-out mice-week7-sample12

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-12


title: oocytes from knock-out mice-week7-sample4

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-4


title: oocytes from knock-out mice-week7-sample1

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-1


title: Hepatoblastoma, LCM-17, Mesenchymal (Cartilage), rep2


title: whole body, sinlge, female, 21 dph, biol rep 2


title: oocytes from wild type mice-week7-sample4

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-wt7-4


title: oocytes from knock-out mice-week7-sample2

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-ko7-2


title: Hepatoblastoma, LCM-17, Mesenchymal (Cartilage), rep1


title: Hepatoblastoma, LCM-17, Mesenchymal (Osteoid)


title: oocytes from wild type mice-week7-sample5

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-wt7-5


title: oocytes from wild type mice-week7-sample2

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-wt7-2


title: oocytes from wild type mice-week7-sample3

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-wt7-3


title: whole body, sinlge, female, 17 dph, biol rep 4

source_name: whole body of single-housed females at 17 dph


title: oocytes from wild type mice-week7-sample1

description:
oocyte_week7_raw_counts.txt
oocyte_week7_deseq2_normalised.txt
o-wt7-1


title: whole body, sinlge, female, 17 dph, biol rep 3

value: whole body of single-housed females at 17 dph


title: Hepatoblastoma, LCM-17, Normal (Pericentral)


title: oocytes from knock-out mice-week4-sample7

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-7


title: whole body, sinlge, female, 17 dph, biol rep 2


title: oocytes from knock-out mice-week4-sample6

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-6


title: Hepatoblastoma, LCM-17, Normal (Midlobular)


title: oocytes from knock-out mice-week4-sample5

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-5


title: oocytes from knock-out mice-week4-sample4

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-4


title: whole body, sinlge, female, 17 dph, biol rep 1


title: Hepatoblastoma, LCM-17, Fetal


title: whole body, sinlge, female, 11 dph, biol rep 4

source_name: whole body of single-housed females at 11 dph


title: Hepatoblastoma, LCM-16, Fetal, rep2


title: oocytes from knock-out mice-week4-sample2

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-2


title: whole body, sinlge, female, 11 dph, biol rep 2

value: whole body of single-housed females at 11 dph


title: oocytes from knock-out mice-week4-sample1

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-1


title: Hepatoblastoma, LCM-16, Fetal, rep1


title: whole body, sinlge, female, 11 dph, biol rep 3


title: oocytes from wild type mice-week4-sample12

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-12


title: whole body, sinlge, female, 11 dph, biol rep 1


title: oocytes from wild type mice-week4-sample7

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-7


title: oocytes from wild type mice-week4-sample9

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-9


title: oocytes from wild type mice-week4-sample10

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-10


title: whole body, sinlge, female, 10 dph, biol rep 4

source_name: whole body of single-housed females at 10 dph


title: Hepatoblastoma, LCM-15, Fetal


title: Hepatoblastoma, LCM-15, Mesenchymal (Osteoid)


title: Hepatoblastoma, LCM-15, Normal (Midlobular)


title: oocytes from wild type mice-week4-sample5

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-5


title: oocytes from wild type mice-week4-sample4

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-4


title: whole body, sinlge, female, 10 dph, biol rep 3

value: whole body of single-housed females at 10 dph


title: Hepatoblastoma, LCM-14, Normal (Pericentral)

value: Untreated


title: oocytes from knock-out mice-week4-sample3

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-ko4-3


title: oocytes from wild type mice-week4-sample3

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-3


title: oocytes from wild type mice-week4-sample6

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-6


title: whole body, sinlge, female, 10 dph, biol rep 2


title: whole body, sinlge, female, 10 dph, biol rep 1


title: oocytes from wild type mice-week4-sample2

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-2


title: oocytes from wild type mice-week4-sample1

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-1


title: oocytes from wild type mice-week4-sample11

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-11


title: Granulosa cells from knock-out mice-6month-Sample6

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-6

value: Granulosa cells


title: Hepatoblastoma, LCM-14, Normal (Midlobular)


title: Hepatoblastoma, LCM-14, Fetal, rep2


title: Granulosa cells from knock-out mice-6month-Sample5

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-5


title: whole body, sinlge, female, 9 dph, biol rep 4

source_name: whole body of single-housed females at 9 dph


title: Hepatoblastoma, LCM-14, Fetal, rep1


title: oocytes from wild type mice-week4-sample8

description:
oocyte_week4_raw_counts.txt
oocyte_week4_deseq2_normalised.txt
o-wt4-8


title: Granulosa cells from knock-out mice-6month-Sample4

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-4


title: whole body, sinlge, female, 9 dph, biol rep 3

value: whole body of single-housed females at 9 dph


title: Hepatoblastoma, LCM-13, Normal (Pericentral)


title: whole body, sinlge, female, 9 dph, biol rep 2


title: whole body, sinlge, female, 9 dph, biol rep 1


title: Granulosa cells from wild type mice-6month-Sample12

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-12


title: Hepatoblastoma, LCM-13, Normal (Midlobular)


title: Granulosa cells from knock-out mice-6month-Sample1

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-1


title: Granulosa cells from knock-out mice-6month-Sample3

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-3


title: Granulosa cells from knock-out mice-6month-Sample2

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-ko6m-2


title: Granulosa cells from wild type mice-6month-Sample10

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-10


title: Hepatoblastoma, LCM-13, Fetal


title: Granulosa cells from wild type mice-6month-Sample11

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-11


title: Granulosa cells from wild type mice-6month-Sample9

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-9


title: whole body, group, female, 35 dph, biol rep 3

source_name: whole body of group-housed females at 35 dph


title: Granulosa cells from wild type mice-6month-Sample6

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-6


title: Hepatoblastoma, LCM-12, Normal (Midlobular)


title: whole body, group, female, 35 dph, biol rep 2

value: whole body of group-housed females at 35 dph


title: Granulosa cells from wild type mice-6month-Sample7

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-7

value: Ovary


title: Hepatoblastoma, LCM-12, Embryonal


title: Granulosa cells from wild type mice-6month-Sample5

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-5


title: Granulosa cells from wild type mice-6month-Sample4

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-4


title: whole body, group, female, 35 dph, biol rep 1


title: Granulosa cells from wild type mice-6month-Sample2

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-2


title: whole body, group, female, 28 dph, biol rep 4

source_name: whole body of group-housed females at 28 dph


title: Granulosa cells from wild type mice-6month-Sample1

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-1


title: Granulosa cells from knock-out mice-Week7-Sample5

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-ko7-5


title: Hepatoblastoma, LCM-11, Normal (Midlobular)


title: Granulosa cells from knock-out mice-Week7-Sample4

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-ko7-4


title: whole body, group, female, 28 dph, biol rep 2

value: whole body of group-housed females at 28 dph


title: Granulosa cells from knock-out mice-Week7-Sample3

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-ko7-3


title: Hepatoblastoma, LCM-12, Normal (Pericentral)

value: Liver


title: Granulosa cells from wild type mice-6month-Sample8

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-8


title: whole body, group, female, 28 dph, biol rep 1


title: Granulosa cells from knock-out mice-Week7-Sample2

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-ko7-2


title: Granulosa cells from wild type mice-Week7-Sample5

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-wt7-5


title: whole body, group, female, 35 dph, biol rep 4


title: Hepatoblastoma, LCM-12, Fetal

value: F


title: Hepatoblastoma, LCM-11, Embryonal


title: Hepatoblastoma, LCM-11, Fetal


title: whole body, group, female, 21 dph, biol rep 4

source_name: whole body of group-housed females at 21 dph


title: Granulosa cells from wild type mice-Week7-Sample2

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-wt7-2


title: Hepatoblastoma, LCM-10, Normal (Midlobular)


title: Granulosa cells from wild type mice-6month-Sample3

description:
granulosa_6months_raw_counts.txt
granulosa_6months_deseq2_normalised.txt
g-wt6m-3


title: Granulosa cells from wild type mice-Week7-Sample1

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-wt7-1


title: Hepatoblastoma, LCM-10, Embryonal


title: Granulosa cells from knock-out mice-Week4-Sample6

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-6


title: whole body, group, female, 21 dph, biol rep 2

value: whole body of group-housed females at 21 dph


title: whole body, group, female, 28 dph, biol rep 3


title: Hepatoblastoma, LCM-10, Fetal

value: Hepatoblastoma


title: whole body, group, female, 21 dph, biol rep 1


title: Granulosa cells from knock-out mice-Week4-Sample5

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-5


title: Amla-2_S17_L001

organism: Emblica officinalis

source_name: exosome-like nanovesicle (ENV)

value: exosome-like nanovesicle (ENV)


title: Hepatoblastoma, LCM-9, Mesenchymal (Osteoid)

value: Treated


title: Granulosa cells from knock-out mice-Week4-Sample4

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-4


title: Hepatoblastoma, LCM-10, Normal (Pericentral)

value: Non-tumor


title: Amla-1_S16_L001


title: Granulosa cells from knock-out mice-Week7-Sample1

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-ko7-1


title: Hepatoblastoma, LCM-9, Normal (Pericentral)


title: Granulosa cells from knock-out mice-Week4-Sample3

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-3


title: RT4 siNUMB siCYR61/CTGF rep1

tag: cell line

value: urothelial bladder cancer


title: Hepatoblastoma, LCM-9, Normal (Midlobular)


title: Hepatoblastoma, LCM-9, Embryonal


title: RT4 siNUMB siCtrl rep1

tag: cell type

value: siCtr


title: Granulosa cells from knock-out mice-Week4-Sample1

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-1


title: whole body, group, female, 17 dph, biol rep 1

source_name: whole body of group-housed females at 17 dph


title: Hepatoblastoma, LCM-8, Normal (Midlobular)

value: M

tag: treatment


title: RT112 siNUMB ROCKi rep1

value: ROCKi


title: Granulosa cells from wild type mice-Week4-Sample7

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-7


title: whole body, group, female, 13 dph, biol rep 4

source_name: whole body of group-housed females at 13 dph


title: Hepatoblastoma, LCM-8, Embryonal

value: Untreated


title: Granulosa cells from wild type mice-Week7-Sample4

description:
granulosa_week7_raw_counts.txt
granulosa_week7_deseq2_normalised.txt
g-wt7-4

value: Granulosa cells


title: RT112 siNUMB Vehicle_ROCKi rep1

value: vehicle


title: whole body, group, female, 13 dph, biol rep 3

value: whole body of group-housed females at 13 dph


title: Granulosa cells from wild type mice-Week4-Sample6

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-6

value: Ovary


title: whole body, group, female, 17 dph, biol rep 3

value: whole body of group-housed females at 17 dph


title: Hepatoblastoma, LCM-8, Fetal

value: Liver


title: RT4 siNUMB ROCKi rep1


title: Granulosa cells from wild type mice-Week4-Sample5

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-5


title: whole body, group, female, 13 dph, biol rep 2


title: Granulosa cells from knock-out mice-Week4-Sample2

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-ko4-2


title: RT4 siNUMB Vehicle_ROCKi rep1


title: whole body, group, female, 13 dph, biol rep 1


title: Hepatoblastoma, LCM-7, Mesenchymal (Osteoid)


title: Hepatoblastoma, LCM-7, Normal (Pericentral)


title: whole body, group, female, 17 dph, biol rep 2


title: Granulosa cells from wild type mice-Week4-Sample3

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-3


title: whole body, group, female, 9 dph, biol rep 4

source_name: whole body of group-housed females at 9 dph


title: Hepatoblastoma, LCM-7, Normal (Midlobular)


title: KK47 siNUMB Verteporfin rep1

value: Verteporfin


title: Granulosa cells from wild type mice-Week4-Sample2

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-2


title: KK47 siNUMB Vehicle_Verteporfin rep1


title: Hepatoblastoma, LCM-7, Embryonal


title: RT112 siNUMB Verteporfin rep1


title: whole body, group, female, 9 dph, biol rep 2

value: whole body of group-housed females at 9 dph


title: whole body, group, female, 9 dph, biol rep 3


title: RT112 siNUMB Vehicle_Verteporfin rep1


title: M1 mouse heart_cKO rep2_Ribo-seq

description:
CKo2
M1 mouse heart_Ribo_raw_counts

data_processing:
For RNA-seq data analysis, the sequencing data was filtered with cutadapt. The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) or rat genome (Rattus_norvegicus.Rnor_6.0) using STAR or HISAT2, respectively. Expression level of gene was calculated by featureCounts and StringTie, respectively. The raw counts were then analyzed using DESeq2.
For Ribo-seq data analysis, the Ribo-seq raw data underwent adapter trimming and low-quality sequence filtering using cutadapt, followed by rRNA sequence removal using bowtie. Subsequently, the clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using STAR. Then ORF analysis and ORF counts analysis were conducted using RiboCode.
For TRAC-seq data analysis, following adapter trimming and quality filtering, the clean sequencing data were initially aligned to the tRNA sequences using Bowtie2. Subsequently, read counts for each tRNA were calculated using the method described in (Cozen et al., 2015).
Assembly: Mus_musculus.GRCm38; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: txt;raw counts
Library strategy: Ribo-seq

source_name: Heart

value: Heart


title: Granulosa cells from wild type mice-Week4-Sample1

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-1


title: whole body, group, female, 9 dph, biol rep 1


title: Granulosa cells from wild type mice-Week4-Sample4

description:
granulosa_week4_raw_counts.txt
granulosa_week4_deseq2_normalised.txt
g-wt4-4


title: Hepatoblastoma, LCM-7, Fetal

value: Hepatoblastoma


title: M1 mouse heart_cKO rep1_Ribo-seq

description:
CKo1
M1 mouse heart_Ribo_raw_counts


title: RT4 siNUMB Verteporfin rep1


title: whole body, sinlge, male, 21 dph, biol rep 4

source_name: whole body of single-housed males at 21 dph


title: M1 mouse heart_Ctrl rep2_Ribo-seq

description:
Ctrl2
M1 mouse heart_Ribo_raw_counts

value: Ctrl


title: Hepatoblastoma, LCM-6, Normal (Midlobular)

value: Non-tumor


title: RT4 siNUMB Vehicle_Verteporfin rep1

value: urothelial bladder cancer


title: whole body, sinlge, male, 21 dph, biol rep 2

value: whole body of single-housed males at 21 dph


title: Triple_culture_O-IAV

city: Vienna

first: Matthias

last: Farlik

state: Vienna

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: Single Cell 5'

library_source: transcriptomic single cell

data_processing:
Raw data files were demultiplexed using the 10X Genomics Cell ranger (v.6.1.2) pipeline for CAF+mono/macro co-culture experiment and 10X Genomics Cell Ranger (v.7.0.0) for Triple culture experiment,  with the command “mkfastq”, assembled, and aligned to the human reference genome using the “count” pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv file containing barcode information for each cell of the sample
Supplementary files format and content: tsv file containing feature information for the sample
Supplementary files format and content: mtx file containing matrix information for the sample

source_name: Macrophages, patient-derived colorectal cancer-associated fibroblasts, patient-derived colorectal cancer organoids

growth_protocol: Monocytes were isolated from the whole blood of healthy volunteers using the EasySep™ Direct Human Monocyte Isolation Kit. For macrophage generation monocytes were attached to cell culture plates for 2 h  in RPMI-1640. Adherent monocytes were further incubated in RPMI-1640 supplemented with 10% fetal calf serum (FCS) and 100 ng/ml M-CSF for 7 days. For triple cultures cells were embedded in Geltrex domes at a ratio of 20:10:1 (CAFs:monocytes:organoid-cells) and cultured in Advanced DMEM/F12 basal medium for 3 days before treatments.

extract_protocol:
Co-cultures of CAFs and monocytes/macrophages were treated with TrypLE to realease the single cells. Triple cultures were subjected to dispase and TrypLE incubation resulting in single-cell suspension.
Libraries were performed using 10x Genomics Chromium Next GEM 3’ v3.1 (CAF+mono/macro experiment) or 5’ v2 (Triple culture experiment) kit and run on a Chromium Single Cell Controller. cDNA recovery, amplification and gene expression libraries were prepared according to the manufacturer’s protocol. Quality control was performed using TapeStation (Agilent) and Qubit Fluorometer (ThermoFisher). Libraries were sequenced on a NovaSeqSP flow cell (Illumina) with 50bp read length in paired-end mode.

treatment_protocol: Triple cultures were infected (using 5*100 TCID50/initially seeded cells) with oncolytic virus  (H1N1-NS1116) for 1 h and cultured in basal medium for further 24 h. For chemotherapy, domes with triple cultures were incubated in ENAS medium containing 20 μM oxaliplatin and 0.5 mM 5-FU for 24 hours.

tag: diagnosis

value: colorectal cancer


title: Hepatoblastoma, LCM-6, Embryonal

value: M


title: Hepatoblastoma, LCM-6, Fetal

value: Untreated


title: Triple_culture_mock

description: Single Cell 5'

value: Macrophages, patient-derived colorectal cancer-associated fibroblasts, patient-derived colorectal cancer organoids

value: mock


title: whole body, sinlge, male, 21 dph, biol rep 1


title: whole body, sinlge, male, 21 dph, biol rep 3


title: M1 mouse heart_cKO rep2_RNA-seq

description:
CKo2
M1 mouse heart_RNA_raw_counts


title: Triple_culture_oxali_5FU

description: Single Cell 5'

value: 20 𝝁M oxaliplatin + 0.5 mM 5-fluorouracil


title: Hepatoblastoma, LCM-5, Mesenchymal (Stromal), rep1

value: F

value: Treated


title: M1 mouse heart_cKO rep1_RNA-seq

description:
CKo1
M1 mouse heart_RNA_raw_counts


title: Hepatoblastoma, LCM-6, Normal (Pericentral)

value: Liver


title: M1 mouse heart_Ctrl rep2_RNA-seq

description:
Ctrl2
M1 mouse heart_RNA_raw_counts


title: Macro_CAF_24h

description: Single Cell 3'

source_name: Macrophages, patient-derived colorectal cancer-associated fibroblasts


title: Macro_CAF_alone

description: Single Cell 3'

value: Macrophages, patient-derived colorectal cancer-associated fibroblasts


title: whole body, sinlge, male, 17 dph, biol rep 4

source_name: whole body of single-housed males at 17 dph


title: Hepatoblastoma, LCM-5, Normal (Pericentral)

source_name: Liver


title: whole body, sinlge, male, 17 dph, biol rep 3

value: whole body of single-housed males at 17 dph


title: Hepatoblastoma, LCM-5, Normal (Midlobular), rep1


title: M1 mouse heart_Ctrl rep1_RNA-seq

description:
Ctrl1
M1 mouse heart_RNA_raw_counts

value: Heart


title: whole body, sinlge, male, 17 dph, biol rep 2


title: Hepatoblastoma, LCM-5, Embryonal, rep1

value: Hepatoblastoma


title: M1 mouse heart_Ctrl rep1_Ribo-seq

description:
Ctrl1
M1 mouse heart_Ribo_raw_counts

value: Ctrl


title: Mono_CAF_24h

description: Single Cell 3'

source_name: Monocytes, patient-derived colorectal cancer-associated fibroblasts


title: DKO3 CD4T

city: Shinjuku

first: Daisuke

last: Aki

state: Tokyo

department: School of Medicine

institute: Keio University

data_processing:
RNA sequencing was performed using Illumina NovaSeq 6000 platform. After trimming adapters using Cutadapt and sequence reads were mapped to Grcm39/mm10 using  bowtie2.
Read counts were normalized to TPM.
Assembly: mm10
Supplementary files format and content: xls file includes raw counts and TPM values for each sample

source_name: liver

extract_protocol:
Total RNA was isolated from the FACS sorted CD4 T cells using RNeasy Mini kit (QIAGEN) and used for library construction.
The libraries were generated using NEBNext UltraII FS DNA Library Prep Kit (NEB) according to manufacture's instruction.

value: liver

value: mouse CD4+ T cell

value: Nr4a1 and Nr4a2 knockout


title: whole body, sinlge, male, 17 dph, biol rep 1


title: DKO2 CD4T


title: whole body, sinlge, male, 11 dph, biol rep 4

source_name: whole body of single-housed males at 11 dph


title: DKO1 CD4T


title: Hepatoblastoma, LCM-4, Normal (Midlobular), rep1

value: Non-tumor