title: SCVI-111_hiPSC_CM_Reporter_1016


title: SCVI-111_hiPSC_CM_Reporter_1015

status: Public on Aug 14 2022

type: SRA

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

state: CA

address: 265 Campus Dr.

department: Cardiovascular Institute

country: USA

institute: Stanford University

description:
Human induced pluripotent stem cells containing a TBX5-lineage tracing system consisting of a TBX5-Cre and CMV Drive lox-stop-lox-TurboGFP construct were differentiated to day 15 hiPSC cardiomyocytes. Cells were dissociated and processed for scRNA-seq using the ICELL8 system.
111_ICELL8_D15_barcodes.tsv.gz
111_ICELL8_D15_features.tsv.gz
111_ICELL8_D15_matrix.mtx.gz

library_source: transcriptomic

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
Droplet Based Sequencing: Data generated using the 10X Genomics 3' scRNA-seq v3.1 kit  were processed using CellRanger v6.0.0 (10X Genomics). Default parameters were used for alignment. The reference genomes used were refdata-gex-GRCh38-2020-A  for Human alignment and refdata-gex-mm10-2020-A for mouse data. References were obtained from the 10X Genomics website.
Samples (SCVI-111_hiPSC-Derived Cardiomyocytes_Day7-30) were multiplexed using the 10X Genomics CellPlex kit were demultiplexed using the CellRanger multi configuration. 10X Genomics cell multiplexing oligos used for each individual sample were as follow: Day7-CMO306, Day11-CMO307, Day13-CMO308, Day15-CMO309, Day30-CMO310.
Smartseq2 Based Sequencing: Data generated using the ICELL8 Takara Smartseq2 kit were processed using STARSolo aligner v2.7.9a software developed by Alexander Dobin. Reference genome used was a custom reference from GRCh38-2020-A (10X Genomics) containing added TurboGFP sequence. Parameters used were:  --soloType SmartSeq --soloStrand Unstranded.
GRCh38 (for Human) and mm10 (for Mouse)
Genome_build: Samples containing tab-delimited files contain output from CellRanger or STARSolo containing file with gene ensembl ID and gene symbols, cell barcodes, and matrix file containing raw counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC-derived Cardiomyocytes

extract_protocol:
Droplet based extraction: HiPSC-derived cardiomyocyte or mouse embryonic heart derived single cells were dissociated and captured and lysed using 10X Genomics Chromium Next GEM Single Cell 3' v3.1 Kit. mRNA was reverse transcribed to cDNA, and cDNA pre-amplification was conducted following manufacturer's protocol.    Smart-seq2 based extraction: HiPSC-derived cardiomyocytes were dissociated into single cell suspensions and captured using the ICELL8 Smartseq2 TAKARA system. mRNA was reverse transcribed to cDNA and cDNA pre-amplification was conducted per manufacturer’s protocol on an ICELL8 nanowell chip.
Droplet based library construction: Libraries for samples processed using 10X Genomics Single Cell 3' v3.1 kit were prepared from pre-amplified cDNA according to manufactrer's protocol. Gene expression libraries were generated for all 10X samples, and CellPlex multiplexing libraries were generated for running hiPSC-CM samples (Day 7, 11, 13,15, 30). Individual library index primers were used for multiplexing libraries on flow cell during sequencing.     Smart-seq2 library construction: Following Takara Smartseq2 ICELL8 protocol, pre-amplified and tagmented cDNA from individual single cells in ICELL8 nanowells received individual index sequencing barcodes for demultiplexing cells during downstream analysis.

tag: cell type

value: hiPSC-derived cardiomyocytes

tag: strain

tag: developmental stage

value: Day 15

tag: cell line

value: SCVI-111 TBX5-Lineage Reporter Line


title: SCVI-111_hiPSC_CM_Reporter_1011


title: SCVI-111_hiPSC_CM_Reporter_1013


title: SCVI-111_hiPSC_CM_Reporter_1010


title: SCVI-111_hiPSC_CM_Reporter_1009


title: SCVI-111_hiPSC_CM_Reporter_1036


title: SCVI-111_hiPSC_CM_Reporter_1008


title: SCVI-111_hiPSC_CM_Reporter_1006


title: SCVI-111_hiPSC_CM_Reporter_1005


title: SCVI-111_hiPSC_CM_Reporter_1007


title: SCVI-111_hiPSC_CM_Reporter_1004


title: SCVI-111_hiPSC_CM_Reporter_1003


title: SCVI-111_hiPSC_CM_Reporter_999


title: SCVI-111_hiPSC_CM_Reporter_1002


title: SCVI-111_hiPSC_CM_Reporter_994


title: SCVI-111_hiPSC_CM_Reporter_996


title: SCVI-111_hiPSC_CM_Reporter_998


title: SCVI-111_hiPSC_CM_Reporter_1001


title: SCVI-111_hiPSC_CM_Reporter_995


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title: SCVI-111_hiPSC_CM_Reporter_1017


title: SCVI-111_hiPSC_CM_Reporter_992


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title: SCVI-111_hiPSC_CM_Reporter_988


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title: SCVI-111_hiPSC_CM_Reporter_984


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title: SCVI-111_hiPSC_CM_Reporter_1014


title: SCVI-111_hiPSC_CM_Reporter_1000


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title: SCVI-111_hiPSC_CM_Reporter_979


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title: SCVI-111_hiPSC_CM_Reporter_968


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title: SCVI-111_hiPSC_CM_Reporter_924


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title: SCVI-111_hiPSC_CM_Reporter_921


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title: SCVI-111_hiPSC_CM_Reporter_920


title: SCVI-111_hiPSC_CM_Reporter_926


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title: SCVI-111_hiPSC_CM_Reporter_915


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title: SCVI-111_hiPSC_CM_Reporter_912


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title: SCVI-111_hiPSC_CM_Reporter_923


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title: SCVI-111_hiPSC_CM_Reporter_895


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title: SCVI-111_hiPSC_CM_Reporter_897


title: SCVI-111_hiPSC_CM_Reporter_884


title: SCVI-111_hiPSC_CM_Reporter_887


title: SCVI-111_hiPSC_CM_Reporter_891


title: SCVI-111_hiPSC_CM_Reporter_898


title: SCVI-111_hiPSC_CM_Reporter_881


title: SCVI-111_hiPSC_CM_Reporter_879


title: SCVI-111_hiPSC_CM_Reporter_885


title: SCVI-111_hiPSC_CM_Reporter_889


title: SCVI-111_hiPSC_CM_Reporter_883


title: SCVI-111_hiPSC_CM_Reporter_886


title: SCVI-111_hiPSC_CM_Reporter_878


title: SCVI-111_hiPSC_CM_Reporter_882


title: SCVI-111_hiPSC_CM_Reporter_893


title: SCVI-111_hiPSC_CM_Reporter_873


title: SCVI-111_hiPSC_CM_Reporter_880


title: SCVI-111_hiPSC_CM_Reporter_877


title: SCVI-111_hiPSC_CM_Reporter_869


title: SCVI-111_hiPSC_CM_Reporter_876


title: SCVI-111_hiPSC_CM_Reporter_868


title: SCVI-111_hiPSC_CM_Reporter_874


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title: SCVI-111_hiPSC_CM_Reporter_872


title: SCVI-111_hiPSC_CM_Reporter_892


title: SCVI-111_hiPSC_CM_Reporter_871


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title: SCVI-111_hiPSC_CM_Reporter_867


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title: SCVI-111_hiPSC_CM_Reporter_859


title: SCVI-111_hiPSC_CM_Reporter_875


title: SCVI-111_hiPSC_CM_Reporter_861


title: SCVI-111_hiPSC_CM_Reporter_847


title: SCVI-111_hiPSC_CM_Reporter_845


title: SCVI-111_hiPSC_CM_Reporter_857


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title: SCVI-111_hiPSC_CM_Reporter_855


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title: SCVI-111_hiPSC_CM_Reporter_849


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title: SCVI-111_hiPSC_CM_Reporter_846


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title: SCVI-111_hiPSC_CM_Reporter_838


title: SCVI-111_hiPSC_CM_Reporter_840


title: SCVI-111_hiPSC_CM_Reporter_858


title: SCVI-111_hiPSC_CM_Reporter_832


title: SCVI-111_hiPSC_CM_Reporter_831


title: SCVI-111_hiPSC_CM_Reporter_842


title: SCVI-111_hiPSC_CM_Reporter_828


title: SCVI-111_hiPSC_CM_Reporter_829


title: SCVI-111_hiPSC_CM_Reporter_834


title: SCVI-111_hiPSC_CM_Reporter_823


title: SCVI-111_hiPSC_CM_Reporter_830


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title: SCVI-111_hiPSC_CM_Reporter_818


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title: SCVI-111_hiPSC_CM_Reporter_807


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title: SCVI-111_hiPSC_CM_Reporter_804


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title: SCVI-111_hiPSC_CM_Reporter_806


title: SCVI-111_hiPSC_CM_Reporter_805


title: SCVI-111_hiPSC_CM_Reporter_802


title: SCVI-111_hiPSC_CM_Reporter_801


title: SCVI-111_hiPSC_CM_Reporter_800


title: SCVI-111_hiPSC_CM_Reporter_816


title: SCVI-111_hiPSC_CM_Reporter_798


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title: SCVI-111_hiPSC_CM_Reporter_795


title: SCVI-111_hiPSC_CM_Reporter_796


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title: SCVI-111_hiPSC_CM_Reporter_788


title: SCVI-111_hiPSC_CM_Reporter_793


title: SCVI-111_hiPSC_CM_Reporter_789


title: SCVI-111_hiPSC_CM_Reporter_791


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title: SCVI-111_hiPSC_CM_Reporter_641


title: SCVI-111_hiPSC_CM_Reporter_644


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title: SCVI-111_hiPSC_CM_Reporter_213


title: SCVI-111_hiPSC_CM_Reporter_234


title: SCVI-111_hiPSC_CM_Reporter_228


title: SCVI-111_hiPSC_CM_Reporter_210


title: SCVI-111_hiPSC_CM_Reporter_208


title: SCVI-111_hiPSC_CM_Reporter_209


title: SCVI-111_hiPSC_CM_Reporter_207


title: SCVI-111_hiPSC_CM_Reporter_203


title: SCVI-111_hiPSC_CM_Reporter_205


title: SCVI-111_hiPSC_CM_Reporter_200


title: SCVI-111_hiPSC_CM_Reporter_204


title: SCVI-111_hiPSC_CM_Reporter_202


title: SCVI-111_hiPSC_CM_Reporter_222


title: SCVI-111_hiPSC_CM_Reporter_206


title: SCVI-111_hiPSC_CM_Reporter_201


title: SCVI-111_hiPSC_CM_Reporter_221


title: SCVI-111_hiPSC_CM_Reporter_199


title: SCVI-111_hiPSC_CM_Reporter_212


title: SCVI-111_hiPSC_CM_Reporter_211


title: SCVI-111_hiPSC_CM_Reporter_197


title: SCVI-111_hiPSC_CM_Reporter_196


title: SCVI-111_hiPSC_CM_Reporter_195


title: SCVI-111_hiPSC_CM_Reporter_193


title: SCVI-111_hiPSC_CM_Reporter_192


title: SCVI-111_hiPSC_CM_Reporter_194


title: SCVI-111_hiPSC_CM_Reporter_191


title: SCVI-111_hiPSC_CM_Reporter_190


title: SCVI-111_hiPSC_CM_Reporter_189


title: SCVI-111_hiPSC_CM_Reporter_188


title: SCVI-111_hiPSC_CM_Reporter_186


title: SCVI-111_hiPSC_CM_Reporter_185


title: SCVI-111_hiPSC_CM_Reporter_182


title: SCVI-111_hiPSC_CM_Reporter_184


title: SCVI-111_hiPSC_CM_Reporter_183


title: SCVI-111_hiPSC_CM_Reporter_181


title: SCVI-111_hiPSC_CM_Reporter_198


title: SCVI-111_hiPSC_CM_Reporter_178


title: SCVI-111_hiPSC_CM_Reporter_173


title: SCVI-111_hiPSC_CM_Reporter_176


title: SCVI-111_hiPSC_CM_Reporter_179


title: SCVI-111_hiPSC_CM_Reporter_175


title: SCVI-111_hiPSC_CM_Reporter_177


title: SCVI-111_hiPSC_CM_Reporter_180


title: SCVI-111_hiPSC_CM_Reporter_172


title: SCVI-111_hiPSC_CM_Reporter_171


title: SCVI-111_hiPSC_CM_Reporter_168


title: SCVI-111_hiPSC_CM_Reporter_169


title: SCVI-111_hiPSC_CM_Reporter_166


title: SCVI-111_hiPSC_CM_Reporter_170


title: SCVI-111_hiPSC_CM_Reporter_163


title: SCVI-111_hiPSC_CM_Reporter_162


title: SCVI-111_hiPSC_CM_Reporter_164


title: SCVI-111_hiPSC_CM_Reporter_160


title: SCVI-111_hiPSC_CM_Reporter_165


title: SCVI-111_hiPSC_CM_Reporter_187


title: HAP1 cell line HD3_KO_3_S52573

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard) based on Picard tools 2.19.2 (http://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options suggested be the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.0.
Genome_build: GRCh38 (hg38) Reference Genome Assembly
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

molecule: total RNA

source_name: HAP1 cell line

growth_protocol: HAP1 cells were grown in IMDM+++ medium (IMDM (12440053, Thermo Scientific), supplemented with Penicillin-Streptomycin (P4333, Sigma-Aldrich, 1% final concentration) and fetal bovine serum (F7524, Sigma-Aldrich, 10% final concentration)) at 37 °C, 5% CO2.

extract_protocol:
Total RNA from knockout (KO) and inactive mutant expressing cells, as well as inhibitor-treated cells (JQ12 1 μM, MS-275 3 μM, both 24 hours) was isolated using Trizol reagent (Thermo Fisher Scientific) as described in the manual. The isolated RNA, dissolved in nuclease-free ddH2O, was then subjected to another precipitation step by adding 1/10 vol. 3 M sodium-acetate (pH 5.2) and 2.5 vol. 96% ethanol. Following overnight-incubation, the samples were centrifuged (12000 rpm, 30 min, 4 °C) and washed with 75% ethanol. Pellets were air-dried and dissolved in a suitable amount of nuclease-free ddH2O (shaking at 300 rpm, 10 min, 55 °C).
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: JQ12 (Siliphaivanh et al., 2007; Stiff et al., 2016) 1 μM, MS-275 (S1053, Selleck Chemicals) 3 μM, both 24 hours

value: HAP1 HDAC3 knockout cell line


title: HAP1 cell line HD3_KO_2_S52574


title: SCVI-111_hiPSC_CM_Reporter_158


title: SCVI-111_hiPSC_CM_Reporter_159


title: HAP1 cell line HAP_MS_2_S52577

value: control cell line treated with MS275


title: SCVI-111_hiPSC_CM_Reporter_161


title: SCVI-111_hiPSC_CM_Reporter_155


title: SCVI-111_hiPSC_CM_Reporter_154


title: HAP1 cell line HAP_1_S52581

value: control cell line


title: HAP1 cell line HD3_KO_1_S52575


title: SCVI-111_hiPSC_CM_Reporter_167


title: HAP1 cell line HAP_143_3_S52583

value: HAP1wt cell line stably expressing the catalytically inactive transgenic version of HDAC8


title: HAP1 cell line HAP_MS_3_S52576


title: SCVI-111_hiPSC_CM_Reporter_152


title: HAP1 cell line HAP_MS_1_S52578


title: SCVI-111_hiPSC_CM_Reporter_157


title: SCVI-111_hiPSC_CM_Reporter_174


title: HAP1 cell line HAP_3_S52579


title: SCVI-111_hiPSC_CM_Reporter_156


title: HAP1 cell line HAP_2_S52580


title: SCVI-111_hiPSC_CM_Reporter_150


title: SCVI-111_hiPSC_CM_Reporter_151


title: SCVI-111_hiPSC_CM_Reporter_153


title: HAP1 cell line HAP_142_2_S52588

value: HAP1wt cell line stably expressing the catalytically inactive transgenic version of HDAC2


title: SCVI-111_hiPSC_CM_Reporter_149


title: SCVI-111_hiPSC_CM_Reporter_147


title: HAP1 cell line HAP_135_3_S52584

value: HAP1wt cell line stably expressing the catalytically inactive transgenic version of HDAC3


title: SCVI-111_hiPSC_CM_Reporter_148


title: HAP1 cell line HAP_135_2_S52587


title: HAP1 cell line HAP_142_3_S52589


title: HAP1 cell line HAP_142_1_S52590


title: HAP1 cell line HD3_wt_A9_3_S52606

value: HAP1 HDAC3 knockout cell line stably expressing the catalytically active transgenic version of HDAC3


title: HAP1 cell line HAP_135_1_S52586


title: SCVI-111_hiPSC_CM_Reporter_143


title: SCVI-111_hiPSC_CM_Reporter_146


title: HAP1 cell line HD3_wt_A9_1_S52608


title: HAP1 cell line HAP_143_1_S52585


title: HAP1 cell line HD3_wt_A9_2_S52605


title: SCVI-111_hiPSC_CM_Reporter_145


title: L(3)mbt mutant brain RNA-seq rep3

city: Bunkyo-ku

first: Soichiro

last: Yamanaka

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls were performed by illumina Hiseq
trim down the base to first 50 bp from 150 bp using seqkit
Reads were alighed to the dm6 genome assembly using HISAT2
only unique reads were extracted
for larval brain sample, read count by using FeatureCounts
Assembly: dm6
Supplementary files format and content: txt file (count data)

organism: Drosophila melanogaster

source_name: L(3)mbt mutant fly larval brain

growth_protocol: Each fly strain was maintained under normal laboratory condition.

extract_protocol:
RNAs were extracted according to NipponGene's instructions accompanying RNA extraction kit(311-07361).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. Poly-A selected mRNAs were brought to library preparation.

treatment_protocol: L3 larval brain grown at 29C for 5-6 days after spawning at 25C

value: L3 larval

tag: tissue

value: brain

tag: genotype

value: L(3)mbt mutant


title: SCVI-111_hiPSC_CM_Reporter_142


title: HAP1 cell line HAP_143_2_S52582


title: L(3)mbt mutant brain RNA-seq rep1


title: Lint-O mutant brain RNA-seq rep3

source_name: Lint-O mutant fly larval brain

value: Lint-O mutant


title: HAP1 cell line HD3_135_G10_3_S52607

value: HAP1 HDAC3 knockout cell line stably expressing the catalytically inactive version of HDAC3


title: L(3)mbt mutant brain RNA-seq rep2


title: HAP1 cell line HD3_135_G10_2_S52593


title: SCVI-111_hiPSC_CM_Reporter_140


title: Lint-O mutant brain RNA-seq rep1


title: SCVI-111_hiPSC_CM_Reporter_138


title: HAP1 cell line HAP_MS3_2_S52595


title: SCVI-111_hiPSC_CM_Reporter_139


title: Lint-O mutant brain RNA-seq rep2


title: SCVI-111_hiPSC_CM_Reporter_144


title: HAP1 cell line HD3_135_G10_1_S52594


title: HAP1 cell line HAP_MS3_3_S52598


title: yw brain RNA-seq rep3

source_name: yw fly larval brain

value: yw


title: yw brain RNA-seq rep2


title: HAP1 cell line HAP_MS3_1_S52596


title: SCVI-111_hiPSC_CM_Reporter_137


title: SCVI-111_hiPSC_CM_Reporter_136


title: SCVI-111_hiPSC_CM_Reporter_141


title: HAP1 cell line HAP_MS1_3_S52600


title: SCVI-111_hiPSC_CM_Reporter_135


title: SCVI-111_hiPSC_CM_Reporter_134


title: HAP1 cell line HAP_MS1_2_S52601


title: SCVI-111_hiPSC_CM_Reporter_133


title: yw brain RNA-seq rep1


title: Kidney - NX - biol rep 1

city: Leuven

first: Jef

last: Van den Eynde

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

data_processing:
To minimize lane effects, all libraries were normalized, and equimolarly pooled before being 100-cycle paired-end sequenced across two lanes of NovaSeq 6000 System flowcell (Illumina, San Diego, CA), generating 2x150 bp.
Individual libraries were separated from multiplexed sequencing data (total yield = 207 Gbases). Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36; the remaining reads had a mean quality score per base of 35.7, with 92.8% of bases having a data quality score ≥Q30.
The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text files include unique hit counts for each Sample

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
RNA was extracted from snap frozen samples and purified with RNeasy Plus Mini kit (Qiagen, 74134) according to manufacturer’s protocol. The concentration and quality of the extracted mRNA was determined with a spectrophotometer (NanoDrop, Thermo Scientific). The samples had a mean 260/280 ratio of 2.10 (range 2.07-2.12) and a mean concentration of 482ng/µL (range 78-1253ng/µL).
The mRNA was reverse transcribed using the GoScript Reverse Transcription System (Promega A5004). All samples were submitted to GENEWIZ (Leipzig, Germany) for RNA library preparations, sequencing reactions and initial bioinformatics analysis. RNA sequencing libraries were prepared based on 500ng input total RNA using poly(A) selection and strand-specific RNA library prep kits (Illumina, San Diego, CA) according to the manufacturer’s instructions. To minimize lane effects, all libraries were normalized, and equimolarly pooled before being 100-cycle paired-end sequenced across two lanes of NovaSeq 6000 System flowcell (Illumina, San Diego, CA), generating 2x150 bp.

treatment_protocol: Rats in the AVF+NX group had undergone a 5/6th partial nephrectomy and a creation of an end-to-side arteriovenous fistula of the jugular vein onto the carotid artery; those in the NX group only received a 5/6th partial nephrectomy; and those in the Sham group underwent sham surgery. All samples were collected 4 weeks after the surgical procedure.

value: Kidney

tag: breed

value: Sprague-Dawley

tag: age

value: 13 weeks old

tag: model

value: NX

tag: time

value: 4 weeks after surgery


title: Kidney - Sham - biol rep 2

value: Sham


title: Kidney - NX - biol rep 4


title: Kidney - Sham - biol rep 4


title: Kidney - NX - biol rep 2


title: Kidney - Sham - biol rep 3


title: Kidney - Sham - biol rep 1


title: Kidney - NX - biol rep 3


title: HAP1 cell line HAP_MS1_1_S52599

value: control cell line treated with MS275


title: Kidney - AVF+NX - biol rep 3

value: AVF+NX


title: HAP1 cell line HAP_JQ_3_S52591

value: control cell line treated with JQ12


title: SCVI-111_hiPSC_CM_Reporter_132

value: hiPSC-derived cardiomyocytes

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: Kidney - AVF+NX - biol rep 4


title: SCVI-111_hiPSC_CM_Reporter_131


title: Kidney - AVF+NX - biol rep 1


title: Kidney - AVF+NX - biol rep 2


title: Heart - Sham - biol rep 2

source_name: Heart

value: Heart


title: HAP1 cell line HAP_JQ_1_S52597


title: HAP1 cell line HAP_JQ_2_S52592


title: SCVI-111_hiPSC_CM_Reporter_130


title: Heart - Sham - biol rep 1


title: Heart - Sham - biol rep 3


title: HAP1 cell line HAP_141_3_S52602

value: HAP1wt cell line stably expressing the catalytically inactive transgenic version of HDAC1


title: SCVI-111_hiPSC_CM_Reporter_129


title: Heart - NX - biol rep 4


title: Heart - NX - biol rep 3


title: SCVI-111_hiPSC_CM_Reporter_128


title: Heart - NX - biol rep 1


title: HAP1 cell line HD8_wt_3_S47243

value: HAP1 HDAC8 knockout cell line stably expressing the catalytically active transgenic version of HDAC8


title: Heart - AVF+NX - biol rep 1


title: Heart - AVF+NX - biol rep 3


title: Heart - AVF+NX - biol rep 2


title: HAP1 cell line HD8_wt_1_S47245


title: CAF27 S63845 18h, biol replicate 4

city: Nantes

first: Frederique

last: Souaze

address: Quai Moncousu

country: France

institute: INSERM

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer

extract_protocol:
Total RNA from cell samples were purified with the NucleoSpin RNA (Macherey Nagel, Hoerdt, France).
the libraries was prepared from 10 ng of total RNA. 15 RNA samples were extracted from hiPS. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse

value: breast cancer

value: cancer associated fibroblast

tag: treatment

value: MCL-1 antagonist


title: CAF27 S63845 18h, biol replicate 2


title: HAP1 cell line HAP_141_1_S52603


title: Heart - NX - biol rep 2

value: Sprague-Dawley


title: SCVI-111_hiPSC_CM_Reporter_125


title: SCVI-111_hiPSC_CM_Reporter_124


title: CAF27 S63845 18h, biol replicate 1


title: CAF27  untreated, biol replicate 2

value: untreated


title: CAF27  untreated, biol replicate 4


title: SCVI-111_hiPSC_CM_Reporter_126


title: Heart - AVF+NX - biol rep 4

value: 13 weeks old


title: SCVI-111_hiPSC_CM_Reporter_123


title: SCVI-111_hiPSC_CM_Reporter_127


title: HAP1 cell line HD8_wt_2_S47244


title: HAP1 cell line HAP_141_2_S52604


title: CAF27  untreated, biol replicate 1


title: HAP1 cell line HD8_143_2_S47256

value: HAP1 HDAC8 knockout cell line stably expressing the catalytically inactive version of HDAC8


title: CAF27 S63845 18h, biol replicate 3


title: CAF27  untreated, biol replicate 3


title: HAP1 cell line HD8_143_3_S47255


title: CAF46 S63845 18h, biol replicate 4


title: SCVI-111_hiPSC_CM_Reporter_122


title: CAF46  untreated, biol replicate 4


title: HAP1 cell line HD2_wt_3_S47249

value: HAP1 HDAC2 knockout cell line stably expressing the catalytically active transgenic version of HDAC2


title: SCVI-111_hiPSC_CM_Reporter_120


title: CAF46 S63845 18h, biol replicate 3


title: CAF46  untreated, biol replicate 3


title: HAP1 cell line HD2_wt_2_S47250


title: HAP1 cell line HD2_wt_1_S47251


title: SCVI-111_hiPSC_CM_Reporter_119


title: CAF48  untreated, biol replicate 4


title: CAF48 S63845 18h, biol replicate 4


title: HAP1 cell line HD1_wt_2_S47253

value: HAP1 HDAC1 knockout cell line stably expressing the catalytically active transgenic version of HDAC1


title: CAF48 S63845 18h, biol replicate 3


title: CAF46  untreated, biol replicate 2


title: CAF46  untreated, biol replicate 1


title: SCVI-111_hiPSC_CM_Reporter_118


title: HAP1 cell line HD1_wt_3_S47252


title: SCVI-111_hiPSC_CM_Reporter_117


title: SCVI-111_hiPSC_CM_Reporter_116


title: CAF48 S63845 18h, biol replicate 2


title: CAF46 S63845 18h, biol replicate 2


title: CAF46 S63845 18h, biol replicate 1


title: CAF48  untreated, biol replicate 1


title: CAF48 S63845 18h, biol replicate 1


title: HAP1 cell line HD8_KO_1_S47284

value: HAP1 HDAC8 knockout cell line


title: HAP1 cell line HD8_KO_2_S47279


title: HAP1 cell line HD1_wt_1_S47254


title: HAP1 cell line HD8_KO_3_S47280


title: CAF48  untreated, biol replicate 2


title: HAP1 cell line HD8_143_1_S47274


title: SCVI-111_hiPSC_CM_Reporter_114


title: HAP1 cell line HD2_142_3_S47278

value: HAP1 HDAC2 knockout cell line stably expressing the catalytically inactive version of HDAC2


title: SCVI-111_hiPSC_CM_Reporter_113

value: hiPSC-derived cardiomyocytes


title: CAF56  untreated, biol replicate 4


title: HAP1 cell line HD2_142_2_S47277


title: CAF56  untreated, biol replicate 1


title: SCVI-111_hiPSC_CM_Reporter_111

value: Day 15


title: CAF56 S63845 18h, biol replicate 3


title: SCVI-111_hiPSC_CM_Reporter_115

value: SCVI-111 TBX5-Lineage Reporter Line


title: CAF56  untreated, biol replicate 3


title: SCVI-111_hiPSC_CM_Reporter_110


title: SCVI-111_hiPSC_CM_Reporter_112


title: CAF36  untreated, biol replicate 4


title: CAF48  untreated, biol replicate 3


title: CAF56  untreated, biol replicate 2


title: CAF56 S63845 18h, biol replicate 2


title: CAF56 S63845 18h, biol replicate 4


title: CAF36 S63845 18h, biol replicate 4


title: HAP1 cell line HD2_142_1_S47276


title: SCVI-111_hiPSC_CM_Reporter_109


title: SCVI-111_hiPSC_CM_Reporter_108


title: CAF36  untreated, biol replicate 3


title: CAF36 S63845 18h, biol replicate 2


title: SCVI-111_hiPSC_CM_Reporter_107


title: CAF36 S63845 18h, biol replicate 3


title: CAF56 S63845 18h, biol replicate 1


title: CAF36 S63845 18h, biol replicate 1


title: HAP1 cell line HD1_141_1_S47281

value: HAP1 HDAC1 knockout cell line stably expressing the catalytically inactive version of HDAC1


title: HAP1 cell line HD1_141_2_S47282


title: CAF36  untreated, biol replicate 1


title: CAF36  untreated, biol replicate 2


title: HAP1 cell line HD2_KO_3_S47259

value: HAP1 HDAC2 knockout cell line


title: SCVI-111_hiPSC_CM_Reporter_105


title: SCVI-111_hiPSC_CM_Reporter_106


title: CAF24  untreated, biol replicate 3


title: CAF24 S63845 18h, biol replicate 3


title: CAF24  untreated, biol replicate 4


title: CAF24 S63845 18h, biol replicate 4


title: CAF24 S63845 18h, biol replicate 2


title: SCVI-111_hiPSC_CM_Reporter_104


title: HAP1 cell line HD1_141_3_S47275


title: HAP1 cell line HD2_KO_1_S47257


title: SCVI-111_hiPSC_CM_Reporter_103


title: CAF24  untreated, biol replicate 2


title: CAF24 S63845 18h, biol replicate 1


title: HAP1 cell line HD1_KO_3_S47258

value: HAP1 HDAC1 knockout cell line


title: SCVI-111_hiPSC_CM_Reporter_102


title: HAP1 cell line HD1_KO_1_S47264


title: CAF24  untreated, biol replicate 1

value: breast cancer


title: SCVI-111_hiPSC_CM_Reporter_101


title: HAP1 cell line HD2_KO_2_S47260


title: HAP1 cell line HD1_KO_2_S47263


title: SCVI-111_hiPSC_CM_Reporter_99


title: Mock_3_48hpi_R1

city: Rochester

first: Joshua

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-8828

department: Biochemistry & Biophysics

institute: University of Rochester

data_processing:
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and gencode 25 human gene annotations using only uniquely aligned reads (default) and including multi-mapping reads (-M).
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36.
Each sample was mapped individually to the human reference genome (GRCh38.p7, primary assembly + gencode 25 annotation) with STAR2.5.2b.
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with a false-discovery rate adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: GRCh38.p7, primary assembly + gencode 25 annotation.
Supplementary files format and content: pre_deSeq2_counts.txt
Supplementary files format and content: deSeq2_Ad_vs_mock.xlsx: Excel file containing gene names, abundance values, log2 fold changes, and significance scores (p-values).

source_name: Human Lung Fibroblasts

growth_protocol: MRC5 fibroblasts (ATCC CCL-171) were cultured in Dulbecco’s modified Eagle serum (DMEM; Invitrogen) supplemented with 10% (vol/vol) FBS, 4.5 g/liter glucose, and 1% penicillin-streptomycin (Life Technologies) at 37oC in a 5% (vol/vol) CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) according to manufacturer's instructions.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer's protocols.

treatment_protocol: Cells were infected for 2 hrs with each indicated virus and then allowed to grow in fresh, serum-free DMEM for 48 hrs.

value: Fibroblasts

tag: infection

value: Mock

tag: time point

value: 48 hpi


title: Mock_2_48hpi_R1


title: Ad_3_48hpi_R1

value: HCMV strain AD169


title: SCVI-111_hiPSC_CM_Reporter_98


title: SCVI-111_hiPSC_CM_Reporter_100


title: Ad_2_48hpi_R1


title: HAP1 cell line HAP_MS_1_S47267

value: control cell line treated with MS275


title: SCVI-111_hiPSC_CM_Reporter_97


title: HAP1 cell line HAP_2_S47265

value: control cell line


title: Mock_1_48hpi_R1


title: SCVI-111_hiPSC_CM_Reporter_96


title: HAP1 cell line HAP_3_S47268


title: HAP1 cell line HAP_MS_3_S47261


title: SCVI-111_hiPSC_CM_Reporter_95


title: Ad_1_48hpi_R1


title: HAP1 cell line HAP_1_S47266


title: SCVI-111_hiPSC_CM_Reporter_94


title: HAP1 cell line HAP_MS_2_S47262


title: SCVI-111_hiPSC_CM_Reporter_121


title: SCVI-111_hiPSC_CM_Reporter_93


title: Uninfected fish 8, skin muscle

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Skin and muscle

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks with sea water

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Fish were batch challenged with M. viscosa. The challenge study was conducted over the course of 34 days, with temperatures ranging from 8-9.5°C throughout the period. Mortality was recorded on a daily basis, and cause of death was confirmed by bacteriological sampling. Ten fish were collected from controls and challenge tanks at 9, 23, 34 days post-challenge (referred to as time points 1, 2, and 3 respectively). Additionally, 10 control fish were taken from the challenge tank prior to introduction of the bacterial culture. For each fish, samples were taken of the head-kidney (HK), as well as from the site of external ulcers, or from the abdomen if the fish did not exhibit visible lesions despite being infected

tag: agent


title: Infected fish 4, day 23, ulcer site

value: Moritella viscosa

value: day 23


title: Uninfected fish 10, skin muscle


title: Infected fish 9, day 9, head kidney

source_name: Head kidney

value: day 9


title: Infected fish 9, day 23, head kidney


title: Infected fish 3, day 23, head kidney


title: Infected fish 2, day 23, head kidney


title: Infected fish 7, day 9, head kidney


title: Uninfected fish 4, skin muscle


title: Infected fish 10, day 9, ulcer site


title: Infected fish 9, day 23, ulcer site


title: Infected fish 6, day 9, head kidney


title: Infected fish 3, day 9, head kidney


title: Infected fish 7, day 34, head kidney

value: day 34


title: Infected fish 3, day 34, head kidney


title: Infected fish 10, day 23, head kidney


title: Infected fish 5, day 34, head kidney


title: SCVI-111_hiPSC_CM_Reporter_90

value: hiPSC-derived cardiomyocytes


title: SCVI-111_hiPSC_CM_Reporter_91

value: Day 15


title: SCVI-111_hiPSC_CM_Reporter_89

value: SCVI-111 TBX5-Lineage Reporter Line


title: SCVI-111_hiPSC_CM_Reporter_92


title: H3122-LR3_Ceritinib

city: Koto-ku

first: Ryohei

last: Katayama

state: Tokyo

department: The Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

description: lung adenocarcinoma, EML4-ALK

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner3000

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

label: biotin

source_name: H3122-LR3,Ceritinib treat,

label_protocol: GeneChip 3'IVT Express Kit

growth_protocol: RPMI with 10%FBS

extract_protocol: RNeasy Mini Kit

treatment_protocol: incubate with 1000 nM of crizotinib or ceritinib for 6 hr

value: Ceritinib


title: Uninfected fish 9, head kidney


title: Infected fish 1, day 34, head kidney


title: SCVI-111_hiPSC_CM_Reporter_88


title: SCVI-111_hiPSC_CM_Reporter_86


title: H3122-LR2_non

description: lung adenocarcinoma, EML4-ALK

source_name: H3122-LR2,non treat


title: Infected fish 1, day 23, ulcer site


title: H3122-LR3_non

description: lung adenocarcinoma, EML4-ALK

source_name: H3122-LR3,non treat


title: Hungatella hathewayi N2-326, Glucose , rep3

city: Qingdao

first: Parkash

middle: Singh

last: Rawat

state: Shanding

address: 72 Binhai Road, Jimo

department: State Key Laboratory for Microbial Technology, School of Life Sciences

country: China

institute: Shandong University

data_processing:
Base calling: FastQ, Base calls quality check: Phred
Data filtering: Cutadapt
Read alignment: Bowtie2
Quality control: FastQC
Assembly: HH50_5.scaffolds.fna
Supplementary files format and content: Expression.xlsx= Read counts and FPKM counts for each transcript, format= xlsx
Supplementary files format and content: Glc_vs_CSA.DESeq.xlsx= differential expression (foldchange and log2foldchange values) for each trasncript, format= xlsx

organism: Hungatella hathewayi

source_name: Bacterium

growth_protocol: Cells were grown in an anaerobic chamber without shaking at 37 °C

extract_protocol:
Bacterial cells at mid-log phase of the growth were centrifuges at 12000 g, 15 minutes, 4 °C. RNA was extracted using the Trizol Reagent (Invitrogen Life Technologies).
Library was constructed using the NEBNext Ultra II RNA Library Prep for Illumina kit by Shanghai Personal Biotechnology Co. Ltd. cDNA was synthesized by using fragmented mRNA as template and random oligonucleotides as primers. Overhangs were converted into blunt ends via exonuclease/exonuclease/polymerase activities and the enzymes were removed. After adenylation of 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated. Library fragments were purified using the  AMPure XP system (Beckman Coulter, Beverly, CA, USA). Library quality detection was performed using Agilent 2100 Bioanalyzer (Agilent, 2100), uing the Agilent high sensitivity DNA Kit (Agilent, 5067-4626). The total library concentration was detected by Pico green (Quantifluor-ST fluorometer, Promega, e6090; Quant iT PicoGreen dsDNA Assay kit, Invitrogen, p7589), and the effective library concentration was quantitatively detected by qPCR (Thermo Scientific StepOnePlus Real-Time PCR Systems).

value: Bacterium

value: WT

value: Growth in 1.5% Glucose


title: Uninfected fish 7, head kidney


title: Hungatella hathewayi N2-326, Glucose , rep2


title: SCVI-111_hiPSC_CM_Reporter_87


title: MI A24

city: fort valley

first: phaneendra

last: batchu

state: georgia

address: 1005 State univerity drive

department: Animal Science

institute: fort valley state university

description: Blood samples collected after 30 minutes of transportation

data_processing:
Data processing was done by Novagene
Methods uploaded with a file name Methods_RNA-seq

organism: Capra hircus

source_name: Blood

extract_protocol:
Blood RNA was extracted using a MagMAX™ Stabilized Blood Tubes RNA Isolation Kit by applied biosystems (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s instructions.
NEBNext® UltraTM  RNA Library Prep kit from Illumina® (NEB, USA) were used to generate the sequencing libraries

value: Blood

tag: group

value: MI

value: 30 minutes of transportation


title: MI A21


title: SCVI-111_hiPSC_CM_Reporter_85


title: MI A27


title: MI A22


title: H3122-LR2_Crizotinib

description: lung adenocarcinoma, EML4-ALK

source_name: H3122-LR2,Crizotinib treat

value: Crizotinib


title: H3122-LR2_Ceritinib

description: lung adenocarcinoma, EML4-ALK

source_name: H3122-LR2,Ceritinib treat,


title: Hungatella hathewayi N2-326, Glucose , rep1


title: Uninfected fish 8, head kidney


title: Uninfected fish 5, head kidney


title: Microdissected Mice Renal PT-S1, UNx1_24h, ATAC-Seq

city: Bethesda

first: Hiroaki

last: Kikuchi

state: MD

address: 10 CENTER DR

department: Epithelial Systems Biology Laboratory, Systems Biology Center

institute: NHLBI

library_source: genomic

data_processing:
Adapter sequences were trimmed for both forward and reverse reads using cutadapt (v 3.4)
Trimmed sequences were aligned to the mouse reference genome mm10 using bowtie (version 2-2.4.5 )
The resulting SAM files were converted to a binary format (BAM), sorted by queryname, and indexed using samtools
Reads that mapped to the mitochondrial genome were removed using samtools
Identically mapping read duplicates were marked using Picard MarkDuplicates (v 2.25.7)
Narrow open chromatin peaks were identified using MACS2 (v2.2.7.1)
Assembly: mm10
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Pathogen-free male C57BL/6 mice (Taconic) weighing 20-30 g had free access to ad libitum drinking water and normal rodent chow before experiment. The mice were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 3 days before the experimental procedures.

extract_protocol:
Three manually dissected proximal tubules (200-300 um) were lysed and transposed simultaneously in 25 ul of transposition mix (0.1% NP40, 0.1% Tween-20, 0.01% digitonin and 5% Tn5 enzyme (Illumina # 15027865) in Tagment DNA Buffer (FC-121–1030; Illumina). The transposition reaction was incubated at 37 C for 30 mins in a thermomixer with shaking at 1,000 rpm. After tagmentation, the reactions were stopped with addition of 80 ul of water, 3 ul of 0.5% EDTA, 1.5 ul of 20% SDS and 5 ul of proteinase K.
The transposed DNA fragments were purified by DNA Purification Kits (Zymo Research, # D4014), and amplified using PCR. The final libraries were purified using AmPure XP magnetic beads (Beckman Coulter, Indianapolis, IN).

treatment_protocol: Seven-week-old mice were assigned to two groups with sham operation or with unilateral nephrectomy (UNx). UNx was performed by the surgical excision method.

value: Kidney

value: UNx


title: H3122_non

description: lung adenocarcinoma, EML4-ALK

source_name: H3122,non treat


title: H3122_Ceritinib

description: lung adenocarcinoma, EML4-ALK

source_name: H3122,Ceritinib treat,


title: Microdissected Mice Renal PT-S1, UNx2_24h, ATAC-Seq


title: H3122_Crizotinib

description: lung adenocarcinoma, EML4-ALK

source_name: H3122,Crizotinib treat


title: MO A15

description: Blood samples collected after 180 minutes of transportation

value: MO

value: 180 minutes of transportation


title: MO A17


title: SCVI-111_hiPSC_CM_Reporter_84

source_name: hiPSC-derived Cardiomyocytes


title: MO A16


title: SCVI-111_hiPSC_CM_Reporter_83


title: SCVI-111_hiPSC_CM_Reporter_81


title: Hungatella hathewayi N2-326, Chondroitin sulfate A , rep1

value: Growth in 1.5% Chondroitin sulfate A


title: MO A13


title: SCVI-111_hiPSC_CM_Reporter_80


title: Microdissected Mice Renal PT-S1, Sham3_24h, ATAC-Seq

source_name: Kidney

value: Sham


title: Microdissected Mice Renal PT-S1, UNx3_24h, ATAC-Seq


title: Microdissected Mice Renal CCD, UNx4_72h, RNA-Seq, Transcriptome 03 [72h_CCD_unx4_3]

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm39.103) using STAR v2.7.61
Transcript abundances in TPM were caculated by  RSEM/1.3.3
Assembly: GRCm39 (Ensembl)
Supplementary files format and content: tab-delimited text files include TPM values for each sample

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MO A11


title: SCVI-111_hiPSC_CM_Reporter_82

value: hiPSC-derived cardiomyocytes


title: Microdissected Mice Renal PT-S1, Sham1_24h, ATAC-Seq


title: Microdissected Mice Renal PT-S1, Sham2_24h, ATAC-Seq


title: Hungatella hathewayi N2-326, Chondroitin sulfate A , rep3


title: SCVI-111_hiPSC_CM_Reporter_79

value: Day 15


title: Hungatella hathewayi N2-326, Chondroitin sulfate A , rep2


title: Microdissected Mice Renal CCD, UNx3_72h, RNA-Seq, Transcriptome 01 [72h_CCD_unx3_1]


title: MO A14


title: SCVI-111_hiPSC_CM_Reporter_77

value: SCVI-111 TBX5-Lineage Reporter Line


title: CL A8

description: Blood samples collected from non transported goats

value: CL

value: non transported goats


title: Slideseq_T1L_Heart_D7PI

city: Ithaca

first: Iwijn

last: De Vlaminck

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: High-resolution spatial RNA sequencing of heart tissue from T1L-infected neonatal mice at 7 dpi

library_source: transcriptomic single cell

data_processing:
Mus musculus genome and gene annotations (assembly: GRCm38) were downloaded from the Ensembl genome browser, and Reovirus strain Type 1 lang genome and gene annotations were downloaded from the NCBI browser. Genomes were processed using the Cell Ranger (10x Genomics) pipeline’s mkref command.
Sequencing data was aligned to a combined mouse and reovirus reference genome (described below) using the STAR Solo (version=2.7.9a) pipeline to derive a feature x bead barcode expression matrix.
Assembly: GRCm38

source_name: Neonatal murine heart

growth_protocol: Confirmed pregnant female C57BL/6J mice were ordered from Jackson Laboratories to be delivered at embryonic stage E14.5. The mice pups were weighed every day until the time points used in the study.

extract_protocol:
Whole hearts were isolated using aseptic technique and placed in ice cold sterile Hank’s Balanced Salt Solution, HBSS.  Blood and other contamination were carefully removed by perfusing the tissues with fresh HBSS. Fresh tissues were immediately embedded in Optimal Cutting Compound (OCT) media and frozen in a liquid-nitrogen-cooled isopentane (EMD Millipore, MX0760) bath for spatial transcriptomics experiments. The tissue blocks were cut into 10µm sections using Thermo Scientific CryoStar NX50 cryostat, and mounted on on a "Curio Seeker Tile (Tile ID #A0004_043, Curio Bioscience). A barcode whitelist and a barcode position file for the corresponding tile were provided by Curio Bioscience.
Slide-seq spatial transcriptomics experiment was performed using the Curio Seeker Kit (Curio Bioscience) according to manufacturer's instructions. Briefly, a tissue section from a fresh-frozen reovirus-infected heart at 7 dpi was mounted on a 3mmx3mm spatially indexed bead surface (Curio Seeker Kit, Tile ID #A0004_043, Curio Bioscience). After RNA hybridization and reverse transcription, the tissue section was digested, and the beads were removed from the glass tile and resuspended. Second strand synthesis was then performed by semi-random priming followed by cDNA amplification. A sequencing library was then prepared using the Nextera XT DNA sample preparation kit. The library was sequenced on an Illumina NextSeq 2K (P3 flow cell) using the 100-cycle kit (Read 1 = 50 bp, Read 2 = 80, Index 1 = 10).

treatment_protocol: Neonatal mice pups weighing 3 gram/ pup were gavaged using intramedic tubing (Becton Dickinson 427401) per os with 50 μl with 107 PFU reovirus type 1 lang (T1L) in phosphate buffered saline (PBS) containing green food color (McCormick) via a 1ml tuburculin slip tip syringe (BD 309659) and 30G x 1/2 needle (BD 305106). Litters treated with PBS alone on the same day were used as mock controls for the respective infection groups.

value: Neonatal murine heart

tag: infection state

tag: days post infection (dpi)

value: 7 dpi


title: Untreated primary HGFs (human gingival fibroblasts ) replicate 2

city: Iowa City

first: Erliang

last: Zeng

state: IOWA

address: 801 Newton Rd, DSB N101-9, College of Dentistry

institute: University of Iowa

data_processing:
DESeq2 R package
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogene pipeline (Remove reads with adaptor contamination, Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%), Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read).  Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Cleaned reads were mapped to the human reference genome hg38 using STAR software.
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) was estimated as gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human gingiva

growth_protocol: Frozen stocks of Sg (ATCC 33399), Streptococcus sanguinis (Ss) (ATCC 10556), Sm (ATCC 49456), and So (ATCC 35037) were thawed and streaked on two Brain heart infusion agar plates (BHI, Becton, Dickinson and Company, MD, USA) and incubated at 37°C 5% CO2 overnight. Each strain was then subcultured in 4 ml BHI medium for 30 min at 37°C before inoculating 60 µl into each well of a 24-well plate containing 2 ml of BHI medium with different concentrations of Sg SCS or DMEM. 1% horse serum (ThermoFisher Scientific) was added to the medium for Sm. The bacteria were then incubated at 37°C 5% CO2 for up to 72 hours. At intervals of 4, 12, and 24 hours, 100 µl of bacteria from each well were measured in duplicates for optical density (OD) using a microplate reader at a wavelength of 600 nm.

extract_protocol:
Total RNA from HGFs was extracted after 24 hrs using the miRNeasy Mini kit and mRNA-seq was performed commercially (Novogen, Sacramento, CA). RNA degradation and contamination was monitored on 1% agarose gels, RNA purity was checked using a Nanophotometer® spectrophotometer, and RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA). A total 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) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: The bacteria were incubated at 37°C in an anaerobic atmosphere until they reached stationary phase. For Pg, 300 µl was inoculated into each culture tube containing 5 ml of BHI media with 5% horse serum and with different concentrations of Sg SCS or DMEM.

value: human gingiva

value: Control


title: Untreated primary HGFs (human gingival fibroblasts ) replicate 1


title: CL A9

value: Blood


title: CL A7


title: Microdissected Mice Renal CCD, UNx1_72h, RNA-Seq, Transcriptome 02 [72h_CCD_unx1_2]

value: WT


title: SCVI-111_hiPSC_CM_Reporter_75

tag: cell type


title: Microdissected Mice Renal CCD, UNx1_72h, RNA-Seq, Transcriptome 01 [72h_CCD_unx1_1]

value: Kidney


title: HGFs (human gingival fibroblasts ) treated with 5% Sg SCS replicate 2

value: 5% Sg SCS


title: Microdissected Mice Renal CCD, UNx2_72h, RNA-Seq, Transcriptome 03 [72h_CCD_unx2_3]

value: UNx


title: CL A4


title: SCVI-111_hiPSC_CM_Reporter_76

tag: strain


title: MO A10

value: MO

value: 180 minutes of transportation


title: HTR-8 cell, si TET, rep3

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
Aligned to hg38 by STAR
Transcript assembly by stringtie
Differential analysis by DEseq2
Assembly: hg38
Supplementary files format and content: csv files include count values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HTR-8 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: trophoblasts

value: TET KD


title: Microdissected Mice Renal CCD, UNx4_72h, RNA-Seq, Transcriptome 02 [72h_CCD_unx4_2]


title: SCVI-111_hiPSC_CM_Reporter_78

value: hiPSC-derived cardiomyocytes

tag: developmental stage

value: Day 15


title: Microdissected Mice Renal CCD, Sham4_72h, RNA-Seq, Transcriptome 02 [72h_CCD_sham4_2]

value: Sham


title: CL A6

value: CL

value: non transported goats


title: HTR-8 cell, control, rep1

tag: cell line


title: HGFs (human gingival fibroblasts ) treated with 5% Sg SCS replicate 1

tag: tissue


title: SCVI-111_hiPSC_CM_Reporter_72

value: SCVI-111 TBX5-Lineage Reporter Line


title: SCVI-111_hiPSC_CM_Reporter_74


title: HTR-8 cell, si TET, rep1

tag: genotype


title: Microdissected Mice Renal CCD, Sham4_72h, RNA-Seq, Transcriptome 01 [72h_CCD_sham4_1]


title: Microdissected Mice Renal CCD, Sham4_72h, RNA-Seq, Transcriptome 03 [72h_CCD_sham4_3]


title: C27 MI

description: Muscle samples collected after 30 minutes of transportation

data_processing:
Data processing was done by Novagene
Methods uploaded

source_name: Muscle

extract_protocol:
Blood RNA was extracted using a MagMAX™ Stabilized Blood Tubes RNA Isolation Kit by applied biosystems (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s instructions. Muscle RNA was extracted by using RNeasy® Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) according to manufacturer’s procedures
NEBNext® UltraTM  RNA Library Prep kit from Illumina® (NEB, USA) were used to generate the sequencing libraries

value: Muscle

value: MI

value: 30 minutes of transportation


title: SCVI-111_hiPSC_CM_Reporter_73


title: SCVI-111_hiPSC_CM_Reporter_70


title: HTR-8 cell, control, rep3

value: WT


title: SCVI-111_hiPSC_CM_Reporter_69


title: EXO3D02

city: Beijing

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
Supplementary files format and content: raw and normalized data

source_name: human umbilical cord mesenchymal stem cells

growth_protocol: hUMSCs were cultivated in serum-free MSCBM containing EliteGro-Adv mixed with 0.1% penicillin-streptomycin.

extract_protocol:
total RNAs were extracted from 200μg exosomes purified from 2D-hUMSCs and 3D-hUMSCs supernatants, and both 2D-Exo and 3D-Exo groups contained 4 samples.
TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) were used to prepare miRNA sequencing libraries.

treatment_protocol: For 3D culture of hUMSCs, hUMSCs were digested when the confluent reached 80%-90%. The optimal cell density was 2×105/ mL, and 2 mL of the cell suspension was inoculated into ultra-low adhesion culture 6-well plate.

value: human umbilical cord  wharton's jelly differentiation


title: Microdissected Mice Renal CCD, Sham1_72h, RNA-Seq, Transcriptome 02 [72h_CCD_sham1_2]

value: Kidney


title: EXO3D04

value: human umbilical cord mesenchymal stem cells


title: CL A1

value: Blood


title: EXO3D05


title: SCVI-111_hiPSC_CM_Reporter_71

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
Droplet Based Sequencing: Data generated using the 10X Genomics 3' scRNA-seq v3.1 kit  were processed using CellRanger v6.0.0 (10X Genomics). Default parameters were used for alignment. The reference genomes used were refdata-gex-GRCh38-2020-A  for Human alignment and refdata-gex-mm10-2020-A for mouse data. References were obtained from the 10X Genomics website.
Samples (SCVI-111_hiPSC-Derived Cardiomyocytes_Day7-30) were multiplexed using the 10X Genomics CellPlex kit were demultiplexed using the CellRanger multi configuration. 10X Genomics cell multiplexing oligos used for each individual sample were as follow: Day7-CMO306, Day11-CMO307, Day13-CMO308, Day15-CMO309, Day30-CMO310.
Smartseq2 Based Sequencing: Data generated using the ICELL8 Takara Smartseq2 kit were processed using STARSolo aligner v2.7.9a software developed by Alexander Dobin. Reference genome used was a custom reference from GRCh38-2020-A (10X Genomics) containing added TurboGFP sequence. Parameters used were:  --soloType SmartSeq --soloStrand Unstranded.
GRCh38 (for Human) and mm10 (for Mouse)
Genome_build: Samples containing tab-delimited files contain output from CellRanger or STARSolo containing file with gene ensembl ID and gene symbols, cell barcodes, and matrix file containing raw counts.

extract_protocol:
Droplet based extraction: HiPSC-derived cardiomyocyte or mouse embryonic heart derived single cells were dissociated and captured and lysed using 10X Genomics Chromium Next GEM Single Cell 3' v3.1 Kit. mRNA was reverse transcribed to cDNA, and cDNA pre-amplification was conducted following manufacturer's protocol.    Smart-seq2 based extraction: HiPSC-derived cardiomyocytes were dissociated into single cell suspensions and captured using the ICELL8 Smartseq2 TAKARA system. mRNA was reverse transcribed to cDNA and cDNA pre-amplification was conducted per manufacturer’s protocol on an ICELL8 nanowell chip.
Droplet based library construction: Libraries for samples processed using 10X Genomics Single Cell 3' v3.1 kit were prepared from pre-amplified cDNA according to manufactrer's protocol. Gene expression libraries were generated for all 10X samples, and CellPlex multiplexing libraries were generated for running hiPSC-CM samples (Day 7, 11, 13,15, 30). Individual library index primers were used for multiplexing libraries on flow cell during sequencing.     Smart-seq2 library construction: Following Takara Smartseq2 ICELL8 protocol, pre-amplified and tagmented cDNA from individual single cells in ICELL8 nanowells received individual index sequencing barcodes for demultiplexing cells during downstream analysis.


title: EXO3D01


title: Microdissected Mice Renal CCD, Sham3_72h, RNA-Seq, Transcriptome 02 [72h_CCD_sham3_2]


title: Microdissected Mice Renal CCD, Sham2_72h, RNA-Seq, Transcriptome 02 [72h_CCD_sham2_2]


title: CL A3


title: Microdissected Mice Renal CCD, Sham1_72h, RNA-Seq, Transcriptome 01 [72h_CCD_sham1_1]


title: C24 MI


title: SCVI-111_hiPSC_CM_Reporter_68


title: C23 MI


title: C26 MI


title: SCVI-111_hiPSC_CM_Reporter_67


title: C25 MI


title: C22 MI


title: Microdissected Mice Renal CCD, UNx3_24h, RNA-Seq, Transcriptome 03 [24h_CCD_unx3_3]

value: UNx


title: Microdissected Mice Renal CCD, UNx3_24h, RNA-Seq, Transcriptome 01 [24h_CCD_unx3_1]


title: EXO2D05


title: SCVI-111_hiPSC_CM_Reporter_65


title: Microdissected Mice Renal CCD, UNx3_24h, RNA-Seq, Transcriptome 02 [24h_CCD_unx3_2]


title: SCVI-111_hiPSC_CM_Reporter_64


title: EXO2D04


title: SCVI-111_hiPSC_CM_Reporter_66


title: C21 MI


title: EXO2D02


title: C20 MI


title: Microdissected Mice Renal CCD, UNx2_24h, RNA-Seq, Transcriptome 01 [24h_CCD_unx2_1]


title: Microdissected Mice Renal CCD, UNx2_24h, RNA-Seq, Transcriptome 03 [24h_CCD_unx2_3]


title: C19 MI


title: Microdissected Mice Renal CCD, UNx1_24h, RNA-Seq, Transcriptome 02 [24h_CCD_unx1_2]


title: SCVI-111_hiPSC_CM_Reporter_62


title: Microdissected Mice Renal CCD, UNx1_24h, RNA-Seq, Transcriptome 01 [24h_CCD_unx1_1]


title: C17 MO

description: Muscle samples collected after 180 minutes of transportation

value: MO

value: 180 minutes of transportation


title: C18 MO


title: n=4, T7, Koku LN 13

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

description:
47
47_Koku_LN_13_S47

data_processing:
Data was processed with Lexogen QuantSeq data analysis pipeline on BlueBee Genomics platform.
Assembly: hg38
Supplementary files format and content: RNA_counts.csv: Expression counts retrieved from Quantseq software as semicolon-separated table.

source_name: LNCaP

extract_protocol:
RNA was extracted with miRNeasy Mini Kit (Qiagen).
Libraries were constructed with Lexogen Quantseq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

value: LNCaP

value: prostate adenocarcinoma cells

tag: condition

value: co-culture

value: seven days


title: n=4, T7, Kon p21

description:
46
46_Kon_p21_S46

value: primary stromal cells

value: control co-culture


title: SCVI-111_hiPSC_CM_Reporter_61

value: hiPSC-derived cardiomyocytes

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: n=4, T7, Kon LN 13

description:
45
45_Kon_LN_13_S45


title: SCVI-111_hiPSC_CM_Reporter_60


title: Microdissected Mice Renal CCD, Sham4_24h, RNA-Seq, Transcriptome 03 [24h_CCD_sham4_3]

value: WT

value: Sham


title: C15 MO

value: Muscle


title: Microdissected Mice Renal CCD, Sham4_24h, RNA-Seq, Transcriptome 02 [24h_CCD_sham4_2]

value: Kidney


title: n=4, T3, Koku p21

description:
44
44_Koku_p21_S44

value: three days


title: n=4, T7, Koku p21

description:
48
48_Koku_p21_S48


title: n=4, T3, Koku LN 13

description:
43
43_Koku_LN_13_S43


title: Microdissected Mice Renal CCD, Sham3_24h, RNA-Seq, Transcriptome 03 [24h_CCD_sham3_3]


title: SCVI-111_hiPSC_CM_Reporter_58


title: SCVI-111_hiPSC_CM_Reporter_63


title: Microdissected Mice Renal CCD, Sham4_24h, RNA-Seq, Transcriptome 01 [24h_CCD_sham4_1]


title: EXO2D01

value: human umbilical cord mesenchymal stem cells

value: human umbilical cord  wharton's jelly differentiation


title: C14 MO

value: MO

value: 180 minutes of transportation


title: SCVI-111_hiPSC_CM_Reporter_57


title: n=4, T3, Kon LN 13

description:
41
41_Kon_LN_13_S41

value: LNCaP

value: prostate adenocarcinoma cells


title: SCVI-111_hiPSC_CM_Reporter_56


title: n=4, T1, Koku p21

description:
40
40_Koku_p21_S40

value: co-culture

value: one day


title: Microdissected Mice Renal CCD, Sham2_24h, RNA-Seq, Transcriptome 03 [24h_CCD_sham2_3]


title: Microdissected Mice Renal CCD, Sham2_24h, RNA-Seq, Transcriptome 01 [24h_CCD_sham2_1]


title: n=4, T1, Koku LN 13

description:
39
39_Koku_LN_13_S39


title: C12 MO


title: SCVI-111_hiPSC_CM_Reporter_53


title: SCVI-111_hiPSC_CM_Reporter_55


title: C11 MO


title: Microdissected Mice Renal CCD, Sham1_24h, RNA-Seq, Transcriptome 03 [24h_CCD_sham1_3]


title: SCVI-111_hiPSC_CM_Reporter_54


title: SCVI-111_hiPSC_CM_Reporter_59


title: n=4, T1, Kon p21

description:
38
38_Kon_p21_S38

value: primary stromal cells

value: control co-culture


title: C10 MO


title: C16 MO


title: SCVI-111_hiPSC_CM_Reporter_52

value: hiPSC-derived cardiomyocytes

value: Day 15


title: C9 CL

value: CL


title: SCVI-111_hiPSC_CM_Reporter_51

value: SCVI-111 TBX5-Lineage Reporter Line


title: Microdissected Mice Renal PT-S1, UNx5_72h, RNA-Seq, Transcriptome 02 [72h_PT_unx5_2]

value: WT

value: UNx


title: Microdissected Mice Renal CCD, Sham1_24h, RNA-Seq, Transcriptome 01 [24h_CCD_sham1_1]

value: Kidney

value: Sham


title: n=4, T1, Kon LN 13

description:
37
37_Kon_LN_13_S37


title: C13 MO

value: Muscle


title: C7 CL

description: Muscle samples collected from non transported goats

value: non transported goats


title: C8 CL


title: n=3, T7, Koku p21

description:
36
36_Koku_p21_S36

value: seven days


title: SCVI-111_hiPSC_CM_Reporter_50


title: n=4, T3, Kon p21

description:
42
42_Kon_p21_S42

value: three days


title: C6 CL


title: n=3, T7, Koku LN 13

description:
35
35_Koku_LN_13_S35

value: LNCaP

value: prostate adenocarcinoma cells


title: Microdissected Mice Renal PT-S1, UNx5_72h, RNA-Seq, Transcriptome 01 [72h_PT_unx5_1]


title: SCVI-111_hiPSC_CM_Reporter_49


title: C5 CL


title: n=3, T7, Kon p21

description:
34
34_Kon_p21_S34


title: Microdissected Mice Renal PT-S1, UNx4_72h, RNA-Seq, Transcriptome 02 [72h_PT_unx4_2]


title: Microdissected Mice Renal PT-S1, UNx4_72h, RNA-Seq, Transcriptome 03 [72h_PT_unx4_3]


title: n=3, T7, Kon LN 13

description:
33
33_Kon_LN_13_S33


title: Microdissected Mice Renal PT-S1, UNx4_72h, RNA-Seq, Transcriptome 01 [72h_PT_unx4_1]


title: SCVI-111_hiPSC_CM_Reporter_48


title: n=3, T3, Koku p21

description:
32
32_Koku_p21_S32

value: co-culture


title: C4 CL


title: SCVI-111_hiPSC_CM_Reporter_47


title: SCVI-111_hiPSC_CM_Reporter_46


title: C3 CL


title: C2 CL


title: Microdissected Mice Renal PT-S1, UNx3_72h, RNA-Seq, Transcriptome 03 [72h_PT_unx3_3]


title: Microdissected Mice Renal PT-S1, UNx3_72h, RNA-Seq, Transcriptome 02 [72h_PT_unx3_2]


title: n=3, T3, Koku LN 13

description:
31
31_Koku_LN_13_S31


title: Microdissected Mice Renal PT-S1, UNx3_72h, RNA-Seq, Transcriptome 01 [72h_PT_unx3_1]


title: SCVI-111_hiPSC_CM_Reporter_45


title: n=3, T3, Kon p21

description:
30
30_Kon_p21_S30

value: primary stromal cells


title: Microdissected Mice Renal PT-S1, UNx2_72h, RNA-Seq, Transcriptome 02 [72h_PT_unx2_2]


title: C1 CL


title: n=3, T3, Kon LN 13

description:
29
29_Kon_LN_13_S29

value: control co-culture


title: SCVI-111_hiPSC_CM_Reporter_44

value: hiPSC-derived cardiomyocytes


title: SCVI-111_hiPSC_CM_Reporter_43

value: Day 15


title: B27 MI

value: MI

value: 30 minutes of transportation


title: Microdissected Mice Renal PT-S1, UNx2_72h, RNA-Seq, Transcriptome 01 [72h_PT_unx2_1]

value: WT


title: B25 MI


title: SCVI-111_hiPSC_CM_Reporter_42

value: SCVI-111 TBX5-Lineage Reporter Line


title: n=3, T1, Koku LN 13

description:
27
27_Koku_LN_13_S27

value: one day


title: n=3, T1, Koku p21

description:
28
28_Koku_p21_S28


title: B26 MI


title: n=3, T1, Kon p21

description:
26
26_Kon_p21_S26


title: Microdissected Mice Renal PT-S1, UNx1_72h, RNA-Seq, Transcriptome 01 [72h_PT_unx1_1]

value: Kidney

value: UNx


title: SCVI-111_hiPSC_CM_Reporter_41


title: B24 MI

value: Muscle


title: Microdissected Mice Renal PT-S1, Sham5_72h, RNA-Seq, Transcriptome 03 [72h_PT_sham5_3]

value: Sham


title: SCVI-111_hiPSC_CM_Reporter_40


title: B23 MI


title: n=3, T1, Kon LN 13

description:
25
25_Kon_LN_13_S25


title: Microdissected Mice Renal PT-S1, Sham5_72h, RNA-Seq, Transcriptome 02 [72h_PT_sham5_2]


title: n=2, T7, Koku p21

description:
24
24_Koku_p21_S24

value: seven days


title: B22 MI


title: n=2, T7, Koku LN 13

description:
23
23_Koku_LN_13_S23

value: LNCaP


title: B21 MI


title: SCVI-111_hiPSC_CM_Reporter_39


title: Microdissected Mice Renal PT-S1, Sham5_72h, RNA-Seq, Transcriptome 01 [72h_PT_sham5_1]


title: Microdissected Mice Renal PT-S1, Sham4_72h, RNA-Seq, Transcriptome 03 [72h_PT_sham4_3]


title: B20 MI


title: SCVI-111_hiPSC_CM_Reporter_36


title: SCVI-111_hiPSC_CM_Reporter_37


title: Microdissected Mice Renal PT-S1, Sham4_72h, RNA-Seq, Transcriptome 02 [72h_PT_sham4_2]


title: n=2, T7, Kon LN 13

description:
21
21_Kon_LN_13_S21

value: prostate adenocarcinoma cells


title: Microdissected Mice Renal PT-S1, UNx1_72h, RNA-Seq, Transcriptome 02 [72h_PT_unx1_2]


title: SCVI-111_hiPSC_CM_Reporter_38


title: B18 MO

value: MO

value: 180 minutes of transportation


title: Microdissected Mice Renal PT-S1, Sham4_72h, RNA-Seq, Transcriptome 01 [72h_PT_sham4_1]


title: SCVI-111_hiPSC_CM_Reporter_34


title: Microdissected Mice Renal PT-S1, Sham3_72h, RNA-Seq, Transcriptome 03 [72h_PT_sham3_3]


title: B17 MO


title: n=2, T3, Koku LN 13

description:
19
19_Koku_LN_13_S19

value: co-culture

value: three days


title: SCVI-111_hiPSC_CM_Reporter_33

value: hiPSC-derived cardiomyocytes

value: Day 15


title: Microdissected Mice Renal PT-S1, Sham3_72h, RNA-Seq, Transcriptome 01 [72h_PT_sham3_1]


title: B16 MO


title: n=2, T3, Kon p21

description:
18
18_Kon_p21_S18

value: primary stromal cells

value: control co-culture


title: SCVI-111_hiPSC_CM_Reporter_32

value: SCVI-111 TBX5-Lineage Reporter Line


title: n=2, T1, Koku p21

description:
16
16_Koku_p21_S16

value: one day


title: n=2, T3, Kon LN 13

description:
17
17_Kon_LN_13_S17


title: SCVI-111_hiPSC_CM_Reporter_31


title: n=2, T7, Kon p21

description:
22
22_Kon_p21_S22


title: Microdissected Mice Renal PT-S1, Sham2_72h, RNA-Seq, Transcriptome 03 [72h_PT_sham2_3]

value: Kidney

value: WT


title: B15 MO

value: Muscle


title: Microdissected Mice Renal PT-S1, Sham2_72h, RNA-Seq, Transcriptome 01 [72h_PT_sham2_1]

value: Sham


title: B19 MI

value: MI

value: 30 minutes of transportation


title: SCVI-111_hiPSC_CM_Reporter_35


title: n=2, T3, Koku p21

description:
20
20_Koku_p21_S20


title: B14 MO


title: n=2, T1, Koku LN 13

description:
15
15_Koku_LN_13_S15

value: LNCaP

value: prostate adenocarcinoma cells


title: B13 MO

value: MO

value: 180 minutes of transportation


title: SCVI-111_hiPSC_CM_Reporter_30


title: Microdissected Mice Renal PT-S1, Sham1_72h, RNA-Seq, Transcriptome 01 [72h_PT_sham1_1]


title: n=2, T1, Kon p21

description:
14
14_Kon_p21_S14


title: Microdissected Mice Renal PT-S1, Sham1_72h, RNA-Seq, Transcriptome 03 [72h_PT_sham1_3]


title: SCVI-111_hiPSC_CM_Reporter_29


title: n=2, T1, Kon LN 13

description:
13
13_Kon_LN_13_S13


title: SCVI-111_hiPSC_CM_Reporter_28


title: Microdissected Mice Renal PT-S1, UNx4_24h, RNA-Seq, Transcriptome 03 [24h_PT_unx4_3]

value: UNx


title: SCVI-111_hiPSC_CM_Reporter_27

value: hiPSC-derived cardiomyocytes


title: Microdissected Mice Renal PT-S1, UNx4_24h, RNA-Seq, Transcriptome 02 [24h_PT_unx4_2]


title: n=1, T7, Koku LN 03

description:
11
11_Koku_LN_03_S11

value: co-culture

value: seven days


title: SCVI-111_hiPSC_CM_Reporter_26

value: Day 15


title: B10 MO


title: SCVI-111_hiPSC_CM_Reporter_24

value: SCVI-111 TBX5-Lineage Reporter Line


title: Microdissected Mice Renal PT-S1, UNx4_24h, RNA-Seq, Transcriptome 01 [24h_PT_unx4_1]


title: SCVI-111_hiPSC_CM_Reporter_25


title: B9 CL

value: CL


title: Microdissected Mice Renal PT-S1, UNx3_24h, RNA-Seq, Transcriptome 03 [24h_PT_unx3_3]

value: Kidney


title: B8 CL

value: non transported goats


title: n=1, T7, Kon LN 03

description:
9
9_Kon_LN_03_S9

value: control co-culture


title: n=1, T7, Kon p21

description:
10
10_Kon_p21_S10

value: primary stromal cells


title: n=1, T3, Koku p21

description:
8
8_Koku_p21_S8

value: three days


title: Microdissected Mice Renal PT-S1, UNx2_24h, RNA-Seq, Transcriptome 02 [24h_PT_unx2_2]

value: WT


title: SCVI-111_hiPSC_CM_Reporter_23


title: Microdissected Mice Renal PT-S1, UNx3_24h, RNA-Seq, Transcriptome 01 [24h_PT_unx3_1]


title: n=1, T3, Koku LN 03

description:
7
7_Koku_LN_03_S7

value: LNCaP


title: B7 CL

value: Muscle


title: Microdissected Mice Renal PT-S1, UNx2_24h, RNA-Seq, Transcriptome 03 [24h_PT_unx2_3]


title: SCVI-111_hiPSC_CM_Reporter_22


title: B6 CL


title: n=1, T7, Koku p21

description:
12
12_Koku_p21_S12


title: B11 MO

value: MO


title: SCVI-111_hiPSC_CM_Reporter_21


title: B12 MO

value: 180 minutes of transportation


title: n=1, T3, Kon p21

description:
6
6_Kon_p21_S6


title: Microdissected Mice Renal PT-S1, UNx1_24h, RNA-Seq, Transcriptome 02 [24h_PT_unx1_2]

value: UNx


title: SCVI-111_hiPSC_CM_Reporter_20

value: hiPSC-derived cardiomyocytes


title: B5 CL


title: B4 CL


title: B3 CL


title: SCVI-111_hiPSC_CM_Reporter_19


title: n=1, T1, Koku p21

description:
4
4_Koku_p21_S4

value: co-culture

value: one day


title: Microdissected Mice Renal PT-S1, Sham3_24h, RNA-Seq, Transcriptome 02 [24h_PT_sham3_2]

value: Sham


title: Microdissected Mice Renal PT-S1, Sham3_24h, RNA-Seq, Transcriptome 03 [24h_PT_sham3_3]


title: n=1, T1, Koku LN 03

description:
3
3_Koku_LN_03_S3

value: prostate adenocarcinoma cells


title: SCVI-111_hiPSC_CM_Reporter_18

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: Microdissected Mice Renal PT-S1, Sham3_24h, RNA-Seq, Transcriptome 01 [24h_PT_sham3_1]

value: Kidney


title: n=1, T1, Kon LN 03

description:
1
1_Kon_LN_03_S1

value: control co-culture


title: Microdissected Mice Renal PT-S1, Sham2_24h, RNA-Seq, Transcriptome 02 [24h_PT_sham2_2]


title: A27 MI

value: Blood

value: MI

value: 30 minutes of transportation


title: n=1, T1, Kon p21

description:
2
2_Kon_p21_S2

value: primary stromal cells


title: SCVI-111_hiPSC_CM_Reporter_16


title: SCVI-111_hiPSC_CM_Reporter_15


title: SCVI-111_hiPSC_CM_Reporter_17


title: Microdissected Mice Renal PT-S1, Sham2_24h, RNA-Seq, Transcriptome 01 [24h_PT_sham2_1]

value: WT


title: A24 MI


title: Microdissected Mice Renal PT-S1, Sham1_24h, RNA-Seq, Transcriptome 03 [24h_PT_sham1_3]