title: Patient 11, BCR-derived cDNA

value: BCR


title: Sample 10-46-L003 [snRNA-seq]

status: Public on Feb 01 2024

type: SRA

city: Stanford

first: Tony

last: Wyss-Coray

state: CA

address: 290 Jane Stanford Way

department: Neurology

country: USA

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Raw gene counts were obtained by aligning reads to the hg38 genome (refdata-gex-GRCh38-2020-A) using CellRanger software (v.4.0.0) (10x Genomics). To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were also counted.
All subsequent analysis was implemented in Python (3.9.12) based on the Scanpy (1.9.1) single-cell data analysis package except when stated otherwise in the corresponfing manuscript.
assembly: hg38

molecule: nuclear RNA

organism: Homo sapiens

source_name: brain (frontal cortex)

extract_protocol:
snRNA-seq libraries were prepared from nuclei using the Chromium Next GEM Single Cell 3ʹ v.3.1 according to the manufacturer’s protocol (10x Genomics).
Nuclei were counted using with a TC20 Automated Cell Counter (Bio-Rad) and loaded into a 10x droplet generator at a concentration of 8,000 nuclei per sample. Thirteen pcr cycles were applied to generate cDNA, and 15 cycles for final library generation. The final snRNA-seq libraries were sequenced on a NovaSeq 6000.

tag: tissue

value: brain (frontal cortex)

tag: disease status

value: AD

tag: genotype

value: APOE 3/3

tag: age

tag: Sex

value: Male

tag: treatment

value: ad apoe 33


title: maternal lung, H2O, 15.11 h, replicate 4

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Basecalling done bg Novogene as part of paid service. Sequencing produced a total of 828 libraries (414 paired end), with a median read depth of 24*106 reads (mean 25*106 reads, min 19.9 and max 46.6106), all of which passed initial QC controls performed by multiqc56. We detected base-pair overrepresentation in the first 11 bp of each read, as expected due to biases in random primers, and removed them using the trimfq command from seqtk (https://github.com/lh3/seqtk). Reads were mapped to gencode mouse transcriptome version M2357, which is an annotation of the genome assembly version GRCm38. In order to perform pseudo-mapping with Salmon58, we created an index using k-mer size 31 bp and supplying the genome in order to create decoy k-mers to account for biases due to un-annotated transcribed genomic regions (as described in Salmon documentation). We mapped libraries to the resulting index using Salmon quant using the following options: gcBias, seqBias, validateMappings, numBootstraps=10 and minScoreFraction=0.8. Finally, we annotated the resulting quant files using the R library tximeta59 and removed all features that lacked annotation. We performed all initial exploratory analyses and plots (e.g. PCA) using TPM-normalized data, and used the raw count data for the differential expression analysis. Before fitting statistical models, we normalised the count data from Salmon using TMM, retained only transcripts with more than 10 reads in at least 70% of the samples of the same condition, and applied voom correction for mean/variance relationship using the limma package60.
Assembly: gencode mouse transcriptome version M23
Supplementary files format and content: TPM matrix summarizing all samples

molecule: polyA RNA

organism: Mus musculus

source_name: maternal lung

growth_protocol: Animals : Nulliparous C57BL/6JRj mice (Janvier, Saint Berthevin Cedex, France) from the same barrier were time-mated and pregnancy confirmed by the presence of vaginal plug the morning after mating (designated gestation day (GD) 0). Dams arrived at the institute at GD 11 or 12 and were allowed to acclimate for 6-7 days prior to exposure. Mice were pair housed in clear 1290D euro standard polypropylene cages with Aspen bedding (Tapvei, Estonia), enrichment (mouse house 80-ACRE011, Techniplast, Italy; small aspen blocks, Tapvei, Estonia) and nesting material (Enviro Dri, Lillico, Biotechnology, UK), under controlled conditions and access to food (Altromin 1314 for breeding, Brogaaarden, Denmark) and tap water ad libitum. Animals were weighed on the day of arrival and the day prior to exposure to confirm pregnancy.

extract_protocol:
Isolation of pups and maternal/fetal organs: At 2, 5, 12 and 24 h, dams were terminally anesthetized by subcutaneous injection of 0.2 ml of Zoletil mixture (tiletamin/zolazepam, xylazin og fentanyl) and killed by exanguination by withdrawal of heart blood into Eppendorf tubes containing 36 ml K2EDTA (n=7-9 per exposure/time point). The uterus was excised and opened. Fetuses were excised from their embryonic sac, their viability confirmed, killed by decapitation, sexed by visual inspection, and their position in the uterus noted. From each litter, the first female fetus encountered in the right uterine horn, counting from the cervix, was selected and saved for analyses. The placenta was dissected into chorion and decidua by blunt/stump dissection under. From dams, the liver and right lung were dissected. Dissected organs were snap frozen in liquid nitrogen and kept at -80ºC. Fetal livers were dissected later. Maternal blood was centrifuged at 2000xg at 4°C for 5 min and plasma was stored in aliquots at -80°C until analysis. A maximum of one female fetus from each dam were used for any one outcome. RNA extraction: Total RNA was isolated from frozen maternal lung and liver, chorion, decidua and fetal liver. Briefly, 20 - 50 mg of tissue was homogenized with a blender in 700 ul lysis buffer with 7 ul mercapto-ethanol. RNA extraction was carried out utilizing magnetic beads technology, on a chemagic Prepito® (Perkin Elmer, Waltham, Massachusetts), as recommended by the manufacturer. Concentration and purity were measured on a NanoDrop1000 spectrophotometer, with all samples showing an A260/280 ratio between 1.9 and 2.1. RNA integrity was analyzed by 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 Pico Kit (Agilent Technologies) as recommended by manufacturer. All samples used for RNAseq displayed RNA integrity number (RIN) above 7. cDNA library construction and paired end sequencing was carried out by Novogene (Hongkong). To exclude ribosomal RNA, polyA selection was done.
Novogene paid service

treatment_protocol: Exposure: Lipopolysaccharide (LPS; E. Coli serotype 00:55 B5 LPS (Sigma Lot nr. 025M4040V)) was diluted to the final concentration (0.02 µg/µl) in double distilled pyrogen-free water (Chem-Lab, Zedelgem, Belgium). In the morning of GD 17, the pregnant mice were divided into control and LPS treatment groups, evenly distributing weights among the groups. Animals were placed in a whole-body inhalation chamber with an attached anaesthetic vaporizer  delivering 3-4% isoflurane in filtered air, and were intratracheally instilled with 50 µl of vehicle (control group) or 1 μg LPS in 50 µl vehicle, followed by 200μl of air. Vehicle and LPS were administered through a 0.58 mm polyethylene tube (Ref: 427411, Becton Dickinson, Brøndby, Denmark) attached to a plastic syringe. After instillation, animals were returned to their cage, briefly placed on heating pads and checked upon regularly until euthanization.

value: maternal lung

value: WT


title: KO_26w_ALF_5.ZT4

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
The expression data was adjusted for biological (sex) and technical (batch) effects using the Bioconductor package limma v3.44.1.
14413 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Genome_build: GRCm38, release 81
Supplementary_files_format_and_content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

molecule: total RNA

source_name: tibialis anterior muscle

extract_protocol:
After homogenization of tibialis anterior muscle with Qiazol reagent (Qiagen #1023537) RNA was isolated using miRNeasy Mini Kit (Qiagen #1038703). RNA quality was checked using Nanodrop and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
RNA-seq libraries were sequenced in paired-end mode with a read length of 150 base pairs with an average of 2 x 25 million reads for each sample at Berry Genomics (Illumina NovaSeq 6000).

treatment_protocol: Tibialis anterior muscle was collected and snap frozen with liquid nitrogen at six different time point intervals during 24hr period (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20).

tag: strain

value: female

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: 26 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

value: whole muscle


title: KO_26w_ALF_4.ZT0

value: male


title: maternal lung, LPS, 15.11 h, replicate 3

value: LPS


title: KO_26w_ALF_9.ZT8


title: Patient 11, mRNA-derived cDNA

city: OULLINS

first: Pierre

last: Sujobert

address: 165 Chemin du Grand Revoyet 1er eta, Faculte Medecine Lyon Sud BP12

country: France

institute: CIRI - Centre International de Recherche en Infectiologie

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
matrix column: Sample

data_processing:
BCL files were converted to FASTQ using CellRanger mkfastq (R1 : 26 base pairs, R2 : 150 base pairs). Raw FASTQ from gene expression libraries were aligned on the GRCh38 human genome and processed using CellRanger Count (10x Genomics Cell Ranger 4.0.0). HTO barcodes were retrieved using CITE-seq-Count and B cell immunoglobulin phenotype reconstruction was performed with CellRanger VDJ (10x genomics Cell Ranger 4.0.0).
Further processing was done with Seurat v4.
Assembly: GRCh38
Supplementary files format and content: Matrixcounts.csv.gz: Raw count matrix (assay "RNA"; slot "counts") from Seurat object (n= 14 samples)
Supplementary files format and content: metadata.csv: metadata file from Seurat object (n= 14 samples)
Supplementary files format and content: barcodes.xlsx: file to demultiplex raw datas

source_name: Lymph node

extract_protocol:
After enzymatic dissociation of the embryo; CFSE+ hCD45+ Live cells were sorted by flow cytometry
Libraries were prepared using Chromium Single Cell 5ʹ v1.1 protocol (10x Genomics).
mRNA libraries were prepared according to the manufacturer's instructions
HTO libraries were prepared according to the manufacturer's instructions. For each sample, the three conditions (before and after graft with RCHOP or vehicle treatment) were done and pooled in the same experiment with the TotalSeq -C listed above
BCR libraries were amplified accoring to 10X Genomics guidelines. 800 pg of amplified sequences was used with Nextera XT reagents (Illumina San Diego, California) to construct the final BCR library of each sample by PCR using i5 forward and Nextera XT i7 reverse primers.
The three libraries were quantified using the Library Quantification Sample Kit Kapa (Illumina-Uni San Diego, California)
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% HTO library and 10% BCR library before sequencing.

value: Lymph node

tag: cell type

value: Immune cells

tag: library type

value: mRNA

tag: antibodies/tags


title: Sample 05-52-L004 [snRNA-seq]

value: brain (frontal cortex)

value: Female


title: maternal lung, H2O, 15.11 h, replicate 3


title: KO_26w_ALF_3.ZT0


title: Patient 10, BCR-derived cDNA

description:
5' BCR library: read1 file contains cell barcode and UMI; read2 file contains V(D)J transcript
matrix column: V / D / J / C Light_Heavy

value: BCR


title: maternal lung, LPS, 5.11 h, replicate 9


title: Sample 05-27-L003 [snRNA-seq]

value: AD

value: APOE 4/4

value: ad apoe 44


title: KO_26w_ALF_2.ZT0


title: Sample 04-44-L004 [snRNA-seq]

value: APOE 3/3

value: Male

value: ad apoe 33


title: KO_26w_ALF_1.ZT0

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: 26 weeks


title: Patient 10, mRNA-derived cDNA


title: Sample 04-44-L003 [snRNA-seq]


title: maternal lung, H2O, 5.11 h, replicate 9

value: maternal lung

value: WT


title: KO_10w_ALF_24.ZT20

value: female

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: Sample 04-44-L002 [snRNA-seq]

value: brain (frontal cortex)


title: Patient 7, BCR-derived cDNA

value: Lymph node

value: Immune cells


title: Patient 7, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
matrix column: Condition

library_source: other

molecule: protein

value: HTO

value: TotalSeq™-C0254; pre-graft / TotalSeq™-C0252; Vehicle / TotalSeq™-C0253; RCHOP


title: maternal lung, H2O, 15.11 h, replicate 2


title: KO_10w_ALF_23.ZT20


title: KO_10w_ALF_22.ZT20

value: male


title: Patient 11, HTO-derived cDNA

value: TotalSeq™-C0252; pre-graft / TotalSeq™-C0254; Vehicle / TotalSeq™-C0253; RCHOP


title: Patient 7, mRNA-derived cDNA

value: mRNA


title: maternal lung, LPS, 15.11 h, replicate 1

value: LPS


title: maternal lung, H2O, 15.11 h, replicate 1


title: KO_10w_ALF_21.ZT20

value: Bmal1(stopFL/stopFL), Cre(-/-)


title: Patient 5, BCR-derived cDNA

value: BCR


title: Sample 04-44-L001 [snRNA-seq]

value: AD

value: APOE 3/3

value: Male

value: ad apoe 33


title: Sample 04-06-L003 [snRNA-seq]

value: APOE 4/4

value: ad apoe 44


title: Sample 03-54-L004 [snRNA-seq]

value: brain (frontal cortex)


title: KO_10w_ALF_20.ZT16

value: female

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: Patient 10, HTO-derived cDNA

value: Lymph node

value: Immune cells

value: HTO


title: maternal lung, TiO2, 5.11 h, replicate 2

value: maternal lung

value: WT


title: KO_10w_ALF_19.ZT16

value: Bmal1(stopFL/stopFL), Cre(-/-)


title: maternal lung, TiO2, 5.11 h, replicate 1


title: Sample 03-54-L003 [snRNA-seq]

value: AD


title: Patient 5, mRNA-derived cDNA

value: mRNA


title: maternal lung, LPS, 15.11 h, replicate 2

value: LPS


title: Sample 03-54-L002 [snRNA-seq]

value: Male


title: Patient 5, HTO-derived cDNA

value: TotalSeq™-C0254; pre-graft / TotalSeq™-C0253; Vehicle / TotalSeq™-C0252; RCHOP


title: KO_10w_ALF_18.ZT16

value: male


title: Sample 03-54-L001 [snRNA-seq]

value: brain (frontal cortex)

value: APOE 4/4

value: ad apoe 44


title: KO_10w_ALF_17.ZT16

value: 10-12 weeks

value: ad libitum


title: Patient 4, HTO-derived cDNA

value: Lymph node

value: TotalSeq™-C0252; pre-graft / TotalSeq™-C0253; Vehicle / TotalSeq™-C0251; RCHOP


title: Patient 4, BCR-derived cDNA

value: Immune cells

value: BCR


title: maternal lung, LPS, 5.11 h, replicate 7

value: maternal lung

value: WT


title: maternal lung, LPS, 5.11 h, replicate 8


title: KO_10w_ALF_15.ZT12

value: female

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: whole muscle


title: Patient 23, BCR-derived cDNA


title: maternal lung, H2O, 5.11 h, replicate 7


title: A2780 cells, si-PART1_2

city: Jinan, Shandong

first: Huan

last: Wu

state: Asia

address: 107 West Wenhua Road

department: Obstetrics and Gynecology

country: China

institute: Qilu Hospital

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: File format: Tab-delimited text file. Content: Raw counts and FPKM values for each sample.

growth_protocol: A2780 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: A2780 cells were transfected with siRNAs (si-NC or si-PART1) using lipo2000 reagent according to the manufacturer's protocol. After that, cells were maintained in 1640 supplemented with 10% FBS for 48 hours before RNA extraction.

tag: cell line

value: Ovarian endometrioid adenocarcinoma cells

value: PART1 knockdown


title: A2780 cells, si-PART1_1


title: Patient 4, mRNA-derived cDNA

value: mRNA


title: maternal lung, LPS, 5.11 h, replicate 6

value: LPS


title: Patient 23, HTO-derived cDNA

value: HTO

value: TotalSeq™-C0251; pre-graft / TotalSeq™-C0252; Vehicle / TotalSeq™-C0253; RCHOP


title: maternal lung, H2O, 5.11 h, replicate 6


title: KO_10w_ALF_14.ZT12

value: male

value: 10-12 weeks


title: KO_10w_ALF_13.ZT12

value: ad libitum


title: A2780 cells, si-NC_3

value: Negative control siRNA


title: Patient 23, mRNA-derived cDNA

value: Lymph node

value: Immune cells


title: maternal lung, LPS, 5.11 h, replicate 5

value: maternal lung


title: A2780 cells, si-NC_1


title: KO_10w_ALF_12.ZT8


title: Patient 3, BCR-derived cDNA

value: BCR


title: maternal lung, H2O, 5.11 h, replicate 8

value: WT


title: maternal lung, H2O, 5.11 h, replicate 5


title: A2780 cells, si-PART1_3


title: KO_10w_ALF_11.ZT8

value: female

value: Bmal1(stopFL/stopFL), Cre(-/-)


title: Patient 3, HTO-derived cDNA

value: TotalSeq™-C0253; pre-graft / TotalSeq™-C0251; Vehicle / TotalSeq™-C0252; RCHOP


title: KO_10w_ALF_16.ZT12

value: whole muscle


title: maternal lung, LPS, 5.11 h, replicate 4


title: KO_10w_ALF_9.ZT8


title: Primary FPD-MM 18 HHT scRNA Seq

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Patient-derived AML cells

growth_protocol: Patient-derived AML cells were cultured in 20% FBS-containing RPMI media.

extract_protocol:
Frozen patient derived AML BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 2 minutes until partially thawed and immediately transferred to a 50 mL conical tube with 1ml of prewarmed media (RPMI1640 supplemented with 10% FBS) and centrifuged (300 g for 5 min). Cells were sequentially diluted 1:1 3 times with prewarmed RPMI containing 10% FBS. Cells were centrifuged at 300 x g for 5 minutes in a swinging bucket centrifuge. After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 1 mL of 2% FBS/PBS, centrifuged at 300 x g for 5 minutes and resuspended in 900 uL of 2% FBS/PBS. To removed dead cells and debris, cells were passed through a 40 micron Flow-mi strainer and the cell concentration of the concentrated cell stock was determined with a Countess counting device.  The desired number of targeted cells (5000-10,000) from the concentrated cell stock were separated on the 10X Chromium Controller.
scRNA Seq libraries were constructed following the 10X Genomics protocol for single cell RNA Seq analysis.

treatment_protocol: PD AML cells were treated with homoharringtonine (100 nM) for 16 hrs at 37°C and cryopreserved in 90% FBS, 10% DMSO until nuclei isolation for multiomics (sc-ATAC + sc-RNA) analysis

value: Patient-derived AML cells

value: Lymphocytes

value: germline mtRunx1

value: 100 nM homoharringtonine


title: Primary FPD-MM 18 Ctrl scRNA Seq

value: Control


title: Patient 3, mRNA-derived cDNA

value: mRNA


title: maternal lung, H2O, 5.11 h, replicate 4


title: maternal lung, LPS, 5.11 h, replicate 3

value: LPS


title: Primary FPD-MM 17 MB 1 [ATAC-seq]

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

growth_protocol: GMR-AML1 cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Bulk ATAC-Seq analysis was performed following the protocol of Buenrostro et al 2015. Tn5 transposase-tagmented genomic DNA was utilized to make libraries for next generation sequencing.
Bulk ATAC Sequencing Libraries were constructed following standard Illumina protocols for paired-end sample indexing with I7 and I5 sequencing indices.

treatment_protocol: AML cells were treated with homoharringtonine (100 nM) for 16 hours or mebendazole (1000 nM) for 24 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.

value: Germline mtRunx1

value: 1000 nM mebendazole


title: Patient 2, BCR-derived cDNA

value: Lymph node

value: Immune cells


title: A2780 cells, si-NC_2

value: Ovarian endometrioid adenocarcinoma cells

value: Negative control siRNA


title: KO_10w_ALF_8.ZT4

value: female

value: 10-12 weeks

value: ad libitum


title: Patient 1, BCR-derived cDNA

value: BCR


title: maternal lung, H2O, 5.11 h, replicate 2

value: maternal lung

value: WT


title: maternal lung, H2O, 5.11 h, replicate 3


title: Patient 2, HTO-derived cDNA

value: HTO

value: TotalSeq™-C0252; pre-graft / TotalSeq™-C0253; Vehicle / TotalSeq™-C0251; RCHOP


title: Primary FPD-MM 17 MB 2 [ATAC-seq]

value: Patient-derived AML cells

value: Lymphocytes


title: maternal lung, LPS, 5.11 h, replicate 2

value: LPS


title: KO_10w_ALF_3.ZT0

value: male

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: whole muscle


title: maternal lung, H2O, 5.11 h, replicate 1


title: Patient 2, mRNA-derived cDNA

value: Lymph node

value: Immune cells

value: mRNA


title: KO_10w_ALF_6.ZT4

value: female


title: KO_10w_ALF_7.ZT4

value: 10-12 weeks


title: Primary FPD-MM 17 Ctrl 2 [ATAC-seq]

value: Germline mtRunx1

value: Control


title: Sample_9_18_CO

city: shanghai

first: zhicheng

last: shao

address: dongan road 130

institute: fudan

description:
Sample 11 as control
Sample 11

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

source_name: astrocyte

growth_protocol: astrocyte was eltrotransfected with OCT4/shp53 factors and growth in neurobasal with B27,BDNF,GDNF,Vc

extract_protocol:
astrocyte was treat by CHIR99021,SB431542,RepSox, Y27632 cocktail and DMSO and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: astrocyte was eltrotransfected with OCT4/shp53 factors and then treat with DMSO and CHIR99021,SB431542,RepSox, Y27632 cocktail for 5 days in neurobasal medium

value: brain

value: astrocyte direct reprogramming into cortical organoid

tag: disease state

value: normal


title: KO_10w_ALF_4.ZT0

value: ad libitum


title: Primary FPD-MM 17 Ctrl 1 [ATAC-seq]

value: Patient-derived AML cells


title: Patient 1, HTO-derived cDNA

value: HTO

value: TotalSeq™-C0251; pre-graft / TotalSeq™-C0252; Vehicle / TotalSeq™-C0253; RCHOP


title: GMR-AML1 HHT 2 [ATAC-seq]

value: Lymphocytes

value: 100 nM homoharringtonine


title: KO_10w_ALF_5.ZT4

value: male

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: whole muscle


title: maternal lung, LPS, 5.11 h, replicate 1

value: maternal lung

value: WT

value: LPS


title: Male - statin - 2

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-seq alignment was performed with STAR v2.4.1a to the mouse genome GRCm38.97.
The read-count per gene was quantified with HTSeq and Ensembl Mus_musculus.GRCm38.97 GTF file.
Differential gene analysis was performed with EdgeR (v3.28.1) with trimmed mean of M values (TMM) normalization. Significance was denoted as p value<0.05 and fold change>1.25.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: CPM_file.csv, this processed data file contains counts per million (CPM) for all 12 samples for all mapped genes.
Supplementary_files_format_and_content: EdgeR_TMM-norm-counts_filtered.csv, this processed data file contains the EdgeR processed counts for all 12 samples, which are TMM normalized and filtered to remove low expression genes.

source_name: Liver

extract_protocol:
Liver tissue was homogenized in trizol and RNA was isolated.
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

value: 0.1g Simvastatin per kg body weight in chow diet (Research Diets D11060903i)

value: Male

value: liver


title: GMR-AML1 Ctrl 1 [ATAC-seq]

value: Germline mtRunx1

value: Control


title: Patient 1, mRNA-derived cDNA

value: Lymph node

value: Immune cells

value: mRNA


title: Primary FPD-MM [ATAC-seq]

value: Patient-derived AML cells


title: Male - statin - 3


title: GMR-AML1 Ctrl 2 [ATAC-seq]

value: Lymphocytes


title: Sample_9_18_SP

description:
Sample 12 as treatment vs Sample 11
Sample 12

value: brain

value: astrocyte direct reprogramming into spinal cord organoid

value: normal


title: GMR-AML1 HHT 1 [ATAC-seq]

value: 100 nM homoharringtonine


title: KO_10w_ALF_1.ZT0

value: female

value: Bmal1(stopFL/stopFL), Cre(-/-)

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: RE-RE_26w_ALF_24.ZT20

value: 26 weeks


title: Male - statin - 1

value: 0.1g Simvastatin per kg body weight in chow diet (Research Diets D11060903i)

value: Male

value: liver


title: Sample_8_8CO

description:
Sample 9 as control
Sample 9

value: astrocyte direct reprogramming into cortical organoid


title: Primary FPD [ATAC-seq]

value: Germline mtRunx1

value: Control


title: Sample_8_8SP

description:
Sample 10 as treatment vs Sample 9
Sample 10


title: RE-RE_26w_ALF_22.ZT20

value: male


title: Female - statin - 3

value: Female


title: KO_10w_ALF_2.ZT0


title: Primary FPD-MM 17 HHT 1

description:
KBr_290_Ctrl_HHT_100_8h_Rep1
KBr_290_Ctrl_HHT_100_8h_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with homoharringtonine (100 nM) for 8/16 hours or mebendazole (1000 nM) for 16/24 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: Patient-derived AML cells

value: Lymphocytes


title: Primary FPD-MM 17 Ctrl 1

description:
KBr_290_Ctrl_16h_Rep1
KBr_290_Ctrl_16h_1


title: Male - chow diet - 2

value: Chow diet (Research Diets D11060903i)


title: RE-RE_26w_ALF_19.ZT16


title: Sample_8_5SP

description:
Sample 8 as treatment vs Sample 7
Sample 8

value: brain

value: astrocyte direct reprogramming into spinal cord organoid

value: normal


title: RE-RE_26w_ALF_21.ZT20

value: female

value: ad libitum


title: Female - statin - 2


title: Sample_8_5CO

description:
Sample 7 as control
Sample 7


title: Sample_SM_3

description:
Sample 6 as treatment vs Sample 3
Sample 6

value: CHIR99021,SB431542,RepSox and Y27632 cocktail treat 5 days


title: Male - chow diet - 1


title: RE-RE_26w_ALF_20.ZT16

value: 26 weeks

value: whole muscle


title: Primary FPD-MM 17 Ctrl 2

description:
KBr_290_Ctrl_16h_Rep2
KBr_290_Ctrl_16h_2


title: RE-RE_26w_ALF_23.ZT20


title: Male - chow diet - 3

value: Male

value: liver


title: RE-RE_26w_ALF_18.ZT16


title: Sample_CON_3

description:
Sample 3 as control
Sample 3

value: DMSO treat 5 days


title: Primary FPD-MM 18 MB 1

description:
KBr_FPD089_1000MB_24h_Rep1
KBr_FPD089_1000_MB_24h_1

value: Germline mtRunx1

value: 1000 nM mebendazole


title: Female - chow diet - 3

value: Female


title: Sample_SM_1

description:
Sample 4 as treatment vs Sample 1
Sample 4

value: CHIR99021,SB431542,RepSox and Y27632 cocktail  treat 5 days


title: Primary FPD-MM 17 HHT 2

description:
KBr_290_Ctrl_HHT_100_8h_Rep2
KBr_290_Ctrl_HHT_100_8h_2

value: Patient-derived AML cells

value: Lymphocytes

value: 100 nM homoharringtonine


title: Primary FPD-MM 18 MB 2

description:
KBr_FPD089_1000MB_24h_Rep2
KBr_FPD089_1000_MB_24h_2


title: Female - statin - 1

value: 0.1g Simvastatin per kg body weight in chow diet (Research Diets D11060903i)


title: Sample_CON_2

description:
Sample 2 as control
Sample 2

value: brain

value: normal


title: RE-RE_26w_ALF_16.ZT12

value: male

value: ad libitum


title: RE-RE_26w_ALF_17.ZT16

value: 26 weeks


title: Sample_SM_2

description:
Sample 5 as treatment vs Sample 2
Sample 5


title: Primary FPD-MM 18 HHT 2

description:
KBr_FPD089_100HHT_16h_Rep2
KBr_FPD089_100_HHT_16h_2


title: Sample_CON_1

description:
Sample 1 as control
Sample 1


title: RE-RE_26w_ALF_15.ZT12

value: female

value: whole muscle


title: Female - chow diet - 1

value: Chow diet (Research Diets D11060903i)

value: liver


title: RE-RE_26w_ALF_14.ZT12


title: Primary FPD-MM 18 Ctrl 2

description:
KBr_FPD089_Ctrl_Rep2
KBr_FPD089_Ctrl_2_RNA

value: Germline mtRunx1

value: Control


title: RE-RE_26w_ALF_13.ZT12


title: WT_Female_5

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
We aligned the reads to the zebrafish reference genome (GRCz10) using RapMap which utilizes the pseudoaligner kallisto
Assembly: GRCz10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: Kidney

extract_protocol:
RNA was harvested using trizol according to manufacturers instructions
RNA libraries for RNA-seq were prepared using  TruSeq RNA Sample Prep Kit version 2 (Illumina) according to manufacturs instructions

value: Kidney

value: WT

value: Female


title: Primary FPD-MM 18 Ctrl 1

description:
KBr_FPD089_Ctrl_Rep1
KBr_FPD089_Ctrl_1_RNA

value: Patient-derived AML cells

value: Lymphocytes


title: 20200706_Allograft_2

city: Chicago

first: Ankit

last: Bharat

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

data_processing:
Initial data processing was performed using the Cell Ranger version 2.0 pipeline (10x Genomics), reads were mapped to mm10 version of the mouse genome, Ensemble build 84.
Downstream single cell RNA-seq analysis was performed using Seurat Package version 3.1.0 following the standard workflow posted on Satija lab website (https://satijalab.org/seurat/) . Specifically, SCTransform with an anchor-based integration approach was used to integrate 4 different samples from two conditions.
Cell types were identified using both manual annotations based on positive markers from FindAllMarkers function in Seruat pipeline and a supervised annotation tool, SingleR .
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Single-cell suspensions from naïve and 24 hours after transplantation mouse lung were prepared as described above for flow cytometry with slight modifications. Allograft was removed and digested with 3 mL dispase (Corning) with DNase I (Sigma), and gently teased using forceps into small (1-2 mm) fragments followed by incubation at room temperature with gentle agitation for 30 minutes. The resulting suspension (in DMEM + 5% FBS) was passed through 70 μm cell strainer, erythrocytes were lysed  andlysed and filtered through 40 μm cell strainers. Cells were counted using AO/PI and Cellometer K2 (Nexcelom), and cell viability exceeded 90%.
Single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell V2 Reagent Kit and Controller (10x Genomics).
Libraries were assessed for quality (TapeStation 4200, Agilent) and then sequenced on NextSeq 500 or HiSeq 4000 instruments.

value: Lung

value: 10 weeks

value: left lung syngeneic transplantation


title: Primary FPD-MM 18 HHT 1

description:
KBr_FPD089_100HHT_16h_Rep1
KBr_FPD089_100_HHT_16h_1

value: 100 nM homoharringtonine


title: 20200706_Allograft_1


title: RE-RE_26w_ALF_12.ZT8

value: male

value: ad libitum


title: WT_Female_4


title: 20200706_Control_2

value: no treatment


title: GMR-AML1 MB 2

description:
KBr_141_Mebend_1000_16hr_Rep2
KBr_141_Mebend_1000_16hr_3

value: 1000 nM mebendazole


title: RE-RE_26w_ALF_11.ZT8

value: 26 weeks

value: whole muscle


title: WT_Female_2


title: GMR-AML1 MB 1

description:
KBr_141_Mebend_1000_16hr_Rep1
KBr_141_Mebend_1000_16hr_1

value: Germline mtRunx1


title: 20200706_Control_1


title: Female - chow diet - 2

value: Chow diet (Research Diets D11060903i)

value: liver


title: WT_Female_1

value: Kidney

value: WT


title: GMR-AML1 Ctrl 4

description:
KBr_141_16hr_Rep2
KBr_141_16hr_3

value: Patient-derived AML cells

value: Control


title: RE-RE_26w_ALF_9.ZT8

value: female


title: GMR-AML1 Ctrl 3

description:
KBr_141_16hr_Rep1
KBr_141_16hr_1

value: Lymphocytes


title: RE-RE_26w_ALF_8.ZT4


title: JM8.N4_C59_Smc3_ChIPSeq

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Homozygote cell line with endogenously tagged CTCF and Rad21 loci

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
Reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g mm --nomodel --extsize 250
bigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 250 --ignoreDuplicates
Genome_build: mm10
Supplementary_files_format_and_content: .bed files containing ChIP-Seq peak genomic coordinates (mm10), length, summit, pileup, pvalue, qvalue and fold enrichment over input as determined by MACS2
Supplementary_files_format_and_content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice.  During the incubation, the lysates were repeatedly pipetted up and down every 5 minutes. Lysates were then centrifuged for 10 min at 4000 rpm.  Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 50 cycles of 30" on and 30" off).  Sonicated lysates were cleared by centrifugation and 400-1600 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 8-16 μg of normal rabbit IgGs, anti-Rad21 or anti-CTCF antibodies.  About 15% of the precleared chromatin was saved as input.  Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 60 μl of water and analyzed by qPCR together with 2% of the input chromatin prior to ChIP-Seq library preparation.
ChIP-seq libraries were prepared using the Illumina TruSeq™ DNA sample preparation kit according to manufacturer instructions with few modifications. We used 100 ng of ChIP input DNA (as measured by Fragment analyzer™) and 50 μl of immunoprecipitated DNA as a starting material; library samples were enriched through 12 cycles of PCR amplification. We assessed library quality and fragment size by qPCR and Fragment analyzer™. We sequenced 7 multiplexed libraries per lane on the Illumina HiSeq4000 sequencing platform (single end-reads, 50 bp long) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.

treatment_protocol: Cells were cross-linked for 5 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final).

value: FLAG-Halo-CTCF/Rad21-SNAPf-V5 Knock-in

tag: chip antibody

value: Smc3 (Bethyl A300-060A)


title: WT_Male 2

value: Male


title: WT_Male 3


title: RE-RE_26w_ALF_7.ZT4

value: ad libitum


title: RE-RE_26w_ALF_6.ZT4

value: male


title: JM8.N4_C59_IgG_ChIPSeq

value: Rabbit normal IgG (Jackson ImmunoResearch 011-000-002)


title: JM8.N4_C59_CTCF_ChIPSeq

value: CTCF (Abcam ab128873)


title: WT_Female_3

value: Female


title: RE-RE_26w_ALF_5.ZT4

value: 26 weeks

value: whole muscle


title: JM8.N4_C59_Smc1a_ChIPSeq

value: Smc1a (Bethyl A300-055A)


title: pool of 10 embryos, Low glucose + BHB, replicat 3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

data_processing:
Raw fastq files were trimmed using fastp (with the option -w 4) then mapped to the reference genome (Bt.Ensembl105) using Kallisto.
Raw count and differential expression analysis were done using the R library DESeq2.
Assembly: bostau9
Supplementary files format and content: xlsx file containing the results of differential expression analysis between CTL vs BHB
Supplementary files format and content: xlsx file containing the results of differential expression analysis between CTL vs LG
Supplementary files format and content: xlsx file containing the results of differential expression analysis between LG vs BHB

organism: Bos taurus

source_name: 8-days blastocystes

growth_protocol: The embryos are incubated in SOF#1 until day 4. On the day 4 of development, the embryos are transferred to in drops of SOF #2 (5mL SOF Base, 0.8% BSA FAF fraction V tested (A-6003), 1X non-essential amino acids, 10uM EDTA, 1mM L-Glutamine, 0.33mM pyruvate, 0,10mM gentamicin), in which they are incubated (5% CO2, 20% O2, 100% H2O) until day 8. The embryos are divided in groups of 20-30 for each 50ul drop of SOF#2. At fay 8, embryos are washed twice in a small dish containing veterinary PBS (no calcium or magnesium) and are retrieved in 0,5mL sterile tubes with a minimal amount of PBS. They are then stored in -80C until RNA extraction,

extract_protocol:
RNA was harvested using Simultaneous Purification of Genomic DNA and total RNA from Animal and Human Cells from the AllPrep DNA/RNA Micro Handbook (QIAGEN, USA). Each 9 samples consist of a pool of 9 to 11 embryos.
Enrichement of mRNA was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs, USA) and libraries were prepared using the NEBNext Ultra II RNA Library kit for Illumina (E7770, E7775, New England Biolabs, USA).

treatment_protocol:
cumulus-oocyte complexes (COCs) were divided in 50ul drops of maturation medium in groups of 10 COCs (4.5mL TCM 199 Gibco 11150-059 with 100ul/mL FBS, 40mM pyruvate, 50mg/mL gentamicin, 0,5ug FSH and 1ul/mL estradiol) between our three treatments, one control with a standard glucose concentration (5.5mM), one low glucose concentration (2.75mM) and one with low glucose concentration (2,75mM) with a supplement of BHB (1.8mM) and finally the drops are covered with mineral oil (M8410 Sigma mineral oil, SOF-BSA). The maturation medium is prepared at least 4 hours in advance and balanced in the incubator (5% CO2, 20% O2, 100% H2O) where the COCs are incubated for 24 hours.
IVF was performed using the three groups of COCs and embryos developded in the same conditions (see growth protocol)

value: 8-days blastocystes

value: Low Glucose + BHB


title: WT_Male 1

value: Kidney

value: WT


title: GMR-AML1 Ctrl 2

description:
KBr_141_8hr_Rep2
KBr_141_8hr_2

value: Patient-derived AML cells

value: Germline mtRunx1

value: Control


title: RE-RE_26w_ALF_4.ZT0


title: JM8.N4_C59_input

value: FLAG-Halo-CTCF/Rad21-SNAPf-V5 Knock-in


title: RE-RE_26w_ALF_10.ZT8

value: female


title: JM8.N4_WT_Smc3_ChIPSeq

value: wild type

value: Smc3 (Bethyl A300-060A)


title: pool of 10 embryos, Low glucose + BHB, replicat 2


title: FPD-MM (2019)

description:
KBr_FPDMM_MI_2019
KBr_FPDMM_MI_2019

value: Lymphocytes


title: JM8.N4_WT_Smc1a_ChIPSeq


title: GMR-AML1 Ctrl 1

description:
KBr_141_8hr_Rep1
KBr_141_8hr_1


title: RE-RE_26w_ALF_3.ZT0

value: ad libitum


title: pool of 10 embryos, Low glucose + BHB, replicat 1


title: WT_Male 4

value: Male


title: FPD (2015)

description:
KBr_873412_2015
KBr_873412_2015


title: GMR-AML1 HHT 2

description:
KBr_141_HHT_100_8hr_Rep2
KBr_141_HHT_100_8hr_3

value: 100 nM homoharringtonine


title: GMR-AML1 HHT 1

description:
KBr_141_HHT_100_8hr_Rep1
KBr_141_HHT_100_8hr_1


title: RE-RE_26w_ALF_2.ZT0

value: male

value: 26 weeks

value: whole muscle


title: pool of 9 embryos, Low glucose, replicat 3

value: 8-days blastocystes

value: Low Glucose


title: JM8.N4_WT_CTCF_ChIPSeq

value: CTCF (Abcam ab128873)


title: RE-RE_26w_ALF_1.ZT0


title: GMR-AML1, H3K27Ac ChIP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing. DNA fragments were PCR amplified for 12 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: 1 x 10^7 Human GMR-AML1 cells  were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analysis.

value: Patient-derived AML cells


title: pool of 11 embryos, Low glucose, replicat 2


title: JM8.N4_WT_IgG_ChIPSeq

value: Rabbit gamma globulin (Jackson ImmunoResearch 011-000-002)


title: RE-RE_10w_ALF_24.ZT20

value: 10-12 weeks


title: GMR-AML1, H3K27Ac Input

value: Germline mtRunx1


title: pool of 9 embryos, Low glucose, replicat 1


title: JM8.N4_WT_input


title: pool of 11 embryos, Control, replicat 3

value: Control


title: RE-RE_10w_ALF_22.ZT20

value: female


title: Random, rep3

city: Hangzhou

first: Xueying

last: Liu

address: No. 150 Dongfang Road, Qiantang District

institute: Hangzhou lnstitute of Medicine Chinese Academy of Sciences

description:
scramble
Random-3

data_processing:
The reference genome sequences were indexed using Hisat2 (v2.0.1), and the clean data were aligned to the reference genome using the same software.
The known gff annotation files were converted into transcripts in fasta format and indexed appropriately.
With the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw counts and FPKM values for each sample.

growth_protocol: Human colon cancer cell line HCT116 (15K cells/well) was cultured in RPMI 1640 (YESEN, 41402ES76) with 10% FBS (Sunrise, SR100180.03) and 1% penicillin/streptomycin (Biosharp) and incubated in a 5% CO2 incubator at 37 ℃.

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
Library construction and sequencing were conducted by GENEWIZ (GENEWIZ Biotechnology Co., Ltd, Suzhou, China) on an Illumina HiSeq instrument with a 2x150 paired-end (PE) configuration, in accordance with the manufacturer's instructions.

treatment_protocol: The HCT116 cells were subjected to treatment with SCAF4_F3_11nt aptamers or NC at a final concentration of 1 µM for 24 hours, followed by collection for Bulk RNA-sequencing.

value: Random


title: RE-RE_10w_ALF_23.ZT20


title: pool of 10 embryos, Control, replicat 2


title: pool of 10 embryos, Control, replicat 1


title: RE-RE_10w_ALF_21.ZT20


title: RE-RE_10w_ALF_20.ZT16


title: 43-O-1, rep3

description:
11nt
43-O-3


title: HCC38 siGRHL2 RNA

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
The row reads were trimmed to remove adaptor sequences using Skewer (v0.2.2).
The reads were mapped to the hg38 genome using STAR (v.2.7.8a).
The mapped reads were then counted using featureCounts (v.2.0.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA-seq libraries were prepared with 10 ng of total RNA using a SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara)

value: cell line

value: breast cancer


title: 43-O-1, rep2

description:
11nt
43-O-2


title: RE-RE_10w_ALF_19.ZT16

value: ad libitum


title: HCC38 siCtrl RNA

value: siCtrl


title: FPD (2014)

description:
KBr_807475_2014
KBr_807475_2014

value: Lymphocytes


title: HiC_DLD1-IAA4d

city: Worcester

first: Nezar

last: Abdennur

state: MA

address: 368 Plantation Street

department: Genomics and Computational Biology

institute: UMass Chan Medical School

data_processing:
Hi-C libraries were processed using the distiller pipeline (https://github. com/open2c/distiller-nf).
Briefly, Hi-C sequencing reads were mapped to the hg38 assembly using bwa mem, and alignments were processed, deduplicated and classified into contact pairs using pairtools (https://github.com/open2c/pairtools).
Hi-C pairs were aggregated into multiresolution contact matrices, filtered and normalized by iterative correction using the cooler package.
Genome browser plots were generated using HiGlass and coolbox. Contact frequency vs distance profiles were calculated using cooltools.
Spectral clustering and analysis were performed on Hi-C from untreated NADNMT1 cells using the inspectro package as described in (Spracklin et al., 2023) applied to the first 10 eigenvectors of the contact matrix at 50kb resolution. We compared the results of k-means with several functional and epigenomic tracks, including H3K9me3 and DNAme (this study), H3K27me3 and RNA-seq (Rokavec et al., 2017), as well as GC content and distance from centromere. Based on cluster metrics and interpretability, we selected k=9 clusters and combined two pairs and one triple of clusters whose functional profiles were largely similar but differed in overall proximity to the centromere to yield 5 IPGs. Comparison of IPGs with labels from SNIPER was generated using bioframe. Summaries of IPG-level observed/expected contact frequency were generated using cooltools.
Assembly: hg38
Supplementary files format and content: mcool

growth_protocol: Cells were cultured at 37 °C in a 5% CO2 atmosphere. DLD-1  cells were maintained in DMEM-GlutaMAX media, supplemented with 10% fetal bovine serum, 100 U/mL penicillin-streptomycin, 0.13% sodium bicarbonate (RPE-1).

extract_protocol:
Hi-C assays were performed with an Arima Hi-C plus kit (Arima Genomics #A510008) according to manufacturer's Instructions starting from 2*106 cells/reaction.
ibraries preparation were performed with a Kapa Hyper Prep Kits with KAPA Library Amplification Primer Mix (Roche, 07962347001), quantified by Qubit (Invitrogen), checked on a Tapestation device (Agilent) and Pair-End sequenced on a NovaSeq platform (Illumina).

treatment_protocol: Auxin indole-3-acetic acid sodium salt (IAA) (I5148, Sigma-Aldric) was used at 500 nM dissolved in water. 2'-deoxy-5-azacytidine (DAC) (A3656, Sigma-Aldrich) was used at 2.5 µM for 96h. GSK-3685032 (HY-139664, MedChemExpress) was used at the indicated time and concentrations. All cell lines were tested negative for mycoplasma contamination. IAA washout was performed by five gentle washes in PBS. Cells were then analyzed at the indicated time points.

value: colorectal adenocarcinoma cell line

value: Auxin 4 days


title: HiC_DLD1-IAA4d-WO4d

value: Auxin 4 days, Washout 4 days


title: HiC_3BKO-NT


title: HiC_3BKO-IAA4d

value: DNMT1-AID;DNMT3b -/-


title: HiC_DLD1-NT


title: RE-RE_10w_ALF_18.ZT16

value: whole muscle


title: Random, rep2

description:
scramble
Random-2


title: RE-RE_10w_ALF_17.ZT16


title: T47D siGRHL2 RNA


title: SCM-3 Donor 3

city: Mountain View

first: Tesfahun

middle: Dessale

last: Admasu

address: 110 pioneer way, ste. j

department: ApoptoSens

institute: SENS Research Foundation

description:
SCM-3
DPP4+ cells isolated
D3SCM3

data_processing:
 After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
 The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
 BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Donor 3

growth_protocol: Cells were mentained with promo cell basal medium MV2 (C-22221) supplemented with Growth Medium MV 2 SupplementPack (C-39221).

extract_protocol:
Cells were collected and RNA was extracted using commercially available kits Quick-RNA Miniprep Kit (Zymo Research, R1055) according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary senescent cells were treated with doxorubicin for 24hrs and secondary senescent cells were treated with conditioned medium collected from doxorubicin treated cells.

value: Endothelial cells

value: Vein

value: wild type

value: Primary Endothelial cells

value: Senescent conditioned medium


title: HiC_3BKO-IAA10d

value: Auxin 10 days


title: T47D siFOXA1 RNA


title: Random, rep1

description:
scramble
Random-1

value: Random


title: RE-RE_10w_ALF_16.ZT12

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
The expression data was adjusted for biological (sex) and technical (batch) effects using the Bioconductor package limma v3.44.1.
14413 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Genome_build: GRCm38, release 81
Supplementary_files_format_and_content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

extract_protocol:
After homogenization of tibialis anterior muscle with Qiazol reagent (Qiagen #1023537) RNA was isolated using miRNeasy Mini Kit (Qiagen #1038703). RNA quality was checked using Nanodrop and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
RNA-seq libraries were sequenced in paired-end mode with a read length of 150 base pairs with an average of 2 x 25 million reads for each sample at Berry Genomics (Illumina NovaSeq 6000).

value: male

value: 10-12 weeks


title: SCM-2 Donor 3

description:
SCM-2
DPP4+ cells isolated
D3SCM2


title: ChIP_DLD1-NT_Input

data_processing:
ChIP-seq data, including data from (Rokavec et al., 2017) were processed following the steps of the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with slight modifications using a simplified custom snakemake workflow as described in (Spracklin et al., 2023).
Reads were mapped to hg38 using bwa mem (Li, 2013).
Alignment files (BAM format) were filtered for quality and duplicates using samtools (Li et al., 2009).
Cross-correlation analysis and fragment length estimation for single-ended datasets was performed using the phantompeakqualtools package (Landt et al., 2012).
Signal track (target over input) generation was performed using MACS2 (Y. Zhang et al., 2008).
ChIP-seq tracks were compared by aggregating bigwig signal at 10-kb resolution using pybbi and generating density scatter plots using the matplotlib extension for datashader.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ChIP assays were carried out as described previously (Scelfo et al., 2019). Briefly, 1% formaldehyde cross-linked chromatin was sonicated to an average size of 300–600 bp and quantified.
100 μg of sonicated chromatin was incubated overnight at 4°C with 2 μg of the indicated antibodies, and recovered by Sepharose protein A beads. DNA from washed beads was column-purified, quantified using the Qubit dsDNA HS, and used for library preparation with KAPA UDI Primer Mixes Kit.


title: HiC_DLD1-IAA10d


title: RE-RE_10w_ALF_15.ZT12

value: ad libitum


title: ChIP_DLD1-NT_H3K9me3


title: SCM-1 Donor 3

description:
SCM-1
DPP4+ cells isolated
D3SCM1


title: 43-O-1, rep1

description:
11nt
43-O-1


title: ChIP_DLD1-NT_H3K27me3

value: H3K27me3 (Cell Signalling Technology, 9733S, RRID:AB_2616029)


title: T47D siFOXA1 ATAC

data_processing:
Fastq files were generated by RTA in Illumina MiSeq or NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to hg38 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: hg38
Supplementary files format and content: peak summit data

extract_protocol:
Briefly, 50,000 cells were lysed to release the nuclei and subjected to a transposition reaction using Tn5 transposase (Illumina). Transposed fragments underwent preamplification, quantification via real-time polymerase chain reaction, and subsequent amplification.
Libraries were prepared with the Omni-ATAC protocol.

value: cell line

value: breast cancer


title: RE-RE_10w_ALF_14.ZT12

value: female


title: NSCM-3 Donor 3

description:
NSCM-3
D3NSCM3

value: Non senescent conditioned medium


title: NSCM-2 Donor 3

description:
NSCM-2
D3NSCM2


title: NSCM-1 Donor 3

description:
NSCM-1
D3NSCM1


title: RE-RE_10w_ALF_13.ZT12


title: RE-RE_10w_ALF_12.ZT8


title: ChIP_3BKO-NT_H3K9me3

value: colorectal adenocarcinoma cell line

value: DNMT1-AID;DNMT3b -/-


title: ChIP_3BKO-NT_H3K27me3


title: T47D siCtrl ATAC

value: siCtrl


title: EGF60-siMSK2_RNA_3

city: Philadelphia

last: Wong

state: PA

address: 3400 Civic Center Blvd., SCTR 9-187

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.20.0.422)
Alignment to hg38 using STAR (v2.7.9a)
Aligned reads were counted using HTseq (v0.13.5)
Assembly: hg38
Supplementary files format and content: HTseq-counted output files (.out)

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using QIAGEN RNeasy kit.
Sequencing libraries were assembled using Nextera XT DNA Library Prepation Kit

treatment_protocol: 10nM of either non-template scramble control siRNA or siRNA targeting MSK2 was added to cell culture media every 24 hours for 72 total hours of incubation. Cells were serum starved for the last 24 hours. Cells were treated with PBS, 750pM EGF for 30 minutes, or 750pM EGF for 60 minutes.

value: human lung fibroblasts

value: EGF

tag: time

value: 60 minutes


title: T47D siCtrl RNA


title: RE-RE_10w_ALF_11.ZT8

value: whole muscle


title: S-3 Donor 3

description:
S-3
DPP4+ cells isolated
D3S3

value: Endothelial cells

value: Vein

value: wild type

value: Primary Endothelial cells

value: Doxorubicin


title: T47D siGRHL2 ATAC


title: S-2 Donor 3

description:
S-2
DPP4+ cells isolated
D3S2


title: ChIP_3BKO-IAA10d_H3K9me3

value: Auxin 10 days


title: EGF60-siMSK2_RNA_1


title: ChIP_3BKO-IAA10d_H3K27me3

value: H3K27me3 (Cell Signalling Technology, 9733S, RRID:AB_2616029)


title: RE-RE_10w_ALF_9.ZT8

value: 10-12 weeks

value: ad libitum


title: EGF30-siMSK2_RNA_4

value: 30 minutes


title: DE2, skin, CD45+

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: Oregon Health & Science University

description: BD Rhapsody

data_processing:
Data preprocessing was performed using the Seven Bridges BD Rhapsody Whole Transcriptome Analysis Pipeline. Samples were demultiplexed and reads were quality filtered and aligned to the hg38/GRCh38 genome prior to quantification.
Assembly: hg38
Supplementary files format and content: Molecules per Cell and Sample Tag Calls CSV files

source_name: skin

extract_protocol:
BD Rhapsody single-cell RNAseq protocol using well-based isolation of individual cells, lysis within those wells, and bead-capture of mRNA using the polyA tail
BD Rhapsody's WTA, Sample Tag (for multiplexing), and AbSeq library preparation protocol and reagents

treatment_protocol: Skin single-cell enzymatic dissociation followed by sample labeling (for multiplexing) and CD45+ and CD45- cell isolation

value: skin

value: non-affected tissue

tag: condition

value: fresh, frozen


title: NS-3 Donor 3

description:
NS-3
D3NS3

tag: tissue

value: no treatment


title: RE-RE_10w_ALF_8.ZT4

value: male


title: S-1 Donor 3

description:
S-1
DPP4+ cells isolated
D3S1


title: RE-RE_10w_ALF_7.ZT4


title: DE2, skin, CD45-

description: BD Rhapsody


title: EGF60-siMSK2_RNA_2

value: human lung fibroblasts

value: EGF

value: 60 minutes


title: NS-1 Donor 3

description:
NS-1
D3NS1

value: Endothelial cells

value: Vein


title: DE1, skin, CD45+

description: BD Rhapsody


title: RE-RE_10w_ALF_6.ZT4

value: female

value: whole muscle


title: EGF30-siMSK2_RNA_2


title: 6.15.22, skin, CD45+

description: BD Rhapsody

value: frozen


title: EGF30-siMSK2_RNA_1


title: EGF30-siMSK2_RNA_3


title: SCM-3 Donor 2

description:
SCM-3
DPP4+ cells isolated
D2SCM3

source_name: Donor 2

value: wild type

value: Primary Endothelial cells

value: Senescent conditioned medium


title: PBS-siMSK2_RNA_4

value: PBS


title: RE-RE_10w_ALF_5.ZT4

value: 10-12 weeks

value: ad libitum


title: SCM-2 Donor 2

description:
SCM-2
DPP4+ cells isolated
D2SCM2


title: RE-RE_10w_ALF_10.ZT8


title: RE-RE_10w_ALF_4.ZT0


title: DBD+ RNASeq rep 3

city: Columbus

first: Ariunaa

last: Bayanjargal

state: OH

address: 700 Children's Dr

institute: Nationwide Childrens Hospital

data_processing:
Low-quality reads (q < 10) and adapter sequences were trimmed
Aligned to hg19 genome using STAR
Reads were counted
Differential analysis performed using DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig files of combined replicates for visualization
Supplementary files format and content: Text files of differential analysis run with DESeq2.

source_name: muscle

growth_protocol: A673 cells were grown at 37C, 5% CO2 in DMEM with 10% fetal bovine serum, 1% P/S/Q, and 1% sodium pyruvate.

extract_protocol:
Total RNAwere extracted using RNeasy Extraction Kit.
cDNA libraries were prepared from total RNA with TruSeq Stranded mRNA Kit (Illumina 20020594)

treatment_protocol: For knockdown of endogenous EWS::FLI in A673, cells were infected with RNAi virus and subsequently infected with the cDNA-containing virus to rescue the cells. After 48 hours, cells were selected with puromycin (100 μg/ul) and hygromycin (150 μg/ul); and allowed to grow for 7-8 days prior to collection

value: muscle

value: Ewing sarcoma cell line

value: KD + DBD+ rescue

value: DBD+ rescue


title: 3.1.22, skin, CD45+

description: BD Rhapsody

value: skin

value: non-affected tissue


title: NSCM-3 Donor 2

description:
NSCM-3
D2NSCM3

value: Endothelial cells

value: Non senescent conditioned medium


title: DBD+ RNASeq rep 2


title: RE-RE_10w_ALF_3.ZT0

city: Barcelona

last: Perdiguero

address: Dr. Aiguader 88

institute: UPF

value: male


title: PBS-siMSK2_RNA_2

value: human lung fibroblasts

value: 60 minutes


title: PBS-siMSK2_RNA_1


title: NSCM-2 Donor 2

description:
NSCM-2
D2NSCM2

value: Vein

value: wild type


title: RE-RE_10w_ALF_2.ZT0

value: female

value: whole muscle


title: EGF60-NTC_RNA_3

value: EGF

value: NTC-siRNA


title: RE-RE_10w_ALF_1.ZT0

value: 10-12 weeks

value: ad libitum


title: DBD RNASeq rep 3

value: muscle

value: Ewing sarcoma cell line

value: KD + DBD rescue

value: DBD rescue


title: Br-RE_26w_ALF_24.ZT20

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 26 weeks


title: DBD+ RNASeq rep 1

value: KD + DBD+ rescue

value: DBD+ rescue


title: DBD RNASeq rep 2


title: Br-RE_26w_ALF_23.ZT20


title: NS-3 Donor 2

description:
NS-3
DPP4+ cells isolated
D2S3

value: Endothelial cells

value: Primary Endothelial cells

value: Doxorubicin


title: EGF60-NTC_RNA_2

value: human lung fibroblasts

value: 60 minutes


title: Br-RE_26w_ALF_22.ZT20

value: male

value: whole muscle


title: NS-2 Donor 2

description:
NS-2
DPP4+ cells isolated
D2S2

value: Vein

value: wild type


title: EGF30-NTC_RNA_4

value: EGF

value: 30 minutes

value: NTC-siRNA


title: EGF60-NTC_RNA_1


title: SCM-1 Donor 2

description:
SCM-1
DPP4+ cells isolated
D2SCM1

value: Senescent conditioned medium


title: PBS-siMSK2_RNA_3

value: PBS


title: NS-1 Donor 2

description:
NS-1
DPP4+ cells isolated
D2S1


title: wtEF RNASeq rep 3

value: muscle

value: Ewing sarcoma cell line

value: KD + wtEF rescue

value: wtEF rescue


title: DBD RNASeq rep 1

value: KD + DBD rescue

value: DBD rescue


title: Br-RE_26w_ALF_20.ZT16

value: female

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 26 weeks

value: ad libitum


title: EGF30-NTC_RNA_3

value: human lung fibroblasts


title: wtEF RNASeq rep 1


title: Br-RE_26w_ALF_19.ZT16

value: male

value: whole muscle


title: S-3 Donor 2

description:
S-3
D2NS3

value: Endothelial cells

value: Vein

value: wild type

value: Primary Endothelial cells

value: no treatment


title: S-2 Donor 2

description:
S-2
D2NS2


title: EGF30-NTC_RNA_2

value: EGF

value: 30 minutes

value: NTC-siRNA


title: Br-RE_26w_ALF_18.ZT16


title: NSCM-1 Donor 2

description:
NSCM-1
D2NSCM1

value: Non senescent conditioned medium


title: NS-2 Donor 3

description:
NS-2
D3NS2


title: EGF30-NTC_RNA_1


title: KD RNASeq rep 3

value: muscle

value: Ewing sarcoma cell line

value: KD of EWS::FLI

value: empty vector rescue


title: S-1 Donor 2

description:
S-1
D2NS1


title: Br-RE_26w_ALF_17.ZT16

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 26 weeks

value: ad libitum


title: KD RNASeq rep 2


title: PBS-NTC_RNA_4

value: human lung fibroblasts

value: PBS

value: 60 minutes


title: Br-RE_26w_ALF_16.ZT12

value: female

value: whole muscle


title: Br-RE_26w_ALF_15.ZT12

value: male


title: DBD+ Rb CnT rep 3

data_processing:
*library strategy: CUT&Tag
Quality control on raw sequencing reads were performed with FastQC (v0.11.4)
Adapter sequences and/or low quality reads were trimmed using trim_galore (0.4.4_dev)
Reads were aligned to human (hg19) and spike-in Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genomes using Bowtie2 (v2.3.4.3)
SamTools (v1.9) (H. Li et al., 2009) was used to convert sam to bam with ‘-bq 10’ option.
Cut and Tag reads were spike-in normalized using DESeq2’s median ratio method (Anders & Huber, 2010)
Spike-in normalized tracks were generated and averaged across biological replicates using deep-Tools (Ramírez et al., 2016).
Peaks were called with spike-in normalization and their corresponding IgG as controls accounting for variation between the biological replicates using MACS2 (v 2.2.7.1) (Zhang et al., 2008), DiffBind (v2.14.0) (Ross-Innes et al., 2012; Stark & Brown, 2011) and DESeq2 (v1.26.0)(Love, Huber, & Anders, 2014).
Assembly: hg19 and E.coli
Supplementary files format and content: Final peak list generated with following thresholds: FRD < 0.05, logFC > 8, counts > 80, IDR < 0.01.
Supplementary files format and content: Bigwig files of combined replicates for visualization.

extract_protocol:
Total DNA (digested with Tn5) was purified using Phenol/Chloroformextraction followed by Ethanol precipitation
CUT&Tag libraries were prepared with NEBNext HiFi 2x PCR Master Mix (NEB M0541S) and indexed primers (Buenrostro, J.D. et al, Nature, 2015)

value: KD + DBD+ rescue

value: DBD+ rescue


title: SCM-2 Donor 1

description:
SCM-2
DPP4+ cells isolated
D1SCM2

source_name: Donor 1

value: Endothelial cells

value: Artery

value: wild type

value: Primary Endothelial cells

value: Senescent conditioned medium


title: SCM-3 Donor 1

description:
SCM-3
DPP4+ cells isolated
D1SCM3


title: DBD+ Rb CnT rep 2

value: muscle

value: Ewing sarcoma cell line


title: SCM-1 Donor 1

description:
SCM-1
DPP4+ cells isolated
D1SCM1


title: PBS-NTC_RNA_3

value: NTC-siRNA


title: KD RNASeq rep 1

value: KD of EWS::FLI

value: empty vector rescue


title: Br-RE_26w_ALF_14.ZT12

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 26 weeks

value: ad libitum


title: Br-RE_26w_ALF_13.ZT12

value: female

value: whole muscle


title: wtEF RNASeq rep 2

value: KD + wtEF rescue

value: wtEF rescue


title: DBD Rb CnT rep 3

value: KD + DBD rescue

value: DBD rescue


title: Br-RE_26w_ALF_12.ZT8

value: male


title: NSCM-3 Donor 1

description:
NSCM-3
D1NSCM3

value: Endothelial cells

value: Artery

value: wild type

value: Primary Endothelial cells

value: Non senescent conditioned medium


title: DBD Rb CnT rep 2

value: muscle

value: Ewing sarcoma cell line


title: Br-RE_26w_ALF_11.ZT8

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)


title: PBS-NTC_RNA_1

value: human lung fibroblasts

value: PBS

value: 60 minutes

value: NTC-siRNA


title: KD Rb CnT rep 3

value: KD of EWS::FLI

value: empty vector rescue


title: NSCM-1 Donor 1

description:
NSCM-1
D1NSCM1


title: S-3 Donor 1

description:
S-3
DPP4+ cells isolated
D1S3

value: Doxorubicin


title: Br-RE_26w_ALF_10.ZT8

value: female

value: 26 weeks

value: ad libitum

value: whole muscle


title: KD Rb CnT rep 2


title: DBD+ CTCF CnT rep3

value: KD + DBD+ rescue

value: DBD+ rescue


title: Br-RE_26w_ALF_9.ZT8

value: male


title: S-2 Donor 1

description:
S-2
DPP4+ cells isolated
D1S2

value: Endothelial cells

value: Artery

value: wild type

value: Primary Endothelial cells


title: PBS-NTC_RNA_2

value: human lung fibroblasts

value: PBS


title: S-1 Donor 1

description:
S-1
DPP4+ cells isolated
D1S1


title: Br-RE_26w_ALF_8.ZT4

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)


title: DBD+ CTCF CnT rep2

value: muscle

value: Ewing sarcoma cell line


title: Br-RE_26w_ALF_7.ZT4


title: NS-3 Donor 1

description:
NS-3
D1NS3

value: no treatment


title: NSCM-2 Donor 1

description:
NSCM-2
D1NSCM2

value: Non senescent conditioned medium


title: DBD CTCF CnT rep 3

value: KD + DBD rescue

value: DBD rescue


title: Br-RE_26w_ALF_5.ZT4

value: 26 weeks

value: ad libitum

value: whole muscle


title: NS-2 Donor 1

description:
NS-2
D1NS2


title: DBD CTCF CnT rep 2


title: KD CTCF CnT rep 3

value: KD of EWS::FLI

value: empty vector rescue


title: NS-1 Donor 1

description:
NS-1
D1NS1

value: Endothelial cells

value: Artery


title: KD CTCF CnT rep 2


title: Br-RE_26w_ALF_4.ZT0

value: female


title: Br-RE_26w_ALF_3.ZT0

value: male


title: Br-RE_26w_ALF_1.ZT0


title: Br-RE_10w_ALF_24.ZT20

value: 10-12 weeks


title: DBD H3K27ac CnT rep 3

data_processing:
*library strategy: CUT&Tag
Quality control on raw sequencing reads were performed with FastQC (v0.11.4)
Adapter sequences and/or low quality reads were trimmed using trim_galore (0.4.4_dev)
Reads were aligned to human (hg19) and spike-in Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genomes using Bowtie2 (v2.3.4.3)
SamTools (v1.9) (H. Li et al., 2009) was used to convert sam to bam with ‘-bq 10’ option.
Cut and Tag reads were spike-in normalized using DESeq2’s median ratio method (Anders & Huber, 2010)
Spike-in normalized tracks were generated and averaged across biological replicates using deep-Tools (Ramírez et al., 2016).
Peaks were called with spike-in normalization and their corresponding IgG as controls accounting for variation between the biological replicates using MACS2 (v 2.2.7.1) (Zhang et al., 2008), DiffBind (v2.14.0) (Ross-Innes et al., 2012; Stark & Brown, 2011) and DESeq2 (v1.26.0)(Love, Huber, & Anders, 2014).
Assembly: hg19 and E.coli
Supplementary files format and content: Final peak list generated with following thresholds: FRD < 0.05, logFC > 8, counts > 80, IDR < 0.01.
Supplementary files format and content: Bigwig files of combined replicates for visualization.
Supplementary files format and content: Bed files of enahncer and super-enhancers called with ROSE.


title: Br-RE_10w_ALF_23.ZT20

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)


title: DBD H3K27ac CnT rep 2

value: muscle


title: Br-RE_10w_ALF_22.ZT20


title: KD H3K27ac CnT rep 3

value: Ewing sarcoma cell line


title: Br-RE_10w_ALF_21.ZT20


title: DBD+ FLAG CnT rep 2

value: KD + DBD+ rescue

value: DBD+ rescue


title: Br-RE_10w_ALF_20.ZT16


title: DBD+ H3K27ac CnT rep 3


title: DBD+ FLAG CnT rep 3


title: Br-RE_10w_ALF_19.ZT16


title: Br-RE_26w_ALF_2.ZT0


title: Br-RE_10w_ALF_18.ZT16


title: DBD+ H3K27ac CnT rep 2


title: Br-RE_10w_ALF_17.ZT16


title: DBD+ FLAG CnT rep 1


title: Br-RE_10w_ALF_16.ZT12


title: HEK001 (insert) in Transwell plate, in KSFM Day 7, rep3

type: RNA

city: Kubang Kerian

first: Ahmad

last: Azlina

state: Kelantan

address: Health Campus, Universiti Sains Malaysia

country: Malaysia

institute: School of Dental Sciences

description: Gene expression of coculture (insert) HEK001 in KSFM at day 7

hyb_protocol: 0.825 μg of Cy3-labelled cRNA with specific activity ≥6 pmol Cy3/µg cRNA was fragmented at 60 °C for 30 min in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent. Then, 25 µl of the mixture were combined with 25 μl of 2x Hi-RPM Hybridization Buffer and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 hours at 65 °C in a rotating Agilent microarray hibridization oven

scan_protocol: Slides were scanned immediately using Agilent SureScan Microarray Scanner (G4900DA) with 3 μm resolution at wavelength of 532 nm (Cy3) using the extended dynamic range (10-100%) setting.

data_processing: The normalized intensities were extracted using the Agilent Feature Extraction Software using default parameters (protocol GE1_1200_Jun14 and grid: 072363_D_F_20150612)

source_name: Human Epithelial Keratinocyte (HEK001)

label_protocol: Cy3 labelled cRNA was purified using RNeasy Mini Kit (Qiagen, Ca) according to manufacturer's instruction

growth_protocol: Stem cells from human exfoliated deciduous teeth (SHED) (AllCells, USA) were cultured in alpha-minimum essential medium (α-MEM) (Gibco, USA) supplemented with 15% of fetal bovine serum (FBS) (Gibco, USA) and 1% of penicillin/streptomycin (Gibco, USA). Meanwhile, human epithelial keratinocyte (HEK001) (ATCC, USA) were cultured in Keratinocyte-Serum Free Medium (KSFM) (1x) (Gibco, USA) containing L-glutamine supplemented with 2.5 µg of Epidermal Growth Factor (EGF) (Gibco, USA) Human Recombinant and 25 mg of Bovine Pituitary Extract (Gibco, USA). Both cells were incubated in 37°C humidified incubator and the media inside the flask was changed every 2 days.

extract_protocol: RNA was prepared using the innuPREP RNA Mini Kit (AnalytikJena, Germany). The qualitative and quantitative analysis of the RNA samples were determined. All RNA samples are subjected to DNase I, RNase-free (Thermo Scientific, USA) to remove genomic DNA.

treatment_protocol: SHED were cultured in 6-well of Transwell with 0.4 µm pore polyester membrane insert (Corning, USA) until day 5. HEK001 were cultured at the top of the co-culture plate while SHED were cultured at the bottom of the co-culture plate. Medium used inside the co-culture was complete KSFM (Gibco, USA).

value: keratinocyte cells

tag: culture type

value: Insert of Transwell (6-well plate)

tag: protocol

value: coculture (insert) HEK001 in KSFM

value: day 7


title: DBD FLAG CnT rep 1

tag: genotype

value: KD + DBD rescue

value: DBD rescue


title: KD H3K27ac CnT rep 2

value: KD of EWS::FLI

value: empty vector rescue


title: DBD FLAG CnT rep 3


title: SHED cultured in Transwell plate, in KSFM Day 7, rep2

description: Gene expression of coculture SHED in KSFM at day 7

source_name: Stem Cell from Human Exfoliated Deciduous Teeth (SHED)

value: stem cells

value: Transwell (6-well plate)

value: coculture SHED in KSFM


title: DBD FLAG CnT rep 2


title: HEK001 (insert) in Transwell plate, in KSFM Day 7, rep1


title: HEK001 (insert) in Transwell plate, in KSFM Day 5, rep3

description: Gene expression of coculture (insert) HEK001 in KSFM at day 5

value: day 5


title: SHED cultured in Transwell plate, in KSFM Day 7, rep3


title: HEK001 (insert) in Transwell plate, in KSFM Day 5, rep1


title: Br-RE_10w_ALF_13.ZT12

first: Eusebio

source_name: tibialis anterior muscle

tag: Sex

value: female

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

tag: age

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: SHED cultured in Transwell plate, in KSFM Day 7, rep1


title: SHED cultured in Transwell plate, in KSFM Day 5, rep2

description: Gene expression of coculture SHED in KSFM at day 5


title: KD FLAG CnT rep 1

value: muscle

value: Ewing sarcoma cell line

tag: treatment


title: SHED cultured in Transwell plate, in KSFM Day 5, rep3


title: SHED cultured in Transwell plate, in KSFM Day 5, rep1


title: HEK001 (insert) in Transwell plate, in KSFM Day 7, rep2

value: keratinocyte cells

value: Insert of Transwell (6-well plate)

value: coculture (insert) HEK001 in KSFM


title: Br-RE_10w_ALF_15.ZT12

tag: strain

value: male

tag: feeding


title: HEK001 (insert) in Transwell plate, in KSFM Day 5, rep2

tag: cell type


title: Br-RE_10w_ALF_14.ZT12

tag: zeitgeber time


title: KD FLAG CnT rep 3

value: KD of EWS::FLI


title: Br-RE_10w_ALF_9.ZT8


title: Br-RE_10w_ALF_8.ZT4


title: KD FLAG CnT rep 2

value: empty vector rescue


title: Br-RE_10w_ALF_6.ZT4


title: Br-RE_10w_ALF_12.ZT8


title: Flag-DHX9, Flag, rep 3

first: Israel

last: Canadas

address: 333 Cottman Ave.

department: Nuclear Dynamics and Cancer Program

institute: Fox Chase Cancer Center

data_processing:
For analysis of RE expression from RIP-seq data, FASTQ reads were trimmed by TrimGalore (version 0.6.4).
The trimmed FASTQ reads were mapped against H. sapiens UCSC hg19 using the Bowtie 2 (version 2.3.5) alignment software.
The counts of RE were calculated by RepEnrich2 using default settings, and were normalized by one million reads as CPM (counts per million).
Assembly: hg19
Supplementary files format and content: Expression data in excel format

extract_protocol:
DHX9-depleted H446 cells, transfected with Flag-MDA5 or Flag-RIG-I vector, were harvested. RNA immunoprecipitation (RIP) was conducted with Flag antibody using a Magna RIP RNA-Binding Protein Immunoprecipitation kit, according to the manufacturer’s instructions. RIP was also conducted with Flag antibody against H446 expressing 3xFlag-DHX9-K417R.
Illumina sequencing libraries were prepared by Novogene, with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). Libraries were quantified using the Qubit 2.0 Fluorometer (Life Technologies).

treatment_protocol: DHX9-depleted H446 cells were transfected with Flag-MDA5 or Flag-RIG-I vector. 3xFlag-DHX9-K417R vector was used for checking DHX9-bound RNA.

value: Small Cell Lung Cancer

value: Flag-IP


title: Br-RE_10w_ALF_2.ZT0

treatment_protocol: Tibialis anterior muscle was collected and snap frozen with liquid nitrogen at six different time point intervals during 24hr period (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20).


title: SHED cultured in KSFM Day 7, rep1

description: Gene expression of SHED in KSFM at day 7

value: stem cells

value: 6-well plate

value: SHED in KSFM

value: day 7


title: SHED cultured in KSFM Day 7, rep3


title: HEK001 cultured in KSFM Day 1, rep1

description: Gene expression of HEK001 in KSFM at day 1

value: HEK001 in KSFM

value: day 1


title: hippocampus, male, wildtype, chow, cohort2_29

city: Atlanta

first: Marise

last: Parent

email: mbparent@gsu.edu, tanderson80@gsu.edu

state: GA

address: PO Box 5030

department: Neuroscience Institute

institute: Georgia State University

data_processing:
Cutadapt with minimum length set to 1 to exclude empty reads.
STAR (version 2.7.0a) was used to align Fastq files to the Rn6.0 genome build from UCSC genome browser with refseq annotations. To limit analyses to canonical gene alignments and generate counts for downstream analyses, “outSAMstrandField intronMotif,” “outFilterIntronMotifs RemoveNoncanonical,” and “quantMode GeneCounts” STAR options were used.
Assembly: Rn6
Supplementary files format and content: tab delimited text file including raw counts for each sample

organism: Rattus norvegicus

source_name: dorsal hippocampus

extract_protocol:
rneasy lipid tissue minikit from snap frozen dorsal hippocampus tissue chunks
PolyA enrichment and NEB Ultra II library prep

value: dorsal hippocampus

value: wildtype

tag: diet

value: chow

tag: cohort


title: SHED cultured in KSFM Day 1, rep3

description: Gene expression of SHED in KSFM at day 1


title: SHED cultured in KSFM Day 1, rep1


title: HEK001 cultured in KSFM Day 1, rep2

value: keratinocyte cells


title: iPSC-CM_Ind6_MTX_24hr

city: Galveston

first: Michelle

middle: C.

last: Ward

email: miward@UTMB.edu, ermatthe@UTMB.edu

state: TX

address: 301 University Blvd., MRB 7.150

department: Biochemistry and Molecular Biology

institute: UTMB-Galveston

data_processing:
Reads were assessed for quality using the MultiQC package (Ewels et al. 2016) in Linux.
Reads were aligned to hg38 using the Subread package (Liao et al. 2013)  with the featureCounts function (Liao et al. 2014) used to quantify  the read number across annotated genes in R.
Assembly: hg38
Supplementary files format and content: RNA-seq counts for all individuals and conditions (72 total samples). Column 1 are Entrez gene IDs by row.  Columns 2-72 are each sample denoted by (treatment.individual.time). Eg. DOX.3.3hr is the DOX-treated sample from individual 3 at 3 hours after treatment.

growth_protocol: Human iPSC-dervied cardiomyocytes were maintained in Cardiomyocyte Maintenance Media (500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (MT35015CV, Corning), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL Penicillin/Streptomycin) on Matrigel-coated dishes at 37°C, 5% CO2 and atmospheric O2.

extract_protocol:
RNA was extracted from ~1.5 million cells using the Zymo dual DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA). All treatments and timepoints per individual were extracted in one batch resulting in 6 extraction batches of 12 samples corresponding to the 6 individuals. Median RIN scores were 9.35, 9.6, 9.3, 9.6, 9.65, and 9.55 across treatments for individuals 1-6, respectively.
RNA-seq libraries were generated using 250 ng of RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L, Ipswich, MA, USA), NEBNext Ultra II RNA library prep with Sample Purification Beads kit (E7775K) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) kit (E6440S). Libraries were prepared in batches of 12 for each individual, following the manufacturer's protocol.

treatment_protocol: 1.5 million iPSC-CMs were plated in 6-well plates. On Days 27-29, iPSC-CMs were treated with 0.5 µM DNR, DOX, EPI, MTX, TRZ, or vehicle in fresh cardiomyocyte maintenance media. iPSC-CMs and cell culture media were collected 3- and 24-hours post-treatment, resulting in 72 samples from 6 individuals.

tag: disease state

value: healthy

tag: cell line

value: induced pluripotent stem cell-derived cardiomyocytes

value: female

value: 0.5 uM mitoxantrone


title: Flag-DHX9, Flag, rep 2


title: Br-RE_10w_ALF_1.ZT0

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: hippocampus, male, alzheimer, western, cohort2_28

value: male

value: alzheimer

value: western


title: Br-RE_10w_ALF_10.ZT8


title: SHED cultured in KSFM Day 7, rep2

value: stem cells

value: 6-well plate

value: SHED in KSFM

tag: time

value: day 7


title: Br-RE_10w_ALF_3.ZT0


title: Flag-RIG-I, input

value: Small Cell Lung Cancer

value: Flag-RIG-I

value: input


title: Flag-DHX9, Flag, rep 1

value: Flag-IP


title: Br-RE_10w_ALF_7.ZT4


title: iPSC-CM_Ind6_DOX_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: female

value: 0.5 uM doxorubicin


title: hippocampus, male, wildtype, western, cohort2_27

value: dorsal hippocampus

value: wildtype


title: iPSC-CM_Ind6_TRZ_24hr

value: 0.5 uM trastuzumab


title: SHED cultured in α-MEM Day 1, rep1

description: Gene expression of SHED in α-MEM at day 1

value: SHED in α-MEM

value: day 1


title: Flag-RIG-I, Flag, rep 2


title: Br-RE_10w_ALF_5.ZT4

value: Bmal1(stopFL/stopFL), Syt10-Cre(-/tg)

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: Mu-RE_26w_ALF_22.ZT20

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks


title: iPSC-CM_Ind6_VEH_3hr

value: 0.5 uM vehicle


title: hippocampus, male, wildtype, chow, cohort2_26

value: male

value: chow


title: SHED cultured in KSFM Day 1, rep2

value: stem cells

value: 6-well plate

value: SHED in KSFM


title: Br-RE_10w_ALF_4.ZT0


title: hippocampus, male, wildtype, western, cohort2_24

value: dorsal hippocampus

value: western


title: iPSC-CM_Ind6_VEH_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: female


title: Flag-DHX9, input

value: Small Cell Lung Cancer

value: input


title: SHED cultured in α-MEM Day 1, rep3

value: SHED in α-MEM

value: day 1


title: SHED cultured in α-MEM Day 1, rep2


title: hippocampus, male, alzheimer, western, cohort2_23

value: alzheimer


title: iPSC-CM_Ind6_DNR_24hr

value: 0.5 uM daunorubicin


title: iPSC-CM_Ind6_MTX_3hr

value: 0.5 uM mitoxantrone


title: hippocampus, male, alzheimer, chow, cohort2_30

value: male


title: iPSC-CM_Ind6_DOX_3hr

value: 0.5 uM doxorubicin


title: Flag-MDA5, Flag, rep 1

value: Flag-IP


title: iPSC-CM_Ind6_EPI_24hr

value: 0.5 uM epirubicin


title: Flag-RIG-I, Flag, rep 3

value: Flag-RIG-I


title: hippocampus, male, alzheimer, chow, cohort2_25

value: dorsal hippocampus

value: chow


title: Mu-RE_26w_ALF_24.ZT20

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks

value: ad libitum

value: whole muscle


title: Mu-RE_26w_ALF_25.ZT20


title: iPSC-CM_Ind6_DNR_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: female


title: Flag-RIG-I, Flag, rep 1

value: Small Cell Lung Cancer


title: Mu-RE_26w_ALF_21.ZT20


title: hippocampus, female, alzheimer, chow, cohort2_19

value: alzheimer


title: iPSC-CM_Ind5_VEH_24hr

value: 0.5 uM vehicle


title: iPSC-CM_Ind6_TRZ_3hr

value: 0.5 uM trastuzumab


title: Jurkat XPO1 C528S cells, PMA Ionomycin, 6 hours, NFAT1 antibody [PMA_Iono_NFAT1_C528S]

city: Cleveland

first: Yi Fan

last: Chen

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

data_processing:
library strategy: CUT&RUN-Seq
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.4.5.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.3
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.4.3
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

source_name: Peripheral blood mononuclear cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies
Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions.
Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM SP100030 treatments were co-administered at the same time and cells were incubated for 6 hours prior ot harvest

tag: antibody

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: PMA Ionomycin


title: hippocampus, female, alzheimer, western, cohort2_18

tag: tissue

value: dorsal hippocampus

value: western


title: Flag-MDA5, input

value: input


title: Mu-RE_26w_ALF_19.ZT16

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks


title: iPSC-CM_Ind5_TRZ_24hr


title: Jurkat XPO1 C528S cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1_C528S]

value: PMA Ionomycin + SP100030


title: Mu-RE_26w_ALF_14.ZT12

value: ad libitum

value: whole muscle


title: Flag-MDA5, Flag, rep 3

value: Flag-IP


title: iPSC-CM_Ind6_EPI_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: female

value: 0.5 uM epirubicin


title: iPSC-CM_Ind5_MTX_24hr

value: 0.5 uM mitoxantrone


title: hippocampus, female, wildtype, western, cohort2_17

value: wildtype


title: Flag-MDA5, Flag, rep 2

value: Small Cell Lung Cancer


title: hippocampus, female, alzheimer, western, cohort2_21

value: alzheimer


title: hippocampus, female, wildtype, chow, cohort2_20

value: dorsal hippocampus

value: chow


title: hippocampus, female, wildtype, chow, cohort2_15


title: Jurkat cells, PMA Ionomycin + Selinexor, 6 hours, NFAT1 [PMA_Iono_Selinexor_NFAT1_rep2]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: WT


title: Mu-RE_26w_ALF_16.ZT12

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks

value: ad libitum


title: hippocampus, female, alzheimer, chow, cohort1_14


title: Jurkat XPO1 C528S cells, PMA Ionomycin + SP100030, 6 hours, NFAT1 antibody [PMA_Iono_SP_NFAT1_C528S]

value: PMA Ionomycin + SP100030


title: Mu-RE_26w_ALF_20.ZT16

value: male

value: whole muscle


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, RUNX3 [PMA_Iono_SP_RUNX3_rep2]


title: Mu-RE_26w_ALF_18.ZT16


title: iPSC-CM_Ind5_TRZ_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: female

value: 0.5 uM trastuzumab


title: hippocampus, female, wildtype, western, cohort2_22

value: wildtype

value: western


title: Mu-RE_26w_ALF_13.ZT12


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, RUNX3 [PMA_Iono_SP_RUNX3_rep1]


title: Mu-RE_26w_ALF_12.ZT8


title: Mu-RE_26w_ALF_7.ZT4


title: iPSC-CM_Ind5_MTX_3hr

value: 0.5 uM mitoxantrone


title: Mu-RE_26w_ALF_15.ZT12


title: iPSC-CM_Ind5_EPI_24hr

value: 0.5 uM epirubicin


title: hippocampus, female, alzheimer, chow, cohort1_10

value: dorsal hippocampus

value: alzheimer

value: chow


title: hippocampus, female, alzheimer, chow, cohort2_16


title: Jurkat XPO1 C528S cells, DMSO, 24 hrs, IgG control antibody [IgG_C528S]

value: IgG

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: DMSO


title: Mu-RE_26w_ALF_11.ZT8

value: male

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks

value: ad libitum

value: whole muscle


title: Mu-RE_26w_ALF_10.ZT8

value: female


title: Jurkat cells, PMA Ionomycin + Selinexor, 6 hours, NFAT1 [PMA_Iono_Selinexor_NFAT1_rep1]

value: WT

value: PMA Ionomycin + SP100030


title: hippocampus, female, wildtype, chow, cohort1_13

value: wildtype


title: Mu-RE_26w_ALF_9.ZT8


title: Jurkat XPO1 C528S cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1_C528S]

value: PMA Ionomycin


title: Mu-RE_26w_ALF_5.ZT4


title: iPSC-CM_Ind5_DOX_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM doxorubicin


title: hippocampus, female, wildtype, western, cohort1_12

value: dorsal hippocampus

value: western


title: iPSC-CM_Ind5_DNR_3hr

value: 0.5 uM daunorubicin


title: hippocampus, male, alzheimer, chow, cohort1_8

value: alzheimer

value: chow


title: Mu-RE_26w_ALF_4.ZT0

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)


title: Mu-RE_26w_ALF_8.ZT4

value: male

value: 26 weeks


title: hippocampus, male, wildtype, chow, cohort1_7


title: iPSC-CM_Ind5_DOX_24hr


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, RUNX1 [PMA_Iono_SP_RUNX1]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells


title: Jurkat cells, PMA Ionomycin, 6 hours, RUNX1 [PMA_Iono_RUNX1]

value: WT


title: hippocampus, female, alzheimer, western, cohort1_11

value: female


title: hippocampus, male, alzheimer, western, cohort1_6


title: Mu-RE_26w_ALF_6.ZT4

value: ad libitum

value: whole muscle


title: hippocampus, male, wildtype, western, cohort1_5

value: wildtype


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, ETS1 [PMA_Iono_SP_ETS1]

value: PMA Ionomycin + SP100030


title: iPSC-CM_Ind5_DNR_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes


title: hippocampus, female, wildtype, chow, cohort1_9

value: dorsal hippocampus


title: Jurkat cells, PMA Ionomycin, 6 hours, RUNX3 [PMA_Iono_RUNX3_rep1]

value: PMA Ionomycin


title: iPSC-CM_Ind5_EPI_3hr

value: 0.5 uM epirubicin


title: iPSC-CM_Ind4_MTX_24hr

value: 0.5 uM mitoxantrone


title: Jurkat cells, DMSO, 6 hours, RUNX3 antibody [DMSO_RUNX3_rep2]

value: DMSO


title: Mu-RE_26w_ALF_2.ZT0

value: male

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks


title: iPSC-CM_Ind4_TRZ_24hr

value: 0.5 uM trastuzumab


title: Jurkat cells, PMA Ionomycin, 6 hours, ETS1 [PMA_Iono_ETS1]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: WT


title: Jurkat cells, PMA Ionomycin, 6 hours, RUNX4 [PMA_Iono_RUNX3_rep2]


title: iPSC-CM_Ind5_VEH_3hr

value: female

value: 0.5 uM vehicle


title: Mu-RE_26w_ALF_1.ZT0

value: ad libitum

value: whole muscle


title: Mu-RE_10w_ALF_23.ZT20

value: 10-12 weeks


title: Mu-RE_26w_ALF_3.ZT0


title: iPSC-CM_Ind4_DOX_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM doxorubicin


title: iPSC-CM_Ind4_VEH_24hr


title: Mu-RE_10w_ALF_24.ZT20


title: hippocampus, male, wildtype, chow, cohort1_4

value: dorsal hippocampus

value: wildtype

value: chow


title: iPSC-CM_Ind4_EPI_24hr

value: 0.5 uM epirubicin


title: hippocampus, male, wildtype, western, cohort1_2

value: male

value: western


title: Jurkat cells, DMSO, 6 hours, RUNX1 antibody [DMSO_RUNX1]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: DMSO


title: Mu-RE_26w_ALF_23.ZT20

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 26 weeks


title: iPSC-CM_Ind4_DNR_24hr

value: female

value: 0.5 uM daunorubicin


title: Jurkat cells, DMSO, 6 hours, ETS1 antibody [DMSO_ETS1]

value: T cells

value: WT


title: hippocampus, male, alzheimer, western, cohort1_1

value: alzheimer


title: Mu-RE_10w_ALF_22.ZT20

value: 10-12 weeks

value: ad libitum

value: whole muscle


title: Mu-RE_10w_ALF_21.ZT20


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_for_RUNX]

value: IgG


title: iPSC-CM_Ind4_TRZ_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM trastuzumab


title: Mu-RE_10w_ALF_20.ZT16

value: male