title: VDJ_TCR-96-PT

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description: Single-cell RNA-seq

data_processing:
The 10X Genomics Cellranger (v3.1.0) mkfastq was applied to demultiplex the Illumina BCL output into FASTQ files.
Cellranger count was then applied to each FASTQ file to align reads to GRCh38 reference genome and generate barcode and UMI counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: .hd5 file, Cell Ranger output

source_name: PBMC

growth_protocol: Peripheral blood leukocytes (PBMC’s) were isolated from patient blood samples via centrifugation with lymphoprep (07851, StemCell Technologies) and SepMate conical tubes (85450, StemCell Technologies).  Samples were then stored in liquid nitrogen for later use and thawed on the day of experiments.  PBMC’s from patient blood were thawed and stained for FACS sorting.   CD45+CD3+CD8+ cells were then sorted using a FACSAria II sorter (BD Biosciences) running FACSDiva v8.0.1 software.  After sorting, cells were washed twice in 1 x PBS + 0.05% BSA and immediately submitted to the Medical Genome Facility (MGF) Genome Analysis Core (GAC) for further processing.

extract_protocol:
The cells were first counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter) and a basic hemocytometer and light microscope.  Barcoded Gel Beads were thawed from -80 oC to room temperature and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Single Cell 3’ v2 library kit (10x Genomics).  The target capture number of cells was 2000-3000, so a volume containing more than 5000 live cells was combined with cDNA master mix.  The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell A chip.  The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were captured into uniquely labeled GEMs (Gel Beads-In-Emulsion).  The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up.
The resulting cDNA was a pool of uniquely barcoded molecules.  Cleaned and measured pooled cDNA continued on to library construction, where standard Illumina sequencing primers and a unique i7 Sample index were added to each cDNA pool.
All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific), Agilent Bioanalyzer High Sensitivity chips (Agilent) and Kapa DNA Quantification reagents (Kapa Biosystems).   Libraries were sequenced at 60,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit.  The flow cells were sequenced as 100 x 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HCS v3.3.52 collection software.  Base-calling was performed using Illumina’s RTA version 2.7.3.

treatment_protocol: Patient blood draws were prior to (BL) or 12 weeks after treatment (PT) with anti-PD-1 infusion therapy, as detailed in the manuscript.

tag: genotype

value: Post-treatment

value: CD8+ T cells

tag: library preparation

value: 10x Genomics, Chromium Single Cell V(D)J


title: FQMR19

status: Public on Feb 18 2022

type: SRA

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

description: mRNA

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using DimerRemover.
Single end reads were aligned using STAR v2.5.3a to the GRCh38 human genome release.
BAMS index were generated using Sambamba v0.6.6.
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: Tab-delimited text files (.tsv) include RAW count for each Sample and DESeq2 output.

molecule: total RNA

organism: Homo sapiens

source_name: innervated muscle fiber derivated from hIPS

growth_protocol: The hIPSc were differentiated into functional muscles according to the protocol described in Mazaleyrat et al. (DOI: 10.3390/cells9061531).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA were evaluated using the RNA 6000 Pico assay (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease

tag: tissue


title: VDJ_TCR-96-BL

country: USA

description: Single-cell RNA-seq

value: Baseline

tag: cell type


title: VDJ_TCR-137-PT

description: Single-cell RNA-seq


title: VDJ_TCR-83-PT

description: Single-cell RNA-seq


title: VDJ_TCR-91-PT

description: Single-cell RNA-seq


title: VDJ_TCR-83-BL

description: Single-cell RNA-seq


title: VDJ_TCR-91-BL

description: Single-cell RNA-seq


title: GEX_TCR-96-PT

description: Single-cell RNA-seq

value: 10x Genomics, Chromium Single Cell 5’


title: GEX_TCR-96-BL

description: Single-cell RNA-seq


title: GEX_TCR-91-PT

description: Single-cell RNA-seq


title: VDJ_TCR-137-BL

description: Single-cell RNA-seq


title: HTG_P_3

city: Changchun

first: Weiwei

last: Cui

state: Jilin

address: Xinmin

country: China

institute: Jilin University

data_processing:
Filtration: we removed reads with adapter and N (N means that the nucleobase information cannot be determined) ≥ 0.002, and low-quality reads from raw data.
Comparative analysis: RNA-Seq sequencing data were compared and analyzed using Tophat2, Hisat2, and STAR software.
Transcript splicing: we used Stringtie software to assemble reads into transcripts and quantify them based on the results of the alignment to the genome.
Transcript screening: we used Cuffmerge software to merge the transcripts obtained from each sample splicing.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: blood

extract_protocol:
For each sample, trizol (TAKARA BIO INC., CA, Japan) was added into the whole blood immediately after the blood samples were collected. The ratio of trizol to whole blood is 3:1. And total RNA was isolated and purified using total RNA extraction kit.The chain-specific library was constructed by removing the ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: disease state

value: prediabetes

tag: bmi


title: GEX_TCR-91-BL

description: Single-cell RNA-seq


title: GEX_TCR-137-PT

description: Single-cell RNA-seq


title: GEX_TCR-83-PT

description: Single-cell RNA-seq


title: GEX_TCR-83-BL

description: Single-cell RNA-seq


title: 737511T.INPUT

city: ZhenJiang

first: Jiabin

last: Huang

state: JiangSu

address: 8 Dianli Road, Runzhou District

institute: Affiliated People's Hospital of Jiangsu University

data_processing:
The RNA concentration of each sample was measured using NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA).
RNA integrity and gDNA contamination were measured by denatured agarose gel electrophoresis
RNA Quantification and Quality Assurance by Qubit3.
Library quality was measured using Agilent 2100 Bioanalyzer.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.
Genome_build: HG19
Supplementary_files_format_and_content: excel format

molecule: polyA RNA

source_name: cancer tissue

extract_protocol:
fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours.
Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: adenocarcinoma of esophagogastric junction

tag: tumer stage

value: Stage IIIB

tag: treatment

value: untreated

value: cancer tissue


title: FQMR28

description: mRNA

value: FSHD1 mosaic isogenic Control

value: innervated muscle fiber derivated from hIPS


title: FQMR18

description: mRNA

value: FSHD1 mosaic


title: GEX_TCR-137-BL

description: Single-cell RNA-seq


title: GEX_TCR-95-PT

description: Single-cell RNA-seq

value: 10x Genomics, Chromium Single Cell 3’ v2


title: GEX_TCR-94-BL

description: Single-cell RNA-seq


title: GEX_TCR-89-BL

description: Single-cell RNA-seq


title: GEX_TCR-89-PT

description: Single-cell RNA-seq


title: Control3_input

city: Nanjing

first: yingjie

last: Zhang

address: No.300 Guangzhou Road

institute: Department of Rehabilitation Medicine, the First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: GRCh38（hg38）
Supplementary_files_format_and_content: text files include FPKM values and annotation for each Sample
Supplementary_files_format_and_content: text files include peak  information for each group

organism: Rattus norvegicus

source_name: myocardial tissue

growth_protocol: Male Sprague-Dawley (SD) rats aged 10 weeks and weighing 250-300g were collected from Beijing Vital River Laboratory Animal Technology Co. Ltd. The current study was carried out in accordance with the guidelines of the Chinese Council on Animal Protection and approved by the Institutional Animal Care and Use Committee of Nanjing Medical University (reference number of 10091).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.
m6A-seq

treatment_protocol: SD rats were randomly divided into the sham operation (SO) group and the myocardial infraction (MI) group. Ligation of left anterior descending coronary artery was conducted in the MI group and myocardial ischemia was confirmed withe elevated ST-segment in electrocardiogram. However, string went through the corresponding myocardial region without ligation in the SO group. Finally, heart samples were collected from the infarction area in the MI group and the corresponding region in the SO group. Heart samples were refrigerated at −80°C for further detection.

value: myocardial tissue

tag: strain

value: Sprague Dawley

value: control

tag: rip antibody


title: MI1_input

value: myocardial infarction (MI) model


title: MI2_input


title: Control2_input


title: MI2_IP

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: MI1_IP


title: MI3_IP


title: NKO_DR.5 RNAseq rep 5

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

institute: J David Gladstone Institutes

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
NKO.5_BGT-15-g4_S15

data_processing:
ChIP seq:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the hg19 reference human genome was performed using Bowtie 2.2.4. Peaks were called using GEM for transcription factors (GATA4, NKX2-5, TBX5, MEIS1, ISL1) and BCP for GLYR1 and H3K36me3.
Bulk RNA seq:
Cluster generation, sequencing, and base calling was performed on Illumina HiSeq 2500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Reads were mapped to the hg19 reference human genome using STAR (v 2.7.3a) and assigned to Ensembl genes. We quantified gene expression using raw counts and kept the protein coding genes that showed an average FPKM value across the samples >0.5 FPKM. We then performed differential expression gene testing with DESeq25 (v.1.24.0 R package) using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: We provide bed ad BigWig files for ChIPseq.       We provide excel files for differential expression analysis for every gene for Bulk RNAseq experiments.

source_name: NKX2-5 KO hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

growth_protocol: For human cardiac differentiation into D6 cardiac progenitors, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al. 2013; Tohyama et al. 2013). Briefly hiPSCs were detached from hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) with accutase (Cat. 07920, Stem Cell Technologies) and reseeded on matrigel at 0.6–1.2x105 cells per 12well in Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) (day-3). We optimized each hiPSC clone individually to identify the best cell seeding density that resulted in high levels of cTNT, NKX2-5, TBX5 and GATA4-positive sheet-like beating CMs at day15 of differentiation. On the next two days, media was changed daily with fresh E8 medium without ROCK inhibitor. On the day of cardiac induction (day0), 6μM CHIR99021 (Cat. 4423, Tocris) was added for 24 hr. in 1ml per well of B27-supplemented (without insulin) RPMI1640 media (Cat. 11875-119, Life Technologies). On day1 media was changed for freshly prepared 6μM CHIR99021 in B27-supplemented (without insulin) (Cat. A1895601, Life Technologies) RPMI1640 media. At day 2 and 3 IWP4 (Cat. 5214, Tocris) in B27-supplemented (without insulin) RPMI1640 media was added to activate Wnt signaling at a final concentration of 5μM. At day 4, IWP4 was removed, and 1ml of B27-supplemented (without insulin) RPMI1640 media per was daily added per well (days 4-6). At day day 6 cells were collected.

extract_protocol:
Total RNA was TRIzol-extracted (Cat. 10296010, Thermo Fisher Scientific) and further purified using the Direct-Zol RNA kit (Cat. R2052, Zymo Research) with DNaseI in-column treatment according to the manufacturer’s instructions and quantified with Nanodrop (Thermo scientific).
After RNA quality control with bioanalyzer Agilent 2100 (Agilent Technologies), Paired-end Poly(A)-enriched RNA libraries were prepared with the Ovation RNA-seq System V2 Kit (Cat. 7102-08, NuGEN; strand specific) from the Gladstone Genomic core. The mRNA-seq libraries were analyzed by Agilent Bioanalyzer and quantified using an Illumina Library Quantification Kit (Cat. KK4824, KAPA Biosystems). Libraries were prepared by the Gladstone Genomics Core (http://labs.gladstone.org/genomics/home). High-throughput sequencing was done using an Illumina HiSeq 2500 instrument (http://humangenetics.ucsf.edu/genomics-services/sample-processing/).

treatment_protocol: To generate the GATA4 and TBX5 knockout lines, WTC11 hiPSCs were dissociated in accutase (Cat. 07920, Stem Cell Technologies), and 250.000 cells were aliquoted per condition and nucleofected with Cas9-ribonucleoprotein complexes (Cas9-RNP) following the Primary Cell Nucleofection P3 Kit manufacturer’s instructions (V4XP-3960, Lonza). For Cas9-RNP complex preparation 180pmol of each synthetic modified sgRNA (Synthego) to target GATA4 (GAGGCCCACUCGGCGGGAGG),  TBX5 (GCTTACCTTGTGGTTCTGGTAGG) or NKX2-5 (TCTATCCACGTGCCTACAGC) and 20pmol of SpCas9-NLS purified protein (QB3 Macrolab, UCB) were diluted into 20μl of nucleofection buffer prepared as indicated in Primary Cell Nucleofection P3 Kit, mixed and incubated at room temperature for 10 min. After 10 min. of incubation, the aliquoted 250.000 cells were resuspended in 20μL nucleofection buffer containing the corresponding Cas9-RNP complexes, mixed 5-6 times and then transferred to the bottom of a nucleofector well (nucleofector 96 well cassette from the Primary Cell Nucleofection P3 Kit). This was repeated for every Cas9-RNP condition. The nucleofector cassette was placed in the nucleofector instrument (Nucleofector 4D system, Lonza) and cells nucleofector using the preset program DS-138. The nucleofection cassette was brought back to sterile hood and 80μL of Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM rho kinase (ROCK) inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) added into each well and incubated for 10 min. at 37°C.  During the incubation time, we removed the hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) from 12 well plates (Corning) pre-coated for 1 hr. at 37°C with 0.5ml per well of matrigel and added 2mL of pre-warmed E8 medium plus 5μM ROCK inhibitor (Y-27632 2HCl) in each well. Then pipetted the nucleofected cells to each of the pre-coted wells with media. After ~3-5 days, wells with surviving clones were expanded to isolate gDNA for screening. A genomic fragment spanning the gRNA target sites was amplified and Sanger sequenced to identify clones with frame-shift insertions/deletions. Synthego ICE analysis was run to identify clones with highest knock-out efficiency (https://ice.synthego.com/#/), which were subsequently subjected to the colony picking and clone sequencing until monoclonal lines were generated. The top 5 sgRNA predicted off-targets (https://horizondiscovery.com/en/products/tools/crispr-specificity-analysis) were verified to be intact by sanger sequencing in the final monoclonal lines and checked for normal karyotype (Cell Line Genetics).

value: hiPSC cardiomyocyte

tag: genotype/variation

value: NKX2-5 KO

tag: cardiomyocyte differentiation day

value: Day 6

tag: type of experiment

value: Bulk RNAseq


title: Control1_IP


title: Control2_IP


title: NKO_DR.3 RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
NKO.3_BGT-13-e4_S13

source_name: NKX2-5  KO hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)


title: Control3_IP


title: GEX_TCR-94-PT

description: Single-cell RNA-seq

value: Post-treatment

value: CD8+ T cells


title: GEX_TCR-119-PT

description: Single-cell RNA-seq


title: NKO_DR.1 RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
NKO.1_BGT-11-c4_S11


title: TKO_DR.4 RNAseq rep 4

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
TKO.4_BGT-9-a4_S9

source_name: TBX5 KO hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

value: TBX5 KO


title: TKO_DR.5 RNAseq rep 5

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
TKO.5_BGT-10-b4_S10


title: NKO_DR.4 RNAseq rep 4

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
NKO.4_BGT-14-f4_S14


title: GEX_TCR-95-BL

description: Single-cell RNA-seq

value: Baseline


title: GEX_TCR-119-BL

description: Single-cell RNA-seq


title: TKO_DR.3 RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
TKO.3_BGT-8-h3_S8


title: TKO_DR.2 RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
3c1_gko_dr5_S105


title: Control1_input


title: gko.3 bulk RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
2b1_gko_dr6b_S11

source_name: GATA4 KO hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

value: GATA4 KO


title: gko.4 bulk RNAseq rep 4

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
2b1_gko_dr6b_S104


title: TKO_DR.1 RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
3c1_gko_dr5_S12


title: gko.2 bulk RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
1a1_gko_dr2_S103


title: WTC11_DR4.2 bulk RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
WT.2_BGT-2-b3_S2

source_name: WT hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)


title: WTC11_DR4.4 bulk RNAseq rep 4

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
WT.4_BGT-4d3_S4


title: gko.1 bulk RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
1a1_gko_dr2_S10


title: WTC11_DR4.1 bulk RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
WT.1_BGT-1-a3_S1


title: WTC11_DR4.5 bulk RNAseq rep 5

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
WT.5_BGT-5-e3_S5


title: NKO_DR.2 RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
NKO.2_BGT-12-d4_S12


title: T13 siControl bulk RNAseq rep 1

description:
processed data file: DE_Table_excluding_siRNA_GLYR1.txt
3-c1-T13Ctrl_S3_L001

source_name: WT hiPSC cardiomyocyte differentiation day 7

growth_protocol: For human cardiac differentiation into D6 cardiac progenitors, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al. 2013; Tohyama et al. 2013). Briefly hiPSCs were detached from hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) with accutase (Cat. 07920, Stem Cell Technologies) and reseeded on matrigel at 0.6–1.2x105 cells per 12well in Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) (day-3). We optimized each hiPSC clone individually to identify the best cell seeding density that resulted in high levels of cTNT, NKX2-5, TBX5 and GATA4-positive sheet-like beating CMs at day15 of differentiation. On the next two days, media was changed daily with fresh E8 medium without ROCK inhibitor. On the day of cardiac induction (day0), 6μM CHIR99021 (Cat. 4423, Tocris) was added for 24 hr. in 1ml per well of B27-supplemented (without insulin) RPMI1640 media (Cat. 11875-119, Life Technologies). On day1 media was changed for freshly prepared 6μM CHIR99021 in B27-supplemented (without insulin) (Cat. A1895601, Life Technologies) RPMI1640 media. At day 2 and 3 IWP4 (Cat. 5214, Tocris) in B27-supplemented (without insulin) RPMI1640 media was added to activate Wnt signaling at a final concentration of 5μM. At day 4, IWP4 was removed, cells were subjecte to siRNA tranfection.

treatment_protocol: For siRNA knockdown experiments during in cardiac progenitor cells, at day 4 of differentiation cells were detached from the plates with 1ml of accutase (Cat. 07920, Stem Cell Technologies) and quenched with 1ml of B27 (minus insulin) RPMI1640 media (Cat. 11875-119, Life Technologies) per well.  All cells were combined and centrifuge at 300xg, supernatant removed and the pellet resuspended in a volume of B27 (minus insulin) RPMI with 5uM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) necessary for 2x the number of wells initially collected. Cells were then seeded in twice the number of 12 well plates originally collected that were pre-coated with fibronectin bovine plasma solution (Cat. F1141, Sigma-Aldrich). Cells were immediately transfected in solution, prior attachment to the well surface using lipofectamine RNAiMax (Cat. 13778075, Invitrogen). For one well of a 12 well plate, mix A (75μl Opti-MEM (Cat. 31985070, Thermo Fisher Scientific) were combined with 3μl of a 10μM siRNA stock) and mix B (75μl Opti-MEM) with 7μl of lipofectamine RNAiMax were prepared. Mix A and B were combined and incubated at RT for 5-10 min. 160μl of lipofectamine siRNA complexes were added dropwise to each well. At day 7 of differentiation, ~72 hrs. after transfection cell were collected, washed, supernatants removed and pellets snap frozen and stored at -80°C until processed. The following siRNA were used: GATA4 Silencer Select Pre-designed SiRNA (Cat. 4392420, ID s535120, Lot. AS02F2E2, Thermo Fisher Scientific), siGLYR1 (siRNA ID: SASI_Hs01_00116796, Millipore-Sigma) and Silencer Select Negative control #1 siRNA (Cat. 4390843, Thermo Fisher Scientific).

value: T13 siControl

value: Day 7


title: T14 siControl bulk RNAseq rep 2

description:
processed data file: DE_Table_excluding_siRNA_GLYR1.txt
5-e1-T14Ctrl_S5_L001

value: T14 siControl


title: WTC11_DR4.3 bulk RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_koStudy_Sigma.csv
WT.3_BGT-3-c3_S3


title: siControl bulk RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
9a2_sicont_sigma_3_S18

value: siControl


title: siGATA4 bulk RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
10b2_sigata4_1_S19


title: siControl bulk RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
8h1_sicont_sigma_2_S17


title: Al-WT-3

city: Qingdao

first: Liu

middle: jia

last: jia

address: NO. 72, Bin Hai Road

institute: shandong university

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The seedlings grew on hydroponically 2% modified MGRL for 7 days, the root of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Roots

value: wild type

value: aluminum treatment


title: CK-WT-3

value: control


title: CK-WT-2


title: CK-WT-1


title: myc-h3x2-wt-HU150spike-x39

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Sensor-carrying cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha factor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals. The number after 'HU' in the sample title indicates the minutes after release into HU.

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

tag: antibody

value: myc

tag: growth condition

value: wt


title: myc-h3x2-wt-HU180spike-x39

tag: genotype


title: T13 siGLYR1bulk RNAseq rep 1

description:
processed data file: DE_Table_excluding_siRNA_GLYR1.txt
4-d1-T13SiGLYR1_S4_L001

value: hiPSC cardiomyocyte

value: T13 siGLYR1

value: Bulk RNAseq


title: myc-h3x2-wt-HU130spike-x39


title: siGATA4 bulk RNAseq rep 3

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
12d2_sigata4_3_S21


title: myc-h3x2-wt-HU90spike-x39


title: myc-h3x2-wt-HU50spike-x39


title: myc-h3x2-wt-HU70spike-x39


title: myc-h3x2-wt-alpha2spike-x39


title: myc-h3x2-wt-HU15spike-x39


title: myc-h3x2-wt-asyncspike-x39

value: asyncspike


title: myc-h3x2-wt-HU40spike-x39


title: myc-h3x2-wt-HU30spike-x39


title: myc-h3x2-wt-alpha1spike-x39


title: myc-h3x2-wt-HU110-s47


title: MI3_input

tag: tissue

value: myocardial tissue

value: Sprague Dawley

value: myocardial infarction (MI) model


title: myc-h3x2-wt-HU090-s47


title: myc-h3x2-wt-HU130-s47


title: myc-h3x2-wt-HU180-s47


title: Al-WT-2


title: myc-h3x2-wt-HU150-s47


title: myc-h3x2-wt-HU040-s47


title: myc-h3x2-wt-HU015-s47


title: myc-h3x2-wt-HU050-s47


title: myc-h3x2-wt-alpha-s47

value: alpha


title: Al-WT-1


title: myc-h3x2-wt-HU110spike-x39


title: myc-h3x2-wt-HU030-s47


title: myc-h3x2-wt-async-s47

value: async


title: myc-h3x2-wt-HU070-s47


title: myc-h3x2-wt-HU130-s43


title: siGATA4 bulk RNAseq rep 2

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
11c2_sigata4_2_S20

tag: cell type

value: Day 7


title: myc-h3x2-wt-HU150-s43


title: myc-h3x2-wt-HU090-s43


title: myc-h3x2-wt-HU070-s43


title: myc-h3x2-wt-HU050-s43


title: myc-h3x2-wt-HU060-s43


title: myc-h3x2-wt-HU040-s43


title: myc-h3x2-wt-HU015-s43


title: myc-h3x2-vps75-HU180-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: myc-h3x2-wt-alpha-s43


title: myc-h3x2-vps75-HU150-s47


title: myc-h3x2-vps75-HU110-s47


title: myc-h3x2-vps75-HU090-s47


title: sma-6-6_S5

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Fastq files generated by bcl2fastq with adapter trimming
Map R1 to WBcel235 as single-end using STAR v2.5.2b
Assign uniquely-mapping read-pairs to transcript exons and splice-junctions using Featurecounts v1.5.2
Filter out genes not accruing 10 reads in at least 1 library
Call differentially expressed genes using Limma Voom with TMM normalization
Genome_build: WBcel235
Supplementary_files_format_and_content: Sma_mutants_Protein_Coding_Only.csv;  comma-separated values format; contains Degust-generated gene-count matrix for samples and Limma-voom estimates for expression levels and significance

organism: Caenorhabditis elegans

source_name: C. elegans whole animal

growth_protocol: Worms were grown on standard NGM plates and fed with E. coli bacteria at 20 degrees celsius

extract_protocol:
RNA was extracted with TRIZOL
RNA was poly-A selected using oligo dT magnetic beads, fragmented and library prepared using TruSeq stranded kit (Illumina)

tag: developmental stage

value: L2 larval stage

value: whole animal


title: myc-h3x2-vps75-HU130-s47


title: myc-h3x2-wt-HU180-s43


title: 4C_YR2_VP3_Rep2

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Library strategy: 4C
Reads were mapped and processed using pipe4C (Krijger et al., 2020) (github.com/deLaatLab/pipe4C) with the following parameters: normalization to 1 million reads in cis, window size 21, top 2 read counts removed
Genome_build: Hybrid ovine genome (UCSC: OAR v3.1) containing BLV genome (GenBank: KT122858.1) at their respective integration site
Supplementary_files_format_and_content: 4C:  interaction coverage file (wig files generated using pipe4C)

organism: Ovis aries

source_name: BLV infected YR2 cell ine

growth_protocol: Cell lines were maintained in Opti-MEM GlutaMAX medium (Life Technologies) supplemented with 10% FBS, 1 mM sodium pyruvate, 2 mM glutamine, non-essential amino acids 1X and 100 μg/ml kanamycin. Cell were maintained at a density of 0.5x10^6 cell/ml, and media was changed each 3 days.

extract_protocol:
4C experiments were performed as described (Krijger et al., 2020). Briefly, 10^7 cells per sample were cross-linked in 2% formaldehyde for 10 min and the reaction was quenched by adding glycine at a final concentration of 0.13M. Then, cells were lysed and the harvested cross-linked chromatin was digested using the restriction enzyme DpnII (NEB). After a ligation step with the T4 DNA ligase (NEB), ligated samples were decross-linked and subjected to a second round of digestion using the restriction enzyme CviQI (NEB). Digested samples were then ligated using T4 DNA ligase and purified before being used as template for inverse PCR.
The 4C library was constructed as described in Krijger et al., 2020.

value: Leukemia derived B-cell

tag: cell line

tag: viewpoint

tag: barcode

value: GCTGCCTATAGTTTTAGAGCTT


title: sma-6-4_S4


title: 4C_YR2_VP3_Rep1


title: 4C_YR2_VP3_Rep3


title: myc-h3x2-vps75-HU050-s47

value: myc


title: T14 siGLYR1 bulk RNAseq rep 2

description:
processed data file: DE_Table_excluding_siRNA_GLYR1.txt
6-f1-T14SiGLYR1_S6_L001

value: T14 siGLYR1


title: myc-h3x2-vps75-HU070-s47


title: myc-h3x2-wt-HU110-s43

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: wt


title: 4C_YR2_VP1_Rep2

value: AAACAATTGGGGGCTCGT


title: myc-h3x2-wt-HU030-s43


title: sma-6-3_S3


title: 4C_YR2_VP1_Rep1


title: myc-h3x2-vps75-HU040-s47


title: myc-h3x2-vps75-HU030-s47


title: sma-6-2_S2


title: myc-h3x2-vps75-HU015-s47


title: myc-h3x2-vps75-async-s47


title: myc-h3x2-vps75-alpha-s47


title: sma-6-1_S1


title: myc-h3x2-vps75-HU190-s44


title: 4C_L267_VP3_Rep2

source_name: BLV infected L267 cell line

value: Lymphoma derived B-cell

value: GGAACTCGACGGCCAAGATC


title: myc-h3x2-vps75-HU150-s44


title: 4C_L267_VP3_Rep1


title: sma-3_9rep_S19


title: myc-h3x2-vps75-HU130-s44


title: myc-h3x2-vps75-HU110-s44


title: 4C_L267_VP1_Rep3


title: myc-h3x2-vps75-HU090-s44


title: myc-h3x2-vps75-HU070-s44


title: 4C_L267_VP1_Rep2


title: sma-3_4_S17


title: 4C_L267_VP1_Rep1


title: myc-h3x2-vps75-HU040-s44


title: sma-3_5_S18


title: 4C_L267_VP3_Rep3


title: myc-h3x2-vps75-HU050-s44


title: 4C_YR2_VP1_Rep3


title: sma-3_3_S16


title: myc-h3x2-vps75-HU030-s44


title: myc-h3x2-vps75-HU015-s44


title: siControl bulk RNAseq rep 1

description:
processed data file: DifferentialExpressionResults_siRNA_gata4_Sigma.csv
7g1_sicont_sigma_1_S16

value: hiPSC cardiomyocyte

value: siControl

value: Bulk RNAseq


title: IonXpress_029

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

description: ex vivo

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.12.1; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.12.1) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome__21K_v1) With TMAP mapper in Torrent Suite version 5.12.1.
hg19 Human genome reference
Genome_build: text files.  Raw read count and normalized reads count (RPM, reads per million).
Supplementary_files_format_and_content: raw counts of sequencing reads _Auto_Ion_AmpliSeq_Transcriptome_Human_Dr_Spaner_Chip02_20200525_s5xl-server_487.bcmatrix

source_name: Blood

growth_protocol: Leukemia cells were purified from the blood and RNA was made 24h after culture in AIM-V media with or without anifrolumab and frozen until used for RNAseq.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA, USA), and cDNA was synthesized from 2 μg of RNA using Superscript II reverse transcriptase (Invitrogen), according to the instructions of the manufacturer.
Complementary DNA (cDNA) libraries were constructed from the total RNA using the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.
Targeted RNA sequencing

treatment_protocol: CLL cells were isolated from blood by negative selection with the Rosette Sep Human B cell enrichment cocktail (StemCell Technologies, Vancouver BC, Canada) and density centrifugation. This method yields percentages of CD19+ and CD19+/CD5+ cells of >98 and >96%, respectively. total RNA was made after 24h culture with AIM V media in the presence or absence of anifrolumab which is a neutralizing antibody against the IFNAR1 that specifically block type I interferon signaling, then samples were frozen in -80C until RNAseq.

value: purified primary CLL-B cells

tag: treatments

value: Pt.3 CON


title: sma-3_2_S15


title: IonXpress_030

description: ex vivo

value: Pt.3 anifrolumab treated


title: N2_L2_5_S14

value: L2 larval stage

value: WT


title: IonXpress_028

description: ex vivo

value: Pt.2 anifrolumab treated


title: myc-h3x2-vps75-alpha-s44

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG

value: alpha

tag: strain


title: RPS6-SW1990

city: Shanghai

first: Zhiyong

last: Liu

state: China

address: changhai road 168

institute: Changhai Hospital

data_processing:
Basecalling was performed using CASAVA version 1.8
During data pre-processing, Fastx was applied to remove adaptor sequences, reads that have no adequate (<50%) bases of quality values greater than 20, bases with quality value lower than 10 at 3'-end, reads shorter than 20bp, base N, and ribosome RNA reads.
Reads were mapped to hg19 genome assembly by TopHat (version 2.0.9) while 2 mismatches are acceptable and for each read, no more than 2 multiple hits are allowed.
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, Cufflink (Ver. 2.1.1) was introduced to quantify mapping result from TopHat.
Genome_build: Ensemble HG19

extract_protocol:
The RNAs targeted with RPS6 in four cancer cell lines (Huh7,HCT116, DU145, SW1990) were isolated, quantified and purified. The sequencing libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit from Illumina according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer cell line

tag: sample type


title: 10-Input-SW1990

value: input


title: RPS6-DU145

value: Prostate cancer cell line


title: N2_L2_3_S12

value: whole animal


title: 10-Input-DU145


title: myc-h3x2-rtt-HU180spike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT

value: myc

value: rtt


title: HCT116-RPS6

value: Colon cancer cell line


title: N2_L2_4_S13


title: N2_L2_2_S11


title: myc-h3x2-vps75-async-s44

value: async


title: myc-h3x2-rtt-HU150spike-x39


title: HCT116-Input


title: IonXpress_025

description: ex vivo

value: purified primary CLL-B cells

value: Pt.1 CON


title: N2_L2_1_S10


title: 3B-RPS6

value: Hepatocellular carcinoma cell line


title: myc-h3x2-rtt-HU130spike-x39


title: myc-h3x2-rtt-HU110spike-x39


title: 112_MRD6.3_3

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

institute: Erasmus MC

description: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of serial dilutations and post-treatment samples from CLL patients enrolled in the CLL11 trial

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

source_name: PBMCs

extract_protocol:
gDNA was available from the CLL11 trial. 1-27 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

tag: sequencing run number

tag: rearrangement/patient number

value: PBMCs

value: Serial dilution


title: 3B-Input


title: myc-h3x2-rtt-HU90spike-x39


title: 112_MRD6.3_1


title: myc-h3x2-rtt-HU70spike-x39


title: 112_MRD6_3


title: myc-h3x2-rtt-HU50spike-x39


title: IonXpress_027

description: ex vivo

value: Pt.2 CON


title: M4_17_DAT10

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

description:
Replicate 1
DAT
MT10

data_processing:
Libraries were pooled, templated and enriched on the Ion OneTouch 2 System and sequenced on the Ion Proton system on P1.1.17 chips using Ion HiQ chemistry.
To ensure sufficient read coverage, the majority of the samples (with the exception of samples M1_3_WT0 and M4_17_DAT10, which had sufficient coverage in the first run) were sequenced twice, and sample M2_13_WT10 three times. Thus there are several raw files for the same sample.
Data was collected with Ion Suite (version 4.4.3. 1).
Reads were mapped to the reference genome with tmap-f3 in Torrent Suite (v4.4.3).
Multiple runs were combined for the same sample.
Genome_build: UCSC dm3 Drosophila reference genome.
Supplementary_files_format_and_content: Files are in txt (tab-delimited) format. All files contain gene and transcript ids, gene official symbol, chromosome location, and the RPKM value.

organism: Drosophila melanogaster

source_name: adult head

growth_protocol: All fly strains were reared on a standard corn meal, yeast, molasses, agar medium at 25°C and 45-47% humidity under a 12:12 h light:dark cycle for 7 days after eclosion.

extract_protocol:
PolyA+ selected libraries were produced from individual whole Drosophila brains (4 heads per group). Specifically, total RNA was prepared using the RNAqueous-Micro kit (Ambion) followed by polyA+ mRNA isolation with the Dynabeads mRNA DIRECT Micro kit (Ambion) according to the manufacturer’s protocols.
Barcoded libraries (Ion XpressRNA) were made using the Ion Total RNA-Seq Kit v2, PCR-amplified, and quantified with Agilent Bioanalyzer (Agilent).

treatment_protocol: Individual aged male flies were then anesthetized briefly with CO2 and placed in polycarbonate tubes containing food consisting of 1% agar and 3% sucrose delivered in water (vehicle) or AMPH solution (10 mM) (Sigma, A5880) for 48 hrs.

value: brain

value: dDATfmn

value: adult

tag: Sex

value: male

tag: treatment

value: 10 mM AMPH


title: M4_21_DAT10

description:
Replicate 3
DAT
MT10


title: myc-h3x2-rtt-HU30spike-x39

tag: sensor


title: M4_18_DAT10

description:
Replicate 2
DAT
MT10


title: IonXpress_026

description: ex vivo

value: Pt.1 anifrolumab treated


title: 112_MRD6_1


title: M2_15_WT10

description:
Replicate 3
XL
WT10

value: WT


title: M2_17_WT10

description:
Replicate 4
XL
WT10


title: 112_MRD6_2


title: 112_MRD5.5_3


title: myc-h3x2-rtt-alpha2spike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT

tag: antibody

value: myc


title: 112_MRD5.5_2


title: M2_14_WT10

description:
Replicate 2
XL
WT10


title: myc-h3x2-rtt-HU15spike-x39

tag: growth condition

value: rtt


title: cdc

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) (https://cran.r-project.org/web/packages/pheatmap/index.html)according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (http://www.bioconductor.org/packages/release/bioc/html/ DESeq2.html)with Q value ≤ 0.05.
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: fpkm, tpm, read_count

organism: Mus musculus

source_name: cardiosphere derived cell

extract_protocol:
Total RNA was extracted from 3 separate samples of cdc,cdc derived epicardial-like cells and primary epicardial cells using Trizol(Life science)and DNA-free kit(Ambion).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: 10uM sb-431542 was added into the culture medium of CDCs, epithelial clones formed in 2 weeks.Then the epithelial clones were picked up through clone cylinders and trasferred to a new plate.Different trypsin digestion time could purify the mesenchymal cells in the epithelial cell clone.

value: heart ventricle epicardium


title: pEpiCs

source_name: primary Epicardial cell


title: myc-h3x2-rtt-alpha1spike-x39

tag: genotype


title: M3_9_DAT0

description:
Replicate 4
DAT
MT00

tag: tissue

value: 0 mM AMPH


title: cPT-QC_run20

source_name: thymus, tonsil and PBMCs

value: qPT-QC

value: thymus, tonsil and PBMCs

value: quality control


title: M2_13_WT10

description:
Replicate 1
XL
WT10


title: 112_MRD6.3_2

value: PBMCs

value: Serial dilution


title: cdc_EpiCs

source_name: cdc derived EpiC-like clone


title: M3_8_DAT0

description:
Replicate 3
DAT
MT00

value: brain


title: 112_MRD5.5_1


title: 112_MRD5_7


title: myc-h3x2-rtt-HU40spike-x39


title: k9ac-h3x2-wt-HU180-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: wt


title: cPT-QC_run19


title: M3_5_DAT0

description:
Replicate 2
DAT
MT00

value: dDATfmn

value: adult

value: male


title: M3_4_DAT0

description:
Replicate 1
DAT
MT00


title: k9ac-h3x2-wt-HU150-s47


title: Water_5F

type: RNA

city: Mions

first: Aline

last: de Conti

address: 16 Route de Corbas

institute: iarc

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Cellegans_UnrestrictedGE_G2519F_020186 Microarray (Agilent Technologies, Santa Clara, CA) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies G2600D SG14324425) using one color scan setting for G3 Microarray format 8x60k (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: Water

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: N2 worm cultures were fed fresh C. elegans modified Habitation Medium (CeHM) and maintained at 20°C on shakers before being subjected to hypochlorite treatment to isolate eggs. Dauer free egg isolates were allowed to hatch overnight in M9 buffer for 19 +/- 1 hr to obtain age-synchronized first larval stage (L1) worms, then resuspended (900 worms per 1mL) and maintained in CeHM until the fourth larval stage (L4).

extract_protocol: Total RNA was extracted from C. elegans using miRNeasy Mini kits (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: At the mid-L4 larval stage, C. elegans were exposed to 25 µM 5-Fluoro-2'-deoxyuridine (FUdR). 24h later, 900 µL of adults in CeHM plus FUdR were dosed with 100µL of freshly made 10x dosing solutions and exposed for 24h (water (control group), 10 µg/ml NaAsO2, 200 µg/ml DMA, 2 µg/ml HgCl2, or 0.5 µg/ml meHgCl).

value: whole body

tag: age

value: Water


title: 112_MRD5_6


title: cPT-QC_run18


title: M1_3_WT0

description:
Replicate 3
XL
WT00

value: WT

tag: developmental stage


title: k9ac-h3x2-wt-HU110-s47


title: 112_MRD5_5


title: k9ac-h3x2-wt-HU090-s47


title: k9ac-h3x2-wt-HU070-s47


title: cPT-QC_run17


title: myc-h3x2-rtt-asyncspike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT

value: myc

value: asyncspike

value: rtt


title: 7760-854

value: CLL11  EOT patient sample


title: M1_13_WT0

description:
Replicate 2
XL
WT00

value: 0 mM AMPH


title: M1_10_WT0

description:
Replicate 1
XL
WT00


title: k9ac-h3x2-wt-HU050-s47


title: 7759-854

value: PBMCs


title: k9ac-h3x2-wt-HU130-s47


title: k9ac-h3x2-wt-HU040-s47


title: m8w

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

country: Germany

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

data_processing:
The raw count data generated from Cell Ranger pipeline was processed using Seurat v3.1 12 by following the standard pipeline.
The 8 Week and 24 Week HSCs were treated and analysed as one entity. Cells were filtered based on quality metrics (number of genes, total UMI counts, percentage of mitochondrial genes).
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

source_name: Bone Marrow

extract_protocol:
HSCs (Lin- Kit+ Sca-1+ CD48- CD150+ CD34- CD201+ LT-HSCs (LSK CD48- CD150+) (3000 cells) from B6 mice were sorted into BSA-coated tube containing 5 µl of PBS with 0.04% BSA.
Single-Cell RNA-seq

treatment_protocol: Untreated mice C57/BL6 were used

tag: cell type

value: Haematopoietic Stem Cells

value: 8 weeks


title: M1_8_WT0

description:
Replicate 4
XL
WT00

value: brain


title: 7667-854


title: meHgCl_5J

source_name: meHgCl

value: meHgCl


title: k9ac-h3x2-wt-HU030-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: wt


title: meHgCl_3J

value: adult


title: HgCl2_5I

value: whole body


title: 7616-854


title: k9ac-h3x2-wt-HU015-s47


title: DMA_5H

source_name: DMA

value: DMA


title: Water_3F

value: Water


title: 6223-854


title: s4_CD38_neg

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENCODE) was used for the alignment.
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read quantification was downloaded from Gencode ().
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

extract_protocol:
HSCs (Lin- Kit+ Sca-1+ CD48- CD150+ CD34- CD201+ CD38hi vs CD38lo) were sorted directly to the lysis buffer from RNAeasy Micro Kit (Qiagen), RNA was isolated base on the protocol from the Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: population

value: CD38 neg

value: 8-16 weeks


title: s5_CD38_pos

value: CD38 pos


title: k9ac-h3x2-wt-async-s47

value: async


title: s6_CD38_neg


title: HgCl2_3I


title: DMA_3H


title: NaAsO2_3G


title: 6828-854

value: CLL11  EOT patient sample


title: Water_4F


title: NaAsO2_5G


title: s3_CD38_pos


title: k9ac-h3x2-wt-alpha-s47

value: alpha


title: 5941-854

value: PBMCs


title: meHgCl_2L


title: DMA_2I


title: s2_CD38_neg

value: Haematopoietic Stem Cells


title: HgCl2_2J


title: k9ac-h3x2-wt-HU180-s43


title: k9ac-h3x2-wt-HU150-s43


title: 5342-854


title: k9ac-h3x2-wt-HU130-s43


title: 5604-854


title: s1_CD38_pos


title: m24w

value: 24 weeks


title: 1842-854


title: 5214-854


title: k9ac-h3x2-wt-HU090-s43


title: TH9 48h cGAMP N=1

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

data_processing:
Raw FASTQ files were trimmed for residual adapter sequences and quality filtered through Trimmomatic software.
Reads were pseudo-aligned against mm10 genome through Kallisto software.
Differential expression analysis was performed with DESeq2 R package.
Genome_build: mm10

source_name: Naive CD4+ T cells

growth_protocol: Naive CD4 T cells (FACS sorted CD4+ CD62L+ cells) isolated from C57BL/6J mouse spleen and lymph nodes were seeded at 3,000,000 cells/mL in 96-well plates coated with anti-CD3 (2 µg.mL-1; Clone 17A2 and anti-CD28 (2 µg.mL-1; Clone PV1). After treatment as described below, cells were polarized in vitro into TH1 or TH9 cells for 16h and 48h in culture medium (RPMI-1640, 10% FBS, 1% PSA,  10 mM Hepes, 1 mM Sodium Pyruvate, 2 mM L-glutamine, MEM NEAA 0.1 mM each AA and 55 µM 2-Mercaptoethanol) supplemented with IL-12 (10 ng.ml-1) and anti-mouse IL-4 (50 μg.ml-1 ) for TH1 cells or TGF-β (2 ng.ml-1), IL-4 (20 ng.ml-1) and anti-mouse IFN-γ (2, 50 μg.ml-1) for TH9 cells.

extract_protocol:
Total RNA was extracted from cells by using Trizol reagent according to the manufacturer's instructions.
500 ng of total RNA were used for library construction. Libraries were prepared thanks to Truseq stranded total RNA with Ribo-zero kit according to manufacturer's instructions.

treatment_protocol: Mouse naive CD4 T cells seeded onto plate-bound anti-CD3 and anti-CD28 were transfected with 80 µg.mL-1 of 2'3'-cGAMP or Control dinucleotide using Lipofectamine 2000 and Opti-MEM according to the manufacturer's intructions for 6h. Transfection medium was carefully removed and replaced by polarization medium.

tag: in vitro polarization

tag: sting activation

tag: time (hours)


title: k9ac-h3x2-wt-HU110-s43

tag: strain


title: 1826-854

tag: sequencing run number

tag: sample type


title: k9ac-h3x2-wt-HU070-s43


title: TH9 48h cGAMP N=3


title: cPT_QC_run16

tag: rearrangement/patient number

value: cPT-QC

value: thymus, tonsil and PBMCs

value: quality control


title: TH9 48h cGAMP N=2


title: TH9 48h Control N=2

value: Control


title: k9ac-h3x2-wt-HU060-s43

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

value: wt


title: 1361-854


title: k9ac-h3x2-wt-HU050-s43


title: 7004-854


title: NaAsO2_2H

value: whole body

value: adult

tag: treatment


title: k9ac-h3x2-wt-HU040-s43

tag: sensor


title: 7002-854


title: Water_2G

value: Water


title: Su9T01_16h_TAS116_3

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent). For comparison among multiple arrays, probe set data were median-normalized per chip.

source_name: 1µM TAS116, 16h, replicate3

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: Total RNA from each cell line was isolated by RNeasy Mini Kit (QIAGEN) in combination with DNase treatment (RNase-Free DNase Set, QIAGEN)

tag: cell line

value: ATL


title: k9ac-h3x2-wt-HU030-s43

source_name: Sensor-carrying cells

tag: antibody

tag: growth condition


title: Su9T01_16h_TAS116_1

source_name: 1µM TAS116, 16h, replicate1


title: TH1 48h cGAMP N=3


title: TH9 48h Control N=3


title: Su9T01_16h_DMSO_2

source_name: DMSO, 16h, replicate2


title: Su9T01_16h_DMSO_3

source_name: DMSO, 16h, replicate3


title: Su9T01_16h_TAS116_2

source_name: 1µM TAS116, 16h, replicate2


title: Su9T01_16h_DMSO_1

source_name: DMSO, 16h, replicate1


title: 5620-854

source_name: PBMCs

tag: tissue


title: 6702-854


title: OATL4_16h_TAS116_3


title: k9ac-h3x2-wt-HU015-s43

tag: genotype


title: TH9 48h Control N=1


title: TH1 48h Control N=3


title: k9ac-h3x2-wt-alpha-s43


title: 5210-854


title: k9ac-h3x2-vps75-HU150-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: k9ac-h3x2-vps75-HU180-s47


title: 5460-854


title: TH1 48h cGAMP N=2


title: TH1 48h Control N=2


title: TH1 48h Control N=1


title: TH1 48h cGAMP N=1


title: OATL4_16h_TAS116_2


title: k9ac-h3x2-vps75-HU130-s47


title: 5207-854


title: TH9 16h cGAMP N=3


title: OATL4_16h_TAS116_1


title: OATL4_16h_DMSO_3


title: OATL4_16h_DMSO_2


title: TH9 16h cGAMP N=2


title: k9ac-h3x2-vps75-HU110-s47


title: 4681-854


title: k9ac-h3x2-vps75-HU090-s47


title: TH9 16h cGAMP N=1


title: 4540-854


title: OATL4_16h_DMSO_1


title: k9ac-h3x2-vps75-HU050-s47


title: 4461-854


title: 4460-854


title: TH9 16h Control N=2


title: k9ac-h3x2-vps75-HU040-s47


title: TH9 16h Control N=3


title: 5179-854


title: TH9 16h Control N=1


title: 2126-854


title: 1902-854


title: HuT102_16h_TAS116_3


title: TH1 16h cGAMP N=3


title: HuT102_16h_TAS116_1


title: HuT102_16h_DMSO_3


title: TH1 16h cGAMP N=2


title: k9ac-h3x2-vps75-HU015-s47


title: k9ac-h3x2-vps75-HU070-s47


title: HuT102_16h_TAS116_2


title: 1900-854


title: k9ac-h3x2-vps75-alpha-s47


title: TH1 16h cGAMP N=1


title: HuT102_16h_DMSO_2


title: k9ac-h3x2-vps75-async-s47

value: async


title: 1624-854

value: CLL11  EOT patient sample


title: TH1 16h Control N=3


title: ED-40515_16h_TAS116_3

extract_protocol: For each probe, the values were expressed as log2(normalized signal/median of normalized signals from DMSO treated samples).


title: HuT102_16h_DMSO_1


title: TH1 16h Control N=2


title: k9ac-h3x2-vps75-HU030-s47


title: k9ac-h3x2-vps75-HU190-s44


title: k9ac-h3x2-vps75-HU150-s44


title: ED-40515_16h_DMSO_3


title: TH1 16h Control N=1


title: 1260-854


title: ChIP_M2241_Input

data_processing:
For genome wide mapping of CTCF and RAD21 reads were mapped using Bowtie 2 v2.3.5.1 with default settings . The mapped reads with mapping quality score <15 and PCR duplicates were discarded using SAMtools v1.9. Bigwig files were generated with DeepTools v.3.3.2 with bin length of 10 bp, extending reads to 200 bp and CPM normalization. CTCF motif and the orientation of each peak was identified using FIMO v5.1.1  with motif MA0139.1 with -max-stored-scores 50000000.
For RAD21 and CTCF localization on the viral genome reads were mapped using Bowtie 2 v2.3.5.1 with settings n1 k2 . PCR duplicates were discarded using SAMtools v1.9. Bigwig files generated with DeepTools v.3.3.2 with bin length of 10 bp, extending reads to 200 bp and CPM normalization.
Genome_build: Hybrid ovine genome (UCSC: OAR v3.1) containing BLV genome (GenBank: KT122858.1) at their respective integration site
Supplementary_files_format_and_content: bigWig files and narrowPeak files

source_name: BLV infected PBMC

growth_protocol: Cell lines were maintained in Opti-MEM GlutaMAX medium (Life Technologies) supplemented with 10% FBS, 1 mM sodium pyruvate, 2 mM glutamine, non-essential amino acids 1X and 100 μg/ml kanamycin. Cell were maintained at a density of 0.5x10^6 cell/ml, and media was changed each 3 days. Primary cells were collected and characterized as described in Rosewick et al. 2017 (PMID 28534499)

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde before lysis followed by sonication of their chromatin (Bioruptor Plus, Diagenode) to obtain DNA fragments of 200–400 bp. Chromatin immunoprecipitations were performed with chromatin from 6x10^6 cells (1x10^6 cells for the epigenetic modifications) and 5μg of antibodies
Library was prepared using the Ovation Ultralow System v2 kit (NuGen) following Manufacter’s instructions. Paired-end sequencing was then performed with the Illumina HiSeq 2000 instrument. More than 20 millions of single reads were obtained for all libraries

value: Primary leukemic B-cells isolated from sheep M2241L

value: PBMC

tag: chip antibody

value: untreated


title: IE9IDO_Triple_1

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description:
VoomCounts_2.csv
3102

data_processing:
Fastq files generated with CASAVA
fastq files mapped to hg38 with STAR aligner
gene count levels obtained from STAR
Voom normalized counts using limma
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: voom normalized counts in csv format

growth_protocol: C57BL/6 mice were challenged intraperitoneally (i.p.) with 1×107 IE9mp1-mIDO1 or IE9mp1-Empty-Vector tumor cells in a final volume of 500ml Dulbecco’s PBS (Corning Cellgro®) and treated by oral gavage with 300mg/kg IDO1 inhibitor INCB023843 (Incyte Corp.) in 200ml 0.5% methylcellulose

extract_protocol:
RNA extraction was performed using Qiagen miRNAeasy mini kit
Total RNA library perp prepared using The KAPA RNA HyperPrep Kit with RiboErase (HMR) with 500ng RNA input.

treatment_protocol: injection 5 days on and two days off from d7-d21, with or without (i) NAMPT inhibitor FK866 (Sigma-Aldrich, 500 μg per mouse i.p.)  once every week for 3 weeks (on day 13, 20, 27); (ii) purinergic receptor A2a or A2b antagonists (Sch 58261 from Sigma-Aldrich or PSB 1115 from Tocris Bioscience, 1mg/kg)

tag: replicate

value: Triple


title: ChIP_M2241_CTCF

tag: cell type

value: CTCF (Millipore, 07-729)


title: 1822-854

value: PBMCs


title: IE9IDO_Triple_2

description:
VoomCounts_2.csv
3103


title: k9ac-h3x2-vps75-HU110-s44


title: ChIP_L267_Input

source_name: BLV infected L267 cell line

value: Lymphoma derived B-cell


title: IE9IDO_A2b_2

description:
VoomCounts_2.csv
395


title: PDX#2

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

country: Italy

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR v2.7.0e with parameters  --runThreadN 8 --outFilterMultimapNmax 20 --alignIntronMax 500000 --quantMode TranscriptomeSAM GeneCounts --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate
Raw counts were determined by STAR v2.7.0e
STAR gene counts were normalized applying the median of ratios method implemented in DESeq2 R package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include DESeq normalized reads
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: patient-derived xenografts (PDXs)

growth_protocol: Isolation, culture and processing of primary epithelial ovarian cancer cells:  Peritoneal ascites was collected through paracentesis upon informed consent from a 59-years old patient of the Gynaecology Division of the European Institute of Oncology (Milan) who presented with ovarian masses and other pelvic lesions. The ascites was collected prior to any surgical or pharmacological treatment. The clinical evaluation and the histological analysis of peritoneal biopsies indicated a diagnosis of FIGO Stage-IIIC HGSOC. The isolation and culture of primary cells were performed as previously described (Cell Rep. 2017;18(13):3242-3256. doi:10.1016/j.celrep.2017.03.015). The purity of the primary culture was examined by immunostaining for the epithelial cytokeratins 5, 7 and 8, and was consistently over 95%. During culture, primary cells underwent spontaneous in vitro immortalization and a stable cell line could be established. The As11 cell line has currently reached more than 80 passages. Both primary early-passage cancer cells and the cell line were cultured on collagen I-coated plates (Collagen Cellware, Biocoat, Corning) at 37°C in a humidified incubator with 5% CO2.  Spheroid formation assay:  The spheroid formation assay was performed as previously described (Stem Cell Reports. 2018;10(4):1412-1425. doi:10.1016/j.stemcr.2018.02.009) seeding single cell suspensions from primary cultures in Poly-(2-hydroxyethyl methacrylate) (P3932-25G, Sigma)-coated dishes at a density of 5x10^3 cells/ml. Spheroid formation was assessed 7 days after seeding. The spheroid-forming efficiency was defined as the ratio between number of spheroids and number of cells seeded. To perform the whole exome sequencing and the mRNA sequencing, first-generation spheroids were dissociated and re-seeded as described above in order to obtain second-generation spheroids. When needed, 20 or 50 uM LY294002 (Cell Signaling Technology, Danvers, MA) was added to suspension cultures on days 0, 2 and 4 after seeding.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s protocol and quantified using the 2100 Bioanalyzer (Agilent)
TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat (Illumina, catalogue number 20020596) was used to prepare sequencing libraries for all samples starting from 100 ng of RNA.

value: High Grade Serous Ovarian Cancer

value: HGSOC cells

tag: tumor stage

value: FIGO Stage-IIIC

tag: passage

tag: age

value: six to eight weeks old


title: PDX#3

tag: strain


title: PDX#4


title: ChIP_YR2_Input

source_name: BLV infected YR2 cell line

value: Leukemia derived B-cell


title: ED-40515_16h_TAS116_2


title: ED-40515_16h_TAS116_1


title: k9ac-h3x2-vps75-HU090-s44

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019


title: IE9IDO_A2b_1

description:
VoomCounts_2.csv
394


title: k9ac-h3x2-vps75-HU050-s44


title: IE9IDO_A2a_4

description:
VoomCounts_2.csv
385


title: CL

source_name: Ovarian carcinoma cells

value: HGSOC primary cells


title: k9ac-h3x2-vps75-HU130-s44


title: OCSC

source_name: Ovarian carcinoma stem cells

value: 2 (second generation spheres)


title: ChIP_YR2_RAD21

data_processing:
For genome wide mapping of CTCF and RAD21 reads were mapped using Bowtie 2 v2.3.5.1 with default settings . The mapped reads with mapping quality score <15 and PCR duplicates were discarded using SAMtools v1.9. Bigwig files were generated with DeepTools v.3.3.2 with bin length of 10 bp, extending reads to 200 bp and CPM normalization. CTCF motif and the orientation of each peak was identified using FIMO v5.1.1  with motif MA0139.1 with -max-stored-scores 50000000.
For RAD21 and CTCF localization on the viral genome reads were mapped using Bowtie 2 v2.3.5.1 with settings n1 k2 . PCR duplicates were discarded using SAMtools v1.9. Bigwig files generated with DeepTools v.3.3.2 with bin length of 10 bp, extending reads to 200 bp and CPM normalization.
genome build: Hybrid ovine genome (UCSC: OAR v3.1) containing BLV genome (GenBank: KT122858.1) at their respective integration site
processed data files format and content: bigWig files and narrowPeak files

value: Rad21 (Abcam, Ab992)


title: PDX#1


title: IE9IDO_A2a_3

description:
VoomCounts_2.csv
384


title: ChIP_L267_RAD21


title: ChIP_YR2_CTCF


title: k9ac-h3x2-vps75-HU030-s44

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG


title: ED-40515_16h_DMSO_2

value: ATL


title: PR


title: ChIP_L267_CTCF


title: AS

source_name: Ascites

value: ascites - tumor cell aggregates


title: k9ac-h3x2-vps75-HU015-s44


title: IE9IDO_A2a_1

description:
VoomCounts_2.csv
381


title: k9ac-h3x2-vps75-HU040-s44


title: k9ac-h3x2-vps75-HU070-s44


title: k9ac-h3x2-vps75-alpha-s44

value: alpha


title: k9ac-h3x2-vps75-async-s44

value: async


title: IE9IDO_vehicle_5

description:
VoomCounts_2.csv
365

value: vehicle


title: IE9IDO_vehicle_4

description:
VoomCounts_2.csv
364


title: IE9IDO_Incyte_1

description:
VoomCounts_2.csv
371

value: Incyte


title: Patient3_16h_TAS116

data_processing: Data analysis  were carried out by a contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

label_protocol: Experiments were carried out by a contract research service at Dragon Genomics Center (Takara Bio, Mie, Japan). Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).


title: IE9IDO_vehicle_3

description:
VoomCounts_2.csv
363


title: IE9IDO_vehicle_2

description:
VoomCounts_2.csv
362


title: Patient3_16h_DMSO

source_name: DMSO, 16h


title: IE9IDO_A2a_2

description:
VoomCounts_2.csv
383


title: WT Day 6 input ChIPseq rep 6 [inp_wt_r1_cpc.1.1]

data_processing:
ChIP seq:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the hg19 reference human genome was performed using Bowtie 2.2.4. Peaks were called BCP for GLYR1.
single cell RNA seq:
Cluster generation, sequencing, and base calling was performed on NovaSeq (Illumina, software v1.5)
6-8 replicate samples (from independent differentiation runs involving either wild-type or P496L mutant cells) were each processed in 3 batches. Reads from each sample were aligned to the hg38 human reference (version 2020-A from 10X Genomics website) using Cell Ranger version 5.0.1. The resulting count matrices for all samples within each batch were aggregated without depth normalization.
Genome_build: hg19 (ChIP-seq); hg38 (RNA-seq)
Supplementary_files_format_and_content: We provide bed ad BigWig files for ChIPseq.
Supplementary_files_format_and_content: We provide the aligned bam files and count matrices in h5 format

source_name: WT hiPSC cardiomyocyte differentiation day 6 (cardiac progenitor stage)

extract_protocol:
For ChIPseq experiments, CPs (30×106 for cTFs and 10×106 for GLYR1 and histone marks) were pelleted and suspended in 10ml DMEM and cross-linked in 1% Formaldehyde solution (Cat. 28906, Thermo Fisher Scientific) by rocking in room temperature for 10 min. Then glycine (final concentration 0.125M) was added to quench the cross-link for 5 min. Samples were centrifuged at 1000 rcf for 5 min. at 4°C. Cells were washed with 10ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Cat. 4693132001 Roche and Cat. 4906837001 Sigma-Aldrich) and the pellets were snap frozen in liquid nitrogen. All samples were stored at −80°C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40, protease/phosphatase inhibitors) for 10 min. on a rotator at 4°C. Nuclei were isolated by centrifugation (2,500 x g, 5 min., 4°C), resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease/phosphatase inhibitors) and incubated on a rotator for 30 min. at 4°C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 15 min. (60 s cycles, 5% duty cycle, 200 cycles/burst, intensity = 6) until DNA was in the 200–700 base pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease/phosphatase inhibitors) and incubated with the corresponding primary antibody at 4°C overnight under rotation. Antibody-protein complexes were immunoprecipitated using 50μl of Dynabeads™ Protein A/Protein G (Cat. 10015D, Invitrogen) per sample at 4°C for 2 h under rotation. After incubation, beads were washed five times (2 min./wash under rotation) with cold RIPA buffer [50 mM HEPES-KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate], followed by one wash in cold final wash buffer [1xTE, 50 mM NaCl]. Immunoprecipitated chromatin was eluted at 65°C with agitation for 30 min. in elution buffer [50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS]. High-salt buffer [250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl] and Proteinase K (Cat. P8107s, New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65°C. Samples were treated with RNase A, and DNA was purified with AMPure XP beads (Cat. A63881, Beckman Coulter). Primary antibodies used for ChIP were: GATA4 (Cat. sc-1237 X, Santa Cruz), TBX5 (Cat. sc-17866 X, Santa Cruz), H3K36me3 (Cat. ab9050, Abcam), GLYR1 (anti-serum 7; provided by James T. Kadonaga’s laboratory), NKX2-5 (Cat. sc-8697 X, Santa Cruz), MEIS1 (Cat. ab19867, Abcam).
Fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat. E7645, New England BioLabs). Samples were ligated to adaptor oligos for multiplex sequencing (Cat. E7335, New England BioLabs), PCR amplified, and sequenced on an Illumina NextSeq 500 at the Gladstone Institutes.

tag: cardiomyocyte differentiation day

value: Day 6

tag: processing batch

tag: comparison analysis

value: P496L GLYR1 mutant versus WT at Day 6 cardiac progenitor stage differential GLYR1 binding


title: Patient2_16h_TAS116


title: IE9IDO_vehicle_1

description:
VoomCounts_2.csv
361

tag: treatment


title: Patient1_16h_TAS116


title: IE9MP1_IDO_FK866_Incyte_5

description:
VoomCounts_2.csv
Grp5-2


title: k56ac-h3x2-wt-HU090-s47

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

value: wt


title: GLYR1 P496L mutant Day 6 input ChIPseq rep 3 [inp_p496l_r4_cpc.3]

growth_protocol: For human cardiac differentiation into D6 cardiac progenitors or D18 cardiomyocytes, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al. 2013; Tohyama et al. 2013). Briefly hiPSCs were detached from hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) with accutase (Cat. 07920, Stem Cell Technologies) and reseeded on matrigel at 0.6–1.2x105 cells per 12well in Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM ROCK inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) (day-3). We optimized each hiPSC clone individually to identify the best cell seeding density that resulted in high levels of cTNT, NKX2-5, TBX5 and GATA4-positive sheet-like beating CMs at day15 of differentiation. On the next two days, media was changed daily with fresh E8 medium without ROCK inhibitor. On the day of cardiac induction (day0), 6μM CHIR99021 (Cat. 4423, Tocris) was added for 24 hr. in 1ml per well of B27-supplemented (without insulin) RPMI1640 media (Cat. 11875-119, Life Technologies). On day1 media was changed for freshly prepared 6μM CHIR99021 in B27-supplemented (without insulin) (Cat. A1895601, Life Technologies) RPMI1640 media. At day 2 and 3 IWP4 (Cat. 5214, Tocris) in B27-supplemented (without insulin) RPMI1640 media was added to activate Wnt signaling at a final concentration of 5μM. At day 4, IWP4 was removed, and 1ml of B27-supplemented (without insulin) RPMI1640 media per was daily added per well (days 4-9) and collected at day 6 cardiac progenitor stage or continue with media changes for cardiomyocyte stage collection. At day 10 the media was changed to regular B27-supplemented (with insulin) (Cat. A1895601, Life Technologies) RPMI1640 hereafter.

treatment_protocol: For the generation of the GLYR1P496L line, the HDR template (12nM):  CCTCAGATATCCTGCAAGGAAACTTTAAGCTTGATTTCTACCTGAAATACATTCAGAAGGA, was added to the Cas9-RNP complexes, prior to transferring into the nucleofector wells. This was repeated for every Cas9-RNP condition. The nucleofector cassette was placed in the nucleofector instrument (Nucleofector 4D system, Lonza) and cells nucleofector using the preset program DS-138. The nucleofection cassette was brought back to sterile hood and 80μL of Essential 8 medium (E8) (Cat. A1517001, Life Technologies) with 5μM rho kinase (ROCK) inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) added into each well and incubated for 10 min. at 37°C.  During the incubation time, we removed the hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) from 12 well plates (Corning) pre-coated for 1 hr. at 37°C with 0.5ml per well of matrigel and added 2mL of pre-warmed E8 medium plus 5μM ROCK inhibitor (Y-27632 2HCl) in each well. Then pipetted the nucleofected cells to each of the pre-coted wells with media. After ~3-5 days, wells with surviving clones were expanded to isolate gDNA for screening. A genomic fragment spanning the gRNA target sites was amplified using primers FW 5’ CACCAGTGCACTCTAGCCT 3’ and REV 5’ TGCAGCAAATGAGGTAGGGT 3’ for GLYR1 with Phusion® High-Fidelity PCR Master Mix with GC Buffer (Cat. M0532S, New England BioLabs) and Sanger sequenced (Quintara Biosciences or MCLAB) to identify clones with frame-shift insertions/deletions. Synthego ICE analysis was run to identify clones with highest knock-out efficiency (https://ice.synthego.com/#/), which were subsequently subjected to the colony picking and clone sequencing until monoclonal lines were generated. The top 5 sgRNA predicted off-targets (https://horizondiscovery.com/en/products/tools/crispr-specificity-analysis) were verified to be intact by sanger sequencing in the final monoclonal lines and checked for normal karyotype (Cell Line Genetics).


title: WT Day 6 input ChIPseq rep 5 [input_cpc_2.3]


title: Patient2_16h_DMSO


title: WT Day 6 input ChIPseq rep 7 [inp_wt_r4_cpc.2]


title: IE9MP1_IDO_FK866_Incyte_4

description:
VoomCounts_2.csv
Grp5-1


title: k56ac-h3x2-wt-HU050-s47


title: AR1547_13

tag: cell line

value: ATL cell line


title: AR1547_14


title: GLYR1 P496L mutant Day 6 input ChIPseq rep 1 [inp_p496l_r1_cpc.1]


title: GLYR1 P496L mutant Day 6 input ChIPseq rep 2 [inp_p496l_r2_cpc.2]


title: k56ac-h3x2-wt-HU130-s47

tag: antibody


title: KK1_16h_TAS116_1


title: k56ac-h3x2-wt-HU110-s47

tag: growth condition


title: k56ac-h3x2-wt-HU040-s47


title: k56ac-h3x2-wt-HU070-s47


title: WT Day 6 GLYR1 ChIPseq rep 7 [glyr1_wt_r4_cpc.2]

value: GLYR1 anti-sera 7

tag: chip antibody vendor

value: James T. Kadonaga Laboratory


title: IE9MP1_IDO_FK866_Incyte_2

description:
VoomCounts_2.csv
Grp4-3


title: k56ac-h3x2-wt-HU150-s47

tag: genotype


title: KK1_16h_DMSO_1


title: ED-40515_16h_DMSO_1


title: k56ac-h3x2-wt-HU030-s47


title: Patient1_16h_DMSO

tag: tissue


title: WT Day 6 GLYR1 ChIPseq rep 6 [glyr1_wt_r1_cpc.1.1]

tag: chip antibody


title: k56ac-h3x2-wt-HU015-s47


title: IE9MP1_IDO_FK866_Incyte_1

description:
VoomCounts_2.csv
Grp4-2

tag: replicate


title: IE9MP1_IDO_FK866_5

description:
VoomCounts_2.csv
Grp3-5


title: IE9MP1_IDO_FK866_4

description:
VoomCounts_2.csv
Grp3-4


title: GLYR1 P496L mutant Day 6 GLYR1 ChIPseq rep 3 [glyr1_p496l_r4_cpc.3]


title: LMY1_16h_TAS116_1


title: k56ac-h3x2-wt-async-s47


title: IE9MP1_IDO_FK866_3

description:
VoomCounts_2.csv
Grp3-3


title: LMY1_16h_DMSO_1


title: k56ac-h3x2-wt-alpha-s47


title: k56ac-h3x2-wt-HU180-s43


title: IE9MP1_IDO_FK866_2

description:
VoomCounts_2.csv
Grp3-2


title: GLYR1 P496L mutant Day 6 GLYR1 ChIPseq rep 2 [glyr1_p496l_r2_cpc.2]


title: AR1547_07


title: GLYR1 P496L mutant Day 6 GLYR1 ChIPseq rep 1 [glyr1_p496l_r1_cpc.1]


title: k56ac-h3x2-wt-HU150-s43


title: AR1547_08


title: WT Day 6 input ChIPseq rep 5 [inp_wt_r1_cpc.1]

value: Day 6 Cardiac Progenitor versus Day 0 hiPSC stage differential GLYR1 binding


title: IE9MP1_IDO_Incyte_4

description:
VoomCounts_2.csv
Grp2-5


title: WT Day 6 GLYR1 ChIPseq rep 5 [glyr1_wt1_cpc.3]


title: WT Day 6 input ChIPseq rep 4 [input_cpc_3.4]

value: Day 6 Cardiac Progenitor versus Day 0 hiPSC stage differential GLYR1 binding AND P496L GLYR1 mutant versus WT at Day 6 cardiac progenitor stage differential GLYR1 binding


title: k56ac-h3x2-wt-HU130-s43


title: AR1547_06


title: AR1547_05


title: IE9MP1_IDO_Incyte_3

description:
VoomCounts_2.csv
Grp2-4


title: k56ac-h3x2-wt-HU110-s43


title: WT hiPSC input ChIPseq rep 6 [inp_wt4_ipsc.4]

source_name: WT hiPSC

growth_protocol: Human iPSCs were maintained on tissue culture-treated polystyrene plates (Cat. 430630, Corning) with hESC-qualified LDEV-free matrigel (Cat. 354277, Corning) in Essential 8 medium (E8) (Cat. A1517001, Life Technologies). The medium was changed daily and the hiPSCs were split every 4 – 6 days using Accutase (Cat. 07920, Stem Cell Technologies). The rho kinase (ROCK) inhibitor (Y-27632 2HCl, Cat. S1049, Selleckchem.com) was included in the medium at 5μM final concentration on the day of passaging.

value: Day 0:hiPSC


title: k56ac-h3x2-wt-HU090-s43

source_name: Sensor-carrying cells


title: WT hiPSC input ChIPseq rep 5 [inp_wt3_ipsc.3]


title: IE9MP1_IDO_Incyte_2

description:
VoomCounts_2.csv
Grp2-3


title: AR1547_03


title: AR1547_04


title: IE9MP1_IDO_Incyte_1

description:
VoomCounts_2.csv
Grp2-2


title: k56ac-h3x2-wt-HU070-s43


title: WT hiPSC input ChIPseq rep 4 [inp_wt2_ipsc.2]


title: senescent cells with corylin treatment (S+C)

city: Taoyuan City

first: chunhao

last: feng

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan (R.O.C.)

department: Graduate Institute of Natural Product

country: Taiwan

institute: Chang Gung University

data_processing:
Raw reads QC: adapter trimming and quality filtering (trimmomatic PE {input.r1} {input.r2} {output.r1_clean} {output.r1_clean_up} {output.r2_clean} {output.r2_clean_up} ILLUMINACLIP:/adapters/{adapter}.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20)
Align against reference genome with reference annotation Aligner: bowtie2 Reference : transcript sequences
Gene expression (RSEM) http://deweylab.github.io/RSEM/
Differential gene expression (EBSeq) https://www.biostat.wisc.edu/~kendzior/EBSEQ/
Pathway enrichment
GO enrichment
Genome_build: hg19/mm10
Supplementary_files_format_and_content: excel file included Expected count (S), Expected count (S-C), Expected count (Y), TPM (S), TPM (S-C), TPM (Y), FPKM (S), FPKM (S-C), FPKM (Y), Fold change (S-C_S), Fold change (S-C_Y), Fold change (S_Y), PPEE (S-C_S), PPEE (S-C_Y), PPEE (S_Y), Description, GO (BP)GO (MF)GO (CC), Pathway (KEGG), EC number

source_name: Bioresource Collection and Research Center, Taiwan

growth_protocol: HUVECs were cultured in M199 supplemented with HEPES, ECGS (Millipore), heparin, NaHCO3, L-glutamine, sodium pyruvate, and FBS (20% final concentration). The cells were grown in an atmosphere of 5% CO2 at 37°C and sub-cultured by trypsinization with trypsin-EDTA (Lonza).

extract_protocol:
RNA was collected from HUVECs and extracted by TRIzol (T9424, Sigma, USA). The extracted RNA samples were sent to Genomics (Taipei, Taiwan) for analysis, and a library was constructed. Briefly, after quality control of raw reads, mRNA was purified using reverse transcriptase and a random primer to synthesize single-strand cDNA, and dUTP was used in place of dTTP to generate double-stranded cDNA. A single ‘A’ nucleotide was added to the 3’ end of ds cDNAs. Then, multiple indexing adapters were ligated to the 5’ and 3’ ends of ds cDNA.
Library was validate on Agilent 2100 Bio-analyzer and Real-Time PCR System.

treatment_protocol: The cells were treated with DNSO or corylin for 24days.

value: Human umbilical vein

tag: pdl

value: treated with corylin for 24 days


title: IE9MP1_IDO_FK866_1

description:
VoomCounts_2.csv
Grp3-1


title: IE9MP1_IDO_vehicle_3

description:
VoomCounts_2.csv
Grp1-3


title: AR1547_02


title: senescent cells (S)

value: treated with DMSO for 24 days


title: WT hiPSC input ChIPseq rep 3 [inp_wt1_ipsc.1]

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes


title: WT hiPSC GLYR1 ChIPseq rep 6 [glyr1_wt4_ipsc.4]


title: IE9MP1_IDO_vehicle_2

description:
VoomCounts_2.csv
Grp1-2


title: k56ac-h3x2-wt-HU050-s43


title: k56ac-h3x2-wt-HU060-s43


title: k56ac-h3x2-wt-HU040-s43