title: Replicate 10, mouse mixed pool, snATAC

city: Pittsburgh

first: Michael

last: Leone

address: 4315 Tesla St

institute: Carnegie Mellon University

description:
SEA2253A67
10x Genomics

library_source: genomic single cell

data_processing:
Bcl files were converted to fastq format using the cellranger mkfastq command line tool. Fastq reads were then aligned to the mm10 genome using Chromap. Subsequent steps were done with the software suite ArchRv1.0. Arrow files were generated from the aligned fragments and doublet scores were generated using ArchR’s built-in doublet algorithm. An ArchR project was then generated from the Arrow files and sample metadata from the sequencing run. Cells were filtered with minimum transcription start site (TSS) enrichment = 8, minimum number of unique fragments 10^3.5, and doublets filtered out with cutoff enrichment threshold of 0.5. Fragment periodicity plots were also inspected for intact periodicity from nucleosomes.
Un-biased clustering of cells was done using Iterative LSI, with variable features looped between 30 and 230. 200 variable features was selected having a favorable resolution of clustering with minimal batch effects. Batch correction was performed with Harmony. Enrichment of marker genes for major cell types was visualized based on gene score, which is a proxy for gene expression based on accessibility at and around the TSS of the gene.
Once neuron clusters were identified by marker genes, two separate neuron and glia ArchR projects were generated and we re-clustered cells again with iterative LSI. Clusters within the neuron sub-project were labeled based on ATAC-RNA integration.  We used the macaque snRNA-seq dataset with conserved dorsal horn cell type labels (along with unlabeled Mid and Ventral neurons) and we named the macaque genes the orthologous mouse gene names, in order to match with annotated mouse gene scores. We then performed unconstrained integration using ArchR’s implementation of Seurat’s label transfer algorithm using the command addGeneIntegrationMatrix. After integration and putative cell labeling, we also visualized in UMAPs the marker gene expression in clusters now labeled as dorsal horn neuron subtypes. We used the macaque and conserved marker genes previously discussed. We then re-combined the neuron and glia projects (ArchR Project: Mouse_DorsalHorn_scATAC). We also provide the neuron subset (ArchR project: Mouse_scATAC_DorsalHorn_neuron2_wDeviations) and we computed motif enrichment and cell-type-specific variability in enrichment (deviations) using ArchR’s implementation of chromVAR.
Code for data processing available at https://github.com/pfenninglab/dorsalhorn_conserved_rna_atac_xen
Assembly: mm10
Supplementary files format and content: the processed, labeled neuron and glia ArchR project (Mouse_DorsalHorn_scATAC.tar.gz), as well as the processed, labeled neuron subset (Mouse_scATAC_DorsalHorn_neuron2_wDeviations.tar.gz) which also contains the deviation matrix from ArchR’s implementation of chromVAR.

source_name: F/M pool of mice 11-20

extract_protocol:
Twenty sex-matched B6 mice were deeply anesthetized with Isoflurane, decapitated and the spinal cord was dissected out. Then, the lumbar spinal cord from L3-5 was mounted on an agarose mold and the dorsal halve was micro dissected on a vibratome (Leica Microsystems). Next, the tissue was Dounce homogenized with a loose pestle in 2ml of Lysis Buffer containing in mM: 10 Tris-Cl, 10 NaCl, 3 MgCl2; ~25 strokes, and filtered through a 70mm cell strainer, followed by a centrifugation step at 400g for 5min at 4ºC. After that, the pellet was resuspended in 2ml of Nuclei Wash and Resuspension Buffer (1X PBS, 1% BSA and RNase inhibitor 0.2U/mL) and filtered-through a 40mm cell strainer to optimize myelin and debris removal. Finally, nuclei viability was assessed by trypan blue staining
Library construction and sequencing were done at the 10X Genomics Core at the University of Pittsburgh according to standard 10x workflow: https://www.10xgenomics.com/support/single-cell-atac/documentation/steps/library-prep

value: dorsal horn of spinal cord

tag: cell line

value: all

tag: age (years)

value: pooled male and female


title: Replicate 9, mouse mixed pool, snATAC

status: Public on Aug 01 2024

type: SRA

country: USA

description:
SEA2253A66
10x Genomics

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: Sex

tag: genotype


title: Replicate 12, mouse mixed pool, snATAC

description:
SEA2253A69
10x Genomics


title: Replicate 8, mouse mixed pool, snATAC

description:
SEA2253A65
10x Genomics


title: Replicate 6, mouse mixed pool, snATAC

description:
SEA2253A63
10x Genomics

source_name: F/M pool of mice 1-10


title: Replicate 4, mouse mixed pool, snATAC

description:
SEA2253A61
10x Genomics


title: Replicate 3, mouse mixed pool, snATAC

description:
SEA2253A60
10x Genomics


title: Replicate 5, mouse mixed pool, snATAC

description:
SEA2253A62
10x Genomics


title: Replicate 1, mouse mixed pool, snATAC

description:
SEA2253A58
10x Genomics


title: Replicate 7, mouse mixed pool, snATAC

description:
SEA2253A64
10x Genomics


title: Replicate 2, mouse mixed pool, snATAC

description:
SEA2253A59
10x Genomics


title: BRAF V600E #3

city: Columbus

first: Alessandro

last: Canella

state: OH

address: 700 Children’s Drive

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
60-80M read pairs
B3_AC

library_source: transcriptomic

data_processing:
Low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64
Features were identified from the GFF file that came with the assembly from Gencode (V28).
Feature coverage counts were calculated using featureCounts
Normalized (TPM) quantification for each sample was done using salmon counts
Assembly: GRCm38.p6 assembly of theMus musculus reference from NCBI
Supplementary files format and content: comma separated file that includes the aggregated normalized salmon TPM counts for all samples

molecule: total RNA

source_name: brain

growth_protocol: DF1-BRAF V600E and DF1-CRE cells were injected intracranially in the right hemisphere of RCAS mice at the age of 2 days.

extract_protocol:
Total RNA from tumor-infiltrating immune cells was isolated using the Qiagen miRNeasy Micro kit (Qiagen) and eluted with 14uL H2O. The quality and quantity of RNA was checked with Bioanalyzer.
Total RNA-seq by Illumina NovaSeq6000

value: brain

tag: tissue type

value: BRAF V600E

value: Tumor infiltrating immune cells

tag: time point

value: at day 3 post-treatment


title: HM_CS_7

city: Frederiksberg C

first: Camilla

middle: Hartmann Friis

last: Hansen

address: Ridebanevej 9, 2nd floor

department: Faculty of Health Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina CASAVA software used for basecalling.
Adaptors trimmed with Fastp, filtered for low quality sequence and mapped to Mus Musculus(GRCm38/mm10) genome with HISAT2 v 2.0.5
Gene count file made using FeatureCounts v 1.5.0
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: adipose

extract_protocol:
Rneasy Lipid Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose

value: Male

tag: treatment


title: BRAF V600E #2

description:
60-80M read pairs
B2_AC


title: BRAF V600E #1

description:
60-80M read pairs
B1_AC


title: no tumor #3

description:
60-80M read pairs
C3_AC

value: no tumor


title: no tumor #2

description:
60-80M read pairs
C2_AC


title: mESC_Zscan10_day0_C2

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

data_processing:
Read quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37)
Reads were aligned to mm10 genome using HISAT2 (Version 2.2.1)
Normalized read counts for all genes were obtained using featureCount (v3.18.1).
Differential expression was determined in each of the pair-wise comparisons between experimental and control groups using DESeq (V1.22.1).
Assembly: mm10
Supplementary files format and content: Tabular files
Supplementary files format and content: Raw counts for each sample

source_name: mESCs

growth_protocol: HM1 mESCs were grown in standard medium (DMEM supplemented with 15% FBS (ES-qualified, ThermoFisher Scientific, 16141-079), 1000 U/mL LIF (Millipore), 1× MEM non-essential amino acids, 1 mM of Sodium Pyruvate, 1× GlutaMAX™ Supplement, 1× Penicillin and streptomycin, and 0.1 mM of 2-mercaptoethanol) supplemented with 1µM MEK1/2 inhibitor (PD0325901, Sigma) and 3 1µM GSK3 inhibitor (CHIR99021, Sigma).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN) following manufacturer’s protocol.
A total of 100ng total RNA was subjected to polyA enrichment and cDNA libraries preparation using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, E7760L).

treatment_protocol: During differenation, LIF, MEK1/2 inhibitor and GSK3 inhibitor were removed from the medium

value: mESCs

value: HM1 mESCs

value: Embryonic stem cells

value: Zscan10 KO

value: Differentiation day0


title: mESC_Zscan10_day0_C1


title: no tumor #1

description:
60-80M read pairs
C1_AC


title: HM_CS_2


title: NASH, Bio Rep 7

city: Tarrytown

first: Yuanqi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: Freshly frozen Spatial Transcriptomics sequencing

data_processing:
Demultiplex:spaceranger-1.3.0 mkfastq
Alignment: spaceranger-1.3.0 count
Assembly: GRCm38 Ensembl release100
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count daata in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Visium Spatial Transcriptomics

source_name: liver

extract_protocol:
Liver section mRNAs were released by permeabilization to the Visium spots, captured by poly-T probes with unique barcodes. The optimal permeabilization time was 18-24 minutes, pre-determined by Visium Tissue Optimization Kit.
Visium Gene Expression v1

value: liver

tag: diet

value: CDAA-HFD

tag: strain

value: male


title: NASH, Bio Rep 5


title: NASH, Bio Rep 4


title: NASH, Bio Rep 1


title: Replicate 11, mouse mixed pool, snATAC

description:
SEA2253A68
10x Genomics

value: dorsal horn of spinal cord

value: all


title: Chow, Bio Rep 6

value: Chow


title: NASH, Bio Rep 3


title: Chow, Bio Rep 4


title: Chow, Bio Rep 3


title: Chow, Bio Rep 5


title: DFCRE04

city: Philadelphia

first: Kathryn

middle: E

last: Wellen

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
fastq files were aligned to Mus musculus reference genome GRCm39 using Kallisto (version 0.46.2).
Transcript quantification data were summarized to genes using the tximport package and normalized using the trimmed mean of M values (TMM) method in edgeR.
Genes with <1 CPM in n+1 of the samples, where n is the size of the smallest group of replicates, were filtered out.
Expression data was normalized using the VOOM function in the Limma package in R.
Differentially expressed genes were identified by linear modeling after correcting for multiple testing using Benjamini-Hochberg using the Limma package.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes log2 counts per million (CPM) values for each sample

growth_protocol: 6-8 week old Acly f/f; Acss2 f/f mice were injected with AAV8-TBG-Cre to generate DKO mice or AAV8-TBG-GFP to generate WT control mice. 1 week after injection, mice were placed on a Western diet (Teklad TD.88137) for 6 weeks prior to tissue collection.

extract_protocol:
RNA was extracted using TRIzol following manufacturer's protocol.
Library construction was performed by Novogene Corporation. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Liver tissue was freeze-clamped at time of collection and frozen in liquid nitrogen immediately.

value: DKO


title: DFCRE06


title: DFCRE03


title: Chow, Bio Rep 1


title: DFCRE02


title: Chow, Bio Rep 2


title: DFCRE01


title: DFGFP04

value: WT


title: NASH, Bio Rep 6


title: DFGFP05


title: DFGFP01


title: DFGFP03


title: NASH, Bio Rep 2


title: DT

city: ZunYi

first: meng meng

last: Guo

state: GuiZhou

address: Zunyi Medical University

department: Immunology

country: China

institute: Zunyi Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: FPKM(.csv)

source_name: mouse NSCLC tumor tissue

extract_protocol:
A total amount of 1-3μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using VAHTS Universal  V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the  manufacturer’s recommendations and index codes were added to attribute sequences to  each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Then we added fragmentation buffer to break the mRNA into short  fragments. First strand cDNA was synthesized using random hexamer primer and  RNase H. Second strand cDNA synthesis was subsequently performed using buffer,  dNTPs, DNA polymerase I and RNase H. And then, the double stranded cDNA was  purified by AMPure P beads or QiaQuick PCR kit. The purified double stranded cDNA  was repaired at the end, added a tail and connected to the sequencing connector, then  the fragment size was selected, and finally the final cDNA library was obtained by PCR  enrichment.
RAN library were prepared for sequencing using standard Illumina protocols

value: mouse NSCLC tumor tissue

value: Taraxasterol combined with DC tumor vaccine


title: PBS

value: PBS


title: DFGFP02


title: DFGFP06


title: Tara

value: Taraxasterol


title: Ptk6-/- female succinate biol 3

city: Chicago

first: Angela

last: Tyner

address: 900 S Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Performed by LC Sciences (Houston, TX)
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. The sequence quality was verified using FastQC.
HISAT2was usedto map reads to the genome. The mapped reads of each sample were assembled using StringTie.
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
StringTie and ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: GRCm39

source_name: distal jejunum

extract_protocol:
RNA was harvested using TRIzol (Invitrogen), genomic DNA was removed using TURBO DNA-free Kit (Invitrogen).
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: distal jejunum

value: 100 mM succinate


title: Ptk6-/- female succinate biol 2


title: DC

value: DC tumor vaccine


title: Ptk6-/- female control biol 3

value: Regular water


title: Ptk6-/- female control biol 2


title: Wildtype female succinate biol 3


title: Ptk6-/- female control biol 1


title: DFCRE05


title: Wildtype female succinate biol 2


title: Wildtype female succinate biol 1


title: Wildtype female control biol 3


title: Wildtype female control biol 1


title: Wildtype female control biol 2


title: Ptk6-/- male succinate biol 3


title: Ptk6-/- male succinate biol 2


title: Ptk6-/- male succinate biol 1


title: Ptk6-/- male control biol 3


title: Ptk6-/- male control biol 2


title: Wildtype male succinate biol 2


title: Wildtype male succinate biol 3


title: Ptk6-/- male control biol 1


title: Wildtype male control biol 1


title: Ptk6-/- female succinate biol 1


title: Wildtype male control biol 2


title: Wildtype male succinate biol 1


title: Wildtype male control biol 3


title: Intestinal lamina propria lymphocytes, IL-22Fc, replicate 2

city: San Diego

first: Peng

last: Zhang

state: CA

address: 9500 Gilman Dr.

institute: UCSD

library_source: transcriptomic single cell

data_processing:
Single cell RNA-Sequencing (scRNA-seq) library preparation was performed by Judith Varner lab using the 10x 3' Continuous Chromium Connect. Approximately 17,000 cells were loaded to achieve 10,000 captured cells per sample to be sequenced. Sequencing was performed by IGM using the NovaSeq 6000 (Illumina) sequencing platform to obtain approximately 200 million reads per sample. Raw scRNA-seq data was converted to FASTQ files and then aligned to the mouse genome [mm10]-2020 A and integrated using default parameters of CellRanger (v7.1.0, 10x Genomics). Quality control and clustering were performed using Loupe Brower 6.5.0. Basic filtering parameters included cells with Unique Molecular Identifiers (UMIs) of minimum 50 and maximum 8500. Cells expressing less than 50 percent mitochondrial related genes were included and CD45+ were removed. After clustering, detected clusters were mapped to cell types or intermediate states using known markers for intestinal epithelial cell subtypes.
Assembly: [mm10]-2020 A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intetstine

extract_protocol:
mesenteric fat tissue and Peyer’s patches were carefully removed and small intestine was opened longitudinally and sliced into small fragments roughly 2 mm in length. The tissue was incubated in 5 mM EDTA–PBS on ice for 90 min. Every 30 min, the tissue was shaken vigorously and the supernatant was collected as fraction 1 in a new conical tube. The final fraction (enriched for crypts) was washed twice in PBS, centrifuged at 300g for 5 min, and dissociated with TrypLE express (Invitrogen) for 5 min at 37 °C. The single-cell suspension was then passed through a 40-μm filter and removed dead cell by using Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) for scRNA-seq. After IEC was removed, the remaining tissue was then minced with scissors and dissociated in RPMI containing 2% FBS, Liberase (31.25μg/ml) and DNase I (50 μg/ml; Sigma) at constant shaking at 37 °C for 35 min (175 rpm). The digested tissue was then filtered through a 70-μm strainer to remove large debris. Viable lamina propria lymphocytes were collected at the interface of a 40%/80% Percoll/RPMI gradient (GE Healthcare). Removed dead cell by using Dead Cell Removal Kit for scRNA-seq.
Library was performed according to the manufacter's instructions (10x 3' Chomium Connect)

value: Small intetstine

value: lamina propria lymphocytes

value: HFD+30% fructose water for 16 weeks, and i.p. injected with IL-22-Fc for last 4 weeks


title: Intestinal lamina propria lymphocytes, IL-22Fc, replicate 1

value: male


title: Intestinal lamina propria lymphocytes, Fc, replicate 1

value: HFD+30% fructose water for 16 weeks, and i.p. injected with Fc for last 4 weeks


title: Intestinal epithelial cells, IL-22Fc, replicate 2

value: epithelial cell


title: Intestinal lamina propria lymphocytes, Fc, replicate 2


title: Intestinal epithelial cells, IL-22Fc, replicate 1


title: HFD iWAT

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Using Cell Ranger, raw sequencing reads were converted to fastq files, aligned to the mm10 genome, and counted per single cell/nucleus.
Assembly: mm10
Supplementary files format and content: tsv.gz; outputs from Cell Ranger v7.1.0 (filtered feature-barcode matrices)

molecule: nuclear RNA

growth_protocol: Wild-type male C57BL/6J mice were subject to either a standard chow diet or a high-fat diet (HFD) from 8 weeks of age for 10 weeks.

extract_protocol:
Nuclei were isolated from frozen epididymal (eWAT) and inguinal (iWAT) white adipose tissues by pulverizing the tissues in liquid nitrogen and homogenizing in chilled Douncers.
Next, the nucleus suspension was subject to nucleus sorting to remove debris and multiplets.
Then, 16,000 nuclei (targeting 10,000) were loaded onto the 10X Genomics Chromium controller.,
Libraries were constructed using the Chromium Single Cell 3' Reagent Kit v3.3 and indexed using sample barcodes.

value: adipose

value: wild-type

value: High-fat diet (HFD)


title: Intestinal epithelial cells, Fc, replicate 1


title: Intestinal epithelial cells, Fc, replicate 2


title: Chow iWAT

value: Chow diet


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-72, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

data_processing:
none provided
Supplementary files format and content: mm10,GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol. iPS cells were differentiated into CMs as described below. On day 0, the medium was replaced with the AscleStem cardiomyocyte differentiation medium kit (CDM; Nacalai Tesque) containing 6 μM CHIR99021 (Tocris, Bristol, UK). On day 2, the medium was replaced with CDM supplemented with 5 μM IWP-2 (Tocris) and 5 μM SB431542 (Wako, Osaka, Japan). From day 4 onward, the medium was replaced with fresh CDM every other day. On day 10, the cells were dissociated into single cells using Liberase solution (Roche) supplemented with DNase I (Roche). On day 11, cells were purified using glucose- and glutamine-free Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies, Carlsbad, CA) and 4 mM lactic acid (Wako). The glucose-free lactic acid medium was changed every 2 days for 6 to 8 days. After purification, the cells were maintained in DMEM containing 10% FBS (Thermo Fisher Scientific) and then subjected to analysis around day 35. Prepared hiPSCMs were treated with DMEM containing 200 ng/mL human recombinant IGFBP7 (#350-09, Pepro Tech) and 9% mouse serum (vaccinated and unvaccinated), and RNA samples were collected for bulk RNA-seq 24 hours later. "
single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.
scRNA-seq, Bulk RNA-seq

value: cardiomyocyte

value: heart

tag: age

value: 6-8 weeks old


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-73, scRNAseq

value: 6-9 weeks old


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-71, scRNAseq


title: Chow eWAT


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-70, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-68, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-66, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-65, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-69, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-63, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-67, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-59, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-58, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-57, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-60, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-54, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-61, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-55, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-64, scRNAseq


title: HFD eWAT


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-62, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-53, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-52, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-51, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-50, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-48, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-56, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-49, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-47, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-46, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-43, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-42, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-41, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-40, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-39, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-44, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-38, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-36, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-37, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-34, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-35, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-33, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-32, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-31, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-28, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-24, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-27, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-25, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-29, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-22, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-26, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-18, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-19, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-30, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-16, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-45, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-23, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-15, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-14, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-13, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-12, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-11, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-8, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-6, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-2, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-5, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-3, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-20, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-21, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-4, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-1, scRNAseq


title: B16F10_MOCK_1

city: Busan

first: Eun-Ji

last: Ko

address: 2, Busandaehak-ro

country: South Korea

institute: Pusan National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCm39 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Skin

growth_protocol: B16-F10 cells were cultured in RPMI1620 containing 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA, USA), 1% penicillin, and L-glutamine (Gibco). All cell lines were maintained at 37 °C in a humidified atmosphere containing 5% CO2 and 90% humidity.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Approximately 18 h after transfection, the cells were treated with 100 μg/mL hygromycin for 2 days.

value: Skin

value: morphology of spindle-shaped and epithelial-like cells

value: Hygromycin

value: Control


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-17, scRNAseq


title: MC3T3-E1 cells, 25(OH)D + ZK191784, Rep 1

city: Rotterdam

first: Bram

middle: CJ

last: van der Eerden

address: Wytemaweg 80

department: Internal medicine

country: Netherlands

institute: Erasmus University MC

data_processing:
Sequencing was performed at 2x150 bp on a NovaSeq 6000 (Illumina, California, USA)
Raw sequence reads were aligned to the mm39 mouse reference genome using STAR (version 2.7.9a) using basic 2-pass mode
Duplicate reads were marked using the Genome Analysis Toolkit (version 4.2.4.0)
Reads were counted per exon in the GENCODE vM30 mouse gene annotation using featureCounts (subread version 2.0.3)
The resulting count table was further processed using the DESeq2 package (version 1.38.2)
Assembly: Mm39
Supplementary files format and content: Text filed including raw count for each sample
Supplementary files format and content: Text file including TMM normalized counts for each sample

source_name: Calvarial bone

growth_protocol: MC3T3-E1 were seeded in 12-wells plate, grown for 2 days in alpha-minimum essential medium (αMEM; A10490-01, Gibco, Paisley, UK), supplemented with 10% fetal bovine serum. Than cells were switched to osteogenic medium (αMEM, 10% FBS, 100 Units/mL penicillin and 100 µg/mL streptomycin, 10 mM β-glycerophosphate (BGP, Sigma-Aldrich, Missouri, United States), 50 µg/ml ascorbic acid (Sigma-Aldrich) and 0.1 µM dexamethasone (Sigma-Aldrich).  Cells were differentiated for 28 days and refreshed 3 times a week.

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions. RNA concentration and size distribution profile were analyzed on an Agilent Bioanalyzer RNA 6000 Pico chip (Thermo Fisher Scientific, USA).
RNA sequencing library was prepared using the QuantSeq 3’ mRNA-Seq library prep kit (Lexogen, Vienna, Austria)

treatment_protocol: At day 27 cells were treated for 24 hours with, 100 µM 25(OH)D, 100 µM 25(OH)D + 4 mM BGP, or 100 µM 25(OH)D + 100 µM ZK191784

value: Calvarial bone

value: Pre-osteoblast

value: WT

value: 100 microM 25(OH)D + 100 microM ZK191784


title: MC3T3-E1 cells, 25(OH)D + BGP, Rep 2

value: 100 microM 25(OH)D + 4 mM BGP


title: MC3T3-E1 cells, 25(OH)D + ZK191784, Rep 3


title: MC3T3-E1 cells, 25(OH)D + ZK191784, Rep 2


title: B16F10_Tjp2KO_1

description: GAAGCTTATGAACCCGACTACGG

value: Tjp2(ZO2) KO cells


title: B16F10_Tjp1KO_1

description: ACGGACCGCCTGTCCGAGCGAGG

value: Tjp1(ZO1) KO cells


title: MC3T3-E1 cells, 25(OH)D + BGP, Rep 3


title: MC3T3-E1 cells, 25(OH)D, Rep 2

value: 100microM 25(OH)D


title: MC3T3-E1 cells, 25(OH)D, Rep 3


title: MC3T3-E1 cells, Control, Rep 3


title: MC3T3-E1 cells, Control, Rep 1


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-10, scRNAseq


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-9, scRNAseq


title: 6 weeks female mouse lymph node, treated with S/Zn-RS, replication 3

city: Xiamen

first: yee

last: chen

state: Fujian

address: Xiangannanlu

department: School of Public Health

institute: Xiamen University

description:
Singleron Matrix GEXSCOPE
S/Zn-RS_3

data_processing:
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.3 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm39
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample

source_name: lymph node

extract_protocol:
The lymph nodes were placed into PBS with 2% (v/v) fetal bovine serum and prepared into single cell suspension by mechanical grinding. Then, we washed samples for 3 times with PBS with 2% (v/v) fetal bovine serum. Finally, the samples were stained with Trypan Blue and the cell viability was evaluated microscopically. Single-cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE Single Cell RNA Library Kits (Singleron) (Ref). Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: 6 weeks

tag: gender

value: female

value: treated with S/Zn-RS

value: lymph node


title: cardiomyocyte,Cdh5Cre-Igfbp7 flox-7, scRNAseq

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: MC3T3-E1 cells, Control, Rep 2


title: 6 weeks female mouse lymph node, treated with S/Zn-RS, replication 2

description:
Singleron Matrix GEXSCOPE
S/Zn-RS_2


title: 6 weeks female mouse lymph node, treated with S/Zn-RS, replication 1

description:
Singleron Matrix GEXSCOPE
S/Zn-RS_1


title: 6 weeks female mouse lymph node, treated with S/AlPi, replication 2

description:
Singleron Matrix GEXSCOPE
S/AlPi_2

value: treated with S/AlPi


title: 6 weeks female mouse lymph node, treated with S/AlPi, replication 3

description:
Singleron Matrix GEXSCOPE
S/AlPi_3


title: 6 weeks female mouse lymph node, treated with STFK, replication 3

description:
Singleron Matrix GEXSCOPE
STFK_3

value: treated with STFK


title: 6 weeks female mouse lymph node, treated with STFK, replication 2

description:
Singleron Matrix GEXSCOPE
STFK_2


title: MC3T3-E1 cells, 25(OH)D + BGP, Rep 1

value: Calvarial bone


title: 6 weeks female mouse muscle, treated with S/Zn-RS 72h, replication 2

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Cleanned sequence reads were mapped to GRcm38 Genome by using Hisat2
Raw count were calculated by using featurecounts
Supplementary files format and content: GRcm39
Supplementary files format and content: tab-delimited txt files include raw count values for each Sample

source_name: muscle

extract_protocol:
1. put the tissue block directly into the mortar, add a small amount of liquid nitrogen, grind quickly, wait for the tissue to soften, add a small amount of liquid nitrogen, and then grind until the grinding is complete. Then, add the tissue sample to 1 ml of Trizol at 50-100 mg and transfer it to a centrifuge tube.2. Add chloroform, which accounts for 1/5 of the total volume. Cap the centrifuge tube tightly and shake vigorously for 15 sec and let stand at room temperature for 2-3min. Then centrifuge at 12,000 rpm at 4°C for 10-15 min. Carefully pipette the upper aqueous phase into a new centrifuge tube and add equal volumes of isopropyl alcohol. Mix upside down and leave at room temperature for 10min. Then centrifuge at 12,000 rpm at 4°C for 10 min. Carefully discard the supernatant and add 1 ml of 75% ethanol prepared with DEPC water. Wash the tube cap and wall well and flick the tube bottom, let the pellet float. Centrifuge at 12,000 rpm at 4°C for 3 min, discard supernatant. Leave at room temperature for 2-3min and let dry. Add an appropriate amount of RNase free water (DEPC water), after complete dissolution, take a small amount for testing, and store the rest at -80°C. 3. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent， USA） and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: muscle

value: treated with S/Zn-RS 72h


title: 6 weeks female mouse muscle, treated with S/Zn-RS 72h, replication 1


title: 6 weeks female mouse lymph node, treated with STFK, replication 1

description:
Singleron Matrix GEXSCOPE
STFK_1


title: MC3T3-E1 cells, 25(OH)D, Rep 1

value: Pre-osteoblast

value: WT


title: 6 weeks female mouse muscle, treated with S/Zn-RS 24h, replication 1

value: treated with S/Zn-RS 24h


title: 6 weeks female mouse muscle, treated with S/AlPi  72h, replication 1

value: treated with S/AlPi  72h


title: 6 weeks female mouse muscle, treated with S/Zn-RS 6h, replication 1

value: treated with S/Zn-RS 6h


title: 6 weeks female mouse muscle, treated with S/AlPi  24h, replication 2

value: 6 weeks

value: treated with S/AlPi  24h


title: 6 weeks female mouse muscle, treated with S/Zn-RS 24h, replication 2

value: female


title: 6 weeks female mouse muscle, treated with S/AlPi  24h, replication 1


title: 6 weeks female mouse muscle, treated with S/AlPi 6h, replication 2

value: treated with S/AlPi 6h


title: MP-8_DMSO_1hrBIC

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
For RNA-Seq, reads were mapped to mm10 using Bowtie2
Counts matrix for DESeq2 was generated using FeatureCounts
For RNA-Seq, BAM files were deduplicated (UMI_tools) and converted to BigWig files (bamCoverage) in a strand specific manner.
For RNA-Seq,DESeq2 was used to call differential gene expression between genotypes, and calculate FPKM.
Assembly: mm10
Supplementary files format and content: Bigwig files (.bw) represent genome coverage by the reads in a strand specific manner. Counts file represent the FeatureCounts output that was used for DESeq2
Library strategy: BrU-Seq

source_name: Brain

growth_protocol: Day in vitro (DIV) primary neuron cultures from mouse cortex

extract_protocol:
Cultures were lysed in Tri-reagent BD (Sigma, T3809) and frozen for future procedures. RNA was purified by phenol-chloroform extraction and isopropaonol precipitation, treated with DNase-I (NEB, M0303) then fragmented by high-magnesium, high-temperature incubation.
One 1μg of Bru-containing  RNA was used for library preparation. The library was prepared in collaboration with the BrU-seq lab of the University of Michigan (Paulsen et al., 2013, 2014)

value: Brain

value: DIV17 Cortical Cultures

tag: drug

value: DMSO

value: 1hr bicuculline


title: MP-6_MM401_1hrH2O

value: 1hr H2O


title: 6 weeks female mouse muscle, treated with S/AlPi 6h, replication 1


title: MP-4_MM401_1hrBIC


title: 6 weeks female mouse muscle, treated with S/AlPi  72h, replication 2


title: MP-3_DMSO_4hrH2O

value: 4hr H2O


title: MP-5_MM401_4hrBIC

value: 4hr bicuculline


title: MP-9_DMSO_4hrBIC


title: MP-2_DMSO_4hrBIC


title: MP-21_MM401_4hrH2O


title: MP-7_MM401_4hrH2O


title: 6 weeks female mouse lymph node, treated with S/AlPi, replication 1

description:
Singleron Matrix GEXSCOPE
S/AlPi_1

value: treated with S/AlPi

value: lymph node


title: MP-1_DMSO_1hrBIC


title: MP-20_MM401_1hrH2O


title: MP-18_MM401_1hrBIC


title: MP-19_MM401_4hrBIC


title: 6 weeks female mouse muscle, treated with S/Zn-RS 6h, replication 2

value: muscle


title: MP-16_DMSO_4hrBIC


title: MP-15_DMSO_1hrBIC


title: MP-17_DMSO_4hrH2O


title: MP-14_MM401_4hrH2O


title: MP-13_MM401_1hrH2O


title: MP-10_DMSO_4hrH2O


title: MP-12_MM401_4hrBIC


title: MP-11_MM401_1hrBIC


title: HFD fed IKO5 mice

city: Beijing

first: Shaocong

last: Hou

address: 1st Nanwei Street

department: State Key Laboratory of Bioactive Substance and Function of Natural Medicines

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to obtain clean reads
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis  was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: Microsoft Excel file includes FPKM values for each sample
Supplementary files format and content: Microsoft Excel file includes raw counts for each sample

source_name: Ileum

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's instructions. RNA degradation and contamination, RNA purity, and RNA integrity was assessed according to the manufacturer's instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Ileum

value: intestinal epithelial cells (IECs)

value: IEC NCoR knock out (IKO)


title: HFD fed IKO7 mice


title: HFD fed IKO3 mice


title: HFD fed IKO2 mice


title: HFD fed WT7 mice

value: WT


title: HFD fed IKO4 mice


title: HFD fed WT3 mice


title: HFD fed WT1 mice


title: HFD fed IKO1 mice


title: HFD fed WT2 mice


title: mESC_WT_day0_C2_RAD21

library_source: genomic

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of ChIP-seq data in fastq files were assessed using QoRTs (v1.2.37)
ChIP-seq raw reads were aligned to the mm10 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq peaks were identified using MACS.
Assembly: mm10
Supplementary files format and content: Bigwig file

growth_protocol: H1 mESCs were grown in standard medium (DMEM supplemented with 15% FBS (ES-qualified, ThermoFisher Scientific, 16141-079), 1000 U/mL LIF (Millipore), 1× MEM non-essential amino acids, 1 mM of Sodium Pyruvate, 1× GlutaMAX™ Supplement, 1× Penicillin and streptomycin, and 0.1 mM of 2-mercaptoethanol) supplemented with 1µM MEK1/2 inhibitor (PD0325901, Sigma) and 3 1µM GSK3 inhibitor (CHIR99021, Sigma).

extract_protocol:
Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10mM Tris-HCl, 1mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: mESCs

value: HM1 mESCs

value: Embryonic stem cells

tag: chip antibody

value: Wild-type

tag: chip-antibody


title: HFD fed WT5 mice


title: mESC_THAP1_day0_C2_RAD21


title: mESC_THAP1_day0_C1_RAD21


title: HFD fed WT4 mice


title: mESC_THAP1_day0_C2_CTCF

value: CTCF


title: mESC_THAP1_day0_C1_CTCF


title: HFD fed IKO6 mice


title: mESC_WT_day0_C1_YY1


title: mESC_THAP1_day0_C1_THAP1


title: mESC_WT_day0_C1_CTCF


title: mESC_WT_day0_C2_CTCF


title: mESC_THAP1_day0_C2_YY1


title: mESC_WT_day0_C2_YY1


title: mESC_THAP1_day0_C1_YY1


title: mESC_WT_day0_C2_THAP1


title: mESC_WT_day0_C1_THAP1


title: JP2CR Sham rep4

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

description: CR-Sham4 counts

data_processing:
Raw files were uploaded as paired reads into and processed by Illumina's BaseSpace hub (basespace.illumina.com). Sequences from the same sample on each of the two lanes were combined into a single "biosample".
Sequences were assessed using the FastQC Version 1.0.0 App and confirmed to be of good quality (scores>30).
First strand sequences were aligned to the mus musculus mm10 genome and gene counts produced using the RNA-Seq Alignment App (v2.0.2; incorporates STAR v2.5.0b, Isis v2.6.25.18, BEDTools v2.17.0, Cufflinks 2.2.1, and BLAST v2.2.26+) and selecting automatic trimming of TruSeq Adapters. All other options are default values.
Pairwise differential expression of STAR aligned sequences was performed using the BaseSpace DESeq2 app (v1.1.0; incorporates DESeq2 v1.6.3, Isis v2.6.25.19, BEDTools v2.17.0, and Picard v1.128).
Assembly: mm10
Supplementary files format and content: comma separated file containing read counts and differential expression information

source_name: Ventricular tissue

growth_protocol: Mice were housed under standard conditions and fed a normal chow diet

extract_protocol:
Ventricles were removed, rinsed in cold saline and flash frozen in liquid nitrogen. Tissue was homozenized and total RNA harvested using an Trizol reagent.
PolyA RNA was enriched and stranded libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA sample preparation kit.

treatment_protocol: Male mice (9-10-weeks-old) underwent sham or TAC (pressure overload) surgery. Heart tissue was isolated five weeks later.

value: Ventricular tissue

value: Male

value: homozygous JP2CR

value: Control operated


title: JP2CR TAC rep4

description: CR-TAC4 counts

value: pressure overload operated


title: HFD fed WT6 mice


title: JP2CR TAC rep1

description: CR-TAC1 counts


title: JP2CR TAC rep3

description: CR-TAC3 counts


title: JP2CR Sham rep1

description: CR-Sham1 counts


title: JP2CR Sham rep3

description: CR-Sham3 counts


title: WT TAC rep4

description: WTcr-TAC4 counts

value: wildtype


title: WT TAC rep3

description: WTcr-TAC3 counts


title: WT TAC rep2

description: WTcr-TAC2 counts


title: WT Sham rep3

description: WTcr-Sham3 counts


title: WT Sham rep4

description: WTcr-Sham4 counts


title: mESC_WT_day0_C1_RAD21


title: WT TAC rep1

description: WTcr-TAC1 counts


title: WT Sham rep1

description: WTcr-Sham1 counts


title: TKO_Notch_13

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
Assembly: mm10
Supplementary files format and content: cellranger derived feature, barcode, matrix files

source_name: prostate

extract_protocol:
12-week-old TKO or TKO-Nicd1 mice were euthanized and half of each prostate, including one of each paired lobes, was pooled for tissue dissociation. Tissue was dissociated with collagenase II in media supplemented with 10 µM Y-27632 ROCK inhibitor and 1nM R1881, followed by trypsinization (0.25%). Filtered cell suspensions were sorted for cell viability using DAPI staining, then cell suspensions counted after Trypan Blue staining using a Countess FL automated cell counter (ThermoFisher).
Mouse organoids were generated from TKO or TKO-Nicd1 prostate tumor tissue isolated from mice at end stage. Tissue was dissociated and cell suspensions cultured in mouse prostate organoid media. TKO or TKO-Nicd1 organoids selected for high EGFP expression were transplanted into SCID mice, and subsequent tumors dissociated for scRNA-seq analysis as described above.
Library was performed according to the manufacter’s instructions (Single Cell 3'GEX v3 protocol, 10x Genomics).

value: prostate

tag: condition

tag: model

value: Organoid Transplant


title: TKO_15

description: 10x Genomics


title: TKO_12

description: 10x Genomics


title: TKO_Notch_12W_NT505

description: 10x Genomics

value: GEMM


title: TKO_Notch_12W_NT504

description: 10x Genomics


title: TKO_Notch_12W_NT497

description: 10x Genomics


title: TKO_Notch_12W_NT449

description: 10x Genomics


title: TKO_12W_T1883

description: 10x Genomics

value: TKO


title: SKO_12W_T2001

description: 10x Genomics

value: SKO


title: TKO_12W_T2789

description: 10x Genomics


title: JP2CR TAC rep2

description: CR-TAC2 counts


title: SKO_45W_T1636

description: 10x Genomics


title: JP2CR Sham rep2

description: CR-Sham2 counts


title: WT Sham rep2

description: WTcr-Sham2 counts


title: ILCP

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

description: 10x Genomics

data_processing:
For each library the reads were aligned to the mouse transcriptome (GRCm38) and expression calculated using the 10X Cellranger (v6.0.1) wrapper for the STAR aligner (Spliced Transcripts Alignment to a Reference, Alexander Dobin)
They were then combined with Cellranger.
Assembly: GRCm38
Supplementary files format and content: Cloupe file

source_name: Lung

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
10X Single cell library preparation was performed using the 10X Genomics technology platform. The 10X Genomics Chromium Single Cell 3’ v3 protocol was followed to obtain separate 3’ libraries for each sample for subsequent sequencing.

treatment_protocol: siLP-ILCPs ("progenitors" CD45+CD3-CD4-CD8-CD11b-CD11c-CD19-FceR1-Ly6G/Ly6C-NK1.1-TER119-IL7Ra+Id2 BFP+KLRG1-NKp46-CCR6-Rorc Kat-PLZF Cit+Bcllb Tom-) were purified by FACS from the small intestinal lamina propria of Bcl11b tm2Peli.Id2 BFP.PLZF Cit. Rorc Kat mice. To analyse the progeny siLP-ILCP were transferred by IV into Rag2-/-Ilr2g-/- mice and allowed to reconstitute for 6-7 weeks. siLP progeny ('LPprogeny") and lung progeny ("ILCP") were purified from recipient (CD45.1) tissues by FACS as CD45.2+Id2 BFP+.

value: Innate lymphoid cells

value: Lung

value: 10-13 weeks old


title: LPProgeny

description: 10x Genomics

source_name: siLP

value: siLP

value: Bcl11b tm2Peli.Id2 BFP.PLZF Cit. Rorc Kat

value: 18-26 weeks old


title: Progenitors

description: 10x Genomics

value: Innate lymphoid cell progenitors

value: 8-16 weeks old


title: mESC_ZFP524_day0_C2

data_processing:
Read quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37).
Reads were aligned to mm10 genome using HISAT2 (Version 2.2.1).
Normalized read counts for all genes were obtained using featureCount (v3.18.1).
Differential expression was determined in each of the pair-wise comparisons between experimental and control groups using DESeq (V1.22.1).
Assembly: mm10
Supplementary files format and content: Tabular files include raw counts for each sample.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN) following manufacturer’s protocol.
A total of 100ng total RNA was subjected to polyA enrichment and cDNA libraries preparation using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, E7760L).

treatment_protocol: During differentiation, LIF, MEK1/2 inhibitor and GSK3 inhibitor were removed from the medium.

tag: cell line

value: Mouse embryonic stem cells (mESCs)

value: ZFP524 KO

value: Differentiation day0


title: mESC_ZFP524_day4_C1

value: Differentiation day4


title: mESC_ZFP524_day4_C2


title: mESC_ZFP524_day0_C1


title: mESC_ZFP764_day4_C2

value: ZFP764 KO


title: TKO_Notch_10

description: 10x Genomics

tag: tissue

value: prostate

value: Organoid Transplant


title: mESC_THAP1_day4_C2

tag: cell type

value: THAP1 KO


title: mESC_THAP1_day4_C1


title: mESC_ZFP764_day0_C1


title: mESC_THAP1_day0_C1


title: mESC_THAP1_day0_C2


title: mESC_WT_day4_C2

value: Wild-type


title: mESC_WT_day4_C1


title: mESC_WT_day0_C2


title: P-8894-T

type: genomic

city: Tampa

first: Anders

last: Berglund

state: Florida

address: 12902 Magnolia Drive

department: Department of Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

hyb_protocol: Bisulfite converted DNA was processed with the Illumina FFPE restoration kit, amplified, fragmented and hybridized to Illumina Infinium Human EPIC Beadchip using standard Illumina protocol

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

data_processing:
Normalization was performed using the minfi preprocessNoob function, which performs the NOOB method for background correction, as well as a dye-bias normalization. beta-values were estimated using the intensity of the methylated signal divided by the sum of both methylated and unmethylated signals. Under performing CpG probes were deleted based on the recommendation by Zhou et al. [PMID: 27924034]. β-values with a corresponding detection p > 0.01 were considered as missing values.
processed value definition: Beta-value

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Prostate

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was obtained from the prostate tissues. DNA was extracted from using QIAamp DNA extraction kit (QIAGEN, Valencia, CA) the marked tumor area on the H&E slides by the pathologist.

value: Prostate

tag: sample type

value: Tumor

tag: gleason

value: Surgery


title: mESC_WT_day0_C1

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

institute: University of Tuebingen

tag: genotype


title: P-8894-N

value: Normal


title: P-8876-T


title: SKO_58W_T2057

description: 10x Genomics

value: SKO

value: GEMM


title: CCA, scRNAseq [SI_GA_B6]

city: Kowloon

first: Wenjun

last: XIONG

state: Hong Kong

address: Tat Chee Avenue

institute: City University of Hong Kong

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.1. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Müller glia

extract_protocol:
2-4 retinas of the same treatment group were pooled in PBS. The retinas were incubated in digesting buffer (87.5mM HEPES PH7.0, 2.5mM L-Cysteine, 0.5mM EDTA PH8.0, 25µl papain suspension, 49µl UltraPura Nuclease-Free Water, HBSS up to 1ml) for 8min at 37°C. Retinas were then washed and triturated to generate a single-cell suspension in sorting buffer (1% w/v BSA, 1mM MgCl2, 50U DNase1, 40U RiboLock RNase Inhibitor in PBS). Cells were passed through a 40μm strainer and then Tdtomato+ MG were sorted using a Sony SH800 Cell Sorter. Gating was performed to isolate intact cells from debris and to isolate positive fluorescent MG-derived cells. Live purified cells were then pelleted at 300g for 10min at 4°C and resuspended in 0.04% BSA in PBS at a concentration of 2,000 cells per μl.
Libraries were constructed using Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit and Chromium Controller (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Tamoxifen (75mg/kg) was injected into P20 Glast-CreER; Rosa26-tdTomato mice daily for five consecutive days to label MG. The mice were split into three group as following.   1) Control treatment: Mice were intravitreally injected with AAV7m8-GFAP-GFP-LacZsh at P28 and retinas were harvested at P51.   2) CCA treatment: Mice were intravitreally injected with AAV7m8-GFAP-cyclin D1-p27sh and AAV7M8-GFAP-GFP-LacZsh (9:1 mixed) at P28. Low-dose AAV7m8-GFAP-GFP-LacZsh was added to serve as an indicator of infection success. Retinas were harvested at P51.  3) CCANT treatment: Mice received CCA treatment at P28 and were further injected with NMDA at P35 and TSA at P37 (CCANT). Retinas were harvested at P51.  For all three treatment groups, the retinas with good AAV infection, as indicated by GFP expression, were collected and MG were sorted by FACS for scRNA-Seq analysis.

value: retina

value: Muller glia

value: Glast-CreERT2; R26-CAG-LSL-Tdt

value: Intravitreal injetion of AAV7m8-GFAP-cyclinD1-p27sh +AAV7m8-GFAP-GFP-LacZsh (9:1 mixed)


title: P-8811-T


title: CCANT, scRNAseq [SI_GA_C6]

description: 10x Genomics

value: Intravitreal injetion of AAV7m8-GFAP-cyclinD1-p27sh +AAV7m8-GFAP-GFP-LacZ-sh(9:1 mixed)+ NMDA+Trichostatin A (TSA)


title: mESC_ZFP764_day0_C2

value: Mouse embryonic stem cells (mESCs)

value: Differentiation day0


title: mESC_ZFP764_day4_C1

value: ZFP764 KO

value: Differentiation day4


title: Control, scRNAseq [SI_GA_A6]

description: 10x Genomics

value: Intravitreal injetion of AAV7m8-GFAP-GFP-LacZsh


title: cardiomyocyte,AAV_Igfbp7, replicate2-63, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,AAV_Igfbp7, replicate2-62, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-64, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-61, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8766-T

value: Prostate

value: Tumor

value: Surgery


title: P-8771-T


title: P-8771-N

value: Normal


title: P-8766-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-59, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8583-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-60, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-58, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8538-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-57, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-53, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8464-T


title: P-8464-N


title: P-8372-T


title: P-8372-N


title: P-8538-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-51, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-55, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-50, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8165-T


title: P-8811-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-49, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-54, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8583-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-52, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8083-T


title: P-8876-N


title: P-8269-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-56, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7725-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-44, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-8165-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-48, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7695-N


title: P-7695-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-46, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-47, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-45, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7725-T


title: P-7690-N


title: P-8269-N


title: P-8083-N


title: P-7583-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-36, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-43, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-37, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-35, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7583-T


title: P-7690-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-42, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-39, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7450-N


title: P-7612-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-40, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-34, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7450-T


title: P-7612-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-33, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-38, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-41, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-7277-T


title: P-7359-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-31, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-30, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-29, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6916-T


title: P-7277-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-28, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6916-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-27, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-25, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-24, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6893-T


title: P-6893-N


title: P-6876-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-23, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6861-T


title: P-6876-N


title: P-6864-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-32, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6861-N


title: P-7359-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-26, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-19, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-21, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6807-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-18, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6807-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-20, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6800-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-22, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-15, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-16, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6714-T


title: P-6800-N


title: P-6714-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-14, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-17, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-13, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6699-T


title: P-6864-T


title: P-6699-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-12, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-10, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-11, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-6669-N


title: P-6669-T


title: P-6212-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-7, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-9, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-6, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-8, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-5691-N


title: P-4260-N


title: P-6212-N


title: cardiomyocyte,AAV_Igfbp7, replicate2-5, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-4242-T


title: P-5691-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-3, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-1, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-4260-T


title: cardiomyocyte,AAV_Igfbp7, replicate2-4, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate2-2, scRNAseq

description:
smartseq2
Igfbp7_AAV_2.xlsx


title: P-3245-T


title: P-3245-N


title: P-3215-T


title: P-4242-N


title: P-3215-N


title: P-3446-N


title: P-3446-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-60, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-64, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-59, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-2516-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-58, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-1374-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-61, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-1374-N


title: P-2516-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-57, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-53, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-1398-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-55, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-56, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-54, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-63, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-52, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-8946-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-62, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7704-N


title: P-7764-N


title: P-7969-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-47, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7568-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-45, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-51, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7513-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-44, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-50, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7920-N


title: P-8820-N


title: P-7952-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-48, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-49, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-43, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-46, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7530-N


title: P-7221-N


title: P-6396-N


title: P-5153-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-41, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-6959-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-40, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-37, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-39, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-38, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7095-N


title: P-7580-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-36, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-5185-N


title: P-4585-N


title: P-7492-N


title: P-4143-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-35, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4241-N


title: P-4256-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-34, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-42, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4093-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-33, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-8946-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-32, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-29, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-28, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-27, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7969-T


title: P-7952-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-26, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7920-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-31, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-24, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-3988-N


title: P-7764-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-25, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7704-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-23, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7580-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-30, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-21, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-22, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-8137-N


title: P-8842-N


title: P-5939-N


title: P-5963-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-20, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-18, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-19, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-16, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-8156-T


title: P-5931-N


title: P-5945-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-15, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-5909-N


title: P-5167-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-14, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-13, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-5184-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-12, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-7568-T


title: cardiomyocyte,AAV_Igfbp7, replicate1-11, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-9, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4991-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-10, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4911-N


title: P-4841-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-17, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4457-N


title: P-4353-N


title: P-4838-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-8, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-5787-N


title: P-3958-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-7, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-6, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-5, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-4006-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-4, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-3897-N


title: cardiomyocyte,AAV_Igfbp7, replicate1-3, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-2, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-3312-N


title: P-3725-N


title: P-3598-N


title: cardiomyocyte,AAV_CTRL, replicate2-94, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-96, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_Igfbp7, replicate1-1, scRNAseq

description:
smartseq2
Igfbp7_AAV_1.xlsx


title: P-5405-T


title: cardiomyocyte,AAV_CTRL, replicate2-95, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-91, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5659-T


title: P-5777-T


title: P-5676-T


title: cardiomyocyte,AAV_CTRL, replicate2-93, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-90, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-92, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3380-N


title: cardiomyocyte,AAV_CTRL, replicate2-89, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5345-T


title: P-5321-T


title: cardiomyocyte,AAV_CTRL, replicate2-88, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-87, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4353-T


title: P-3958-T


title: P-4006-T


title: cardiomyocyte,AAV_CTRL, replicate2-84, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3897-T


title: cardiomyocyte,AAV_CTRL, replicate2-83, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-85, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-82, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-81, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5281-T


title: P-3380-T


title: P-3598-T


title: cardiomyocyte,AAV_CTRL, replicate2-80, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3312-T


title: cardiomyocyte,AAV_CTRL, replicate2-77, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-76, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-2118-T


title: cardiomyocyte,AAV_CTRL, replicate2-75, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-86, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1514-T


title: P-2011-T


title: P-1913-T


title: P-1477-T


title: cardiomyocyte,AAV_CTRL, replicate2-73, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-74, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1412-T


title: P-3725-T


title: P-1055-T


title: cardiomyocyte,AAV_CTRL, replicate2-71, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-2118-N


title: P-1345-T


title: cardiomyocyte,AAV_CTRL, replicate2-70, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-2011-N


title: cardiomyocyte,AAV_CTRL, replicate2-68, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-79, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-67, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1913-N


title: cardiomyocyte,AAV_CTRL, replicate2-66, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1514-N


title: P-1412-N


title: cardiomyocyte,AAV_CTRL, replicate2-64, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-63, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1345-N


title: cardiomyocyte,AAV_CTRL, replicate2-62, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-65, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-7513-T


title: P-7530-T


title: cardiomyocyte,AAV_CTRL, replicate2-61, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-60, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-72, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-7492-T


title: cardiomyocyte,AAV_CTRL, replicate2-58, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-7221-T


title: cardiomyocyte,AAV_CTRL, replicate2-59, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-6959-T


title: cardiomyocyte,AAV_CTRL, replicate2-69, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-7095-T


title: cardiomyocyte,AAV_CTRL, replicate2-57, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-56, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5331-T


title: P-6396-T


title: cardiomyocyte,AAV_CTRL, replicate2-54, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-55, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1477-N


title: P-1055-N


title: P-3318-N


title: P-3625-N


title: P-3288-N


title: cardiomyocyte,AAV_CTRL, replicate2-51, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3184-N


title: cardiomyocyte,AAV_CTRL, replicate2-52, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-1635-N


title: P-2521-N


title: cardiomyocyte,AAV_CTRL, replicate2-47, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-48, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-50, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-49, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3914-T


title: P-1242-N


title: cardiomyocyte,AAV_CTRL, replicate2-46, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3318-T


title: P-3625-T


title: cardiomyocyte,AAV_CTRL, replicate2-45, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-43, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3914-N


title: cardiomyocyte,AAV_CTRL, replicate2-53, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-42, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-3184-T


title: P-1635-T


title: cardiomyocyte,AAV_CTRL, replicate2-40, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-2521-T


title: cardiomyocyte,AAV_CTRL, replicate2-41, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-39, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8842-T


title: P-1242-T


title: cardiomyocyte,AAV_CTRL, replicate2-38, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8137-T


title: P-5945-T


title: cardiomyocyte,AAV_CTRL, replicate2-36, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-35, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-37, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-44, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5909-T


title: P-3288-T


title: cardiomyocyte,AAV_CTRL, replicate2-34, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-32, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-30, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5931-T


title: P-5787-T


title: P-5939-T


title: P-4991-T


title: cardiomyocyte,AAV_CTRL, replicate2-33, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5184-T


title: cardiomyocyte,AAV_CTRL, replicate2-26, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4841-T


title: cardiomyocyte,AAV_CTRL, replicate2-25, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-29, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5167-T


title: cardiomyocyte,AAV_CTRL, replicate2-28, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4911-T


title: cardiomyocyte,AAV_CTRL, replicate2-27, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-24, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8768-N


title: cardiomyocyte,AAV_CTRL, replicate2-22, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-21, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4838-T


title: P-5963-T


title: P-4457-T


title: P-8306-N


title: cardiomyocyte,AAV_CTRL, replicate2-31, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-23, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-19, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8759-N


title: P-8215-N


title: cardiomyocyte,AAV_CTRL, replicate2-18, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8757-N


title: cardiomyocyte,AAV_CTRL, replicate2-20, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-16, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8428-N


title: cardiomyocyte,AAV_CTRL, replicate2-17, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8156-N


title: P-8820-T


title: cardiomyocyte,AAV_CTRL, replicate2-15, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-13, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8768-T


title: P-8759-T


title: cardiomyocyte,AAV_CTRL, replicate2-14, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-11, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8556-N


title: P-8757-T


title: cardiomyocyte,AAV_CTRL, replicate2-12, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8556-T


title: cardiomyocyte,AAV_CTRL, replicate2-10, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-9, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8306-T


title: P-8428-T


title: cardiomyocyte,AAV_CTRL, replicate2-8, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-7, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-8215-T


title: P-5153-T


title: cardiomyocyte,AAV_CTRL, replicate2-6, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4256-T


title: cardiomyocyte,AAV_CTRL, replicate2-4, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-5, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-5185-T


title: P-4585-T


title: cardiomyocyte,AAV_CTRL, replicate2-2, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4143-T


title: P-5361-T


title: P-4241-T


title: cardiomyocyte,AAV_CTRL, replicate2-3, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: P-4093-T


title: cardiomyocyte,AAV_CTRL, replicate1-93, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate2-1, scRNAseq

description:
smartseq2
CTRL_AAV_2.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-92, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-3988-T


title: cardiomyocyte,AAV_CTRL, replicate1-91, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5777-N


title: P-5659-N


title: cardiomyocyte,AAV_CTRL, replicate1-89, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-90, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5676-N


title: P-5405-N


title: cardiomyocyte,AAV_CTRL, replicate1-88, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5361-N


title: cardiomyocyte,AAV_CTRL, replicate1-87, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5345-N


title: cardiomyocyte,AAV_CTRL, replicate1-86, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5281-N


title: cardiomyocyte,AAV_CTRL, replicate1-85, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: P-5321-N


title: cardiomyocyte,AAV_CTRL, replicate1-83, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-82, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 +AM580 Pre-Sorting

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

library_source: other

data_processing:
Barcode amplicon reads were processed using a custom pipeline available at: https://github.com/mpiersonsmela/barcode-matching
Assembly: n/a
Supplementary files format and content: barcode_counts_GEO.csv: barcode counts for each sample
Library strategy: Amplicon sequencing

molecule: other

growth_protocol: Plasmids for doxycycline-inducible expression of TFs were integrated into reporter hiPSCs. Pooled PiggyBac plasmid libraries (Figure 3A/B) were integrated into 1 million hiPSCs per replicate, using a Lonza nucleofector with 100 µL of P3 buffer. 250 fmol transposon pool and 2.5 µg transposase plasmid were used for each nucleofection. Puromycin selection was performed between days 2-7 post-nucleofection. Subsequently, DDX4+ iOLCs were induced using the protocol described above. In follow-up rounds of screening, cells were treated with 5 µM GSK-3484862, and some replicates were additionally treated with the retinoic acid receptor agonist AM580 (1 µM).

extract_protocol:
DNA was extracted from sorted DDX4+ cells using the Qiagen DNEasy Micro kit, and from unsorted and pre-induction cells using the Qiagen DNEasy kit.
Barcode amplification and sequencing was performed as previously described (Smela et al., eLife 2023). For fold-change calculations, barcode abundances in the DDX4+ cells were separately compared to unsorted cells and to pre-induction cells.

value: Differentiated hiPSCs (pre-sorting)

value: iOLC induction, + 1 µM AM580


title: PGP1 Pre-Induction

value: hiPSCs

value: undifferentiated hiPSCs


title: F3 -AM580 Pre-Sorting

value: iOLC induction


title: PGP1 -AM580 Pre-Sorting


title: cardiomyocyte,AAV_CTRL, replicate1-80, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-81, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PGP1 +AM580 Pre-Sorting


title: cardiomyocyte,AAV_CTRL, replicate1-78, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 -AM580 sorted REC8+

value: Sorted GFP+ cells


title: cardiomyocyte,AAV_CTRL, replicate1-76, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-75, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-77, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 +AM580 sorted REC8+


title: cardiomyocyte,AAV_CTRL, replicate1-74, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 -AM580 sorted DDX4+

value: Sorted DDX4+ cells


title: cardiomyocyte,AAV_CTRL, replicate1-73, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-72, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 Pre-Induction


title: cardiomyocyte,AAV_CTRL, replicate1-84, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 +AM580 sorted DDX4+


title: PGP1 -AM580 sorted REC8+


title: cardiomyocyte,AAV_CTRL, replicate1-71, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PGP1 -AM580 sorted CD38+

value: Sorted CD38+ cells


title: PGP1 -AM580 sorted DDX4+


title: cardiomyocyte,AAV_CTRL, replicate1-68, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-79, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PGP1 +AM580 sorted REC8+


title: cardiomyocyte,AAV_CTRL, replicate1-69, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: cardiomyocyte,AAV_CTRL, replicate1-67, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: PGP1 +AM580 sorted DDX4+


title: F3 -AM580 sorted CD38+


title: cardiomyocyte,AAV_CTRL, replicate1-66, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx


title: F3 +AM580 sorted CD38+


title: cardiomyocyte,AAV_CTRL, replicate1-64, scRNAseq

description:
smartseq2
CTRL_AAV_1.xlsx