title: 2799

city: Boston

first: Christina

last: Codden

state: MA

address: 800 Washington Stree

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing:
Demultiplexing, read alignment, and read counting, and nuclei calls were done with Cellranger 3.0
Quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression was performed using the development version of the R package Seurat in R 3.5.0
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.  For each feature, its feature ID and names are stored in the first and second column of the features.tsv file.  The third column of this file indentifies that it is a gene expression feature.  The actual gene cell matrix, .mtx file, is stored in the Market Exchange Format (MEX) for sparse matrices.

molecule: nuclear RNA

source_name: Adult human myectomy tissue

extract_protocol:
Nuclei were released from the tissue via dounce homogenization and then nuclei were processed using 10x genomics Chromium Single Cell 3' reagent V2 kit
10x Genomics Chromium Single Cell 3' reagent v2 kit

value: adult heart IVS

tag: gender

value: Male

tag: age


title: s.NJA01801.E06

status: Public on May 20 2021

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

molecule: total RNA

organism: Mus musculus

source_name: colon

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

tag: strain

tag: tissue

value: colon

tag: facs cellnumber

value: Singlet

tag: age (days)


title: s.NJA01801.E07


title: s.NJA01801.E05


title: 3_Serum_0Gy

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Adapter trimming and quality filtering (at level 30) was performed using fastp (https://academic.oup.com/bioinformatics/article/34/17/i884/5093234).
UMI extraction and deduplication was performed with umi_tools (https://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract) using following regex expression: .+(?P<discard_1>AACTGTAGGCACCATCAAT)(?P<umi_1>.{12})(?P<discard_2>.+)
Mapping to miRbase mature (version 22) was perfomed using bowtie (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25) and allowed for 1 mismatch.
Created bam files were sorted and indexed using samtools (https://www.ncbi.nlm.nih.gov/pubmed/21903627) and then picard (https://broadinstitute.github.io/picard/).
Files with counts were collected to table. Counts were converted to TPM and log10 transformed (logTPM) using edgeR without library normalization and prior equal 0.001 (hence -3 as minimum). This utlized OmicSelector (https://biostat.umed.pl/OmicSelector).
Genome_build: miRbase version 22
Supplementary_files_format_and_content: counts and logTPM values

organism: Homo sapiens

source_name: Serum

extract_protocol:
Blood samples were collected at pre-specified timepoints via venipuncture. Samples were centrifuged and frozen to -80oC within 4 hours of collection. Exosomes were isolated from selected serum samples using the Qiagen miRCURY Exosome Serum/Plasma Kit. Total RNA was isolated using the Qiagen miRNeasy Serum/Plasma Kit.
After RNA extraction, small RNA-seq (next generation sequencing) indexed sequencing libraries were prepared from 200 ng total RNA according to QIAseq miRNA Library Kit Handbook (version 11/2016).

tag: body fluid

value: Serum

tag: irradiation dose


title: s.NJA01801.E04


title: PBL_NAIVE_1789

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

data_processing:
Reads were mapped to hg38, using STAR to generate bam files. The mapped libraries were then TMM normalized accounting for differences in size and dispersion using the default parameters of EdgeR for gene abundance levels.
Genome_build: hg38
Supplementary_files_format_and_content: TMM normalized expression values for all ENSEMBLE genes

molecule: polyA RNA

source_name: Naïve B cell

extract_protocol: 1-10 ng of total RNA was used as input for the mRNA HyperPrep Kit (Kapa Biosystems) according to the manufacturer's instructions.  Following adapter ligation cDNA was PCR amplified for 12 cycles.

tag: patient

tag: ethnicity

value: African American

value: Female

tag: sorting markers

value: PBMC


title: PBL_NAIVE_955

value: Caucasian


title: PBL_NAIVE_1792


title: NP_ASC_1809

source_name: Antibody secreting cell

value: Nasal polyp


title: NP_NAIVE_1789


title: NP_NAIVE_955


title: PBL_NAIVE_1809


title: NP_NAIVE_1792


title: s.NJA01801.D22


title: s.NJA01801.E01


title: NP_ASC_1792


title: 1_Serum_0Gy


title: NP_ASC_1789


title: s.NJA01801.D20


title: s.NJA01801.D19


title: s.NJA01801.D21


title: s.NJA01801.D18


title: s.NJA01801.D16


title: s.NJA01801.D17


title: Donor: TSL49 Cell Line: ILC2

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Normalized expression values were generated through the TMM and  voom methods using the limma and edgeR Libraries in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as TMM normalized voom transformed expression values.

source_name: tonsil

growth_protocol: in vivo

extract_protocol:
Cells were sorted directly into RLT lysis buffer with beta mercaptoethanol added and then flash frozen on dry ice. RNA was isolated using Qiagen's RNeasy Micro kit (cat# 74004). 300 pg of total RNA was used to generate cDNA with Takara's SMARTSeq v4 Ultra Low Input RNA Kit for Seuencing (cat# 634892). Illumina's Nextera XT DNA kit (cat# FC-131-1096) was used with 1 ng of unsheared cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on a NextSeq 550 instrument in a Paired-End 75 bp configuration.

tag: cell population

tag: donor id


title: Donor: TSL49 Cell Line: ILC1


title: Donor: TSL49 Cell Line: ILCFR

value: ILCFR


title: s.NJA01801.D15


title: Donor: TSL49 Cell Line: ILC3


title: Donor: TSL49 Cell Line: Treg

value: Treg


title: Donor: TSL49 Cell Line: GCTFH

value: GCTFH


title: s.NJA01801.D14


title: Donor: TSL49 Cell Line: GCB

value: GCB


title: s.NJA01801.D13


title: s.NJA01801.E02


title: s.NJA01801.D12


title: Donor: TSL73 Cell Line: ILC1


title: Donor: TSL73 Cell Line: ILCFR


title: s.NJA01801.D09


title: Donor: TSL73 Cell Line: Treg


title: s.NJA01801.D10


title: s.NJA01801.D08


title: Donor: TSL73 Cell Line: GCTFH


title: s.NJA01801.D07


title: s.NJA01801.D06


title: Donor: TSL73 Cell Line: GCB


title: s.NJA01801.D05


title: Donor: TSL32 Cell Line: ILCFR


title: Donor: TSL32 Cell Line: ILC3


title: s.NJA01801.D02


title: s.NJA01801.D04


title: s.NJA01801.D03


title: Donor: TSL73 Cell Line: ILC2


title: s.NJA01801.D11


title: s.NJA01801.D01


title: Donor: TSL32 Cell Line: GCB


title: s.NJA01801.C21


title: s.NJA01801.C20


title: Donor: TSL32 Cell Line: GCTFH


title: s.NJA01801.C22


title: Donor: TSL65 Cell Line: ILCFR


title: s.NJA01801.C19


title: Donor: TSL65 Cell Line: ILC2


title: Donor: TSL73 Cell Line: ILC3


title: Donor: TSL65 Cell Line: ILC1


title: s.NJA01801.C18


title: Donor: TSL65 Cell Line: ILC3


title: Donor: TSL32 Cell Line: ILC2


title: s.NJA01801.C16


title: Donor: TSL65 Cell Line: GCTFH


title: Donor: TSL65 Cell Line: Treg


title: s.NJA01801.C14


title: s.NJA01801.C13


title: Donor: TSL32 Cell Line: ILC1


title: Donor: TSL32 Cell Line: Treg


title: Donor: TSL65 Cell Line: GCB


title: s.NJA01801.C12


title: Donor: TSL29 Cell Line: ILC3


title: s.NJA01801.C10


title: s.NJA01801.C11


title: s.NJA01801.C09


title: Donor: TSL29 Cell Line: ILC2


title: Donor: TSL29 Cell Line: ILCFR


title: Donor: TSL29 Cell Line: Treg


title: s.NJA01801.C08


title: s.NJA01801.C07


title: Donor: TSL29 Cell Line: GCTFH


title: s.NJA01801.C06


title: Donor: TSL55 Cell Line: ILC2


title: Donor: TSL29 Cell Line: GCB


title: s.NJA01801.C05


title: s.NJA01801.E03


title: s.NJA01801.C03


title: Donor: TSL55 Cell Line: ILCFR


title: s.NJA01801.C04


title: s.NJA01801.C02


title: Donor: TSL55 Cell Line: ILC1


title: s.NJA01801.C01


title: Donor: TSL55 Cell Line: Treg


title: Donor: TSL55 Cell Line: ILC3


title: s.NJA01801.B21


title: Donor: TSL55 Cell Line: GCTFH


title: s.NJA01801.B20


title: s.NJA01801.B19


title: Donor: TSL29 Cell Line: ILC1


title: Donor: TSL56 Cell Line: ILCFR


title: Donor: TSL55 Cell Line: GCB


title: s.NJA01801.B18


title: Donor: TSL56 Cell Line: ILC3


title: s.NJA01801.B17


title: Donor: TSL56 Cell Line: Treg


title: Donor: TSL56 Cell Line: ILC1


title: Sample422 [Rectal biopsy]

first: Angela

last: Mo

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Using FastQC, the single end 150 bp reads were trimmed and adapters were removed.
Reads were mapped to human genome hg19 using hisat2.
The aligned reads were converted into read counts per gene with SAMtools and HTSeq in the default union mode.
The raw read counts were normalized via trimmed mean of M-values normalization with the edgeR R package.
Further adjustment and removal of batch effects was performed with SVA and (SNM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for each sample.
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene expression for each sample.

source_name: Rectal biopsy

extract_protocol:
Rectal biopsy specimens were obtained during diagnostic colonoscopy. RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced on the Illumina NextSeq as single-end 150-bp reads.

tag: individual

value: M

tag: age at diagnosis

tag: time of sampling

value: 52wk FU

tag: initial treatment

value: CS-IV

tag: colectomy

tag: disease

value: pediatric ulcerative colitis


title: Lucap 145 Matched Normal Sample

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: Lucap 145 Matched Normal Sample

library_source: genomic

data_processing:
Library strategy: exome-seq
Sequencing was performed using an Illumina HiSeq 2500 in high-output mode and  employed a paired-end, 100 base read length (PE100) sequencing strategy.
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.66.3 software, followed by demultiplexing of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Raw sequencing reads produced by Illumina’s bcl2fastq 1.8.4 software were processed to exclude read pairs failing default (PF filtering) quality checks. Short reads from the LuCaP PDX specimens were aligned to both human reference genome hg19  and mouse reference genome mm9 separately using TopHat (version 2.0.14). An in-house developed software was applied to retain the reads with higher fidelity to hg19 for further downstream analysis., only reads aligning to standard  chromosomes (chr 1:22, X,Y,M) were retained for further analysis The reads with low quality were filtered and duplicates were marked using Picard. MuTect v1 and Strelka version 1.0.15 were used to identify somatic single nucleotide variants  within the 5’ UTR for each tumor and matched normal pair.
Genome_build: hg19
Supplementary_files_format_and_content: VCF files from Mutect and Strelka are included as processed data files.

molecule: genomic DNA

source_name: Matched Normal tissue

growth_protocol: Genomic DNA from frozen tissue was extracted using the Qiagen Gentra Puregene Tissue Kit (Qiagen).

extract_protocol:
DNA was sheared using a Covaris LE220 ultrasonicator targeting 200bp, and sequencing adaptors added by ligation
Individually barcoded libraries were pooled 4-plex before capture. Libraries were hybridized to SeqCap EZ Choice probes of the 50 Mb Human UTR Design (Roche)

treatment_protocol: Sequencing libraries were prepped with the KAPA HyperPrep kit (Roche) using 1 μg of DNA

value: muscle

tag: sample type

value: normal sample


title: Lucap 147 Matched Normal Sample

description: Lucap 147 Matched Normal Sample

tag: tissue

value: liver


title: Lucap 145 Tumor Sample

description: Lucap 145 Tumor Sample

source_name: Prostate cancer tissue

value: prostate cancer

value: tumor sample


title: Sample420 [Rectal biopsy]

tag: gender

value: F


title: Sample421 [Rectal biopsy]

value: CS-Oral


title: Lucap 81 Matched Normal Sample

description: Lucap 81 Matched Normal Sample

value: kidney


title: Sample419 [Rectal biopsy]


title: Donor: TSL56 Cell Line: GCB


title: Lucap 81 Tumor Sample

description: Lucap 81 Tumor Sample


title: Sample418 [Rectal biopsy]


title: Lucap 78 Matched Normal Sample

description: Lucap 78 Matched Normal Sample


title: Donor: TSL56 Cell Line: ILC2


title: Lucap 78 Tumor Sample

description: Lucap 78 Tumor Sample


title: Sample417 [Rectal biopsy]


title: Sample415 [Rectal biopsy]


title: Sample414 [Rectal biopsy]


title: Sample416 [Rectal biopsy]


title: GM12878_Nailseq_EH_EdUHU_HU023_LY073c

city: Beijing

first: Chen

last: Ai

address: Yiheyuan Road No.5

country: China

institute: Peking University

description: nascent DNA strand

data_processing:
Library strategy: NAIL-seq
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
Mapping for NAIL-seq: R1 and R2 reads were stitched using PEAR [74] and the bridge adapter sequences were trimmed with custom scripts. The stitched reads were aligned to the human genome (assembly hg19) or mouse genome (assembly mm10) by BWA-MEM (-k 20). PCR duplicates were distinguished by random molecular barcodes (RMBs) and only one was kept. Then the reads with MAPQ (mapping quality) >= 30 were kept for further analysis. We used samtools to convert .sam files into .bam files.
To generate genome tracks, we converted the .bam files into .BigWig. For NAIL-seq or ORC2 ChIP-seq, files were generated by the bamCoverage (in deepTools) with the parameter --binSize 1000 --normalizeUsing RPKM. For MCM5 ChIP-seq, the fold change value of ChIP-ed samples over input was generated by bamCompare with parameter --binSize 1000, --normalizeUsing RPKM –operation ratio. The data was presented by IGV 2.4.14.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: BigWig

growth_protocol:
K562/GM12878: GM12878 and K562 (3111C0001CCC000039, National Infrastructure of Cell line resource, China) cells were cultured in RPMI1640 media supplied with 15% FBS as described (Rao SS et al., 2014, Cell and Chiarle R. et al., 2011, Cell). For G1 arrest, GM12878 or K562 were incubated with 1 µM or 5 µM palbociclib (SelleckChem) for 36 hours, respectively.
mouse splenic B: The wild-type C57BL/6NCr mice at 6-8 weeks old were used for splenic B cell purification, following the manufacturer’s instructions (EasySep Mouse B cell isolation kit by STEMCELL). Both male and female mice were indiscriminately used in this study. Mice were housed and handled according to the standards set by Peking University laboratory animal center and all animal experiments were approved by the institutional animal care and use committee at Peking University. Naïve splenic B cells were isolated and activated with LPS (25 mg/mL; Sigma) and IL-4 (5 ng/mL; Sigma).
mESC: Murine embryonic stem V6.5 (mES-V6.5) cells were grown in 2i media containing 15% FBS, 1 µM PD0325901 (SelleckChem), 3 µM CHIR99021 (SelleckChem), 1000 U/mL mouse LIF (Millipore) and other described essential supplements. mES-V6.5 cells were always cultured on 0.2% gelatin (Sigma)-treated plates and synchronized by thymidine and nocodazole as described (Ballabeni A et al., 2011, PNAS).

extract_protocol:
Cells were harvested, washed with PBS, and applied to genomic DNA (gDNA) extraction with Proteinase K digestion as described previously.  Purified genomic DNA was subjected to Click reaction with 100 µM Biotin-PEG-azide, 2 mM CuSO4, 4 mM THPTA, and 10 mM Sodium ascorbate at 25℃ for 1 hour, followed by DNA precipitation. The copper in the click reaction hydrolyzes gDNA and fragments it into small fragments (around 200~400 bp in length), resulting in that each fragmented nascent DNA has little chance to contain both EdU and BrdU, simultaneously. Dissolved DNA was denatured at 95℃ for 5 min and phosphorylated by T4 PNK at 37℃ for 30 min.  For EdU/HU-labeled samples, T4 PNK-treated DNA was incubated with C1 beads alone. All of the enrichment steps were performed at room temperature for 4 hours.  Isolated EdU-labeled ssDNA were ligated on-beads with two types of bridge adapters (Bridge adapter -1 and -2, see the resource table for sequence details), simultaneously, at room temperature for at least 4 hours as follow: 1 µM Bridge adapters each, 1,600 U T4 DNA ligase and 15% PEG-8000.
After that, ligated DNA was harshly washed and tagged with Illumina P5-I5 and P7-I7 sequences as described (Yin J, et al., 2019, Cell Discov.).All the libraries were subjected to 2 × 150 bp Hiseq sequencing.

treatment_protocol:
K562/GM12878: For EdU/HU treatment, G1-synchronized GM12878 or K562 cells were released into fresh media with 10 µM EdU plus 5 or 10 mM HU for 24 or 12 hours, respectively. The concentration of EdU is comparable with the endogenous dTTP [68], and EdU can be incorporated into nascent DNA in a very efficient way and 2 minutes are sufficient for EdU to label nascent Okazaki fragments in OK-seq . Moreover, the G1-released K562 cells requires additional 2.5 hours to reach the G1/S transition. Therefore, the initiation sites are hard to escape from EdU labelling in the EdU/HU assay. For ⍺-amanitin or DRB mediated-RNA polymerase II inhibition, G1-arrest K562 cells were released into fresh media containing indicated concentrations of ⍺-amanitin, or DRB, plus HU and EdU for 12 hours.
mouse splenic B:The B cells were treated with 10 mM HU and 10 µM EdU for 28 hours from activation. For ⍺-amanitin treatment, primary B cells were incubated with 10 mM HU, 10 µM EdU, and ⍺-amanitin for 28 hours once LPS and IL-4 were added.
mESC: Mitotically arrested cells were shaken off, washed by pre-warmed 2i media, cultured in fresh media for 1.5 hours. To reduce replication fork progression speed, M phase synchronized mES cells were released into fresh media and incubated with 4 mM HU and 50 µM EdU for 3 hours. For the degradation of RNA polymerase II, the homozygous mAID-tagged RNA polymerase II cells were synchronized as wild-type cells. 1 ug/mL Doxycycline (Dox) was added to induce the production of OsTIR1. 500 uM IAA was added at 1 hour before releasing from nocodazole to induce the degradation of RNA polymerase II. The nocodazole-arrested cells were then cultured in the presence of Dox, IAA, EdU, and HU for 3 hours before harvesting.

tag: cell line

tag: cell type

value: B-Lymphocyte

tag: technique

value: NAIL-seq

tag: nail-seq labeling strategy

value: EdU/HU

tag: treatment

value: WT untreated

tag: cell phase

value: S

tag: purified antibody/biotin

value: EdU

tag: protocol

value: Protocol 2:NAIL-seq EdU/HU


title: s.NJA01801.B16

tag: strain

value: colon

tag: facs cellnumber

value: Singlet

tag: age (days)


title: Sample413 [Rectal biopsy]

tag: individual

value: M

tag: age at diagnosis

tag: time of sampling

value: 52wk FU

tag: initial treatment

value: CS-IV

value: pediatric ulcerative colitis


title: Lucap 147 Tumor Sample

description: Lucap 147 Tumor Sample

tag: tissue

value: prostate cancer

tag: sample type

value: tumor sample


title: GM12878_Nailseq_EB_BrdU_rep2_HU041_LY105d

description: nascent DNA strand

growth_protocol: GM12878 and K562 (3111C0001CCC000039, National Infrastructure of Cell line resource, China) cells were cultured in RPMI1640 media supplied with 15% FBS as described (Rao SS et al., 2014, Cell and Chiarle R. et al., 2011, Cell). For G1 arrest, GM12878 or K562 were incubated with 1 µM or 5 µM palbociclib (SelleckChem) for 36 hours, respectively.

extract_protocol:
Cells were harvested, washed with PBS, and applied to genomic DNA (gDNA) extraction with Proteinase K digestion as described previously.  Purified genomic DNA was subjected to Click reaction with 100 µM Biotin-PEG-azide, 2 mM CuSO4, 4 mM THPTA, and 10 mM Sodium ascorbate at 25℃ for 1 hour, followed by DNA precipitation. The copper in the click reaction hydrolyzes gDNA and fragments it into small fragments (around 200~400 bp in length), resulting in that each fragmented nascent DNA has little chance to contain both EdU and BrdU, simultaneously. Dissolved DNA was denatured at 95℃ for 5 min and phosphorylated by T4 PNK at 37℃ for 30 min.  For EdU- and BrdU-labeled samples, the denatured and modified DNA were purified by anti-BrdU (BU1/75) and Protein G beads for BrdU-labelled proportion, and the supernatants were denatured again and then incubated with Streptavidin C1 beads (Dynabeads) to isolate EdU-labeled proportion.  Isolated EdU- or BrdU-labeled ssDNA were ligated on-beads with two types of bridge adapters (Bridge adapter -1 and -2, see the resource table for sequence details), simultaneously, at room temperature for at least 4 hours as follow: 1 µM Bridge adapters each, 1,600 U T4 DNA ligase and 15% PEG-8000.
After that, ligated DNA was harshly washed and tagged with Illumina P5-I5 and P7-I7 sequences as described (Yin J, et al., 2019, Cell Discov.).All the libraries were subjected to 2 × 150 bp Hiseq sequencing.

treatment_protocol: For EdU and BrdU dual-labeling experiments, G1-arrested GM12878 and K562 cells were washed with pre-warmed RPMI1640 and released into fresh medium for 3 or 2.5 hours, respectively. Then the cells were cultured with 10 µM EdU for 15 min followed by a wash with pre-warmed RPMI1640 and then cultured with 50 µM BrdU for an additional 15 min.

tag: cell line

value: E+B

value: BrdU

value: Protocol 1:NAIL-seq EdU+BrdU


title: GM12878_Nailseq_EB_EdU_rep2_HU041_LY105h

description: nascent DNA strand

tag: cell type

value: B-Lymphocyte

value: NAIL-seq


title: Lucap 92 Matched Normal Sample

description: Lucap 92 Matched Normal Sample

value: spleen

value: normal sample


title: Sample412 [Rectal biopsy]

tag: gender

value: F

tag: colectomy

tag: disease


title: Lucap 92 Tumor Sample

description: Lucap 92 Tumor Sample


title: GM12878_Nailseq_EB_BrdU_rep1_HU041_LY105c

description: nascent DNA strand

tag: technique

tag: nail-seq labeling strategy

tag: treatment

value: WT untreated

tag: cell phase

value: S


title: Donor: TSL56 Cell Line: GCTFH

tag: cell population

value: GCTFH

tag: donor id


title: Sample411 [Rectal biopsy]

tag: individual

value: M

value: CS-Oral


title: Sample410 [Rectal biopsy]

tag: age at diagnosis

value: 52wk FU

value: CS-IV


title: K562_ChIPseq_MCM5-input_HU026_LY076a

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
Mapping for ChIP-seq: First, we trimmed the adapter sequences in the reads using cutadapt (-g NGGGGGGGGG -g GGGGG --times=2 --minimum-length=70 --error-rate=0.2 -O 3) . Then we aligned reads to the human genome (assembly hg19) using BWA-MEM (-k 20). Then the reads with MAPQ (mapping quality) >= 30 were kept for further analysis. We used samtools to convert .sam files into .bam files.
To generate genome tracks, we converted the .bam files into .BigWig. For NAIL-seq or ORC2 ChIP-seq, files were generated by the bamCoverage (in deepTools) with the parameter --binSize 1000 --normalizeUsing RPKM. For MCM5 ChIP-seq, the fold change value of ChIP-ed samples over input was generated by bamCompare with parameter --binSize 1000, --normalizeUsing RPKM –operation ratio. The data was presented by IGV 2.4.14.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: BigWig

growth_protocol: K562 (3111C0001CCC000039, National Infrastructure of Cell line resource, China) cells were cultured in RPMI1640 media supplied with 15% FBS as described (Rao SS et al., 2014, Cell and Chiarle R. et al., 2011, Cell).

extract_protocol:
For ORC2 ChIP-seq, the supernatants were pre-cleared by 40 µL protein G dynabeads for 1 hour and then incubated with 40 µL Streptavidin T1 beads (Dynabeads) for 6 hours at 4℃. Beads were harshly washed by freshly-made 2% SDS, high-salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0), LiCl buffer (0.25 M LiCl; 1% NP-40; 10 mM Tris-HCl; pH 8.0, 1 mM EDTA) and TE buffer. The beads-bound chromatin was eluted with the elution buffer (20 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) at 65℃ overnight. For MCM5 ChIP-seq, the soluble fractions were directly applied to anti-MCM5 (1:50) enrichment at 4℃ overnight. Then protein G dynabeads were added and incubated for 1 hour. Beads were washed as those of ORC2/5 ChIP, except that the wash with 2% SDS was removed. Chromatin on beads was eluted twice with elution buffer at 65℃ for 15 min.   The eluate fraction was digested by RNase A and incubated with Proteinase K overnight. DNA was purified, end-repaired, and poly-dC tailing as described [72]. After poly-dC tailing, DNA was tagged with a biotinylated primer, captured by Streptavidin C1 beads, and ligated with an indicated bridge adapter (see the resource table) overnight at room temperature. The ligated products were then washed and tagged with Illumina P5-I5 and P7-I7 sequences via PCR for 13 cycles.
Sequencing was performed on the Illumina Hiseq platform (2 × 150 bp).

treatment_protocol: For the ChIP-seq of ORC2, ORC2 tagged with Avi-tag at its N-terminal was inserted into pMAX-GFP (Lonza) backbone to replace GFP (Fairhead et al., 2015, Methods Mol Biol.). BirA from bacteria was inserted into pX330 to replace Cas9. Ten million K562 cells transfected with 30 µg BirA and 30 µg Avi-ORC2 plasmids were immediately arrested at the G1 phase by 5 µM palbociclib for 36 hours and then incubated with or without 10 µg/mL ⍺-amanitin for 12 hours in the presence of palbociclib. For MCM5, wild-type K562 cells were treated with palbociclib for 36 hours, and then cultured in the presence or absence of 10 µg/mL ⍺-amanitin for 12 hours with palbociclib.  Cells were fixed by 1% formaldehyde (F1635, Sigma) for 10 min at room temperature and quenched by 125 mM glycine for 5 min. Ten million fixed cells were washed twice with PBS and lysed with ice-cold NP40 lysis buffer (10 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.05% NP40) on ice for 15 min. The cell lysate was separated by 24% (w/v) sucrose in the NP40 lysis buffer. The nuclei pellet was washed with PBS /1 mM EDTA and resuspended with glycerol buffer (20 mM Tris-HCl, pH 8.0; 75 mM NaCl; 0.5 mM EDTA; 0.85 mM DTT; 50% glycerol) and lysed by nuclei lysis buffer (10 mM HEPES, pH 7.6; 1 mM DTT; 7.5 mM MgCl2; 0.2 mM EDTA; 0.3 M NaCl; 1 M Urea; 1% NP40). Chromatin pellets were washed twice with PBS / 1 mM EDTA and resuspended in the sonication buffer (20 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM EDTA; 0.1% SDS; 1% Triton X-100; 4 mM CaCl2) supplied with 40 U MNase for 15 min at 37℃. The Nuclease was quenched by adding 5 mM EDTA and 5 mM EGTA. The chromatin was further fragmented by sonication and separated for the soluble fraction.

value: human blood (chronic myelogenous leukemia)

value: ChIP-seq

value: WT

tag: purified antibody/biotin

tag: protocol

value: Protocol 3 ORC2/MCM5 ChIP-seq


title: K562_ChIPseq_MCM5-ama_HU026_LY076d

value: WT ama 10ug/mL


title: K562_ChIPseq_MCM5-ama-input_HU026_LY076b


title: Sample408 [Rectal biopsy]

tag: time of sampling

tag: initial treatment

value: pediatric ulcerative colitis


title: Sample407 [Rectal biopsy]


title: Sample409 [Rectal biopsy]


title: GM12878_Nailseq_EB_EdU_rep1_HU041_LY105g

description: nascent DNA strand

tag: cell line

value: B-Lymphocyte

value: NAIL-seq

value: E+B

value: EdU

value: Protocol 1:NAIL-seq EdU+BrdU


title: Sample405 [Rectal biopsy]

value: F


title: Sample406 [Rectal biopsy]


title: K562_ChIPseq_MCM5_HU026_LY076c

tag: cell type

value: WT untreated


title: Sample403 [Rectal biopsy]

tag: gender


title: K562_Nailseq_EH_DRB30_HU020_LY068f

description: nascent DNA strand

value: EdU/HU

value: WT DRB 30 uM

value: S

value: Protocol 2:NAIL-seq EdU/HU


title: K562_Nailseq_EH_DRB5_HU020_LY068c

description: nascent DNA strand

value: human blood (chronic myelogenous leukemia)

value: WT DRB 5 uM


title: K562_Nailseq_EH_DRB0_HU020_LY068b

description: nascent DNA strand


title: Sample402 [Rectal biopsy]

value: 52wk FU

value: CS-IV

tag: colectomy


title: Sample401 [Rectal biopsy]

tag: disease


title: K562_Nailseq_EH_ama10_HU018_LY064d

description: nascent DNA strand

tag: technique

value: WT ama 10ug/mL


title: K562_Nailseq_EH_ama2_HU018_LY064c

description: nascent DNA strand

tag: nail-seq labeling strategy

value: WT ama 2ug/mL


title: K562_Nailseq_EH_ama0_HU018_LY064b

description: nascent DNA strand

tag: treatment


title: Sample396 [Rectal biopsy]

value: CS-Oral

value: pediatric ulcerative colitis


title: K562_Nailseq_EB_BrdU_rep2_HU041_LY105b

description: nascent DNA strand

value: NAIL-seq

value: E+B

tag: cell phase

value: BrdU


title: Sample397 [Rectal biopsy]

value: M


title: Sample398 [Rectal biopsy]


title: K562_Nailseq_EB_EdU_rep2_HU041_LY105f

description: nascent DNA strand

value: WT untreated

value: EdU

value: Protocol 1:NAIL-seq EdU+BrdU


title: Sample393 [Rectal biopsy]

value: F


title: K562_ChIPseq_ORC2_HU047_LY111d

value: ChIP-seq

value: Protocol 3 ORC2/MCM5 ChIP-seq


title: K562_ChIPseq_ORC2-ama_HU047_LY111e

value: human blood (chronic myelogenous leukemia)


title: K562_Nailseq_EB_BrdU_rep1_HU041_LY105a

description: nascent DNA strand

value: S


title: K562_Nailseq_EH_EdUHU_HU021_LY058e

description: nascent DNA strand

value: EdU/HU

value: Protocol 2:NAIL-seq EdU/HU


title: Sample394 [Rectal biopsy]

value: 52wk FU


title: K562_Nailseq_EB_EdU_rep1_HU041_LY105e

description: nascent DNA strand


title: Tubuli sample-RNA-seq_rep30 [HK472T]

city: Philadelphia

first: Xin

last: Sheng

institute: University of Pennsylvania

description:
processed data file: TubSamplesTPM.txt.gz
HK472

data_processing:
Sequence quality was assessed with FastQC. Adaptors and low-quality bases were trimmed using Trim-galore (v0.4.4). RNA-seq reads were then aligned to the human genome (hg19/GRCh37) using STAR (v2.4.1d) based on GENCODE v19 annotations. Gene-level read count quantifications were estimated using RSEM (v1.3.1). The estimated read counts of each sample were normalized using DESeq2 (v1.22.2) and then log-transformed with an offset of 1. Genes, with log-transformed value > 1 in > 5% of samples, were retained. The resulting read counts were then centered and unit-normalized. Next, we conducted hierarchically cluster on the resulting matrix based on average and cosine distance. We calculated a two-sided chi2 P-value based on Mahalanobis distance from the center of a 20-dimensional PC space. 5 samples (3 for tubule and 2 for glomerular) were identified as outliers (≥60% samples with Bonferroni-adjusted p-values <0.05) and excluded. Sex compatibility checks were conducted based on XIST, and genes located on chromosome Y. 5 samples, with inconsistent gender were removed from the downstream analysis. 15 samples with age below 20 were further excluded. The estimated read counts were normalized across samples using TMM methods implemented in edgeR (v3.24.3), and gene expression levels were estimated as transcripts per million (TPM). Only genes with at least 0.1 TPM in at least 20% samples for each kidney compartment were considered as expressed and used for the downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: Tubuli sample-RNA-seq

growth_protocol: De-identified human kidney samples were obtained from unaffected portion of tumor nephrectomies. Samples were de-identified and no HPI was collected via an honest broker via the CHTN. The study was deemed IRB exempt (exemption IV).

extract_protocol:
The human kidney tissue was manually microdissected for glomerular and tubular compartments in RNAlater. Generally, 60-150 glomeruli that readily released from the capsule were collected and placed into RNeasy RNA Tissue Lysis Buffer Solution (Qiagen no. 741006).
Only samples with RIN scores above 7 and a minimum total RNA of 100 ng were used for cDNA production. Nonstrand-specific, poly A+ - selected RNA-seq libraries were generated using the Illumina TruSeq protocol. Libraries were sequenced to a median depth of 35 million 100-bp Single reads.

tag: age

value: Male

tag: race

value: White

tag: disease state

value: Healthy

tag: tissue

value: Tubuli


title: Sample392 [Rectal biopsy]

tag: individual

tag: age at diagnosis

value: pediatric ulcerative colitis


title: Sample390 [Rectal biopsy]

value: M

tag: time of sampling

value: CS-Oral


title: Sample389 [Rectal biopsy]

tag: initial treatment


title: Tubuli sample-RNA-seq_rep29 [HK504T]

description:
processed data file: TubSamplesTPM.txt.gz
HK504


title: Sample391 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep28 [HK522T]

description:
processed data file: TubSamplesTPM.txt.gz
HK522

value: Female


title: Tubuli sample-RNA-seq_rep27 [HK353T]

description:
processed data file: TubSamplesTPM.txt.gz
HK353

value: African American


title: Tubuli sample-RNA-seq_rep26 [HK17T]

description:
processed data file: TubSamplesTPM.txt.gz
HK17


title: Sample399 [Rectal biopsy]

value: F

value: CS-IV


title: Sample388 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep25 [HK339T]

description:
processed data file: TubSamplesTPM.txt.gz
HK339


title: Tubuli sample-RNA-seq_rep24 [HK196T]

description:
processed data file: TubSamplesTPM.txt.gz
HK196


title: Sample387 [Rectal biopsy]


title: Sample395 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep23 [HK232T]

description:
processed data file: TubSamplesTPM.txt.gz
HK232


title: Tubuli sample-RNA-seq_rep22 [HK464T]

description:
processed data file: TubSamplesTPM.txt.gz
HK464

value: Hispanic


title: Sample385 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep21 [HK520T]

description:
processed data file: TubSamplesTPM.txt.gz
HK520


title: Sample386 [Rectal biopsy]


title: Sample384 [Rectal biopsy]


title: Sample383 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep20 [HK519T]

description:
processed data file: TubSamplesTPM.txt.gz
HK519


title: Sample380 [Rectal biopsy]


title: Sample382 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep19 [HK517T]

description:
processed data file: TubSamplesTPM.txt.gz
HK517


title: Tubuli sample-RNA-seq_rep17 [HK512T]

description:
processed data file: TubSamplesTPM.txt.gz
HK512


title: Tubuli sample-RNA-seq_rep18 [HK513T]

description:
processed data file: TubSamplesTPM.txt.gz
HK513


title: Sample379 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep16 [HK511T]

description:
processed data file: TubSamplesTPM.txt.gz
HK511


title: Sample378 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep15 [HK508T]

description:
processed data file: TubSamplesTPM.txt.gz
HK508


title: Tubuli sample-RNA-seq_rep14 [HK503T]

description:
processed data file: TubSamplesTPM.txt.gz
HK503


title: Sample377 [Rectal biopsy]


title: Sample376 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep13 [HK501T]

description:
processed data file: TubSamplesTPM.txt.gz
HK501


title: Sample375 [Rectal biopsy]


title: Sample373 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep12 [HK479T]

description:
processed data file: TubSamplesTPM.txt.gz
HK479


title: Sample374 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep11 [HK473T]

description:
processed data file: TubSamplesTPM.txt.gz
HK473


title: Tubuli sample-RNA-seq_rep10 [HK462T]

description:
processed data file: TubSamplesTPM.txt.gz
HK462


title: Sample372 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep9 [HK441T]

description:
processed data file: TubSamplesTPM.txt.gz
HK441


title: Sample400 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep8 [HK39T]

description:
processed data file: TubSamplesTPM.txt.gz
HK39


title: Sample381 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep7 [HK398T]

description:
processed data file: TubSamplesTPM.txt.gz
HK398


title: Sample370 [Rectal biopsy]


title: Sample369 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep5 [HK282T]

description:
processed data file: TubSamplesTPM.txt.gz
HK282


title: Sample367 [Rectal biopsy]


title: Sample368 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep4 [HK254T]

description:
processed data file: TubSamplesTPM.txt.gz
HK254

value: Multiracial


title: Sample366 [Rectal biopsy]


title: Sample365 [Rectal biopsy]


title: Sample364 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep1 [HK224T]

description:
processed data file: TubSamplesTPM.txt.gz
HK224


title: Sample362 [Rectal biopsy]


title: Sample363 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep38 [HK567G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK567G_GAGTGG

source_name: Glomeruli sample-RNA-seq

value: Glomeruli


title: Tubuli sample-RNA-seq_rep3 [HK241T]

description:
processed data file: TubSamplesTPM.txt.gz
HK241


title: Glomeruli sample-RNA-seq_rep35 [HK558G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK558G_ACTTGA


title: Sample361 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep36 [HK559G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK559G_GTTTCG


title: Sample360 [Rectal biopsy]


title: Sample359 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep2 [HK233T]

description:
processed data file: TubSamplesTPM.txt.gz
HK233


title: Glomeruli sample-RNA-seq_rep33 [HK556G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK556G_GTGAAA


title: Sample358 [Rectal biopsy]


title: Sample371 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep37 [HK560G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK560G_CGTACG


title: Glomeruli sample-RNA-seq_rep34 [HK557G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK557G_GTGGCC


title: Sample357 [Rectal biopsy]


title: Tubuli sample-RNA-seq_rep6 [HK283T]

description:
processed data file: TubSamplesTPM.txt.gz
HK283


title: Sample356 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep32 [HK554G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK554G_GTCCGC


title: Glomeruli sample-RNA-seq_rep31 [HK552G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK552G_ATTCCT


title: Sample355 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep30 [HK551G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK551G_CCGTCC


title: Glomeruli sample-RNA-seq_rep29 [HK549G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK549G_AGTTCC


title: Glomeruli sample-RNA-seq_rep28 [HK544G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK544G_AGTCAA


title: Sample353 [Rectal biopsy]

value: Baseline


title: Sample354 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep27 [HK541G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK541G_CAGATC


title: Sample351 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep26 [HK540G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK540G_GCCAAT


title: Sample352 [Rectal biopsy]


title: Sample350 [Rectal biopsy]


title: Sample349 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep25 [HK538G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK538G_TGACCA


title: Sample348 [Rectal biopsy]


title: Sample347 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep23 [HK534G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK534G_CGATGT


title: Glomeruli sample-RNA-seq_rep22 [HK531G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK531G_GATCAG


title: Sample346 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep21 [HK529G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK529G_ACTGAT


title: Sample344 [Rectal biopsy]


title: Sample342 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep20 [HK528G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK528G_GAGTGG


title: Glomeruli sample-RNA-seq_rep19 [HK526G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK526G_CGTACG


title: Sample343 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep18 [HK522G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK522G_GTTTCG


title: Sample341 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep17 [HK520G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK520G_GTGGCC


title: Sample340 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep16 [HK519G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK519G_ACTTGA


title: Sample339 [Rectal biopsy]


title: Sample337 [Rectal biopsy]


title: Sample338 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep15 [HK512G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK512G_ACAGTG


title: Glomeruli sample-RNA-seq_rep14 [HK504G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK504G_ATTCCT


title: Sample336 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep11 [HK479G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK479G_CCGTCC


title: Glomeruli sample-RNA-seq_rep24 [HK536G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK536G_TAGCTT


title: Sample334 [Rectal biopsy]


title: Sample332 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep9 [HK472G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK472G_AGTCAA


title: Sample333 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep8 [HK466G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK466G_CTTGTA


title: Sample331 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep7 [HK464G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK464G_GGCTAC


title: Sample330 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep4 [HK39G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK39G_ACTTGA


title: Glomeruli sample-RNA-seq_rep5 [HK444G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK444G_GATCAG


title: Sample327 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep6 [HK463G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK463G_TAGCTT


title: Glomeruli sample-RNA-seq_rep3 [HK331G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK331G_CGATGT


title: Sample326 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep2 [HK315G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK315G_GCCAAT


title: Sample325 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep13 [HK503G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK503G_TGACCA


title: Sample335 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep12 [HK481G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK481G_TTAGGC


title: Sample323 [Rectal biopsy]


title: Sample324 [Rectal biopsy]


title: Glomeruli sample-RNA-seq_rep1 [HK238G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK238G_TGACCA


title: 12 hpi replicate 2 control

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

data_processing:
Raw RNA-Sequencing (RNA-Seq) reads were obtained from McMaster University as 50 bp paired-end reads in FASTQ format with a minimum of 21 million reads per sample. Reads were analyzed for various quality control parameters including: per base sequence quality, per sequence GC content, sequence length distribution and sequence duplication levels and Kmer content using the FastQC tool.
Paired-end sequencing reads were mapped to the human reference transcriptome (GRCh37.67) obtained from the ENSEMBL database using the ‘quant’ function of Salmon, transcript counts summarized at the gene-level using the corresponding transcriptome GTF file mappings obtained from ENSEMBL
Transcript count data was normalized using DeSeq2's 'estimateSizeFactors' function using the default 'median ratio method’.
Genome_build: GRCh37.67
Supplementary_files_format_and_content: EXCEL DeSeq2 normalized counts

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 12 hours post-infecttion (hpi).

growth_protocol: Calu-3 cells (human lung adenocarcinoma derived; ATCC) were cultured as cited previously in Physiol Rep 7, e14249 (2019).

extract_protocol:
RNA was isolated using TRIzol reagent (Invitrogen, CA, USA). Sample quality was first assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer G2938C, Aligent RNA 6000 Nano Kit, Agilent; Santa Clara, CA, USA ), then enriched (NEBNext Poly(A) mRNA Magnetic Isolation Module; NEB, Ipswich, MA, USA).
Library preparations were conducted using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) and library fragment size distribution verified using Agilent TapeSection D1000 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cells (Calu-3) were infected with SARS-CoV-2 at a multiplicity of infection (MOI) of 2. One hour post infection, the inoculum was removed and the clock was set to zero. poly-A enriched RNA was extracted at 0, 1, 2, 3, 6 and 12 hours post infection (hpi).

value: control

tag: time

value: 12 hpi

value: human lung epithelial cells

tag: cell line


title: 12 hpi replicate 3 control

tag: cell type


title: Sample321 [Rectal biopsy]

tag: gender

tag: colectomy


title: Glomeruli sample-RNA-seq_rep10 [HK473G]

description:
processed data file: GlomSamplesTPM.txt.gz
HK473G_AGTTCC


title: Sample320 [Rectal biopsy]

tag: disease


title: Sample329 [Rectal biopsy]


title: Sample328 [Rectal biopsy]


title: Sample318 [Rectal biopsy]


title: 12 hpi replicate 2 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 12 hours post-infecttion (hpi).

value: SARS-CoV-2 infection


title: Sample319 [Rectal biopsy]


title: Sample317 [Rectal biopsy]


title: Sample322 [Rectal biopsy]


title: Sample314 [Rectal biopsy]


title: Sample315 [Rectal biopsy]


title: 6 hpi replicate 2 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 6 hours post-infecttion (hpi).

value: 6 hpi


title: 6 hpi replicate 3 infected


title: 6 hpi replicate 1 control

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 6 hours post-infecttion (hpi).


title: 6 hpi replicate 3 control


title: 6 hpi replicate 2 control


title: Sample312 [Rectal biopsy]


title: Sample311 [Rectal biopsy]


title: 6 hpi replicate 1 infected


title: Sample309 [Rectal biopsy]


title: 3 hpi replicate 3 control

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 3 hours post-infecttion (hpi).

value: 3 hpi


title: 12 hpi replicate 3 infected


title: 3 hpi replicate 1 control


title: 3 hpi replicate 2 control


title: 12 hpi replicate 1 control


title: 12 hpi replicate 1 infected


title: Sample308 [Rectal biopsy]

value: pediatric ulcerative colitis


title: 3 hpi replicate 3 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 3 hours post-infecttion (hpi).


title: Sample310 [Rectal biopsy]


title: Sample316 [Rectal biopsy]

value: M


title: Sample307 [Rectal biopsy]

value: CS-Oral


title: 3 hpi replicate 2 infected


title: Sample305 [Rectal biopsy]


title: 3 hpi replicate 1 infected


title: Sample306 [Rectal biopsy]


title: 2 hpi replicate 3 control

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 2 hours post-infecttion (hpi).

value: 2 hpi


title: 2 hpi replicate 1 control


title: 2 hpi replicate 3 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 2 hours post-infecttion (hpi).


title: 2 hpi replicate 2 infected


title: Sample301 [Rectal biopsy]


title: 2 hpi replicate 1 infected


title: 2 hpi replicate 2 control


title: Sample302 [Rectal biopsy]


title: Sample300 [Rectal biopsy]


title: Sample299 [Rectal biopsy]


title: 1 hpi replicate 3 control

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 1 hours post-infecttion (hpi).

value: 1 hpi


title: Sample298 [Rectal biopsy]

value: F


title: 1 hpi replicate 1 control


title: Sample297 [Rectal biopsy]


title: 1 hpi replicate 2 control


title: Sample295 [Rectal biopsy]


title: Sample296 [Rectal biopsy]


title: 1 hpi replicate 1 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 1 hours post-infecttion (hpi).


title: 0 hpi replicate 3 control

source_name: Human lung epithelial cells (Calu-3) not infected with SARS-CoV-2 (control). RNA sampled at 0 hours post-infecttion (hpi).

value: 0 hpi


title: 1 hpi replicate 2 infected


title: Sample293 [Rectal biopsy]

value: CS-IV


title: 0 hpi replicate 2 control


title: Sample304 [Rectal biopsy]


title: Sample294 [Rectal biopsy]


title: 0 hpi replicate 1 control


title: Sample303 [Rectal biopsy]


title: Sample292 [Rectal biopsy]


title: Sample291 [Rectal biopsy]


title: 0 hpi replicate 2 infected

source_name: Human lung epithelial cells (Calu-3) infected with SARS-CoV-2. RNA sampled at 0 hours post-infecttion (hpi).


title: Sample290 [Rectal biopsy]

source_name: Rectal biopsy


title: Sample289 [Rectal biopsy]


title: Sample288 [Rectal biopsy]


title: Sample287 [Rectal biopsy]


title: 1 hpi replicate 3 infected


title: Sample286 [Rectal biopsy]


title: C4-2B-ENZR cell with KIF15 knockdown 2

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university

description: This sample is of C4-2B-ENZR transfected with siRNA of KIF15.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C4-2B-ENZR cells transfected with siRNA are referred as C4-2B-ENZR_NC and C4-2B-ENZR_siKIF15.

value: prostate cancer cell line C4-2B-ENZR

tag: genotype/variation

value: KIF15 knocked down


title: C4-2B-ENZR cell with KIF15 knockdown 1


title: C4-2B-ENZR cell as control 3

description: This sample is of C4-2B-ENZR transfected with siRNA of negtive control.

value: negative control


title: Sample285 [Rectal biopsy]

value: Baseline


title: Sample284 [Rectal biopsy]


title: C4-2B-ENZR cell as control 2


title: Sample283 [Rectal biopsy]


title: C4-2B-ENZR cell as control 1


title: Sample282 [Rectal biopsy]


title: Cardiac organoid timecourse Day 27 CHIR8-quantseq [CM_Organoid_D27_t10_C8_C-103303.3-quantseq]

city: Vienna

first: Pablo

last: Hofbauer

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

description:
CM_Organoid_D27_t10_C8_C-103303.3-quantseq
mRNA

data_processing:
Trimming was performed for Smart-Seq2 experiments using trim-galore v0.5.0 and for QuantSeq 3' mRNA-Seq experiments using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10  minlength=20).
Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and UCSC gene annotation provided in the iGenomes UCSC hg38 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Reads were aligned to the hg38 genome using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files with per gene read counts.

source_name: Cardiac organoid differentiation timecourse Day 27 (Maintenance, CHIR99021 8 µM, WTC)

growth_protocol: hPSCs were harvested at around 70% confluency. 5000 cells/well were subsequently seeded into ultra-low attachment 96-well plates (Corning) containing E8 + ROCKi (Y-27632, Tocris) and collected by spinning for 5 minutes at 200G. After 24h, formed aggregates were induced with FLyAB(Ins) containing 4-8 µM (WTC) or 1-3 µM (H9) CHIR99021. Cardiac differentiation was performed as described for 2D cultures. For maintenance of the obtained cardiac organoids, medium was changed to CDM-I and exchanged every second day.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen, #74104). Generation of the RNA-seq libraries was performed according to manufacturer’s instructions with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, #015). After the preparation of the libraries, samples were checked for an adequate size distribution with a fragment analyzer (Advanced Analytical Technologies, Inc) and were submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing. For Smart-Seq2 analysis, 400 cells were sorted into lysis buffer and stored at -80C until further processing. Samples were QC’d/libraries prepared and sequenced by the VBCF NGS facility using a home-made Smart-Seq2 kit.

tag: genotype

value: Cardiac organoid differentiation timecourse Day 27 (Maintenance, CHIR99021 8 uM, WTC)

tag: sequencing type

value: quant-seq


title: Sample281 [Rectal biopsy]


title: Sample280 [Rectal biopsy]


title: Sample279 [Rectal biopsy]


title: 0 hpi replicate 3 infected

tag: treatment

value: SARS-CoV-2 infection

value: human lung epithelial cells


title: Sample278 [Rectal biopsy]


title: 0 hpi replicate 1 infected


title: Cardiac organoid timecourse Day 27 CHIR8-quantseq [CM_Organoid_D27_t10_C8_C-103302.2-quantseq]

description:
CM_Organoid_D27_t10_C8_C-103302.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 27 CHIR8-quantseq [CM_Organoid_D27_t10_C8_C-103301.1-quantseq]

description:
CM_Organoid_D27_t10_C8_C-103301.1-quantseq
mRNA


title: Sample277 [Rectal biopsy]


title: Cardiac organoid timecourse Day 10 CHIR8-quantseq [CM_Organoid_D10_t9_C8_C-103291.3-quantseq]

description:
CM_Organoid_D10_t9_C8_C-103291.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 10 (Maintenance, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 10 (Maintenance, CHIR99021 8 uM, WTC)


title: Cardiac organoid timecourse Day 10 CHIR8-quantseq [CM_Organoid_D10_t9_C8_C-103290.2-quantseq]

description:
CM_Organoid_D10_t9_C8_C-103290.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 10 CHIR8-quantseq [CM_Organoid_D10_t9_C8_C-103289.1-quantseq]

description:
CM_Organoid_D10_t9_C8_C-103289.1-quantseq
mRNA


title: Sample276 [Rectal biopsy]

value: pediatric ulcerative colitis


title: C4-2B-ENZR cell with KIF15 knockdown 3


title: Sample275 [Rectal biopsy]


title: Cardiac organoid timecourse Day 7.5 CHIR8-quantseq [CM_Organoid_D7.5_t8_C8-103284.2-quantseq]

description:
CM_Organoid_D7.5_t8_C8-103284.2-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 7.5 (Cardiomyocyte Specification, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 7.5 (Cardiomyocyte Specification, CHIR99021 8 uM, WTC)


title: Cardiac organoid timecourse Day 7.5 CHIR8-quantseq [CM_Organoid_D7.5_t8_C8-103283.1-quantseq]

description:
CM_Organoid_D7.5_t8_C8-103283.1-quantseq
mRNA


title: Sample274 [Rectal biopsy]

value: M

value: CS-Oral


title: Cardiac organoid timecourse Day -1-quantseq [Pluri_D0_t0-103236.2-quantseq]

description:
Pluri_D0_t0-103236.2-quantseq
mRNA

source_name: induced pluripotent stem cells (WTC)

growth_protocol: Human pluripotent stem cell lines (H9, WiCell; WT and modified WTC, Allen Institute for Cell Science) were cultured in a modified in-house medium based on the E8 culture system (Thomson 2008). The original E8 recipe was supplemented with 0.5% BSA (Europa Biosciences) and in-house produced FGF2. Cells were grown on either Corning or Eppendorf tissue culture-treated plates coated with Vitronectin (Stem Cell Technologies) and passaged using either TrypLE Express Enzyme (Gibco) or PBS-EDTA every 3-4 days.

value: induced pluripotent stem cells (WTC)


title: Cardiac organoid timecourse Day -1-quantseq [Pluri_D0_t0-103235.1-quantseq]

description:
Pluri_D0_t0-103235.1-quantseq
mRNA


title: Sample272 [Rectal biopsy]

value: F


title: Cardiac organoid timecourse Day -1-quantseq [Pluri_D0_t0-103237.3-quantseq]

description:
Pluri_D0_t0-103237.3-quantseq
mRNA


title: Sample273 [Rectal biopsy]


title: Sample270 [Rectal biopsy]


title: Sample269 [Rectal biopsy]


title: Sample271 [Rectal biopsy]


title: Cardiac organoid timecourse Day 27 CHIR4-quantseq [CM_Organoid_D27_t10_C4_C-103300.3-quantseq]

description:
CM_Organoid_D27_t10_C4_C-103300.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 27 (Maintenance, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 27 (Maintenance, CHIR99021 4 uM, WTC)


title: Sample266 [Rectal biopsy]


title: Cardiac organoid timecourse Day 10 CHIR4-quantseq [CM_Organoid_D10_t9_C4_C-103288.3-quantseq]

description:
CM_Organoid_D10_t9_C4_C-103288.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 10 (Maintenance, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 10 (Maintenance, CHIR99021 4 uM, WTC)


title: Sample265 [Rectal biopsy]


title: Cardiac organoid timecourse Day 7.5 CHIR8-quantseq [CM_Organoid_D7.5_t8_C8-103285.3-quantseq]

description:
CM_Organoid_D7.5_t8_C8-103285.3-quantseq
mRNA


title: Cardiac organoid timecourse Day 10 CHIR4-quantseq [CM_Organoid_D10_t9_C4_C-103287.2-quantseq]

description:
CM_Organoid_D10_t9_C4_C-103287.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 27 CHIR4-quantseq [CM_Organoid_D27_t10_C4_C-103299.2-quantseq]

description:
CM_Organoid_D27_t10_C4_C-103299.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 10 CHIR4-quantseq [CM_Organoid_D10_t9_C4_C-103286.1-quantseq]

description:
CM_Organoid_D10_t9_C4_C-103286.1-quantseq
mRNA


title: Sample264 [Rectal biopsy]

value: CS-IV


title: Cardiac organoid timecourse Day 7.5 CHIR4-quantseq [CM_Organoid_D7.5_t8_C4-103282.3-quantseq]

description:
CM_Organoid_D7.5_t8_C4-103282.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 7.5 (Cardiomyocyte Specification, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 7.5 (Cardiomyocyte Specification, CHIR99021 4 uM, WTC)


title: Sample262 [Rectal biopsy]


title: Sample261 [Rectal biopsy]


title: Sample260 [Rectal biopsy]


title: Cardiac organoid timecourse Day 7.5 CHIR4-quantseq [CM_Organoid_D7.5_t8_C4-103280.1-quantseq]

description:
CM_Organoid_D7.5_t8_C4-103280.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 6.5 CHIR8-quantseq [CM_Organoid_D6.5_t7_C8-103279.3-quantseq]

description:
CM_Organoid_D6.5_t7_C8-103279.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 6.5 (Cardiomyocyte Specification, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 6.5 (Cardiomyocyte Specification, CHIR99021 8 uM, WTC)


title: Sample259 [Rectal biopsy]

value: Baseline


title: Cardiac organoid timecourse Day 6.5 CHIR8-quantseq [CM_Organoid_D6.5_t7_C8-103277.1-quantseq]

description:
CM_Organoid_D6.5_t7_C8-103277.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 6.5 CHIR8-quantseq [CM_Organoid_D6.5_t7_C8-103278.2-quantseq]

description:
CM_Organoid_D6.5_t7_C8-103278.2-quantseq
mRNA


title: Sample258 [Rectal biopsy]


title: Sample268 [Rectal biopsy]


title: Cardiac organoid timecourse Day 27 CHIR4-quantseq [CM_Organoid_D27_t10_C4_C-103298.1-quantseq]

description:
CM_Organoid_D27_t10_C4_C-103298.1-quantseq
mRNA


title: Sample256 [Rectal biopsy]


title: Cardiac organoid timecourse Day 6.5 CHIR4-quantseq [CM_Organoid_D6.5_t7_C4-103274.1-quantseq]

description:
CM_Organoid_D6.5_t7_C4-103274.1-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 6.5 (Cardiomyocyte Specification, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 6.5 (Cardiomyocyte Specification, CHIR99021 4 uM, WTC)


title: Sample257 [Rectal biopsy]


title: Sample267 [Rectal biopsy]


title: Sample255 [Rectal biopsy]


title: Cardiac organoid timecourse Day 6.5 CHIR4-quantseq [CM_Organoid_D6.5_t7_C4-103275.2-quantseq]

description:
CM_Organoid_D6.5_t7_C4-103275.2-quantseq
mRNA

value: quant-seq


title: Sample263 [Rectal biopsy]


title: Cardiac organoid timecourse Day 5.5 CHIR8-quantseq [CM_Organoid_D5.5_t6_C8-103273.3-quantseq]

description:
CM_Organoid_D5.5_t6_C8-103273.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 5.5 (Cardiac Mesoderm, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 5.5 (Cardiac Mesoderm, CHIR99021 8 uM, WTC)


title: Sample254 [Rectal biopsy]


title: Cardiac organoid timecourse Day 5.5 CHIR8-quantseq [CM_Organoid_D5.5_t6_C8-103272.2-quantseq]

description:
CM_Organoid_D5.5_t6_C8-103272.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 7.5 CHIR4-quantseq [CM_Organoid_D7.5_t8_C4-103281.2-quantseq]

description:
CM_Organoid_D7.5_t8_C4-103281.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 5.5 CHIR8-quantseq [CM_Organoid_D5.5_t6_C8-103271.1-quantseq]

description:
CM_Organoid_D5.5_t6_C8-103271.1-quantseq
mRNA


title: Sample253 [Rectal biopsy]


title: Sample251 [Rectal biopsy]


title: Sample252 [Rectal biopsy]


title: Cardiac organoid timecourse Day 5.5 CHIR4-quantseq [CM_Organoid_D5.5_t6_C4-103270.3-quantseq]

description:
CM_Organoid_D5.5_t6_C4-103270.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 5.5 (Cardiac Mesoderm, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 5.5 (Cardiac Mesoderm, CHIR99021 4 uM, WTC)


title: Cardiac organoid timecourse Day 5.5 CHIR4-quantseq [CM_Organoid_D5.5_t6_C4-103269.2-quantseq]

description:
CM_Organoid_D5.5_t6_C4-103269.2-quantseq
mRNA


title: Sample250 [Rectal biopsy]


title: Cardiac organoid timecourse Day 5.5 CHIR4-quantseq [CM_Organoid_D5.5_t6_C4-103268.1-quantseq]

description:
CM_Organoid_D5.5_t6_C4-103268.1-quantseq
mRNA


title: Sample249 [Rectal biopsy]


title: Cardiac organoid timecourse Day 6.5 CHIR4-quantseq [CM_Organoid_D6.5_t7_C4-103276.3-quantseq]

description:
CM_Organoid_D6.5_t7_C4-103276.3-quantseq
mRNA


title: Sample248 [Rectal biopsy]


title: Cardiac organoid timecourse Day 4.5 CHIR8-quantseq [CM_Organoid_D4.5_t5_C8-103267.3-quantseq]

description:
CM_Organoid_D4.5_t5_C8-103267.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 4.5 (Cardiac Mesoderm, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 4.5 (Cardiac Mesoderm, CHIR99021 8 uM, WTC)


title: Cardiac organoid timecourse Day 4.5 CHIR8-quantseq [CM_Organoid_D4.5_t5_C8-103265.1-quantseq]

description:
CM_Organoid_D4.5_t5_C8-103265.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 4.5 CHIR8-quantseq [CM_Organoid_D4.5_t5_C8-103266.2-quantseq]

description:
CM_Organoid_D4.5_t5_C8-103266.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 4.5 CHIR4-quantseq [CM_Organoid_D4.5_t5_C4-103264.3-quantseq]

description:
CM_Organoid_D4.5_t5_C4-103264.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 4.5 (Cardiac Mesoderm, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 4.5 (Cardiac Mesoderm, CHIR99021 4 uM, WTC)


title: Sample246 [Rectal biopsy]

value: pediatric ulcerative colitis


title: Sample245 [Rectal biopsy]

value: M


title: Cardiac organoid timecourse Day 4.5 CHIR4-quantseq [CM_Organoid_D4.5_t5_C4-103263.2-quantseq]

description:
CM_Organoid_D4.5_t5_C4-103263.2-quantseq
mRNA


title: Sample242 [Rectal biopsy]


title: Sample243 [Rectal biopsy]


title: Cardiac organoid timecourse Day 4.5 CHIR4-quantseq [CM_Organoid_D4.5_t5_C4-103262.1-quantseq]

description:
CM_Organoid_D4.5_t5_C4-103262.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 3.5 CHIR8-quantseq [CM_Organoid_D3.5_t4_C8-103259.1-quantseq]

description:
CM_Organoid_D3.5_t4_C8-103259.1-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 3.5 (Cardiac Mesoderm, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 3.5 (Cardiac Mesoderm, CHIR99021 8 uM, WTC)


title: Cardiac organoid timecourse Day 3.5 CHIR8-quantseq [CM_Organoid_D3.5_t4_C8-103260.2-quantseq]

description:
CM_Organoid_D3.5_t4_C8-103260.2-quantseq
mRNA


title: Sample241 [Rectal biopsy]


title: Sample240 [Rectal biopsy]

value: 52wk FU


title: Cardiac organoid timecourse Day 3.5 CHIR4-quantseq [CM_Organoid_D3.5_t4_C4-103258.3-quantseq]

description:
CM_Organoid_D3.5_t4_C4-103258.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 3.5 (Cardiac Mesoderm, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 3.5 (Cardiac Mesoderm, CHIR99021 4 uM, WTC)


title: Cardiac organoid timecourse Day 3.5 CHIR4-quantseq [CM_Organoid_D3.5_t4_C4-103256.1-quantseq]

description:
CM_Organoid_D3.5_t4_C4-103256.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 3.5 CHIR8-quantseq [CM_Organoid_D3.5_t4_C8-103261.3-quantseq]

description:
CM_Organoid_D3.5_t4_C8-103261.3-quantseq
mRNA


title: Cardiac organoid timecourse Day 2.5 CHIR8-quantseq [CM_Organoid_D2.5_t3_C8-103255.3-quantseq]

description:
CM_Organoid_D2.5_t3_C8-103255.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 2.5 (Cardiac Mesoderm, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 2.5 (Cardiac Mesoderm, CHIR99021 8 uM, WTC)


title: Sample237 [Rectal biopsy]

source_name: Rectal biopsy


title: Sample239 [Rectal biopsy]


title: Sample235 [Rectal biopsy]

value: F

value: CS-Oral


title: Sample247 [Rectal biopsy]


title: Cardiac organoid timecourse Day 2.5 CHIR8-quantseq [CM_Organoid_D2.5_t3_C8-103254.2-quantseq]

description:
CM_Organoid_D2.5_t3_C8-103254.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 2.5 CHIR8-quantseq [CM_Organoid_D2.5_t3_C8-103253.1-quantseq]

description:
CM_Organoid_D2.5_t3_C8-103253.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 3.5 CHIR4-quantseq [CM_Organoid_D3.5_t4_C4-103257.2-quantseq]

description:
CM_Organoid_D3.5_t4_C4-103257.2-quantseq
mRNA


title: Sample234 [Rectal biopsy]

value: CS-IV


title: Cardiac organoid timecourse Day 2.5 CHIR4-quantseq [CM_Organoid_D2.5_t3_C4-103252.3-quantseq]

description:
CM_Organoid_D2.5_t3_C4-103252.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 2.5 (Cardiac Mesoderm, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 2.5 (Cardiac Mesoderm, CHIR99021 4 uM, WTC)


title: Sample244 [Rectal biopsy]

value: Baseline


title: Sample233 [Rectal biopsy]


title: Cardiac organoid timecourse Day 2.5 CHIR4-quantseq [CM_Organoid_D2.5_t3_C4-103251.2-quantseq]

description:
CM_Organoid_D2.5_t3_C4-103251.2-quantseq
mRNA


title: Sample231 [Rectal biopsy]


title: Sample236 [Rectal biopsy]


title: Cardiac organoid timecourse Day 2.5 CHIR4-quantseq [CM_Organoid_D2.5_t3_C4-103250.1-quantseq]

description:
CM_Organoid_D2.5_t3_C4-103250.1-quantseq
mRNA


title: Cardiac organoid timecourse Day 1.5 CHIR8-quantseq [CM_Organoid_D1.5_t2_C8-103249.3-quantseq]

description:
CM_Organoid_D1.5_t2_C8-103249.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 1.5 (Mesoderm Induction, CHIR99021 8 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 1.5 (Mesoderm Induction, CHIR99021 8 uM, WTC)


title: Sample232 [Rectal biopsy]


title: Cardiac organoid timecourse Day 1.5 CHIR8-quantseq [CM_Organoid_D1.5_t2_C8-103248.2-quantseq]

description:
CM_Organoid_D1.5_t2_C8-103248.2-quantseq
mRNA

value: quant-seq


title: Sample229 [Rectal biopsy]


title: Sample230 [Rectal biopsy]


title: Sample238 [Rectal biopsy]


title: Cardiac organoid timecourse Day 1.5 CHIR8-quantseq [CM_Organoid_D1.5_t2_C8-103247.1-quantseq]

description:
CM_Organoid_D1.5_t2_C8-103247.1-quantseq
mRNA


title: Sample227 [Rectal biopsy]


title: Cardiac organoid timecourse Day 1.5 CHIR4-quantseq [CM_Organoid_D1.5_t2_C4-103246.3-quantseq]

description:
CM_Organoid_D1.5_t2_C4-103246.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 1.5 (Mesoderm Induction, CHIR99021 4 µM, WTC)

value: Cardiac organoid differentiation timecourse Day 1.5 (Mesoderm Induction, CHIR99021 4 uM, WTC)


title: Sample228 [Rectal biopsy]


title: Cardiac organoid timecourse Day 1.5 CHIR4-quantseq [CM_Organoid_D1.5_t2_C4-103245.2-quantseq]

description:
CM_Organoid_D1.5_t2_C4-103245.2-quantseq
mRNA


title: Cardiac organoid timecourse Day 1.5 CHIR4-quantseq [CM_Organoid_D1.5_t2_C4-103244.1-quantseq]

description:
CM_Organoid_D1.5_t2_C4-103244.1-quantseq
mRNA


title: Sample313 [Rectal biopsy]


title: Sample225 [Rectal biopsy]


title: Sample220 [Rectal biopsy]


title: Sample223 [Rectal biopsy]


title: Sample222 [Rectal biopsy]


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C8-103243.3-quantseq]

description:
Pluri_D1_t1_C8-103243.3-quantseq
mRNA

source_name: Cardiac organoid differentiation timecourse Day 0 (3D aggregated Pluripotent Stem Cells, WTC)


title: Sample224 [Rectal biopsy]


title: Sample217 [Rectal biopsy]


title: Sample219 [Rectal biopsy]


title: Sample216 [Rectal biopsy]


title: Sample215 [Rectal biopsy]


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C8-103242.2-quantseq]

description:
Pluri_D1_t1_C8-103242.2-quantseq
mRNA

value: Cardiac organoid differentiation timecourse Day 0 (3D aggregated Pluripotent Stem Cells, WTC)


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C4-103240.3-quantseq]

description:
Pluri_D1_t1_C4-103240.3-quantseq
mRNA


title: Sample221 [Rectal biopsy]


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C4-103238.1-quantseq]

description:
Pluri_D1_t1_C4-103238.1-quantseq
mRNA


title: 3D_Cardiac_Organoid_CM_Day7.5_+Sunitinib_WTC-quantseq [CM_Organoid_D7_Sun-114942.2-quantseq]

description:
CM_Organoid_D7_Sun-114942.2-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 7.5, WTC)

treatment_protocol: 100 ng/ml Sunitinib was added from Cardiac Mesoderm stage onward.


title: 3D_Cardiac_Organoid_CM_Day7.5_+Sunitinib_WTC-quantseq [CM_Organoid_D7_Sun-114946.3-quantseq]

description:
CM_Organoid_D7_Sun-114946.3-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 7.5, WTC)


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C4-103239.2-quantseq]

description:
Pluri_D1_t1_C4-103239.2-quantseq
mRNA


title: Pluripotent Stem Cells_H9-quantseq [Pluri_H9-75577.5-quantseq]

description:
Pluri_H9-75577.5-quantseq
mRNA

source_name: Pluripotent stem cells (H9)

value: Wild-type

value: Pluripotent stem cells (H9)


title: Cardiac organoid timecourse Day 0-quantseq [Pluri_D1_t1_C8-103241.1-quantseq]

description:
Pluri_D1_t1_C8-103241.1-quantseq
mRNA


title: 3D_Cardiac_Organoid_CM_Day7.5_WTC-quantseq [CM_Organoid_D7-114948.5-quantseq]

description:
CM_Organoid_D7-114948.5-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes (Day 7.5, WTC)


title: 3D_Cardiac_Organoid_CM_Day7.5_+Sunitinib_WTC-quantseq [CM_Organoid_D7_Sun-114938.1-quantseq]

description:
CM_Organoid_D7_Sun-114938.1-quantseq
mRNA


title: Sample213 [Rectal biopsy]

value: pediatric ulcerative colitis


title: 3D_Cardiac_Organoid_CM_Day27_+Sunitinib_WTC-quantseq [CM_Organoid_D27_Sun-114968.3-quantseq]

description:
CM_Organoid_D27_Sun-114968.3-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 27, WTC)


title: Sample214 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CM_Day27_+Sunitinib_WTC-quantseq [CM_Organoid_D27_Sun-114966.2-quantseq]

description:
CM_Organoid_D27_Sun-114966.2-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 27, WTC)


title: Sample212 [Rectal biopsy]

value: M


title: Sample226 [Rectal biopsy]


title: Sample211 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CM_Day7.5_WTC-quantseq [CM_Organoid_D7-114940.4-quantseq]

description:
CM_Organoid_D7-114940.4-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes (Day 7.5, WTC)


title: Sample218 [Rectal biopsy]


title: Sample209 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CM_Day27_WTC-quantseq [CM_Organoid_D27-114964.4-quantseq]

description:
CM_Organoid_D27-114964.4-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes (Day 27, WTC)


title: 3D_Cardiac_Organoid_CM_Day10_+Sunitinib_WTC-quantseq [CM_Organoid_D10_Sun-114954.2-quantseq]

description:
CM_Organoid_D10_Sun-114954.2-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 10, WTC)


title: Sample210 [Rectal biopsy]


title: Sample206 [Rectal biopsy]


title: Sample208 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CM_Day27_WTC-quantseq [CM_Organoid_D27-114970.5-quantseq]

description:
CM_Organoid_D27-114970.5-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes (Day 27, WTC)


title: 3D_Cardiac_Organoid_CM_Day10_+Sunitinib_WTC-quantseq [CM_Organoid_D10_Sun-114958.3-quantseq]

description:
CM_Organoid_D10_Sun-114958.3-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes + Sunitinib (Day 10, WTC)


title: 3D_Cardiac_Organoid_CM_Day10_WTC-quantseq [CM_Organoid_D10-114956.5-quantseq]

description:
CM_Organoid_D10-114956.5-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes (Day 10, WTC)


title: 3D_Cardiac_Organoid_CM_Day27_+Sunitinib_WTC-quantseq [CM_Organoid_D27_Sun-114962.1-quantseq]

description:
CM_Organoid_D27_Sun-114962.1-quantseq
mRNA


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-99045.1-quantseq]

description:
CMEC_Organoid_D7_H9-99045.1-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 7.5, H9)

growth_protocol: Pluripotency maintenance medium was refreshed 6h prior to seeding cells. Then, 2500-3000 hPSC were seeded into ultra-low cluster 96-well plates (Corning) in FLyAB(Ins) medium with CHIR99021 (5-6 µM for WTC, 1.5 µM for H9) and ROCKi (5 µM) for 36h-40h. Next, medium was exchanged to BFIIWPRa with the addition of VEGF-A (200 ng/ml, Peprotech) for 4 days with medium exchanged every day. Subsequently, medium was exchanged to BFI + VEGF-A (100 ng/ml) for 2 days with a medium change after 1 day. For maintenance, CDM medium with 100 ng/ml of VEGF-A was used and exchanged every second day. For Smart-Seq2 analysis, Day 7.5 organoids containing cardiomyocytes and endothelial cells were dissociated using the StemDiff cardiomyocyte dissociation kit (Stem Cell Technologies, Catalog #05010) and GFP+ CMs and Tomato+ ECs as well as GFP-/Tomato- cells were FACS-sorted into lysis buffer.


title: Sample203 [Rectal biopsy]

value: CS-Oral


title: Sample200 [Rectal biopsy]

value: F


title: Sample205 [Rectal biopsy]


title: Sample201 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-99046.2-quantseq]

description:
CMEC_Organoid_D7_H9-99046.2-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 7.5, H9)


title: 3D_Cardiac_Organoid_CM_Day10_+Sunitinib_WTC-quantseq [CM_Organoid_D10_Sun-114950.1-quantseq]

description:
CM_Organoid_D10_Sun-114950.1-quantseq
mRNA


title: 3D_Cardiac_Organoid_CM_Day10_WTC-quantseq [CM_Organoid_D10-114952.4-quantseq]

description:
CM_Organoid_D10-114952.4-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes (Day 10, WTC)


title: Sample199 [Rectal biopsy]

value: Baseline


title: Sample202 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-104273.5-quantseq]

description:
CMEC_Organoid_D7_H9-104273.5-quantseq
mRNA

value: quant-seq


title: Sample197 [Rectal biopsy]

value: CS-IV


title: Sample198 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-104272.6-quantseq]

description:
CMEC_Organoid_D7_H9-104272.6-quantseq
mRNA


title: Sample207 [Rectal biopsy]


title: Sample204 [Rectal biopsy]


title: Sample196 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-104271.4-quantseq]

description:
CMEC_Organoid_D7_H9-104271.4-quantseq
mRNA


title: 3D_Cardiac_Organoid_CM_Day10_WTC-quantseq [CM_Organoid_D10-114960.6-quantseq]

description:
CM_Organoid_D10-114960.6-quantseq
mRNA


title: 3D_Cardiac_Organoid_CMEC_Day7.5_H9-quantseq [CMEC_Organoid_D7_H9-99047.3-quantseq]

description:
CMEC_Organoid_D7_H9-99047.3-quantseq
mRNA


title: 3D_Cardiac_Organoid_CMEC_Day7.5_WTC-quantseq [CMEC_Organoid_D7-104253.3-quantseq]

description:
CMEC_Organoid_D7-104253.3-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 7.5, WTC)


title: Sample194 [Rectal biopsy]


title: Sample193 [Rectal biopsy]


title: Sample195 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day27_WTC-quantseq [CMEC_Organoid_D27-104264.4-quantseq]

description:
CMEC_Organoid_D27-104264.4-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 27, WTC)


title: 3D_Cardiac_Organoid_CMEC_Day7.5_WTC-quantseq [CMEC_Organoid_D7-104251.2-quantseq]

description:
CMEC_Organoid_D7-104251.2-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 7.5, WTC)


title: 3D_Cardiac_Organoid_CMEC_Day27_WTC-quantseq [CMEC_Organoid_D27-104265.5-quantseq]

description:
CMEC_Organoid_D27-104265.5-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 27, WTC)


title: 3D_Cardiac_Organoid_CMEC_Day7.5_WTC-quantseq [CMEC_Organoid_D7-104249.1-quantseq]

description:
CMEC_Organoid_D7-104249.1-quantseq
mRNA


title: Sample189 [Rectal biopsy]


title: Sample191 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day27_WTC-quantseq [CMEC_Organoid_D27-104261.1-quantseq]

description:
CMEC_Organoid_D27-104261.1-quantseq
mRNA


title: 3D_Cardiac_Organoid_CMEC_Day27_WTC-quantseq [CMEC_Organoid_D27-104262.2-quantseq]

description:
CMEC_Organoid_D27-104262.2-quantseq
mRNA


title: Sample190 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day10_WTC-quantseq [CMEC_Organoid_D10-104276.3-quantseq]

description:
CMEC_Organoid_D10-104276.3-quantseq
mRNA

source_name: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 10, WTC)


title: Sample188 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day10_WTC-quantseq [CMEC_Organoid_D10-104275.2-quantseq]

description:
CMEC_Organoid_D10-104275.2-quantseq
mRNA

value: 3D cardiac organoids containing cardiomyocytes and endothelial cells (Day 10, WTC)


title: Sample186 [Rectal biopsy]


title: 3D_Cardiac_Organoid_CMEC_Day10_WTC-quantseq [CMEC_Organoid_D10-104274.1-quantseq]

description:
CMEC_Organoid_D10-104274.1-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-75617.8-quantseq]

description:
Assembled_CM_D27_H9-75617.8-quantseq
mRNA

source_name: 3D Assembled Cardiomyocytes Day 27 (H9)

growth_protocol: For the generation of assembled/aggregated cardiomyocytes, cardiomyocytes maintained until Day 21 were dissociated using the StemDiff cardiomyocyte dissociation kit (Stem Cell Technologies) and re-seeded as aggregates in AggreWell400 plates (Stem Cell Technologies) at 1000 cells/well in CDM-I and 5% FBS (PAA). After 2 days, formed aggregates were transferred to ultra-low cluster 96-well plates (Corning) in CDM-I and put on a shaker at 58 rpm, 37C and 5% CO2. After 4 days, with a medium change after 2 days, the aggregates were used for analysis.

value: 3D Assembled Cardiomyocytes Day 27 (H9)


title: Sample184 [Rectal biopsy]

source_name: Rectal biopsy

value: pediatric ulcerative colitis


title: 3D_Cardiac_Organoid_CMEC_Day27_WTC-quantseq [CMEC_Organoid_D27-104263.3-quantseq]

description:
CMEC_Organoid_D27-104263.3-quantseq
mRNA


title: Sample185 [Rectal biopsy]


title: Sample183 [Rectal biopsy]


title: Sample187 [Rectal biopsy]


title: Sample182 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70018.6-quantseq]

description:
Assembled_CM_D27_H9-70018.6-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-75616.7-quantseq]

description:
Assembled_CM_D27_H9-75616.7-quantseq
mRNA


title: Sample192 [Rectal biopsy]


title: Sample181 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70016.5-quantseq]

description:
Assembled_CM_D27_H9-70016.5-quantseq
mRNA


title: Sample180 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70013.4-quantseq]

description:
Assembled_CM_D27_H9-70013.4-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70012.3-quantseq]

description:
Assembled_CM_D27_H9-70012.3-quantseq
mRNA


title: Sample179 [Rectal biopsy]


title: Sample178 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70008.1-quantseq]

description:
Assembled_CM_D27_H9-70008.1-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_H9-quantseq [Assembled_CM_D27_H9-70009.2-quantseq]

description:
Assembled_CM_D27_H9-70009.2-quantseq
mRNA


title: Sample176 [Rectal biopsy]


title: Sample175 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-99059.8-quantseq]

description:
Assembled_CM_D27-99059.8-quantseq
mRNA

source_name: 3D Assembled Cardiomyocytes Day 27 (WTC)


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-99058.7-quantseq]

description:
Assembled_CM_D27-99058.7-quantseq
mRNA

value: 3D Assembled Cardiomyocytes Day 27 (WTC)


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-99055.6-quantseq]

description:
Assembled_CM_D27-99055.6-quantseq
mRNA


title: Sample172 [Rectal biopsy]


title: Sample171 [Rectal biopsy]


title: Sample170 [Rectal biopsy]

value: M


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-99053.4-quantseq]

description:
Assembled_CM_D27-99053.4-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-88282.3-quantseq]

description:
Assembled_CM_D27-88282.3-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-88281.2-quantseq]

description:
Assembled_CM_D27-88281.2-quantseq
mRNA


title: Sample168 [Rectal biopsy]


title: Sample167 [Rectal biopsy]


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-88280.1-quantseq]

description:
Assembled_CM_D27-88280.1-quantseq
mRNA


title: Sample166 [Rectal biopsy]


title: Sample165 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75627.12-quantseq]

description:
2D_CM_D27_H9-75627.12-quantseq
mRNA

source_name: 2D differentiated cardiomyocytes_Day 27 (H9)

growth_protocol: hPSCs were seeded at 160-175,000 cells/24 well plate in E8 + ROCKi (Y-27632, Tocris) for 24h. Cells were then induced for 36h-40h with CDM medium (Mendjan et al. 2014) containing FGF2 (30 ng/ml, Cambridge University), LY294002 (5 µM, Tocris), Activin A (50 ng/ml, Cambridge University), BMP4 (10 ng/ml, R&D Systems), CHIR99021 (1-1.5 µM for H9, 3-4 µM for WTC, Tocris). 1 µg/ml of Insulin (Roche/Sigma-Aldrich, #11376497001) was optionally added to increase cell viability during this stage. This medium was termed FLyABCH(Ins). Following 36h-40h, cells were induced with CDM medium containing BMP4 (10ng/ml), FGF2 (8 ng/ml), Insulin (10 µg/ml), IWP2 (5µM, Tocris) and Retinoic Acid (0.5 µM, Sigma Aldrich) for 4 days with medium change every day. This medium was termed BFIIWPRa. Subsequently, the medium was changed to CDM medium containing BMP4 (10ng/ml), FGF2 (8 ng/ml) and Insulin (10 µg/ml) for 2 days with medium change every day. This medium was termed BFI. For maintenance of the obtained cardiomyocytes, medium was changed to CDM medium containing Insulin (10 µg/ml) and half the medium exchanged every day.


title: Sample177 [Rectal biopsy]


title: Sample164 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75621.11-quantseq]

description:
2D_CM_D27_H9-75621.11-quantseq
mRNA

value: 2D differentiated cardiomyocytes_Day 27 (H9)


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75619.9-quantseq]

description:
2D_CM_D27_H9-75619.9-quantseq
mRNA


title: Sample163 [Rectal biopsy]


title: Sample173 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75620.1-quantseq]

description:
2D_CM_D27_H9-75620.1-quantseq
mRNA


title: 3D_Assembled_Cardiomyocytes_Day27_WTC-quantseq [Assembled_CM_D27-99054.5-quantseq]

description:
Assembled_CM_D27-99054.5-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-73344.5-quantseq]

description:
2D_CM_D27_H9-73344.5-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-73328.8-quantseq]

description:
2D_CM_D27_H9-73328.8-quantseq
mRNA


title: Sample169 [Rectal biopsy]


title: Sample160 [Rectal biopsy]


title: Sample162 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-73327.7-quantseq]

description:
2D_CM_D27_H9-73327.7-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-73326.6-quantseq]

description:
2D_CM_D27_H9-73326.6-quantseq
mRNA


title: Sample156 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-70005.4-quantseq]

description:
2D_CM_D27_H9-70005.4-quantseq
mRNA


title: Sample157 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75629.14-quantseq]

description:
2D_CM_D27_H9-75629.14-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-70003.3-quantseq]

description:
2D_CM_D27_H9-70003.3-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-75628.13-quantseq]

description:
2D_CM_D27_H9-75628.13-quantseq
mRNA


title: Sample155 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-70002.2-quantseq]

description:
2D_CM_D27_H9-70002.2-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_H9-quantseq [2D_CM_D27_H9-70001.1-quantseq]

description:
2D_CM_D27_H9-70001.1-quantseq
mRNA


title: Sample153 [Rectal biopsy]


title: 2D_Cardiomyocytes_Day 27_WTC-quantseq [2D_CM_D27-99051.1-quantseq]

description:
2D_CM_D27-99051.1-quantseq
mRNA

source_name: 2D differentiated cardiomyocytes_Day 27 (WTC)


title: Sample161 [Rectal biopsy]


title: Sample151 [Rectal biopsy]


title: Sample152 [Rectal biopsy]


title: Sample150 [Rectal biopsy]


title: Sample159 [Rectal biopsy]


title: Sample149 [Rectal biopsy]


title: Pluripotent Stem Cells_H9-quantseq [Pluri-43416.7-quantseq]

description:
Pluri-43416.7-quantseq
mRNA

value: Wild-type

value: Pluripotent stem cells (H9)


title: Sample158 [Rectal biopsy]


title: Sample147 [Rectal biopsy]


title: Pluripotent Stem Cells_H9-quantseq [Pluri-61465.5-quantseq]

description:
Pluri-61465.5-quantseq
mRNA


title: 2D_Cardiomyocytes_Day 27_WTC-quantseq [2D_CM_D27-99057.3-quantseq]

description:
2D_CM_D27-99057.3-quantseq
mRNA

value: 2D differentiated cardiomyocytes_Day 27 (WTC)


title: 2D_Cardiomyocytes_Day 27_WTC-quantseq [2D_CM_D27-99052.2-quantseq]

description:
2D_CM_D27-99052.2-quantseq
mRNA


title: Pluripotent Stem Cells_H9-quantseq [Pluri-61464.4-quantseq]

description:
Pluri-61464.4-quantseq
mRNA


title: Sample146 [Rectal biopsy]


title: Pluripotent Stem Cells_H9-quantseq [Pluri-43410.6-quantseq]

description:
Pluri-43410.6-quantseq
mRNA


title: Pluripotent Stem Cells_H9-quantseq [Pluri-80938.3-quantseq]

description:
Pluri-80938.3-quantseq
mRNA


title: Sample145 [Rectal biopsy]


title: Pluripotent Stem Cells_H9-quantseq [Pluri-88602.2-quantseq]

description:
Pluri-88602.2-quantseq
mRNA


title: Pluripotent Stem Cells_H9-quantseq [Pluri-88601.1-quantseq]

description:
Pluri-88601.1-quantseq
mRNA


title: Sample143 [Rectal biopsy]


title: Sample144 [Rectal biopsy]

value: CS-Oral


title: Epicardium_Day9-quantseq [AntD9-115478.6-quantseq]

description:
AntD9-115478.6-quantseq
mRNA

source_name: 2D Epicardium Day 9 (H9)

growth_protocol: ~70% confluent hPSCs were seeded at 55,000 cells/24 well plate in E8 + ROCKi (Y-27632, Tocris) 24h prior differentiation. Cells were induced with CDM medium (Mendjan et al. 2014) containing FGF2 (30 ng/ml, Cambridge University), LY294002 (7.5 µM, Tocris), BMP4 (10 ng/ml, R&D Systems) and CHIR99021 (1.5 µM, Tocris) (similar to Iyer et al., 2016.). Following 36h-40h, differentiation medium was exchanged to CDM medium containing BMP4 (10ng/ml), FGF2 (8 ng/ml), Insulin (10 µg/ml), IWR-1 (1µM, Tocris) and Retinoic Acid (1 µM, Sigma Aldrich) for 2 days with medium change every day. Subsequently, the medium was changed to CDM medium containing BMP4 (10 ng/ml), Insulin (10 µg/ml) and Retinoic Acid (1 µM) for 5 days with one medium change in-between (similar to Guadix et al., 2017). For maintenance of the obtained epicardium, cells were seeded at the end of differentiation onto Bovine Fibronectin (2 µg/ml, Sigma) coated plates in CDM medium containing Insulin (10 µg/ml) and SB431542 (10 µM, Tocris) supplemented with ROCKi for the first day of seeding. This medium was termed CDM-SBI. The replated epicardium was routinely passaged at 80-90% confluency every 3-5 days at 1:3 ratio;

value: 2D Epicardium Day 9 (H9)


title: Sample142 [Rectal biopsy]

value: F


title: Sample141 [Rectal biopsy]

value: Baseline


title: Epicardium_Day9-quantseq [AntD9-115477.5-quantseq]

description:
AntD9-115477.5-quantseq
mRNA

value: quant-seq


title: Epicardium_Day9-quantseq [AntD9-80953.4-quantseq]

description:
AntD9-80953.4-quantseq
mRNA


title: Epicardium_Day9-quantseq [AntD9-80952.3-quantseq]

description:
AntD9-80952.3-quantseq
mRNA


title: Sample140 [Rectal biopsy]


title: Sample139 [Rectal biopsy]

value: CS-IV


title: Sample148 [Rectal biopsy]


title: Epicardium_Day9-quantseq [AntD9-88620.2-quantseq]

description:
AntD9-88620.2-quantseq
mRNA


title: Sample138 [Rectal biopsy]


title: TS543_DMSO_IgG_chip-seq

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

source_name: TS543 glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

tag: agent

value: DMSO

value: glioma

tag: chip antibody

value: IgG


title: 2D_replated_Epicardium-quantseq [Ant_replated-115482.1-quantseq]

description:
Ant_replated-115482.1-quantseq
mRNA

source_name: 2D replated epicardial cells (H9)

value: 2D replated epicardial cells (H9)


title: TS543_ETO_IgG_chip-seq

value: ETO


title: 2D_replated_Epicardium-quantseq [Ant_replated-115481.9-quantseq]

description:
Ant_replated-115481.9-quantseq
mRNA


title: Sample137 [Rectal biopsy]

value: pediatric ulcerative colitis


title: Sample136 [Rectal biopsy]

value: M


title: 2D_replated_Epicardium-quantseq [Ant_replated-115480.8-quantseq]

description:
Ant_replated-115480.8-quantseq
mRNA


title: Epicardium_Day9-quantseq [AntD9-88619.1-quantseq]

description:
AntD9-88619.1-quantseq
mRNA


title: 2D_replated_Epicardium-quantseq [Ant_replated-115479.7-quantseq]

description:
Ant_replated-115479.7-quantseq
mRNA