title: qNHA cells, mRNA-seq, DMSO, BR1

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

data_processing:
Sequencing reads were trimmed with using Cutadapt (v1.10) with " -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 50 ".
Trimmed reads were aligned using STAR (v2.5.4b) (STAR  --runMode alignReads  --runThreadN 6  --genomeDir <reference directory>  --readFilesIn <R1.fastq.gz> <R2.fastq.gz>  --readFilesCommand zcat  --outFileNamePrefix <name.out>  --outSAMtype BAM SortedByCoordinate  --outSAMstrandField intronMotif   --outSAMattributes NH HI NM MD AS XS  --outSAMunmapped Within  --outSAMheaderHD @HD VN:1.4  --outFilterMultimapNmax 20  --outFilterScoreMinOverLread 0.33  --outFilterMatchNminOverLread 0.33  --alignIntronMax 500000  --alignMatesGapMax 1000000  --twopassMode Basic).
hg38
bedgraph

source_name: brain

extract_protocol:
mRNA from GSCs and primary cells was extracted using Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific, 61011). We enriched for 5’-capped mRNA by digesting mRNA extraction with Terminator exonuclease digestion (Lucigen, TER51020) following manufacture’s recommendations.
RNA-seq library was generated using TruSeq RNA Library Prep Kit v.2 (Illumina, RS-122–2001).

value: brain

value: HA

value: Human Astrocytes


title: qhFB cells, mRNA-seq, DMSO, BR2

status: Public on Jun 05 2024

type: SRA

state: MO

department: Genetics

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

tag: tissue

value: skin

tag: cell line

value: HDFa

tag: cell type

value: primary dermal fibroblast

tag: treatment

value: DMSO


title: qNHA cells, mRNA-seq, DMSO, BR2


title: AGS-GM-CSF cells, siAPE1, rep3

city: Lianyungang

first: Baoming

last: Zhang

address: No. 6 Zhenhua East Road

country: China

institute: The First Peoples Hospital of Lianyungang

data_processing:
Raw data in fastq format were filtered with PERL SCRIPT to obtain the clean reads that were then mapped to mouse genome (GRCm39/mm39) using HISAT2
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo

source_name: AGS

extract_protocol:
Total RNA was extracted using the Trizol reagent and subjected to quality detection. mRNA was enriched with magnetic bead containing Oligo, and 1.5μg of total RNA was used for construction of sequencing libraries
The library was then sequenced on the MGISEQ-T7 platform after determining the insert size and effective concentration.

value: AGS

value: Human gastric adenocarcinoma cells

tag: genotype

value: APE1 knockdown

value: GM-CSF incubation


title: qhFB cells, mRNA-seq, DMSO, BR1


title: MRL-KO_3

city: Chicago

first: Joseph

middle: G

last: O'Brien

state: IL

address: 445 E Ohio St, Apt 1818

institute: Northwestern

data_processing:
Sequences were trimmed for adapter sequence based on quality of the reads using fastqc/0.11.5
Trimmed sequences were aligned to the mm10 reference genome using tophat/2.1.0
Read count extraction and normalization was gathered using Bioconductor edgeR open source software
Assembly: mm10
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample
Supplementary files format and content: Tab-deliminated text file includes CPM values for each sample

organism: Mus musculus

source_name: Quadriceps

growth_protocol: 3 Female mice per cohort, aged 16 weeks

extract_protocol:
RNA was extracted from whole quadriceps using TRIzol and filted with Aurum Total RNA Mini-kit. RNA was suspended in 30ul of RNase-Free Water
The Illumina RNA Sample Prep Kit version 2.0 generated libraries and aligned to the mm10 reference

value: Quadriceps

tag: Sex

value: Female

tag: age

value: 16 weeks


title: MCF7-Veh biol rep 1

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
counts_01_DMSO
2022-07-30_Annotated_read_counts.csv
Vehicle_1

data_processing:
Reads were aligned using Hisat2 (Version 2.2.1)
Reads were counted using featureCounts program in the Subread (Version 2.0.1) package
Assembly: hg38
Supplementary files format and content: comma separated value (.csv) files containing raw read counts

source_name: Breast

growth_protocol: Phenol red-free DMEM + 10% charcoal-stripped FBS for 3 days

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN). mRNA was selectively isolated from total RNA (1 ug input) using poly-T oligos attached to magnetic beads according to the manufacturer’s guidelines in the NEBNext poly(A) mRNA magnetic isolation module (Cat. #: E7490, NEB, Ipswich, MA).
The library preparation from the enriched mRNA was conducted according to NEBNext Ultra II Directional RNA kit

treatment_protocol: DMSO,  1 nM E2, 100 nM Fulv, or 100 nM Fulv +1 nM E2, for 24 hours

value: Breast

value: Epithelial


title: DGM-13206_Sample_79

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Raw reads from 240 sequenced samples pooled from the 3 healthy, nonsmoker subjects were processed with Salmon to obtain gene and transcript levels as estimated read counts and transcripts per million (TPM) using the Ensembl release 79 transcriptome.
Samples with <10e6 reads or for which less than 80% of fragments mapped to non-mitochondrial protein coding genes were excluded from the final analysis, leaving data from a total of 157 single cells.
For all analyses, TPM values were log transformed as log2(1+TPM). Genes which were not expressed in any sample were excluded, leaving a total of 21,757 genes after filtering. Eighteen samples with no visible cell captured and <10e6 mapped reads (“no cell” wells) were used to estimate background levels of RNA contamination for each gene detected. For 855 genes expressed in at least 20% of no cell wells, background levels were estimated from estimated read counts by fitting an exponential distribution. Estimated read counts for affected genes were corrected by subtracting background levels (to a minimum of 0) and TPM values were recalculated using the corrected read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: log TPM text files include the Ensembl unique ID and gene symbol and log2(1+TPM) values for all samples.

source_name: small airway epithelium brushing

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Fluidigm C1 system following the manufacturer’s protocol. To enrich the cell capture of club cells and basal cells, and minimize the inclusion with larger differentiated ciliated and mucin-secreting cells, the single cell suspension (15 μl; 400~600 cells/μl) were loaded into the medium-sized (10 to 17 μm in diameter) microfluidic RNA-seq chip after priming (Fluidigm). The cells were captured using an Olympus-phase contrast microscope to examine the cell numbers in each capture site. Only single cells in the capture site were used.
The Fluidigm C1 system was used for single cell RNA purification and cDNA synthesis by using the SMARTer Ultra Low RNA kit, and the single cell cDNAs were transferred to a 96 well-plate. The single cell library preparation and RNA sequencing were performed following a Fluidigm protocol.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

tag: individual id

tag: smoking status

value: nonsmoker

value: SAE


title: MRL-KO_2


title: AGS-GM-CSF cells, siNC, rep2

value: WT


title: MRL-KO_1


title: DGM-13206_Sample_76


title: qNHA cells, mRNA-seq, DACPano, BR1

value: brain

value: HA

value: Human Astrocytes

value: 1uM DAC 6 days, 100nM Pano 2 days


title: DGM-13206_Sample_7


title: DGM-13206_Sample_81


title: DGM-13206_Sample_72


title: AGS-GM-CSF cells, siAPE1, rep2


title: D2-WT_2


title: Reactivated.4

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

data_processing:
Raw reads were cleaned from adaptors and low-quality regions using cutadapt.
Clean reads were mapped to Pisum sativum genome using HISAT2.
Per gene read counting was done using htseq-count.
DESeq2 with default parameters was used to perform differential expression analysis.
Assembly: Pisum sativum v1a
Supplementary files format and content: TSV (tab-separated values) text file with per gene read counts for each sample.

organism: Lathyrus oleraceus

source_name: Shoot Apical Meristem

growth_protocol: Pisum sativum plants were grown in standard conditions in vermiculite (hydroponic growth with automatic watering). Plants were watered with Hoagland No.1 solution suplemented with trace elements. Greenhouse conditions: Long Day photoperiod (16 hours of light and 8 hours of darkness) with natural light supplemented with artificial light using 400 W mercury vapor lamps. Temperature fluctuated between 21.5ºC during the day and 15ºC during the night.

extract_protocol:
RNA from Shoot Apical Meristem samples at the different stages described was extracted using the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Turbo DNA-free kit INVITROGEN; Ref-AM1907) following the manufacturer’s instructions. The quality of the RNA was checked on an Agilent 2100 Bioanalyzer instrument using the RNA6000 nano kit.
Eukaryotic Transcriptome Library/Strand specific libray (mRNA-seq poly A enrichment) was constructed using Illumina NovaSeq 6000

treatment_protocol: Samples were collected at different stages of development: 1.- Proliferative: SAM was collected of young plants that just started flowering. The samples were collected after the production of the first flower bud, before anthesis. 2.- GPA (UPDATED TO PA): SAM was collected just when plants undergo Proliferative Arrest. 3.- Pruned: SAM collected the same day as 2, but in plants that had been continiously pruned (never sensed seeds), avoiding the arrest of the meristem. 4.- Reactivated: SAM collected 24 hours after removing all fruits and flowers of arrested plants. 4 biological replicates for each sample. Shoot apical meristems were collected macroscopically, by removing as much leaves and flower buds as possible.

value: Shoot Apical Meristem

value: Cameor Wild Type

tag: developmental stage

value: Reactivated after Proliferative Arrest, Meristem Active


title: MRL-WT_1


title: Reactivated.3


title: Reactivated.2


title: DGM-13206_Sample_74


title: qhFB cells, mRNA-seq, DACPano, BR2

value: skin

value: HDFa

value: primary dermal fibroblast


title: Pruned.4

value: Continiously deflowered, SAM Active


title: Pruned.3


title: AGS-GM-CSF cells, siNC, rep1

value: AGS

value: Human gastric adenocarcinoma cells

value: GM-CSF incubation


title: qhFB cells, mRNA-seq, DACPano, BR1


title: DGM-13206_Sample_69

value: nonsmoker


title: 94595

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
Tophat2 was used to align RNA-seq reads to the human genome
HTSeq was used to quantify gene expression levels
normalization and differential expression analyses were performed by DESeq2
Assembly: hg19
Supplementary files format and content: read counts

source_name: Skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
Libraries were constructed from polyadenylated RNA on the Illumina Genome Analyzer Iix

value: Skin

value: Keratinocyte

value: control


title: DGM-13206_Sample_68

value: SAE


title: Reactivated.1


title: GPA.4

value: SAM arrested


title: AGS-GM-CSF cells, siNC, rep3

value: WT


title: qNHA cells, mRNA-seq, DACPano, BR2

value: brain

value: HA

value: Human Astrocytes

value: 1uM DAC 6 days, 100nM Pano 2 days


title: DGM-13206_Sample_67


title: NHA cells, mRNA-seq, DMSO, BR1

value: DMSO


title: Pruned.2

value: Shoot Apical Meristem

value: Cameor Wild Type


title: NHA cells, mRNA-seq, DMSO, BR2


title: DGM-13206_Sample_66


title: AGS-GM-CSF cells, siAPE1, rep1

value: AGS

value: APE1 knockdown


title: NHA cells, mRNA-seq, DACPano, BR1


title: Pruned.1

value: Continiously deflowered, SAM Active


title: hFB cells, mRNA-seq, DMSO, BR1

value: skin

value: HDFa

value: primary dermal fibroblast


title: DGM-13206_Sample_62

value: nonsmoker


title: Proliferative.3

value: Pre-Anthesis, SAM active


title: hFB cells, mRNA-seq, DACPano, BR2


title: DGM-13206_Sample_64

value: SAE


title: GPA.2

value: SAM arrested


title: DGM-13206_Sample_63


title: hFB cells, mRNA-seq, DMSO, BR2


title: Proliferative.2


title: Proliferative.1


title: hFB cells, mRNA-seq, DACPano, BR1


title: B66 cells, mRNA-seq, DMSO, BR2

value: brain

value: glioblastoma stem cell


title: DGM-13206_Sample_58


title: DGM-13206_Sample_61


title: AsPC-1 treated with U0126

city: Tokyo

first: Toru

last: Furukawa

address: 8-1 Kawadacho, Shinjuku-ku

department: Institute for Integrated Medical Sciences

country: Japan

institute: Tokyo Women's Medical University

data_processing:
HISAT
StringTie
Assembly: GRCh38
Supplementary files format and content: txt

source_name: Pancreas

growth_protocol: Human pancreatic cancer cell lines AsPC-1, MIA PaCa-2, and PCI-35 were used in this study. AsPC-1 and MIA PaCa-2 were obtained from the American Type Culture Collec-tion (Manassas, VA, USA), and PCI-35 was provided by Dr. Hiroshi Ishikura [Int J Cancer 1993;54:972-977]. Unless otherwise stated, AsPC-1 and PCI-35 were cultured with RPMI-1640 with 10% fetal bovine serum, and MIAPaCa-2 was cultured with Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction.
The isolated total RNA was used for construction of a fragment library using TruSeq Stranded Total RNA LT Sample Prep Kit Gold (Illumina, San Diego, CA, USA).

treatment_protocol: Cells of the human pancreatic cancer cell lines were seeded at 5 × 105 cells per dish in 10-cm culture dishes and cultured under 37°C in 5% CO2. After 24 hours, the medium was replaced with medium containing U0126 (Sigma-Aldrich, St. Louis, MO, USA), a MAP2K inhibitor, dissolved in dimethyl sulfoxide (DMSO) to a final concentration of 10 μmol/L, or with medium containing only the same amount of DMSO without U0126 as a control. After incubation for 24 hours, cells were dissociated for RNA isolation.

value: Pancreas

value: pancreatic cancer cell lines


title: PCI-35 treated with U0126


title: PCI-35 treated with DMSO

value: DMSO (control)


title: GPA.1

value: Shoot Apical Meristem


title: DGM-13206_Sample_6


title: GPA.3

value: Cameor Wild Type


title: DGM-13206_Sample_55


title: Proliferative.4


title: B66 cells, mRNA-seq, DMSO, BR1

value: DMSO


title: MIA PaCa-2 treated with U0126

value: MIA PaCa-2


title: MIA PaCa-2 treated with DMSO


title: B66 cells, mRNA-seq, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: DGM-13206_Sample_57


title: NHA cells, mRNA-seq, DACPano, BR2

value: HA

value: Human Astrocytes


title: HT29 cells, no transduction, light, biological replicate 3

city: Urbana

first: Kai

address: 600 South Mathews Avenue

department: Biochemistry

institute: University of Illinois at Urbana-Champaign

data_processing:
The read counts were quantified using Salmon (version 1.9.0)[79] indexed with Genome assembly GRCh38.p14 (NCBI RefSeq Sequence GRCh38.p14.GCF_000001405.40). The count quant.sf files were analyzed using the R package DESeq [https://github.com/hbctraining/DGE_workshop_salmon].
Assembly: GRCh38.p14 (NCBI RefSeq Sequence GRCh38.p14.GCF_000001405.40)
Supplementary files format and content: LaRIPK3_Normalized_Log2counts_salmon.xlsx contains the normalized log2 counts for each condition
Supplementary files format and content: DESEQ2_LaRIPK3_Light_Over_Dark.xlsx compares enriched genes between LaRIPK3 light and dark; DESEQ2_LaRIPK3_Light_R3i_Over_Notreat.xlsx compares enriched genes between RIPK3 kinase inhibitor treatment and no treatment.

growth_protocol: HT-29 cells were grown in McCoy's 5A Medium with supplemented with 10% fetal bovine serum and antibiotics (penicillin and streptomycin) in a humidified 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA of each sample and replicate was extracted using the RNA purification kit (Thermofisher) and treated with DNase (Promega) for 1 h in a 37 °C incubator to degradation of genomic DNA, followed by re-purification of RNA. Finally, the integrity of each RNA sample (300 ng) was assayed through 1% Bleach agarose gel with ethidium bromide. 100-300ng of RNA was submitted for construction of the sequencing libraries.
RNA libraries for RNA-seq were underdone quality check using AATI Fragment Analyzer, followed by PolyA-selected mRNA library construction and MiSeq Titration.

treatment_protocol: HT-29 cells transduced with LaRIPK3-encoding lentivirus were stimulated with intermittent blue light for 12 h (455 nm, 0.5-0.7 mW/cm2, 15 s on and 15 off). For TNF stimulation, cells were treated with 20ng/uL TNF for 1 h.

value: colon, epithelial

value: wild tyoe

value: Light


title: B66 cells, mRNA-seq, DACPano, BR1


title: DGM-13206_Sample_54

value: nonsmoker

value: SAE


title: HT29 cells, no transduction, light, biological replicate 1


title: DGM-13206_Sample_53


title: HT29 cells, no transduction, light, biological replicate 2


title: HT29 cells, no transduction, dark, biological replicate 3

value: Dark


title: HT29 cells, no transduction, dark, biological replicate 1


title: HT29 cells, no transduction, TNFα, biological replicate 3

value: TNF


title: AsPC-1 treated with DMSO

value: Pancreas


title: B49 cells, mRNA-seq, DMSO, BR1

value: brain

value: glioblastoma stem cell


title: B49 cells, mRNA-seq, DMSO, BR2


title: HT29 cells, no transduction, TNFα, biological replicate 2


title: HT29 cells, La-RIPK3 expression, light, RIPK3 kinase inhibitor, biological replicate 3

value: LaRIPK3 positive


title: DGM-13206_Sample_52


title: HT29 cells, La-RIPK3 expression, light, RIPK3 kinase inhibitor, biological replicate 2


title: HT29 cells, no transduction, dark, biological replicate 2


title: HT29 cells, no transduction, TNFα, biological replicate 1


title: DGM-13206_Sample_50


title: B49 cells, mRNA-seq, DACPano, BR1


title: B49 cells, mRNA-seq, DACPano, BR2


title: DGM-13206_Sample_51


title: HT29 cells, La-RIPK3 expression, light, biological replicate 2


title: DGM-13206_Sample_5


title: HT29 cells, La-RIPK3 expression, light, biological replicate 1


title: HT29 cells, La-RIPK3 expression, light, biological replicate 3


title: B36 cells, mRNA-seq, DMSO, BR2


title: HT29 cells, La-RIPK3 expression, dark, biological replicate 3


title: HT29 cells, La-RIPK3 expression, dark, biological replicate 2


title: DGM-13206_Sample_48


title: HT29 cells, La-RIPK3 expression, dark, biological replicate 1


title: B36 cells, mRNA-seq, DACPano, BR2


title: DGM-13206_Sample_49


title: HT29 cells, La-RIPK3 expression, light, RIPK3 kinase inhibitor, biological replicate 1


title: B36 cells, mRNA-seq, DMSO, BR1


title: DGM-13206_Sample_46


title: qNHA cells, nanoCAGE, DMSO, BR2

data_processing:
Sequencing reads were trimmed with using Cutadapt (v1.10) with "-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A TGCTGGAGACCTTCAGTTCGACTAGTGTAG --minimum-length 50".
Trimmed reads were aligned using STAR (v2.5.4b) (STAR  --runMode alignReads  --runThreadN 6  --genomeDir <reference directory>  --readFilesIn <R1.fastq.gz> <R2.fastq.gz>  --readFilesCommand zcat  --outFileNamePrefix <name.out>  --outSAMtype BAM SortedByCoordinate  --outSAMstrandField intronMotif   --outSAMattributes NH HI NM MD AS XS  --outSAMunmapped Within  --outSAMheaderHD @HD VN:1.4  --outFilterMultimapNmax 20  --outFilterScoreMinOverLread 0.33  --outFilterMatchNminOverLread 0.33  --alignIntronMax 500000  --alignMatesGapMax 1000000  --twopassMode Basic).
hg38
bedgraph

extract_protocol:
mRNA from GSCs and primary cells was extracted using Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific, 61011). We enriched for 5’-capped mRNA by digesting mRNA extraction with Terminator exonuclease digestion (Lucigen, TER51020) following manufacture’s recommendations.
We followed the standard nanoCAGE protocol (Salimullah et al., Cold Spring Harbor Protocol, 2011)


title: qNHA cells, nanoCAGE, DMSO, BR1


title: IEC21_3_4C_S59

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

data_processing:
RNA seq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) (Martin 2011) was used to trim adapters from the reads and HISAT2 (version 2.2.1) (Kim et al. 2019) was used to map the reads to the GRCh38.p13 human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M40). HISAT2 output was converted and sorted by chromosomal position using Samtools (version 1.9) (Danecek et al. 2021). RSeQC (v3.0.1) (Wang et al. 2012) and PRINSEQ (v0.20.4) (Schmieder and Edwards 2011) were used for quality control. HTSeq (version 0.11.2) (Anders et al. 2015) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) (Ritchie et al. 2015) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, nonspecific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least one triplicate. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0) (Robinson et al. 2009; McCarthy et al. 2012; Chen et al. 2016). Counts were transformed to log2 (counts per million; cpm) values and associated precision weights, and entered into the limma analysis pipeline. Differentially expressed genes were identified by using generalized linear models that incorporate empirical Bayes methods.
Assembly: GRCh38.p13
Supplementary files format and content: Text file including the normalized counts for each sample.

source_name: CS83iCTR-33n1 hiPSC

growth_protocol: Human colorectal adenocarcinoma cells (Caco-2, HTB-37) were obtained from American Type Culture Collection (ATCC, Manassas, VA). Cells were cultured in a humidified incubator (37⁰C, 5% CO2) in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, Thermo Fisher Scientific, Waltham, MA), 1% non-essential amino acids (Gibco) and 1% penicillin/streptomycin (Sigma). The human EpiIntestinal small intestinal microtissues, consisting of epithelial cells and an underlying lamina propria containing intestinal fibroblasts, were obtained from MatTek Life Sciences (Ashland, USA). Cell culture inserts were placed in 12-well plates and cells were maintained in 100 µl maintenance medium (MatTek Life Sciences) in the apical compartment and 5 ml maintenance medium in the basolateral compartment upon arrival. The hiPSC cell line (CS83iCTR-33n1) was  cultured on human embryonic stem cell qualified Matrigel-coated (Corning #354277) cell culture plates in mTeSR1 medium (Stem Cell Technologies, Vancouver, Canada) and were passaged using gentle cell dissociation reagent (Stem Cell Technologies). For differentiation, hiPSC were dissociated into single cells using accutase (Stem Cell Technologies) and cultured on human embryonic stem cell qualified Matrigel-coated 24-well plates in mTeSR1 supplemented with 10 µM Y-27632 (Stem Cell Technologies) for 1 day. Human iPSCs were subsequently differentiated into definitive endoderm (DE) by incubation in RPMI1640 medium containing 1% non-essential amino acids (Gibco) and 100 ng/ml Activin A (Cell Guidance Systems, Cambridge, UK), with increasing concentrations of fetal bovine serum (0%, 0.2% and 2% on day 1, 2 and 3, respectively). 50 ng/ml BMP4 (R&D Systems, Minneapolis, MN) was also added during the first day of definitive endoderm formation. For differentiation into IECs, definitive endoderm cells were subsequently differentiated into intestinal stem cells by changing medium into DMEM/F12 containing 2% fetal bovine serum, 1% GlutaMAX (Gibco) and 250 ng/ml FGF2 (R&D Systems). After 4 days, cells were dissociated using Accutase and seeded onto polyester transwell inserts (0.4 µm, Corning) coated with Growth Factor Reduced Matrigel #356231. Cells were cultured for 7 days in intestinal differentiation medium (DMEM/F-12 containing 2% fetal bovine serum, 1% non-essential amino acids (Gibco), 1 × B27 (Gibco), 1 × N2 (Gibco), 1% penicillin/streptomycin (Gibco) and 2 mM L-glutamine (Gibco)) supplemented with 20 ng/ml EGF (R&D Systems) and 30 µM Forskolin (Sigma). ROCK inhibitor, y-27632 (final concentration 10 µM; Stem Cell Technologies), was added during the initial 24 h after seeding to reduce cell death. The cells were subsequently cultured for 12 days in intestinal differentiation medium supplemented with 20 ng/ml EGF, 30 µM Forskolin, 5 µM 5-aza-2′-deoxycytidine (Sigma), 20 µM PD98059 (Stem Cell Technologies), and 0.5 µM A-83-01 (Sigma). Definitive endoderm cells were also differentiated into human intestinal organoids (HIOs). Briefly, definitive endoderm cells were differentiated into hindgut endoderm using FGF4 (R&D Systems) and Chiron99021 (Stemgent). After 4 days, free-floating spheroids were collected and embedded into domes of Matrigel (Corning #354234) and further differentiated using 50ng/ml EGF (R&D Systems), 100ng/ml Noggin (R&D Systems) and 500ng/ml RSpondin-1 (R&D Systems) for 38 days. Medium was refreshed every 2-3 days and HIOs were passaged every 10-14 days. To promote intestinal differentiation, 0.5 µM A-83-01 (Sigma), 20 µM PD98059 (Stem Cell Technologies), 5 µM 5-aza-2’-deoxycytidine (Sigma), and 5 µM DAPT (Sigma) was added to the medium the last 7 days.

extract_protocol:
RNA was extracted from Caco-2 cells, hiPSC-derived IEC layers or EpiIntestinal microtissues using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands). Total RNA was extracted from hiPSC-derived organoids using the NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany).
Approximately 1 microgram total RNA was used for RNA library preparations using a TruSeq Stranded mRNA Sample Prep kit (Illumina). After polyA based mRNA selection, RNA was further processed including subsequent fragmentation, first and second strand cDNA synthesis, adapter ligation and final library amplification resulting in RNA seq libraries including unique dual indexes, all following manufacturer’s protocol. Final libraries were eluted in 30 µl elution buffer followed by library quality assessment using a Fragment Analyzer (Agilent Technologies) and quantified by Qubit fluorescence measurements (Life Technologies). Prepared libraries were pooled in an equimolar manner and combined with other indexed libraries for sequencing on an Illumina NovaSeq 6000 system. Final sequencing was done using an S2 and S4 type flow cell, both with an XP loading workflow and settings specific for 2x150 nt paired end reads plus dual indexes reads. All steps for sequencing were carried out according to manufacturer’s protocol. Demultiplexing of reads per sample by corresponding indexes was done using bcl2fastq v2.20.0.422 (Illumina Inc, San Diego, CA, USA).

value: CS83iCTR-33n1 hiPSC

value: intestinal epithelial cells

tag: group

value: hiPSC-derived IEC layers


title: IEC21_3_4B_S58


title: DGM-13206_Sample_45


title: qNHA cells, nanoCAGE, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: IEC21_3_4A_S57


title: HIO1913b_2C_S33

value: human intestinal organoid

value: hiPSC-derived HIOs


title: DGM-13206_Sample_44


title: HIO1913b_2B_S32


title: qNHA cells, nanoCAGE, DACPano, BR1

value: HA

value: Human Astrocytes


title: DGM-13206_Sample_43


title: Mat20_1_3_S30

source_name: EpiIntestinal small intestinal microtissues

value: human primary model for the intestine


title: cc1_1c_S18

value: Caco-2 cell layers


title: Mat20_1_2_S29

value: EpiIntestinal small intestinal microtissues


title: cc1_1a_S16


title: qhFB cells, nanoCAGE, DMSO, BR1

value: skin

value: HDFa

value: primary dermal fibroblast

value: DMSO


title: Mat20_1_1_S28


title: cc1_1b_S17


title: qhFB cells, nanoCAGE, DMSO, BR2


title: Brachial artery 2

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2). The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.
Assembly: GRCh38
Supplementary files format and content: barcodes files are text file lists of all the cell barcodes identified per sample
Supplementary files format and content: features files are tab seperated text files of all the genes analyzed in the experiment
Supplementary files format and content: matrix files are a tab seperated text file that quantifies the expression of each gene for each barcode

source_name: Brachial artery

extract_protocol:
Brachial arteries approximately 2 cm in length were cut longitudinally with a sterile scalpel and then into 1-2 mm square sections. Samples were enzymatically digested for 90 minutes at 37°C with shaking using a combination of collagenase type II, soybean trypsin inhibitor, elastase, Dispase, DNAse I, collagenase type XI, hyaluronidase type I, and HEPES in HBSS with Ca2+ and Mg2+. After 90 minutes, an equal volume of Accumax was added to the dissociation mix and incubated for an additional 5 minutes. Single cells were filtered through a 40 μM strainer, washed with HBSS twice, and incubated with red blood cell lysis buffer for 5-10 min. Cells were washed once again with HBSS and resuspended in 0.1% BSA in PBS for counting and RNA sequencing.
Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and subsequently run on a thermocycler (Eppendorf). Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA) and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000.

value: Brachial artery

value: Male

tag: age (years)

tag: race/ethnicity

value: White


title: qhFB cells, nanoCAGE, DACPano, BR2


title: DGM-13206_Sample_42

value: nonsmoker

value: SAE


title: S051 artery (vein accession no. GSM7418767)

data_processing:
Raw sequence data was processed by the on-instrument Real Time Analysis software (v.2.4.11) to basecall files.
Basecall files were converted to de-multiplexed FASTQ files with the Illumina supplied scripts in the BCL2FASTQ software (v2.17).
The quality of reads was determined with the FASTQC software to evaluate per base sequence quality, duplication rates, and overrepresented k-mers.
Illumina adapters were trimmed from the ends of the reads using the Trim Galore! Package.
Reads were aligned to the human reference genome (GRCh38) with the STAR aligner (v2.5.0a).
Gene count quantification was performed using the GeneCounts function within STAR against the GENCODE v38 human transcript .gtf file.
Assembly: GRCh38
Supplementary files format and content: Processed file is a tab delimited matrix file with the first column representing the Ensembl gene ID, second column gene biotype, third column gene name, fourth column gene chromosomal coordinates in GRCh38, and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

extract_protocol:
RNAlater-preserved samples were ground in liquid nitrogen and isolated with Trizol (Thermo Fisher Scientific) followed by column purification (EZNA Total RNA Kit I, Omega Bio-tek).
500 ng of total RNA was used as input for the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero to generate ribosomal RNA-depleted sequencing libraries. Each sample was sequenced to >40 million raw reads in a single end 75 bp sequencing run on the Illumina NovaSeq.

value: F


title: S044 artery (vein accession no. GSM7418761)

value: M

value: Black


title: DGM-13206_Sample_35


title: Brachial artery 3

value: Hispanic


title: S067 artery (vein accession no. GSM7418774)


title: DGM-13206_Sample_40


title: HIO1913b_2A_S31

value: CS83iCTR-33n1 hiPSC

value: human intestinal organoid

value: hiPSC-derived HIOs


title: qhFB cells, nanoCAGE, DACPano, BR1

value: 1uM DAC 6 days, 100nM Pano 2 days


title: Brachial artery 1

value: Female


title: B36 cells, mRNA-seq, DACPano, BR1

value: brain

value: glioblastoma stem cell


title: DGM-13206_Sample_41


title: S037 artery (vein accession no. GSM7418754)


title: DGM-13206_Sample_33


title: NHA cells, nanoCAGE, DMSO, BR2

value: HA

value: Human Astrocytes

value: DMSO


title: S042 artery (vein accession no. GSM7418759)

value: Brachial artery


title: DGM-13206_Sample_37

value: nonsmoker


title: NHA cells, nanoCAGE, DACPano, BR1


title: NT2-27 P22D56 T200 [77_S21]

first: Jens

last: Hansen

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Treated with Trastuzumab 200ug/mL for 48hs

data_processing:
Read alignment using STAR
Read counts calculation using featureCounts (Rsubread)
Assembly: hg38
Supplementary files format and content: Bulk-RNAseq-Read-Counts.Unique.hg38.20200206.txt: Read counts for each gene in each sample

molecule: nuclear RNA

growth_protocol: iPSCs were maintained in StemFlex media. iPSCs were, I differentiated to iPSC-CMs using monolayer differentiation protocol using CHIR and IWR1 in RPMI1640 supplemented with B27 minus insulin. iPSC-CMs were maintained in RPMI1640 supplemented with B27.

extract_protocol:
RNA isolation was perfomed via treatment with Trizol followed by phenol-chloroform extraction protocol. 500 ug of RNA was used for library prep
RNA libraries for RNA-seq was performed using Illumina TruSeq-stranded mRNA library prep kit using manufacturer protocol

treatment_protocol: iPSC-CMs at days 45-60 were treated with 0ug/mL or 200ug/mL of Trastuzumab for 48 hours

value: iPSC derived cardiomyocyte

tag: subject status

value: Control patient


title: NHA cells, nanoCAGE, DMSO, BR1


title: NHA cells, nanoCAGE, DACPano, BR2


title: DGM-13206_Sample_4

value: SAE


title: DGM-13206_Sample_32


title: S039 artery (vein accession no. GSM7418755)

value: M

value: White


title: NT2-27 P22D56 T0 [76_S54]

description: No drug treatment

value: CTRL


title: DGM-13206_Sample_31


title: TX3-12 P33D35 T200 [75_S51]

value: Cardiotoxic patients


title: TX3-11 P43D33 T200 [73_S71]


title: TX3-12 P33D35 T0 [74_S06]

description: No drug treatment


title: DGM-13206_Sample_30


title: hFB cells, nanoCAGE, DMSO, BR1

value: skin

value: HDFa

value: primary dermal fibroblast


title: TX3-11 P40D45 T0 [70_S74]

description: No drug treatment


title: DGM-13206_Sample_3


title: TX3-1 P45D38 T200 [69_S69]


title: hFB cells, nanoCAGE, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: Li_Ribo_1

city: chengdu

first: Yixin

last: Wang

state: sichuan

address: 211 huimin street

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

institute: Sichuan Agricultural University

description: Generated from present study

data_processing:
Five raw RNA-seq data downloaded from GEO (GSE116775) were aggregated into the Ribo group before data processing. Trimmomatic (0.39) was used to remove the adapter sequence and low-quality reads (Q < 20).
The clean reads were aligned to the bovine reference genome (Bos taurus ARS-UCD1.2) using STAR (2.7.9a) with the detection of chimeric (fusion) alignments (--chimSegmentMin 10)
The aligned reads were used for circRNAs identification through CIRCexplorer2 (https://circexplorer2.readthedocs.io/en/latest/)4 with annotating pipeline.
The high-confident circRNAs (BSJ reads ≥ 2, detected in at least all replicates of one method) were maintained to explore the intersection among six methods using TBtools (https://github.com/CJ-Chen/TBtools/releases)
The high confident circRNAs of liver and rumen were integrated, then converted into the human genome position (GRCh38.p13) using UCSC LiftOver with the chain file (bosTau9ToHg38.over.chain.gz)
The genome position of human circRNAs was downloaded from circAtlas database and used to search for overlap regions with cattle circRNAs on human genome position using bedtools (2.30.0)
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Excel sheet include circRNA information and BSJ read count of each individual sample

organism: Bos taurus

source_name: Liver

growth_protocol: The three cross-bred (Kinsella Composite) beef steers are managed based on the guidelines established by the Canadian Council on Animal Care (https://ccac.ca/en/standards/guidelines/)

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation Kit (Ambion, Carlsbad, CA, USA) according to the manufacturer's instructions.
The purified circRNAs were used to build the sequencing libraries following the guidance of TruSeq® Stranded Total RNA cDNA library construction kit

treatment_protocol: The total RNA of each sample was subjected to circRNA enrichment using the following six methods, respectively: The ribosome RNA (rRNA) of total RNA was removed through Ribo-zero (defined as Ribo); the linear RNA of total RNA was removed through RNase R (defined as R); both linear RNA and some lariat RNA were removed through RNase R following polyadenylation and poly (A)+ RNA depletion (defined as RTP); both rRNA and linear RNA were removed through Ribo-zero and following with RNase R (defined as Ribo-R); rRNA, linear RNA and RNA with poly (A) structure were removed through Ribo-zero and following with RNase and poly (A)+ RNA depletion (defined as Ribo-RP); rRNA, linear RNA and lariat RNA were removed through Ribo-zero and following RNase R then polyadenylation and poly (A)+ RNA depletion (defined as Ribo-RTP)

tag: breed

value: Kinsella Composite beef

value: steer

tag: sampling age

value: 15 months old

value: Liver

value: Ribosomal RNAs removal (Ribo)


title: DGM-13206_Sample_29

value: nonsmoker


title: TX3-1 P45D38 T0 [68_S11]

description: No drug treatment

value: iPSC derived cardiomyocyte


title: TX3-1 P39D32 T200 [67_S63]


title: hFB cells, nanoCAGE, DACPano, BR1


title: Long bone MSCs, primary, sample 1

city: NEDLANDS

first: Vincent

last: Kuek

state: WA

address: Telethon Kids Institute, Northern Entrance, Perth Children's Hospital,  15 Hospital Ave

department: Telethon Kids Cancer Centre

country: Australia

institute: Telethon Kids Institute

description: pMSCs 1 FPKM

data_processing:
Quality control: reads containing the adaptor, unknown base N content greater than 5% and low-quality reads were removed from raw data using SOAPnuke software (v1.5.2, BGI).
Read alignment: Clean reads (58-71 million/sample) were aligned to the reference genome (Mus_musculus, NCBI, version: GCF_000001635.26_GRCm38.p6) using HISAT2 (v2.0.4). Alignment to reference gene was conducted using Bowtie2 (v2.2.5).
Gene expression profilling: The gene expression level for each sample was calculated using RSEM (v1.2.8).
Differentially expressed genes (DEGs) analysis: DEGs were defined (Log2FC|≥2, q-value≤0.01) and calculated using the DEseq2 method.
Data analyses: Principle component analysis (PCA), gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) was performed using BGI’s Dr Tom software.
Assembly: Mus_musculus, NCBI, version: GCF_000001635.26_GRCm38.p6.
Supplementary files format and content: Excel worksheet file including FPKM values for each sample.

source_name: mesenchymal stem cells

growth_protocol: Heterogenous cell population from collagenase IV-digested long bones were cultured in MesenCult media (Stem Cell Technologies) supplemented with 100 Units/ml penicillin, 100μg/ml streptomycin (Thermo Fisher Scientific), 1% L-glutamine (Thermo Fisher Scientific) and 0.1% MesenPure (Stem Cell Technologies) for 10 days, followed by FACS sorting to isolate pure cMSC population.

extract_protocol:
RNA was harvested using Rneasy microkit kit (Qiagen). The quality and quantity of RNA samples were determined using an Agilent 2100 BioAnalyzer to confirm acceptable RNA integrity number (>6.5).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) following manufacturer's protocols.

treatment_protocol: pMSCs were directly sorted from heterogenous cell population derived from collagenase IV-digested long bones via FACs.

tag: strain

value: Female

value: mesenchymal stem cells

value: Freshly isolated without culture

value: Wild Type


title: B66 cells, nanoCAGE, DMSO, BR2

tag: tissue

value: brain

value: glioblastoma stem cell

value: DMSO


title: Long bone MSCs, primary, sample 2

description: pMSCs 2 FPKM


title: DGM-13206_Sample_28

value: SAE


title: Long bone MSCs, cultured, sample 4

description: cMSCs 4 FPKM

value: Cultured for a single passage


title: B66 cells, nanoCAGE, DMSO, BR1

tag: cell line


title: B66 cells, nanoCAGE, DACPano, BR2

tag: cell type

value: 1uM DAC 6 days, 100nM Pano 2 days


title: TX2-40 P40D37 T200 [65_S60]

value: Cardiotoxic patients

tag: treatment


title: DGM-13206_Sample_27


title: hFB cells, nanoCAGE, DMSO, BR2

value: skin

value: HDFa

value: primary dermal fibroblast


title: DGM-13206_Sample_26


title: DGM-13206_Sample_25


title: TX3-11 P40D33 T0 [72_S75]

description: No drug treatment

value: CTRL


title: Long bone MSCs, cultured, sample 2

description: cMSCs 2 FPKM

tag: genotype


title: TX2-40 P37D36 T400 [63_S14]

description: Treated with Trastuzumab 400ug/mL for 48hs


title: TX2-40 P40D37 T0 [64_S44]

description: No drug treatment


title: B66 cells, nanoCAGE, DACPano, BR1


title: DGM-13206_Sample_24

value: nonsmoker


title: TX3-1 P39D32 T0 [66_S46]

description: No drug treatment

value: iPSC derived cardiomyocyte


title: B49 cells, nanoCAGE, DMSO, BR2


title: Long bone MSCs, cultured, sample 3

description: cMSCs 3 FPKM

tag: Sex

value: Female


title: AGS_shEHF [ATAC-seq]

city: Guangzhou

first: Li

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

library_source: genomic

data_processing:
Clean reads were mapped to the reference genome.
MACS were used to call peaks.
Assembly: hg19
Supplementary files format and content: peaks

molecule: genomic DNA

source_name: GEA cell lines

growth_protocol: Gastroesophageal adenocarcinoma (GEA) cell lines AGS were cultured in F12K, DMEM (Thermo, USA) supplemental with 10% FBS (Gibco, USA) and penicillin & streptomycin (Hyclone, USA) in an incubator with 5% CO2 at 37°C.

extract_protocol:
The indicated live cells were harvested, counted and treated with cold lysis buffer. A nuclear pellet was acquired and immediately incubated with transposition reaction mix, which included Tn5 transposase.
After purification and PCR amplification, the libraries were sequenced on a BGIseq500 (BGI-Shenzhen, China).

treatment_protocol: shRNA

value: AGS

value: EHF shRNA


title: B36 cells, nanoCAGE, DMSO, BR2


title: DGM-13206_Sample_19


title: B49 cells, nanoCAGE, DACPano, BR2


title: TX2-40 P37D36 T200 [62_S16]


title: JUB-AGS

data_processing:
For the analysis of ChIP-seq data, Bowtie2 was used to align sequencing reads onto the human reference genome hg19.
MACS2 was used to call peaks, deeptools was used to rorate bigwig files, and ROSE was used to identify SEs.
Assembly: hg19
Supplementary files format and content: peak text files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with indicated antibodies.
The purified ChIP DNA samples and their input DNA were diluted and send to BGI Genomics for library construction and sequencing.

treatment_protocol: No special treatment

value: Gastroesophageal adenocarcinoma (GEA) cell line

tag: chip antibody

value: JUB

value: untreated


title: AGS_shJUB [ATAC-seq]

value: JUB shRNA


title: B49 cells, nanoCAGE, DMSO, BR1

value: brain

value: glioblastoma stem cell

value: DMSO


title: DGM-13206_Sample_22

tag: individual id

value: SAE


title: AGS_shNC [ATAC-seq]

value: NC shRNA


title: DGM-13206_Sample_21

tag: smoking status


title: TX2-40 P37D36 T0 [61_S62]

description: No drug treatment

value: Cardiotoxic patients


title: B49 cells, nanoCAGE, DACPano, BR1

value: 1uM DAC 6 days, 100nM Pano 2 days


title: TX2-35 P43D41 T200 [59_S29]


title: TX2-35 P43D41 T0 [58_S04]

description: No drug treatment

value: CTRL


title: TX2-35 P43D41 T400 [60_S59]


title: TX2-35 P28D32 T200 [57_S33]


title: DGM-13206_Sample_23

value: nonsmoker


title: AGS-input 2


title: B36 cells, nanoCAGE, DACPano, BR2


title: B36 cells, nanoCAGE, DMSO, BR1


title: Long bone MSCs, cultured, sample 1

description: cMSCs 1 FPKM

value: mesenchymal stem cells

value: Cultured for a single passage

value: Wild Type


title: H3K4Me1-AGS

value: AGS


title: DGM-13206_Sample_15


title: EHF-AGS

value: Gastroesophageal adenocarcinoma (GEA) cell line

value: EHF


title: DGM-13206_Sample_14


title: DGM-13206_Sample_16


title: TX1-83 P69D33 T0 [54_S20]

description: No drug treatment

value: iPSC derived cardiomyocyte


title: AGS-H3K4me3

value: untreated


title: DGM-13206_Sample_11


title: AGS-H3K27ac


title: TX2-35 P28D32 T0 [56_S72]

description: No drug treatment


title: B36 cells, nanoCAGE, DACPano, BR1

value: brain


title: TX1-83 P49D69 T0 [52_S28]

description: No drug treatment


title: Input (EHF)_AGS


title: DGM-13206_Sample_2


title: DGM-10500_Sample_7


title: TX1-34 P29D39 T0 [50_S65]

description: No drug treatment


title: TX1-83 P69D33 T200 [55_S09]


title: qNHA cells, ATAC, DMSO, BR2

data_processing:
Sequencing reads were trimmed with using Cutadapt (v1.10) with "-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff=15,10 --minimum-length=36"
Trimmed reads were aligned to hg38 reference genome using bowtie2 (v2.3.4.1) with " --very-sensitive -X 2000".
Reads aligned to chrM were eliminated.
Duplicated reads were discarded using Picard (v2.8.1, http://broadinstitute.github.io/picard/).
Only properly paired reads with at least 10 mapping quality were retained
hg38
bigwig

extract_protocol:
We followed the omniATAC protocol (Corces et al., Nature Methods, 2017)
We followed the omniATAC protocol (Corces et al., Nature Methods, 2017)

value: HA

value: Human Astrocytes


title: OE33_siNC(JUB)_rep1 [RNA-seq]

data_processing:
The RNA-seq data was filtered with SOAPnuke, and clean reads were obtained.
The clean data were mapped to reference genome using HISAT2, and were aligned to reference coding gene set by Bowtie2.
Then, expression of genes was calculated using by RESM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Total RNA from HCC cells were extracted using Trizol method.
Total RNA was extracted from the cells using Trizol (Invitrogen, USA), qualified and quantified using a Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, USA). Afterwards, oligo(dT)-attached magnetic beads were purified mRNA. First-strand cDNA and second-strand cDNA were respectively synthesized. The single strand circle DNA was formatted as the final library, and then was subjected to sequencing on BGIseq500 platform. The library preparation and sequencing were conducted by BGI Genomics (Shenzhen, China).

treatment_protocol: siRNAs targeting EHF or AJUBA and a negative control (NC) were transfected into GEA cell lines by RNAiMAX reagents (Invitrogen, USA)

value: NC siRNA


title: DGM-13206_Sample_13

value: SAE


title: qNHA cells, ATAC, DMSO, BR1

value: DMSO


title: TX1-83 P49D69 T200 [53_S39]

value: Cardiotoxic patients


title: DGM-13206_Sample_12


title: qNHA cells, ATAC, DACPano, BR2

value: 1uM DAC 6 days, 100nM Pano 2 days


title: AGS-input


title: qNHA cells, ATAC, DACPano, BR1


title: TX1-34 P29D39 T200 [51_S53]


title: DGM-10500_Sample_45

value: nonsmoker


title: NT3-46 P32D41 T200 [47_S27]

value: Control patient


title: OE33_siJUB#5_rep1 [RNA-seq]

value: JUB siRNA #5


title: NHA cells, ATAC, DMSO, BR2


title: OE33_siJUB#1_rep2 [RNA-seq]

value: EHF siRNA #1


title: qhFB cells, ATAC, DMSO, BR2

value: skin

value: HDFa

value: primary dermal fibroblast


title: OE33_siNC(JUB)_rep2 [RNA-seq]

value: Gastroesophageal adenocarcinoma (GEA) cell line


title: NHA cells, ATAC, DMSO, BR1


title: qhFB cells, ATAC, DMSO, BR1


title: DGM-10500_Sample_46


title: TX1-34 P36D32 T200 [49_S26]

value: iPSC derived cardiomyocyte


title: DGM-10500_Sample_8


title: qhFB cells, ATAC, DACPano, BR2


title: qhFB cells, ATAC, DACPano, BR1


title: NT3-46 P26D30 T0 [44_S32]

description: No drug treatment

value: CTRL


title: OE33_siJUB#5_rep2 [RNA-seq]


title: DGM-10500_Sample_44


title: NT3-46 P32D41 T0 [46_S10]

description: No drug treatment


title: DGM-10500_Sample_43


title: NT3-46 P26D30 T200 [45_S36]


title: DGM-10500_Sample_39


title: NT3-4 P50D37 T0 [42_S01]

description: No drug treatment


title: DGM-10500_Sample_4


title: NHA cells, ATAC, DACPano, BR1

value: brain

value: HA


title: DGM-10500_Sample_40


title: OE33_siJUB#1_rep1 [RNA-seq]


title: NHA cells, ATAC, DACPano, BR2

value: Human Astrocytes


title: AGS_siJUB#5_rep1 [RNA-seq]

value: AGS


title: hFB cells, ATAC, DACPano, BR2


title: NT3-4 P50D37 T200 [43_S37]


title: AGS_siNC(JUB)_rep2 [RNA-seq]

value: NC siRNA


title: AGS_siNC(JUB)_rep1 [RNA-seq]


title: DGM-10500_Sample_3

value: SAE


title: hFB cells, ATAC, DMSO, BR2

value: DMSO


title: AGS_siJUB#5_rep2 [RNA-seq]


title: NT2-23 P43D41 T200 [39_S45]


title: AGS_siJUB#1_rep1 [RNA-seq]


title: NT3-4 P35D37 T200 [41_S61]


title: NT3-4 P35D37 T0 [40_S66]

description: No drug treatment


title: DGM-10500_Sample_38

value: nonsmoker


title: S056 artery (vein accession no. GSM7418769)

value: Brachial artery

value: M

value: Hispanic


title: DGM-10500_Sample_29


title: DGM-10500_Sample_28


title: AGS_siJUB#1_rep2 [RNA-seq]

value: EHF siRNA #1


title: NT2-23 P43D41 T0 [38_S40]

description: No drug treatment

value: Control patient


title: DGM-10500_Sample_27


title: B66 cells, ATAC, DACPano, BR2

value: glioblastoma stem cell

value: 1uM DAC 6 days, 100nM Pano 2 days


title: NT2-23 P23D32 T200 [37_S42]

value: iPSC derived cardiomyocyte


title: OE33_siNC(EHF)_rep1 [RNA-seq]

value: Gastroesophageal adenocarcinoma (GEA) cell line


title: DGM-10500_Sample_34


title: NT2-23 P23D32 T0 [36_S52]

description: No drug treatment

value: CTRL


title: hFB cells, ATAC, DMSO, BR1

value: skin

value: HDFa

value: primary dermal fibroblast


title: OE33_siEHF#3_rep2 [RNA-seq]

value: EHF siRNA #3


title: hFB cells, ATAC, DACPano, BR1


title: DGM-10500_Sample_26

value: SAE


title: DGM-10500_Sample_21


title: NT2-22 P40D37 T200 [33_S15]


title: NT2-22 P43D36 T200 [35_S49]


title: B49 cells, ATAC, DMSO, BR1

value: brain

value: DMSO


title: B66 cells, ATAC, DACPano, BR1


title: OE33_siEHF#1_rep1 [RNA-seq]


title: NT2-22 P40D37 T0 [32_S02]

description: No drug treatment


title: B49 cells, ATAC, DACPano, BR2


title: OE33_siEHF#3_rep1 [RNA-seq]


title: AGS_siNC(EHF)_rep3 [RNA-seq]

value: AGS

value: NC siRNA


title: B49 cells, ATAC, DACPano, BR1


title: DGM-10500_Sample_22

value: nonsmoker


title: DGM-10500_Sample_19


title: DGM-10500_Sample_17


title: AGS_siNC(EHF)_rep2 [RNA-seq]


title: B49 cells, ATAC, DMSO, BR2


title: NT2-22 P43D36 T0 [34_S07]

description: No drug treatment


title: DGM-10500_Sample_16


title: B66 cells, ATAC, DMSO, BR2


title: B36 cells, ATAC, DMSO, BR1


title: OE33_siNC(EHF)_rep2 [RNA-seq]


title: B66 cells, ATAC, DMSO, BR1


title: OE33_siEHF#1_rep2 [RNA-seq]

value: EHF siRNA #1


title: AGS_siEHF#3_rep3 [RNA-seq]


title: NT1-32 P36D35 T200 [28_S12]

value: Control patient


title: DGM-10500_Sample_13


title: NT1-32 P35D37 T400 [26_S41]


title: DGM-10500_Sample_2


title: NT2-22 P25D35 T200 [31_S08]


title: AGS_siEHF#3_rep1 [RNA-seq]


title: NT1-32 P36D35 T400 [29_S19]


title: AGS_siNC(EHF)_rep1 [RNA-seq]


title: NT2-22 P25D35 T0 [30_S30]

description: No drug treatment


title: NT1-32 P36D35 T0 [27_S13]

description: No drug treatment


title: B36 cells, ATAC, DACPano, BR2

value: glioblastoma stem cell


title: AGS_siEHF#3_rep2 [RNA-seq]


title: Nalm-6_Spinner flask control day 6

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed and reads from all untreated and DMSO-treated control samples were summed to generate a single control sgRNA distribution.
Supplementary_files_format_and_content: sgRNA read counts per sample as a tab-delimited text file

source_name: Nalm-6 pre-B lymphoid cell line

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Genomic DNA was extracted and purified using the Gentra Cell Puregene kit (QIAGEN, cat. # 158388).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample with multiple collected time-points was grown in T-175 spinner flasks.

value: pre-B lymphoid cell line

tag: treatment/time point

value: Spinner flask control day 6

tag: experiment type

value: pooled sgRNA library

tag: molecule subtype

value: sgRNAs PCR-amplified from genomic DNA


title: B36 cells, ATAC, DMSO, BR2


title: DGM-10500_Sample_1

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Raw reads from 240 sequenced samples pooled from the 3 healthy, nonsmoker subjects were processed with Salmon to obtain gene and transcript levels as estimated read counts and transcripts per million (TPM) using the Ensembl release 79 transcriptome.
Samples with <10e6 reads or for which less than 80% of fragments mapped to non-mitochondrial protein coding genes were excluded from the final analysis, leaving data from a total of 157 single cells.
For all analyses, TPM values were log transformed as log2(1+TPM). Genes which were not expressed in any sample were excluded, leaving a total of 21,757 genes after filtering. Eighteen samples with no visible cell captured and <10e6 mapped reads (“no cell” wells) were used to estimate background levels of RNA contamination for each gene detected. For 855 genes expressed in at least 20% of no cell wells, background levels were estimated from estimated read counts by fitting an exponential distribution. Estimated read counts for affected genes were corrected by subtracting background levels (to a minimum of 0) and TPM values were recalculated using the corrected read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: log TPM text files include the Ensembl unique ID and gene symbol and log2(1+TPM) values for all samples.

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Fluidigm C1 system following the manufacturer’s protocol. To enrich the cell capture of club cells and basal cells, and minimize the inclusion with larger differentiated ciliated and mucin-secreting cells, the single cell suspension (15 μl; 400~600 cells/μl) were loaded into the medium-sized (10 to 17 μm in diameter) microfluidic RNA-seq chip after priming (Fluidigm). The cells were captured using an Olympus-phase contrast microscope to examine the cell numbers in each capture site. Only single cells in the capture site were used.
The Fluidigm C1 system was used for single cell RNA purification and cDNA synthesis by using the SMARTer Ultra Low RNA kit, and the single cell cDNAs were transferred to a 96 well-plate. The single cell library preparation and RNA sequencing were performed following a Fluidigm protocol.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500


title: B36 cells, ATAC, DACPano, BR1

value: 1uM DAC 6 days, 100nM Pano 2 days


title: NT1-32 P35D37 T200 [25_S23]

value: iPSC derived cardiomyocyte


title: AGS_siEHF#1_rep3 [RNA-seq]

value: Gastroesophageal adenocarcinoma (GEA) cell line


title: AGS_siEHF#1_rep2 [RNA-seq]


title: NT1-21 P45D35 T400 [23_S38]


title: NT1-32 P35D37 T0 [24_S56]

description: No drug treatment

value: CTRL


title: DGM-10500_Sample_15

value: SAE


title: DGM-10161_Sample_95


title: Nalm-6_Spinner flask control day 4

value: Spinner flask control day 4


title: DGM-10161_Sample_96


title: AGS_siEHF#1_rep1 [RNA-seq]


title: Nalm-6_Spinner flask control day 2

value: Spinner flask control day 2


title: Nalm-6_Spinner flask control day 0

value: Spinner flask control day 0


title: DGM-10500_Sample_14


title: Nalm-6_Spinner flask control day 8

value: Spinner flask control day 8


title: DGM-10500_Sample_10

value: nonsmoker


title: NT1-21 P45D35 T200 [22_S47]


title: NT1-21 P45D35 T0 [21_S50]

description: No drug treatment


title: DGM-10161_Sample_94


title: DGM-10161_Sample_92


title: NT1-21 P43D37 T400 [20_S48]


title: Nalm-6_Untreated control T-75 flask

value: Untreated control T-75 flask


title: NT1-21 P43D37 T200 [19_S55]

value: Control patient


title: DGM-10161_Sample_91


title: Nalm-6_EMI7 70nM inactive control

description: EGFR_inhibitor_inactive_control_EMI7_0_07uM_S10

value: EMI7 70nM inactive control


title: DGM-10161_Sample_89


title: DGM-10161_Sample_88


title: NT1-21 P43D37 T0 [18_S31]

description: No drug treatment


title: NT1-21 P43D42 T400 [17_S34]


title: trmA truB dKO, rep2

city: Winnipeg

first: Ute

last: Kothe

state: MB

address: 144 Dysart Road

department: Chemistry

institute: University of Manitoba

data_processing:
Data processing was performed by Azenta.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides  with poor quality using Trimmomatic v.0.36.
The trimmed reads were then mapped to the Escherichia_coli_BW25113 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene feature in the annotation file. Only unique reads that fell within gene regions were counted.
DESeq2 was used to compare gene expresion between strains. The Wald test was  used to generate p-values and log2 fold changes
Assembly: ASM75055v1
Supplementary files format and content: tab delimited text files of raw counts for each sample
Supplementary files format and content: comma separated value files include data from DESeq2

organism: Escherichia coli

growth_protocol: E. coli cultures were grown from single colonies overnight in LB media containing 50 µg/mL kanamycin (ΔtrmA, ΔtruB, and ΔtrmAΔtruB strains)  or lacking antibiotic (wildtype). Saturated cultures were centrifuged, resuspended in fresh LB media containing 2% (w/v) sodium formate, and cultures were prepared in LB media containing 2% (w/v) sodium formate at an OD600 of ~0.1. Cultures were grown at 37°C until reaching an OD600 between 0.3 and 0.4, when 15 mL of each culture was harvested by centrifugation, shock frozen, and stored at -80°C until RNA extraction.

extract_protocol:
Cells were  opened in 300 µL of a cell opening buffer (100 mM Tris, 10 mM EDTA, 0.5% SDS, 286 mM β-mercaptoethanol) containing 10 mg/mL lysozyme, 0.1 U/µL DNase I, and 0.1 U/µL RiboLock RNase inhibitor (ThermoFisher)  and incubated at 37 °C for 5 minutes. Subsequently, Proteinase K was added to a final concentration of 0.5 mg/mL and lysates were incubated at 50 °C for 10 minutes. RNA extractions were performed using TRIzol per the manufacturer's instructions.
Strand-specific RNA-seq (2x150 bp, single index) with rRNA depletion (bacteria) library preparation was performed by Azenta.

value: trmA truB deletion


title: Nalm-6_EMI1 70nM

value: pre-B lymphoid cell line

value: EMI1 70nM


title: trmA truB dKO, rep3


title: DGM-10161_Sample_84


title: NT1-21 P43D42 T0 [15_S03]

description: No drug treatment


title: DGM-10161_Sample_87


title: Syn20190114

first: YING

last: CAO

state: Michigan

address: 615 N Main St

institute: university of michigan

description: 10 X genomics

data_processing:
For alignment and digital gene expression matrix generation, 10X Genomics Cell Ranger  v3.0.0 workflow was utilized in the preprocessing of the raw data. Specifically, the raw base call  (BCL) files generated by Illumina NovaSeq were demultiplexed into fastq files using the  CellRanger mkfastq function. Then, the Cell Ranger count function was used to align and filter  reads, count the barcodes and UMIs, and generate Digital Gene Expression matrices. Mouse  genome mm10 was used as the reference for alignment. R Package Seurat v.4.0.4 was used for  subsequent steps of the analysis 68. For cell filtering, normalization and data scaling, the starting pool of 9,578 cells and  20,902 genes was filtered by excluding cells with fewer than 1,000 or more than 8,100 detected  genes, or with >8% of its transcripts corresponding to mitochondria-encoded genes, or fewer  than 500 or more than 60,000 UMIs. These filters resulted in 5,523 cells, for which the average  number of detected genes was 4,430 (IQR 3,120 - 5,824), and the average UMIs was 16,618  (IQR 7,450 - 24,231). Transcript counts were normalized across cells by using the global-scaling method called “LogNormalize” (Seurat function NormalizeData), which divided the UMI counts  by the total UMI count per cell, multiplied with a scale factor of 10,000 (default), and log- transformed. Subsequently, normalized counts for each gene were centered and scaled across  cells by using the Seurat function ScaleData, so that the mean and variance across cells are 0 and 1, respectively. For dimensionality Reduction and Louvain-Jaccard Clustering, we performed principal  component analysis (PCA) on the normalized, scaled expression data by using the top 2,000  highly variable genes selected by using the Seurat function RunPCA. We used the elbow point in the scree plot and chose the top 20 PC scores for downstream clustering. We obtained 8 clusters  by using Louvain-Jaccard clustering with the Seurat functions FindNeighbors and FindClusters  (with resolution 0.05). UMAP were utilized to visualize the clusters (Extended Data Fig. 1a).
Assembly: Mouse genome mm10
Supplementary files format and content: barcodes\matrix
Supplementary files format and content: gene

extract_protocol:
Five mice at postnatal day 5 were euthanized by isoflurane inhalation followed by  decapitation. The brain was isolated and embedded in 4% agarose II in artificial cerebrospinal  fluid (ACSF) and sectioned at 200um thickness on a VT 1000S vibratome (Leica). The caudal  NTS tissue and adjacent regions in the dorsal vagal complex were manually dissected based on  the morphology (the relative position to area postrema, 4th ventricle, and central canal), and  referred as the NTS.
Tissue was pulled together in hibernate A solution (Gibco), followed by  digestion with 20 u/ml papain (Worthington Biochemical Corporation) and serial trituration by  Pasteur pipets to generate single cell suspension. The cells were stained with 0.2% DyeCycle  Ruby (Invitrogen) at 37 degree for 15 minutes before passing through a 70um cell strainer  (Falcon). The live cell suspensions were sorted and collected by a BD FACSAria III Cell Sorter  (BD Biosciences) with a nozzle diameter of 100 um. The FACS sample was loaded to the 10X  Chromium platform for capturing. The following cDNA synthesis with PCR and library  preparation were done according to the manufacturer’s protocol.

value: brain

value: Nerve cells

tag: age

value: postnatal day 5


title: truB KO, rep3

value: truB deletion


title: NT1-15 P25D29 T200 [14_S35]

value: iPSC derived cardiomyocyte

tag: subject status


title: DGM-10161_Sample_83

value: SAE


title: hippocampal microglia, young male, 4 mon, mouse #5

city: Los Angeles

first: Helen

middle: S.

last: Goodridge

state: CA

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

data_processing:
Indexed libraries were pooled and cleaned up, and the pooled library size was verified on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified via Qubit (Thermo Fisher Scientific).
Sample libraries were sequenced on a NovaSeq 6000 (Illumina) with a 1x75 bp read length and coverage of over 30M reads/sample.
Sequence reads were aligned to the mouse reference genome (mm10) using STAR (v.2.7.7a).
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file incudes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro kit (QIAGEN).
The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for subsequent library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA).

value: Hippocampus

value: hippocampal microglia

value: WT

value: male

value: 4 months


title: DGM-10161_Sample_81

value: nonsmoker


title: Nalm-6_0.1% DMSO control

value: 0.1% DMSO control

value: pooled sgRNA library

value: sgRNAs PCR-amplified from genomic DNA


title: truB KO, rep2


title: hippocampal microglia, young male, 4 mon, mouse #4


title: NT1-15 P25D29 T0 [13_S43]

description: No drug treatment

value: Control patient

value: CTRL


title: DGM-10161_Sample_8


title: 102-4R P29D32 T200 [11_S18]

value: Healthy human


title: NT1-21 P43D42 T200 [16_S24]


title: DGM-10161_Sample_79


title: 102-4R P29D32 T0 [10_S25]

description: No drug treatment


title: truB KO, rep1


title: hippocampal microglia, young male, 4 mon, mouse #2


title: DGM-10161_Sample_78


title: trmA KO, rep3

value: trmA deletion


title: hippocampal microglia, young male, 4 mon, mouse #3


title: trmA KO, rep2


title: trmA truB dKO, rep1

value: trmA truB deletion


title: 102-4R P28D48-2 T400 [09_S58]


title: DGM-10161_Sample_77


title: 102-4R P28D48-2 T200 [08_S57]


title: hippocampal microglia, young male, 4 mon, mouse #1


title: trmA KO, rep1


title: hippocampal microglia, young female, 4mon, mouse #5

value: female


title: 102-4R P28D48-1 T400 [06_S22]

value: iPSC derived cardiomyocyte


title: hippocampal microglia, young female, 4mon, mouse #4


title: hippocampal microglia, young female, 4mon, mouse #3


title: 102-4R P28D48-2 T0 [07_S73]

description: No drug treatment


title: BW25113 wildtype, rep2

value: wildtype


title: DGM-10161_Sample_75

value: SAE


title: 102-4R P28D48-1 T200 [05_S67]


title: BW25113 wildtype, rep1


title: DGM-10161_Sample_74


title: hippocampal microglia, young female, 4mon, mouse #2

value: Hippocampus

value: hippocampal microglia


title: BW25113 wildtype, rep3


title: DGM-10161_Sample_72


title: DGM-10161_Sample_69


title: hippocampal microglia, young female, 4mon, mouse #1

value: WT


title: CD_fl_36_Input_2

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) with the options ‘-p 40 --very-sensitive --end-to-end --no-unal --phred33’. For analysis at repetitive elements, multimapping reads where kept but only the best alignment was reported. For reads with multiple equally good alignments, a single alignment was selected for reporting using a pseudo-random number generator. High quality-mapped reads, that we considered as mapping uniquely, were identified with samtools v1.15 (Danecek et al., 2021) using ‘samtools view -q 30’. SAM files containing either all reads or only unique reads were filtered using bedtools v2.30.0 (Quinlan and Hall, 2010) to exclude reads overlapping with the mm10 blacklist (Amemiya et al., 2019; Consortium, 2012). Duplicates were removed with the “Picard Toolkit.” from the Broad Institute (GitHub Repository: https://broadinstitute.github.io/picard/) using ‘java -jar picard.jar MarkDuplicates’. BigWig files were generated using deeptools v3.5.1 (Ramirez et al., 2016) using the RPKM normalization method and visualized on the IGV browser (Robinson et al., 2011).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Spleen

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Recombination of the floxed allele was achieved by culturing cells in the presence of 4OHT for 36h.
libraries were generated using Thruplex DNA-seq Kit from Takara according to manufacturer's instructions.

value: Spleen

value: resting B cells

value: 4OHT, 36h


title: DGM-10161_Sample_68

value: nonsmoker


title: 102-4R P24D39 T400 [03_S64]


title: DGM-10161_Sample_67


title: 102-4R P28D48-1 T0 [04_S68]

description: No drug treatment


title: hippocampal microglia, old male, 25 mon, mouse #5

value: male

value: 25 months


title: wt_wt_36_Input_2


title: hippocampal microglia, old male, 25 mon, mouse #4


title: 102-4R P24D39 T0 [01_S70]

description: No drug treatment

value: CTRL


title: hippocampal microglia, old male, 25 mon, mouse #3


title: DGM-10161_Sample_64


title: DGM-10161_Sample_66


title: 102-4R P24D39 T200 [02_S05]

value: Healthy human


title: wt_fl_36_Input_2


title: CD_fl_36_H3K9me3 IP_2


title: DGM-10161_Sample_63


title: wt_fl_36_H3K9me3 IP_2


title: mCMs biological replicate 2

city: Boston

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
10x Genomics
mCM_2

data_processing:
Downstream differential expression and clustering analysis was performed using the Seurat V.4.0 package, as described in the tutorials (http://satijalab.org/seruat/). CellRanger matrices were imported for each sample with default parameters, and distributions of gene number, UMI number and % mitochondrial gene expression were examined for each sample to filter out cells of low quality. Cells with greater than 20% of genes coming from mitochondrial genes were selected against, as well as those with fewer than 200 genes or 400 UMIs. The doublets were detected and removed using DoubletFinder (v2.0.3). The resulting subset Seurat objects were normalized using the scTransform workflow and further scaled and normalized the RNA assay in order to perform downstream differential expression analysis and marker visualization utilizing the FindMarkers and FeaturePlot functions on the RNA assay. Uniform manifold approximation and projection (UMAP) was performed and iteratively modified after performing marker gene expression and examining expression of key markers. Cell scores for chamber-specific gene expression and CM maturation were determined by evaluating the average expression of a set of representative marker genes for each metric.
Assembly: Grc38
Supplementary files format and content: Processed data file is the seurat object containing the analysis of all of the libraries used in the paper.
Supplementary files format and content: combined_seurat.rds

extract_protocol:
Collagenase II dissociated hiPSC-CMs on day 15 of cardiac differentiation and counted using a hemocytometer. Cells were resuspended in PBS + BSA (0.04%).
Libraries were generated using the Chromium platform (10x Genomics) with the Next GEM Single Cell 3ʹ Reagent Kit v3.1, using an input of 1 million cells per mL. Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was then fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent Technologies). Libraries were sequenced using NextSeq 500 (Illumina) at Harvard Medical School.

value: Wild type

value: human induced pluripotent stem cell

tag: cell population

value: mCMs

tag: disease state

value: Healthy

value: monolayer differentiation


title: DGM-10161_Sample_62

first: Yael

address: 1300 York Avenue

institute: Weill Cornell Medical College

value: SAE


title: hippocampal microglia, old male, 25 mon, mouse #1

tag: strain

value: Hippocampus


title: bCMs biological replicate2

description:
10x Genomics
bCM_2

value: bCMs

value: bioreactor differentiation


title: hippocampal microglia, old female, 25 mon, mouse #5

tag: tissue

value: hippocampal microglia

value: WT

value: female


title: wt_wt_36_H3K9me3 IP_2

value: Spleen

value: resting B cells

value: 4OHT, 36h


title: DGM-10161_Sample_61

value: nonsmoker


title: CD_fl_36_Input_1


title: bCOs biological replicate 1

description:
10x Genomics
bCO

tag: cell line

value: bCOs

value: bioreactor cardiac organoids


title: DGM-10161_Sample_60

tag: cell type


title: bCMs biological replicate 1

description:
10x Genomics
bCMs

value: Wild type

value: human induced pluripotent stem cell

tag: treatment


title: hippocampal microglia, old male, 25 mon, mouse #2

tag: genotype

value: male

value: 25 months


title: wt_fl_36_Input_1


title: wt_wt_36_Input_1


title: DGM-10161_Sample_6

value: SAE


title: hippocampal microglia, old female, 25 mon, mouse #4

value: Hippocampus

tag: Sex


title: CD_fl_36_H3K9me3 IP_1


title: hippocampal microglia, old female, 25 mon, mouse #3


title: A09161-NSC-0.6 µM TG

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

data_processing:
Raw fastq sequence files were generated and demultiplexed using Illumina bcl2fastq software (Illumina, Inc., San Diego, CA, USA).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4.1 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4.1 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The gene expression values as raw counts of sequencing reads were obtained and log2 transformation and ‘DESeq’ normalization was applied.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw sequencing read counts formatted as genes-vs-samples matrix table.

source_name: iPSC-derived neural stem cells

growth_protocol: Existing validated iPSCs were differentiated into a highly uniform population of NSCs using a commercially available Gibco PSC neural induction medium (Thermo Fisher Scientific, Waltham, MA, USA) and following the manufacturer's instructions. Briefly, the iPSCs maintained in feeder-free conditions were dissociated and then seeded as 50 – 200 µm size cell aggregates in a Geltrex (Thermo Fisher Scientific, Waltham, MA, USA) coated tissue culture vessel and mTeSR-1 medium (Stem Cell Technologies Inc., Cambridge, MA, USA) supplemented with 10 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA). The iPSCs were seeded at a cell density that reached 15-25%  cell confluency after 24 hours when the cell culture medium was switched to Gibco PSC neural induction medium (Thermo Fisher Scientific, Waltham, MA, USA). Thereafter medium was changed every other day. On day 7, the differentiated NSCs were dissociated with Stem Pro Accutase (Thermo Fisher Scientific, Waltham, MA, USA) and then reseeded in a Geltrex-coated tissue culture vessel, and at a cell density of 0.1 million/cm2. The seeded NSCs were cultured in an NSC expansion medium containing 50% Neurobasal medium, 50% Advanced DMEM/F12, and 1X neural induction supplement (all from Thermo Fisher Scientific, Waltham, MA, USA) until reaching confluence. The NSC expansion medium was supplemented with 5 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA) for the first 24 hours. The generated NSCs from passage one were used for characterization and all downstream ER stress challenge experiments.

extract_protocol:
Total RNA from both control and ER stress-challenged NSCs was extracted using a commercially available RNeasy Mini Kit (Qiagen, Germantown, MD, USA) and by following the manufacturer’s instructions. RNA quality and quantity were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA).
1 µg of high-quality total RNA per sample and the reagents supplied in Illumina Stranded mRNA sample preparation kit v2 (Illumina, Inc., San Diego, CA, USA) were used to prepare mRNA sequencing libraries.

treatment_protocol: After the ICC and transcriptomic characterization, the generated NSCs were seeded on the Geltrex-coated surface and maintained in the NSC expansion medium (described above) until 60 – 70% confluent. One part of the NSC culture was then vehicle-treated (control) and the other two parts were ER stress-challenged using two different concentrations of 0.3 µM and 0.6 µM Thapsigargin (TG) for 24 hours. Both, vehicle-treated and ER stress-challenged NSCs were then quantitatively measured for cell proliferation, apoptotic cell death, protein aggregation, oxidative stress, mitochondrial function cellular phenotypes by high content screening (HCS) analysis and for genome-wide gene expression using deep mRNA sequencing.

value: iPSC-derived neural stem cells

value: not applicable

value: neural stem cell

value: 0.6 uM Thapsigargin (TG)


title: hippocampal microglia, old female, 25 mon, mouse #2

value: hippocampal microglia

value: WT

value: female


title: DGM-10161_Sample_59

last: Strulovici-Barel


title: A02287-NSC-0.6 µM TG


title: wt_fl_36_H3K9me3 IP_1

value: Spleen

value: resting B cells

value: 4OHT, 36h


title: hippocampal microglia, old female, 25 mon, mouse #1


title: A09161-NSC-0.3 µM TG

value: 0.3 uM Thapsigargin (TG)


title: DGM-10161_Sample_58

value: nonsmoker


title: wt_wt_36_H3K9me3 IP_1


title: mCMs biological replicate 1

description:
10x Genomics
mCMs

value: Wild type

value: human induced pluripotent stem cell

value: mCMs

value: Healthy

value: monolayer differentiation


title: DGM-10161_Sample_57

value: SAE


title: A02287-NSC-0.3 µM TG

value: iPSC-derived neural stem cells

value: not applicable


title: A09161-NSC-Control

value: neural stem cell

value: vehicle-treated control


title: Lung-DC-6h-GEX

city: Research Triangle Park

first: Hideki

last: Nakano

state: NC

address: 111 TW Alexander Drive

department: Immunity, Inflammation and Disease Laboratory

institute: NIEHS

description: polyA RNA

data_processing:
CellRanger 3.1.0 'count' was used to align reads to the mm10-1.2.0 reference.
Seurat v3.0 (R 3.6.1) was used to process and filter the raw counts.  Only good quality cells were retained; applied filters included 1000-6000 detected features, 250-50000 total RNA counts, 0.02-0.08 proportion cycling, and 0.005-0.075 proportion of mitochondrial RNA.
Assembly: mm10
Supplementary files format and content: List of features (GEX and ADT) in tab-delimited text format.
Supplementary files format and content: List of barcodes with basic annotations (sample, QC status pass/fail, and assigned cluster) in tab-delimited text format.
Supplementary files format and content: Counts matrix files in tab-delimited text format; one file per assay (GEX or ADT) per sample.
Library strategy: CITE-seq

source_name: Lung

extract_protocol:
CD11b+cDC2s from mouse lungs were purified by flow cytometry, and stained withTotal A-Seq oligo-conjugated antibodies according to manufacturer’s instruction (BioLegend).The cells were counted and examined for viability using a TC-20 cell counter (Bio-Rad). 10,000live cells at 3×105cells/mL concentration with 90% or above viability were loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Controller (10x Genomics). The cDNA for antibody derived transcripts (ADT) and gene derived transcripts was generated and amplified according to manufacturer’s instructions (10x Genomics and BioLegend).
The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v3 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library).

treatment_protocol: C57BL/6J mice were given house dust extract (10 microlitters) together with ovalbumin (100 micrograms) in 50 microlitter PBS 6 and 18 hours prior to the analysis. Untreated C57BL/6J mice were used for 0 hour samples.

value: Lung

value: primary cells

value: CD11b+ conventional dendritic cells

value: wildtype (C57BL/6J)

value: Oropharyngeal aspiration of house dust extract and ovalbumin, 6h timepoint

tag: library type

value: polyA RNA


title: DGM-10161_Sample_56

city: New York

tag: individual id

value: nonsmoker


title: IEC, Zinc+TNF, rep 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm39 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples

source_name: intestinal epithelial cells

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate a sequencing libary for the illumina nextseq 500 usi,g the truseq stranded libary prep kit accorting to the manufacturers instructions

treatment_protocol: mice were punt in zinc containg or normal drinking water for 7 days. Afterwards, the mice were injected with PBS or TNF and the small intestine was isolated after 8h and and IEC were isolated

value: intestinal epithelial cells

value: WT

value: Zinc+TNF

tag: time


title: IEC, Zinc+TNF, rep 3


title: DGM-10161_Sample_55

tag: smoking status


title: Lung-DC-0h-GEX

description: polyA RNA

value: untreated


title: Lung-DC-18h-GEX

description: polyA RNA

value: Oropharyngeal aspiration of house dust extract and ovalbumin, 18h timepoint


title: A02287-NSC-Control


title: DGM-10161_Sample_54

value: SAE


title: Lung-DC-18h-ADT

description: Antibody-derived oligonucleotide (ADT)

library_source: other

molecule: protein

value: ADT

tag: adt


title: IEC, Zinc+TNF, rep 2


title: IEC, Zinc+TNF, rep 1


title: Lung-DC-6h-ADT

description: Antibody-derived oligonucleotide (ADT)


title: DGM-10161_Sample_52


title: Lung-DC-0h-ADT

description: Antibody-derived oligonucleotide (ADT)


title: DGM-10161_Sample_51


title: KF(CD74+)-ctr-2

city: Changsha

first: Jingheng

last: Zhang

address: 87 Xiangya Rd

institute: Xiangya Hospital, Central South Uniiversity

data_processing:
For RNA-seq data analysis, raw fastq files were processed with trim_galore (version 0.6.7).
Filtered reads were mapped with STAR (version 2.7.10b).
Mapped reads were quantified with featurecounts (version 2.0.5) . All steps were done in Linux (Red Hat 7.9).
Assembly: hg38
Supplementary files format and content: The csv file contains raw counts for each sample.

source_name: Keloid

growth_protocol: Human foreskin fibroblasts (HFF, CTCC-001-0346) were isolated from human male foreskin biopsies. Keloid fibroblasts (KF, CTCC-185-HUM) were isolated from human keloid specimen. Both cell lines were cultured in Dulbecco’s MEM (C3113, Vivacell) with 10% fetal bovine serum (CTCC-002-001, Meisen) and 0.2% Primocin (ant-pm-05, Invivogen).

extract_protocol:
Total RNA was isolated using RNAiso plus (9109, Takara) and quantified using Nanodrop One. The quality of RNA was determined by Bioanalyzer 2100 (Agilent Technologies).
After the RNA was purified by poly-T magnetic beads, sequencing libraries was generated, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina) with PE150 strategy.

treatment_protocol: 8*10^4 cells were seeded into each elastomer and were allowed to adhere for 24 hours. Then, the elastomer was installed on the cell stretching device and stretched for the indicated time.

value: Keloid

value: Unstretched KF(CD74+) cells


title: 10x scRNAseq, 3' Gene Expression

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
10x Genomics
filtered_feature_bc_matrix.tar.gz

data_processing:
For bulk RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
For scRNA-seq: 10x Genomics Cellranger v6.1.1 was used to process fastq files and generate the bam file and matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.0.
Assembly: mm10
Supplementary files format and content: RSEM extracted TPM matrix filtered by expressed protein-coding genes as one csv file
Supplementary files format and content: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz

source_name: small intestine and colon

growth_protocol: All mice were housed in specific-pathogen-free conditions at 22-24℃ with humidity of 40%–70% and a light/dark cycle of 12 hours, and were used and maintained in accordance with the Institutional Animal Care and Use Committee Guidelines of Westlake University

extract_protocol:
RNA were extracted from cells using AMPure XP beads (Backman)
Full-length Smart-seq2 and 10x genomics scRNA-seq

treatment_protocol: For bulk RNA-seq exepriments, a total of 1.5×105 CFU Candida albicans (strain SC5314) or vehicle (PBS) were i.v. injected into the mice. For the scRNA-seq experiment, the mice were at the steady state.

value: small intestine and colon

value: 12 weeks

value: male

value: ILCs

value: Fcer1g f/f (control) andRorc-cre+Fcer1g f/f (CKO)

value: No


title: DGM-10161_Sample_50

source_name: small airway epithelium brushing


title: IEC, TNF, rep 4

value: TNF


title: KF(CD74+)-ctr-1


title: 10x scRNAseq, HTO

molecule: other


title: DGM-10161_Sample_5

value: nonsmoker


title: KF-18h-2

value: KF cells stretched for 18 hours


title: DGM-10161_Sample_49


title: KF-18h-1


title: IEC, TNF, rep 2

value: intestinal epithelial cells

value: WT


title: Tamoxifen (double knockout) S08

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

description: dKO - 8088

data_processing:
To generate gene-expression matrices, fastq files were processed and mapped to the GRCm39.109 reference genome, using the Parse Biosciences SplitPipe v1.0.4 with default parameters (Parse Biosciences, Seattle, WA).
The downstream analysis was performed using the R 4.2.2 and Seurat v4.3.0 R package
Low-quality cells with less than 200 genes detected and all genes expressed in less than 3 cells were removed, leaving 31,089 cells and 37,725 genes for further analysis. Data was normalized using Seurat’s NormalizeData function with LogNormalize as a method and a scale factor equal to 10,000.
Principal Component Analysis was performed on a submatrix of the top 2,000 most-variable genes, using the function FindVariableGenes from the Seurat package. The number of top Principal Components (PC) was evaluated by the elbow method keeping 20 PCs for clustering and data visualization. The batch effect between samples was removed using the package Harmony v0.1.1. The cells were clustered using a shared nearest-neighbor modularity optimization-based clustering algorithm (FindClusters in the Seurat package).
To visualize cells in two dimensions the Uniform Manifold Approximation and Projection was applied. The cluster-specific genes were computed using FindAllMarkers from the Seurat package, using the MAST test with the number of Unique Molecular Identifiers detected as a latent variable. The same test was used to compute differentially expressed genes between genotypes or treatment groups within cell clusters. Cell clusters were annotated by assessing known cell-type-specific markers. All plots were created using ggplot2 v3.4.1. Labels in the volcano plots were created using ggrepel v0.9.3.
Assembly: GRCm39
Supplementary files format and content: ExpressionMatrix.mtx.gz - a sparse matrix with read counts
Supplementary files format and content: CellIDs.txt.gz - a comma-separated archive of barcodes (columns of the expression matrix)
Supplementary files format and content: Genes.txt.gz - a tab-delimited archive of genes (rows of the expression matrix)
Supplementary files format and content: MetaData.txt.gz - a tab-delimited archive containing an additional description of the samples (columns of the expression matrix)

source_name: retina

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle, fed ad libitum, and maintained using standard procedures.

extract_protocol:
Animals were sacrificed and eyes were enucleated. Under a microscope, the anterior chamber, consisting of the cornea, lens, and iris was removed. The retina then carefully peeled from the posterior eye cup. The retina was then disassociated into single cells with the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions. 2mL of papain solution was used per animal.
8 sublibraries were generated and sequenced independently on Illumina NovaSeq6000 at an average sequencing depth of 50,000 reads/cell, for a projected total of 5 billion reads for the entirety of the 100,000 cell barcoded library. Reads from identical cells from each of the 8 sublibraries were consolidated during analysis and processing of raw reads.

treatment_protocol: Animals were treated at post-natal day 28 (P28) for five consective days via intraperitoneal injection - control animals were administered corn oil vehicle, while dKO animals were treated with 75mg/kg of tamoxifen dissolved in corn oil. Tamoxifen was stored at 4 deg C in the dark.

value: retina

value: 6 months

value: Tamoxifen, P28


title: DGM-10161_Sample_48

value: SAE


title: KF-12h-2

value: Keloid

value: KF cells stretched for 12 hours


title: Tamoxifen (double knockout) S09

description: dKO - 8122


title: KF(CD74+)-6h-2

value: KF(CD74+) cells stretched for 6 hours


title: Tamoxifen (double knockout) S07

description: dKO - 8078


title: KF(CD74+)-6h-1


title: IEC, TNF, rep 1


title: IEC, Zinc, rep 2

value: Zinc+PBS


title: DGM-10161_Sample_47


title: IEC, Zinc, rep 1


title: IEC, PBS, rep 2

value: PBS


title: KF-6h-2

value: KF cells stretched for 6 hours


title: Tamoxifen (double knockout) S06

description: dKO - 8078


title: IEC, PBS, rep 1


title: DGM-10161_Sample_41


title: Tamoxifen (double knockout) S05

description: dKO - 8076


title: Corn_oil (control) S04

description: Control - 8087

value: Corn oil, P28


title: BRDK98 treated cells, 60min LipidA [Exp4_60min_BRDK98_rep2]

city: La Jolla

first: Jingwen

last: Liao

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using analyzeRepeats.pl within HOMER with -strand both -count exons -condenseGenes –noadj and then by getDiffExpression.pl within HOMER
Assembly: GRCm38 (mm10)
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-20) dataValue.
Supplementary files format and content: Exp2_ARID1AKO_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-18) dataValue.
Supplementary files format and content: Exp3_PBRM1KO_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-14) dataValue.
Supplementary files format and content: Exp4_early_tpm.txt: Columns: (1) RefSeq acc (2) chrom (3) chromStart (4) chromEnd (5) strand (6) length (7) copies (8) annotation (9-26) dataValue.
Supplementary files format and content: Exp1_ACBI1_BRM014_BRDK98_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-20) normalized Log2 read count for experiment (21-23) Log2 fold change, p-value, adjusted p-value 1hr_Ctrl vs 0hr_Ctrl (24-26) Log2 fold change, p-value, adjusted p-value of 4hr_Ctrl vs 0hr_Ctrl (27-29) Log2 fold change, p-value, adjusted p-value of 4hr_ACBI1 vs 4hr_Ctrl (30-32) Log2 fold change, p-value, adjusted p-value of 4hr_BRM014 vs 4hr_Ctrl (33-35) Log2 fold change, p-value, adjusted p-value of 4hr_BRDK98 vs 4hr_Ctrl
Supplementary files format and content: Exp2_ARID1AKO_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-18) normalized Log2 read count for experiment (19-21) Log2 fold change, p-value, adjusted p-value 1hr_Ctrl vs 0hr_Ctrl (22-24) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (25-27) Log2 fold change, p-value, adjusted p-value of 1hr_ARID1AKO vs 1hr_Ctrl (28-30) Log2 fold change, p-value, adjusted p-value of 4hr_ARID1AKO vs 4hr_Ctrl
Supplementary files format and content: Exp3_PBRM1KO_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) normalized Log2 read count for experiment (15-17) Log2 fold change, p-value, adjusted p-value 4hr_Ctrl vs 0hr_Ctrl (18-20) Log2 fold change, p-value, adjusted p-value of 4hr_PBRM1KO vs 4hr_Ctrl
Supplementary files format and content: Exp4_early_DESeq2.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-26) normalized Log2 read count for experiment (27-29) Log2 fold change, p-value, adjusted p-value 20min_Ctrl vs 0min_Ctrl  (30-32) Log2 fold change, p-value, adjusted p-value 60min_Ctrl vs 0min_Ctrl  (33-35)  Log2 fold change, p-value, adjusted p-value of 20min_ACBI1 vs 20min_Ctrl  (36-38) Log2 fold change, p-value, adjusted p-value of 20min_BRM014 vs 20min_Ctrl  (39-41) Log2 fold change, p-value, adjusted p-value of 20min_BRDK98 vs 20min_Ctrl  (42-44) Log2 fold change, p-value, adjusted p-value of 60min_ACBI1 vs 60min_Ctrl (45-47) Log2 fold change, p-value, adjusted p-value of 60min_BRM014 vs 60min_Ctrl (48-50) Log2 fold change, p-value, adjusted p-value of 60min_BRDK98 vs 60min_Ctrl

source_name: BMDM

extract_protocol:
RNA was harvested using Zymo Research Quick-RNA miniprep kit and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded messenger ribonucleic acid (mRNA) kit following manufacturer's protocols.
RNA-seq 50bp single-end sequencing

value: BMDM

value: BRDK98 treated

tag: stimulation

value: 60min LipidA

tag: molecule type

value: strand specific polyA+ RNA


title: KF-ctr-2

value: Unstretched KF cells


title: BRDK98 treated cells, 60min LipidA [Exp4_60min_BRDK98_rep1]


title: IEC, TNF, rep 3

value: intestinal epithelial cells

value: WT

value: TNF


title: Corn_oil (control) S03

description: Control - 8081

value: retina

value: 6 months


title: DGM-10161_Sample_39

value: nonsmoker

value: SAE


title: BRM014 treated cells, 60min LipidA [Exp4_60min_BRM014_rep2]

value: BRM014 treated


title: KF-12h-1

value: Keloid

value: KF cells stretched for 12 hours


title: Corn_oil (control) S02

description: Control - 8080


title: KF-ctr-1


title: DGM-10161_Sample_37


title: HFF-18h-2

source_name: Skin

value: Skin

value: HFF cells stretched for 18 hours


title: BRM014 treated cells, 60min LipidA [Exp4_60min_BRM014_rep1]

value: BMDM


title: DGM-10161_Sample_36


title: DGM-10161_Sample_44


title: HFF-18h-1