title: SUS-LNA-48


title: YAP.Mm rep 2

status: Public on Jul 25 2022

type: SRA

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

library_source: transcriptomic

data_processing:
HiSeq 2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 (Patro et al. 2017). Gene level summaries were prepared using tximport version 1.20.0 (Soneson, Love, and Robinson 2015) running under R version 4.1.0 (R Core Team 2021).
Genome_build: zv11 with an ensembl version 104 annotation
Supplementary_files_format_and_content: gphelps_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary_files_format_and_content: gphelps_l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset

molecule: total RNA

organism: Danio rerio

source_name: cells isolated from 5 dpf larvae that express a mitfa:GFP reporter

extract_protocol:
RNeasy Micro Kit (Qiagen)
Samples were analyzed for RNA integrity using a Femto Analyzer, and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT (Illumina) and sequenced on a HiSeq2000 (Illumina) using 40nt single end reads.

treatment_protocol: Zebrafish 5 dpf larvae (100-1,000 per sample) were anesthetized in 0.1% tricaine.

tag: genetic background

value: AB/Tubingen (TAB5/14)

tag: transgene

tag: genotype

value: mitfa null (w2/w2); half tp53_M214K/+, half tp53_+/+


title: SUS-NEG-26

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using HTSeq-count software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files

organism: Mus musculus

source_name: Blood

extract_protocol:
Blood RNA from 6–7 individual mice per group was used in this study. Male mice submandibular blood was collected using 20-G hypodermic needles into EDTA-coated tubes. The tubes were centrifuged at 1000xg for 20 min at 4°C, and 100 μl of the blood cell fractions were put in RNAprotect animal blood tubes (Qiagen,) and stored at -80°C. Total RNA, including miRNAs, was extracted using RNeasy Protect animal blood kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies) and RNA integrity was checked using 4200 TapeStation.
rRNA depletion along with globin depletion was performed using QIAGEN FastSelect rRNA HMR/Globin Kit. RNA-seq library preparation used NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs were fragmented for 15 min at 94°C. The first and second cDNA strands were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends, and a universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using Agilent Tapestation 4200 and quantified using Qubit 2.0 Fluorometer. Sequencing libraries were multiplexed and clustered on the Illumina HiSeq instrument according to the manufacturer’s instructions. The samples were sequenced using a 150 paired end configuration.

tag: tissue

value: Blood

tag: Sex

value: male

value: stress susceptible (SUS)

tag: treatment

value: NEG (scrambled control oligonucleotide)


title: Q.Mp rep 1

value: wild-type mitfa


title: CON-NEG-54

value: CON


title: YAP.Mp rep 3

value: wild-type mitfa; half tp53_M214K/+, half tp53_+/+


title: CON-NEG-53


title: YAP.Mp rep 2


title: wt1_15

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description: Library of 92 cells

library_source: transcriptomic single cell

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Assembly: mm10
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary files format and content: cellbarcodes_cellid.csv is a supplemetary file contains cellds and one of the 192  unique cellbarcode associated with the cell id.

molecule: polyA RNA

source_name: dermal mast cells

growth_protocol: Mast cells were isolated from ear skin of C57BL/6J  wt and Tln knockout mice.

extract_protocol:
Mast cells were isolated from ear skin of C57BL/6J Mcpt5-Cre wt and Tln knockout mice .
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.

treatment_protocol: no treatment

tag: strain

value: C57BL/6J Mcpt5 Cre R26LSLYFP

value: Ear skin

tag: reporter/marker

value: Mcpt5 Cre+/-


title: Q.Mm rep 1

value: mitfa null (w2/w2)


title: CON-NEG-33


title: SUS-NEG-12


title: YAP.Mm rep 4


title: p53.Mp rep 4


title: SUS-LNA-51

value: LNA (antisense oligonucleotide of microRNA 144-3p)


title: YAP.Mm rep 3


title: Q.Mm rep 3


title: Q.Mm rep 4


title: p53.Mp rep 2


title: SUS-LNA-49


title: Q.Mp rep 4


title: SUS-LNA-20


title: SUS-LNA-44


title: CON-NEG-90


title: iecs_baseline_dko _biol rep 3

city: Philadelphia

first: Monica

last: Jimenez

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

data_processing:
STAR alignment for 150bp paired-end reads
Assembly: mm10
Supplementary files format and content: .csv files of counts as determined via STAR

source_name: colon

extract_protocol:
RNA was isolated from Percolled colonic IECs using a Purelink RNA kit. QC, library preparation, and library sequencing was performed by Azenta. Extracted RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR.

treatment_protocol: WT and DKO mice were treated with 2% DSS for 7 days and allowed to recover for 2 days. Colonic IECs were isolated from mice and lymphocytes removed by resuspending in isotonic 40% Percoll diluted in complete media.

value: colon

tag: cell type

value: intestinal epithelial cells

value: miR-181 DKO

value: baseline


title: Q.Mp rep 2

value: AB/Tubingen (TAB5/14)


title: Q.Mp rep 3


title: CON-NEG-80

value: Blood


title: p53.Mm rep 3

value: mitfa null (w2/w2); half tp53_M214K/+, half tp53_+/+


title: CON-NEG-46

value: male


title: p53.Mm rep 2


title: iecs_dss_dko_biol rep 3

value: dss


title: p53.Mp rep 1


title: p53.Mp rep 3


title: iecs_dss_dko_biol rep 1


title: iecs_baseline_dko _biol rep 2


title: Q.Mm rep 2


title: iecs_baseline_dko _biol rep 1


title: NTG.Mp rep 2

value: wild-type mitfa


title: iecs_baseline_wt _biol rep 1

value: wt


title: iecs_dss_wt_biol rep 3


title: NTG.Mp rep 1


title: iecs_baseline_wt _biol rep 2


title: iecs_dss_dko_biol rep 2


title: NTG.Mm rep 4


title: p53.Mm rep 1


title: NTG.Mp rep 3


title: iecs_dss_wt_biol rep 2


title: iecs_dss_wt_biol rep 1


title: NTG.Mm rep 3


title: nonCM_MI_day1_2

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description: Chronium (10X Genomics)

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.027 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.2b)
The reads aligned to exon were counted using featureCounts
For nonCM RNA-seq, raw data was processed using Cell Ranger (version 4.0.0)
For spatial transcriptome, raw data was processed using Space Ranger (version 1.2.1)
Genome_build: For single-cardiomyocyte RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 23, https://www.gencodegenes.org/)
Genome_build: For nonCM RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz.
Genome_build: For spatial transcrptome, the reference transcript data and the gene annotation file for mouse was downloaded from https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz.
Supplementary_files_format_and_content: ReadCounts file generated using featureCounts.
Supplementary_files_format_and_content: Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger or Space Ranger.

source_name: non-cardiomyocyte

growth_protocol: All the animal experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines for animal experiments of the University of Tokyo (Approved Number P14-106). All of wild type C57BL/6 male mice were purchased from CLEA JAPAN. All mouse were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described7. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2500 (Illumina) in rapid mode

treatment_protocol: Myocardial infarction (MI) was induced as previously described25. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

tag: operation

value: sham

tag: region

value: non-cardiomyocyte

tag: name in supplementary file


title: nonCM_MI_day1_1

description: Chronium (10X Genomics)


title: nonCM_MI_day7_2

description: Chronium (10X Genomics)


title: nonCM_MI_day7_1

description: Chronium (10X Genomics)


title: NTG.Mm rep 2


title: BRAF.Mp rep 4


title: NTG.Mm rep 1


title: BRAF.Mp rep 3


title: Sham_2_42

description:
Smart-seq2
ReadCounts.xlsx

source_name: Cardiomyocyte

value: single-cardiomyocyte


title: nonCM_Sham_2

description: Chronium (10X Genomics)


title: Sham_2_41

description:
Smart-seq2
ReadCounts.xlsx


title: BRAF.Mp rep 1


title: Sham_2_40

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_39

description:
Smart-seq2
ReadCounts.xlsx


title: BRAF.Mm rep 4


title: Sham_2_44

description:
Smart-seq2
ReadCounts.xlsx


title: BRAF.Mm rep 3


title: BRAF.Mm rep 2


title: BRAF.Mm rep 1


title: nonCM_Sham_1

description: Chronium (10X Genomics)


title: Sham_2_43

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_37

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_RNASeq_LSL_3d_rep4

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Differential gene expression and expression quantification (eRPKM) were calculated from GSE83865 RNA-Seq published data
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing differential expression results (DESeq2) and eRPKM after YAP overexpression (3 days and 7 days in LSL system, 4 weeks in LapTTA system)

extract_protocol:
total RNA was purified from homogenized livers
Library preparation was performed with the TruSeq RNA Sample Prep Kits v2 (Illumina)

tag: strain background

value: ROSA26-rtTA-IRES-EGFP; tetYAP

value: doxycycline food for 3 days

value: Liver


title: Sham_2_36

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_RNASeq_LSL_3d_rep3


title: Liver_RNASeq_LSL_7d_rep3

value: doxycycline food for 7 days


title: murine kidney_non-pathogenic Leptospira spp.-infected_7day_biological rep1

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

description:
P104
Expression data from infected mice kidney tissue.
Non-pathogenic L. biflexa serovar Patoc (ATCC number 23582).
After infection at day 7

data_processing:
Primary sequencing data was produced by Illumina Hiseq 2000 and 4000 Sequencing System (Flowcell ID: 0416 and HL2F3BBXX).
Fastq files are quality checked with FastQC, v0.11.5 (Babraham Bioinformatics, Cambridge, UK).
Sequenced reads were trimmed using the CLC Genomics Workbench V9.5 on the basis of the per base sequence quality score (Q) >= 20.
After this trimming step, sequenced reads were mapped to Mus_musculus GRCM38 using the CLC Genomics Workbench V9.5.
RPKM, Reads Per Kilobase of exon model per Million mapped reads, values for estimating transcript expression levels were done using the CLC Genomics Workbench V9.5.
Genome_build: Mus_musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain gene name, ID, reads and RPKM values.

source_name: Kidney from mice infected with non-pathogenic L. biflexa after 7 days

growth_protocol: C57BL/6 female mice aged 6–8 weeks were used for this study. All animal experiments were handled under Animal Biosafety Level 2 conditions and followed all appropriate guidelines for the use of infected animals.

extract_protocol:
Total RNA was extracted from kidney tissues using the TRIzol reagent (Invitrogen, Carlsbad, CA) with DNaseI digestion. The quantity and integrity of extracted RNA were verified using a Nano-Drop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Total RNA samples were converted to cDNA using the Ovation RNA-seq System V2 (NuGEN). Library construction was performed using the Ovation Ultralow Library System V2 1-96 (NuGEN).

treatment_protocol: Bacteria were propagated at 28 °C under aerobic conditions in medium containing 10% Leptospira enrichment Elinghausen-McCullough-Johnson-Harris (EMJH) medium (BD Diagnostics) and 90% Leptospira medium base EMJM medium (Difco, Sparks, MD). The number of motile leptospires was counted using dark-field microscopy and a Petroff-Hausser counting chamber for experimental infections. Mice were inoculated using intraperitoneal challenge with 10^9 Leptospira spp. in 0.1 ml EMJH medium and the control groups were inoculated with sterile EMJH medium.

value: WT

tag: gender

value: Female

tag: age

value: 6-8 weeks

value: Kidney

tag: infection

value: L. biflexa serovar Patoc

tag: infection time

value: 7 days


title: murine kidney_non-infected_7day_biological rep1

description:
E423
Expression data from non-infected mice kidney tissue.
Sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium.
After inoculation at day 7

source_name: Kidney from mice inoculated with sterile EMJH medium after 7 days


title: Liver_RNASeq_LSL_7d_rep2


title: murine kidney_pathogenic Leptospira spp.-infected_7day_biological rep2

description:
C408
Expression data from infected mice kidney tissue.
Pathogenic L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) isolate recovered from kidneys of hamsters.
After infection at day 7

source_name: Kidney from mice infected with pathogenic L. interrogans after 7 days


title: Liver_RNASeq_LSL_WT_rep4

value: ROSA26-rtTA-IRES-EGFP; WT


title: Liver_RNASeq_LSL_WT_rep3


title: Liver_RNASeq_LSL_3d_rep1


title: Sham_2_35

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_RNASeq_LSL_7d_rep1


title: Sham_2_30

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_27

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_34

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_33

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_31

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_29

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_28

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_32

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_38

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_24

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_H3K122Ac_LapTTA_4W_rep2

description:
processed data file: Liver_ChIPSeq_H3K122Ac_LapTTA_4W.bw.gz
processed data file: Liver_H3K122Ac_LapTTA_4W_broad_peaks.bed.gz

library_source: genomic

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Replicates of the same condition were merged after alignment to a single BAM file for the analyses
Transcription factors Yap and Tead at 4W: peak calling with MACS version 1.4;  --mfold=7,30 -g mm -p 0.00001
Other trancription factor (Hnf4a,Brd4,Pol2): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K27Ac, H3K122Ac, H3K4me3): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Input for peak calling was taken from GSE83863 published data
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt.gz files: bed files of transcription factors ChIP-Seq;  *_broad_peaks.bed.gz files: bed files of histone marks ChIP-Seq; *bw.gz: compreed bigWig files

molecule: genomic DNA

extract_protocol:
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, HNF4a, BRD4, Histone Marks, RNAPol2 ChIP dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate)  and 1% formaldehyde (FA).                           For ATAC seq experiments, 100,000 cells obtained from liver perfused mice were lysed to obtain nuclei. Transposition reaction and DNA purification were then performed.
For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. For ATAC seq, libraries were prepared for Illumina sequencing with index primers.

tag: genotype/variation

value: tetYAP

tag: chip antibody

value: H3K122Ac (Abcam ab33309)


title: Sham_2_20

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_26

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_RNASeq_LSL_WT_rep1

tag: genotype


title: Sham_2_19

description:
Smart-seq2
ReadCounts.xlsx

tag: tissue


title: Sham_2_25

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_22

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_H3K122Ac_LapTTA_4W_rep3


title: Liver_ChIPSeq_Hnf4a_LapTTA_4W_rep1

description:
processed data file: Liver_ChIPSeq_Hnf4a_LapTTA_4W.bw.gz
processed data file: Liver_Hnf4a_LapTTA_4W_peaks.bed.gz

value: HNF4a (Abcam, ab41898)


title: Liver_ChIPSeq_Pol2_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_Pol2_LapTTA_4W.bw.gz
processed data file: Liver_Pol2_LapTTA_4W_peaks.txt.gz

value: Pol2 N20-X (Santa Cruz, sc-899)


title: Liver_ChIPSeq_H3K4me3_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_H3K4me3_LapTTA_4W.bw.gz
processed data file: Liver_H3K4me3_LapTTA_4W_broad_peaks.bed.gz

value: H3K4me3 (Active Motif, #39159)


title: Sham_2_17

description:
Smart-seq2
ReadCounts.xlsx

value: sham

value: single-cardiomyocyte


title: Sham_2_16

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_RNASeq_LSL_3d_rep2

value: ROSA26-rtTA-IRES-EGFP; tetYAP

value: doxycycline food for 3 days


title: Liver_ChIPSeq_H3K122Ac_LapTTA_4W_rep1

value: Liver


title: Sham_2_23

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Tead_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_Tead_LapTTA_4W.bw.gz
processed data file: Liver_Tead_LapTTA_4W_peaks.txt.gz

value: ChIPseq and ATAC seq analysis were performed on liver of WT LaptTA or LaptTA tetYAP mice activated for 4W


title: Liver_ChIPSeq_Brd4_LapTTA_4W_rep2

description:
processed data file: Liver_ChIPSeq_Brd4_LapTTA_4W.bw.gz
processed data file: Liver_Brd4_LapTTA_4W_peaks.txt.gz


title: Liver_ChIPSeq_Brd4_LapTTA_4W_rep3


title: Sham_2_21

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Hnf4a_LapTTA_4W_rep2


title: Liver_RNASeq_LSL_WT_rep2

value: doxycycline food for 7 days


title: Liver_ChIPSeq_Brd4_LapTTA_4W_rep1


title: Liver_ChIPSeq_H3K4me1_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_H3K4me1_LapTTA_4W.bw.gz
processed data file: Liver_H3K4me1_LapTTA_4W_broad_peaks.bed.gz

value: H3K4me1 (Abcam, ab8895)


title: Liver_ChIPSeq_H3K27Ac_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_H3K27Ac_LapTTA_4W.bw.gz
processed data file: Liver_H3K27Ac_LapTTA_4W_broad_peaks.bed.gz

value: H3K27ac (Abcam, ab4729)


title: Sham_2_14

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_12

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_13

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_18

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Hnf4a_LapTTA_WT_rep2

description:
processed data file: Liver_ChIPSeq_Hnf4a_LapTTA_WT.bw.gz
processed data file: Liver_Hnf4a_LapTTA_WT_peaks.txt.gz

value: WT


title: Sham_2_10

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LapTTA_4W

description:
processed data file: Liver_ChIPSeq_Yap_LapTTA_4W.bw.gz
processed data file: Liver_Yap_LapTTA_4W_peaks.txt.gz


title: Sham_2_9

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_8

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_11

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_H3K122Ac_LapTTA_WT_rep3

description:
processed data file: Liver_ChIPSeq_H3K122Ac_LapTTA_WT.bw.gz
processed data file: Liver_H3K122Ac_LapTTA_WT_broad_peaks.bed.gz


title: Sham_2_15

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_6

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_5

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_H3K122Ac_LapTTA_WT_rep1


title: Liver_ChIPSeq_Brd4_LapTTA_WT_rep1

description:
processed data file: Liver_ChIPSeq_Brd4_LapTTA_WT.bw.gz
processed data file: Liver_Brd4_LapTTA_WT_peaks.txt.gz


title: Liver_ChIPSeq_H3K122Ac_LapTTA_WT_rep2


title: Sham_2_7

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Brd4_LapTTA_WT_rep2


title: Liver_ChIPSeq_Tead_LSL_7d_rep4

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Replicates of the same condition were merged after alignment to a single BAM file for the analyses
Peak calling was carried out with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g mm -p 0.00001
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Input for peak calling was taken from GSE83863 published data
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt files: bed files of transcription factors; *.bw.gz: compressed bigWig files

extract_protocol:
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate)  and 1% formaldehyde (FA).
For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

value: liver

value: TEAD (Aviva Systems Biology, ARP38276)


title: Liver_ChIPSeq_Brd4_LapTTA_WT_rep3


title: Liver_ChIPSeq_Tead_LSL_7d_rep3


title: Sham_2_3

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_4

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_2

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LapTTA_WT

description:
processed data file: Liver_ChIPSeq_Yap_LapTTA_WT.bw.gz
processed data file: Liver_Yap_LapTTA_WT_peaks.txt.gz


title: Sham_1_43

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Tead_LSL_7d_rep2


title: Sham_1_44

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_2_1

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_42

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Hnf4a_LapTTA_WT_rep1


title: Liver_ChIPSeq_Tead_LSL_7d_rep1


title: Liver_ChIPSeq_Yap_LSL_7d_rep3


title: Sham_1_41

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LSL_7d_rep2


title: Liver_ChIPSeq_Yap_LSL_7d_rep1


title: Sham_1_39

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_40

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Tead_LSL_3d_rep2


title: Liver_ChIPSeq_Tead_LSL_3d_rep3


title: Liver_ChIPSeq_Tead_LSL_3d_rep1


title: Sham_1_38

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_37

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LSL_3d_rep3


title: Sham_1_36

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_31

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_32

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_35

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LSL_3d_rep1


title: Liver_ChIPSeq_Tead_LSL_WT_rep3

value: ROSA26-rtTA-IRES-EGFP; WT


title: Sham_1_30

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_29

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LSL_3d_rep2


title: Liver_ChIPSeq_Yap_LSL_WT_rep3


title: Liver_ChIPSeq_Tead_LSL_WT_rep2


title: Liver_ChIPSeq_Yap_LSL_WT_rep1


title: Sham_1_34

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Tead_LSL_WT_rep1


title: Sham_1_28

description:
Smart-seq2
ReadCounts.xlsx


title: Liver_ChIPSeq_Yap_LSL_WT_rep2


title: Sham_1_27

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_26

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_23

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_33

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_22

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_24

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_21

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_19

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_16

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_17

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_25

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_20

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_15

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_13

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_14

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_11

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_12

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_10

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_18

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_9

description:
Smart-seq2
ReadCounts.xlsx


title: C6 TAZ

type: RNA

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

description: Gene expression profiling of well annotated genes

hyb_protocol: Following fragmentation and labeling , 5.5 ug of cDNA were hybridized for 16 hr at 45C, washed and stained in the Affymetrix Fluidics Station 450/250

scan_protocol: GeneChips were scanned using GeneTitan MC instrument and the GCC GeneTitan control software

data_processing: Expression Console TM software

label: Biotin

organism: Rattus norvegicus

source_name: Rat C6 glioma cells

label_protocol: 5.5 µg of cDNA is required for labeling and is labelled according to GeneChip Whole transcript (WT) expression arrays

growth_protocol: Cells were cultured in DMEM supplemented with 3% FBS and 1% (v/v) penicillin/streptomycin (growth medium) at 37 °C in humidified air atmosphere with 5% CO2.

extract_protocol: InnuPrep RNA Mini kit 2.0 from Analytik Jena was used according to manufacturers protocol

treatment_protocol: Rat C6 glioma cells (ACC550) were purchased from the DSMZ (Braunschweig, Germany). Tafazzin (TAZ) was knocked out in C6 cells (C6 TAZ) using the CRISPR-Cas9 system as described in Gürtler at al. 2019 (Biochim Biophys Acta Mol Cell Biol Lipids 1864, 452-465).

value: glioma cells

tag: cell line

value: TAZ knockout


title: Sham_1_8

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_6

description:
Smart-seq2
ReadCounts.xlsx


title: C6


title: Sham_1_4

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_7

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_3

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_1

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_5

description:
Smart-seq2
ReadCounts.xlsx


title: Sham_1_2

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_39

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: remote


title: MI_D7_RZ_2_38

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_37

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_62

type: genomic

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Raw IDATs were processed with R (v4.1.1) package ‘SeSAMe’ with noob background correction, non-linear dye bias correction, and non-detection masking. P-value threshold was set at 0.1. Probe masking was performed using the standard mask list in SeSAMe, including probes that overlap with SNPs and repeat elements.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Skin, sacrum

label_protocol: Cy3 and Cy5

extract_protocol: Frozen cell pellets were thawed and lysed using QIAshredder spin columns (Qiagen).  Genomic DNA was extracted from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen), then stored at -80°C before analysis.

tag: subexperiment

value: TERT immortalization

value: 16 fetal weeks

value: female

value: Ambient

value: Full

value: TERT

tag: subculture

tag: growth protocol

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

tag: treatment protocol

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: FSF1_TERT_64


title: MI_D7_RZ_2_36

description:
Smart-seq2
ReadCounts.xlsx

tag: strain

tag: operation

value: single-cardiomyocyte


title: MI_D7_RZ_2_35

description:
Smart-seq2
ReadCounts.xlsx

tag: region

tag: name in supplementary file


title: FSF1_TERT_55


title: FSF1_TERT_61


title: FSF1_TERT_57


title: FSF1_TERT_60


title: FSF1_TERT_53


title: FSF1_TERT_59


title: FSF1_TERT_52


title: FSF1_TERT_46


title: FSF1_TERT_51


title: FSF1_TERT_49


title: FSF1_TERT_48


title: FSF1_TERT_42


title: FSF1_TERT_41


title: FSF1_TERT_65


title: FSF1_TERT_50


title: FSF1_TERT_54


title: FSF1_TERT_45


title: FSF1_TERT_63


title: FSF1_TERT_40


title: FSF1_TERT_47


title: FSF1_TERT_44


title: MI_D7_RZ_2_31

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_43


title: MI_D7_RZ_2_30

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_28

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_27

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_26

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_39


title: FSF1_TERT_56


title: MI_D7_RZ_2_25

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_33

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_23

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_22

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_37


title: FSF1_TERT_58


title: MI_D7_RZ_2_24

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_34

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_38


title: MI_D7_RZ_2_20

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_19

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_17

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_21

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_32

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 18

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: Rainbow Blvd.

department: Otolaryngology Head and Neck Surgery

institute: University of Kansas School of Medicine

hyb_protocol: Using an Affymetrix GeneChip WT Pico labeling kit, the entire yield of total RNA was TdT end labeled with biotin and hybridized on an Affymetrix miRNA 4.0 array.

scan_protocol: After washing and staining each chip was read with an Affymetrix GeneChip Scanner 3000 7G using a single scan with default normalization.

data_processing: The arrays were background corrected, normalized and gene-level summarized using the Robust Multichip Average (RMA) algorithm. In order to ascertain which miRNAs were significantly expressed in each array, a detection p-value was computed based on a Wilcoxon Rank-Sum test of the miRNA probe set signals compared to the distribution of a GC matched background signal comprising anti-genomic pr  obes in the same array. The detection p-values were adjusted for multiple hypothesis testing (FDR) using the Benjamini and Hochberg method. These analyses were performed using Affymetrix Expression Console Software. miRNAs with a normalized log2 signal intensity ™ 7 and an adjusted detection p-value (FDR) ˜ 0.05 were considered significantly expressed.

label: biotin

source_name: Perilymph

extract_protocol: Total RNA was extracted with Trizol reagent (Thermofisher, cat #15596018) and purified by centrifuging with phase lock heavy gel (Tiagen, cat # WMS-2302830).  RNA was analysed with an Agilent RNA6000 Pico kit using an Agilent Bioanalyzer 2100, and samples yielded on average of 0.5-2 ng of total RNA

value: Perilymph

tag: pta air


title: MI_D7_RZ_2_15

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_18

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 17

label_protocol: Using an Affymetrix GeneChip WT Pico labeling kit, the entire yield of total RNA was TdT end labeled with biotin and hybridized on an Affymetrix miRNA 4.0 array.


title: Patient 16


title: MI_D7_RZ_2_14

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_16

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_36


title: FSF1_TERT_34


title: FSF1_TERT_33


title: MI_D7_RZ_2_12

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_13

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_29

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_10

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_11

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 15


title: MI_D7_RZ_2_9

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_8

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 14


title: Patient 12


title: MI_D7_RZ_2_7

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_31


title: Patient 13


title: MI_D7_RZ_2_6

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_5

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_4

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_2

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_1

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_3

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_65

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 11


title: FSF1_TERT_32


title: Patient 10


title: FSF1_TERT_27


title: Patient 9


title: FSF1_TERT_35


title: FSF1_TERT_24


title: MI_D7_RZ_1_64

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_63

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_26


title: Patient 8


title: FSF1_TERT_22


title: FSF1_TERT_23


title: MI_D7_RZ_1_61

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_62

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_60

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_25


title: MI_D7_RZ_1_59

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 7


title: MI_D7_RZ_1_57

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_21


title: MI_D7_RZ_1_58

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_20


title: Patient 5


title: MI_D7_RZ_1_56

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_18


title: MI_D7_RZ_1_55

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_19


title: MI_D7_RZ_1_54

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_17


title: MI_D7_RZ_1_53

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 3


title: FSF1_TERT_28


title: FSF1_TERT_30


title: FSF1_TERT_29


title: MI_D7_RZ_1_51

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_52

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 4


title: Patient 2


title: MI_D7_RZ_1_49

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_48

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_50

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 1


title: FSF1_TERT_14


title: FSF1_TERT_15


title: FSF1_TERT_16


title: MI_D7_RZ_1_44

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_47

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_45

description:
Smart-seq2
ReadCounts.xlsx


title: Patient 6


title: S2_RTnTag_m6A_5knuclei_n1_(220309_NK_dm_1189)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RT&Tag for m6A in S2 cells, 5k nuclei, replicate 1

data_processing:
Genome_build: UCSC dm6
1. We used trim-galore 0.6.4_dev with parameters "-q 20 --length 20" to trim adapters from 50bp or 100bp single-end reads. 2. We used hisat2 2.1.0 with parameters "--max-intronlen 5000" to map the trimmed reads to the reference sequence for Drosophilia melanogaster, dm6 from UCSC. 3. We used deepTools 3.3.1 bedCoverage to with parameters "--normalizeUsing CPM" to make bigwig files (Supplementary file .bw).

organism: Drosophila melanogaster

source_name: RT&Tag

tag: antibody

value: m6A Megabase cat# AP60500

tag: cell type

value: S2 cell line


title: MI_D7_RZ_1_46

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_m6A_5knuclei_n2_(220309_NK_dm_1209)

description: RT&Tag for m6A in S2 cells, 5k nuclei, replicate 2


title: S2_RTnTag_m6A_25knuclei_n2_(220309_NK_dm_1206)

description: RT&Tag for m6A in S2 cells, 25k nuclei, replicate 2


title: MI_D7_RZ_1_43

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_m6A_25knuclei_n1_(220309_NK_dm_1186)

description: RT&Tag for m6A in S2 cells, 25k nuclei, replicate 1


title: MI_D7_RZ_1_41

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_42

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_m6A_100knuclei_n1_(220309_NK_dm_1183)

description: RT&Tag for m6A in S2 cells, 100k nuclei, replicate 1


title: MI_D7_RZ_1_39

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_12


title: MI_D7_RZ_1_38

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_13


title: MI_D7_RZ_1_40

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_IgG_5knuclei_n2_(220309_NK_dm_1207)

description: RT&Tag for IgG in S2 cells, 5k nuclei, replicate 2

value: IgG Abcam cat# ab172730


title: MI_D7_RZ_1_37

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_36

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_35

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_IgG_5knuclei_n1_(220309_NK_dm_1187)

description: RT&Tag for IgG in S2 cells, 5k nuclei, replicate 1


title: MI_D7_RZ_1_33

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_34

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_32

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_31

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_29

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_30

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_IgG_25knuclei_n1_(220309_NK_dm_1184)

description: RT&Tag for IgG in S2 cells, 25k nuclei, replicate 1


title: S2_RTnTag_IgG_25knuclei_n2_(220309_NK_dm_1204)

description: RT&Tag for IgG in S2 cells, 25k nuclei, replicate 2


title: MI_D7_RZ_1_28

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_11


title: MI_D7_RZ_1_27

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_IgG_100knuclei_n2_(220309_NK_dm_1201)

description: RT&Tag for IgG in S2 cells, 100k nuclei, replicate 2


title: S2_RTnTag_m6A_100knuclei_n2_(220309_NK_dm_1203)

description: RT&Tag for m6A in S2 cells, 100k nuclei, replicate 2


title: MI_D7_RZ_1_26

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_IgG_100knuclei_n1_(220309_NK_dm_1181)

description: RT&Tag for IgG in S2 cells, 100k nuclei, replicate 1


title: FSF1_TERT_10


title: MI_D7_RZ_1_25

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_8


title: MI_D7_RZ_1_24

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_H3K27me3_5knuclei_n2_(220309_NK_dm_1208)

description: RT&Tag for H3K27me3 in S2 cells, 5k nuclei, replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733


title: MI_D7_RZ_1_23

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_H3K27me3_5knuclei_n1_(220309_NK_dm_1188)

description: RT&Tag for H3K27me3 in S2 cells, 5k nuclei, replicate 1


title: MI_D7_RZ_1_21

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_4


title: FSF1_TERT_9


title: MI_D7_RZ_1_20

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_H3K27me3_25knuclei_n2_(220309_NK_dm_1205)

description: RT&Tag for H3K27me3 in S2 cells, 25k nuclei, replicate 2


title: MI_D7_RZ_1_18

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_5


title: FSF1_TERT_7


title: S2_RTnTag_H3K27me3_25knuclei_n1_(220309_NK_dm_1185)

description: RT&Tag for H3K27me3 in S2 cells, 25k nuclei, replicate 1


title: MI_D7_RZ_1_17

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_6


title: MI_D7_RZ_1_22

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_16

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERT_2


title: S2_RTnTag_H3K27me3_100knuclei_n1_(220309_NK_dm_1182)

description: RT&Tag for H3K27me3 in S2 cells, 100k nuclei, replicate 1


title: FSF1_TERT_3


title: MI_D7_RZ_1_13

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_15

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_10

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_12

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_9

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERTCtl_9

value: Hygromycin B resistance

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vector encoding hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured through replicative senescence, in triplicate.


title: MI_D7_RZ_1_8

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: remote


title: LN_MHCII

city: Daejeon

first: Ji Hoon

last: Ahn

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Institute for Basic Science

description: FACS sorted

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mosue reference genome.
Aligned reads were then read by Seurat (v4.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes), doublets (cells with more than twice the median of detected gene numbers), potential dead cells (>5% mitochondrial gene percentage) and contaminating non-BAMP cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for CNS BAMPs

source_name: mouse deep cervical lymph nodes MHCII high BAMPs

extract_protocol:
FACS sorted MHCII high BAMPs were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

treatment_protocol: Cell labeling was performed according to an adapted BioLegend cell hashing protocol (TotalSeq™-C Antibodies and Cell Hashing with 10x Single Cell 5' Reagent Kit v3 3.1 Protocol, Biolegend)

tag: age

value: Adult

tag: library type

value: single cell RNA


title: LN_MHCII_surf

description: FACS sorted and labeling by TotalSeq™-C antibodies

growth_protocol: 10x single cell RNA sequencing 3' NEXT GEM v3.1

value: mouse deep cervical lymph nodes MHCII high BAMPs

value: single cell surface tagged oligos


title: FSF1_TERTCtl_4

value: TERT immortalization

value: 16 fetal weeks

value: female

value: Ambient

value: Full


title: MI_D7_RZ_1_19

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: FSF1_TERT_1

value: TERT

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: FSF1_TERTCtl_3

value: Hygromycin B resistance


title: FSF1_TERTCtl_7

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vector encoding hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured through replicative senescence, in triplicate.


title: NFF2_LOWO2_32

source_name: Foreskin

value: Reduced oxygen

value: 0 years

value: male

value: Low 3% O2

value: b

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_RZ_1_7

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: remote


title: MI_D7_RZ_1_14

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_TERTCtl_6

value: TERT immortalization

value: 16 fetal weeks

value: female


title: Dura_MHCII_surf

source_name: mouse dural MHCII high BAMPs

value: Adult

value: mouse dural MHCII high BAMPs

value: single cell surface tagged oligos


title: MI_D7_RZ_1_6

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: CP_MHCII_surf

source_name: mouse choroid plexus MHCII high BAMPs

value: mouse choroid plexus MHCII high BAMPs


title: MI_D7_RZ_1_5

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_4

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_1_3

description:
Smart-seq2
ReadCounts.xlsx


title: S2_RTnTag_H3K27me3_100knuclei_n2_(220309_NK_dm_1202)

description: RT&Tag for H3K27me3 in S2 cells, 100k nuclei, replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: FSF1_TERTCtl_8

value: Ambient

value: Full

value: Hygromycin B resistance

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vector encoding hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured through replicative senescence, in triplicate.


title: CP_MHCII

description: FACS sorted

value: single cell RNA


title: FSF1_TERTCtl_1


title: MI_D7_RZ_1_1

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: remote


title: MI_D7_RZ_1_11

description:
Smart-seq2
ReadCounts.xlsx


title: Brain_MHCII_surf

source_name: mouse brain cortex and subdural meninges MHCII high BAMPs


title: Dura_MHCII

description: FACS sorted


title: MI_D7_RZ_2_65

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_64

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_62

description:
Smart-seq2
ReadCounts.xlsx


title: Brain_MHCII

description: FACS sorted

value: mouse brain cortex and subdural meninges MHCII high BAMPs


title: FSF1_TERTCtl_5

value: TERT immortalization

value: 16 fetal weeks

value: female


title: MI_D7_RZ_2_61

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_63

description:
Smart-seq2
ReadCounts.xlsx


title: Dura_EC

description: FACS sorted

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mosue reference genome.
Aligned reads were then read by Seurat (v4.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes), doublets (cells with more than twice the median of detected gene numbers), potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for CNS border ECs

source_name: mouse dural endothelial cells (EC)

extract_protocol:
FACS sorted endothelial cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

value: mouse dural endothelial cells (EC)

value: Adult


title: NFF2_LOWO2_30

value: Reduced oxygen

value: 0 years

value: male

value: Low 3% O2

value: b

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_RZ_2_60

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: FSF1_TERTCtl_2

value: Ambient

value: Full

value: Hygromycin B resistance

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vector encoding hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured through replicative senescence, in triplicate.


title: MI_D7_RZ_2_59

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: remote


title: MI_D7_RZ_2_58

description:
Smart-seq2
ReadCounts.xlsx


title: CP_EC

description: FACS sorted

source_name: mouse choroid plexus endothelial cells (EC)


title: MI_D7_RZ_1_2

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_33

value: a


title: MI_D7_RZ_2_56

description:
Smart-seq2
ReadCounts.xlsx


title: Brain_EC

description: FACS sorted

source_name: mouse brain cortex and subdural meninges endothelial cells (EC)


title: MI_D7_RZ_2_55

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_26


title: MI_D7_RZ_2_57

description:
Smart-seq2
ReadCounts.xlsx


title: P7_dura_CD45_2

description: FACS sorted

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mosue reference genome.
Aligned reads were then read by Seurat (v4.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 300 genes), doublets (cells with more than twice the median of detected gene numbers), potential dead cells (>10% mitochondrial gene percentage) and contaminating cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural immune cells

source_name: P7 mouse dural immune cells

extract_protocol:
FACS sorted immune cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

treatment_protocol: Mice were intracardially injected with CD45-FITC (11-0451-85, 30-F11, Invitrogen) antibody and perfused after 30 seconds. Immune cells were gated with an antibody with a different clone, CD45-APC/cyanine7 (109824, 104, Biolegend), and Singlet+Live+CD45+CD45iv- cells were collected.

value: P7 mouse dural immune cells

value: Pup


title: MI_D7_RZ_2_53

description:
Smart-seq2
ReadCounts.xlsx

source_name: Cardiomyocyte


title: MI_D7_RZ_2_52

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_54

description:
Smart-seq2
ReadCounts.xlsx


title: P28_dura_CD45

description: FACS sorted

source_name: P28 mouse dural immune cells

value: P28 mouse dural immune cells

value: Adult


title: P7_dura_CD45_1

description: FACS sorted


title: NFF2_LOWO2_28

value: Reduced oxygen

value: 0 years

value: male


title: NFF2_LOWO2_27

value: Low 3% O2

value: b

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_RZ_2_50

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: NFF2_LOWO2_31

value: Full


title: MI_D7_RZ_2_51

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_49

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_47

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_23


title: NFF2_LOWO2_24


title: MI_D7_RZ_2_48

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_46

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_25


title: MI_D7_RZ_2_44

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_45

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_43

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_41

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_RZ_2_40

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_61

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic


title: MI_D7_RZ_2_42

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_58

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_59

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_60

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_56

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_22


title: NFF2_LOWO2_29


title: MI_D7_IZ_2_54

description:
Smart-seq2
ReadCounts.xlsx


title: AS-1258_D10Tam_Autoch_plus_mTmGFrag_NSGFrag

first: Simon

last: Joost

state: NY

address: 1275 York Avenue

department: Cell Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw sequencing data from cDNA and hash libraries was demultiplexed and aligned with the 10X Genomics CellRanger pipeline (v.5.5.0) to a custom GRCm38/mm10 reference genome including the GFP and tdTomato transgenes used in this study.
Assembly: mm10
Supplementary files format and content: Count matrices from all samples were combined into a single h5. file with all relevant metadata. Please not that not all samples in this file were used in the final analysis.
Supplementary files format and content: Jupyter notebooks detailing all downstream processing and data analysis steps can be found at https://github.com/sim-joo/Pitter_et_al_Cancer_Research

source_name: pancreatic ductal adenocarcinoma (PDAC)

extract_protocol:
Primary PDAC tumors from KPCT and KPF; RosamTmG/+; Lgr5CreER mice were digested following method: tumors were finely chopped with scissors and incubated with digestion buffer containing collagenase IV (17104019, ThermoFisher Scientific, 0.1 U/ml ), Dispase (#354235, Corning, 0.6 U/ml), DNase I (#69182–3; Sigma Aldrich, 10 U/ml), and Soybean Trypsin Inhibitor (#T9003, Sigma Aldrich, 0.1 mg/ml) dissolved in HBSS with Mg2+ and Ca2+ (#14025076, Thermo Fisher Scientific) in gentleMACS C Tubes (Miltenyi Biotec) for 42 min at 37°C using the gentleMACS Octo Dissociator (#130–096-427, Miltenyi Biotech). After enzymatic dissociation, samples were washed with HBSS + Mg2+ and Ca2+ and filtered through a 100 μm cell strainer and spun at 300 g for 5 min at room temperature. Cells were then washed with media and pelleted at 300 g for 5 min at 4°C. The supernatant was removed, and the pellet resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 2% of heat-inactivated FBS in PBS) before being passed through a 40 μm strainer. At this point cells were used either for direct orthotopic implantations, for generation of 2D and 3D cells cell lines, or were prepared for FACS.  For FACS staining, cell suspensions were next blocked for 5 min at room temperature with rat anti-mouse CD16/CD32 with Fcblock (#553142, BD Biosciences) in FACS buffer, and incubated for 30min with a mix of four APC-conjugated antibodies against: CD45 (#559864, BD Biosciences, 1:500) + CD31 (#561814, BD Biosciences, 1:500) + CD11b (#561690, BD Biosciences, 1:500) and TER-119 (#561033, BD Biosciences, 1:500) and 300 nM DAPI as live-cell marker. Sorts were performed on a BD FACSAria sorter (Becton Dickinson) for either (CD45/CD31/CD11b/TER119)−/tdTomato+/DAPI− live cells (KPCT mice) and/or for (CD45/CD31/CD11b/TER119)−/tdTomato+/GFP+/DAPI− live cells (KPF; RosamTmG/+; Lgr5CreER mice) in lineage tracing experiments and as indicated in figures. Sorted cells were collected directly into S-MEM with 2% of heat-inactivated FBS for scRNA-seq or for scATAC-seq. If samples were hashed towards scRNA-seq sequencing, individual tumor cell suspension were incubated for 30 min with hashing antibodies (see table below) in addition to FACS antibodies.
PDAC tumors were harvest, dissociated, and tumor cells isolated via FACS as described above. The scRNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3. Briefly, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Between 20,000 to 25,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium following TotalSeq B cell hashing protocol  [49]. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells

tag: tumor model

value: PDAC autochthonous or fragment transplant; Lgr5 lineage tracing

tag: treatment

value: 10d tamoxifen; individual mice hashed

tag: hash


title: MI_D7_IZ_2_55

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

tag: tissue


title: MI_D7_IZ_2_57

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_20

tag: subexperiment

value: a


title: MI_D7_IZ_2_51

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_19

tag: subculture


title: MI_D7_IZ_2_53

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_52

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_18

tag: growth protocol


title: MI_D7_IZ_2_48

description:
Smart-seq2
ReadCounts.xlsx


title: OG-1331_Day3_100621_HTO

value: PDAC autochthonous; Lgr5 lineage tracing

value: 3d tamoxifen; individual mice hashed


title: MI_D7_IZ_2_50

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_49

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_17

value: Reduced oxygen


title: NFF2_LOWO2_15

value: 0 years


title: OG-1331_Day3_100621


title: MI_D7_IZ_2_46

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_45

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_47

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_16

value: male


title: OG-1221_KPT_081021

value: PDAC orthotopic; different transplant models; individually hashed

value: untreated


title: OG-1221_KPT_081021_HTO


title: MI_D7_IZ_2_44

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_14

value: Low 3% O2

value: b

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_IZ_2_42

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic

value: single-cardiomyocyte


title: KPT_072021_HTO

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells


title: AS-1258_D10Tam_Autoch_plus_mTmGFrag_NSGFrag_HTO

value: PDAC autochthonous or fragment transplant; Lgr5 lineage tracing

value: 10d tamoxifen; individual mice hashed


title: MI_D7_IZ_2_41

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7


title: NFF2_LOWO2_21

value: Full


title: MI_D7_IZ_2_43

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_7

value: a


title: NFF2_LOWO2_8

value: Reduced oxygen


title: KPT_071221_HTO


title: MI_D7_IZ_2_38

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_072021


title: NFF2_LOWO2_9

value: 0 years


title: NFF2_LOWO2_12

value: male


title: MI_D7_IZ_2_39

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_40

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_11


title: NFF2_LOWO2_4


title: NFF2_LOWO2_10


title: NFF2_LOWO2_3


title: NFF2_LOWO2_5


title: MI_D7_IZ_2_37

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_35

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_32

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_6


title: MI_D7_IZ_2_34

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_070721_HTO

value: PDAC orthotopic; different transplant models; individually hashed


title: MI_D7_IZ_2_31

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_062821_HTO

value: untreated


title: KPT_070721


title: NFF2_LOWO2_2

value: Low 3% O2


title: MI_D7_IZ_2_30

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_LOWO2_13


title: MI_D7_IZ_2_29

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_062521_HTO


title: KPT_062521


title: MI_D7_IZ_2_26

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_27

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_25

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_24

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_23

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_062821


title: KPT_062221_HTO


title: MI_D7_IZ_2_28

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_22

description:
Smart-seq2
ReadCounts.xlsx


title: KPT_062221


title: MI_D7_IZ_2_20

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_21

description:
Smart-seq2
ReadCounts.xlsx


title: 2D_3D_Cells_HTO

value: PDAC cell lines cultured in different conditions; individually hashed


title: MI_D7_IZ_2_18

description:
Smart-seq2
ReadCounts.xlsx


title: 2D_3D_Cells


title: MI_D7_IZ_2_17

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_16

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_19

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_13

value: Ambient

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_IZ_2_15

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic

value: single-cardiomyocyte


title: KPT_071221

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells


title: MI_D7_IZ_2_14

description:
Smart-seq2
ReadCounts.xlsx


title: Day_10_Veh_LGK_HTO

value: PDAC orthotopic; fragment transplant

value: 10d Veh or LGK-974 treated; individually hashed


title: MI_D7_IZ_2_13

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7


title: NFF2_LOWO2_1

value: Full


title: MI_D7_IZ_2_12

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_10

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_11

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_36

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_33

description:
Smart-seq2
ReadCounts.xlsx


title: Day_10_Veh_LGK


title: NFF2_AMBO2_12

value: Reduced oxygen

value: a


title: MI_D7_IZ_2_9

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_9

value: 0 years

value: male


title: AK1471_82_83_HTO

value: PDAC autochthonous

value: untreated; invidual mice hashed


title: LGK_Day_20

value: 20d LGK-974 treated; individual mice hashed


title: LGK_Day_20_HTO


title: MI_D7_IZ_2_6

description:
Smart-seq2
ReadCounts.xlsx


title: AK1471_82_83


title: MI_D7_IZ_2_5

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_4

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_3

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_10

value: Ambient


title: AJ1207_08_12_HTO

value: PDAC orthotopic; different transplant models; individually hashed

value: untreated

value: B0307_TotalSeqB':'NSG_fragment', 'B0309_TotalSeqB':'NSG_fragment',  'B0310_TotalSeqB':'NSG_sorted'


title: NFF2_AMBO2_8

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: NFF2_AMBO2_5


title: NFF2_AMBO2_6


title: AJ1207_08_12

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells


title: MI_D7_IZ_2_1

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic

value: single-cardiomyocyte


title: MI_D7_IZ_1_90

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7


title: MI_D7_IZ_2_2

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_2_8

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_89

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_11

value: Reduced oxygen

value: Full


title: Veh_Day_10_HTO

value: PDAC orthotopic; fragment transplant

value: 10d Veh treated; individual mice hashed


title: MI_D7_IZ_1_88

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_87

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_14

value: 0 years

value: male

value: a


title: MI_D7_IZ_2_7

description:
Smart-seq2
ReadCounts.xlsx


title: Veh_Day_10


title: MI_D7_IZ_1_86

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_4

value: Ambient


title: Gem_Day_10_HTO

value: 10d gemcitabine treated; individual mice hashed


title: MI_D7_IZ_1_85

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_7


title: NFF2_AMBO2_1


title: MI_D7_IZ_1_84

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_2


title: MI_D7_IZ_1_80

description:
Smart-seq2
ReadCounts.xlsx


title: NFF2_AMBO2_3


title: NFF2_AMBO2_15


title: MI_D7_IZ_1_83

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_78

description:
Smart-seq2
ReadCounts.xlsx


title: Gem_Day_10


title: FSF1_SW_15_11

value: Growth arrest:Serum withdrawal

value: 16 fetal weeks

value: female

value: c

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: FSF1_SW_15_12

value: b


title: LGK_Day_10_HTO

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells

value: 10d LGK-974 treated; individual mice hashed


title: mTmG_Day_3_HTO

value: PDAC orthotopic; fragment transplant; Lgr5 lineage tracing

value: 3d tamoxifen; individual mice hashed


title: MI_D7_IZ_1_77

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: ischemic

value: single-cardiomyocyte


title: FSF1_SW_15_13

value: a


title: FSF1_SW_15_10

value: Ambient


title: MI_D7_IZ_1_76

description:
Smart-seq2
ReadCounts.xlsx


title: mTmG_Day_3


title: MI_D7_IZ_1_75

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_79

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_15_6


title: 1918-1922_HTO

value: 20d tamoxifen; individual mice hashed


title: FSF1_SW_15_8

value: Growth arrest:Serum withdrawal


title: MI_D7_IZ_1_81

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_73

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_72

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_74

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_71

description:
Smart-seq2
ReadCounts.xlsx


title: 1918-1922


title: MI_D7_IZ_1_82

description:
Smart-seq2
ReadCounts.xlsx


title: 1920_24_29_HTO


title: MI_D7_IZ_1_70

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_69

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_68

description:
Smart-seq2
ReadCounts.xlsx


title: 1920_24_29


title: MI_D7_IZ_1_66

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_65

description:
Smart-seq2
ReadCounts.xlsx


title: KW1718_CD_LGK

value: PDAC autochthonous

value: LGK-974 treated

value: no hash


title: MI_D7_IZ_1_67

description:
Smart-seq2
ReadCounts.xlsx


title: LGK_Day_10

value: PDAC orthotopic; fragment transplant


title: MI_D7_IZ_1_64

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_63

description:
Smart-seq2
ReadCounts.xlsx


title: KW1714_CD_LGK


title: MI_D7_IZ_1_62

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_61

description:
Smart-seq2
ReadCounts.xlsx


title: XZ1386_veh

value: Veh treated


title: MI_D7_IZ_1_59

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_15_9

value: 16 fetal weeks

value: female

value: b

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: FSF1_SW_15_7


title: MI_D7_IZ_1_57

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_58

description:
Smart-seq2
ReadCounts.xlsx


title: YY1017_YY1021_HTO

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells

value: LGK-974 treated; individual mice hashed


title: KW1710_veh


title: FSF1_SW_15_2

value: c


title: MI_D7_IZ_1_56

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: ischemic

value: single-cardiomyocyte


title: MI_D7_IZ_1_55

description:
Smart-seq2
ReadCounts.xlsx


title: YY1017_YY1021


title: FSF1_SW_15_4

value: Growth arrest:Serum withdrawal

value: Ambient

value: a


title: MI_D7_IZ_1_54

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_53

description:
Smart-seq2
ReadCounts.xlsx


title: YY1010_YY1024_HTO

value: PDAC autochthonous

value: Veh treated; individual mice hashed


title: MI_D7_IZ_1_60

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_51

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_52

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_50

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_49

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_48

description:
Smart-seq2
ReadCounts.xlsx


title: Sample3_GH2807

value: untreated

value: no hash


title: FSF1_SW_5_6

value: 16 fetal weeks

value: female

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 5% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: FSF1_SW_15_1

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_IZ_1_46

description:
Smart-seq2
ReadCounts.xlsx


title: Sample2_GH2798

value: pancreatic ductal adenocarcinoma (PDAC)

value: tumor cells


title: MI_D7_IZ_1_45

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_47

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_44

description:
Smart-seq2
ReadCounts.xlsx


title: YY1010_YY1024


title: Sample1_GH2593_luc_live


title: FSF1_SW_15_5


title: FSF1_SW_15_3

value: b


title: BMDM_KO_LPS_24h 3

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

data_processing:
Purity-filtered reads were pre-processed using fastp (v. 0.19.11)
STAR v2.7.3a (Spliced Transcripts Alignment To a Reference) was used to align reads to the mouse mm10 genome and generate raw counts.
Assembly: Mus musculus mm9
Supplementary files format and content: Tab-separated .txt files with gene-level read counts

source_name: Bone-marrow

extract_protocol:
RNA was extracted from cells or tissue using RNeasy Plus Mini or Micro kit (Qiagen)
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara) from 10ng of total RNA. This protocol includes a first step of RNA fragmentation using a proprietary fragmentation mix at 94°C. The time of incubation was set up for all samples at 4 min, based on the RNA quality, and according to the manufacturer’s recommendations. After fragmentation, indexed cDNA synthesis and amplification were performed followed with a ribodepletion step using probes targeting mammalian rRNAs. PCR amplification was finally achieved on ribodepleted cDNAs, using 12 cycles estimated in accordance to the input quantity of total RNA.
Sequencing was carried out using a pair-end 2 x 100 bp mode on the NovaSeq 6000 system (Illumina), targeting between 10 and 15M clusters per sample

value: Bone-marrow

tag: cell line

value: Bone-marrow-derived macrophage

tag: genotype

value: KO

value: LPS

tag: time


title: MI_D7_IZ_1_41

description:
Smart-seq2
ReadCounts.xlsx

tag: strain

tag: operation

value: MI day7

tag: region

value: ischemic

value: single-cardiomyocyte


title: FSF1_SW_5_8

value: Growth arrest:Serum withdrawal

value: Ambient


title: FSF1_SW_5_4


title: FSF1_SW_5_7

value: c


title: MI_D7_IZ_1_40

description:
Smart-seq2
ReadCounts.xlsx

tag: name in supplementary file


title: FSF1_SW_5_5

value: 16 fetal weeks

value: a


title: MI_D7_IZ_1_39

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_LPS_24h 1


title: MI_D7_IZ_1_38

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_LPS_24h 2


title: FSF1_SW_5_3

value: female

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 5% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_IZ_1_37

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_palmitate_24h 3

value: palmitate


title: MI_D7_IZ_1_36

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_35

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_palmitate_24h 2


title: FSF1_SW_5_2


title: MI_D7_IZ_1_33

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_34

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_palmitate_24h 1


title: MI_D7_IZ_1_32

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_31

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_42

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_Control_24h 3

value: Control


title: FSF1_SW_1_3

value: b

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 1% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: MI_D7_IZ_1_29

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_43

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_1_2


title: BMDM_KO_Control_24h 2

value: Bone-marrow

value: Bone-marrow-derived macrophage


title: MI_D7_IZ_1_28

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_5_1


title: MI_D7_IZ_1_30

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_1_1


title: BMDM_KO_LPS_2h 3

value: KO

value: LPS


title: MI_D7_IZ_1_27

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: ischemic


title: MI_D7_IZ_1_26

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: MI_D7_IZ_1_25

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_24

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_23

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_LPS_2h 2


title: BMDM_KO_Control_24h 1


title: MI_D7_IZ_1_22

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_05_1

value: Growth arrest:Serum withdrawal

value: Ambient

value: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 0.5% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. Passaging occurred as cells became approximately 90% confluent.


title: FSF1_SW_1_4

value: 16 fetal weeks

value: c


title: MI_D7_IZ_1_21

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_LPS_2h 1


title: FSF1_SW_05_4

value: female

value: a


title: BMDM_KO_palmitate_2h 3

value: palmitate


title: FSF1_SW_05_3


title: MI_D7_IZ_1_19

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_20

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_17

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_16

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_palmitate_2h 2


title: MI_D7_IZ_1_15

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_palmitate_2h 1


title: MI_D7_IZ_1_13

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_Control_2h 3

value: Control


title: MI_D7_IZ_1_18

description:
Smart-seq2
ReadCounts.xlsx


title: FSF1_SW_05_2

value: b


title: ASF1_GA_5

source_name: Skin, arm

value: Growth arrest:MMC

value: 31 years

value: male

value: MMC

value: Full

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

tag: treatment protocol

value: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate growth-arrest subcultures were derived from the initial recovered plate. Cells were treated with D intercalating agent mitomycin C reconstituted in DMSO at a fil concentration of 10ug/ml. Cells were incubated for 3 hours at 37°C before media containing MMC was removed, cells rinsed with PBS, and basal media replaced. Cells were collected on days 18 and 25.


title: MI_D7_IZ_1_12

description:
Smart-seq2
ReadCounts.xlsx

value: MI day7

value: ischemic

value: single-cardiomyocyte


title: MI_D7_IZ_1_11

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_10

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_Control_2h 2

value: Bone-marrow

value: Bone-marrow-derived macrophage

value: KO


title: MI_D7_IZ_1_9

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_KO_Control_2h 1


title: MI_D7_IZ_1_8

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_7

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_LPS_24h 3

value: WT

value: LPS


title: MI_D7_IZ_1_6

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_5

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_4

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_LPS_24h 2


title: ASF1_GA_1

value: Ambient


title: MI_D7_IZ_1_3

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D7_IZ_1_2

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_LPS_24h 1


title: ASF1_GA_parent


title: ASF1_GA_6


title: MI_D7_IZ_1_1

description:
Smart-seq2
ReadCounts.xlsx


title: ASF1_GA_4


title: ASF1_GA_2


title: MI_D7_IZ_1_14

description:
Smart-seq2
ReadCounts.xlsx


title: ASF1_GACtl_6

value: control

value: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate vehicle subcultures were derived from the initial recovered plate. Vehicle DMSO was added to media and incubated for 3 hours at 37°C before media containing vehicle was removed, cells rinsed with PBS, and basal media replaced. Cells were passaged normally.


title: ASF1_GACtl_5

value: Growth arrest:MMC

value: 31 years


title: BMDM_WT_palmitate_24h 2

value: palmitate


title: MI_D1_RZ_3_82

description:
Smart-seq2
ReadCounts.xlsx

value: MI day1

value: remote


title: MI_D1_RZ_3_80

description:
Smart-seq2
ReadCounts.xlsx


title: AVSMC1_GA_parent

source_name: Iliac vein

value: 19 years

value: male

value: Full

value: Vascular smooth muscle cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 10% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: MI_D1_RZ_3_81

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: BMDM_WT_palmitate_24h 1

value: Bone-marrow

value: Bone-marrow-derived macrophage


title: BMDM_WT_Control_24h 3

value: WT

value: Control


title: ASF1_GA_3

value: Ambient

value: MMC

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate growth-arrest subcultures were derived from the initial recovered plate. Cells were treated with D intercalating agent mitomycin C reconstituted in DMSO at a fil concentration of 10ug/ml. Cells were incubated for 3 hours at 37°C before media containing MMC was removed, cells rinsed with PBS, and basal media replaced. Cells were collected on days 18 and 25.


title: BMDM_WT_palmitate_24h 3


title: MI_D1_RZ_3_79

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_78

description:
Smart-seq2
ReadCounts.xlsx


title: ASF1_GACtl_1

value: Growth arrest:MMC

value: 31 years

value: control

value: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate vehicle subcultures were derived from the initial recovered plate. Vehicle DMSO was added to media and incubated for 3 hours at 37°C before media containing vehicle was removed, cells rinsed with PBS, and basal media replaced. Cells were passaged normally.


title: ASF1_GACtl_4


title: ASF1_GACtl_2


title: MI_D1_RZ_3_76

description:
Smart-seq2
ReadCounts.xlsx

value: MI day1

value: remote


title: BMDM_WT_Control_24h 2


title: MI_D1_RZ_3_77

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_75

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_Control_24h 1


title: MI_D1_RZ_3_74

description:
Smart-seq2
ReadCounts.xlsx


title: AVSMC1_GA_3

value: 19 years

value: male

value: Full


title: MI_D1_RZ_3_73

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: MI_D1_RZ_3_72

description:
Smart-seq2
ReadCounts.xlsx


title: ASF1_GACtl_3


title: MI_D1_RZ_3_83

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_70

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_71

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_LPS_2h 2

value: Bone-marrow

value: Bone-marrow-derived macrophage

value: LPS


title: AVSMC1_GA_6

value: Ambient

value: Vascular smooth muscle cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 10% v/v fetal bovine serum on plates pre-coated with gelatin. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: BMDM_WT_LPS_2h 3

value: WT


title: AVSMC1_GA_4

value: MMC

value: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate growth-arrest subcultures were derived from the initial recovered plate. Cells were treated with D intercalating agent mitomycin C reconstituted in DMSO at a fil concentration of 10ug/ml. Cells were incubated for 3 hours at 37°C before media containing MMC was removed, cells rinsed with PBS, and basal media replaced. Cells were collected on days 18 and 25.


title: MI_D1_RZ_3_69

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_67

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_palmitate_2h 3

value: palmitate


title: BMDM_WT_LPS_2h 1


title: MI_D1_RZ_3_84

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_RZ_3_65

description:
Smart-seq2
ReadCounts.xlsx


title: BMDM_WT_palmitate_2h 2