title: FFPE sample 14091 B11

description:
Genomic DNA from FFPE sample 14091 B11
207030420105_R08C01

value: Tumor&Normal

value: Gleason's pattern 7 (3+4), grade group 2


title: Uninfected primary mouse astrocytes, control-in-TC-83-infection, biol rep1

status: Public on Mar 30 2026

type: SRA

city: Albuquerque

first: Steven

last: Bradfute

state: NM

address: 1 University of New Mexico

country: USA

institute: University of New Mexico Health Sciences Center

description:
Library name: Sample10
column name in VEEV_infected_vs_control_All_counts.tsv: MAT11

library_source: transcriptomic

data_processing:
After checking the reads quality using FASTQC, the Fasta reference genome was indexed using Samtools. STAR aligner used to generate genome indecies for alignment and to map the reads to the reference genome. The read counts were generated using HTSEQ. DESeq2 was used to perform differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Tab seperated value (tsv) file contains the raw counts for all the samples

molecule: total RNA

organism: Mus musculus

source_name: Brain mixed primary mouse astrocytes

growth_protocol: Mouse C57 brain mixed primary astrocytes were grown in ABM Basal Medium supplemented with AGM SingleQuots and maintained at 37 °C and 5% CO2 for 24 hours. Primary mouse cortical neurons were grown in Neurobasal Medium supplemented with 0.5 mM GlutaMAX-I and 2% (v/v) B-27 and maintained at 37°C and 5% CO2 for 4 days.

extract_protocol:
Total RNA extracted from infected cells at 16 and 24hpi and from uninfected cells using Direct-Zol RNA Microprep Kit following the manufacturer's protocol.
Ribosomal RNA was depleted using the RiboGone Kit according to the manufacturer's instructions. The RNA was prepared for sequencing using the SMARTer Universal Low  Input RNA Kit for Sequencing following the manufacturer's instructions. Samples were  then prepared using the Ion Plus Fragment Library Kit (Ion Torrent) at the UNM ATG core facility, starting at the Ligation and Nick Repair step, with the only modification being the use of 80% ethanol instead of 70% ethanol for bead washes.

treatment_protocol: At 24h post-seeding primary mouse astrocytes were incubated with either VEEV TrD or VEEV TC-83 (MOI 5) for 1h. The medium changed to fresh medium and cells were maintained at 37C and 5% CO2 for 16h and 24h. The infection was done for primary mouse neurons at 4days after seeding following a similar protocol that used for astrocytes.

tag: cell type

value: Brain mixed primary mouse astrocytes

tag: treatment

value: Untreated


title: ChIP_gH2AX_KO_XRAY_rep2

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

description: Library name: ChIP_gH2AX_KO_XRAY_rep2

library_source: genomic

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: broadPeak files contain peaks as called by macs

molecule: genomic DNA

source_name: TTF

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H2A.X antibody (ab20669, Abcam), or anti-ɣH2AX (Sigma, 05-636-I). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

treatment_protocol: Cells were treated with 5Gy of Xrays and allowed to recover for 30 minutes

tag: chip antibody

tag: Sex

value: Female

value: TTF

tag: strain

value: C57BL6/CAST hybrid

value: 5Gy XRAY

tag: genotype


title: ChIP_gH2AX_KO_XRAY_rep1

description: Library name: ChIP_gH2AX_KO_XRAY_rep1


title: FFPE sample 14082 A4

type: genomic

city: Washington

first: Bernard

last: Kwabi-Addo

state: DC

address: 520 W. Street N.W.

department: Biochemistry and Molecular Biology

institute: Howard University College of Medicine

description:
Genomic DNA from FFPE sample 14082 A4
207030420105_R06C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudio Methylation Module V2011.1
[processed value definition] Average Beta

label: Cy3, Cy5

organism: Homo sapiens

source_name: Prostate

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extracted from FFPE samples using Zymo Quick-DNA FFPE kit according to standard instructions

tag: disease state

tag: tissue

value: Prostate

tag: diagnosis

value: Adenocarcinoma

tag: gleason

tag: age

tag: smoking

value: Y

tag: drinking


title: FFPE sample 14083 A8

description:
Genomic DNA from FFPE sample 14083 A8
207030420105_R07C01

value: N


title: VEEV TrD-infected primary mouse astrocytes, 16hpi, biol rep1

description:
Library name: Sample4
column name in VEEV_infected_vs_control_All_counts.tsv: MAr12

value: VEEV TrD infected -16hpi


title: VEEV TrD-infected primary mouse astrocytes, 24hpi, biol rep3

description:
Library name: Sample9
column name in VEEV_infected_vs_control_All_counts.tsv: MAr43

value: VEEV TrD infected - 24hpi


title: ChIP_H2AX_WT_XRAY_rep1

description: Library name: ChIP_H2AX_WT_XRAY_rep1

value: WT


title: ChIP_gH2AX_WT_XRAY_rep2

description: Library name: ChIP_gH2AX_WT_XRAY_rep2


title: ChIP_H2AX_WT_XRAY_rep2

description: Library name: ChIP_H2AX_WT_XRAY_rep2


title: VEEV TrD-infected primary mouse astrocytes, 16hpi, biol rep3

description:
Library name: Sample6
column name in VEEV_infected_vs_control_All_counts.tsv: MAr42


title: FFPE sample 14081 A1

description:
Genomic DNA from FFPE sample 14081 A1
207030420105_R05C01

value: Normal


title: Uninfected primary mouse astrocytes, control-in-TrD-infection, biol rep2

description:
Library name: Sample2
column name in VEEV_infected_vs_control_All_counts.tsv: MAr31


title: ChIP_H2AX_KO_XRAY_rep2

description: Library name: ChIP_H2AX_KO_XRAY_rep2


title: Uninfected primary mouse astrocytes, control-in-TrD-infection, biol rep3

description:
Library name: Sample3
column name in VEEV_infected_vs_control_All_counts.tsv: MAr41


title: FFPE sample 14064 A13

description:
Genomic DNA from FFPE sample 14064 A13
207030420105_R04C01


title: Uninfected primary mouse astrocytes, control-in-TrD-infection, biol rep1

description:
Library name: Sample1
column name in VEEV_infected_vs_control_All_counts.tsv: MAr11


title: ChIP_H2AX_KO_XRAY_rep1

description: Library name: ChIP_H2AX_KO_XRAY_rep1


title: Xenspi, scRNAseq

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

library_source: transcriptomic single cell

data_processing:
Cell Ranger v5.0 software (10X Genomics)
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: Tab-separated values and matrix files

molecule: polyA RNA

organism: Xenotilapia spiloptera

source_name: intestine

extract_protocol:
Intestinal samples were flushed, chopped and dissociated at 25ºC for 20 minutes in pre-warmed DMEM/F-12 medium 1X (Fisher Scientific) supplemented with 1 mg / mL of dispase II (Sigma). Suspensions were centrifuged at 500 rcf for 7 minutes at 4ºC, resuspended in 10% Fetal Bovine Serum (FBS) in DMEM/F-12, filtered with a 20 µm cell strainer (CellTrics), centrifuged again with the same conditions, resuspended in 10% FBS in DMEM/F-12, and centrifuged one last time at low speed (200-250 rcf) for 5 minutes at 4ºC.
Following instructions from 10X Genomics Chromium Next GEM  Gene Expression 3' v3.1

value: intestine


title: FFPE sample 14063 A10

description:
Genomic DNA from FFPE sample 14063 A10
207030420105_R03C01


title: Trioto, scRNAseq

organism: Triglachromis otostigma


title: VEEV TrD-infected primary mouse astrocytes, 16hpi, biol rep2

description:
Library name: Sample5
column name in VEEV_infected_vs_control_All_counts.tsv: MAr32


title: Boumic, scRNAseq

organism: Boulengerochromis microlepis


title: FFPE sample 14092 A25

description:
Genomic DNA from FFPE sample 14092 A25
207030420105_R02C01

value: Tumor&Normal


title: MIV_7D_3 RNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: MIV_7D_3

data_processing:
Samples with a RIN (RNA Integrity Number) greater than six were selected for sequencing
The sequencing was performed using the 150 nucleotide paired-end reads protocol, generating approximately 20 million reads per sample
Software for the original image data file conversion into sequenced reads: CASAVA base recognition
Reads filters: uncertain nucleotides N > 10% or low-quality nucleotides, Base Quality < 5, constituted more than 50% of the read
Alignments software: HISAT2. Non-directional library
Assembly: Ensembl Rattus norvegicus genome (rnor_6_0_gca_000001895_4)
Supplementary files format and content: Tab-delimited table reporting the gene read counts

organism: Rattus norvegicus

source_name: Median nerve

extract_protocol:
RNA was isolated using TRIzol Reagent (Life Technologies) following the manufacturer’s protocol. Briefly, 500 μl of TRIzol reagent were added directly to frozen nerve samples, which were mechanically dissociated using a pestle. The resulting RNA pellet was resuspended in 12 μl of sterile RNase-free water.
The non-directional library construction was performed as follows: the mRNA was purified from 350 ng of total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers, and the second-strand cDNA synthesis was performed with dTTP. The subsequent steps included end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked using Qubit and real-time PCR, and size distribution was analysed using a bioanalyzer. Libraries were pooled and sequenced on Illumina platforms, based on the effective library concentration and the required data volume

value: Median nerve

value: Repair after cut injury and MIV

tag: time

value: Day 7


title: Telvit, scRNAseq

organism: Telmatochromis vittatus


title: MIV_7D_2 RNA-Seq

description: Library name: MIV_7D_2


title: VEEV TrD-infected primary mouse astrocytes, 24hpi, biol rep1

description:
Library name: Sample7
column name in VEEV_infected_vs_control_All_counts.tsv: MAr13

value: Brain mixed primary mouse astrocytes


title: FFPE sample 14061 A18

description:
Genomic DNA from FFPE sample 14061 A18
207030420105_R01C01

value: Gleason's pattern 7 (3+4), grade group 2


title: INPUT_Male_KO_XRAY_rep2

description: Library name: INPUT_Male_KO_XRAY_rep2

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched H2AX ChIP as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: broadPeak files contain peaks as called by macs

source_name: MEF

value: Male

value: MEF


title: MIV_3D_2 RNA-Seq

description: Library name: MIV_3D_2

value: Day 3


title: MIV_3D_3 RNA-Seq

description: Library name: MIV_3D_3


title: MIV_7D_1 RNA-Seq

description: Library name: MIV_7D_1


title: FFPE sample 14059 D26

description:
Genomic DNA from FFPE sample 14059 D26
206702520021_R07C01

value: Prostate

value: Adenocarcinoma


title: FFPE sample 14060 A7

description:
Genomic DNA from FFPE sample 14060 A7
206702520021_R08C01


title: MIV_3D_1 RNA-Seq

description: Library name: MIV_3D_1


title: INPUT_Female_WT_XRAY_rep1

description: Library name: INPUT_Female_WT_XRAY_rep1

value: Female

value: 5Gy XRAY


title: EV_7D_3 RNA-Seq

description: Library name: EV_7D_3

value: Repair after cut injury


title: INPUT_Male_KO_XRAY_rep1

description: Library name: INPUT_Male_KO_XRAY_rep1


title: INPUT_Female_WT_XRAY_rep2

description: Library name: INPUT_Female_WT_XRAY_rep2

value: WT


title: EV_7D_2 RNA-Seq

description: Library name: EV_7D_2


title: INPUT_Male_WT_XRAY_rep1

description: Library name: INPUT_Male_WT_XRAY_rep1


title: FFPE sample 14058 D17

description:
Genomic DNA from FFPE sample 14058 D17
206702520021_R06C01

value: Normal


title: INPUT_Male_WT_XRAY_rep2

description: Library name: INPUT_Male_WT_XRAY_rep2


title: EV_3D_2 RNA-Seq

description: Library name: EV_3D_2


title: EV_3D_1 RNA-Seq

description: Library name: EV_3D_1


title: FFPE sample 14057 B15

description:
Genomic DNA from FFPE sample 14057 B15
206702520021_R05C01

value: N


title: EV_3D_3 RNA-Seq

description: Library name: EV_3D_3


title: CTR_VEIN_3 RNA-Seq

description: Library name: CTR_VEIN_3

source_name: Healthy epigastric vein

value: Healthy epigastric vein

value: No treatment

value: Day 0


title: INPUT_Female_KO_XRAY_rep2

description: Library name: INPUT_Female_KO_XRAY_rep2


title: FFPE sample 14056 B7

description:
Genomic DNA from FFPE sample 14056 B7
206702520021_R04C01


title: FFPE sample 14055 A26

description:
Genomic DNA from FFPE sample 14055 A26
206702520021_R03C01

value: Tumor&Normal


title: CTR_VEIN_2 RNA-Seq

description: Library name: CTR_VEIN_2


title: CTR_NERVE_4 RNA-Seq

description: Library name: CTR_NERVE_4

source_name: Healthy median nerve

value: Healthy median nerve


title: CTR_NERVE_3 RNA-Seq

description: Library name: CTR_NERVE_3


title: EV_7D_1 RNA-Seq

description: Library name: EV_7D_1

value: Median nerve

value: Day 7


title: CTR_NERVE_5 RNA-Seq

description: Library name: CTR_NERVE_5


title: FFPE sample 14054 A10

description:
Genomic DNA from FFPE sample 14054 A10
206702520021_R02C01


title: ChIP_gH2AX_Male_WT_XRAY_rep1

description: Library name: ChIP_gH2AX_Male_WT_XRAY_rep1

value: Male

value: MEF


title: CTR_NERVE_2 RNA-Seq

description: Library name: CTR_NERVE_2


title: FFPE sample 14053 A24

description:
Genomic DNA from FFPE sample 14053 A24
206702520021_R01C01

value: Prostate


title: ChIP_gH2AX_Male_KO_XRAY_rep2

description: Library name: ChIP_gH2AX_Male_KO_XRAY_rep2


title: CTR_NERVE_1 RNA-Seq

description: Library name: CTR_NERVE_1


title: INPUT_Female_KO_XRAY_rep1

description: Library name: INPUT_Female_KO_XRAY_rep1


title: CTR_MUSCLE_3 RNA-Seq

description: Library name: CTR_MUSCLE_3

source_name: Healthy adductor muscle

value: Healthy adductor muscle


title: ChIP_gH2AX_Male_WT_XRAY_rep2

description: Library name: ChIP_gH2AX_Male_WT_XRAY_rep2


title: FFPE sample 14051 A15

description:
Genomic DNA from FFPE sample 14051 A15
206702520182_R07C01

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: Y


title: ChIP_gH2AX_Female_WT_XRAY_rep2

description: Library name: ChIP_gH2AX_Female_WT_XRAY_rep2

value: Female

value: 5Gy XRAY

value: WT


title: FFPE sample 14052 A17

description:
Genomic DNA from FFPE sample 14052 A17
206702520182_R08C01

value: Gleason's pattern 7 (3+4), grade group 3

value: Former


title: CTR_MUSCLE_1 RNA-Seq

description: Library name: CTR_MUSCLE_1

value: No treatment

value: Day 0


title: ChIP_gH2AX_Male_KO_XRAY_rep1

description: Library name: ChIP_gH2AX_Male_KO_XRAY_rep1


title: vHD_ACA_PPGL

city: Shinjuku

first: Tomohiro

last: Tamura

state: Tokyo

address: Shinanomachi 35

department: Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory

country: Japan

institute: Keio University School of Medicine

description:
Library name: vHD_ACA_PPGL
FFPE sample

data_processing:
Visium HD FASTQ files were processed with Space Ranger v4.0.1 (spaceranger count) using the GRCh38-2024-A reference transcriptome and the Visium Human Transcriptome Probe Set v2.1.0 (GRCh38-2024-A).
Tissue brightfield and CytAssist images were provided, and fiducial-based alignment was applied using a Loupe alignment JSON file.
Nucleus segmentation was enabled and nuclei were expanded by 8 µm (--nucleus-expansion-distance-micron=8) for quantification.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: tissue_positions.parquet
Library strategy: Spatial Transcriptomics

source_name: TUMOR

extract_protocol:
FFPE tissue samples were used for RNA extraction.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's recommendation.

value: TUMOR

value: FFPE


title: CTR_VEIN_1 RNA-Seq

description: Library name: CTR_VEIN_1

value: Healthy epigastric vein


title: FFPE sample 14050 A20

description:
Genomic DNA from FFPE sample 14050 A20
206702520182_R06C01

value: Normal


title: FFPE sample 14071 A23

description:
Genomic DNA from FFPE sample 14071 A23
206702520182_R05C01


title: Bladder tissue and PBMC, BCG unresponsive, sample 08

city: Chicago

last: Meeks

state: IL

address: 303 East Superior Street

institute: Northwestern University

description:
Library name: P19
BD Rhapsody

data_processing:
The libraries were subjected to sequencing using 150 bp paired end sequencing using the Novaseq X Plus by Admera Health (New Jersey). Blood and tissue samples from the same patient were multiplexed using BD sample tag oligos prior to library preparation. Demultiplexing was performed computationally based on sample tag reads. The BD Rhapsody fastq files were processed using the BD Rhapsody WTA pipeline, available on the Seven Bridges Genomics cloud server. Briefly the pipeline had steps which involved filtering of the reads, identifying the cell ID and the UMI, aligning the reads to the the hg38 reference genome or in the case of Abseq data, the Abseq reference file. The raw counts were error corrected, putative cells identified and the final processed file contained reads per cell for the samples generated along with the quality control metrics.
Assembly: hg38
Supplementary files format and content: Seurat RDS file output, contains all cells with appropriate sample tags

source_name: bladder tissue; blood

extract_protocol:
Tissue was transported in DMEM with 10% FBS to preserve stability at room temperature to preserve temperature sensitive granulocytes. Tissue was minced and digested in two rounds (20 minutes and 15 minutes) in DMEM without FBS using Liberase TM (Sigma) in a 37 °C water bath with gentle manual inversion. The digested tissue was resuspended in FACs buffer passed through a 70 uM strainer (Corning), centrifuged and subjected to CD45 enrichment using the Miltenyi biotech CD45 microbeads as per the manufacturer’s instructions. In parallel, 1 ml of blood from blood isolated in EDTA coated tubes was also processed to isolate leukocytes using whole blood lysis protocol recommended by 10X Genomics (CG000392) using eBioscience 1X RBC Lysis Buffer (Thermo fisher) with PBS washes and low speed centrifugation
To combine the matched tissue and blood samples to load on a single BD Rhapsody cartridge, the processed matched tissue and blood samples were labeled with sample tags using the BD Single-cell Multiplexing kit in accordance with the manufacturer’s protocol. The individual samples were resuspended in BD Rhapsody sample buffer (BD Biosciences) and stained with DRAQ7 and Calcein AM florescent dyes to enable visualization for counting and calculation of quality control metrics in the BD Rhapsody single cell system.  The cells were counted, and blood-tissue samples mixed, passed through a 70 micron strainer and up to 10,000 cells loaded in the BD Rhapsody microwell cartridge system. Magnetic capture beads were then loaded close to saturation so that each microwell contains one magnetic bead.  Each of the cells were isolated in the microwells, lysed and the polyadenylated mRNA molecules from each cell captured by individual magnetic capture beads containing unique molecular identifiers (UMIs) and cell specific barcodes. The capture beads were retrieved from the BD Rhapsody single cell system and cDNA reverse transcription carried out with cDNA with UMI and cell specific barcode information added to the cDNA molecules. 3’ end whole transcriptome amplification (WTA), sample tag libraries were prepared according to the BD Rhapsody WTA and sample tag preparation protocol. For quantification and quality control purposes the libraries were subjected to Qubit and Tape station analyses. For calculation of total paired end reads, sequencing depth of 60,000 reads per cell were used for the WTA library analyses, for the sample tag libraries sequencing depth 1200 reads per cell. The WTA and sample tag libraries were mixed according to custom BD Rhapsody calculations.

value: bladder tissue; blood

value: immune

tag: sample group

value: BCG unresponsive

value: BCG


title: ChIP_gH2AX_Female_KO_XRAY_rep2

description: Library name: ChIP_gH2AX_Female_KO_XRAY_rep2

value: MEF


title: Bladder tissue and PBMC, BCG naïve, sample 07

description:
Library name: P18
BD Rhapsody

value: BCG naïve


title: ChIP_gH2AX_Female_WT_XRAY_rep1

description: Library name: ChIP_gH2AX_Female_WT_XRAY_rep1

value: Female


title: CTR_MUSCLE_2 RNA-Seq

description: Library name: CTR_MUSCLE_2

value: Healthy adductor muscle


title: Bladder tissue and PBMC, BCG unresponsive, sample 06

description:
Library name: P16
BD Rhapsody


title: FFPE sample 14070 A14

description:
Genomic DNA from FFPE sample 14070 A14
206702520182_R04C01

value: Tumor&Normal

value: Prostate

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: N

value: Y


title: Bladder tissue and PBMC, BCG unresponsive, sample 07

description:
Library name: P17
BD Rhapsody


title: Bladder tissue and PBMC, BCG unresponsive, sample 04

description:
Library name: P14
BD Rhapsody


title: ChIP_gH2AX_Female_KO_XRAY_rep1

description: Library name: ChIP_gH2AX_Female_KO_XRAY_rep1

value: 5Gy XRAY


title: Bladder tissue and PBMC, BCG unresponsive, sample 05

description:
Library name: P15
BD Rhapsody


title: Bladder tissue and PBMC, BCG responsive, sample 06

description:
Library name: P12
BD Rhapsody

value: BCG responsive


title: ChIP_H2AX_Male_WT_XRAY_rep2

description: Library name: ChIP_H2AX_Male_WT_XRAY_rep2

value: Male

value: WT


title: FFPE sample 14069 A16

description:
Genomic DNA from FFPE sample 14069 A16
206702520182_R03C01


title: Bladder tissue only, BCG unresponsive, sample 03

description:
Library name: P13
BD Rhapsody

source_name: bladder tissue

value: bladder tissue

value: immune

value: Bladder tissue only, BCG unresponsive


title: FFPE sample 14068 A11

description:
Genomic DNA from FFPE sample 14068 A11
206702520182_R02C01

value: Normal


title: Bladder tissue and PBMC, BCG responsive, sample 03

description:
Library name: P9
BD Rhapsody

value: bladder tissue; blood

value: BCG


title: FFPE sample 13967 A18

description:
Genomic DNA from FFPE sample 13967 A18
206702520183_R08C01


title: Bladder tissue and PBMC, BCG responsive, sample 02

description:
Library name: P8
BD Rhapsody


title: ChIP_H2AX_Male_KO_XRAY_rep2

description: Library name: ChIP_H2AX_Male_KO_XRAY_rep2

value: MEF


title: ChIP_H2AX_Male_WT_XRAY_rep1

description: Library name: ChIP_H2AX_Male_WT_XRAY_rep1


title: Bladder tissue and PBMC, BCG responsive, sample 04

description:
Library name: P10
BD Rhapsody


title: Bladder tissue and PBMC, BCG responsive, sample 05

description:
Library name: P11
BD Rhapsody


title: Bladder tissue and PBMC, BCG naïve, sample 06

description:
Library name: P7
BD Rhapsody

value: BCG naïve


title: FFPE sample 14067 C7

description:
Genomic DNA from FFPE sample 14067 C7
206702520182_R01C01

value: Tumor&Normal

value: Prostate


title: Bladder tissue and PBMC, BCG naïve, sample 05

description:
Library name: P6
BD Rhapsody


title: FFPE sample 13966 A6

description:
Genomic DNA from FFPE sample 13966 A6
206702520183_R07C01

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: Former


title: Bladder tissue and PBMC, BCG naïve, sample 04

description:
Library name: P5
BD Rhapsody


title: FFPE sample 13964 A9

description:
Genomic DNA from FFPE sample 13964 A9
206702520183_R06C01


title: Bladder tissue and PBMC, BCG responsive, sample 01

description:
Library name: P4-P
BD Rhapsody


title: ChIP_H2AX_Female_WT_XRAY_rep2

description: Library name: ChIP_H2AX_Female_WT_XRAY_rep2

value: Female

value: 5Gy XRAY


title: Bladder tissue and PBMC, BCG naïve, sample 02

description:
Library name: P3
BD Rhapsody


title: Bladder tissue and PBMC, BCG unresponsive, sample 02

description:
Library name: P2-P
BD Rhapsody

value: BCG unresponsive


title: FFPE sample 13963 A6

description:
Genomic DNA from FFPE sample 13963 A6
206702520183_R05C01

value: Y


title: Bladder tissue and PBMC, BCG naïve, sample 03

description:
Library name: P4
BD Rhapsody


title: FFPE sample 13960 A16

description:
Genomic DNA from FFPE sample 13960 A16
206702520183_R04C01


title: ChIP_H2AX_Female_KO_XRAY_rep2

description: Library name: ChIP_H2AX_Female_KO_XRAY_rep2


title: Bladder tissue and PBMC, BCG unresponsive, sample 01

description:
Library name: P1-P
BD Rhapsody


title: ChIP_H2AX_Female_KO_XRAY_rep1

description: Library name: ChIP_H2AX_Female_KO_XRAY_rep1


title: ChIP_H2AX_Male_KO_XRAY_rep1

description: Library name: ChIP_H2AX_Male_KO_XRAY_rep1

value: Male


title: VOA-10841

city: Melbourne

first: Kathleen

last: Pishas

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 14
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-10841

data_processing:
Gene definitions were based on the GENCODE v4643 human reference gene annotation, with promoters defined as the 3,000 bp upstream and 1,000 bp downstream of the transcription start site (TSS). All methylation profiles were quantile normalized for downstream analysis.
Assembly: Gene definitions were based on the Human reference gene annotation database GENCODE v46
Supplementary files format and content: A CSV file containing quantile-normalized mean methylation levels for promoter UMRs for all samples
Library strategy: EM-seq

source_name: cell line

growth_protocol: LGSOC cell lines were grown for 72 hours (reaching 70–80%) with cell pellets collected. Cell lines were maintained in a 1:1 mixture of M199 and MCDB105 media (Sigma-Aldrich) supplemented with 10% HyClone FBS and 1% Penicillin-Streptomycin (Sigma-Aldrich). Cells were cultured at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol, which included optional  RNase A treatment. 1ug of total DNA was used for the construction of sequencing libraries
Library preparation was conducted using the Human Methylome Panel (Twist Bioscience), and sequencing was performed on the Illumina NovaSeq platform with pairedend 150 bp reads, achieving a minimum depth of 50x coverage.

treatment_protocol: Cell media only.

value: cell line

tag: cell line

value: Low Grade Serous Ovarian

value: NRAS (Q61K)


title: Bladder tissue and PBMC, BCG naïve, sample 01

description:
Library name: P2
BD Rhapsody

value: bladder tissue; blood

value: immune


title: FFPE sample 13959 A12

description:
Genomic DNA from FFPE sample 13959 A12
206702520183_R03C01

value: Normal


title: FFPE sample 14008 A1

description:
Genomic DNA from FFPE sample 14008 A1
206702520183_R02C01

value: Benign

value: Benign Prostate Hyperplasia


title: iOvCa241

description:
Library name: Sample 12
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: iOvCa241

value: KRAS (G12D)


title: ChIP_H2AX_Female_WT_XRAY_rep1

description: Library name: ChIP_H2AX_Female_WT_XRAY_rep1

value: MEF

value: WT


title: VOA-6406

description:
Library name: Sample 11
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-6406

value: NRAS (Q61R)


title: FFPE sample 13990 A1

description:
Genomic DNA from FFPE sample 13990 A1
206702520183_R01C01

value: Prostate


title: scRNAseq_KO2

city: Bangalore

first: Kushagra

last: Bansal

state: Karnataka

address: Jakkur

department: MBGU

country: India

institute: JNCASR

description:
Library name: Sample34
scRNA-seq

data_processing:
The fastq files were trimmed to 50bp and low-quality reads were removed using fastx (v0.0.13) and sickle (v1.33.0) respectively. These 50bp reads were aligned to mouse genome (mm10). bamcoverage was used to generate bigwig files. Juicer was used to generate .hic files. scRNA-seq fastq files were processed through cell rnager to obtain barcodes, features and matrix files.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: hic
Supplementary files format and content: barcodes
Supplementary files format and content: features
Supplementary files format and content: matrix

source_name: spleen

extract_protocol:
splenic cDCs, splenic pDCs, and bone marrow pre-DCs from 6-8 weeks old Smc3-WT and Smc3-cKO mice were isolated through flow cytometry. RNA was isolated using TRIzol and quantified using tapestation.
RNA-seq libraries were prepared using Takara SMARTer® Stranded Total RNA-seq v2 pico input kit following manufacturer’s instructions. ChIP-seq libraries were prepared using an inhouse protocol detailed in the methods. Hi-C libraries were prepared using Arima Hi-C+ kit from Arima Genomics. Single cell RNA-seq libraries were prepared using Chromium Single Cell 3′ Reagent Kit targeting 10,000 cells.

value: spleen

value: RBC depleted splenocytes


title: VOA-4627

description:
Library name: Sample 8
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-4627

value: MAPK Wildtype


title: FFPE sample 13989 A1

description:
Genomic DNA from FFPE sample 13989 A1
206772660053_R08C01

value: N

value: Y


title: VOA-4698

description:
Library name: Sample 7
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-4698

value: cell line

value: Low Grade Serous Ovarian


title: SLC58

description:
Library name: Sample 13
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: SLC58

value: USP9X Mutant


title: HUF

description:
Library name: Sample 9
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: HUF

value: HUF

value: Primary uterine fibroblast


title: AOCS2

description:
Library name: Sample 6
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: AOCS2


title: scRNAseq_KO1

description:
Library name: Sample33
scRNA-seq


title: VOA-1056

description:
Library name: Sample 5
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-1056


title: scRNAseq_WT2

description:
Library name: Sample32
scRNA-seq


title: FFPE sample 13988 A9

description:
Genomic DNA from FFPE sample 13988 A9
206772660053_R07C01

value: Benign


title: VOA-7681

description:
Library name: Sample 4
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-7681

value: KRAS (G12V)


title: FFPE sample 13987 A1

description:
Genomic DNA from FFPE sample 13987 A1
206772660053_R06C01

value: Benign Prostate Hyperplasia


title: VOA-3448

description:
Library name: Sample 10
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-3448


title: FFPE sample 13986 A5

description:
Genomic DNA from FFPE sample 13986 A5
206772660053_R05C01


title: HiC_cDC_KO2

description:
Library name: Sample30
Hi-C

value: cDC


title: IOSE-523

description:
Library name: Sample 3
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: IOSE-523

value: Normal Ovary


title: FFPE sample 13985 A1

description:
Genomic DNA from FFPE sample 13985 A1
206772660053_R04C01


title: genomic DNA from white matter 20

city: Berlin

first: Leonille

last: Schweizer

address: Charitépl. 1

country: Germany

institute: Charité - Universitätsmedizin

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation array data were processed in R (version 3.5.0) applying Bioconductor packages minfi (version 1.28.4)

label: Cy3 and Cy5

source_name: white matter 20

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA extraction of formalin-fixed and paraffin embedded (FFPE) tissue was conducted from white matter areas with increased cell density avoiding cortical regions with neuronal cells using the Maxwell Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol.

value: white matter

value: male

tag: case

value: p

tag: multiregion


title: VOA-3723

description:
Library name: Sample 1
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-3723

tag: cell type


title: S3D1 NC1

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

description: Library name: L6

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: filtered_feature_bc_matrix

source_name: differentiating cells S3D1

extract_protocol:
The harvested stem cell islets were treated with Triple solution for 30 minutes at 37 °C with shaking at 95 rpm. Following treatment, the islets were washed with 1× DPBS and viability was assessed, ensuring a viability rate of over 90%. The cells were then stored in a buffer containing PBS supplemented with 1% w/v BSA. Subsequently, the Single Cell 3.1 protocol was initiated immediately.
Library construction was performed according to the manufacturer’s instructions (Chromium Single Cell 3' v3.1 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded into the Chromium Controller with partitioning oil and barcoded Gel Beads to generate Gel Bead-in-Emulsion (GEMs). Within each GEM, the poly-A RNA from the cell lysate was reverse transcribed into cDNA. This cDNA contained the Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x barcode. The pooled barcoded cDNA was cleaned using Silane DynaBeads, then amplified by PCR. The appropriate fragment sizes were selected using SPRIselect reagent to ensure the cDNA was suitable for library construction. During the library construction, the Illumina R2 primer sequence, paired-end constructs with P5 and P7 adapters, and a sample index were added to each fragment for sequencing.

value: differentiating cells S3D1

value: induced pluripotent stem cells

value: non carrier

tag: treatment

value: Differentiation to stem cell islets


title: S3D1 HNF1A-MODY

description: Library name: L5


title: HCM-CSHL-0078-C25 (model, metastatic), HCM-CSHL-0089-C25 (model, metastatic)

city: New York

first: Luca

last: Zanella

state: New York

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

description:
Library name: AG013
10x Genomics

data_processing:
Each .h5 processed file was generated with 'cellranger count' using the 10X Genomics' Cell Ranger software (v8.0.1)
Each .h5ad file was generated through genotype-based demultiplexing, assigning barcodes to individual samples.
Assembly: GRCh38-2024-A
Supplementary files format and content: Each processed .h5 file was generated using 'cellranger count' by aligning to the reference genome, and contains the UMI count expression matrix for each batch, along with corresponding barcodes and features. Each .h5ad file was generated after demultiplexing with 'demuxlet', assigning barcodes to individual sample, and contains the UMI counts matrix with associated barcodes and features.

molecule: nuclear RNA

source_name: Lymph nodes, Lymph nodes

extract_protocol:
Frozen samples were obtained from the BPC Nationwide Children's Hospital, DFCI and ATCC and processed using the Chromium Nuclei Isolation Kit (Cat. no. 1000494: Chromium Nuclei Isolation Kit WITH RNase inhibitor). The samples were homogenized using a pestle in Lysis Buffer and passed through a column. Debris was removed via centrifugation in Debris Removal Buffer and the isolated nuclei were then washed and resuspended.
Isolated nuclei were loaded onto the 10X Chromium for GEM generation and barcoding. The samples went through post GEM-RT cleanup and cDNA amplification. After cDNA QC and quantification, the samples were processed through the 10X Chromium 3’ gene expression library construction protocol according to the manufacturer's user guide. The library was then sequenced using the Illumina NovaSeq X Plus at the Columbia University Single Cell Analysis Core to generate the single-nucleus RNA-seq data collection.

value: Lymph nodes, Lymph nodes

value: Pancreatic Ductal Adenocarcinoma (Lymph node metastatis), Pancreatic Ductal Adenocarcinoma (Lymph node metastasis)

tag: sample type

value: Frozen-Metastatic, Frozen-Metastatic

tag: tumor or_model

value: Model, Model

tag: batch


title: FFPE sample 13981 A1

description:
Genomic DNA from FFPE sample 13981 A1
206702520037_R08C01

tag: disease state

value: Prostate

value: N


title: HCM-CSHL-0078-C25 (tumor, metastatic), HCM-CSHL-0089-C25 (tumor, metastatic)

description:
Library name: AG012
10x Genomics

tag: tissue

value: Tumor, Tumor


title: S3D1 NC2

description: Library name: L7

tag: genotype


title: HiC_cDC_WT1

description:
Library name: Sample27
Hi-C

value: spleen


title: FFPE sample 13983 A1

description:
Genomic DNA from FFPE sample 13983 A1
206772660053_R02C01

value: Benign

tag: diagnosis

value: Benign Prostate Hyperplasia

tag: gleason

value: Y


title: HCM-CSHL-0078-C25 (tumor, primary), HCM-CSHL-0089-C25 (tumor, primary)

description:
Library name: AG010
10x Genomics

source_name: Pancreas, Pancreas

value: Pancreas, Pancreas

value: Pancreatic Ductal Adenocarcinoma, Pancreatic Ductal Adenocarcinoma

value: Frozen-Primary, Frozen-Primary


title: HiC_cDC_KO1

description:
Library name: Sample29
Hi-C

value: cDC


title: FFPE sample 13984 A1

description:
Genomic DNA from FFPE sample 13984 A1
206772660053_R03C01

tag: age

tag: smoking


title: HCM-BROD-0110-C25 (tumor), HCM-CSHL-0073-C25 (tumor)

description:
Library name: AG008
10x Genomics

value: Pancreatic Adenocarcinoma, Pancreatic Ductal Adenocarcinoma


title: HCM-CSHL-0078-C25 (model, primary), HCM-CSHL-0089-C25 (model, primary)

description:
Library name: AG011
10x Genomics


title: FFPE sample 13982 A1

description:
Genomic DNA from FFPE sample 13982 A1
206772660053_R01C01

tag: drinking


title: scRNAseq_WT1

description:
Library name: Sample31
scRNA-seq

value: RBC depleted splenocytes


title: HiC_cDC_WT2

description:
Library name: Sample28
Hi-C


title: VOA-14202

description:
Library name: Sample 2
Column name in lgsoc_methylome_gene_promoter_cell_lines.csv: VOA-14202

value: cell line

value: Low Grade Serous Ovarian

value: KRAS (G12V)


title: FFPE sample 13980 A1

description:
Genomic DNA from FFPE sample 13980 A1
206702520037_R07C01


title: genomic DNA from white matter 4

source_name: white matter 4

value: white matter

tag: Sex

value: male

value: p


title: HCM-BROD-0110-C25 (model), HCM-CSHL-0073-C25 (model)

description:
Library name: AG009
10x Genomics

value: Model, Model


title: Input_cDC_WT1

description:
Library name: Sample25
ChIP-seq

value: spleen


title: HCM-BROD-0213-C71 (model), HCM-BROD-0416-C71 (model)

description:
Library name: AG007
10x Genomics

source_name: Brain, Brain

value: Brain, Brain

value: Glioblastoma Multiforme, Glioblastoma Multiforme

value: Frozen-Recurrent, Frozen-Primary


title: H3K27Ac_cDC_KO2

description:
Library name: Sample24
ChIP-seq

tag: chip antibody

value: anti-H3K27Ac, ab4729, Abcam


title: Input_cDC_WT2

description:
Library name: Sample26
ChIP-seq


title: FFPE sample 13979 A1

description:
Genomic DNA from FFPE sample 13979 A1
206702520037_R06C01

source_name: Prostate

value: Benign

value: Prostate

value: Benign Prostate Hyperplasia

value: Y


title: H3K27Ac_cDC_KO1

description:
Library name: Sample23
ChIP-seq

value: cDC


title: H3K27Ac_cDC_WT2

description:
Library name: Sample22
ChIP-seq


title: FFPE sample 13977 A1

description:
Genomic DNA from FFPE sample 13977 A1
206702520037_R04C01


title: HCM-BROD-0213-C71 (tumor), HCM-BROD-0416-C71 (tumor)

description:
Library name: AG006
10x Genomics

value: Tumor, Tumor


title: H3K27Ac_cDC_WT1

description:
Library name: Sample21
ChIP-seq


title: HCM-BROD-0001-C18 (model), HCM-BROD-0028-C71 (model)

description:
Library name: AG005
10x Genomics

value: Colon adenocarcinoma, Glioblastoma Multiforme

value: Frozen-Metastatic, Frozen-Primary


title: HCM-BROD-0002-C71 (tumor), HCM-BROD-0415-C71 (tumor)

description:
Library name: AA016
10x Genomics

value: Frozen, Frozen


title: HCM-BROD-0001-C18 (tumor), HCM-BROD-0028-C71 (tumor)

description:
Library name: AG004
10x Genomics


title: Spleen, P2 mice, 7 merged samples

city: BARCELONA

first: Elvira

last: Gonzalez-Saiz

state: BARCELONA

address: CARRER BALDIRI REIXAC 10

country: Spain

institute: IRB BARCELONA

description:
Library name: SpleenP2
10x Genomics

data_processing:
The gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
For more detailed information regarding the processing see code availability section of the present manuscript or contact daniel.fernandez@irbbarcelona.org, elvira.gonzalez@irbbarcelona.org.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrices

source_name: Spleen

growth_protocol: E19 HSCs and P2 HSCs have been grown in the mouse embryo/pups until HSC isolation.

extract_protocol:
Fetal liver and spleen was collected, chopped and filtered through a 100 um strainer. Bone marrow was collected from the femur, tibia, pelvis, sternum and column through mechanical bone crushing. Cells were filtered through a 100um strainer and resuspended in PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). Cells were then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no. 130-091-224). The resulting cKit-enriched fraction was washed and stained with fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend, Catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, Catalog no. 108114), Pacific Blue anti-mouse Lineage Cocktail (Biolegend, Catalog no. 133310) and PE anti-mouse CD201 (EPCR) (Biolegend, Catalog no. 141504). Cells were then washed and HSCs were purified through Flow Cytometry Cell Sorting using a CytoFLEX SRT (Beckman Coulter, Catalog no. C71883).
Unperturbed P2 and E19 HSC isolation and sequencing were performed in different days and loaded on different reactions per tissue. Labeled P2 pups were stained and isolated as following: Pup1 BM - Totalseq #1, Pup2 BM - Totalseq #2, Pup1 Spl - Totalseq #3, Pup2 Spl - Totalseq #4. Then TdTomato+ from one pup was pooled with the TdTomato- of the other and viceversa: Tube 1 - 145 tdtomato positive from Pup1 (both BM and spleen mixed) + 5500 tdtomato negative from Pup2 (both BM and spleen mixed) and Tube 2 - 5156 tdtomato negative from Pup1 (both BM and spleen mixed) + 180 tdtomato positive from Pup2 (both BM and spleen mixed). These tubes were loaded into 2 single-cell reactions. Single-cell libraries using Chromium Single Cell 3’ Reagent Kits (v3) following the manufacturer’s guidelines (10X Genomics).

treatment_protocol: 2 P2 Tppp3CreER LSLTdTomato pups (P2 replicates) were treated with tamoxifen at P0.

value: Spleen

tag: sex donor_mice

value: Unknown

value: WT

value: 2 days after birth (P2)


title: HCM-BROD-0002-C71 (model), HCM-BROD-0415-C71 (model)

description:
Library name: AA017
10x Genomics

value: Brain, Brain

value: Model, Model


title: HCM-BROD-0012-C71 (model), HCM-BROD-0199-C71 (model)

description:
Library name: AA015
10x Genomics

value: Glioblastoma Multiforme, Glioblastoma Multiforme


title: PU1_cDC_KO2

description:
Library name: Sample20
ChIP-seq

value: spleen

value: anti-PU.1, 2266S, Cell Signaling Technologies


title: HCM-CSHL-0143-C20 (tumor), HCM-CSHL-0247-C18 (tumor), HCM-CSHL-0322-C20 (tumor)

description:
Library name: AG001
10x Genomics

source_name: Rectum, Cecum, Rectosigmoid junction

value: Rectum, Cecum, Rectosigmoid junction

value: Adenocarcinoma (NOS), Adinocarcinoma (NOS), Adinocarcinoma (NOS)

value: Tumor, Tumor, Tumor


title: PU1_cDC_KO1

description:
Library name: Sample19
ChIP-seq

value: cDC


title: FFPE sample 13978 A1

description:
Genomic DNA from FFPE sample 13978 A1
206702520037_R05C01

value: Benign

value: Prostate

value: Benign Prostate Hyperplasia

value: Y


title: HCM-BROD-0012-C71 (tumor), HCM-BROD-0199-C71 (tumor)

description:
Library name: AA014
10x Genomics

value: Frozen, Frozen

value: Tumor, Tumor


title: NAc, Br6471

type: RNA

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

label: Xenium probe set

source_name: nucleus accumbens

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: CG000581_RevC

value: nucleus accumbens

tag: tissue preservation method

value: Fresh Frozen

tag: donor id


title: Liver, P2 mice, 7 merged samples

description:
Library name: LiverP2
10x Genomics

source_name: Liver

value: Liver

value: Unknown

value: WT

tag: cell type

value: 2 days after birth (P2)


title: FFPE sample 14085 A2

description:
Genomic DNA from FFPE sample 14085 A2
206702520037_R01C01

value: Tumor&Normal

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: N


title: NAc, Br6432


title: FFPE sample 14086 A2

description:
Genomic DNA from FFPE sample 14086 A2
206702520037_R02C01

value: Gleason's pattern 8 (4+4),  grade group 2


title: Bone Marrow, P2 mice, 7 merged samples

description:
Library name: BoneMarrowP2
10x Genomics

source_name: Bone Marrow

value: Bone Marrow


title: PU1_cDC_WT2

description:
Library name: Sample18
ChIP-seq

value: spleen

value: cDC

value: anti-PU.1, 2266S, Cell Signaling Technologies


title: WES.WM4008_R.Vehicle.Early

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
Library name: WES.WM4008_R.Vehicle.Early
BCL2_WES_BCL2_WES_WM4008.vcf

data_processing:
Raw reads were aligned vs hg19 version of human genome using STAR for RNA-seq and BWA for WES. RSEM with Ensemble transcriptome information was used to estimate gene expression counts. Somatic mutations were called using GATK/Mutect2 tools
Assembly: hg19
Supplementary files format and content: RNA-seq data contains gene expresison counts for each gene. WES mutation results are in .vcf format

source_name: pdx

extract_protocol:
DNA and RNA were purified from snap-frozen PDX tumors following using QIAamp DNA mini kit (Qiagen) and mirVana mRNA isolation kit (Invitrogen) respectively and sequenced at the Broad Institute Genomics core facility
RNA-seq was performed using Illumina TruSeq strand-specific protocol. PCR-Free Human WGS - 60x v2 was used for whole exome DNA sequencing, with sample preparation utilizing custom Broad indices (IDT) and Kapa Biosciences HyperPrep library construction kit

value: pdx

tag: treatment

value: Vehicle


title: FFPE sample 14049 A35

description:
Genomic DNA from FFPE sample 14049 A35
206702520027_R03C01

value: Prostate

value: Gleason's pattern 8 (3+5), grade group 2


title: HCM-CSHL-0143-C20 (model), HCM-CSHL-0247-C18 (model), HCM-CSHL-0322-C20 (model)

description:
Library name: AG002
10x Genomics

value: Rectum, Cecum, Rectosigmoid junction

value: Adenocarcinoma (NOS), Adinocarcinoma (NOS), Adinocarcinoma (NOS)

tag: sample type

tag: tumor or_model

value: Model, Model, Model


title: WES.WM4008_R.DTN.Late

description:
Library name: WES.WM4008_R.DTN.Late
BCL2_WES_BCL2_WES_WM4008.vcf

value: DTN

tag: batch


title: PU1_cDC_WT1

description:
Library name: Sample17
ChIP-seq

tag: tissue


title: FFPE sample 14048 B10

description:
Genomic DNA from FFPE sample 14048 B10
206702520027_R02C01

tag: disease state

value: Tumor&Normal

value: Geason's score 9 (5+4), grade group 2

value: Y


title: WES.WM3960_R.Vehicle.Early

description:
Library name: WES.WM3960_R.Vehicle.Early
BCL2_WES_BCL2_WES_WM3960.vcf


title: WES.WM3960_R.DTN.Late

description:
Library name: WES.WM3960_R.DTN.Late
BCL2_WES_BCL2_WES_WM3960.vcf


title: NAc, Br2720

value: nucleus accumbens

value: Fresh Frozen


title: FFPE sample 5780 A3

description:
Genomic DNA from FFPE sample 5780 A3
206702520113_R06C01

tag: diagnosis

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: N


title: FFPE sample 14090 A15

description:
Genomic DNA from FFPE sample 14090 A15
206702520027_R05C01

tag: gleason

value: Former


title: SMC1A_cDC_KO1

description:
Library name: Sample15
ChIP-seq

value: spleen

value: cDC

tag: genotype

value: anti-SMC1A, A300-055A, Bethyl laboratories


title: NAc, Br6522


title: FFPE sample 3793 18

description:
Genomic DNA from FFPE sample 3793 18
206702520113_R05C01

value: Prostate

value: 7 (4+3), Tertiary Gleason 5 also present

tag: age

tag: smoking


title: WM43802_R.Vehicle.Late

description:
Library name: WM43802_R.Vehicle.Late
BCL2_RNAseq.txt

value: pdx

value: Vehicle


title: WM43802_R.VA.Late

description:
Library name: WM43802_R.VA.Late
BCL2_RNAseq.txt

value: VA


title: mouse skin single cell Transcriptome-1

city: Shanghai

first: Shenbin

last: Liu

address: 131 Dongan road

department: Fudan University

country: China

institute: MOE Frontiers Center for Brain Science

description:
Library name: Control-1
Skin CD45 cells from MC903-treated mice

data_processing:
For skin CD45 cell: scRNA-seq data were analyzed in R v3.6.0 using Seurat v5.1.0, or batched analysis was performed using the Seaborn Python package; For sympathetic ganglia: All downstream single-cell analyses were performed using Cell Ranger and Seurat (37). Briefly, for each gene and each cell barcode (filtered by Cell Ranger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat: A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Cell Ranger reanalyzes feature barcode matrices produced by Cell Ranger count or Ranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using Cell Ranger default parameter settings. The Seurat package was used to normalize data, dimensionality reduction, clustering, and differential expressions. The Seurat alignment method of canonical correlation analysis (CCA) (38) was used to integrate the datasets. For clustering, highly variable genes were selected, and the principal components based on those genes were used to build a graph segmented with a resolution of 0.6. Based on the filtered gene expression matrix by Seurat, differential expression analysis was carried out between samples using the edge R package to obtain zone-specific marker genes. Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P-values less than 0.05 were considered significantly enriched by the marker gene. KEGG (39) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism, and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high throughput experimental technologies. We used the cluster Profiler R package to test the statistical enrichment of marker genes in KEGG pathways. Reactome pathway-based analysis of marker genes was implemented by the ReactomePA R package. We identified TH+ noradrenergic sympathetic neurons based on Snap25, Tubb3, Th, and Dbh expression but negative for Chat transcripts. We then visualized the gene expression of each cluster in R v3.6.0 using Seurat v5.1.0.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Skin

extract_protocol:
For scRNA-seq of skin CD45+ cells, the tissues from EtOH- and MC903-treated mice were surgically removed and digested as described above (see the procedure of “flow cytometry”). After digestion, the samples were sieved through a 40 µM cell strainer and centrifuged at 300 g for 10 minutes. The obtained cell pellet was resuspended in 90 μL MACS buffer (supplemented with 0.5% bovine serum albumin (9048-46-8, Vetec) and 2 mM EDTA (60-00-4, Sigma-Aldrich) and 10 μL CD45 Microbeads (130-052-301, Miltenyi Biotec) per 107 cells, and the cells were incubated for 15 minutes at 4°C in the refrigerator. CD45+ cells were subsequently sorted as described above. Single cells were stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). For sNucRNA-seq of sympathetic neurons, sympathetic ganglia (SCG, STG, T2-T4, CG) were dissected from thirty MC903-challenged mice and placed in the cold (4°C) artificial cerebrospinal fluid (ACSF) solution (in mM: 125 NaCl, 3 KCl, 20 NaHCO3, 1.25 NaH2PO4, 2 MgCl2, 20 D-glucose, 2 CaCl2, 0.0001 tetrodotoxin, 0.02 6,7-dinitroquinoxaline-2,3-dione, 0.05 DL-2-amino-5-phosphonovaleric acid), continually bubbled with 95%O2 and 5%CO2. Harvested tissue was homogenized at 4°C in a buffer containing 0.3% IGEPAL CA-630 and a protease inhibitor cocktail (ab65621, Abcam), and the following components (in mM): 250 sucrose, 25 KCl, 20 NaHCO3, 1.25 NaH2PO4, 5 MgCl2, 20 Tricine-KOH, 0.15 spermine, 0.5 spermidine, and 1 dithiothreitol. Samples were filtered through 70 mM strainers, diluted with iodixanol to a final concentration of 25%, and layered on an iodixanol gradient (30% and 40% iodixanol containing 0.04% BSA and RNasin (Promega N2611, 64 units/mL). The samples were centrifuged at 10,000 g for 20 minutes at 4°C, and the nuclei were collected from the 30-40% iodixanol interface.
The BD Rhapsody system was used to capture transcriptomic information of the single cells. Single-cell capture was achieved by randomly distributing a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation to ensure a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcode capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow, which included random priming and extension (RPE), RPE amplification PCR, and WTA index PCR.

value: Skin

value: immune cell


title: SMC1A_cDC_WT2

description:
Library name: Sample14
ChIP-seq


title: mouse skin single cell Transcriptome-2

description:
Library name: RHS-1
Skin CD45 cells from RHS- and MC903-treated mice


title: FFPE sample 5296 C11

description:
Genomic DNA from FFPE sample 5296 C11
206702520113_R04C01

value: Tumor&Normal

tag: drinking

value: Y


title: Ileum, with in situ Polyadenylation, Stereoseq (STOmics)

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

data_processing:
Raw sequencing reads were trimmed using Cutadapt to remove polyA, polyG, and sequences related to the STOmics library preparation. The trimmed reads were then aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations. Unmapped reads were taxonomically classified using Kraken2(kraken2.09) to generate a taxon-by-spot barcode matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 files contain the raw gene expression count matrix (UMI counts) per spot barcode, along with complementary information, including spot barcode assignments to cells based on segmentation and the raw microbial NCBI taxid presence count matrix (UMI counts) per spot barcode
Library strategy: Spatial transcriptomics

source_name: Ileum

extract_protocol:
Cryosection was obtained from the Ileum of a female, 17 weeks old mouse. The tissue section (10 µm thick) was processed with a modified Stereoseq (STOmics) protocol. The collected section had visible signs of neoplasia adjacent to the lumen. The section was mounted onto STOmics mini chip chip ID C02929E514) and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol. In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix. The chambers were sealed and incubated at 37°C for 25 minutes. After enzyme removal, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: Ileum

tag: Sex

value: female

value: ApcMin/+

tag: strain

value: 17 weeks


title: preDC_KO2

description:
Library name: Sample12
RNA-seq

source_name: bone marrow

value: bone marrow

value: preDC


title: WM43802_R.NA.Late

description:
Library name: WM43802_R.NA.Late
BCL2_RNAseq.txt


title: WM43802_R.DTA.Late

description:
Library name: WM43802_R.DTA.Late
BCL2_RNAseq.txt

value: DTA


title: preDC_KO1

description:
Library name: Sample11
RNA-seq


title: SMC1A_cDC_KO2

description:
Library name: Sample16
ChIP-seq

source_name: spleen

value: spleen

value: cDC

tag: chip antibody

value: anti-SMC1A, A300-055A, Bethyl laboratories


title: FFPE sample 5305 D8

description:
Genomic DNA from FFPE sample 5305 D8
206702520027_R01C01

value: Prostate

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2

value: Former


title: MFascicularis_exp3_chip3_CRISPR

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

institute: Ludwig-Maximilians-Universität München

description: Library name: MFascicularis_exp3_chip3_CRISPR_lib

library_source: other

data_processing:
Per batch and library type, the experimental workflow yielded up to 128 FASTQ files due to the different combinations of 10x and flow cell lanes as well as the paired-end setup. All FASTQ data were processed using Cell Ranger (10x Genomics, v7.0.0). Reads of the GEX libraries were aligned to the hg38 and macFas6 reference genomes extended by the sequence of the dCas9 insert, while reads of the CRISPR libraries were aligned to a custom reference containig the gRNA protospacer sequences.
We demultiplexed the reads by species using cellsnp-lite (v1.2.2) and vireo (v0.2.3), based on a list of single nucleotide polymorphisms (SNPs) derived from bulk RNA-seq data of the wild-type cell lines.
We assigned perturbations to the cells based on the gRNA calls.  We only kept cells that contained a single dominant gRNA (i.e., all other detected gRNAs in the cell contributed <10% of gRNA UMIs and <1000 UMIs combined) and with >10 UMIs supporting the dominant gRNA. To generate the subset of data presented in this repository, we filtered the FASTQ files, count matrices, and gRNA calls to include only POU5F1-perturbed and control cells.
Assembly: GRCh38/hg38 GENCODE release 32 and Macaca fascicularis 6.0/macFas6 ENSEMBL release 105, both extended by the sequence of the dCas9 insert
Supplementary files format and content: Hierarchical data format 5 (h5)  files - filtered count matrices output by Cell Ranger
Supplementary files format and content: Comma-separated values (csv) files - gRNA calls per cell output by Cell Ranger

molecule: other

organism: Macaca fascicularis

growth_protocol: For standard maintenance, iPSCs were grown in geltrex-coated 12-wells in StemFit Basic03. Medium was changed every other day.

extract_protocol:
To quantify mRNA and gRNAs of the cells, cells were dissociated to single cells using Accumax, washed and stored in PBS +0.04 % Bsa. Human and cynomolgus cells were pooled to equal cell numbers per cell line, then the single cell suspension was loaded on a 10x Genomics Chromium Controller for GEM generation. RT and cDNA amplification were conducted according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening; USER GUIDE: CG000510 Rev B).
We performed three CRISPRi screens in total, using one 10x chip in the first two and three 10x chips in the third experiment (5 batches in total). Per 10x chip and lane, two libraries were generated: a gene expression library and a CRISPR library (identified as GEX and CRISPR lib in the sample names). For details see the manufacturer’s protocol.

treatment_protocol: To conduct single-cell CRISPRi screens, iPSCs were seeded as single-cells in geltrex-coated wells. Cells were transduced with lentiviral gRNA libraries (MOI 0.1). Transduced cells were selected with puromycin, then they were expanded for 5 days, while also inducing KRAB-dCas9 expression by adding doxycycline to the SF03 medium.

tag: cell line

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus

tag: library type

value: 10x Genomics 5' CRISPR Guide Capture


title: FFPE sample 14046 B9

description:
Genomic DNA from FFPE sample 14046 B9
206702520113_R01C01

value: Tumor&Normal

value: Gleason's pattern 7 (4+3) with tertiary pattern 5, Grade group 3

value: N


title: WM4262_R.Vehicle.Late

description:
Library name: WM4262_R.Vehicle.Late
BCL2_RNAseq.txt

value: pdx

tag: treatment

value: Vehicle


title: FFPE sample 14047 D18

description:
Genomic DNA from FFPE sample 14047 D18
206702520113_R02C01

value: Gleason's pattern 7 (3+4), Grade group 2


title: SMC1A_cDC_WT1

description:
Library name: Sample13
ChIP-seq

tag: cell type


title: MFascicularis_exp3_chip3_GEX

description: Library name: MFascicularis_exp3_chip3_GEX_lib

value: 10x Genomics 5' Gene Expression


title: preDC_WT2

description:
Library name: Sample10
RNA-seq

value: bone marrow

value: preDC


title: FFPE sample 14043 A8

description:
Genomic DNA from FFPE sample 14043 A8
206702520068_R07C01

value: Gleason's pattern 7 (3+4), Grade group 3


title: FFPE sample 14044 A15

description:
Genomic DNA from FFPE sample 14044 A15
206702520027_R04C01

value: Prostate

value: Y


title: WM4262_R.DTV.Late

description:
Library name: WM4262_R.DTV.Late
BCL2_RNAseq.txt

value: DTV


title: WM43802_R.Azd.Late

description:
Library name: WM43802_R.Azd.Late
BCL2_RNAseq.txt

value: Azd


title: pDC_KO2

description:
Library name: Sample8
RNA-seq

value: spleen

value: pDC


title: MFascicularis_exp3_chip2_GEX

description: Library name: MFascicularis_exp3_chip2_GEX_lib

value: induced pluripotent stem cell

value: KRAB-dCas9-HA-P2A-mCherry insertion at AAVS1 locus


title: WM4262_R.DTV.Early

description:
Library name: WM4262_R.DTV.Early
BCL2_RNAseq.txt


title: FFPE sample 14042 B3

description:
Genomic DNA from FFPE sample 14042 B3
206702520068_R06C01

value: Tumor&Normal

value: Adenocarcinoma


title: MFascicularis_exp3_chip2_CRISPR

description: Library name: MFascicularis_exp3_chip2_CRISPR_lib

value: 10x Genomics 5' CRISPR Guide Capture


title: pDC_KO1

description:
Library name: Sample7
RNA-seq


title: MFascicularis_exp3_chip1_GEX

description: Library name: MFascicularis_exp3_chip1_GEX_lib


title: MFascicularis_exp3_chip1_CRISPR

description: Library name: MFascicularis_exp3_chip1_CRISPR_lib


title: WM4262_R.DTN.Late

description:
Library name: WM4262_R.DTN.Late
BCL2_RNAseq.txt

value: pdx

value: DTN


title: FFPE sample 14041 A13

description:
Genomic DNA from FFPE sample 14041 A13
206702520068_R05C01

value: Gleason's pattern 7 (3+4), Grade group 2

value: Former


title: preDC_WT1

description:
Library name: Sample9
RNA-seq

value: bone marrow

value: preDC


title: FFPE sample 14040 C15

description:
Genomic DNA from FFPE sample 14040 C15
206702520068_R04C01

value: Prostate

value: N


title: pDC_WT2

description:
Library name: Sample6
RNA-seq


title: MFascicularis_exp2_chip1_CRISPR

description: Library name: MFascicularis_exp2_chip1_CRISPR_lib


title: pDC_WT1

description:
Library name: Sample5
RNA-seq


title: FFPE sample 14039 A23

description:
Genomic DNA from FFPE sample 14039 A23
207166150136_R08C01

value: Gleason's pattern 7 (3+4), grade group 2


title: cDC_KO2

description:
Library name: Sample4
RNA-seq

value: cDC


title: WM4257_SCR.Vehicle.Late

description:
Library name: WM4257_SCR.Vehicle.Late
BCL2_RNAseq.txt

value: Vehicle


title: MFascicularis_exp2_chip1_GEX

description: Library name: MFascicularis_exp2_chip1_GEX_lib

value: 10x Genomics 5' Gene Expression


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 3

city: Bethesda

first: Ian

middle: L

last: Morgan

state: MD

address: 50 Center Dr.

institute: National Heart Lung and Blood Institute

description: Library name: pos_sc_Mt_gyrase_Del_CTD_cip_rep3

data_processing:
Trimmomatic to trim adapters from reads
BWA-MEM to align the reads to the reference sequence
SAMtools to index the reads
Pysam to extract reads, count enzyme-cleaved DNA ends, and normalize counts by spikein reads
Assembly: pBR322_plus_spikes.fa
Supplementary files format and content: TXT file with number and location of enzyme-cleaved DNA ends from forward and reverse reads

organism: Synthetic plasmid

source_name: Synthetic plasmid

growth_protocol: Supercoiled pBR322 DNA was treated with  M. tuberculosis gyrase CTD deletion mutant.

extract_protocol:
Qiagen PCR Clean-up Kit
SHAN-seq

value: Synthetic plasmid

value: 100 uM ciprofloxacin

tag: sample group


title: FFPE sample 14038 C17

city: Washington

last: Kwabi-Addo

address: 520 W. Street N.W.

institute: Howard University College of Medicine

description:
Genomic DNA from FFPE sample 14038 C17
206702520068_R02C01

data_processing:
Illumina GenomeStudio Methylation Module V2011.1
[processed value definition] Average Beta

extract_protocol: DNA extracted from FFPE samples using Zymo Quick-DNA FFPE kit according to standard instructions

value: Tumor&Normal


title: cDC_KO1

description:
Library name: Sample3
RNA-seq

value: spleen


title: FFPE sample 8843 C15

description:
Genomic DNA from FFPE sample 8843 C15
207166150136_R07C01

value: Adenocarcinoma

value: Y


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 2

description: Library name: pos_sc_Mt_gyrase_Del_CTD_cip_rep2


title: WM4257_MCL1.Vehicle.Late

description:
Library name: WM4257_MCL1.Vehicle.Late
BCL2_RNAseq.txt

value: pdx

tag: batch


title: cDC_WT2

description:
Library name: Sample2
RNA-seq

tag: tissue


title: WM4257_MCL1.TV.Early

description:
Library name: WM4257_MCL1.TV.Early
BCL2_RNAseq.txt

value: TV


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 1

description: Library name: pos_sc_Mt_gyrase_Del_CTD_cip_rep1


title: FFPE sample 5306 C8

description:
Genomic DNA from FFPE sample 5306 C8
207166150136_R05C01

tag: disease state


title: cDC_WT1

description:
Library name: Sample1
RNA-seq


title: FFPE sample 5299 C9

description:
Genomic DNA from FFPE sample 5299 C9
207166150136_R06C01

tag: diagnosis

value: Former


title: WM4257_SCR.TV.Late

description:
Library name: WM4257_SCR.TV.Late
BCL2_RNAseq.txt


title: RiboTag IP-Camk2 | WT | female | S1 | Sample 97

city: Los Angeles

first: Anand

last: Suresh

state: CA

address: 650 CHARLES E YOUNG DR S, MED RECEIVING CHS, RM 76-200C

department: Neurology

institute: University of California Los Angeles

description: Library name: 97-C24-WT-F-S1-IP

data_processing:
Samples were checked for QC, demultiplexed reads were aligned using STAR aligner to the mouse genome (reference genome ID: mm10) and gene level quantification calculated by Salmon. Outliers were calculated by measuring connectivity between samples, using the WCGNA package and removing samples >2 SD from the mean for Bulk and IP samples. Genes with counts < 20 were excluded.All analysis was performed using R4.4.2.  Counts were VST transformed, Differential gene analysis was performed using limma-voom with FDR of 0.05
Assembly: Demultiplexed reads were aligned using STAR aligner to the mouse genome (reference genome ID: mm10)
Supplementary files format and content: 1CSV file includes raw counts for both cell-type

source_name: somatosensory cortex (brain)

extract_protocol:
For each mRNA isolation experiment, mice were anaesthetized with isoflurane, followed by cardiac perfusion with ice cold choline ACSF containing 132 mM choline, 2.5 mM KCl, 1.25 mM NaH2PO4, 25 mM NaHCO3, 7 mM MgCl2, 0.5 mM CaCl2, and 8 mM D-glucose). Coronal sections (1.5 mm thick) containing S1 (A/P -0.5 to +1.82 mm, M/L 3.0 to 4.0 mm) and V1 (A/P +3.5 to 5.5 mm, M/L 1.5 to 3.0 mm) were collected using Stainless-Steel Brain Matrices (Zivic instruments) in chilled choline, from which S1 and V1 were dissected bilaterally. Samples were independently homogenized with a 2 mL Dounce homogenizer in 1 mL of supplemented homogenization buffer containing 1% w/v, HB-S: 1 mM DTT, protease inhibitors (1X), RNAsin (200 units/mL), cycloheximide (2 mg/l), and heparin (1 mg/mL). 100 μL of the homogenate was used for isolating bulk RNA from S1-V1. To isolate mRNA of HA-tagged Pvalb-Cre or Camk2a-Cre from non-HA tagged ribosomes, samples were incubated for 4 h with an anti-HA antibody (1:180, 5 μL in 900 μL of homogenate; 901513 Covance Anti-HA antibody), followed by overnight incubation with magnetic beads (Pierce Protein A/G Magnetic Beads 88802, 200 μL) at 4oC at 15 rpm centrifugation. The supernatant was washed 3 times with 800 μL of high-salt buffer (Tris 50 mM, KCl 300 mM, MgCl2 12 mM, 10% NP-40 (1%), DTT 1 mM, cycloheximide 100 μg/mL, dH2O), centrifuged at 15 rpm for 10 min at 4 oC. For RNA extraction, we used Zymo Research Direct-zol RNA Miniprep kit (R2051) for the homogenate (input), and the Zymo Research Direct-zol RNA Microprep kit (R2061) for the bead-antibody-protein sample (IP); RNA was eluted with DNAase/RNAse-free water. RNA Integrity Number (RIN) scores were used to evaluate the integrity of RNA through the ratio of 28S:18S ribosomal RNA (Agilent TapeStation 4200). We set a minimum RIN score of 7 for our samples.
RNA-seq libraries were prepared using Ovation® RNA-Seq System V2. Libraries were multiplexed for paired end 100 bp sequencing on NovaSeq S2, with a read depth of ~45 million reads on average.

value: somatosensory cortex (brain)

value: WT

value: Batch 2


title: WM4262_R.DTN.Early

description:
Library name: WM4262_R.DTN.Early
BCL2_RNAseq.txt

value: DTN


title: FFPE sample 13968 A6

first: Bernard

description:
Genomic DNA from FFPE sample 13968 A6
206702520025_R05C01

value: Prostate

tag: gleason

value: Gleason's pattern 7 (3+4), Grade group 2


title: WM4257_SCR.TV.Early

description:
Library name: WM4257_SCR.TV.Early
BCL2_RNAseq.txt


title: WM4257_MCL1.TV.Late

description:
Library name: WM4257_MCL1.TV.Late
BCL2_RNAseq.txt


title: FFPE sample 5308 B12

description:
Genomic DNA from FFPE sample 5308 B12
206702520025_R06C01

value: Gleason's pattern 7 (3+4), grade group 2


title: RiboTag IP-Camk2(Excitatory) | WT | female | S1 | Sample 94

description: Library name: 94-C20-WT-F-S1-IP

source_name: Somatosensory Cortex (brain)

value: Somatosensory Cortex (brain)

value: Excitatory (Camk2)

tag: genotype

value: Batch 1


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 2

description: Library name: neg_sc_Mt_gyrase_Del_CTD_cip_rep2

value: Synthetic plasmid

value: 100 uM ciprofloxacin


title: WM4070_R.Vehicle.Late

description:
Library name: WM4070_R.Vehicle.Late
BCL2_RNAseq.txt

value: Vehicle


title: RiboTag IP-Camk2(Excitatory) | WT | female | S1 | Sample 96

description: Library name: 96-C23-WT-F-S1-IP


title: FFPE sample 13965 A9

description:
Genomic DNA from FFPE sample 13965 A9
206702520025_R04C01

value: Tumor&Normal

value: Adenocarcinoma

tag: age

value: N


title: Cphfro, scRNAseq

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

institute: University of Basel

data_processing:
Cell Ranger v5.0 software (10X Genomics)
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: Tab-separated values and matrix files

organism: Cyphotilapia frontosa

source_name: intestine

extract_protocol:
Intestinal samples were flushed, chopped and dissociated at 25ºC for 20 minutes in pre-warmed DMEM/F-12 medium 1X (Fisher Scientific) supplemented with 1 mg / mL of dispase II (Sigma). Suspensions were centrifuged at 500 rcf for 7 minutes at 4ºC, resuspended in 10% Fetal Bovine Serum (FBS) in DMEM/F-12, filtered with a 20 µm cell strainer (CellTrics), centrifuged again with the same conditions, resuspended in 10% FBS in DMEM/F-12, and centrifuged one last time at low speed (200-250 rcf) for 5 minutes at 4ºC.
Following instructions from 10X Genomics Chromium Next GEM  Gene Expression 3' v3.1

value: intestine


title: RiboTag IP-Camk2(Excitatory) | WT | female | S1 | Sample 93

description: Library name: 93-C19-WT-F-S1-IP


title: WM4070_R.DTV.Late

description:
Library name: WM4070_R.DTV.Late
BCL2_RNAseq.txt

value: pdx

value: DTV


title: RiboTag IP-Camk2(Excitatory) | WT | female | S1 | Sample 92

description: Library name: 92-C18-WT-F-S1-IP

value: WT


title: FFPE sample 14089 A3

description:
Genomic DNA from FFPE sample 14089 A3
206702520025_R02C01

value: Gleason's pattern 7 (3+4), Grade group  2

tag: smoking

value: Former

value: Y


title: RiboTag IP-Camk2(Excitatory) | WT | male | S1 | Sample 91

description: Library name: 91-C16-WT-M-S1-IP


title: Permic, scRNAseq

organism: Perissodus microlepis


title: Julorn, scRNAseq

organism: Julidochromis ornatus


title: WM4070_R.DTN.Late

description:
Library name: WM4070_R.DTN.Late
BCL2_RNAseq.txt

value: DTN


title: FFPE sample 13951 A22

description:
Genomic DNA from FFPE sample 13951 A22
206702520025_R01C01

value: Prostate

value: Gleason's pattern 7 (3+4),

tag: drinking


title: WM4070_R.Vehicle.Early

description:
Library name: WM4070_R.Vehicle.Early
BCL2_RNAseq.txt


title: FFPE sample 13956 A17

description:
Genomic DNA from FFPE sample 13956 A17
206702520025_R03C01

value: Gleason's pattern 7 (3+4), Grade group 2


title: WM4070_R.DTN.Early

description:
Library name: WM4070_R.DTN.Early
BCL2_RNAseq.txt


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase CTD deletion with cip replicate 1

description: Library name: neg_sc_Mt_gyrase_Del_CTD_cip_rep1

value: Synthetic plasmid


title: Hapmic, scRNAseq

organism: Haplotaxodon microlepis


title: Lepatt2_p5, bulkRNA

data_processing:
Trimmomatic, STAR, HTSeq
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

organism: Lepidiolamprologus attenuatus

extract_protocol:
Each intestine was divided into five equally long parts along the anterior-posterior axis, and each section was processed independently. The sections were first mechanically chopped with a razor blade, then homogenized on a FastPrep 24 instrument (MP BioMedicals), and total RNA was extracted using a Zymo Direct-Zol RNA Miniprep kit (Zymo Research), following the manufacturer’s protocol.
Illumina Truseq library preparation protocol


title: WM4070_R.DTV.Early

description:
Library name: WM4070_R.DTV.Early
BCL2_RNAseq.txt


title: Lepatt, scRNAseq


title: WM3960_R_MCL1.DTN.Late

description:
Library name: WM3960_R_MCL1.DTN.Late
BCL2_RNAseq.txt


title: RiboTag IP-Camk2(Excitatory) | KO | male | S1 | Sample 88

description: Library name: 88-C12-KO-M-S1-IP

value: Somatosensory Cortex (brain)

value: Excitatory (Camk2)

value: Fmr1 KO

value: Batch 1


title: Lepatt2_p4, bulkRNA


title: Limdar, scRNAseq

organism: Limnotilapia dardennii


title: WM3960_R_SCR.DTN.Early

description:
Library name: WM3960_R_SCR.DTN.Early
BCL2_RNAseq.txt


title: RiboTag IP-Camk2(Excitatory) | KO | female | S1 | Sample 85

description: Library name: 85-C7-KO-F-S1-IP


title: Lepatt2_p3, bulkRNA


title: Petort, scRNAseq

organism: Petrochromis orthognathus


title: Trezeb, scRNAseq

organism: Trematocara zebra


title: Lepatt2_p2, bulkRNA


title: RiboTag IP-Camk2(Excitatory) | KO | female | S1 | Sample 84

description: Library name: 84-C6-KO-F-S1-IP

organism: Mus musculus


title: WM3908_R.Vehicle.Late

description:
Library name: WM3908_R.Vehicle.Late
BCL2_RNAseq.txt

organism: Homo sapiens

value: Vehicle


title: RiboTag IP-Camk2(Excitatory) | WT | male | S1 | Sample 90

description: Library name: 90-C15-WT-M-S1-IP


title: Erecya, scRNAseq

organism: Eretmodus cyanostictus

value: intestine


title: RiboTag IP-Camk2(Excitatory) | KO | female | S1 | Sample 89

description: Library name: 89-C14-KO-F-S1-IP


title: RiboTag IP-Camk2(Excitatory) | KO | female | S1 | Sample 83

description: Library name: 83-C5-KO-F-S1-IP


title: Erecya2_p5, bulkRNA


title: Neobre, scRNAseq

organism: Neolamprologus brevis


title: Lepatt2_p1, bulkRNA


title: WM3908_R.DTV.Late

description:
Library name: WM3908_R.DTV.Late
BCL2_RNAseq.txt

value: pdx


title: RiboTag IP-Camk2(Excitatory) | KO | male | S1 | Sample 82

description: Library name: 82-C4-KO-M-S1-IP


title: Erecya2_p4, bulkRNA


title: WM3908_R.DTV.Early

description:
Library name: WM3908_R.DTV.Early
BCL2_RNAseq.txt

value: DTV


title: Lepatt1_p4, bulkRNA


title: Erecya2_p3, bulkRNA


title: RiboTag IP-Camk2(Excitatory) | WT | female | S1 | Sample 80

description: Library name: 80-C2-WT-F-S1-IP

value: WT


title: WM3908_R.Vehicle.Early

description:
Library name: WM3908_R.Vehicle.Early
BCL2_RNAseq.txt


title: RiboTag IP-Camk2(Excitatory) | KO | male | S1 | Sample 81

description: Library name: 81-C3-KO-M-S1-IP


title: WM3908_R.DTN.Late

description:
Library name: WM3908_R.DTN.Late
BCL2_RNAseq.txt


title: Erecya2_p2, bulkRNA


title: Lepatt1_p2, bulkRNA


title: Lepatt1_p1, bulkRNA


title: Erecya1_p5, bulkRNA


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 77

description: Library name: 77-C23-WT-F-V1-IP

source_name: Visual Cortex (brain)

value: Visual Cortex (brain)


title: Lepatt1_p5, bulkRNA


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 76

description: Library name: 76-C20-WT-F-V1-IP


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 78

description: Library name: 78-C24-WT-F-V1-IP


title: Erecya2_p1, bulkRNA


title: Erecya1_p4, bulkRNA


title: Lepatt1_p3, bulkRNA


title: Erecya1_p3, bulkRNA


title: Dyrk1aKO_dDAVP_48h_rep_3

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description: Library name: sample_43

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 113). Transcripts per million (TPM) and expected counts were generated by RSEM. Computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Assembly: Ensemble release 113
Supplementary files format and content: TPM values in txt format

source_name: kidney

growth_protocol: Cells were cultured in DMEM/Ham’s F12 mediaum (DMEM/F12, Gibco) containing 5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin, and 2% fetal bovine serum which is referred to complete media at 37ºC.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Microprep kit (R2062, Zymo Research) following the manufacturer’s instructions.
First-strand and double-stranded cDNA was synthesized and amplified from 1 ng of total RNA using SMART-Seq® mRNA HT Kit (634796, TAKARA). Amplified cDNA were purified using AMPure XP beads (A63880, Beckman Coulter), and quantified using a Qubit dsDNA HS DNA assay kit (Q32851, Invitrogen). One nanogram of the synthesized cDNAs were fragmented and tagged with index primers (FC-131-1024, Nextera XT DNA library Preparation Kit, Illumina) for high-throughtput sequencing. Libraries were purified by AmPure XP beads, and quantified using a Qubit dsDNA HS DNA assay kit. Equal amounts of indexed libraries were pooled and sequenced on an Illumina platform.

treatment_protocol: To polarize the cells, cells were maintained on permeable membrane filters (3450, Corning) in complete medium for 4 days. Cells were then incubated in serum-free/hormone-deprived medium [containing 50 nM dexamethasone, 60 nM sodium selenite, and 5 μg/mL transferrin], referred to as simple medium, for another 24 hours. Cells were subsequently treated under four experimental conditions: vehicle-treated, 0.1 nM dDAVP (1-desamino-8-D-arginine-vasopressin, V1005, Sigma), 1 ng/mL TGF-β + 0.1 nM dDAVP, and 10 ng/mL TGF-β + 0.1 nM dDAVP in simple medium. dDAVP was applied to the basolateral side, whereas TGF-β was applied to both the apical and basolateral sides of polarized cells. After 24 hours, the medium was replaced with fresh simple medium containing the same treatments. Cells were harvested at the 48-h time point for sample preparation.

value: kidney

value: mpkCCD

value: mouse cortical collecting duct cell

value: Dyrk1a KO

value: dDAVP 0.1 nM, 48 hrs


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 74

description: Library name: 74-C18-WT-F-V1-IP


title: WM3908_R.DTN.Early

description:
Library name: WM3908_R.DTN.Early
BCL2_RNAseq.txt

value: DTN


title: WM3903_R.DTN.Late

description:
Library name: WM3903_R.DTN.Late
BCL2_RNAseq.txt


title: WM3903_R.DTV.Late

description:
Library name: WM3903_R.DTV.Late
BCL2_RNAseq.txt


title: WM3903_R.DTV.Early

description:
Library name: WM3903_R.DTV.Early
BCL2_RNAseq.txt


title: WM3903_R.DTN.Early

description:
Library name: WM3903_R.DTN.Early
BCL2_RNAseq.txt


title: WM3903_R.Vehicle.Late

description:
Library name: WM3903_R.Vehicle.Late
BCL2_RNAseq.txt


title: Dyrk1aKO_dDAVP_48h_rep_1

description: Library name: sample_41


title: Erecya1_p1, bulkRNA


title: Erecya1_p2, bulkRNA


title: Dyrk1aKO_dDAVP_48h_rep_2

description: Library name: sample_42


title: RiboTag IP-Camk2(Excitatory) | WT | male | V1 | Sample 73

description: Library name: 73-C16-WT-M-V1-IP


title: Dyrk1aKO_dDAVP_48h_rep_4

description: Library name: sample_44


title: RiboTag IP-Camk2(Excitatory) | WT | male | V1 | Sample 72

description: Library name: 72-C15-WT-M-V1-IP


title: WM4376.TN.Late

description:
Library name: WM4376.TN.Late
BCL2_RNAseq.txt

value: TN


title: S_35 (G6PD-tg, non-trained, male, muscle sample)

city: Madrid

first: Jose

middle: Luis

last: Cabrera

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

description: Library name: S_35

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Adaptors from RNAseq were removed from reads and low quality reads filtered using the trimgalore v-0.6.6 and cutadapt v-1.18 software.
Trimmed reads were mapped and quantified on the transcriptome GRCm38 gene-build 91 using RSEM v-1.3.1 (calling STAR aligner).
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method, included in edgeR Bioconductor package).
Assembly: GRCm38 gene-build 91
Supplementary files format and content: Counts for mapped reads obtained with STAR v2.5.1 and RSEM v1.3.1

source_name: Muscle

extract_protocol:
RNA was extracted from mice tissues using the RNeasy® Mini Kit (Qiagen), following standard protocols
RNA libraries were produced using the NEBNext Ultra II Directional RNA kit (Illumina) and sequenced on a NextSeq 2000 (Illumina) platform.

value: Muscle


title: WT_dDAVP_48h_rep_4

description: Library name: sample_40


title: WM4376.Vehicle.Late

description:
Library name: WM4376.Vehicle.Late
BCL2_RNAseq.txt


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 75

description: Library name: 75-C19-WT-F-V1-IP

value: Excitatory (Camk2)


title: S_34 (G6PD-tg, non-trained, male, muscle sample)

description: Library name: S_34


title: WM4257.TN.Late

description:
Library name: WM4257.TN.Late
BCL2_RNAseq.txt


title: WM4257.Vehicle.Late

description:
Library name: WM4257.Vehicle.Late
BCL2_RNAseq.txt


title: WT_dDAVP_48h_rep_3

description: Library name: sample_39


title: WT_dDAVP_48h_rep_2

description: Library name: sample_38


title: S_33 (G6PD-tg, non-trained, male, muscle sample)

description: Library name: S_33


title: WM4224.TN.Late

description:
Library name: WM4224.TN.Late
BCL2_RNAseq.txt


title: S_32 (G6PD-tg, non-trained, male, muscle sample)

description: Library name: S_32


title: WM4224.Vehicle.Late

description:
Library name: WM4224.Vehicle.Late
BCL2_RNAseq.txt


title: Stk11KO_dDAVP_48h_rep5

description: Library name: sample_36

value: Stk11 KO


title: S_31 (G6PD-tg, non-trained, male, muscle sample)

description: Library name: S_31


title: RiboTag IP-Camk2(Excitatory) | KO | female | V1 | Sample 65

description: Library name: 65-C5-KO-F-V1-IP

value: Fmr1 KO

value: Batch 1


title: RiboTag IP-Camk2(Excitatory) | KO | male | V1 | Sample 64

description: Library name: 64-C4-KO-M-V1-IP


title: S_30 (Wild type, trained, male, muscle sample)

description: Library name: S_30


title: RiboTag IP-Camk2(Excitatory) | KO | female | V1 | Sample 71

description: Library name: 71-C14-KO-F-V1-IP


title: WM4061.DTN.Late

description:
Library name: WM4061.DTN.Late
BCL2_RNAseq.txt


title: Stk11KO_dDAVP_48h_rep4

description: Library name: sample_35


title: RiboTag IP-Camk2(Excitatory) | KO | female | V1 | Sample 67

description: Library name: 67-C7-KO-F-V1-IP


title: Stk11KO_dDAVP_48h_rep3

description: Library name: sample_34


title: Stk11KO_dDAVP_48h_rep2

description: Library name: sample_33


title: WM4200_R.DTN.Early

description:
Library name: WM4200_R.DTN.Early
BCL2_RNAseq.txt


title: S_28 (Wild type, trained, male, muscle sample)

description: Library name: S_28


title: WT_dDAVP_48h_rep_1

description: Library name: sample_37


title: RiboTag IP-Camk2(Excitatory) | KO | female | V1 | Sample 66

description: Library name: 66-C6-KO-F-V1-IP


title: RiboTag IP-Camk2(Excitatory) | WT | female | V1 | Sample 61

description: Library name: 61-C1-WT-F-V1-IP


title: WM4200_R.Vehicle.Late

description:
Library name: WM4200_R.Vehicle.Late
BCL2_RNAseq.txt

value: Vehicle


title: S_29 (Wild type, trained, male, muscle sample)

description: Library name: S_29


title: Stk11KO_dDAVP_48h_rep1

description: Library name: sample_32


title: S_27 (Wild type, trained, male, muscle sample)

description: Library name: S_27


title: WM4061.Vehicle.Late

description:
Library name: WM4061.Vehicle.Late
BCL2_RNAseq.txt

value: pdx


title: RiboTag IP-PV (Parvalbumin) | WT | male | S1 | Sample 60

description: Library name: 60-P27-WT-M-S1-IP

value: Somatosensory Cortex (brain)

value: Pvalb


title: WT_dDAVP_48h_rep5

description: Library name: sample_31

value: WT


title: RiboTag IP-PV (Parvalbumin) | WT | male | S1 | Sample 59

description: Library name: 59-P26-WT-M-S1-IP


title: RiboTag IP-Camk2(Excitatory) | KO | male | V1 | Sample 63

description: Library name: 63-C3-KO-M-V1-IP

value: Visual Cortex (brain)


title: RiboTag IP-PV (Parvalbumin) | KO | male | S1 | Sample 58

description: Library name: 58-P25-KO-M-S1-IP


title: WM4008_R.DTN.Late

description:
Library name: WM4008_R.DTN.Late
BCL2_RNAseq.txt


title: S_25 (Wild type, non-trained, male, muscle sample)

description: Library name: S_25


title: WM4008_R.Vehicle.Late

description:
Library name: WM4008_R.Vehicle.Late
BCL2_RNAseq.txt


title: WT_dDAVP_48h_rep3

description: Library name: sample_29

value: kidney

value: mpkCCD


title: S_24 (Wild type, non-trained, male, muscle sample)

description: Library name: S_24


title: WT_dDAVP_48h_rep4

description: Library name: sample_30

value: mouse cortical collecting duct cell


title: S_26 (Wild type, trained, male, muscle sample)

description: Library name: S_26


title: WM3983_R.DTN.Late

description:
Library name: WM3983_R.DTN.Late
BCL2_RNAseq.txt


title: RiboTag IP-PV (Parvalbumin) | KO | male | S1 | Sample 57

description: Library name: 57-P24-KO-M-S1-IP


title: WM3983_R.Vehicle.Late

description:
Library name: WM3983_R.Vehicle.Late
BCL2_RNAseq.txt


title: RiboTag IP-PV (Parvalbumin) | KO | female | S1 | Sample 56

description: Library name: 56-P23-KO-F-S1-IP


title: RiboTag IP-PV (Parvalbumin) | WT | male | S1 | Sample 55

description: Library name: 55-P22-WT-M-S1-IP


title: S_23 (Wild type, non-trained, male, muscle sample)

description: Library name: S_23


title: WT_dDAVP_48h_rep2

description: Library name: sample_28

value: dDAVP 0.1 nM, 48 hrs


title: S_22 (Wild type, non-trained, male, muscle sample)

description: Library name: S_22


title: WT_dDAVP_48h_rep1

description: Library name: sample_27


title: RiboTag IP-PV (Parvalbumin) | WT | male | S1 | Sample 54

description: Library name: 54-P21-WT-M-S1-IP


title: WM3965_R.DTN.Early

description:
Library name: WM3965_R.DTN.Early
BCL2_RNAseq.txt

value: DTN


title: Stk11KO_veh_48h_rep4

description: Library name: sample_25


title: WM3965_R.Vehicle.Early

description:
Library name: WM3965_R.Vehicle.Early
BCL2_RNAseq.txt


title: Stk11KO_veh_48h_rep5

description: Library name: sample_26


title: S_21 (Wild type, non-trained, male, muscle sample)

description: Library name: S_21


title: S_15 (G6PD-tg, non-trained, female, muscle sample)

description: Library name: S_15


title: RiboTag IP-PV (Parvalbumin) | WT | female | S1 | Sample 53

description: Library name: 53-P20-WT-F-S1-IP


title: WM3960_R.DTN.Late

description:
Library name: WM3960_R.DTN.Late
BCL2_RNAseq.txt


title: RiboTag IP-PV (Parvalbumin) | WT | female | S1 | Sample 52

description: Library name: 52-P18-WT-F-S1-IP


title: Stk11KO_veh_48h_rep3

description: Library name: sample_24


title: WM3960_R.Vehicle.Late

description:
Library name: WM3960_R.Vehicle.Late
BCL2_RNAseq.txt


title: S_14 (G6PD-tg, non-trained, female, muscle sample)

description: Library name: S_14


title: WM3960_R.DTN.Early

description:
Library name: WM3960_R.DTN.Early
BCL2_RNAseq.txt


title: RiboTag IP-PV (Parvalbumin) | KO | male | S1 | Sample 51

description: Library name: 51-P12-KO-M-S1-IP


title: Stk11KO_veh_48h_rep2

description: Library name: sample_23


title: RiboTag IP-PV (Parvalbumin) | KO | female | S1 | Sample 50

description: Library name: 50-P11-KO-F-S1-IP


title: Muscle,Ang II-induced 28D,rep3

city: Guangzhou

first: Xing

last: Fu

address: jinsui road NO.9

institute: Guangzhou Medical University

description: Library name: sample9

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)
1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5) .
The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Aorta

extract_protocol:
RNA was harvested using TRIzol/chloroform/isoamyl alcohol. 1.0 ug of total RNA was used for the construction of sequencing lilbraries.
RNA libraries for RNA-seg were prepared using MGIEaSy mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: Aorta

value: tissue

value: ApoE knock out

value: The mini osmotic pump for Ang II-induction


title: S_12 (G6PD-tg, non-trained, female, muscle sample)

description: Library name: S_12

value: Muscle


title: WT_veh_48h_rep5

description: Library name: sample_21


title: S_11 (G6PD-tg, non-trained, female, muscle sample)

description: Library name: S_11


title: RiboTag IP-PV (Parvalbumin) | KO | female | S1 | Sample 49

description: Library name: 49-P10-KO-F-S1-IP

value: Fmr1 KO

value: Batch 1


title: RiboTag IP-PV (Parvalbumin) | KO | female | S1 | Sample 48

description: Library name: 48-P9-KO-F-S1-IP


title: WT_veh_48h_rep4

description: Library name: sample_20

value: Vehicle


title: WT_veh_48h_rep3

description: Library name: sample_19


title: S_9 (Wild type, trained, female, muscle sample)

description: Library name: S_9


title: RiboTag IP-PV (Parvalbumin) | KO | female | S1 | Sample 47

description: Library name: 47-P8-KO-F-S1-IP

value: Somatosensory Cortex (brain)


title: S_13 (G6PD-tg, non-trained, female, muscle sample)

description: Library name: S_13


title: S_10 (Wild type, trained, female, muscle sample)

description: Library name: S_10


title: Muscle,Ang II-induced 14D,rep3

description: Library name: sample6


title: S_8 (Wild type, trained, female, muscle sample)

description: Library name: S_8


title: Muscle,Ang II-induced 28D,rep1

description: Library name: sample7


title: WT_veh_48h_rep2

description: Library name: sample_18


title: Stk11KO_veh_48h_rep1

description: Library name: sample_22

value: Stk11 KO


title: RiboTag IP-PV (Parvalbumin) | KO | male | S1 | Sample 46

description: Library name: 46-P6-KO-M-S1-IP

value: Pvalb


title: Muscle,Ang II-induced 28D,rep2

description: Library name: sample8


title: WT_veh_48h_rep1

description: Library name: sample_17

value: WT


title: RiboTag IP-PV (Parvalbumin) | KO | male | S1 | Sample 45

description: Library name: 45-P5-KO-M-S1-IP


title: S_7 (Wild type, trained, female, muscle sample)

description: Library name: S_7


title: Muscle,Ang II-induced 14D,rep2

description: Library name: sample5


title: RiboTag IP-PV (Parvalbumin) | WT | female | S1 | Sample 44

description: Library name: 44-P4-WT-F-S1-IP


title: S_6 (Wild type, trained, female, muscle sample)

description: Library name: S_6


title: RiboTag IP-PV (Parvalbumin) | WT | female | S1 | Sample 43

description: Library name: 43-P3-WT-F-S1-IP


title: Muscle,sham control,rep3

description: Library name: sample3

value: sham control


title: 10Tgf_dDAVP_rep4

description: Library name: sample_16

value: kidney

value: mpkCCD

value: 10 ng/mL TGF-b+dDAVP 0.1 nM, 48 hrs


title: 10Tgf_dDAVP_rep3

description: Library name: sample_15

value: mouse cortical collecting duct cell


title: Muscle,sham control,rep2

description: Library name: sample2

value: Aorta


title: Muscle,Ang II-induced 14D,rep1

description: Library name: sample4

value: tissue


title: S_5 (Wild type, non-trained, female, muscle sample)

description: Library name: S_5


title: S_4 (Wild type, non-trained, female, muscle sample)

description: Library name: S_4


title: 10Tgf_dDAVP_rep2

description: Library name: sample_14