title: w1118_TG2_IgG

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

institute: John Curtin School of Medical Research, The Australian National University

description:
Library name: w1118_TG2_IgG
w1118_TG2_IgG

data_processing:
RNA-seq: RNA-seq libraries were made using the Illumina Truseq Total RNA library Prep Kit LT. Sequencing was performed on the Illumina Hiseq2500 platform. Following the trimming of adapter sequences with Trimmomatic, RNA-seq reads from replicated wild type (x3) and mutant samples (x3) were aligned to the Drosophila melanogaster (dm6) genome assembly utilizing HISAT2. Gene annotations were sourced from UCSC. The DESeq2 Bioconductor package was employed to identify differentially expressed mRNAs between w1118 and the hamPR/hamPR mutant, as well as between +/Df and hamSK1/Df mutant, with a subsequent estimation of the false discovery rate (FDR). Genes with an FDR < 10% and absolute Log2FC>0 were considered differentially expressed.
CUT&Tag: We mapped the CUT&TAG samples of w1118 and pBAC_ham_sfGFP in TE and TG tissues to the dm6 genome assembly using Bowtie2 with the following parameters: bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The coverage for these samples was generated using bedtools genomeCoverageBed and normalized to library depth to yield reads per million per base (RPM).
Assembly: dm6
Supplementary files format and content: bigwig
Supplementary files format and content: RNAseq counts matrix
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: Testis and genital disc

growth_protocol: Standard Drosophila melanogaster culture condition

extract_protocol:
Total RNA was extracted from finely dissected genital discs or testis samples from 18-25h APF animals using Trizol reagent (Invitrogen). Standard protocol was used for CUT&Tag.
RNA-seq libraries were made using the Illumina Truseq Total RNA library Prep Kit LT. CUT&Tag libraries were generated by PCR using a Universal i5 primer, a uniquely barcoded i7 primer, and PCR master mix (NEB Phusion® High-Fidelity PCR Master Mix with HF Buffer, M0531).

value: Testis and genital disc

tag: genotype

tag: antibodies

value: Rabbit IgG


title: abl_62

status: Public on Mar 21 2025

type: SRA

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

country: USA

institute: OMRF

library_source: transcriptomic

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to human reference genome GRCh38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes  ENSEMBL id  and FPKM values for each gene, in each sample

molecule: total RNA

organism: Homo sapiens

source_name: LNCap-abl cell

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: prostate; derived from LNCaP cells grown in the absence of androgens

tag: sirna

value: siGUGUUUGC (seed)

tag: growth condition

value: 10% CSS RPMI


title: A06

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

institute: Albert Einstein College of Medicine

data_processing:
FastQC run to determine quality of samples
Trim Galore used to trim adaptor/low quality sequences
Trimmed reads were aligned to GRCh38/hg38 genome and read counts extracted using STAR alignment software
Read counts of the two different runs for each sample were added together (L001 and L002)
Normalization was performed using DESeq R package
Assembly: hg38
Supplementary files format and content: a single comma-separated value file containing normalized counts for all samples

source_name: Primary CD4+ T Cells

extract_protocol:
Zymo RNA Extraction Kit
Kapa stranded mRNA kit and Kap mRNA Hyper prep

tag: group

value: healthy weight children

tag: cell type

value: Primary CD4+ T Cells


title: abl_61


title: CBC 0.0 μM (control), biological rep3

type: RNA

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 0.0 μM (control)

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: Data were processed using the Affymetrix Transcriptome Analysis Console (TAC) software (v.4.0).

label: biotin

source_name: iPSC-derived hepatocytes exposed to CBCa at 0.0 μM (control)

label_protocol: The total RNA samples (100 ng each) were labeled using the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Commercial iPSC-derived hepatocytes (iCell Hepatocytes 2.0) from FUJIFILM Cellular Dynamics (Madison, WI) were cultured following the manufacturer’s protocols.

extract_protocol: Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBC at varying concentrations (0.1-40 µM) in triplicate for 24 h.

value: hepatocyte


title: CBC 0.1 μM, biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 0.1 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 0.1 μM


title: d16NC_RNA-3

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

description: Library name: iMT_d16NC_RNA-3

data_processing:
Raw fastq files were processed using Cutadapt [v3.5] to remove adapter sequences (-a CTGTCTCTTATACACA and -A CTGTCTCTTATACACA), with the parameters set to a minimum read length of 20 (-m 20) and a minimum overlap of 12 bases for adapter matching (-O 12). Processed fastq files were aligned to mouse reference mm10 using STAR [v 2.7.10a]. Processed fastq files were aligned to the mouse reference mm10 using STAR [v2.7.10a] and converted to BAM files. The aligned BAM files were used with FeatureCounts [v1.6.0] to generate count files, with parameters [-T 10 -t exon -g gene_id -p].
Assembly: GRCm38
Supplementary files format and content: counts files recording results of FeatureCounts captured by RNA-seq

organism: Mus musculus

source_name: MEFs

growth_protocol: MEFs were isolated from E14.5 B6/C57 mouse embryos. Head, vertebral column, dorsal root ganglia and all internal organs were removed and discarded and the remaining embryonic tissue was manually cut into pieces and incubated in 0.25% trypsin for 5 min. Cells from embryos were plated onto a 15cm tissue culture dish in MEF medium containing DMEM (Life Technologies) and 10% fetal bovine serum (FBS, Gemini). MEFs were seeded at a density of 20 000 cells per 35 mm dish. The next day, MEF medium was replaced with the iMT media containing DMEM (Life Technologies) supplemented with 15% FBS (Gbico), 2 mM GlutaMax supplement (Life Technologies), 1% nonessential amino acids (Life Technologies), 0.1 mM β-mercaptoethanol (Sig- ma) and 40 ng/ml basic fibroblast growth factor (bFGF, Stemgent), as well as chemical components 6TCF (E616452,Tranylcypromine, CHIR99021, FSK) ). Media were changed every 4 days.

extract_protocol:
Cell dissociation
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01) according to the manufacturer's instructions. Subsequently, add 2 µL of RNA with a total amount of approximately 100-400 ng to a PCR tube containing 1 µL of dNTP and 1 µL of TSO-oligodT. Incubate the PCR tube at 65°C for 5 minutes and then place it immediately on ice for 2 minutes. 0.4 μL of ddH2O, 2 μL of 5× PrimeScript II Buffer (Takara), 2 μL of Betaine (Sigma), 0.5 μL of 100 mM DTT, 0.15 μL of 0.4 M MgCl2, 0.2 μL of 50 mM TSO LNA primer, 0.25 μL of RNase inhibitor (Vazyme), and 0.5 μL of PrimeScript II RTase (Takara) were added. The reaction was gently mixed and carried out in a PCR thermocycler programmed as follows: 42°C 120 minutes, 70°C, 10 minutes; 10°C hold. Following the reaction, a PCR amplification mix was prepared with 12.5 μL of 2×HiFi HotStart ReadyMix, 1 μL of TSO-PCR primer (10 μM), and 1.5 μL of ddH2O. The PCR program was as follows: 95°C for 3 minutes; 7-16 cycles (adjust cycles based on RNA input) of 98°C for 30 seconds, 65°C for 15 seconds, and 72°C for 6 minutes; 72°C for 5 minutes; and 10°C hold. Purification was then performed using 0.9 × of VAHTS DNA Clean Beads according to the manufacturer's instructions. Sequencing library construction was using TruePrep DNA Library Prep Kit for MGI (Vazyme, TDM503-01) according to the manufacturer's instructions.

tag: strain

value: MEFs

tag: time

tag: treatment

value: no treatment


title: CBC 0.0 μM (control), biological rep1


title: CBC 0.0 μM (control), biological rep2


title: B11

value: obese children with asthma


title: d16NC_RNA-1

description: Library name: iMT_d16NC_RNA-1


title: w1118_TG1_IgG

country: Australia

description:
Library name: w1118_TG1_IgG
w1118_TG1_IgG

library_source: genomic

molecule: genomic DNA


title: abl_42

value: siGUGUGUA (seed)


title: abl_43


title: w1118_TG2_Ham

description:
Library name: w1118_TG2_Ham
w1118_TG2_Ham

value: Rabbit anti-Ham


title: w1118_TG1_Ham

description:
Library name: w1118_TG1_Ham
w1118_TG1_Ham


title: d2_RNA-3

description: Library name: iMT_d2_RNA-3


title: B10


title: B09


title: d16_RNA-3

description: Library name: iMT_d16_RNA-3


title: d16_RNA-2

description: Library name: iMT_d16_RNA-2


title: abl_41


title: w1118_Te2_Ham

description:
Library name: w1118_Te2_Ham
w1118_Te2_Ham

source_name: Testis

value: Testis


title: A05


title: d16_RNA-1

description: Library name: iMT_d16_RNA-1


title: B08


title: w1118_Te2_IgG

description:
Library name: w1118_Te2_IgG
w1118_Te2_IgG


title: abl_NT2

value: Non target


title: d12NC_RNA-3

description: Library name: iMT_d12NC_RNA-3


title: d12NC_RNA-1

description: Library name: iMT_d12NC_RNA-1


title: w1118_Te1_IgG

description:
Library name: w1118_Te1_IgG
w1118_Te1_IgG


title: B05


title: w1118_Te1_Ham

description:
Library name: w1118_Te1_Ham
w1118_Te1_Ham


title: abl_NT1


title: d12_RNA-3

description: Library name: iMT_d12_RNA-3


title: A03


title: abl_NT3


title: Rv1D_AR2

value: prostate; derived from xenograft serially propagated in mice

value: siAR

value: 10$ CSS RPMI + DHT


title: Rv1D_AR3


title: Ham_GFP_TG2_IgG

description:
Library name: Ham_GFP_TG2_IgG
Ham_GFP_TG2_IgG

value: Testis and genital disc

value: Rabbit IgG


title: B04


title: A02


title: Rv1D_AR1


title: Ham_GFP_TG1_IgG

description:
Library name: Ham_GFP_TG1_IgG
Ham_GFP_TG1_IgG


title: Rv1D_63

value: siGUGUUUGC (seed)


title: C02

value: obese children without asthma


title: Ham_GFP_TG2_GFP

description:
Library name: Ham_GFP_TG2_GFP
Ham_GFP_TG2_GFP

value: Rabbit anti-GFP


title: d12_RNA-1

description: Library name: iMT_d12_RNA-1


title: d12_RNA-2

description: Library name: iMT_d12_RNA-2


title: Ham_GFP_TG1_GFP

description:
Library name: Ham_GFP_TG1_GFP
Ham_GFP_TG1_GFP


title: Rv1D_62


title: d0NC_RNA-3

description: Library name: iMT_d0NC_RNA-3


title: d0NC_RNA-2

description: Library name: iMT_d0NC_RNA-2


title: d0NC_RNA-1

description: Library name: iMT_d0NC_RNA-1


title: Rv1D_61


title: Ham_GFP_Te1_GFP

description:
Library name: Ham_GFP_Te1_GFP
Ham_GFP_Te1_GFP


title: Rv1D_42


title: day35-6

data_processing:
Base-calls were performed with MGI software
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Cell dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: transdifferentiating MEF

tag: age

tag: chemical component


title: IPD5,male, 50d

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

library_source: transcriptomic single cell

data_processing:
The pre-processing of the fastq files was conducted using CeleScopeÂ® (v.1.14.1; www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies GmbH) to generate gene count matrices with default parameters
Low-quality reads were removed.
Sequences were mapped using STAR (https://github.com/alexdobin/STAR) to the human genome reference version GRCh38 and genes were annotated using Ensembl 92
The reads were assigned to genes using featureCount (https://subread.sourceforge.net/) and the cell calling was performed by fitting a negative bimodal distribution and determining the threshold between empty wells and cell-associated wells to generate a count matrix file containing the number of Unique Molecular Identifier (UMI) for each gene within each cell.
Downstream analysis was done using Seurat single-cell analysis toolkit (v. 5.0.1) in R computing language (v. 4.3.2).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and count matrix

source_name: midbrain organoid

growth_protocol: Organoids were generated and cultured as described in Nickels et al. 2020.

extract_protocol:
Midbrain organoids were collected from their culture medium and washed with 1x PBS (phosphate-buffered saline, Gibco, Cat#10010-015). Organoids were transferred to a 1.5ml Eppendorf tube and digested in 1 ml sCelLive™ Tissue Dissociation Solution (Singleron Biotechnologies, Cat#1190062) diluted 1:2 with PBS. The organoids were placed in a thermal shaker at 750 rpm at 37°C for 45 minutes. The state of dissociation was checked at regular intervals under a light microscope. Following digestion, the suspension was filtered using a 40-µm sterile strainer (Greiner, Cat#542040). The cells were centrifuged at 350xg for 5 minutes at 4°C, and the cell pellets were resuspended in 300µl PBS. Cells were stained with Acridine Orange/Propidium Iodide Stain (Logos Biosystems, Cat#F23001), and the cell number and viability were calculated using LUNA-FX7™ Automated Cell Counter (Logos Biosystems, Villeneuve d’Ascq, France).
The single-cell RNA-seq libraries were constructed using GEXSCOPE™ Single Cell RNAseq Library Kit (Singleron Biotechnologies, Cat#4180011) according to the manufacturer´s instructions.

value: midbrain organoid

tag: cell line

value: male

tag: disease state

value: idiopathic PD

value: 50 days of culture


title: Ham_GFP_Te1_IgG

description:
Library name: Ham_GFP_Te1_IgG
Ham_GFP_Te1_IgG


title: IPD6,male, 50d


title: scATAC_Day6_4

description: Library name: iMT_scATAC_Day6_4

library_source: genomic single cell

data_processing:
Raw fastq files were processed using Cutadapt [v3.5] to remove adapter sequences (-a CTGTCTCTTATACACA and -A CTGTCTCTTATACACA), with the parameters set to a minimum read length of 20 (-m 20) and a minimum overlap of 12 bases for adapter matching (-O 12). Processed fastq files were aligned to mouse reference mm10 using bowtie2 [v2.3.4.3]. Duplicates were removed using Picard [v2.27.5] MarkDuplicates. Aligned reads were converted to BAM and sorted using Samtools [v1.14], with quality filter (“-q”) set to 2. Reads were then cleaned and sorted by BEDTools [v2.28.0]. In the end, only properly paired mapped reads were kept.
Assembly: GRCm38
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

source_name: fibroblast

value: fibroblast


title: IPD4,male, 50d


title: day35-4


title: day35-5


title: CTRL6,male, 50d

value: healthy control


title: Rv1D_43

value: siGUGUGUA (seed)


title: scATAC_Day6_2

description: Library name: iMT_scATAC_Day6_2


title: day35-3


title: scATAC_Day6_3

description: Library name: iMT_scATAC_Day6_3


title: Rv1D_NT1

value: Non target


title: B03

value: obese children with asthma

value: Primary CD4+ T Cells


title: CTRL4,male, 50d


title: Rv1D_NT3

value: prostate; derived from xenograft serially propagated in mice

value: 10$ CSS RPMI + DHT


title: day35-2


title: Rv1D_NT2


title: scATAC_Day0_2

description: Library name: iMT_scATAC_Day0_2

value: no treatment


title: scATAC_Day6_1

description: Library name: iMT_scATAC_Day6_1


title: IPD3,female, 50d

value: female


title: scATAC_Day0_1

description: Library name: iMT_scATAC_Day0_1


title: LN_63

source_name: LNCaP cells

value: prostate; derived from metastatic site:left supraclavicular lymph node

value: siGUGUUUGC (seed)

value: 10% FBS RPMI


title: day16-5

value: transdifferentiating MEF


title: IPD2,female, 50d

value: midbrain organoid


title: LN_62


title: H37Rv_EMB+BTZ@16ug/mL+64ng/mL+48h_b11_3

city: Seattle

first: Ethan

last: Bustad

state: WA

address: 1900 Ninth Ave.

department: CGIDR

institute: Seattle Children's Research Institute

description: Library name: EMB.BTZ48_r3

data_processing:
Libraries were sequenced at the National Center for Genomic Analysis (CNAG, Barcelona, Spain). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM (transcripts per million) reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_INDIGO4JoseManuel_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_INDIGO4JoseManuel_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.

organism: Mycobacterium tuberculosis

source_name: Bacteria

growth_protocol: Mycobacterium tuberculosis was routinely grown in Middlebrook 7H9 broth supplemented with 0.2% glycerol-ADC and 0.05% Tyloxapol or 0.025% Tween80 (v/v) at 37°C on a rotary shaker.

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using a custom-designed set of biotinylated oligonucleotides based on the method described in PMID: 32317317.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

value: Bacteria

value: Wildtype

value: EMB 16 µg/mL + BTZ 64 ng/mL

tag: batch

value: 48 hours


title: day16-4


title: IPD1,female, 50d

value: idiopathic PD

value: 50 days of culture


title: LN_61


title: H37Rv_EMB+BTZ@16ug/mL+64ng/mL+48h_b11_2

description: Library name: EMB.BTZ48_r2


title: Rv1D_41

value: siGUGUGUA (seed)


title: CTRL3,female, 50d

value: healthy control


title: H37Rv_EMB+BTZ@16ug/mL+64ng/mL+48h_b11_1

description: Library name: EMB.BTZ48_r1


title: CTRL2,female, 50d


title: LN_43


title: CTRL5,male, 50d

value: male


title: LN_42


title: CTRL1,female, 50d


title: H37Rv_BTZ@64ng/mL+48h_b11_3

description: Library name: BTZ48_r3

value: BTZ, 64 ng/mL


title: day16-2


title: day16-1


title: LN_41


title: H37Rv_BTZ@64ng/mL+48h_b11_2

description: Library name: BTZ48_r2


title: LN_NT3

value: Non target


title: H37Rv_BTZ@64ng/mL+48h_b11_1

description: Library name: BTZ48_r1


title: day8-6


title: day8-5


title: day8-4


title: LN_NT2


title: H37Rv_BTZ@16ng/mL+16h_b11_3

description: Library name: BTZ16_r4

value: BTZ, 16 ng/mL

value: 16 hours


title: day35-1


title: LN_NT1

value: prostate; derived from metastatic site:left supraclavicular lymph node


title: H37Rv_BTZ@16ng/mL+16h_b11_2

description: Library name: BTZ16_r3


title: day8-3


title: H37Rv_BTZ@16ng/mL+16h_b11_1

description: Library name: BTZ16_r2


title: Rv1_AR3

value: prostate; derived from xenograft serially propagated in mice

value: siAR

value: 10% CSS RPMI


title: day8-2

value: transdifferentiating MEF


title: H37Rv_EMB@16ug/mL+48h_b11_3

description: Library name: EMB48_r4

value: Bacteria

value: Wildtype

value: EMB, 16 µg/mL


title: Rv1_AR2


title: BL_BL_2

city: Barcelona

first: Juan

middle: Ángel

last: Recio

state: Cataluña

address: Passeig Vall d'Hebron 119-129

department: Oncology

country: Spain

institute: Vall d'Hebron Research Institute (VHIR)

description: Gene expression data from mouse melanocytes (4OHT)

hyb_protocol: The hybridization protocol was performed using GeneChipTM Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific)

scan_protocol: Scannig was performed using aGene-Chip scanner 3000 7G

data_processing: RMA

label: Biotin

source_name: Mouse melanocytes primary culture: treated with 4OHT (1µM;48h)

label_protocol: After generating the cDNA using WT PLUS Reagent kit-HT (Thermo Fisher scientific, Waltham, MA, USA) 5,5 ng of cDNA (sense strand) were fragmented and biotin labeled with FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific).

growth_protocol: For both models, Tyr::CreERT2;BRafCA and Tyr::CreERT2;BRafCA;Lkb1F/F back skin of neonates was collected. The protocol was adapted from (Damsky et al., 2015). Briefly, the skin was removed from one- or two-days old pups, sterilized by immersion into 70% ethanol for five seconds, and immediately washed with PBS. The skin was then treated with 0.05% trypsin-EDTA (Gibco, Waltham, MA, USA) at 37°C in a 5% CO2 incubator for 1-2 hours. Next, the epidermis was separated from the dermis using sterile forceps and mechanistically digested with a scalpel. Melanocytes were then cultured using a selective medium, consisting in DMEM-F12 (Biowest, Riverside, MO, USA) containing 5% FBS (Gibco), 200 pM Cholera Toxin (Sigma), 200 nM phorbol esters (TPA) (Sigma), 2 mM L-Glutamine (Gibco), 10 U/ml penicillin and 10 μg/ml streptomycin (Gibco).

extract_protocol: For RNA purification Direct-Zol RNA kit (Zymo Research, Irvine, CA, USA) was used. The isolation procedure was performed according to the manufacturer’s recommendations. RNA was analyzed with a 2100 Bioanalyzer (Agilent) to confirm amount and integrity of the sample. Only high-quality samples were used for following applications.

treatment_protocol: Mouse models-derived melanocytes were subjected to 4OHTx treatment for in vitro recombination and UVR. Tamoxifen was added at a concentration of 1 μM for 48 hours. For UVR a Stratagene UV Crosslinker 1800/2400 was used. Cells were irradiated with 30 J/m2 UVB at 60%–70% confluence after removal of medium and the plate lid. For combined treatments, cells were irradiated 48 hours after 4OHTx induction. After treatment, fresh medium was added back, and cells were incubated for 27 days prior to RNA isolation.

value: Mouse melanocytes primary culture

value: treated with 4OHT (1µM;48h)


title: day8-1


title: H37Rv_EMB@16ug/mL+48h_b11_2

description: Library name: EMB48_r2

value: 48 hours


title: Rv1_AR1


title: day4-10


title: Rv1_63

value: siGUGUUUGC (seed)


title: H37Rv_EMB@4ug/mL+16h_b11_3

description: Library name: EMB16_r3

value: EMB, 4 µg/mL


title: day4-9


title: B_B+UV_4 [re-analyzed]

description: Gene expression data from mouse melanocytes (4OHT+UVB)

source_name: Mouse melanocytes primary culture: treated with 4OHT (1µM;48h) + UVB (30J/m2)


title: BL_BL_1


title: B_B+UV_3 [re-analyzed]

value: treated with 4OHT (1µM;48h) + UVB (30J/m2)


title: B_B+UV_2 [re-analyzed]


title: H37Rv_EMB@4ug/mL+16h_b11_2

description: Library name: EMB16_r2


title: BL_BL_3


title: B_B+UV_1 [re-analyzed]


title: Rv1_61


title: day4-8


title: day4-7


title: B_B_4 [re-analyzed]


title: H37Rv_EMB@4ug/mL+16h_b11_1

description: Library name: EMB16_r1


title: Rv1_43

value: siGUGUGUA (seed)


title: day4-6


title: B_B_3 [re-analyzed]


title: H37Rv_EMB@16ug/mL+48h_b11_1

description: Library name: EMB48_r1


title: H37Rv_Untreated@0+48h_b11_3

description: Library name: NoDrug48_r4

value: Untreated


title: H37Rv_Untreated@0+48h_b11_2

description: Library name: NoDrug48_r2


title: B_B_2 [re-analyzed]


title: Rv1_41


title: day4-5


title: H37Rv_Untreated@0+48h_b11_1

description: Library name: NoDrug48_r1


title: Rv1_62


title: Rv1_NT3

value: Non target


title: B_B_1  [re-analyzed]


title: day4-3


title: day16-3


title: Rv1_NT2


title: H37Rv_Untreated@0+16h_b11_3

description: Library name: NoDrug16_r4

value: 16 hours


title: B_B+UV_4


title: B_B+UV_3


title: H37Rv_Untreated@0+16h_b11_2

description: Library name: NoDrug16_r3


title: day4-2


title: H37Rv_Untreated@0+16h_b11_1

description: Library name: NoDrug16_r1


title: day4-1


title: day0-6

value: MEF

value: no treatment


title: H37Rv_TYL@0.0005+16h_b5_3

description: Library name: Untreated_7H9_GOT_R3_S43


title: Rv1_42

value: prostate; derived from xenograft serially propagated in mice

value: 10% CSS RPMI


title: R3(GC)

city: Guiyang

first: hong

last: luo

address: 9 Beijing Road, Yunyan District

institute: Guizhou medical university

description: Library name: samble6

data_processing:
HISAT2 software was used to align the clean reads after quality control with the mouse reference genome, and the HTSeq-count tool was used to calculate the gene expression level according to the alignment results.Differential expression results between groups were obtained using DESeq2. Differentially expressed genes (DEGs) were obtained with the screening criteria of P < 0.05 and an absolute fold change ≥ 2. Using the Metascape tool, with P < 0.01 as the standard, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathways were analyzed for the DEGs.
Assembly: mm10
Supplementary files format and content: Results from differential expression analysis, including gene identifiers.

extract_protocol:
Total RNA was extracted from the GC-treated group and the control group by the TRIzol method. RNA was quantified, RNA purity was detected by a NanoDrop 2000 spectrophotometer (A260/280 between 1.8 and 2.2), and RNA integrity was detected by an Agilent 2100 bioanalyzer.
The mRNAs were randomly disrupted with divalent cations in NEB Fragmentation Buffer, and libraries were constructed utilizing the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Beijing, China).

value: glucocorticoid (GC)


title: R2(GC)

description: Library name: samble5


title: day4-4

value: transdifferentiating MEF


title: day0-5


title: B_B+UV_1


title: B_B_4


title: R1(GC)

description: Library name: samble4


title: H37Rv_TYL@0.0005+16h_b5_2

description: Library name: Untreated_7H9_GOT_R2_S42

value: Bacteria

value: Wildtype


title: H37Rv_TYL@0.0005+16h_b5_1

description: Library name: Untreated_7H9_GOT_R1_S41


title: B_B_3

value: Mouse melanocytes primary culture

value: treated with 4OHT (1µM;48h)


title: day0-4


title: S3(control)

description: Library name: samble3

value: control


title: B_B_1


title: S2(control)

description: Library name: samble2


title: B_B_2


title: day0-2


title: Rv1_NT1


title: B_B+UV_2


title: day0-3


title: H37Rv_Untreated@0+16h_b5_2

description: Library name: Untreated_7H9_GO_R2_S30


title: H37Rv_Untreated@0+16h_b5_3

description: Library name: Untreated_7H9_GO_R3_S31


title: S1(control)

description: Library name: samble1


title: B_CONTROL_3

description: Gene expression data from mouse melanocytes (untreated)

source_name: Mouse melanocytes primary culture: control


title: Eberryi Adult Hemocyte scRNA-seq, replicate 3, scRNA-seq

status: Public on Mar 20 2025

city: Onna

first: Daria

last: Gavriouchkina

state: Kunigami District, Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

description:
Hemocytes_rep3_genes.tsv
Hemocytes_rep3_barcodes.tsv
Blood3_11Aligned.sortedByCoord.out.bam.bg.bw

data_processing:
RNA-seq reads were aligned to the genome using STAR (v2.5.2b)
RNA-seq counts were obtained using featureCounts v1.6.1
scRNA-seq: scRNA-seq reads were aligned to the genome using STAR Solo (v.2.5.2b)
scRNA-seq: scRNA-seq analysis was carried out using Seurat v.4
Supplementary files format and content: RNA-seq: bam files
Supplementary files format and content: RNA-seq: bigwig file for signal visualisation
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files
Supplementary files format and content: scRNA-seq: Robject files containing Seurat Objects
Supplementary files format and content: scRNA-seq: bigwig file for signal visualisation
Assembly: The genome of the animal  (E.berryi) has been submitted to ENA under project name PRJEB52690

organism: Euprymna berryi

source_name: Hemocytes

extract_protocol:
RNA-seq: Total RNA extraction was carried  out using TRIzol reagent (Invitrogen) for lysis followed by on-column purification using PureLink RNA Mini Kit (Invitrogen)  as described in TRIzol Plus RNA Purification instructions from manufacturer. RNA extraction was followed by Turbo DNase treatment (Thermo Fisher Scientific) to remove genomic DNA according to manufacturer’s instructions.
RNA-seq: For organ-specific transcriptomes, library preparation was achieved by using TruSeq Stranded mRNA Library Prep for NeoPrepTM (Illumina). For stage-specific transcriptomes,  NEBNExt Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used.
RNA-seq
scRNA-seq: Tissues were dissociated using a 1%  Papain solution in filtered natural seawater containing 0.1% sodium thioglycolate for retinas, and a 1% Pronase solution for non-retinal tissues on a nutator with gentle trituration. Cell clumps were filtered out using either  30µm MACS SmartStrainers (Miltenyi Biotec) for v2 sample  or using 40µm and 70µm cell strainers (flowmi). Cells were resuspended in a 50% L15 medium in sterile-filtered natural seawater.
scRNA-seq:single cell transcriptomes were obtained using 10x Genomics v.2 and v.3.1 protocols as per manufacturer's instructions
scRNA-seq

value: Hemocytes

tag: Sex

value: Male

tag: developmental stage

value: 80 days  post-hatching

tag: 10x genomics_chemistry

value: Wild-type


title: Eberryi Adult Hemocyte scRNA-seq, replicate 4, scRNA-seq

description:
Hemocytes_rep4_genes.tsv
Hemocytes_rep4_matrix.mtx
Blood4_12Aligned.sortedByCoord.out.bam.bg.bw


title: Eberryi Mature Perioesophageal brain, replicate 4, scRNAseq

description:
Brains_rep4_genes.tsv
Brains_rep4_matrix.mtx
RenamedClusters_Brains.Robj

source_name: Perioesophageal brain lobes (not including optic lobes)

value: 80-days post-hatching


title: Eberryi Adult Hemocyte scRNA-seq, replicate 2, scRNA-seq

description:
Hemocytes_rep2_genes.tsv
Hemocytes_rep2_barcodes.tsv
Blood2_10Aligned.sortedByCoord.out.bam.bg.bw


title: Eberryi Adult Hemocyte scRNA-seq, replicate 1, scRNA-seq

description:
Hemocytes_rep1_genes.tsv
Hemocytes_rep1_matrix.mtx
Blood1_9Aligned.sortedByCoord.out.bam.bg.bw


title: Evs from Treg cells 3

city: Napoli

first: Paola

last: De Candia

address: via Pansini 5

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI NAPOLI FEDERICO II - Dipartimento di Medicina molecolare e Biotecnologie mediche

description: Test

data_processing: Matrix worksheet reports not normalized signal.

label: SYBR Green

source_name: Peripheral blood mononuclear cells

label_protocol: A fixed volume of RNA sample was used as input for reverse transcription reaction by miRCURY-LNA RT Kit according to manufacturer’s instruction (Qiagen, U.S.A.). EV-associated miRNAs (n = 752) were profiled by using the complete human miRCURY LNA miRNA panel I+II (V5, Qiagen, U.S.A.).

growth_protocol: CD4+CD25+ T cells (Treg cells) were purified from peripheral blood mononuclear cells (PBMCs) from buffy coats of human healthy donors by magnetic cell separation with the Dynabeads Regulatory T Cell Kit (Invitrogen), allowing the separation of a 95–99% pure cell population by FACS analysis.

extract_protocol: Total RNA extracted using RNAqueous-4PCR Kit (Ambion, U.S.A.)

treatment_protocol: Cells were then stimulated in vitro for 72 hours in serum-free AIMV Medium AlbuMAX supplement (Gibco) in the presence of anti-CD3 and anti-CD28-coated Dynabeads (0.2 beads per cell) (Invitrogen).

value: Human Treg cells


title: Evs from Treg cells 4

description: Test


title: Evs from Treg cells 5

description: Test


title: B_CONTROL_1


title: Evs from Treg cells 1

description: Test


title: Evs from Treg cells 2

description: Test


title: Eberryi Mature Perioesophageal brain, replicate 3, scRNAseq

description:
Brains_rep3_genes.tsv
Brains_rep3_matrix.mtx
RenamedClusters_Brains.Robj

value: Perioesophageal brain lobes (not including optic lobes)


title: Eberryi Mature Optic lobe, replicate 3, scRNAseq

description:
Optic_Lobes_rep3_genes.tsv
Optic_Lobes_rep3_matrix.mtx
RenamedClusters_EbAdOLs.Robj

source_name: Optic Lobes

value: Optic Lobes

value: Unknown

value: 80 days post-hatching


title: Eberryi Mature Optic lobe, replicate 1, scRNAseq (NovaSeq)

value: Adult - Over 100 days post hatching


title: Eberryi Hatchling Optic lobe, replicate 5, scRNAseq

description:
HatchlingOLs_rep5_genes.tsv
HatchlingOLs_rep5_matrix.mtx
Hatchling_OLs.Robj

value: 1st day post hatching


title: Eberryi Hatchling Optic lobe, replicate 4, scRNAseq

description:
HatchlingOLs_rep4_genes.tsv
HatchlingOLs_rep4_matrix.mtx
Hatchling_OLs.Robj


title: H37Rv_Untreated@0+16h_b5_1

description: Library name: Untreated_7H9_GO_R1_S29

value: Bacteria

tag: genotype

value: Untreated

value: 16 hours


title: Eberryi Hatchling Optic lobe, replicate 3, scRNAseq

description:
HatchlingOLs_rep3_genes.tsv
HatchlingOLs_rep3_matrix.mtx
Hatchling_OLs.Robj

tag: tissue


title: Eberryi Mature Optic lobe, replicate 4, scRNAseq

description:
Optic_Lobes_rep4_genes.tsv
Optic_Lobes_rep4_matrix.mtx
RenamedClusters_EbAdOLs.Robj


title: day0-1

value: MEF

value: no treatment


title: Eberryi Hatchling Optic lobe, replicate 1, scRNAseq

description:
HatchlingOLs_rep1_genes.tsv
HatchlingOLs_rep1_matrix.mtx
Hatchling_OLs.Robj


title: Eberryi Retina, replicate 6, scRNAseq

description:
Retina_rep6_genes.tsv
Retina_rep6_matrix.mtx
Retinas.Robj

source_name: Retina

value: Retina


title: Eberryi Retina, replicate 5, scRNAseq

description:
Retina_rep5_genes.tsv
Retina_rep5_matrix.mtx
Retinas.Robj

value: Male


title: Eberryi Mature Optic lobe, replicate 1, scRNAseq (MiSeq)


title: Eberryi Retina, replicate 1, scRNAseq (MiSeq)

description:
Retina_rep1_genes.tsv
Retina_rep1_matrix.mtx
Retinas.Robj


title: Eberryi Retina, replicate 4, scRNAseq

description:
Retina_rep4_genes.tsv
Retina_rep4_matrix.mtx
Retinas.Robj


title: B_CONTROL_2

description: Gene expression data from mouse melanocytes (untreated)

value: Mouse melanocytes primary culture

value: control


title: Eberryi Mature Perioesophageal brain, replicate 2, scRNAseq

description:
Brains_rep2_genes.tsv
Brains_rep2_matrix.mtx
RenamedClusters_Brains.Robj

value: 60 days post hatching

value: Wild-type


title: Eberryi Retina, replicate 2, scRNAseq

description:
Retina_rep2_genes.tsv
Retina_rep2_matrix.mtx
Retinas.Robj


title: Whole embryo, St 28, RNA-seq

description:
St_28
St_28.bw
Eberryi_stages.counts.txt.gz

source_name: Whole embryo

value: Whole embryo

value: St 28


title: Whole embryo, St 26 (replicate 1) , RNA-seq

description:
St_26_rep1
St_26_rep1.bw
Eberryi_stages.counts.txt.gz

value: Unknown

value: St 26


title: Whole embryo, St 27  (replicate 2), RNA-seq

description:
St_27_rep2
St_27_rep2.bw
Eberryi_stages.counts.txt.gz

value: St 27


title: Whole embryo, St 26 (replicate 2) , RNA-seq

description:
St_26_rep2
St_26_rep2.bw
Eberryi_stages.counts.txt.gz


title: Eberryi Retina, replicate 1, scRNAseq (NovaSeq)

value: Adult - Over 100 days post hatching


title: Whole embryo, St. 25.5 , RNA-seq

description:
St_25_5_R1
St_25.5.bw
Eberryi_stages.counts.txt.gz


title: Eberryi Hatchling Optic lobe, replicate 2, scRNAseq

description:
HatchlingOLs_rep2_genes.tsv
HatchlingOLs_rep2_matrix.mtx
Hatchling_OLs.Robj

value: Optic Lobes

value: 1st day post hatching


title: Whole embryo, St 23 (replicate 2), RNA-seq

description:
St_23_rep2
St_23_rep2.bw
Eberryi_stages.counts.txt.gz

value: St 23


title: Whole embryo, St 25 (replicate 1) , RNA-seq

description:
St_25_rep1
St_25_rep1.bw
Eberryi_stages.counts.txt.gz

value: St 25


title: Whole embryo, St 22 (replicate 2) , RNA-seq

description:
St_22_rep2
St_20_rep2.bw
Eberryi_stages.counts.txt.gz

value: St 22


title: Whole embryo, St 23 (replicate 1), RNA-seq

description:
St_23_rep1
St_23_rep1.bw
Eberryi_stages.counts.txt.gz


title: Whole embryo, St 20 (replicate 2) , RNA-seq

description:
St_20_rep2
St_20_rep2.bw
Eberryi_stages.counts.txt.gz

value: St 20


title: Whole embryo, St 20(replicate 1) , RNA-seq

description:
St_20_rep1
St_20_rep1.bw
Eberryi_stages.counts.txt.gz


title: Whole embryo, St 22 (replicate 1) , RNA-seq

description:
St_22_rep1
St_22_rep1.bw
Eberryi_stages.counts.txt.gz


title: Whole embryo, St 24 (replicate 1) , RNA-seq

description:
St_24_rep1
St_24_rep1.bw
Eberryi_stages.counts.txt.gz

value: St 24


title: Whole embryo, St 24 (replicate 2) , RNA-seq

description:
St_24_rep2
St_24_rep2.bw
Eberryi_stages.counts.txt.gz


title: Whole embryo, St10-11/Gastrula (replicate 2), RNA-seq

description:
Gastrula_St10_11_rep2
St10-11_rep2.bw
Eberryi_stages.counts.txt.gz

value: Stage 10-11/Gastrula


title: Whole embryo, St 15 , RNA-seq

description:
St_15_16
St15-16.bw
Eberryi_stages.counts.txt.gz

value: St 15


title: Whole embryo, St 19  (replicate 1), RNA-seq

description:
St_19_rep1
St_19_rep1.bw
Eberryi_stages.counts.txt.gz

value: St 19


title: Eberryi Retina, replicate 3, scRNAseq

description:
Retina_rep3_genes.tsv
Retina_rep3_matrix.mtx
Retinas.Robj

value: Retina

value: Male

value: 80 days post-hatching

value: Wild-type


title: Whole embryo, St 19 (replicate 2) , RNA-seq

description:
St_19_rep2
St_19_rep2.bw
Eberryi_stages.counts.txt.gz

value: Whole embryo

value: Unknown


title: Whole embryo, St10-11/Gastrula (replicate 1), RNA-seq

description:
Gastrula_St10_11_rep1
St10-11_rep1.bw
Eberryi_stages.counts.txt.gz


title: Eberryi Mature Perioesophageal brain, replicate 1, scRNAseq

description:
Brains_rep1_genes.tsv
Brains_rep1_matrix.mtx
RenamedClusters_Brains.Robj

value: Perioesophageal brain lobes (not including optic lobes)

value: Adult - Over 100 days post hatching


title: Eberryi Retina, replicate 1, scRNAseq (HiSeq)


title: Whole embryo, St 27 (replicate 3) , RNA-seq

description:
St_27_rep3
St_27_rep3.bw
Eberryi_stages.counts.txt.gz

value: St 27


title: Brachia (entire organ - replicate2) , RNA-seq

description:
Brachia4
Brachia4.bw
Eberryi_organs.counts.txt.gz

source_name: Brachia

value: Brachia

value: male

value: Adult


title: Whole embryo, St 27 (replicate 1), RNA-seq

description:
St_27_rep1
St_27_rep1.bw
Eberryi_stages.counts.txt.gz


title: Whole embryo, St 25 (replicate 2) , RNA-seq

description:
St_25_rep2
St_25_rep2.bw
Eberryi_stages.counts.txt.gz

value: St 25


title: Eberryi Mature Optic lobe, replicate 1, scRNAseq (HiSeq)

description:
Optic_Lobes_rep1_genes.tsv
Optic_Lobes_rep1_matrix.mtx
RenamedClusters_EbAdOLs.Robj

value: Optic Lobes


title: Brachia (entire organ), RNA-seq

description:
Brachia3
Brachia3.bw
Eberryi_organs.counts.txt.gz


title: Brachia (anterior-most portion) , RNA-seq

description:
Brachia1
Brachia1.bw
Eberryi_organs.counts.txt.gz


title: Brachia (posterior-most portion) , RNA-seq

description:
Brachia2
Brachia2.bw
Eberryi_organs.counts.txt.gz


title: Retina (Right), RNA-seq

description:
Retina2
Retina2.bw
Eberryi_organs.counts.txt.gz


title: Retina (Left), RNA-seq

description:
Retina1
Retina1.bw
Eberryi_organs.counts.txt.gz


title: Sperm, RNA-seq

description:
Sperm
Sperm.bw
Eberryi_organs.counts.txt.gz

source_name: Sperm

value: Sperm


title: Testes, RNA-seq

description:
Testes
Testes.bw
Eberryi_organs.counts.txt.gz

source_name: Testes

value: Testes


title: Optic Lobe (Right), RNA-seq

description:
OpticLobe2
OpticLobe2.bw
Eberryi_organs.counts.txt.gz

source_name: Optic lobe

value: Optic lobe


title: Optic Lobe (Left), RNA-seq

description:
OpticLobe1
OpticLobe1.bw
Eberryi_organs.counts.txt.gz


title: Optic nerve, RNA-seq

description:
Optic nerve
Optic_nerve.bw
Eberryi_organs.counts.txt.gz

source_name: Optic nerve

value: Optic nerve


title: Mantle, RNA-seq

description:
Mantle
Mantle.bw
Eberryi_organs.counts.txt.gz

source_name: Mantle

value: Mantle


title: Pancreatic Diverticulum, RNA-seq

description:
PancreaticDiverticulum
Pancreatic_Diverticulum.bw
Eberryi_organs.counts.txt.gz

source_name: Pancreatic Diverticulum

value: Pancreatic Diverticulum


title: Optic Lobes (Left and right) , RNA-seq

description:
OpticLobe3
OpticLobe3.bw
Eberryi_organs.counts.txt.gz

value: Wild-type


title: Hepatopancreas (replicate 2) , RNA-seq

description:
Hepatopancreas2
Hepatopancreas2.bw
Eberryi_organs.counts.txt.gz

source_name: Hepatopancreas

value: Hepatopancreas


title: Hepatopancreas (replicate 1) , RNA-seq

description:
Hepatopancreas1
Hepatopancreas1.bw
Eberryi_organs.counts.txt.gz


title: Buccal mass, RNA-seq

description:
BuccalMass
Buccal_mass.bw
Eberryi_organs.counts.txt.gz

source_name: Buccal mass

value: Buccal mass


title: Systemic Heart, RNA-seq

description:
SystemicHeart
Systemic_Heart.bw
Eberryi_organs.counts.txt.gz

source_name: Systemic Heart

value: Systemic Heart


title: WT-GM_IL6

city: Tianjin

first: Yunhuan

address: No. 94, Weijin Road, Nankai District, Tianjin, China

institute: Nankai University

description: Library name: Sample 2

data_processing:
All the reads were mapped to the human reference genome (GRCh38.p13,) using STAR aligner (v2.5.0c).
Assembly: hg38
Supplementary files format and content: tab-demilited text files includs raw counts for each sample
Supplementary files format and content: tab-demilited text files includ FPKM values for each sample

source_name: Peripheral blood mononuclear cells induced macrophages

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq

value: mononuclear cells induced macrophages

value: macrophages

value: shNC


title: NC_1

description: Library name: Sample 1

value: Peripheral blood mononuclear cells induced macrophages

value: WT


title: Brachial_Heart, RNA-seq

description:
BrachialHeart
Brachial_Heart.bw
Eberryi_organs.counts.txt.gz

value: male

value: Adult


title: Mometasone furoate + Indacaterol + Carbachol rep5 18h

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

description: Library name: H20

data_processing:
bcl2fastq v2.17.1.14 for base calling; STAR v2.4.2a for alignment and coverage counting;
Assembly: GRCh38.78
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM) values for each sample for each gene described by its HGNC symbol

source_name: Lung

growth_protocol: BEAS-2B cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10 % Canada origin FBS, L-glutamine (2.5 mM) and NaHCO3 (0.15 % w/v) followed by overnight incubation in serum-free medium.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) and quantified using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE) according to manufacturer's instructions.
Illumina TruSeq

treatment_protocol: Confluent BEAS-2B cells were treated for one, two, six and eighteen hours with vehicle (NS), indacaterol (100 nM), carbachol (10 µM), mometasone (100 nM), or the combination of mometasone and indacaterol, mometasone and carbachol, indacaterol and carbachol, or all three in combination.

value: Lung

value: BEAS-2B human airway epithelial cell line

value: Mometasone + indacterol + carbachol


title: Mometasone furoate + Indacaterol + Carbachol rep5 6h

description: Library name: H19


title: Mometasone furoate + Indacaterol + Carbachol rep5 2h

description: Library name: H18


title: Mometasone furoate + Indacaterol + Carbachol rep5 1h

description: Library name: H17


title: Tentacle suckers, RNA-seq

description:
TentacleSuckers
Tentacle_Suckers.bw
Eberryi_organs.counts.txt.gz

source_name: Suckers from tentacles

value: Suckers from tentacles


title: Retina (Left and right) , RNA-seq

description:
Retina3
Retina3.bw
Eberryi_organs.counts.txt.gz

value: Retina


title: Mometasone furoate + Indacaterol + Carbachol rep4 6h

description: Library name: H15


title: Mometasone furoate + Indacaterol + Carbachol rep4 2h

description: Library name: H14


title: Arm suckers, RNA-seq

description:
ArmSuckers
ArmSuckers.bw
Eberryi_organs.counts.txt.gz

source_name: Suckers from arms

value: Suckers from arms


title: mature leaf, third leaf of tender shoot

city: Hefei

first: Qiang

last: Wang

state: Anhui

address: Changjiang RD 130

institute: Anhui Agriculture University

data_processing:
Single-cells were sequenced with an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150 bp) by LC-Bio Technology co. ltd., (Hangzhou, China).
Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 2.20).
Sample demultiplexing, barcode processing and single-cell 3’ gene counting was done by using the Cell Ranger (version 5.0.1) and scRNA-seq data were aligned to the tea chromosome-level genome from the Tea Plant Information Archive (TPIA) (http://tpia.teaplant.org).
Single cell captured from 1L and 3L were processed using 10XGenomics Chromium Single Cell 3’ Solution. The Cell Ranger output was loaded into Seurat (version 3.1.1) which was used for dimensional reduction, clustering, and analysis of scRNA-seq data.
All genes expressed in less than one cell were removed, number of genes expressed per cell was >500 and <5000 as low and high cut-off, respectively, UMI counts were less than 500, the percent of mitochondrial-DNA derived gene-expression was <25%, doublets were removed by DoubletFinder with default settings (version 2.0.2).
Assembly: shuchazao_V2.genome.fas.gz
Supplementary files format and content: Each mtx file contains the entire gene expression matrix for all cells in each sample

organism: Camellia sinensis

source_name: leaf

growth_protocol: Tender shoots of the current year of 6 years old C. sinensis var. sinensis cv. “shuchazao” trees were collected from a tea plantation of Anhui Agriculture University (Hefei, China) in June.

extract_protocol:
The complete 1st leaf (1L) and 3rd leaf (3L) blades were picked and surface sterilized with 75% alcohol for the following experiments. About 0.6 g of fresh leaf blades were cut and immediately put in a digestion solution for protoplast and tissue isolation. The digestion solution for leaf tissue and protoplast single cell preparation contained 0.4 M D-mannitol (Sigma, USA), 1.5% cellulase R10 (Yakult, Japan), 0.5% macerozyme R10 (Yakult, Tokyo, Japan), 0.7% snailase (YEASEN, Shanghai, China), 20 mM 4-morpholineethanesulfonic acid (pH = 5.5), 20 mM KCl (Sigma, USA), 10 mM CaCl2 (Sigma, USA), 10 mM β-mercaptoethanol and 0.1% BSA (Sigma, USA). Entire intact leaf blades were cut into strips and immersed into 30 mL of digest solution in a glass dish. The strips were evacuated for 5 min and then incubated in the enzyme solution in an incubator at 25 °C for 4 hrs. The digestion mixture was filtered through a 40 μm nylon mesh sieve. Protoplasts were collected after gentle washing twice (centrifugation at 100 g for 2 min with a swinging bucket rotor) and were re-suspended in 8% D-mannitol solution. The number of isolated protoplasts was measured with a hemocytometer counting chamber, and the viability of the protoplasts was assessed by 2 μg mL-1 fluorescein diacetate. The concentration of protoplasts was adjusted to 1500-2000 cells μL-1 by 0.4 M D-mannitol for loading onto the chromium controller of the 10xGenomics platform.
The scRNA-seq libraries were constructed using the 10x Genomics 3' Reagent Kits v3.

value: leaf

value: shuchazao


title: Mometasone furoate + Indacaterol + Carbachol rep4 1h

description: Library name: H13


title: CD163-GM_IL6

description: Library name: Sample 3


title: Mometasone furoate + Indacaterol + Carbachol rep3 2h

description: Library name: H10


title: Mometasone furoate + Indacaterol + Carbachol rep3 18h

description: Library name: H12


title: R-C patterned orgnaoid

city: BALTIMORE

first: Feiyu

last: Yang

state: Maryland

address: Ross Research Building

institute: Johns Hopkins University

description:
Library name: sampleRC
R-C patterned orgnaoid at different ages and conditions

data_processing:
The spatial transcriptomics data were process using the Seurat package.
Seurat objects for all samples were saved as Rds format
Assembly: NCBI
Supplementary files format and content: Rds
Library strategy: Spatial Transcriptomics

source_name: Brain organoid

growth_protocol: Human brain organoids were grow in the device described in the paper, and were differentiated for up to 25 days for regional specific patterning or long-term cultured with agitations.

extract_protocol:
Organoids were sections into 10µm slides for spatial transcriptomic analysis.
Library was constructed using "Visium Human Transcriptome Prove Set v2.0" accordance with the Visium CytAssist Spatial Gene Expression Reagent Kit User Guideline (CG000495).

treatment_protocol: Human brain organoids were treated with morphogen gradients for D-V or R-C axial patternings.

value: Brain organoid

value: Neuron/progenitors

value: Wnt or RA gradient


title: Mometasone furoate + Indacaterol + Carbachol rep3 1h

description: Library name: H9


title: Mometasone furoate + Indacaterol + Carbachol rep4 18h

description: Library name: H16


title: D-V patterned forebrain organoid

description:
Library name: sampleDV
D-V patterned forebrain organoids at different ages

value: SHH/Wnt-inhibitor gradient


title: Mometasone furoate + Indacaterol + Carbachol rep2 18h

description: Library name: H8


title: Iridescent layer surrounding retina, RNA-seq

description:
IridiscentRetina
IridescentLayerAroundRetina.bw
Eberryi_organs.counts.txt.gz

source_name: Iridescent layer surrounding retina

value: Iridescent layer surrounding retina

value: Wild-type


title: Mometasone furoate + Indacaterol + Carbachol rep2 6h

description: Library name: H7

value: WT


title: Skin containing chromophores , RNA-seq

description:
SkinChromatophores
Skin_containing_chromatophores.bw
Eberryi_organs.counts.txt.gz

source_name: Skin containing chromophores

value: Skin containing chromophores

value: male


title: Mometasone furoate + Indacaterol + Carbachol rep2 2h

description: Library name: H6

value: Lung


title: S, rep5

city: Cambridge

first: Cory

middle: Adam

last: Perugino

state: MA

address: 600 Main Street

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
The reads in each sample were mapped to human reference genome GrCh38 using STAR software (version 2.7.9a). On average, we obtained ~11.3 million uniquely mapped reads per sample. Raw read count matrix (the number of reads for each gene in each sample) was obtained using HTSeq python package (version 2.0.1)
Assembly: GrCh38
Supplementary files format and content: CSV file of read count matrix

source_name: B cell

extract_protocol:
Naïve (CD19+ CD20+ IgD+ CD27- CXCR5+ CD11c-), DN1 (CD19+ CD20+ IgD- CD27- CXCR5+ CD11c-), and switched memory (CD19+ CD20+ IgD- CD27+ CXCR5+ CD11c-) B cells were FACS purified from cryopreserved PBMC’s using a FACS Aria Fusion cell sorter. Total RNA was isolated from sorted B cell populations using the RNAeasy Plus Micro kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed via Agilent 4200 Tapestation and RNA concentration was determined using a Qubit Flex (Fisher Scientific).
Total RNA (4 ng/sample) was processed using the SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian (Takara) to create RNA-seq libraries.

value: B cell

value: S


title: N, rep6

value: N


title: N, rep5


title: Mometasone furoate + Indacaterol + Carbachol rep1 18h

description: Library name: H4

value: BEAS-2B human airway epithelial cell line

value: Mometasone + indacterol + carbachol


title: Mometasone furoate + Indacaterol + Carbachol rep2 1h

description: Library name: H5


title: S, rep4


title: Mometasone furoate + Indacaterol + Carbachol rep1 6h

description: Library name: H3


title: Mometasone furoate + Indacaterol + Carbachol rep1 2h

description: Library name: H2


title: N, rep4


title: Mometasone furoate + Indacaterol + Carbachol rep1 1h

description: Library name: H1


title: D, rep3

value: D


title: Mometasone furoate + Indacaterol + Carbachol rep3 6h

description: Library name: H11


title: young leaf, first leaf of tender shoot

value: leaf

value: shuchazao


title: S, rep6


title: Inadacterol + Carbachol rep5 18h

description: Library name: G20

value: Indacterol + carbachol


title: Inadacterol + Carbachol rep5 2h

description: Library name: G18


title: N, rep3


title: D, rep2


title: Inadacterol + Carbachol rep5 6h

description: Library name: G19


title: Eberryi Mature Optic lobe, replicate 2, scRNAseq

description:
Optic_Lobes_rep2_genes.tsv
Optic_Lobes_rep2_matrix.mtx
RenamedClusters_EbAdOLs.Robj

source_name: Optic Lobes

value: Optic Lobes

value: Unknown

value: 60 days post hatching


title: Inadacterol + Carbachol rep5 1h

description: Library name: G17


title: D, rep5


title: S, rep2


title: Inadacterol + Carbachol rep4 18h

description: Library name: G16


title: D, rep6


title: S, rep3


title: N, rep2


title: D, rep1


title: Inadacterol + Carbachol rep4 6h

description: Library name: G15


title: D, rep4


title: Inadacterol + Carbachol rep4 2h

description: Library name: G14


title: Inadacterol + Carbachol rep3 18h

description: Library name: G12


title: S, rep1


title: Inadacterol + Carbachol rep4 1h

description: Library name: G13


title: N, rep1


title: BMDM_atac_6.5_LPS_E2

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

description: Nextseq 500 1st_run samples

data_processing:
Paired-end sequencing was performed with Next-seq 500 and Nextseq 2000 with paired end reads of 38 base pairs and 59 base pairs respectivly.
Reads were then mapped to the mm10 mouse genome with Bowtie2 using the option -k 10 -X 1000 --end-to-end --very-sensitive”.
Sam files were converted to Bam files, and read duplicates were removed using Picard. Blacklist regions and mitochondrial genomic reads were removed using BEDTools and Picard, respectively.
Bam files were converted to Bed files also using BEDTools, and MACS2 was used to call peaks using the converted bed file. Macs2 call-peak options used were “-f BED -g mm -q 0.05 -- nomodel --shift -75 --extsize 150 --keep-dup all”. Macs2 peaks from each condition were concatenated and then overlapping regions merged using mergeBed from BEDTools. To count the number of reads in each merged peak, featureCounts  was used. Read counts from featureCounts were normalized using the TMM method in EdgeR.
Bigwig files were generated using using the bamCoverage (Deeptools) tool with the options --binSize 10 -p max --normalizeUsing None --effectiveGenomeSize 2864785220  --extendReads –scaleFactor X”. The scale factor “X” was derived from the TMM normalization.
Assembly: mm10
Supplementary files format and content: narrowPeak bed files from MACS2
Supplementary files format and content: bigWig files generated with Deeptools

source_name: bone marrow-derived macrophage

growth_protocol: Bone marrow-derived macrophages are differentiated from bone marrow cells and cultured in macrophage growth medium (MGM) (RPMI + 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 200 U/mL penicillin/streptomycin, 10% FBS, 50 µM 2-mercaptoethanol and 30% L929-conditioned media).

extract_protocol:
Cell suspensions were counted and ~ 50,000 cells were used for constructing each ATAC-seq library according to the protocol detailed by Buentrostro et. al, 2015, Molecular Cell.
Cell suspensions were counted and ~ 50,000 cells were used for constructing each ATAC-seq library according to the protocol detailed by Buentrostro et. al, 2015, Molecular Cell.

treatment_protocol: pH medium was prepared using special RPMI-1640 without sodium bicarbonate. The media pH was adjusted to desired pH value using HCl (1 M) or NaOH (1 M). The cells were incubated at the indicated pH for at least 4 hours, followed by treatment with 10 ng/mL LPS or PBS for 4 hours in the respective conditions. BMDMs were plated on non-TC plates for ATAC-seq analysis. Cells were conditioned with pH 7.4 or 6.5 growth medium for 4 hours and stimulated with 10 ng/mL LPS for another 4 hours before harvesting with 3 mM ice-cold PBS-EDTA.

value: bone marrow-derived macrophage

value: wild-type

value: pH 6.5, 4 hrs LPS


title: Inadacterol + Carbachol rep2 18h

description: Library name: G8

value: WT


title: Inadacterol + Carbachol rep3 2h

description: Library name: G10

value: Lung


title: BMDM_atac_7.4_LPS_E2

description: Nextseq 500 1st_run samples

value: pH 7.4, 4 hrs LPS


title: Inadacterol + Carbachol rep3 1h

description: Library name: G9


title: Inadacterol + Carbachol rep3 6h

description: Library name: G11


title: BMDM_atac_6.5_UT_E2

description: Nextseq 500 1st_run samples

value: pH 6.5, untreated


title: BMDM_atac_7.4_UT_E2

description: Nextseq 500 1st_run samples

value: pH 7.4, untreated


title: BMDM_atac_6.5_LPS_E1

description: Nextseq 500 1st_run samples


title: BMDM_atac_7.4_LPS_E1

description: Nextseq 500 1st_run samples


title: Inadacterol + Carbachol rep2 2h

description: Library name: G6

value: BEAS-2B human airway epithelial cell line


title: Inadacterol + Carbachol rep2 6h

description: Library name: G7


title: Inadacterol + Carbachol rep2 1h

description: Library name: G5


title: BMDM_atac_7.4_UT_E1

description: Nextseq 500 1st_run samples


title: Inadacterol + Carbachol rep1 18h

description: Library name: G4


title: MP7ZZ3

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: 10X genomics

data_processing:
Demultiplexed with CellRanger v.7.
Downstream analyses were done with Seurat v.4 (Hao* & Hao* et al., 2021).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Total thymic stroma (CD45-)

extract_protocol:
Excess blood vessels, connective tissues, and adipocytes were carefully removed in ice-chilled 4 sterile 1X PBS (w/o Ca2+, Mg2+). Thymi were finely cut into 1~2 mm3 fragments and transferred into digestion buffer (2% FBS/1640 RPMI (w/ 25mM HEPES), DNase I (20µg/µL), Collagenase/Dispase (1mg/mL)). Tubes containing the thymic fragments with digestion buffer were incubated in a 37 water bath for 20 minutes, 3 times. The solution was gently mixed up and down with transfer pipettes in between the incubations, 100 times each. To remove undigested thymic fragments, the solution was passed into a new tube, through a 70µm cell strainer. Single-cell suspension was then centrifuged for 10 minutes at 300rcf, 4, a condition for centrifugation throughout this protocol. After decanting the supernatant, erythrocytes were lysed with a 2-minute-long incubation in 2mL RBC Lysis Buffer (10X) (BioLegend 420301). After another centrifugation & decantation, cells were resuspended in MACS buffer (filtered and degassed 0.5% BSA/2mM EDTA/1X PBS (w/o Ca2+, Mg2+)). Post cell counting with a hemocytometer, cells underwent CD45 separation as per MACS separation guidelines with mouse CD45 microbeads (Miltenyi Biotec 130-052-301) to collect CD45- cells.
Library was constructed according to the manufacturer's instructions (single cell 3', 10X genomics).

value: Total thymic stroma (CD45-)

value: Z/Z


title: Inadacterol + Carbachol rep1 6h

description: Library name: G3


title: Inadacterol + Carbachol rep1 2h

description: Library name: G2


title: Mometasone furoate + Carbachol rep5 18h

description: Library name: F20

value: Mometasone + carbachol


title: MP7WT1

description: 10X genomics

value: Wild-type


title: MP7ZZ2

description: 10X genomics


title: Mometasone furoate + Carbachol rep5 6h

description: Library name: F19


title: Inadacterol + Carbachol rep1 1h

description: Library name: G1

value: Indacterol + carbachol


title: Mometasone furoate + Carbachol rep5 2h

description: Library name: F18


title: MP7WT2

description: 10X genomics


title: MP3ZZ3

description: 10X genomics


title: MP3ZZ2

description: 10X genomics


title: Mometasone furoate + Carbachol rep5 1h

description: Library name: F17


title: BMDM_atac_6.5_UT_E1

description: Nextseq 500 1st_run samples


title: MP3ZZ1

description: 10X genomics


title: MP3WT3

description: 10X genomics


title: Mometasone furoate + Carbachol rep4 6h

description: Library name: F15


title: Mometasone furoate + Carbachol rep4 18h

description: Library name: F16


title: Mometasone furoate + Carbachol rep4 2h

description: Library name: F14


title: MP3WT2

description: 10X genomics


title: Mometasone furoate + Carbachol rep4 1h

description: Library name: F13


title: MP3WT1

description: 10X genomics


title: MP7ZZ1

description: 10X genomics


title: MP14ZZ2

description: 10X genomics


title: Mometasone furoate + Carbachol rep3 18h

description: Library name: F12


title: Mometasone furoate + Carbachol rep3 6h

description: Library name: F11


title: MP14ZZ1

description: 10X genomics


title: MP14WT2

description: 10X genomics


title: MP14WT1

description: 10X genomics


title: Mometasone furoate + Carbachol rep3 1h

description: Library name: F9


title: Mometasone furoate + Carbachol rep3 2h

description: Library name: F10


title: Mometasone furoate + Carbachol rep2 18h

description: Library name: F8


title: FP3ZZ2

description: 10X genomics


title: Mometasone furoate + Carbachol rep2 6h

description: Library name: F7


title: FP3ZZ1

description: 10X genomics


title: FP3WT2

description: 10X genomics


title: FP14ZZ2

description: 10X genomics


title: FP3WT1

description: 10X genomics


title: FP14ZZ1

description: 10X genomics


title: Mometasone furoate + Carbachol rep1 6h

description: Library name: F3


title: FP14WT2

description: 10X genomics


title: Mometasone furoate + Carbachol rep1 1h

description: Library name: F1


title: Lactating_WT_6

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: 10x Genomics Chromium

data_processing:
Demultiplexing, barcoding, alignment, and feature counting were performed with 10x Genomics CellRanger software v5.0.1 mkfastq and count commands.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Ileum

growth_protocol: Mice were fed a standard diet whilst breeding or in maintenance colonies; RM3 during breeding and RM1 for maintenance and experiment (Special Diets Services)

extract_protocol:
Cells were partitioned and barcoded using the 10X Genomics Chromium Controller, according to the manufacturer’s instructions. The harvested cDNA was assessed and quantified using the Agilent 2100 Bioanalyser and library construction performed using the 10X Single Cell 3' Library Kit v3.1. Libraries were quality controlled by shallow sequencing, balanced, and deep-sequenced.
scRNA-Seq libraries were prepared according to the manufacturer's instructions using the 10X Single Cell 3' Library Kit v3.1

treatment_protocol: Lactating mice of Slc5a4a KO (-/-) and WT (+/+) at day 7 lactation and age-matched virgin females were used.

value: Ileum

tag: mating status

value: Lactating

value: Female


title: Mometasone furoate + Indacaterol rep5 18h

description: Library name: E20

value: Mometasone + indacaterol


title: Mometasone furoate + Indacaterol rep5 6h

description: Library name: E19


title: Lactating_WT_5

description: 10x Genomics Chromium


title: Lactating_WT_4

description: 10x Genomics Chromium


title: FP14WT1

description: 10X genomics


title: Mometasone furoate + Indacaterol rep5 2h

description: Library name: E18


title: Mometasone furoate + Indacaterol rep5 1h

description: Library name: E17


title: Lactating_WT_2

description: 10x Genomics Chromium


title: Lactating_WT_1

description: 10x Genomics Chromium


title: Mometasone furoate + Indacaterol rep4 6h

description: Library name: E15


title: Mometasone furoate + Carbachol rep2 2h

description: Library name: F6


title: Mometasone furoate + Carbachol rep2 1h

description: Library name: F5


title: Lactating_KO_1

description: 10x Genomics Chromium

value: SGLT3a KO


title: Lactating_KO_3

description: 10x Genomics Chromium


title: Lactating_KO_2

description: 10x Genomics Chromium


title: Lactating_WT_3

description: 10x Genomics Chromium


title: Mometasone furoate + Carbachol rep1 18h

description: Library name: F4


title: Mometasone furoate + Indacaterol rep4 2h

description: Library name: E14


title: Mometasone furoate + Indacaterol rep4 1h

description: Library name: E13


title: Mometasone furoate + Indacaterol rep3 18h

description: Library name: E12


title: Mometasone furoate + Indacaterol rep3 6h

description: Library name: E11


title: VF_Ileum_6

data_processing:
Sequenced samples were quality controlled using FastQC v0.11.5, followed by alignment to the mouse genome and feature counting using STAR (v2.7.7a)
Differential expression analysis was conducted in R using the DESeq2 package (v1.34.0)
Quality assessments were performed, including PCA and hierarchical clustering, prior to analysis of differential expression using the Wald test with a specified FDR (alpha<0.05)
Where samples were collected and sequenced separately, contributions from this potential confounding factor were removed by batch correction using the RUVg methodology
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files containing raw read counts

molecule: polyA RNA

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) and RNeasy Plus Mini Kit (Qiagen). 200 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepard using NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module following manufacturer's protocols.

treatment_protocol: Lactating mice at day 7 lactation, and age-matched virgin females and males were used.

value: Virgin


title: Mometasone furoate + Indacaterol rep3 2h

description: Library name: E10

value: WT


title: VM_Ileum_6

value: Male


title: LF_Ileum_6


title: Mometasone furoate + Indacaterol rep3 1h

description: Library name: E9

value: Lung


title: VM_Ileum_5


title: Mometasone furoate + Indacaterol rep2 18h

description: Library name: E8


title: Mometasone furoate + Indacaterol rep2 6h

description: Library name: E7


title: LF_Ileum_5


title: Mometasone furoate + Indacaterol rep2 2h

description: Library name: E6


title: VF_Ileum_5


title: VF_Ileum_4


title: Mometasone furoate + Indacaterol rep2 1h

description: Library name: E5


title: VM_Ileum_4


title: Mometasone furoate + Indacaterol rep1 18h

description: Library name: E4


title: Mometasone furoate + Indacaterol rep1 2h

description: Library name: E2


title: Carbachol rep5 2h

description: Library name: D18

value: Carbachol (10 µM)


title: Carbachol rep5 6h

description: Library name: D19


title: Mometasone furoate + Indacaterol rep1 1h

description: Library name: E1


title: VF_Ileum_2


title: LF_Ileum_3


title: Carbachol rep5 1h

description: Library name: D17


title: VF_Ileum_3


title: VM_Ileum_1


title: Carbachol rep4 18h

description: Library name: D16


title: VM_Ileum_3


title: Carbachol rep4 2h

description: Library name: D14


title: VF_Ileum_1


title: Carbachol rep5 18h

description: Library name: D20


title: LF_Ileum_4


title: Carbachol rep4 6h

description: Library name: D15


title: LF_Ileum_2


title: Mometasone furoate + Indacaterol rep1 6h

description: Library name: E3


title: VF_Duodenum_6

source_name: Duodenum

value: Duodenum


title: Carbachol rep4 1h

description: Library name: D13

value: BEAS-2B human airway epithelial cell line


title: Carbachol rep3 18h

description: Library name: D12


title: VM_Duodenum_6


title: Carbachol rep3 6h

description: Library name: D11


title: LF_Ileum_1


title: Carbachol rep3 1h

description: Library name: D9


title: LF_Jejunum_6

source_name: Jeunum

value: Jeunum


title: VM_Ileum_2


title: Carbachol rep2 1h

description: Library name: D5


title: Carbachol rep3 2h

description: Library name: D10


title: VM_Jejunum_6


title: Carbachol rep2 6h

description: Library name: D7


title: VF_Jejunum_5


title: VF_Jejunum_6


title: VM_Jejunum_5


title: Carbachol rep2 2h

description: Library name: D6


title: Carbachol rep1 18h

description: Library name: D4


title: Carbachol rep2 18h

description: Library name: D8


title: VM_Duodenum_4


title: Carbachol rep1 1h

description: Library name: D1


title: LF_Jejunum_5


title: LF_Duodenum_5


title: VF_Duodenum_5


title: VM_Duodenum_5


title: LF_Duodenum_6


title: Carbachol rep1 2h

description: Library name: D2


title: VM_Jejunum_4


title: Carbachol rep1 6h

description: Library name: D3


title: VF_Duodenum_4


title: Indacaterol rep5 6h

description: Library name: C19

value: Indacaterol (100 nM)


title: VF_Jejunum_4


title: Indacaterol rep5 18h

description: Library name: C20


title: Indacaterol rep5 2h

description: Library name: C18


title: LF_Duodenum_4


title: LF_Jejunum_4


title: Indacaterol rep5 1h

description: Library name: C17


title: Indacaterol rep4 18h

description: Library name: C16


title: VM_Duodenum_3


title: Indacaterol rep4 6h

description: Library name: C15


title: Indacaterol rep4 2h

description: Library name: C14


title: VF_Duodenum_3


title: Indacaterol rep4 1h

description: Library name: C13


title: VM_Jejunum_3


title: VF_Jejunum_3


title: tumor tissue of squamouspapillary craniopharyngioma from case CP9, biological replicate1

city: minatoku toranomon

first: Tatsuma

last: Matsuda

address: tokyo

institute: toranomon hospital

description:
Library name: CP9rep1
10x Genomics

data_processing:
ASTQ files were aligned using the 103 Genomics CellRanger 6.0.0. pipeline to the human GRCh38 reference transcriptome to generate gene-expression count matrices with the ‘‘exclude the introns’’ option.
Assembly: GRCh38
Supplementary files format and content: separated barcode file and features file, matrix file

source_name: tumor tissue

extract_protocol:
A single-cell suspension of the craniopharyngioma samples was digested via stirring at 37_x000E_C for 90 min using collagenase I 60 (160 mL, 100 mg/ mL) and collagenase VII 61 (400 mL, 100 mg/mL; Worthington, OH, USA) immediately after surgical removal. The suspension was then filtered through a 40-mm cell strainer (Corning, NY, USA) to remove debris and undigested large tissue fragments. After allowing the cells to settle, red blood cells were isolated using ACK lysing buffer (Thermo Fisher Scientific, MA, USA), and dead cells were removed using a dead cell removal kit (Miltenyi Biotec, Bergisch Gladbach, Germany); the resultant cell suspension contained approximately 20,000 cells per sampl
The obtained cell suspension was prepared following the specifications of 103 Genomics, using 103 Chromium Next GEM single-cell 3ʹ re- agent kits and the library construction kit (103 Genomics, CA, USA). The cell suspension was loaded into the 103 Genomics Chromium Controller, creating gel beads in emulsion (GEM). After generating the GEM, the suspension was incubated at 53_x000E_C for 45 min in a thermal cycler (Veriti, Applied Biosystems, MA, USA). A barcode-linked polyA cDNA with barcodes at the 5ʹ end was produced via adding template switch oligos linked to cell barcodes and unique molecular identifiers (UMIs). The GEMs were then disrupted, and single-stranded cDNA was cleaned using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). The cDNA was amplified (98_x000E_C for 3 min, 11 cycles of 98_x000E_C for 15 s, 63_x000E_C for 20 s, and 72_x000E_C for 1 min) and the quality was assessed using Agilent TapeStation (Agilent Technologies, CA, USA). The cDNA was enzymatically fragmented, end-repaired, A-tailed, and subjected to size selection on both ends using SPRIselect beads (Beckman Coulter, CA, USA). It was then ligated with adapters provided in the kit. Sample-specific indices were introduced into each library via 14-cycle poly- merase chain reaction amplification using kit-supplied indices (98_x000E_C for 45 s, 14 cycles of 98_x000E_C for 20 s, 54_x000E_C for 30 s, 72_x000E_C for 20 s, 72_x000E_C for 1 min, and holding at 4_x000E_C). Indexed libraries underwent a second round of size selection. The library was quantified and quality was assessed using Agilent TapeStation. Libraries were clustered on a NovaSeq 6000 paired-end read flow cell (Illumina, CA, USA). Sequencing was per- formed with reads for R1 (containing 103 barcodes and UMIs), I7 index (8 cycles; sample index), and R2 (89 cycles; transcript). The 103 Ge- nomics Cell Ranger Single-Cell Software was used for sample demultiplexing, alignment to the human reference genome (hg19), filtering, UMI counting, single-cell 3ʹ end gene counting, and QC as per manufacturer’s instructions.

value: tumor tissue

value: male


title: tumor tissue of squamouspapillary craniopharyngioma from case CP10, biological replicate1

description:
Library name: CP10rep1
10x Genomics


title: Indacaterol rep3 2h

description: Library name: C10


title: LF_Duodenum_3


title: LF_Jejunum_3


title: VM_Duodenum_2


title: Indacaterol rep3 6h

description: Library name: C11


title: tumor tissue of adamantinomatous craniopharyngioma from case CP5, biological replicate2

description:
Library name: CP5rep2
10x Genomics

value: female


title: tumor tissue of adamantinomatous craniopharyngioma from case CP7

description:
Library name: CP7
10x Genomics


title: tumor tissue of adamantinomatous craniopharyngioma from case CP6

description:
Library name: CP6
10x Genomics


title: tumor tissue of ciliated craniopharyngioma from case CP8

description:
Library name: CP8
10x Genomics


title: Mometasone furoate + Carbachol rep1 2h

description: Library name: F2

value: Mometasone + carbachol


title: Indacaterol rep3 1h

description: Library name: C9


title: tumor tissue of squamouspapillary craniopharyngioma from case CP10, biological replicate2

description:
Library name: CP10rep2
10x Genomics


title: tumor tissue of adamantinomatous craniopharyngioma from case CP4, biological replicate2

description:
Library name: CP4rep2
10x Genomics


title: tumor tissue of squamouspapillary craniopharyngioma from case CP9, biological replicate2

description:
Library name: CP9rep2
10x Genomics


title: tumor tissue of adamantinomatous craniopharyngioma from case CP4, biological replicate1

description:
Library name: CP4rep1
10x Genomics


title: VF_Duodenum_2


title: Indacaterol rep2 6h

description: Library name: C7


title: VM_Jejunum_2


title: Indacaterol rep3 18h

description: Library name: C12


title: tumor tissue of adamantinomatous craniopharyngioma from case CP1

description:
Library name: CP1
10x Genomics


title: tumor tissue of adamantinomatous craniopharyngioma from case CP2

description:
Library name: CP2
10x Genomics


title: tumor tissue of adamantinomatous craniopharyngioma from case CP3

description:
Library name: CP3
10x Genomics


title: Indacaterol rep2 2h

description: Library name: C6


title: VF_Jejunum_2


title: LF_Duodenum_2

value: Lactating


title: RNA profiles of MIA PaCa-2 cells treated with Cannabichromene (CBC)

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

description:
Library name: MIACBC
Column name in raw_counts_All_Samples.txt: MIACBC

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 was used for basecalling.
Illumina adapter sequences were removed using the using cutadapt software (version 2.7), and the remaining reads sequences were aligned to the Homo sapiens reference genome (GRCh38) using STAR software with default parameters.
The number of reads mapped to gene features (GTF file of GRCh38.89) was counted using HTSeq.
The read counts for the samples were normalized using the TMM normalization of the edgeR package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: MIA PaCa-2

extract_protocol:
Total RNA was isolated using Trizol reagent (Ambion, North Greenbush, NJ, USA). The isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria), according to the manufacturer’s instructions.
RNA libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK), according to the standard Illumina protocols

treatment_protocol: pancreatic cancer cells were treated with PBS or CBC for 24 hours

value: MIA PaCa-2

value: human pancreatic cancer cell line

value: Cannabichromene (CBC)


title: RNA profiles of PANC-1 cells treated with Cannabichromene (CBC)

description:
Library name: PANCCBC
Column name in raw_counts_All_Samples.txt: PANCCBC


title: Indacaterol rep2 1h

description: Library name: C5


title: VM_Duodenum_1

value: Virgin


title: RNA profiles of MIA PaCa-2 cells treated with PBS

description:
Library name: MIAcon
Column name in raw_counts_All_Samples.txt: MIAcon

value: WT

value: PBS


title: Indacaterol rep1 6h

description: Library name: C3

value: Lung


title: LF_Jejunum_2

value: Female


title: Indacaterol rep1 18h

description: Library name: C4


title: VF_Duodenum_1

value: Duodenum


title: Indacaterol rep1 2h

description: Library name: C2

value: BEAS-2B human airway epithelial cell line


title: Indacaterol rep2 18h

description: Library name: C8


title: Mometasone furoate rep5 18h

description: Library name: B20

value: Mometasone furoate (100 nM)


title: VF_Jejunum_1

value: Jeunum


title: Mometasone furoate rep5 2h

description: Library name: B18


title: Mometasone furoate rep5 6h

description: Library name: B19


title: Pregnant_6

data_processing:
Sequenced samples were quality controlled using FastQC v0.11.5 and aligned using HISAT2 v2.0.4
Gene counts were produced for the same annotations using featureCounts within subread v2.0.0
Analysis of differential expression was performed within R using the DESeq2 package (v1.24.0)
Quality assessments were performed, including PCA and hierarchical clustering, prior to analysis of differential expression using the Wald test with a specified FDR (alpha<0.05)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files containing raw read counts

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (Qiagen). 200 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepard using NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module following manufacturer's protocols.

value: Ileum

value: Pregnant


title: Pseudo_6

value: Pseudopregnant


title: Mometasone furoate rep4 18h

description: Library name: B16


title: Mometasone furoate rep5 1h

description: Library name: B17


title: LF_Jejunum_1


title: Virgin_6


title: Pseudo_5


title: RNA profiles of PANC-1 cells treated with PBS

description:
Library name: PANCcon
Column name in raw_counts_All_Samples.txt: PANCcon


title: Mometasone furoate rep4 2h

description: Library name: B14


title: Pregnant_5


title: Mometasone furoate rep4 1h

description: Library name: B13


title: VM_Jejunum_1

value: Male


title: Indacaterol rep1 1h

description: Library name: C1

value: Indacaterol (100 nM)


title: Mometasone furoate rep3 18h

description: Library name: B12


title: Pregnant_4


title: Virgin_4


title: Pseudo_3


title: LF_Duodenum_1

value: Lactating


title: Mometasone furoate rep2 18h

description: Library name: B8


title: Pregnant_3


title: Mometasone furoate rep2 6h

description: Library name: B7


title: Virgin_3


title: Pregnant_2


title: Mometasone furoate rep2 2h

description: Library name: B6


title: Pseudo_2


title: Mometasone furoate rep1 18h

description: Library name: B4


title: Mometasone furoate rep2 1h

description: Library name: B5


title: Virgin_2


title: Pregnant_1


title: Mometasone furoate rep1 6h

description: Library name: B3


title: Pseudo_1


title: Mometasone furoate rep1 1h

description: Library name: B1


title: Mometasone furoate rep3 6h

description: Library name: B11


title: Mometasone furoate rep3 2h

description: Library name: B10


title: Virgin_5


title: Mometasone furoate rep1 2h

description: Library name: B2


title: Mometasone furoate rep3 1h

description: Library name: B9


title: Virgin_1


title: Mometasone furoate + Indacaterol rep4 18h

description: Library name: E16

value: Mometasone + indacaterol


title: NS rep5 6h

description: Library name: A19

value: Vehicle


title: NS rep5 18h

description: Library name: A20


title: C6661, Treated 48hr replicate 1, scRNA-seq

city: Hong Kong

first: Xinlei

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

institute: HKUST

description:
Library name: C6661-NaB48h-01
10x Genomics
C6661_data.tar.gz
T481

data_processing:
The raw data were processed using Cell Ranger 4.0.0, which includes demultiplexing of raw base call (BCL) files into FASTQ files, alignment, and Unique Molecular Identifier (UMI) counting. Reads were aligned to the Homo sapiens genome assembly GRCh38 (hg38).
Assembly: GRCh38  and chrEBV_Akata_inverted (https://github.com/flemingtonlab/public/blob/master/annotation/chrEBV_Akata_inverted_2.fa)
Supplementary files format and content: gene expression mtx, gene annotation tsv, cell barcode tsv, UMAP coordinates csv, and cell annotations csv

source_name: NPC tumors

growth_protocol: C666-1 cells, derived from patient-derived xenografts (Xeno-666, established from the NPC tissue of a male patient), were maintained in RPMI 1640 medium (Gibco 23400021) supplemented with 10% FBS (Gibco 10270106).

extract_protocol:
Cells were harvested from T75 flasks, washed twice with 1x phosphate-buffered saline (PBS) (Gibco 10010049), and filtered using a Falcon strainer (Falcon 100-0087). Cell viability was assessed using an automated cell counter with trypan blue staining. Subsequently, cells were diluted to a concentration of 5 × 105 cells/ml in PBS, and dead cells were labeled with Propidium iodide (PI, 3 μM). Single cells were isolated using the BD Influx cell sorter before being loaded onto the 10X Chromium Controller.
The single-cell RNA-seq (scRNA-seq) library was prepared following the Chromium Single Cell 3’ Reagent Kits User Guide (V3.1 Chemistry) from 10X GENOMICS.

treatment_protocol: To induce lytic activation in C666-1 cells, the cells were cultured in fresh RPMI 1640 medium supplemented with 3 mM NaB.

value: NPC tumors

value: tumor cells

value: TPA treated for 48 hours


title: Mometasone furoate rep4 6h

description: Library name: B15

source_name: Lung

value: Lung

value: WT


title: NS rep5 2h

description: Library name: A18


title: C6661, Treated 24hr replicate 1, scRNA-seq

description:
Library name: C6661-NaB24h
10x Genomics
C6661_data.tar.gz
T241

value: TPA treated for 24 hours


title: C6661, Untreated, replicate 2, scRNA-seq

description:
Library name: C6661-Untreat-02
10x Genomics
C6661_data.tar.gz
UT2

value: Untreat


title: NS rep4 18h

description: Library name: A16

value: BEAS-2B human airway epithelial cell line


title: C6661, Untreated, replicate 1, scRNA-seq

description:
Library name: C6661-Untreat-01
10x Genomics
C6661_data.tar.gz
UT1


title: NS rep5 1h

description: Library name: A17


title: Pseudo_4

value: Female


title: NS rep4 6h

description: Library name: A15


title: OSRC2, DMSO, Rep3

city: Boston

first: Nitin

middle: H.

last: Shirole

address: 450 Brookline Avenue, M448, Dana Farber Cancer Institute

institute: Dana Farber Cancer Institute

description:
OSRC2_DMSO_F._normD1.12.bw
OSRC2_DMSO_R._normD1.12.bw

data_processing:
Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools. Read pairs were trimmed using cutadapt 1.14. The UMI length was trimmed off the end of both reads to prevent read-through into the UMI of the other end of the sequence, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq, to preserve a single mate orientation during alignment.
The paired-end reads were then mapped to a combined genome index, including both the spike (dm6, drosophila) and primary (hg19, human) genomes, using bowtie2. Properly paired-end reads were retained. These read pairs were then separated based on the genome (i.e. spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated, again using UMI-tools. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-” strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution. Samples displayed highly comparable recovery of spike-in reads; thus samples were normalized based on the DESeq2 size factors. Combined bedGraphs were generated by summing counts per nucleotide across replicates for each condition.
Annotated transcription start sites were obtained from human (GRCh37.87) GTFs from Ensembl. After removing transcripts with biotypes, PRO-Seq signal in each sample was calculated in the window from the annotated transcription start site (TSS) to +150 nt downstream
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: Precision Run-On (PRO)-seq

growth_protocol: OSRC2 cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in RPMI-1640 (Gibco 11875119) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122).

extract_protocol:
Cells (Human or Drosophila) were washed with RT PBS, trypsinized for 1-2 min at 37°C, quenched with ice-cold DMEM +10% FBS and transferred to 50 ml conical tubes. After harvesting, cells were always kept on ice. 5×106 to 1×107 cells per condition were collected by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cell pellets were gently resuspended in 10 ml ice-cold PBS, followed by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cells were resuspended in 250 ml wash buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.5 mM DTT (Thermo Fisher Scientific 707265ML), 0.2 ml/ml RNase inhibitor (Invitrogen AM2696) and 1× protease inhibitor (Thermo Fisher Scientific A32965)]. The cell pellets were gently pipetted using wide bore filtered pipette tips (Thermo Fisher Scientific 2079GPK) to create a single-cell suspensions. The cell suspension was passed through a cell strainer once (Falcon 352235) to avoid cell clumps. 10 ml permeabilization buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.1 % (v/v) IGEPAL CA-630, 0.05% (v/v) Tween-20, 0.5 mM DTT, 0.2 l/ml RNase inhibitor and 1× protease inhibitor] was slowly (over 5-10 seconds) added to the single-cell suspension along the wall of the conical tube. The samples were then incubated on ice for 5 min before centrifugation at 400×g for 4 min at 4°C. The supernatant was removed by gently inverting the tubes after which 1 ml of ice-cold wash buffer was added to each of the pellets to dilute out the residual permeabilization buffer followed by gently pipetting 2-3 times to achieve a single cell suspension. Next an additional 9 ml of ice-cold wash buffer was added to each tube and the samples were pelleted by centrifugation at 400×g for 4 min at 4°C. This wash procedure (1 ml wash buffer followed by 9 ml wash buffer) was repeated an additional 2 times. After the washes, the cell pellets were resuspended in 250 l freezing buffer [50 mM Tris-HCl, pH 8.0, 40% (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, 1 l/ml RNase inhibitor] and transferred to 1.5 ml low binding tubes (Thermo Fisher Scientific Pl90410). 250 l freezing buffer/tube was also added to the 50 ml conical tubes, followed by gentle pipetting, to collect any residual cells, which were then pooled with the first resuspension (bringing the total volume to 500 l, which was further resuspended by gentle pipetting). Trypan blue-stained cell number was determined using a hemocytomer after which the cells were diluted using freezing buffer to the concentration of 1×106 cell/100 l. Aliquots of 5×106 permeabilized cells per 1.5 ml low binding tube were flash frozen in liquid nitrogen and stored at -80°C prior to use. To conduct nuclear run-ons and library preparation, aliquots of frozen permeabilized cells were thawed on ice, pipetted gently, and recounted using a Luna II automated cell counter (Logos Biosystems). For each sample, 1×106 permeabilized Human cells were used for nuclear run-ons, with 5×104 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run-on assays and library preparation were performed as described in (Reimer et al, Mol Cell, 2021) with modifications. Briefly, nascent RNA was labeled by a run-on assay in which an equal volume of 2× nuclear run-on buffer [10 mM Tris-HCl, pH 8.0, 300 mM KCl, 1% sarkosyl, 10 mM MgCl2, 1 mM DTT, 20 M/ea biotin-11-NTPs (Perkin Elmer NEL543001EA), 0.8 U/l RNase inhibitor)] was added into permeabilized cell mixture and incubated for 5 min at 37°C. RNA was purified by the Total RNA Purification Kit (Norgen Biotek Corp 17200) per manufacturer’s instructions, eluted in 100 l H2O, and fragmented by base hydrolysis by adding 25 l 5× fragmentation solution (375 mM Tris-HCl, pH 8.3, 562.5 mM KCl, 22.5 mM MgCl2) followed by incubation for 5 min at 94°C. Fragmentation was stopped by adding 125 l ice-cold 0.1 M EDTA. To enrich for biotin-labeled nascent RNA, 10 ml of streptavidin C1 magnetic beads (Invitrogen 65001) were washed, rendered RNase free per manufacturer’s instructions, and resuspended in 50 ml binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.1% Triton X-100) before being added to the fragmented RNA. The samples were rotated end-to-end for 20 min at RT. The streptavidin magnetic beads were then washed twice with high salt buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl, 0.5% Triton X-100), twice with binding buffer (listed above), and twice with low salt buffer (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). The beads were next resuspended in 500 ml TRIzol Reagent (Invitrogen 15596026) and incubated at 65°C for 5 min to elute RNA from the beads. This elution step was repeated once and the first and second eluates for a given sample were pooled. The RNA was subsequently purified by adding 2.75× volumes of 100% ethanol to the 400 l solution recovered from aqueous phase of TRIzol in the presence of 20 g of Ultrapure glycogen (Invitrogen 10814010). The pelleted RNA was subsequently washed per manufacturer’s instructions and resuspended in 5 l of 10 M App-VRA3_6N 3’ end adapter prepared using the 5' DNA Adenylation Kit (New England Biolabs M2611A) and ligated using T4 RNA ligase 2, truncated KQ (New England Biolabs M0373) per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. 180 ml of betaine binding buffer [1.42g of betaine (Sigma-Aldrich 61962) in 10 ml with binding buffer] was mixed with ligations and incubated for 5 min at 65°C and then for 2 min on ice. Capture on Streptavidin beads was again performed as above to enrich for ligated nascent RNAs except for the addition of a final wash with 1× MDE buffer (New England Biolabs B0608S) after the washes with high salt buffer, binding buffer, and low salt buffer. To prepare nascent RNA for 5’ end adapter ligation, the 5’ ends of the RNA were first decapped by mRNA decapping enzyme (New England Biolabs M0608S) for 1 h at 37°C. The beads were washed once in high, once with low salt buffer, and then once in 1× T4 PNK reaction buffer. The samples were then treated with T4 polynucleotide kinase (New England Biolabs M0201) for 1 h at 37°C for 5’-hydroxyl repairs, followed by one wash with high salt buffer, one wash with low salt buffer, and one wash with 0.25× T4 RNA ligase reaction buffer prior to resuspension in 5 ml of 10 pmol 5' RNA adapter VRA5_6N. Next T4 RNA ligase 1 (New England Biolabs M0204L) was used to ligate the 5’ RNA adapter per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. Following the 5’ end ligation, beads were washed twice with high salt buffer, twice with binding buffer, and twice with low salt buffer, then once with 0.25× SuperScript IV reaction buffer. Reverse transcription was performed using SuperScript IV Reverse Transcriptase (Invitrogen 18090010) and the cDNA was eluted from the beads by heating the samples twice for 30 seconds at 95°C.
The eluted cDNA was initially amplified for 5-cycles of "preCR" [NEBNext Ultra II Q5 master mix (New England Biolabs M0544S) with Illumina TruSeq PCR primers RP-1 and RPI-X for indexing] following the manufacturer's suggested PCR cycling protocol for library construction]. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Libraries were amplified by 3 additional cycles of PCR (8 cycles in total). The amplified library was purified using the ProNex Size-Selective Purification System (Promega) and sequenced using the Illumina NovaSeq platform.

treatment_protocol: 3 x 106 OSRC2/dish were plated on day 0 in triplicate in 150 mm TC-treated cell culture dishes. On day 3 the media was replaced with media containing PT2399 or DMSO and the cells were harvested 6 hrs later. The cells were detached by a brief incubation with 0.25% Trypsin-EDTA (Gibco, 25200072) at 37oC. The Trypsin was then quenched with ice-cold DMEM +10% FBS. The cells were then transferred to 50 ml conical tubes and kept on ice for the remainder of their processing.

value: ccRCC

value: DMSO

value: 6 hrs


title: OSRC2, DMSO, Rep2


title: NS rep4 2h

description: Library name: A14


title: OSRC2, PT2399, Rep1

description:
OSRC2_PT_6h_F._normD1.27.bw
OSRC2_PT_6h_R._normD1.27.bw


title: C6661, Treated 48hr replicate 2, scRNA-seq

description:
Library name: C6661-NaB48h02
10x Genomics
C6661_data.tar.gz
T482