title: HTR5-HA

city: Shanghai

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

institute: Fudan University

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The trimmed reads were mapped to the Arabidopsis reference genome by Bowtie2 and the reads mapped to chloroplast or mitochondrial genomes were filtered.
SAMtools was used to remove reads with low mapping quality and potential PCR duplicates.
BamCoverage and computeMatrix tool in deepTools were used to calculate the enrichment level (RPKM) from 1kb upstream of the TSS to 1kb downstream of the TTS.
Average density profile was plotted in R and a heatmap was generated using the plotHeatmap tool in deepTools.
SICER was used to find peaks and differentially enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigwig

growth_protocol: Arabidopsis thaliana seedlings were grown on MS medium under 16-h light/8-h dark conditions at 22°C for 14 days.

extract_protocol:
ChIP experiment was referred to the previous study (PMID: 28138017).
ChIP-seq library construction was referred to the previously study (PMID: 31278262).

value: seedlings

value: anti-HA


title: Molm-13 cells treated by TP-0184, replicate #3

status: Public on Apr 01 2023

type: SRA

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

country: USA

institute: Houston Methodist Cancer Center

description:
Molm_13_Treated_3
Genes_fpkm_expression.xlsx, Column S, FPKM values
Genes_fpkm_expression.xlsx, Column AN, Raw Counts

library_source: transcriptomic

data_processing:
Used Cutadapt to remove low quality bases, followed by FastQC
Used HISAT2 to map reads to reference genome
Used StringTie for read assembly
Used gffcompare to reconstruct the transcriptome
Used StringTie and edgeR to estimate expression levels for all transcripts
Assembly: Release 101 (August 2020) of the Homo Sapiens reference genome from Ensemble
Supplementary files format and content: Excel file including PRKM and raw count for each gene in each sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Following treatment, the cells were washed with PBS, and RNA extraction was performed with a QIAGEN RNA extraction kit according to the manufacturer’s protocol.
A poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: FLT3-mutated AML cells were cultured and treated with TP-0184 at 200 nM for 48 h

tag: cell line

tag: cell type

value: AML cell

tag: genotype

value: FLT3 mutated

tag: treatment

value: TP-0184 at 200nM for 48 hours


title: Molm-14 cells treated by TP-0184, replicate #1

description:
Molm_14_Treated_1
Genes_fpkm_expression.xlsx, Column T, FPKM values
Genes_fpkm_expression.xlsx, Column AO, Raw Counts


title: Col-Input

country: China

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

tag: chip antibody


title: Col-HA


title: Adult_nphx_1398

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

molecule: total RNA

organism: Mus musculus

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: strain

value: FACS sorted


title: Molm-14 cells treated by TP-0184, replicate #2

description:
Molm_14_Treated_2
Genes_fpkm_expression.xlsx, Column U, FPKM values
Genes_fpkm_expression.xlsx, Column AP, Raw Counts


title: HTR5-Input


title: arp6_input

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The trimmed reads were mapped to the Arabidopsis reference genome by Bowtie2 and the reads mapped to chloroplast or mitochondrial genomes were filtered.
SAMtools was used to remove reads with low mapping quality and potential PCR duplicates.
BamCoverage and computeMatrix tool in deepTools were used to calculate the enrichment level (RPKM) from 1kb upstream of the TSS to 1kb downstream of the TTS.
Average density profile was plotted in R and a heatmap was generated using the plotHeatmap tool in deepTools.
SICER was used to find peaks and differentially enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigwig format

source_name: seedlings

tag: ecotype

tag: tissue


title: hiPS_MFN2KO_11-8_1

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

country: Japan

institute: Fujita Health University

description:
hMFN2 knockout hiPS cells
hiPS_MFN2KO_11-8_1_S7

data_processing:
After trimming adaptor sequences and low-quality bases with cutadapt-1.18.
the sequenced reads were mapped to the reference genome with STAR v 2.6.0c, with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for each gene were calculated using htseq-count v0.11.2 with the GENCODE gtf file.
Gene expression levels were determined as transcripts per million (TPM) , and differentially expressed genes were identified with DESeq2 v1.30.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: MFN2-/- (tet-MYOD1)

growth_protocol: Human iPS cells were cultured on iMatrix-coated dishes in StemFit AK02 medium.

extract_protocol:
NucleoSpin RNA plus XS (Macherey-Nagel)
The 100 ng of total RNAs were used as starting materials to generate RNA-seq libraries with the TruSeq Stranded mRNA LT sample prep kit (Illumina).

value: iPS

value: StemFit AK02


title: Molm-13 cells treated by TP-0184, replicate #2

description:
Molm_13_Treated_2
Genes_fpkm_expression.xlsx, Column R, FPKM values
Genes_fpkm_expression.xlsx, Column AM, Raw Counts


title: arp6_H3


title: Adult_nphx_1396


title: Adult_nphx_1397


title: hiPS_MYOD_11_3

description:
control hiPS cells 2
hiPS_MYOD_11_3_S6

source_name: wildtype control (tet-MYOD1)


title: hiPS_MFN2KO_11-8_2

description:
hMFN2 knockout hiPS cells
hiPS_MFN2KO_11-8_2_S8


title: Molm-13 cells treated by TP-0184, replicate #1

description:
Molm_13_Treated_1
Genes_fpkm_expression.xlsx, Column Q, FPKM values
Genes_fpkm_expression.xlsx, Column AL, Raw Counts


title: Adult_nphx_1395


title: atchz1ab_input


title: arp6_H2AZ


title: Treatment1

city: Charlottesville

first: Agnieszka

last: Swiatecka-Urban

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia School of Medicine

data_processing:
The microRNA sequencing data were analyzed using the GeneGlobe Data Analysis bioinformatics pipeline from Qiagen
The raw QIAseq miRNA sequencing files were uploaded to GeneGlobe Data Analysis Center (Qiagen) for quality control, alignment to the human reference genome (GRCh38), and expression quantification.
Briefly, 3’adapter and low-quality bases were trimmed off from reads using Cutadapt. Reads with less than 16 bp insert sequences or with less than 10 bp unique molecular identifier (UMI) sequences were discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2. All reads assigned to a particular miRNA or piRNA ID were counted and the associated UMIs were clustered to count unique molecules.
The primary analysis output file was downloaded from GeneGlobe.
Assembly: GRCh38
Supplementary files format and content: Differential analysis results in an excel file.

source_name: Parental CFBE 41o-Cells, TGF-beta, 24hrs

extract_protocol:
Total RNA was isolated by using Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. An on-column DNase (Zymo Research) treatment was added to remove contamination with genomic DNA
The starting material, 100 ng of total RNA was used with the QIAseqTM miRNA Library Kit (Qiagen, Maryland, MD, USA), following the manufacturer’s instruction. The RNA quantity and quality were verified by Qubit 2.0 Fluorometer, and Agilent Bioanalyzer Tapestation 2200. In short, 3’ and 5’ adapters were ligated to total input RNA. Reverse transcription, followed by PCR, was used to create cDNA constructs. This process selectively enriches those fragments that have adapter molecules on both ends. PCR was performed with primers that anneal to the ends of the adapters. Quality was examined using Agilent Bioanalyzer Tapestation 2200 and Qubit 2.0 Fluorometer with miRNA library pre-sequencing QC protocol mentioned in the QIAseqTM miRNA Library Kit. The cDNA libraries were pooled at a final concentration of 2.5 pM
Cluster generation and 75 base-pair (bp) single-read single-indexed sequencing was performed on Illumina NextSeq 500

value: Parental CFBE 41o-Cells

value: Epithelial Cells

value: WT

value: TGF-beta


title: MV4-11 cells treated by TP-0184, replicate #3

description:
MV4_11_Treated_3
Genes_fpkm_expression.xlsx, Column P, FPKM values
Genes_fpkm_expression.xlsx, Column AH, Raw Counts


title: atchz1ab_H3


title: Adult_nphx_1394


title: Adult_nphx_1393


title: hiPS_201B7_3

description:
control hiPS cells 1
hiPS_201B7_3_S3

source_name: wildtype control (201B7)


title: atchz1ab_H2AZ


title: MV4-11 cells treated by TP-0184, replicate #2

description:
MV4_11_Treated_2
Genes_fpkm_expression.xlsx, Column O, FPKM values
Genes_fpkm_expression.xlsx, Column AG, Raw Counts


title: MV4-11 cells treated by TP-0184, replicate #1

description:
MV4_11_Treated_1
Genes_fpkm_expression.xlsx, Column N, FPKM values
Genes_fpkm_expression.xlsx, Column AF, Raw Counts


title: Adult_nphx_1392


title: Col_input


title: Col_H3


title: hiPS_201B7_2

description:
control hiPS cells 1
hiPS_201B7_2_S2


title: Adult_nphx_1391


title: T cell receptor single cell library replicate 3

city: Seattle

first: Thomas

middle: Heyward

last: Pulliam

state: WA

address: 850 Republican St.

institute: University of Washington

description:
V(D)J TCR library
Z1471C_TCR

library_source: other

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Raw sequencing reads were aligned to the hg38 genome using Cell Ranger v.3.1. Filtered counts matrices of transcripts and feature barcoding counts were loaded into a SingleCellExperiment object for further analyses in R (v.4.1.2).  Sample hash deconvolution was performed using DropletUtils (v.1.14.2). Doublets detection and removal was performed using scds (v.1.10.0) in conjunction with doublets detected during hash deconvolution. Cells with less than 800 transcript reads, less than 250 genes detected or more than 10% of mitochondrial DNA were excluded as low quality.
Assembly: GRCh38
Supplementary files format and content: Feature barcode samples (ie ADT): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

source_name: Tumor & Blood

growth_protocol: Fresh MCC tumor specimens from needle cores, punch biopsies, or surgical excisions were processed into single-cell digests by mincing them into small pieces with sterile forceps and scissors, followed by incubation in 20 mL of digestion medium composed of RPMI plus 0.002g DNase (Worthington Biochemical, Lakewood NJ), 0.008g collagenase (Worthington Biochemical, Lakewood NJ), and 0.002 g hyaluronidase (Worthington Biochemical, Lakewood NJ) in a 10 cm dish at 37°C with frequent, gentle swirling. After 3 hours of digestion, cells were strained through a 70 μm filter, centrifuged, resuspended in freezing medium , and cryopreserved. Heparinized whole blood from MCC patients was processed at the Specimen Processing Lab (Fred Hutchinson Cancer Center). Peripheral blood mononuclear cells (PBMC) were isolated by routine Ficoll density gradient centrifugation and cryopreserved in liquid nitrogen.

extract_protocol: Viable cells were enriched via FACS and brought to a concentration of 700-1,200 viable cells per microliter using a hemacytometer. These single cell suspensions were then loaded into the appropriate microfluidic chip (chip G; 10x Genomics) and run through a Chromium controller to obtain Gel Beads-in-Emulsion (10x Genomics). Resulting cell suspensions then went through a library preparation process for single-cell RNA sequencing (scRNA-seq) along with paired scV(D)J-seq for T-cell receptor (TCR) clonotypes using the 5′ transcriptome kit with feature barcoding (V1.1; 10x Genomics) following the manufacturer's guidelines. The complementary DNA libraries were then sequenced with 2 × 92 base pair paired-end reads aiming for an average of 25,000 reads/cell for gene expression librareis and 5,000 reads/cell for ADT and V(D)J libraries

value: Tumor & Blood

value: T cells expanded with phytohemagglutinin-purified mitogen, IL2 and IL15

tag: library type

value: TCR


title: Col_H2AZ


title: T cell receptor single cell library replicate 2

description:
V(D)J TCR library
Z1471B_TCR


title: Adult_nphx_1390


title: hiPS_MYOD_11_2

description:
control hiPS cells 2
hiPS_MYOD_11_2_S5


title: atchz1ab arp6_rep3

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the genome of Arabidopsis thaliana (TAIR10) using Hisat2.
SAMtools was used to obtain high mapping quality reads.
FeatureCounts was used to calculate the reads count of genes.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include featureCounts for each Sample

extract_protocol:
RNA was extracted using RNAprep pure Plant Kit (Tiangen Biotech).
RNA-seq library construction was performed according to the instructions of KAPA stranded mRNA-seq Kit (Kapa Biosystems).

value: atchz1ab arp6-1


title: T cell receptor single cell library replicate 1

description:
V(D)J TCR library
Z1471A_TCR


title: Normal pancreatic tissue 1 [CR560569]

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

data_processing:
The sequence data were demultiplexed and converted to FASTQ files using Illumina’s bcl2fastq Conversion Software (v2.19).
The adapter contamination and poor-quality sequences were removed from FASTQ files using the program Trimmomatic (v0.36).
FASTQ files were then mapped to the human reference genome GRCh38 using the RNA-seq aligner STAR (v2.5b: https://github.com/alexdobin/STAR).
The JE-Suite procedure was used to estimate duplication levels, using a Unique Molecule Identifier program to deduplicate, and then mark the reads that are the result of PCR amplification.
The reads per transcript were counted using the program FeatureCounts (v1.4.6p5) followed by normalisation, modeling and differential expression analysis using the SARTools (v1.3.2) package.
Assembly: GRCh38
Supplementary files format and content: PDAC-vs-Normal-Pancreas-RNA-seq.xlsx

source_name: pancreas

extract_protocol:
RNA was extracted using the Maxwell® RSC SimplyRNA Tissue Kit (Promega Ltd UK, Cat # AS1340)
RNA-seq libraries were generated using the KAPA mRNA Library HyperPrep Kit for Illumina® following the manufacturer’s instructions and sequenced using an Illumina NextSeq 500 instrument.

value: pancreas

tag: tissue type

value: Normal pancreatic tissue


title: Normal pancreatic tissue 3 [CR561640]


title: hiPS_MYOD_11_1

description:
control hiPS cells 2
hiPS_MYOD_11_1_S4


title: Normal pancreatic tissue 2 [CR562915]


title: Adult_nphx_1389


title: Adult_nphx_1388


title: Gene expression and antibody derived tags replicate 2

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1471B_GEX

value: GEX/ADT


title: atchz1ab arp6_rep2

value: seedlings


title: Moderately differentiated PDAC 2 [R2700]

value: Moderately differentiated PDAC


title: Adult_nphx_1387


title: Gene expression and antibody derived tags replicate 1

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1471A_GEX


title: atchz1ab arp6_rep1


title: hiPS_201B7_1

description:
control hiPS cells 1
hiPS_201B7_1_S1


title: single cell V(D)J (T cell receptor) library from patient w876

description:
V(D)J TCR library
w876_TCR


title: Moderately differentiated PDAC 1 [R2824]


title: arp6_rep3


title: Adult_nphx_1386


title: Gene expression and antibody derived tags replicate 3

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1471C_GEX


title: Adult_nphx_1385


title: arp6_rep2


title: single cell V(D)J (T cell receptor) library from patient Z1493

description:
V(D)J TCR library
Z1493_TCR


title: Poorly differentiated PDAC 2 [R2944]

value: Poorly differentiated PDAC


title: Poorly differentiated PDAC 1 [R2971]


title: arp6_rep1


title: Adult_nphx_1384

value: FACS sorted


title: atchz1ab hta9hta11_rep3

value: atchz1ab hta9-1hta11-2


title: Adult_nphx_1382


title: Adult_nphx_1381


title: Adult_nphx_1383


title: miRNA-Seq cancer 1

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

description:
cancer 1
Qiagen Rneasy (b-mercaptoethanol lysis buffer)
ACCAGT

data_processing:
Single-end reads were aligned to Ensembl GRCh38 human genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Assembly: hsa38
Supplementary files format and content: tab-delimited text file include table with raw gene counts for every gene and every sample

source_name: endothelial cell line

growth_protocol: Endothelial cells were established according to the method previously described  [21]  (CNRS patent  99-16169).  The  samples  of  healthy  tissue  and  primary  breast  tumor  were  named  HBH.MEC  and  HBCa.MEC, respectively. Both cell lines were seeded at density 5 × 104cells/10cm2on Primaria Tissue  Culture Flask (Corning, NY, USA, #353808) in the presence of Opti-MEM I Reduced Serum Medium  (Gibco, Paisley, UK #31985070) supplemented with 2% (vol/vol) fetal bovine serum (Gibco, Paisley,  UK #A3840402). Cell lines were maintained at 37 °C and 5% CO2  in humidified atmosphere. After  cell culture in the described conditions, the cell were detached with Accutase supplied in Dulbecco’s  PBS  containing  0.5  mM  EDTA  and  phenol  red  (Invitrogen,  Carlsbad,  CA,  USA  #E136579).  Additionally, all cells were negative for mycoplasma (PromoKine, Hamburg, Germany #PK-CA91- 1096).

extract_protocol:
Total RNA was extracted from endothelial cells  using RNeasy Mini Kit (Qiagen, Germany). The samples were freed from DNA using TURBO DNA-free kit (Thermo Fisher Scientific, USA) .
RNA concentration and integrity was measured with UV-Vis spectrophotometry (Nanodrop  2000c,  Thermo  Fisher)  and  the  Fragment  Analyzer  System  using  the  DNF-471  RNA  Kit  (15  nt)  (Agilent,  Santa  Clara,  CA,  USA),  respectively.  As  per  manufacturer’s  protocol,  the  libraries  were  generated using 100ng RNA samples with Small RNA-SeqLibrary Prep Kit (Lexogen,  Vienna, Austria,  #052UG128V0110). Then, cDNA library with adapters for sequencing was prepared and pooled in an  equimolar ratio. The concentration and the size distribution of the final lane mix was analyzed by Qubit  dsDNA HS assay (Thermo Fisher Scientific, Waltham, MA, USA) and by a Fragment Analyzer system  using the DNF-474 HS NGS Fragment Kit (1–6000 bp) (Agilent, Santa Clara, CA, USA). Dilution of  the lane mix (2 nm) was denatured and diluted to loading concentration for sequencing on a NextSeq  500  instrument  with  a  SR75  High  Output  Kit  (Illumina).  Differentially  expressed  miRNA  (DEmiRNAs) were classified according to −1 < logFC > 1, adjusted p-value—FDR (False Discovery  Rate) <0.05.

treatment_protocol: Cell culture as above

value: cancer tissue

tag: replicate

value: biol replicate 1


title: single cell V(D)J (T cell receptor) library from patient Z1249

description:
V(D)J TCR library
Z1249_TCR


title: single cell V(D)J (T cell receptor) library from patient Z1493 (a tech rep at a later date to increase the no. of cells)

description:
V(D)J TCR library
Z1493B_TCR


title: miRNA-Seq cancer 2

description:
cancer 2
Qiagen Rneasy (b-mercaptoethanol lysis buffer)
TGCACG

value: biol replicate 2


title: atchz1ab hta9hta11_rep1


title: atchz1ab hta9hta11_rep2


title: single cell V(D)J (T cell receptor) library from patient Z1308

description:
V(D)J TCR library
Z1308_TCR


title: miRNA-Seq healthy 2

description:
healthy 2
Qiagen Rneasy (b-mercaptoethanol lysis buffer)
GATCAC

value: normal tissue


title: miRNA-Seq healthy 1

description:
healthy 1
Qiagen Rneasy (b-mercaptoethanol lysis buffer)
CAGCGT


title: single cell V(D)J (T cell receptor) library from patient Z1227

description:
V(D)J TCR library
Z1227_TCR


title: hta9hta11_rep3


title: Adult_nphx_1380


title: Adult_nphx_1379


title: single cell V(D)J (T cell receptor) library from patient Z1082

description:
V(D)J TCR library
Z1082_TCR


title: hta9hta11_rep2


title: hta9hta11_rep1


title: Adult_nphx_1378


title: Gene Expression and surface protein counts from patient w876

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
w876_GEX


title: Adult_nphx_1377

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv


title: Human, normal, rep1

city: La Jolla

first: Takuya

last: Nakagawa

state: CA

address: 3855 Health Sciences Dr

department: Moores Cancer Center

institute: UC San Diego

library_source: transcriptomic single cell

data_processing:
We used Cell Ranger 2.1.1 for primary analysis and used Seurat R package for the secondary analysis
we used the count function in Cell Ranger to align reads to the hg19 reference genome (v.1.2.0 prepared by 10X Genomics). [https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/1.2/]
Cells with >5% mitochondrial reads and <30 features were determined to be low quality and were removed from the dataset.
We used the IntegrateData function from Seurat to align datasets by common sources of variation.
Cluster markers of differentially expressed genes were determined by the Wilcoxon rank sum test using Seurat function FindMarkers
Assembly: hg19
Supplementary files format and content: barcodes.tsv, genes.tsv, and matrix.mtx files.

molecule: nuclear RNA

source_name: Salivary gland

growth_protocol: mammalian organism

extract_protocol:
gentleMACS
Chromium Single-Cell 3′ Library Construction Kit v3 (10x Genomics, 1000075)
single nucleus RNA-seq

value: Salivary gland

value: normal salivary gland cell

value: no treatment


title: Human, normal, rep2


title: Human, normal, rep3


title: Gene Expression and surface protein counts from patient Z1493

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1493_GEX

value: Tumor & Blood


title: atchz1ab_rep3


title: Adult_nphx_1376


title: single cell V(D)J (T cell receptor) library from patient Z1210

description:
V(D)J TCR library
Z1210_TCR

value: TCR


title: SYK_A_PHH_siMARC1_Plate_2_FFA_800uM_Rep5

city: Oxford

first: Robert

last: Kitchen

address: Novo Nordisk Ltd, Innovation Building, Roosevelt Drive

institute: Novo Nordisk

data_processing:
Quality control and adaptor trimming were performed with FastQC (v. 0.11.9) and Trim Galore! (v. 0.6.4_dev).
STAR (v. 2.7.3a) was used for alignment and gene-level quantification against the Ensembl (v91) GRCh38 transcriptome annotation.
Assembly: GRCh38 genome and Ensembl v91 annotation
Supplementary files format and content: counts_matrix_for_GEO_final.csv: Comma-separated text file

source_name: PHH

growth_protocol: Cryoplatable PHH (BioreclamationIVT, M00995-P and F00995-P) were thawed and plated in INVITROGRO CP Medium (BioreclamationIVT, Z99029) containing TORPEDO™ Antibiotic Mix (BioreclamationIVT, Z99000) at a seeding density of 58,000-70,000 cells/well into collagen-coated 96-well plates (Perkin Elmer collagen-coated CellCarrier-96 Ultra, 6055708). 24 hours post thaw cells were washed with PBS and fed with modified 5C PHH maintenance medium, all components (except B27) listed in Supplementary Table 4 were combined and filtered using a 0.22 µm sterile filter after which B27 minus Insulin was added and media was refreshed every 2-3 days. PHH donors used are presented in Supplementary Table 5. PHH were transfected 7 days post seeding at a final concentration of 30nM siRNA, and 0.3µL RNAiMAX (Invitrogen, 13778-150) in OptiMEM (Gibco, 31985062).

extract_protocol:
For transcriptome sequencing, mRNA was isolated from siRNA transfected PHH treated with either 0 or 800 µM FFA mix using the Dynabeads mRNA DIRECT Purification Kit (Invitrogen, 61012).
Extracted mRNA was used to prepare Illumina compatible sequencing libraries with QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Cat. No: 15) based on the manufacturer’s protocol. The final sequencing libraries were pooled and sequenced using the Illumina NextSeq 500 system.

treatment_protocol: Dharmacon ON-TARGETplus human SMARTpool siRNAs for MTARC1 (L019358020010), DGAT2 (L009333000005) and NT (D0018101020) were used. FFA mix was produced as described previously, with a modified FFA ratio for oleic acid (Sigma, O1008), palmitic acid (Sigma, P0500), linoleic acid (Sigma, L1376), and ɑ-linolenic acid (Sigma, L039) of 45:30:24:0.01. Cells were treated with either 0 or 800 µM FFA mix diluted in modified 5C PHH maintenance medium for 72 hours at 37 ˚C and 5% CO2 prior to collection. The 800 µM FFA mix condition was supplemented with 2 mM Fructose (Sigma, F3510) and the 0 µM FFA mix condition used 10% (w/v) BSA (Sigma, A8806) in place of the FFA mix.

value: PHH

value: primary human hepatocyte

value: WT

tag: sirna

tag: donor id

value: SYK

tag: perturbation


title: atchz1ab_rep2

value: seedlings


title: Adult_nphx_1375


title: SYK_A_PHH_siMARC1_Plate_2_FFA_800uM_Rep4


title: Col_rep3

value: wild-type


title: atchz1ab_rep1


title: Adult_nphx_1374

value: FACS sorted


title: Col_rep2


title: SYK_A_PHH_siMARC1_Plate_2_FFA_800uM_Rep3


title: Adult_nphx_1373


title: Gene Expression and surface protein counts from patient Z1249

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1249_GEX

value: GEX/ADT


title: Gene Expression and surface protein counts from patient Z1308

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1308_GEX


title: SYK_A_PHH_siMARC1_Plate_2_FFA_800uM_Rep2


title: Gene Expression and surface protein counts from patient Z1493 (a tech rep at a later date to increase the no. of cells)

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1493B_GEX


title: Gene Expression and surface protein counts from patient Z1227

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1227_GEX


title: SYK_A_PHH_siMARC1_Plate_2_FFA_800uM_Rep1


title: Adult_nphx_1372


title: Gene Expression and surface protein counts from patient Z1210

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1210_GEX


title: Col_rep1


title: SYK_A_PHH_siMARC1_Plate_2_FFA_0uM_Rep5


title: SP70leaf_PARE

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Library strategy: PARE-Seq
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file

organism: Saccharum hybrid cultivar SP70-1143

source_name: young leaf

extract_protocol: Small RNA libraries and PARE libraries were constructed from total RNA isolated from young leaves of sugarcane using Trizol Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). And the PARE library preparation protocol is based on Illumina’s TruSeq RNA  Sequencing Sample Preparation Guide (Illumina, San Diego, CA) The libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE).

value: young leaf

tag: cultivar

tag: age

value: mature plants


title: SP70leaf_sRNA

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file


title: Adult_nphx_1371


title: SYK_A_PHH_siMARC1_Plate_2_FFA_0uM_Rep4


title: SYK_A_PHH_siMARC1_Plate_2_FFA_0uM_Rep3


title: Gene Expression and surface protein counts from patient Z1082

description:
Antibody or MHC multimer-derived oligonucleotide (ADT)
Z1082_GEX


title: Adult_nphx_1369


title: Sbarleaf_PARE

organism: Saccharum barberi

value: Khagzi


title: SYK_A_PHH_siMARC1_Plate_2_FFA_0uM_Rep2


title: SYK_A_PHH_siMARC1_Plate_2_FFA_0uM_Rep1


title: Adult_nphx_1368


title: Sbarleaf_sRNA


title: RBleaf_PARE

organism: Saccharum hybrid cultivar RB867515


title: Expanded_TIL_TCR_4B

description: V(D)J TCR library

data_processing:
Raw sequencing reads were aligned to the hg38 genome using Cell Ranger v.3.1. Filtered counts matrices of transcripts and feature barcoding counts were loaded into a SingleCellExperiment object for further analyses in R (v.4.1.2).  Sample hash deconvolution was performed using DropletUtils (v.1.14.2). Doublets detection and removal was performed using scds (v.1.10.0) in conjunction with doublets detected during hash deconvolution. Cells with less than 800 transcript reads, less than 250 genes detected or more than 10% of mitochondrial DNA were excluded as low quality.
Assembly: GRCh38
Supplementary files format and content: Feature barcode samples (ie ADT): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) without gene expression library sequencing

source_name: Tumor

growth_protocol: To expand T cells from tumors, tumor tissue was chopped into small pieces and placed in a culture along with 106 allogenic irradiated peripheral blood mononuclear cells (PBMCs), Remel phytohemagglutinin-purified mitogen (1.6 μg/mL; ThermoFisher), human recombinant IL15 (10 ng/mL; R&D Systems), and human natural interleukin 2 (32 U/mL; Hemagen, Columbia, MD).

extract_protocol: Multimer binding CD8 T cells were enriched via FACS and brought to a concentration of 700-1,200 viable cells per microliter using a hemacytometer. These single cell suspensions were then loaded into the appropriate microfluidic chip (chip G; 10x Genomics) and run through a Chromium controller to obtain Gel Beads-in-Emulsion (10x Genomics). Resulting cell suspensions then went through a library preparation process for single-cell RNA sequencing (scRNA-seq) along with paired scV(D)J-seq for T-cell receptor (TCR) clonotypes using the 5′ transcriptome kit with feature barcoding (V1.1; 10x Genomics) following the manufacturer's guidelines. The complementary DNA libraries were then sequenced with 2 × 92 base pair paired-end reads aiming for an average of 5,000 reads per cell per library according to 10x Genomics guidelines.

value: Tumor

value: T cells expanded with phytohemagglutinin-purified mitogen, IL2 and IL15


title: Expanded_TIL_TCR_3A

description: V(D)J TCR library


title: Adult_nphx_1366


title: Expanded_TIL_TCR_3B

description: V(D)J TCR library


title: Adult_nphx_1367


title: Adult_nphx_1365


title: Expanded_TIL_TCR_2B

description: V(D)J TCR library


title: RBleaf_sRNA


title: SYK_A_PHH_siCtrl_Plate_2_FFA_800uM_Rep4

value: siCtrl


title: Expanded_TIL_TCR_2A

description: V(D)J TCR library


title: SYK_A_PHH_siCtrl_Plate_2_FFA_800uM_Rep5


title: SYK_A_PHH_siCtrl_Plate_2_FFA_800uM_Rep3


title: Adult_nphx_1370


title: Adult_nphx_1364


title: SYK_A_PHH_siCtrl_Plate_2_FFA_800uM_Rep2


title: SI-GA-F1

city: Helsinki

first: Jenni

last: Lahtela

address: Tukholmankatu 8

department: Institute for Molecular Medicine Finland FIMM

country: Finland

institute: University of Helsinki

description: poly-A-tail captured mRNA

data_processing:
26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 98bp (Read 2).
Cell Ranger v1.3 mkfastq pipeline was used to demultiplex and convert Chromium single cell 3’ RNA-sequencing barcode and read data to FASTQ files.
Cell Ranger v1.3 count pipeline was used to generate align reads and gene-cell matrix.
The gene-barcode matrixes were analysed using Seurat 2.0.1 package [Macosco et al. 2015, Satija et al. 2015] along with R 3.4.0 . First, the data was normalized to 10,000 molecules and log-scaling was performed as described in Macosco et al. 2015. Genes that were detected only in a one cell were excluded from the analysis. No further filtering based on total UMIs (unique molecular identifier) or the percentage of mitochondrial genes was performed. Also, no removal of variation originating from UMIs or mitochondrial UMI counts was performed.
Assembly: GRCh38
Supplementary files format and content: RBC_SC_transcriptome.txt: Tab-delimited text file

source_name: Red blood cell unit

extract_protocol:
Leukoreduced red blood cell preparation.
10x Genomics Chromium Single Cell 3’ Library preparation protocol.

value: Peripheral blood

value: Leukoreduced red blood cell unit


title: SI-GA-E1

description: poly-A-tail captured mRNA

source_name: Fresh red blood cell extract

value: Fresh red blood cell extract


title: Expanded_TIL_TCR_1A

description: V(D)J TCR library

value: TCR


title: Adult_nphx_1363


title: Expanded_TIL_Feature_barcodes_4B

description: Antibody or MHC multimer-derived oligonucleotide (ADT)

molecule: protein

value: ADT


title: Expanded_TIL_TCR_4A

description: V(D)J TCR library


title: F-C6 post 7 days assay

first: Matteo

last: Righi

state: London

address: The MediaWorks, 191 Wood Ln

institute: Autolus Therapeutics

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: CAR-T cells

extract_protocol:
mRNA was extracted with the illustra™ RNAspin Mini RNA Isolation Kit (GE Healthcare)
Roughly 40 million paired end reads (150 bp) were sequenced on Illumina Hiseq sequencer (GeneWiz)

tag: cell donor

value: T cells

tag: time

value: post 7 days assay


title: Adult_nphx_1362

tag: cell type


title: F-C5 post 7 days assay


title: Expanded_TIL_Feature_barcodes_4A


title: F-C1 post 7 days assay

value: NT


title: SYK_A_PHH_siCtrl_Plate_2_FFA_0uM_Rep5

tag: cell line

value: PHH

value: primary human hepatocyte

tag: genotype

value: WT

value: SYK


title: Expanded_TIL_Feature_barcodes_3B


title: Adult_nphx_1360

value: FACS sorted


title: SYK_A_PHH_siCtrl_Plate_2_FFA_0uM_Rep4


title: S-C3 pre assay

tag: treatment

value: pre assay


title: Expanded_TIL_Feature_barcodes_3A

value: Tumor


title: S-C1 pre assay


title: SYK_A_PHH_siCtrl_Plate_2_FFA_0uM_Rep3


title: SYK_A_PHH_siCtrl_Plate_2_FFA_0uM_Rep2


title: Expanded_TIL_Feature_barcodes_2B

value: T cells expanded with phytohemagglutinin-purified mitogen, IL2 and IL15


title: Adult_nphx_1359

tag: strain


title: SYK_A_PHH_siCtrl_Plate_2_FFA_0uM_Rep1

value: siCtrl


title: SYK_A_PHH_siCtrl_Plate_2_FFA_800uM_Rep1


title: Adult_nphx_1357


title: F-B5 post 7 days assay


title: Adult_nphx_1356


title: F-B6 post 7 days assay


title: Expanded_TIL_Feature_barcodes_2A


title: F-B1 post 7 days assay


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep4

value: XWQ


title: Adult_nphx_1355


title: S-B3 pre assay


title: Adult_nphx_1361


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep3


title: RNAseq_siTEAD4_1

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

data_processing:
The sequencing adapters were removed from the raw RNA-seq reads, and the obtained clean data were aligned to the human reference genome (hg38) using HISAT2 software (version 2.1.0.).
To quantify gene expression, we counted the sequencing reads within each gene and normalized the counts using edgeR
Enriched GO terms were identified with MGI Gene Ontology Term Finder.| log2FC| > 1 and p value < 0.05 were used as thresholds.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include RPKM values for all samples.

source_name: Human umbilical cord

extract_protocol:
For total RNA analysis and data processing, the total RNA was extracted using a TRIzol reagent following a standard protocol. The RNA integrity was checked on Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies).
Library construction and high-throughput RNA-Seq were performed with the Illumina Hiseq-PE150 platform to a depth of 1.5 × 107 reads.

value: Human umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: TEAD4 knockdown

value: siRNA


title: Adult_nphx_1354


title: S-B1 pre assay

value: T cells


title: Adult_nphx_1353


title: Adult_nphx_1358


title: RNAseq_PD42_2


title: F-A6 post 7 days assay

value: post 7 days assay


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep2


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep5


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep5


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep1


title: Adult_nphx_1351


title: Adult_nphx_1352


title: Expanded_TIL_Feature_barcodes_1A

value: ADT


title: RNAseq_PD42_1


title: RNAseq_siTEAD4_2


title: RNAseq_siCtrl

value: Ctrl knockdown


title: F-A5 post 7 days assay


title: Adult_nphx_1350


title: Adult_nphx_1349


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep4

value: PHH

value: primary human hepatocyte


title: RNAseq_PD26_2

value: WT


title: S-A3 pre assay


title: F-A1 post 7 days assay

value: NT


title: RNAseq_PD26_1


title: RNAseq_PD2_2


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep3


title: S-A1 pre assay

value: pre assay


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep2


title: Adult_nphx_1348

value: FACS sorted


title: cancer stage IA2 [CR_9]

first: Pavel

middle: Vladimirovich

last: Dobrynin

email: pdobrynin@gmail.com, pdobrynin2@uh.edu

state: Texas

address: 3620 SOUTHMORE BLVD APT 20

department: Psychology

institute: University of Houston

data_processing:
Galaxy community server
Quality control with FastQC and Cutadapt
Mapping to reference with RNA STAR
Normolised counts with HTSEQ
Assembly: GRCh38
Supplementary files format and content: One tab-delimited text file include CPM values for all Samples

source_name: Cervical tissue

extract_protocol:
Total RNA was isolated using TriZOL reagent (Invitrogen). The quality and quantity of isolated RNA were assessed using Fragment Analyzer automated system (Advanced Analytical).
cDNA libraries were constructed using TruSeq Stranded Total RNA (with RiboZero, Illumina) kit, reverse transcriptase SuperScript III (Invitrogen), and AMPure XP Beads (Beckman) following standard manufacturers’ protocols
The adaptors-ligated fragments were loaded onto the flow cell using MiSeq v3 sequencing kit; 75 bp end-reads were generated on the MiSeq platform (Illumina).

treatment_protocol: Cervical tissue samples were placed in IntactRNA stabilization reagent at +4°C immediately after excision (during surgery)

value: Cervical tissue

tag: Stage

value: cancer stage IA2


title: RNAseq_PD2_1

tag: tissue


title: XWQ_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep1

value: XWQ


title: Adult_nphx_1347

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs


title: CUTTag_PD42_H3K27ac

data_processing:
For CUT&Tag data processing, FASTQC was used to measure the date quality distribution.
The clean reads were then aligned to reference genome sequences using the bwa program.
Peaks were called using MACS2 peak caller with q-value < 0.05.
Genome-wide normalized signal coverage tracks were visualized in the IGV.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.
Library strategy: CUT&Tag

growth_protocol: hTERT RPE-1 cells (ATCC, CRL-4000) were cultured in F12/DMEM (1:1) supplemented with 10% fetal bovine serum (FBS, Gemini, 900-108) and 0.01mg/ml hygromycin B under 5% CO2 at 37°C.

extract_protocol:
The primary human umbilical cord mesenchymal stem cells (UC-MSCs) were obtained from fetuses with natural labor in Central People's Hospital of Zhanjiang. The experiment has been approved by Institutional Ethics Committee of Central People's Hospital of Zhanjiang (IIT-2022-057-01). Briefly, the fresh umbilical cord was cut off into clumps and were digested with 1 g/L collagenase II for 1 h. The digested clumps were then cultured in DMEM supplemented with 20% fetal bovine serum (FBS, Gibco, 12800), 100 U/mL penicillin, and 100 U/mL streptomycin at 37°C under 5% CO2. After 16 days, the clumps were removed carefully and cells were serially passaged after reaching 80−90% confluence. Cells are qualified for microbiology and virology tests. The population doublings were calculated with PD = log2 (Ne/N0), where N0 represents the number of seeds and Ne represents the number of counts. Cumulative PD numbers represent the sum of PDs from all previous passages, with cells derived from the primary culture considered PD = 0.
CUT&Tag analysis was performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) as described by the manufacturers with some modifications. Briefly, nuclei were extracted from the 10,000 fresh cells, and added the ConA beads incubating at room temperature for 10 min. The mixed complexes were the incubated with H3K27ac and TEAD4 specific primary antibodies with IgG antibody as a control, and the next day, followed by the secondary antibody. A diluted pA-Tn5 adapter complex was then added to the above system and incubated at room temperature for 1 h. After extensive washing, system were subsequently sheared by adding 5 × TTBL. Subsequent proteinase K and DNA extract beads were used for obtaining eluted DNA. Finally, the sequencing libraries were established after 12 cycles of PCR amplification.

value: Human umbilical cord

tag: antibody


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep5

value: siCtrl


title: cancer stage IA1 [CR_8]

value: cancer stage IA1


title: cancer stage IIB [CR_7]

value: cancer stage IIB


title: CUTTag_PD42_IgG

value: Human umbilical cord mesenchymal stem cells

value: IgG


title: Adult_nphx_1345


title: CUTTag_PD42_TEAD4


title: CUTTag_PD2_H3K27ac


title: Adult_nphx_1344


title: cancer stage IB2/IIA1 [CR_6]

value: cancer stage IB2/IIA1


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep3


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep2


title: Adult_nphx_1343


title: cancer stage IA1 [CR_4]


title: cancer stage IA1 [CR_3]


title: Adult_nphx_1342


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep5


title: CUTTag_PD2_IgG


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep1


title: Adult_nphx_1341


title: cancer stage IB1 [CR_2]

value: cancer stage IB1


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep4

value: PHH


title: Adult_nphx_1340


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep4

value: primary human hepatocyte


title: cancer stage IA1 [CR_1]


title: Adult_nphx_1346


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep3

value: WT


title: CIN1 [CIN_5]


title: cancer stage IB1 [CR_5]


title: ATACseq_siCtrl

data_processing:
For ATAC-Seq data processing, FastQC (version 0.11.7) was used to evaluate the quality of the sequencing data, and Trimmomatic was explored to remove the adaptor sequences to obtain the clean data.
The clean data were subsequently aligned to the hg38 reference genome using BWA.
Multiply mapped reads were removed using SAMtools (version 1.3.1) and the MASCS2 was applied to call significant peaks with q-value < 0.05.
Differential peaks were identified by DESeq2 (version 1.16.0) with the thresholds |log2FC| > 2 and p < 0.05
Genomic features of peaks were annotated using ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig files include peaks for each sample, respectively.

extract_protocol:
The primary human umbilical cord mesenchymal stem cells (UC-MSCs) were obtained from fetuses with natural labor in Central People's Hospital of Zhanjiang. The experiment has been approved by Institutional Ethics Committee of Central People's Hospital of Zhanjiang (IIT-2022-057-01). Briefly, the fresh umbilical cord was cut off into clumps and were digested with 1 g/L collagenase II for 1 h. The digested clumps were then cultured in DMEM supplemented with 20% fetal bovine serum (FBS, Gibco, 12800), 100 U/mL penicillin, and 100 U/mL streptomycin at 37°C under 5% CO2. After 16 days, the clumps were removed carefully and cells were serially passaged after reaching 80−90% confluence. Cells are qualified for microbiology and virology tests. The population doublings were calculated with PD = log2 (Ne/N0), where N0 represents the number of seeds and Ne represents the number of counts. Cumulative PD numbers represent the sum of PDs from all previous passages, with cells derived from the primary culture considered PD = 0.
DNA libraries were constructed after 8 cycles of PCR amplification using the TruePrep DNA Library Prep Kit and sequenced on the Illumina Hiseq-PE150 platform to a depth of 4.0 × 107 reads.

value: Ctrl knockdown

value: siRNA


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep2


title: Adult_nphx_1338

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: FACS sorted


title: CIN3 (carcinoma in situ) [CIN_4]

value: Cervical tissue

value: CIN3 (carcinoma in situ)


title: CUTTag_PD2_TEAD4


title: Adult_nphx_1337


title: XWQ_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep1

value: XWQ


title: ONR_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep5

value: ONR


title: ATACseq_PD42_2

value: Human umbilical cord


title: Adult_nphx_1336


title: CIN3 (carcinoma in situ) [CIN_2]


title: ATACseq_siTEAD4_2

value: TEAD4 knockdown


title: ATACseq_PD42_1


title: Adult_nphx_1335


title: ONR_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep4


title: Cervical intraepithelial neoplasia grade 3 (CIN3) [CIN_1]


title: ONR_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep3


title: ATACseq_PD26_2


title: morphologically normal cervical epithelium [Norm2]

tag: tissue type


title: ATACseq_siTEAD4_1


title: Adult_nphx_1339


title: ATACseq_PD2_2


title: ONR_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep2


title: Adult_nphx_1333


title: Adult_nphx_1334


title: ONR_A_PHH_siMARC1_Plate_1_FFA_800uM_Rep1


title: ATACseq_PD2_1


title: Adult_nphx_1332


title: morphologically normal cervical epithelium [Norm1]


title: Adult_nphx_1331


title: Smooth Muscle, Nuclear Localization STUB1, Replicate 3

city: Milwaukee

first: Adeleye

middle: J.

last: Afolayan

state: Wisconsin

address: 8701 Watertown Plank Rd., PD278, CRI TBRC, Rm C3278

institute: Medical College of Wisconsin

description:
smc_gene_exp.diff
Stub1 FPKM data file.xlsx
SMSTUB_NLS_3

data_processing:
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
Assembly: UCSC hg37, GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pulmonary Smooth Muscle

growth_protocol: Pulmonary-derived arterial endothelial cells or smooth muscle cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

extract_protocol:
Cells were collected using trypsin and RNA was gathered using the Qiagen RNeasy kit (cat. 74004)
Libraries were prepared according to Lexogen's instruction accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Cat. 015). Briefly, total RNA was reverse transcribed by oligodT priming, RNA template was removed, and the second strand was synthesized by random priming using DNA polymerase. After bead purification, library is amplified by PCR and sequences required for cluster generation are introduced. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were transfected at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest.

value: Pulmonary Smooth Muscle

value: HPSMC

value: Stub1 NLS transfection


title: Smooth Muscle, Nuclear Localization STUB1, Replicate 2

description:
smc_gene_exp.diff
Stub1 FPKM data file.xlsx
SMSTUB_NLS_2


title: T72h_minusBI_2

city: Beijing

first: Xiaochun

state: China

address: Equipment No.2, Peking University, Beijing, China

department: College of Future Technology

institute: Peking University

data_processing:
Quality control: The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. 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). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two  conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler R package（3.8.1） to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis: Gene Set Enrichment Analysis (GSEA) is a computational approach to  determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were  tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、Reactome、DO and DisGeNET data sets were used for GSEA independently. SNP analysis GATK (4.1.1.0) software was used to analyse SNP calling, and SnpEff (4.3.1q) software was used to annotate SNP. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10). AS analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event. PPI analysis of differentially expressed genes PPI analysis of differentially expressed genes was based on the STRING database, which is available to known and predicted Protein-Protein Interactions.For the species that exist in the database, we build a network by extracting the list of target genes from the database. Otherwise, the Diamond software (0.9.14) was used to compare the target  gene sequence with the selected reference protein sequence, and then the network was established according to the known interaction of the selected reference species. Fusion Analysis Fusion gene refers to the chimeric gene formed by the fusion of all or part of the sequences of two genes, which is generally caused by chromosome translocation, deletion and other reasons. We used SATR-fusion software (1.9.0) to detect genes that are fused. SATR-fusion is a software package uses fusion output results of STAR alignment to detect fusion transcripts, including SATR alignment, SATR fusion. predict, SATR-fusion.filter was used to correct the predicted results of Star-fusion to ensure the accuracy of the results. Weighted correlation network analysis WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing , FPKM can be used as gene expression data.
Assembly: Homo Sapiens genome GRCh38/hg38
Supplementary files format and content: FPKM calculated from the original data were presented in Excel file (.xls and .xlsx)

growth_protocol: All pluripotent and differentiation cells were maintained at 37 °C in the cell incubator (LS-C0150, Thermo), with 5% CO2 and atmospheric (21%) O2. Human induced pluripotent stem cell (iPSC), iPS-18 (Y00300, TaKaRa), iPS-B1 (CA4025106, CELLapy), iPS-M (RC01001-A, Nuwacell), iPS-F (RC01001-B, Nuwacell), and human embryonic stem cell (ESC) lines WIBR3 (Whitehead Institute Center for Human Stem Cell Research, Cambridge, MA) and H9 were routinely cultured in PGM1 medium (CELLAPY) or mTeSR1 (Stemcell Technologies) on growth factor–reduced Matrigel-coated (Corning) plate. iPSCs and ESCs were passaged every 3-5 days using Versene (Gibco) depending on the cell density. 3-5 μM Y27632 (Selleck Chemicals) dissolved in dimethyl sulfoxide (DMSO) was added for the first 12-24h after passage. The pluripotent cells were seeded in 6-well plates.

extract_protocol:
RNA was extracted using the EasyPure® RNA Kit (TransGen). RNA quantification and qualification: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, 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 (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.
Clustering and sequencing: After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

treatment_protocol:
iPSC treated without 0-48h BI-1347 and with 16 μM 0-48h CHIR. CHIR were withdrawn at 48h from the medium. Samples were collected at 72h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-derived CMs

value: iPSC treated without 0-48h BI-1347 and with 16 uM 0-48h CHIR. CHIR were withdrawn at 48h from the medium. Samples were collected at 72h.


title: CIN2/3 [CIN_3]


title: ONR_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep4

value: PHH


title: Adult_nphx_1330


title: Adult_nphx_1329


title: ATACseq_PD26_1

value: Human umbilical cord mesenchymal stem cells


title: ONR_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep3

value: primary human hepatocyte

value: WT


title: T72h_minusBI_1


title: ONR_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep2


title: T72h_plusBI_2

treatment_protocol:
iPSC treated with 0.5 μM  0-48h BI-1347 and 16 μM 0-48h CHIR. Small molecules were withdrawn at 48h from the medium. Samples were collected at 72h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 0.5 uM  0-48h BI-1347 and 16 uM 0-48h CHIR. Small molecules were withdrawn at 48h from the medium. Samples were collected at 72h.


title: Adult_nphx_1328

value: FACS sorted


title: Smooth Muscle, Control, Replicate 2

description:
Stub1 FPKM data file.xlsx
SMCCTRL_2


title: T72h_plusBI_1


title: Adult_nphx_1327


title: Smooth Muscle, Control, Replicate 1

description:
Stub1 FPKM data file.xlsx
SMCCTRL_1


title: ONR_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep5

value: siCtrl


title: T48h_minusBI_2

treatment_protocol:
iPSC treated without BI-1347 and with 16 μM CHIR. Samples were collected at 48h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated without BI-1347 and with 16 uM CHIR. Samples were collected at 48h.


title: ONR_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep5


title: Endothelial Cell, Control, Replicate 3

description:
Stub1 FPKM data file.xlsx
ECCTRL_3

source_name: Pulmonary Endothelia

value: Pulmonary Endothelia

value: HPAEC


title: Adult_nphx_1326


title: ONR_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep4

value: ONR


title: Adult_nphx_1325


title: Endothelial Cell, Control, Replicate 2

description:
Stub1 FPKM data file.xlsx
ECCTRL_2


title: ONR_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep3


title: Smooth Muscle, Control, Replicate 3

description:
Stub1 FPKM data file.xlsx
SMCCTRL_3


title: Endothelial Cell, Control, Replicate 1

description:
Stub1 FPKM data file.xlsx
ECCTRL_1


title: T24h_minusBI_2

treatment_protocol:
iPSC treated without BI-1347 and with 16 μM CHIR. Samples were collected at 24h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated without BI-1347 and with 16 uM CHIR. Samples were collected at 24h.


title: Endothelial Cell, Nuclear Localization STUB1, Replicate 3

description:
stub_nls_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NLS_3


title: T24h_minusBI_1


title: ONR_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep1


title: Smooth Muscle, Nuclear Localization STUB1, Replicate 1

description:
smc_gene_exp.diff
Stub1 FPKM data file.xlsx
SMSTUB_NLS_1

value: Pulmonary Smooth Muscle


title: ONR_A_PHH_siMARC1_Plate_1_FFA_0uM_Rep1


title: ONR_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep5


title: T24h_plusBI_2

treatment_protocol:
iPSC treated with 0.5 μM BI-1347 and 16 μM CHIR. Samples were collected at 24h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 0.5 uM BI-1347 and 16 uM CHIR. Samples were collected at 24h.


title: T48h_minusBI_1


title: ONR_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep4


title: Adult_nphx_1320


title: T24h_plusBI_1


title: Endothelial Cell, Nuclear Localization STUB1, Replicate 1

description:
stub_nls_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NLS_1

value: Stub1 NLS transfection


title: Endothelial Cell, Nuclear Exclusion STUB1, Replicate 3

description:
stub_nes_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NES_3

value: Stub1 NES transfection


title: ONR_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep3


title: hiPSC_02

treatment_protocol:
iPS-B1 cultured in PGM1
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC

value: maitained iPSC


title: hiPSC_01


title: ONR_A_PHH_siCtrl_Plate_1_FFA_800uM_Rep2

value: PHH


title: Adult_nphx_1324


title: Adult_nphx_1319


title: Adult_nphx_1321


title: T48h_plusBI_1

treatment_protocol:
iPSC treated with 0.5 μM BI-1347 and 16 μM CHIR. Samples were collected at 48h.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-derived CMs

value: iPSC treated with 0.5 uM BI-1347 and 16 uM CHIR. Samples were collected at 48h.


title: Adult_nphx_1323


title: Endothelial Cell, Nuclear Exclusion STUB1, Replicate 1

description:
stub_nes_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NES_1


title: Adult_nphx_1318


title: Adult_nphx_1322


title: CM_minusBI_2

treatment_protocol:
iPSC-derived CM on day 15. The cells were treated without BI-1347 0.5 μM 0-48h at stage I.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: WT

value: iPSC-CM without BI-1347 (induced by CHIR 8 uM 0-48h)


title: Endothelial Cell, Nuclear Exclusion STUB1, Replicate 2

description:
stub_nes_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NES_2


title: Endothelial Cell, Nuclear Localization STUB1, Replicate 2

description:
stub_nls_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NLS_2


title: ONR_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep1

value: primary human hepatocyte

value: siCtrl


title: Adult_nphx_1317

description:
Adult_nphx_lec
Adult_nphx_normalized_expression_matrix.csv

value: FACS sorted


title: CM_minusBI_1


title: HC_BC000289_TCPY_11_rep1

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
RNA-seq raw files in FASTQ format were processed in a customized pipeline. For each sample, we first filtered out reads that failed vendor check or are too short (<15nt) after removing the low-quality ends or possible adaptor contamination by using fastq-mcf with options of “-t 0 –x 10 –l 15 –w 4 –q 10 –u”. We then checked the quality using FastQC and generated k-mer profile using kpal for the remaining reads. Reads were then mapped to the human genome (GRCh37/hg19) using Tophat (v2.0.8) by allowing up to 2 mismatches and 100 multiple hits. Reads mapped to ribosomal RNAs or to the mitochondrial genome were excluded from downstream analysis. Gene expression levels were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Only uniquely mapped reads were used to estimate FPKM. To calculate normalized FPKM, we first ran Cuffquant (v2.2.1) with default arguments for genes annotated in GENCODE (v19), and then ran Cuffnorm with parameters of “-total-hits-norm –library-norm-method quartile” on the CBX files generated from Cuffquant
For circRNA identification, we first extracted the chimerically aligned RNAseq reads using Tophat-fusion and then called circRNAs using circExplorer (v2.0). To identify circRNAs that are not back-spliced from a canonical exon border, we ran circExplorer2 with a customized gene annotation file and the “--low-confidence” option. CircRNAs with at least two unique back-spliced reads in overall samples are categorized as “being expressed” and kept as circRNA candidates. CircRNA expression is quantified by normalized reads per million (RPM) at the back-splicing sites for each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each circRNA in each sample

source_name: Temporal cortex pyramidal neuron

extract_protocol:
Total RNA was isolated and treated with DNase (Qiagen) using the Arcturus Picopure method (Applied Biosystems), yielding approximately 7-8 ng RNA per subject. Total RNA was linearly amplified into 5~10 µg of double-stranded cDNA using the validated, precise, isothermal RNA amplification method implemented in the Ovation RNA-seq System V2 (NuGen)
Sequencing libraries were generated from 500 ng of the double-stranded (ds) cDNA using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's protocol. The cDNA was fragmented, and end repair, A-tailing, adapter ligation was performed for library construction.

tag: source sampleid

tag: source subjectid

tag: disease state

value: HC

value: TCPY

tag: batch

tag: replicate


title: CM_minusBI_3


title: Adult_nphx_1316


title: HC_BC000288_TCPY_11_rep1

value: AD


title: D3-30

city: Farmington

first: Olusegun

middle: B

last: Babaniyi

state: CT

address: 400 Farmington avenue

department: Genetics and Developmental Biology

institute: UCONN Health

data_processing:
Base calling was performed on the Illumina NextSeq 500 platform
Fastq files were trimmed of adaptors and low quality sequence using Sickle v1.33
trimmed paired-end reads were alligned to hg38 genome with STAR v2.5.3a
count files for each library was generated using Htseq on anaconda 2.4.0
Assembly: GRCh38.p10
Supplementary files format and content: count files generated from each cDNA library

source_name: Dex treated neural culture 3

growth_protocol: hESCs were cultured on irradiated or mitomycin-treated mouse embryonic fibroblasts (MEFs) feeder cultures and passaged every 7 days. Cultures were fed with hESC media composed of DMEM-F12 (Thermo Scientific) supplemented with 20% knock-out serum replacer (KOSR) (Thermo Scientific), 100 µM nonessential amino-acids, 1 mM L-glutamine, 100 mM β-Mercaptoethanol (Sigma-Aldrich), and 8 ng/mL basic FGF (PeproTech). hESC media was completely replaced every 24 hours. hESC-derived neural cultures were generated from hESC lines using a dual SMAD inhibition protocol over a period of 10 weeks, prior to dexamethasone treatment. Mature neural cultures were maintained in neural differentiation media (NDM), composed of neurobasal medium combined with 2% B-27 supplement, 1x non-essential amino acids, 1 mM L-glutamine (Thermo Scientific), and supplemented with 1 µM ascorbic acid, 200 nM cyclic-AMP, and 10 ng/mL each of brain-derived neurotrophic factor (BDNF) and glial-derived neurotrophic factor (GDNF) (PeproTech). Neural cultures were fed twice a week by replacing half of their culturing medium.

extract_protocol:
Total mRNA was purified from culture lysate of each sample using a phenol-chloroform protocol
cDNA libraries were prepared according to Illumina’s protocol for total mRNA library preparation, using oligoDT beads to enrich for polyadenylated transcripts. cDNA libraries were pooled and sequenced across two high density flow cells using a NextSeq 500 sequencer using equal amounts of each library.

treatment_protocol: 3 sister cultures were treated with 1uM Dexamethasone supplimented into culturing medium (NDM). 3 sister cultures were treated with DMSO vehicle supplimented into culture media as control samples.

value: hESC-derived neural culture

tag: condition

value: 6 hour 1µM Dexamethasone


title: iPS3


title: ONR_A_PHH_siCtrl_Plate_1_FFA_0uM_Rep2

tag: sirna

tag: donor id

value: ONR

tag: perturbation


title: D2-29

source_name: Dex treated neural culture 2

tag: cell line


title: D1-28

source_name: Dex treated neural culture 1


title: HC_BC000287_TCPY_11_rep1

tag: cell type


title: Adult_nphx_1314

first: Myung Jin

institute: Institute for Basic Science


title: iPS1

tag: genotype

tag: treatment


title: Adult_nphx_1313

tag: strain


title: C3-27

source_name: Vehicle treated neural culture 3

tag: tissue

value: 6 hour DMSO


title: HC_BC000286_TCPY_11_rep1


title: HC_BC000285_TCPY_11_rep1


title: iPS2

value: iPSC


title: Adult_nphx_1311


title: C2-26

source_name: Vehicle treated neural culture 2


title: CM_plusBI_1

treatment_protocol:
iPSC-derived CM on day 15. The cells were treated with BI-1347 0.5 μM 0-48h at stage I.
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC-CM with BI-1347 (induced by CHIR 12 uM 0-48h and BI-1347 0.5 uM 0-48h)


title: HC_BC000284_TCPY_11_rep1


title: C1-25

source_name: Vehicle treated neural culture 1


title: D3-18


title: Adult_nphx_1312


title: Adult_nphx_1310


title: CM_plusBI_2


title: HC_BC000282_TCPY_11_rep1


title: Adult_nphx_1309


title: Adult_nphx_1315


title: CM_plusBI_3


title: HC_BC000281_TCPY_11_rep1


title: D2-17


title: m_8_36

treatment_protocol:
iPSC treated with 8 μM 0-36h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: CHIR treated iPSC

value: iPSC treated with 8 uM 0-36h CHIR


title: T48h_plusBI_2

value: iPSC-derived CMs

value: iPSC treated with 0.5 uM BI-1347 and 16 uM CHIR. Samples were collected at 48h.


title: D1-16


title: Adult_nphx_1308


title: Adult_nphx_1307


title: HC_BC000280_TCPY_11_rep1


title: Adult_nphx_1306


title: C3-15


title: HC_BC000277_TCPY_11_rep1


title: m_6_48

treatment_protocol:
iPSC treated with 6 μM 0-48h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: WT

value: iPSC treated with 6 uM 0-48h CHIR


title: C2-14


title: HC_BC000278_TCPY_11_rep1


title: m_6_24

treatment_protocol:
iPSC treated with 6 μM 0-24h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 6 uM 0-24h CHIR


title: C1-13


title: HC_BC000283_TCPY_11_rep1


title: HC_BC000276_TCPY_11_rep1


title: Adult_nphx_1304

value: FACS sorted


title: ips

treatment_protocol:
iPS-18 cultured in PGM1
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: maitained iPSC


title: HC_BC000275_TCPY_11_rep1

value: TCPY


title: Donor63_Day3_Osteo_2 [H63-d3-Ost-3]

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The default RNA-seq pipeline of DolphinNext platform was used for data processing https://dolphinnext.umassmed.edu/
RSEM v1.3.1 was used to align RNA-Seq reads to reference transcripts hg19 and estimates gene and isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

source_name: subcutaneous white adipose tissue

extract_protocol:
RNA was extracted using TriPure TRIzol reagent. Chloroform was added in a 1:5 ratio by volume and phase separation was performed. The RNA-containing layer was mixed with an equal volume of 100% isopropanol and incubated overnight at -20 °C for precipitation. RNA was pelleted and washed with 80% ethanol and resuspended in nuclease-free water.
Library preparation was performed using Illumina TruSeq Stranded mRNA Low-Throughput Sample Prep Kit (Cat# 20020594) according to manufacturer’s instruction.

value: subcutaneous white adipose tissue

value: primary adipose-tissue derived mesenchymal progenitors

value: Osteogenic


title: Adult_nphx_1305

last: Yang


title: m_10_24

treatment_protocol:
iPSC treated with 10 μM 0-24h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 10 uM 0-24h CHIR


title: Donor63_Day3_Osteo_1 [H63-d3-Ost-1]


title: HC_BC000274_TCPY_11_rep1

value: AD


title: Adult_nphx_1302


title: HC_BC000273_TCPY_11_rep1

value: HC


title: Donor63_Day3_Adipo_2 [H63-d3-MDI-3]

value: Adipogenic


title: Adult_nphx_1301


title: Donor63_Day3_Adipo_1 [H63-d3-MDI-1]


title: RNA_6_36

treatment_protocol:
iPSC treated with 6 μM 0-36h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: CHIR treated iPSC

value: iPSC treated with 6 uM 0-36h CHIR


title: RNA_2_48

treatment_protocol:
iPSC treated with 2 μM 0-48h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 2 uM 0-48h CHIR


title: HC_BC000272_TCPY_11_rep1


title: m_10_48

treatment_protocol:
iPSC treated with 10 μM 0-48h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: iPSC treated with 10 uM 0-48h CHIR


title: RNA_12_24

treatment_protocol:
iPSC treated with 12 μM 0-24h CHIR
PSCs were split into E8 medium (Cauliscell Inc) at the ratio of 1:10 or 1:12 for the last passage before beginning differentiation. Cells differentiated in 24-well plates or 96-well plates. When they reached ∼80 to 90% confluence, the medium was changed to RPMI + B27- medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 without insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies). At stage I (from iPSC to mesoderm, day 0-3), PSCs were initially treated with CHIR (Selleck Chemicals). CHIR concentration and duration depended on the cell lines and experiment design, ranging from 2-20 μM and 24-48h respectively. After CHIR treatment, the medium was replaced with RPMI + B27- medium until 72h (day 3). At stage II (CPC stage, day 4-6), the RPMI + B27- medium was renewed and supplemented with 5 μM IWR1 (Selleck Chemicals) for 48 hours.  CPCs could be induced on day 6. At stage III (CM stage, day 7-~12), CPCs continued their differentiation process to CMs in RPMI + B27 medium, consisting of RPMI 1640 (RPMI, Gibco), 2% B27 with insulin (Gibco), and 1% Penicillin-Streptomycin (Life Technologies).

value: WT

value: iPSC treated with 12 uM 0-24h CHIR


title: Donor63_Day3_DMEM_2 [H63-d3-DM-3]

value: Non-induced

value: DMEM


title: Donor63_Day3_Chondro_2 [H63-d3-Cho-3]

value: Chondrogenic


title: Adult_nphx_1299

value: FACS sorted


title: HC_BC000270_TCPY_11_rep1

value: TCPY


title: Adult_nphx_1300


title: HC_BC000271_TCPY_11_rep1


title: Donor63_Day3_Chondro_1 [H63-d3-Cho-1]

value: subcutaneous white adipose tissue

value: primary adipose-tissue derived mesenchymal progenitors


title: Adult_nphx_1298