title: 10H_M_2739


title: 10H_M_2741

status: Public on Apr 18 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain

tag: Sex

value: male


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title: 10H_M_1348


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title: 10H_M_337


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title: 10H_M_331


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title: 10H_M_330


title: Hu5/KD3_3

city: Nagakute

first: Yohei

last: Okada

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Neural iPSC Research, Institute for Medical Science of Aging

country: Japan

institute: Aichi Medical University

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to hg38 whole-genome using STAR v.2.7.5a with parameters -twopassMode
Reads counts of transcripts (feature counts) were calculated using FeatureCounts of the Rsubread package.
Ensembl gene annotation (Homo_sapiens.GRCh38.100.chr.gtf) was used for the transcripts counts.
For all 25 samples, the data normalization was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Ensembl_ENSG_ID and normalized feature counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Skeletal muscles derived from MYOD1-hiPSCs were cultured for 2, 3, and 6 days in myotube differentiation medium. Undifferentaited hiPSCs were cultured in StemFit medium (AK02N). Skeletal muscles derived from Hu5/KD3 was cultured in differentiation medium for 3 days.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit.
Strand-Specific Transcriptome Library Construction Protocol or BGISEQ-500 RNA-Seq Library Preparation Protocol (DNBSEQ)

tag: cell line

tag: cell type

value: human myoblast cell line-derived Skeletal Mucles


title: 10H_M_352


title: Hu5/KD3_2


title: 10H_M_334


title: 10H_M_345


title: Hu5/KD3_1


title: 10H_M_328


title: TIGE9_d6

value: iPSC derived Skeletal Muscles


title: YFE16_d6


title: 10H_M_327


title: 10H_M_332


title: EKN3_d6

description: EKN3 3HA-MYOD1


title: 10H_M_325


title: 10H_M_329


title: TIGE9_d3


title: 10H_M_324


title: 10H_M_323


title: YFE16_d3


title: 10H_M_321


title: 10H_M_322


title: EKN3_d3

description: EKN3 3HA-MYOD1


title: 10H_M_320


title: 409B2_d2

description: 409B2 MYOD1


title: G418 clone 6_d2

description: 201B7 3HA-MYOD1_G418 clone 6


title: G418 clone 5_d2

description: 201B7 3HA-MYOD1_G418 clone 5


title: 10H_M_191


title: 10H_M_319


title: 10H_M_190


title: G418 clone 2_d2

description: 201B7 3HA-MYOD1_G418 clone 2


title: 10H_M_189


title: 10H_M_326


title: G418 clone 1_d2

description: 201B7 3HA-MYOD1_G418 clone 1


title: 10H_M_188


title: G418 bulk_d2

description: 201B7 3HA-MYOD1_G418 bulk


title: Puro clone 6_d2

description: 201B7 3HA-MYOD1_Puro clone 6


title: Puro clone 5_d2

description: 201B7 3HA-MYOD1_Puro clone 5


title: 10H_M_186


title: 10H_M_187


title: Puro clone 3_d2

description: 201B7 3HA-MYOD1_Puro clone 3


title: 10H_M_185


title: Puro clone 2_d2

description: 201B7 3HA-MYOD1_Puro clone 2


title: Puro bulk_d2

description: 201B7 3HA-MYOD1_Puro bulk


title: Puro clone 4_d2

description: 201B7 3HA-MYOD1_Puro clone 4


title: G418 bulk_Undiff

description: 201B7 3HA-MYOD1_G418 bulk

value: Undifferentiated iPSCs


title: 409B2_Undiff

description: 409B2 MYOD1


title: Puro bulk_Undiff

description: 201B7 3HA-MYOD1_Puro bulk


title: 10H_M_181


title: 10H_M_183


title: 10H_M_179


title: 10H_M_182


title: 10H_M_178


title: G418 clone 4_d2

description: 201B7 3HA-MYOD1_G418 clone 4


title: EC from young mouse 3

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

description:
Endothelial cells from young mouse 3
EC6

data_processing:
CASAVA version 1.7 software
Sequenced reads were trimmed to adaptor sequence, and masked for low complexity sequencing, then mapped to mm8 genome assembly using bowtie v0.12.2
Reads per kilobase of 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.exon per Megabase of library size (RPKM) were
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm8
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: Vascular endothelial cells

extract_protocol:
Tissues were removed, homogenized for RNA extraction. Illumina TrueSeq RNA sample prepration kit was used with 1 ug of total RNA.
Libraries were prepared according to standard Illumina's instructions.

value: young

tag: treatment

value: acid injury

tag: tissue

value: lung

value: Endothelial cells


title: EC from young mouse 2

description:
Endothelial cells from young mouse 2
EC5


title: 10H_M_176


title: EC from old mouse 3

description:
Endothelial cells from old mouse 3
EC3

value: old


title: 10H_M_175


title: EC from old mouse 2

description:
Endothelial cells from old mouse 2
EC2


title: 10H_M_174


title: 10H_M_184


title: 10H_M_173


title: EC from old mouse 1

description:
Endothelial cells from old mouse 1
EC1


title: 10H_M_171


title: 10H_M_172


title: 10H_M_170


title: 10H_M_180


title: 10H_M_169


title: 10H_M_168


title: 204001350089_R08C01

type: genomic

city: Pavia

first: Jessica

last: Garau

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: main analyses

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPICBeadchip using standard Illumina protocol

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

data_processing:
R environnment and packages Minfi and ChAMP
Average Beta

label: Cy5 and Cy3

source_name: PBMCs

label_protocol: Standard Illumina Protocol

growth_protocol: cells obtained from patients PBMCs

extract_protocol: genomic DNA was extracted from PBMCs/kits according to manufacturer instructions

treatment_protocol: no treatment

tag: subject

value: Control

tag: gender

value: Female

tag: patient group


title: 204001350089_R07C01

description: main analyses

value: Male


title: 204001350088_R07C01

description: main analyses


title: 204001350088_R05C01

description: main analyses

value: Patient

value: Severe


title: 10H_M_177


title: 10H_M_165


title: 204001350088_R08C01

description: main analyses


title: 10H_M_166


title: 204001350088_R02C01

description: main analyses

value: Mild


title: 10H_M_164


title: 10H_M_167


title: 10H_M_163


title: EC from young mouse 1

description:
Endothelial cells from young mouse 1
EC4


title: 204001350088_R01C01

description: main analyses


title: 204001350085_R07C01

description: main analyses


title: 204001350085_R08C01

description: main analyses


title: 10H_M_161


title: 10H_M_162


title: 204001350085_R06C01

description: main analyses


title: 10H_M_160


title: 204001350085_R03C01

description: main analyses


title: 10H_M_157


title: 10H_M_159


title: 204001350088_R06C01

description: main analyses


title: 204001350085_R02C01

description: main analyses


title: 204001350088_R04C01

description: main analyses


title: 10H_M_156


title: 204001350085_R01C01

description: main analyses


title: 204001350088_R03C01

description: main analyses


title: 10H_M_154


title: 10H_M_153


title: 10H_M_152


title: 10H_M_151


title: MVP-3

city: Nanjing

first: Yanhu

last: Wu

state: Jiangsu Province

address: 300 Guang Zhou Road, Nanjing, Jiangsu Province, China

country: China

institute: Jiangsu Province People's Hospital

data_processing:
Illumina bcl2fastq software used for basecalling
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by tophat2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
RQ1 DNase (Promega) was added to total RNA to remove DNA. Smartspec plus (BioRad) was used to measure the absorbance at 260nm/280nm (A260/A280) to determine the quality and quantity of the purified RNA. RNA integrity was further verified by 1.5% agarose gel
For each sample, RNA-seq library was prepared by using 1 μg of total RNA. mRNAs were captured by VAHTS mRNA capture Beads（Vazyme, N401）. The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544). Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). After purification of ligation product and size fractioning to 300-500bps , the ligated products were amplified，purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.
Manufacturer's instructions was followed for high-throughput sequencing and the libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

value: peripheral blood mononuclear cells

value: mitral valve prolapse patient


title: MVP-2


title: MVP-5


title: MVP-1


title: MVP-4


title: 10H_M_150

value: male


title: Control-5

value: healthy individual


title: Control-4


title: 10H_M_148


title: 10H_M_149


title: Control-3


title: Control-2


title: 204001350085_R05C01

description: main analyses


title: 10H_M_147


title: 10H_M_158


title: 10H_M_146


title: Control-1


title: 10H_M_145


title: 10H_M_144


title: 10H_M_155


title: 10H_M_142


title: 40kPa_CAF05_rep2

city: Urbana

first: Taher

last: Saif

state: IL

address: 105 S Mathews Ave

department: Grainger College of Engineering

institute: University of Illinois at Urbana-Champaign

data_processing:
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used the first 33nt for adaptor trimming).
Trimmed sequences were mapped to GRCh38/hg38 using HISAT2
Gene counts were quantified using HTSeq
Assembly: GRCh38
Supplementary files format and content: tab-delimited files for raw HTSeq gene counts for each sample

source_name: Colorectal cancer

growth_protocol: Human primary colorectal tumor CAFs, CAF05 (Neuromics), were maintained in VitroPlus III Low Serum, Complete medium (Neuromics) supplemented with 1% penicillin-streptomycin (Lonza).  Cells were grown at 37°C in a humidified incubator with 5% CO2. No additional supplements were provided.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer instructions. Samples for RNA-seq were further cleaned up by RNeasy Mini Kit (QIAGEN).
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) . Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

treatment_protocol: CAFs were grown on polyacrylamide hydrogel (PA gel) substrates of 1 kPa, 10 kPa and 40 kPa elastic modulus. Fibronectin coating were applied on the substrates. Cell were also grown on plastic dish that has an elastic modulus of 3.4 GPa.

value: Colorectal cancer

value: Cancer Associated Fibroblast

tag: genotype

value: WT

value: 40kPa substrate stiffness


title: 3.4GPa_CAF05_rep3

value: 3.4GPa substrate stiffness


title: 40kPa_CAF05_rep3


title: 10H_M_141


title: 3.4GPa_CAF05_rep1


title: 3.4GPa_CAF05_rep2


title: 40kPa_CAF05_rep1


title: 10kPa_CAF05_rep3

value: 10kPa substrate stiffness


title: 10H_M_138


title: 10H_M_137


title: 10kPa_CAF05_rep1


title: 10kPa_CAF05_rep2


title: 10H_M_136


title: 1kPa_CAF05_rep3

value: 1kPa substrate stiffness


title: 1kPa_CAF05_rep2


title: 1kPa_CAF05_rep1


title: 10H_M_135


title: 10H_M_134


title: 10H_M_133


title: 10H_M_132


title: 10H_M_131


title: 10H_M_340


title: 10H_M_130


title: 10H_M_143


title: HCC44_Tumor

city: Bellinzona

first: Roger

last: Geiger

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
For initial quality control of sequencing data, FastQC (https://www.bioinformatics.ba) and MultiQC were used.
The reads were trimmed to remove sequencing adapters using Trimmomatic.
Transcript abundance estimates for all transcripts were performed using Kallisto to generate counts files.
Count files were imported to R using the 'tximport' R package and summarized to gene level abundances. Only protein-coding genes with valid chromosomal mappings were retained.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

molecule: polyA RNA

source_name: HCC

extract_protocol:
Frozen cell pellets were re-suspended in lysis buffer from the GenElute™Mammalian Total RNA Miniprep Kit (SIGMA). mRNA was purified following manufacturer’s instructions.
The RNA sample was checked for quality and quantity using a NanoDrop spectrophotometer and an Agilent Bioanalyzer. Poly(A) mRNA was enriched from the total RNA using oligo(dT) magnetic beads. The enriched mRNA was fragmented into smaller pieces using divalent cations under elevated temperature. The fragmented mRNA was used as a template to synthesize first-strand cDNA using random hexamer primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. he double-stranded cDNA was treated with T4 DNA polymerase and Klenow DNA polymerase to create blunt ends, followed by adapter ligation using T4 DNA ligase. The adapter-ligated cDNA fragments were size-selected using agarose gel electrophoresis or bead-based methods, and then PCR amplified to generate the final cDNA library.

value: HCC

value: CD14+ cells

value: Primary


title: HCC47_Tumor


title: HCC40_Tumor


title: SYN+WNT 83i

city: Los Angeles

first: Wensen

last: Jiang

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ format by using bcl2fastq v2.20 (Illumina, San Diego, California). More than 200 million reads were obtained for each sample. Reads were mapped to the human GRCh38 genome and count quantification was done using 10x Genomics Cell Ranger v.7.0.0.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files

extract_protocol: The cells were collected and resuspended in PBS at 1,500 cells/mL and 100uL of the cell solutions was processed for single-cell RNA sequencing. Single-cell RNA-Seq libraries were prepared per the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California) using the 10x Genomics Chromium Controller. Barcoded sequencing libraries were quantified by quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific, Waltham, MA). Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) as per the Single Cell 3′ v3.1 Reagent Kits User Guide, with a sequencing depth of ~40,000 reads/cell.

treatment_protocol: iPSC (D0) were treated with factors and differentiated into Presomitic Mesoderm (PSM, D4), Somite (SM, D8), Sclerotome (SCL, D11), Early Syndetome (SYN, D32). Another attempt was made from iPSC to syndetome, but at D8, WNT-C59 was added to prevent the formation of neural cluster. The product was obtained as improved Syndetome (SYN+WNT). The improved assay was tested on another cell line 83i (WNT+83i)

value: iPSC

tag: cell type (differentiated)

value: improved Syndetome (SYN+WNT+83i)

value: Growth Factor + WNT inhibitor


title: 10H_M_140


title: SCL

description: 10x Genomics

value: Sclerotome (SCL, D11)

value: Growth Factor


title: SYN

description: 10x Genomics

value: Early Syndetome (SYN, D32)


title: 10H_M_128

value: male


title: 10H_M_129


title: 10H_M_126


title: SYN+WNT

description: 10x Genomics

value: improved Syndetome (SYN+WNT)


title: SM

description: 10x Genomics

value: Somite (SM, D8)


title: 10H_M_125


title: 10H_M_127


title: 10H_M_139


title: PSM

description: 10x Genomics

value: Presomitic Mesoderm (PSM, D4)


title: iPSC

description: 10x Genomics

value: iPSC (D0)


title: 10H_M_123


title: 10H_M_124


title: T_cells_ChronicallyActivated_stimulated_Donor3

source_name: Blood

growth_protocol: Sorted naïve CD8+ T cells were re-suspended in complete RPMI medium (RPMI-1640, 10% FBS, 1X GlutaMax, 1X Peninicilin/Streptomycin, 1X Hepes, 1X non-essential aminoacids, 1X Sodium Pyruvate, 0.01% β-mercaptoethanol) containing rIL-2 (40 U/mL, made in house) and 150,000 cells per well were stimulated with plate-bound anti-CD3 (1 mg/mL, clone TR66, made in house) and anti-CD28 antibodies (0.5 ug/mL, BD) in 96-well Nunc Cell Culture Plates (ThermoFisher)

treatment_protocol: For chronic stimulation, cells were cultured for 14 days in a humified CO2 incubator at 37 ̊C with and cells were split 1:2 every third day and transferred into plates freshly coated with anti-CD3 and anti-CD28 antibodies. For transient activation naïve CD8+ T cells were stimulated for 3 days and then transferred into 96 U bottom plates and rested in the presence of rhIL-2 only for the remaining 11 days of culture. For re-stimulation experiments, T cells were activated, rested 8 days, and then re-stimulated from day 11 to 14. At day 14 T cells were collected and washed.

value: Blood

value: Tcell

value: 14 days activated


title: 10H_M_122


title: T_cells_Reactivated_stimulated_Donor3

value: 3d act, 8d rested, 3d act


title: 10H_M_120


title: 10H_M_121


title: T_cells_ChronicallyActivated_stimulated_Donor2


title: 10H_M_119


title: T_cells_Reactivated_stimulated_Donor2


title: 10H_M_118


title: T_cells_TransientlyActivated_stimulated_Donor2

value: 3d activated, 11d rested


title: T_cells_ChronicallyActivated_stimulated_Donor1


title: 10H_M_117


title: T_cells_Reactivated_stimulated_Donor1


title: T_cells_TransientlyActivated_stimulated_Donor1


title: TC28a2 cells transfected with ZEB1 overexpression vector, replicate 3

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
Raw FASTQ files were aligned using HISAT2 and assigned to genomic features with the featureCounts function of the Subread package.
Assembly: GRCh38
Supplementary files format and content: Counts matrix

extract_protocol:
Total RNA was isolated from TC28a2 cells transfected with a vector control (n=3) or ZEB1 overexpression vector (n=3) 48 hours post-transfection using TRIzol. RNA quality was confirmed using NanoDrop measurements of OD 260/280 and 260/230.
DRUG-seq (high throughput low-cost RNA-Seq) libraries were generated for all replicas and the libraries sequenced on Illumina NextSeq 2000.

value: chondrocytes

value: ZEB1 overexpression vector


title: 10H_M_115


title: TC28a2 cells transfected with ZEB1 overexpression vector, replicate 1


title: TC28a2 cells transfected with ZEB1 overexpression vector, replicate 2


title: TC28a2 cells transfected with control vector, replicate 3 [TC28_ZEB1_DRUGseq]

value: control vector


title: TC28a2 cells transfected with control vector, replicate 2 [TC28_ZEB1_DRUGseq]


title: TC28a2 cells transfected with control vector, replicate 1 [TC28_ZEB1_DRUGseq]


title: 10H_M_113


title: 10H_M_112


title: AML-9-9-FLT3-iPSC-PDX

first: Nataly

last: Cruz

address: 1470 Madison Ave

institute: Mount Sinai

description:
10x Genomics
AML9_harmony_integrated_seurat_object.rds

data_processing:
Sequenced fastq files were aligned, filtered, barcoded and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version6.1.0, by 10X Genomics with Cell Ranger, GRCh38database (version2020-A) as the human genome reference.
Each dataset was filtered to retain cells with >=1000 UMIs, >=400 genes expressed, and <25% of the reads mapping to the mitochondrial genome. UMI counts were then normalized so that each cell had a total of 10,000 UMIs across all genes and these normalized counts were log-transformed with a pseudocount of 1 using the "LogNormalize" function in the Seurat package. The top 2000 most highly variable genes were identified using the "vst" selection method of "FindVariableFeatures" function and counts were scaled using the "ScaleData" function. Datasets were processed using the Seurat package
Principal component analysis was performed using the top 2000 highly variable features ("RunPCA" function) and the top 30 principal components were used in the downstream analysis.  Datasets for each patient were integrated separately by using the "RunHarmony" function in the harmony package (version 0.1.0). K-Nearest Neighbor graphs were obtained by using the "FindNeighbors" function whereas the UMAPs were obtained by the "RunUMAP" function (Korsunsky et. al., 2019). The Louvain algorithm was used to cluster cells based on expression similarity. The resolution was set at 0.4 for the AML-4 integrated dataset, and at 0.2 for AML-9 and AML-47 datasets for optimal clustering. Cell density estimations were performed using the stat_density_2d function of the ggplot2 (version 3.3.5) package.
Harmony integrated seurat objects samples were save as RDS files using the "saveRDS" function for R (v4.1.0)
Assembly: hg38
Supplementary files format and content: CellRanger-generated files (barcodes.tsv, features.tsv, matrix.mtx); Seurat object

source_name: hematopoietic

growth_protocol: Culture of human iPSCs on mitotically inactivated MEFs was performed as previously described (Chang et al., 2018) . Hematopoietic differen tiation was performed using a spin-EB protocol previously described (Chang et al., 2018). In the end of the differentiation culture, the cells were collected and dissociated with accutase into single cells and used for flow cytometry, cytological analyses or clonogenic assays

extract_protocol:
CD45-sorted
Library was performed according to the manufacter's instructions (Chromium 10x Genomics 3' protocol (v3.0).

value: iPSC-PDX

value: hematopoietic


title: T_cells_TransientlyActivated_stimulated_Donor3


title: TC28a2 cells transfected with FAP overexpression vector, replicate 2

extract_protocol:
Total RNA was isolated from TC28a2 cells transfected with a vector control (n=3) or FAP overexpression vector (n=3) 48 hours post-transfection using TRIzol. RNA quality was confirmed using NanoDrop measurements of OD 260/280 and 260/230.
DRUG-seq (high throughput low-cost RNA-Seq) libraries were generated for all replicas and the libraries sequenced on Illumina NextSeq 2000.

value: FAP overexpression vector


title: TC28a2 cells transfected with FAP overexpression vector, replicate 3


title: 10H_M_111


title: TC28a2 cells transfected with control vector, replicate 3


title: TC28a2 cells transfected with control vector, replicate 2


title: TC28a2 cells transfected with FAP overexpression vector, replicate 1


title: AML-47-iPSC-PDX-Secondary

description:
10x Genomics
AML47_harmony_integrated_seurat_object.rds

value: iPSC-HSPC-PDX


title: AML-47-iPSC-PDX


title: TC28a2 cells transfected with control vector, replicate 1


title: 10H_M_109

value: male


title: AML-47-iPSC-HSPCs

value: iPSC-HSPC


title: 10H_M_114


title: AML-47-Primary

value: Primary AML


title: AML-9-9-iPSC-PDX


title: 10H_M_108


title: 10H_M_116


title: Exo7T-seq_Ankrd31.EA.null_14dpp_rep2

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer C

data_processing:
After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.  Base calls were perfomed using bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500 or NextSeq 2000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).  Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Adaptors were swapped for some samples (indicated by sample names), and reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped. Maps were analyzed using R versions 3.3.1 to 4.0.3 <http://www.r-project.org>.
Assembly: mm10
Supplementary files format and content: bigWig files contain read counts at positions of ssDNA. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.
Library strategy: Exo7T-seq

source_name: testis

extract_protocol:
Testis cells from 14.5-dpp juvenile mice were obtained as described previously (ref. 1). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 1). In-plug overhang removal with exonuclease VII and exonuclease T and adaptor ligation were performed as described previously (ref. 1, 2, 3) with minor modifications. In brief, plugs were washed in 1 ml of exonuclease VII buffer for 15 min twice, treated with 50 units of exonuclease VII in 100 µl of exonuclease VII buffer at 37°C for 60 min and washed once with 1ml TE. Then plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min. After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 1, 2, 3). (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 3) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.  Base calls were perfomed using bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500 or NextSeq 2000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.  Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).  Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.  Reads for Exo7T-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Maps were analyzed using R versions 3.3.1 to 4.0.3 <http://www.r-project.org>.

value: Spermatocytes

value: testis

value: 14 days post partum


title: 10H_M_107


title: AML-9-iPSC-PDX-Secondary


title: ATCC13883-replicate2

city: Baotou

first: Guo

middle: qing

last: Liu

state: Inner Mongolia

address: 7 Arding street

department: School of Life Science and Technology

institute: Inner Mongolia University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis-natural antisense transcripts. It can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes. Then, we extract upstream 700bp sequence of Transcription Start Site for predicting promoter using TDNN.(Time-DelayNeural Network)
Rockhopper was used to identify new intergenic region transcripts, and Blastx was compared with the nr library to annotate the newly predicted transgenic regions, and the unmarked transcripts were used as candidate non-coding sRNAs. RNA fold and Inta RNA were used to predict secondary structure and target gene respectively.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Assembly: Klebsiella pneumoniae (GCA_000240185.2)
Supplementary files format and content: tab-delimited text files include COUNT and RPKM  values for each Sample

organism: Klebsiella pneumoniae

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.


title: KPN16-replicate3


title: ATCC13883-replicate1


title: AML-9-iPSC-PDX_2


title: KPN16-replicate2


title: KPN16-replicate1


title: 10H_M_106


title: Exo7T-seq_Ankrd31.EA.null_14dpp_rep1


title: 10H_M_104


title: Exo7T-seq_Ankrd31.EA.trunc_14dpp_rep2


title: AML-9-iPSC-HSPCs_2


title: AML-9-Primary-PDX

value: AML-PDX


title: Exo7T-seq_Ankrd31.EA_14dpp_rep2


title: Exo7T-seq_Ankrd31.EA_14dpp_rep1


title: 10H_M_110


title: AML-9-Primary


title: Exo7T-seq_Ankrd31.trunc_14dpp_rep1


title: Exo7T-seq_Ankrd31.trunc_14dpp_rep2


title: ATCC13883-replicate3


title: 10H_M_103


title: AML-4-iPSC-PDX

description:
10x Genomics
AML4_harmony_integrated_seurat_object.rds


title: AML-4-Primary


title: iFIRKO

city: Bunkyo-ku

first: yoshihiro

last: niitsu

state: Tokyo

address: 1-5-45 Yushima

institute: Tokyo medical and dental univercity

data_processing:
Sequence reads were analyzed on GeneGlobe Data Analysis Center (Qiagen).
Read count normalization were performed by RPM method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized data by RPM method for each sample.

source_name: Extracellular vesicles

extract_protocol:
Total RNA of the serum extracellular vesicles was isolated using miRNeasy Micro Kit (Qiagen).
Libraries were generated from the total RNA using QIAseq miRNA Library Kit (Qiagen)

treatment_protocol: Seven-week-old male iFIRKO and control mice were intraperitoneally injected with 100 mg/kg tamoxifen for 5 consecutive days and were analyzed 3 days after the last administration of tamoxifen treatment.

value: Extracellular vesicles

value: Adipoq-CreERT2; Insr flox/flox

value: tamoxifen injection

tag: time

value: Day 3


title: 10H_M_102


title: Exo7T-seq_Ankrd31.null_14dpp_rep2


title: AML-4-iPSC-HSPC


title: 10H_M_105


title: control

value: WT


title: 10H_M_101


title: Exo7T-seq_Spo11.null_14dpp_rep2


title: AML-4-Primary-PDX


title: Exo7T-seq_Ankrd31.null_14dpp_rep1


title: 10H_M_98


title: 10H_M_100


title: Exo7T-seq_Ankrd31.EA.trunc_14dpp_rep1


title: #3_shMfn2+Dox+TNF

city: Chicago

first: Jalees

last: Rehman

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

description: Gene expression data from human lung microvascular endothelial cells

data_processing:
The sequenced reads from all samples were aligned to the human (hg38) reference   genome with STAR v. 2.4.2, and the aligned reads were used to quantify mRNA expression by   using HTSeq-count v. 0.6.1.
Genome_build: hg38

source_name: endothelial cells

growth_protocol: Human lung microvascular endothelial cells (HLMVECs) were purchased from  Lonza and cultured with EGM2 (Lonza) including all supplements and 10% FBS (Hyclone) until  passage 8.

extract_protocol: Total RNA was isolated by using   phenol/chloroform and TRIzol Reagent, and its quality was evaluated with gel QC.

treatment_protocol: The cells were transduced with doxycycline inducible lentiviral shMfn2 RNA with  1:2000 dilution polybrene (Millipore, TR-1003-G) for 24h and then the media was changed. After  48h, the cells were treated with doxycycline (200 ng/mL) or DMSO (control) for 72h to knock-  down endogenous Mfn2. For an exact biological control, we used lenti-Mfn2 shRNA expressing    cells which were treated with DMSO and represented as Control. Mfn2-KD ECs were treated  with doxycycline.

tag: lentivirus

value: shMfn2 RNA

value: doxycycline (200 ng/mL) + TNF


title: NanogKO:Esrrb:Nanog (44JN) rep3 S9/3

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
Raw reads where processed with bcl2fastq (v 2.19.1)
Cutadapt trimming (v 2.2.0)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.4.1) flags (-b -f3 -F4 -F8 -q7)
Normalised bigwigs for visualisation was generated with bamCoverage (v 4.4.0) using binsize 5 and RPKM.
Peaks were called using macs2 (v 2.2.0) -f BAMPE, -q 0.001
Consensus peaks pr condition was defined as peaks present in all 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak bed (except for Input sample)

growth_protocol: SL (Serum:Lif) medium: GMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco), 100 μM 2-mercaptoethanol (Sigma), 1× MEM non-essential amino acids, 2 mM l-glutamine, 1 mM sodium pyruvate (all from Gibco), 1,000 U ml−1 leukaemia inhibitory factor (LIF) (made in house)

extract_protocol:
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter, for PECAM+PDGFRA- cells.
Nuclei preparation and transposase treatment was carried out as described in (Stewart-Morgan et al. 2019)
NEBNext Ultra II DNA library kit

value: ESC


title: Exo7T-seq_wt_14dpp_rep1

value: wt


title: SB3

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell line

extract_protocol:
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq2 (Keren-Shaul et al, Nature Protocols 2019)
single cell RNA-seq for gene expression quantitation

value: cell line


title: #3_shMfn2+Dox

value: Human lung microvascular endothelial cells (HLMVECs)

value: doxycycline (200 ng/mL)


title: NanogKO:Esrrb:Nanog (44JN) rep2 S6


title: 10H_M_97

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: male


title: Exo7T-seq_Spo11.null_14dpp_rep1

value: Spermatocytes


title: NanogKO:Esrrb:Nanog (44JN) rep1 S3


title: #3_shMfn2+TNF

value: TNF


title: 10H_M_99


title: 10H_M_95


title: NanogKO:Esrrb (44J) rep2 S5


title: #2_shMfn2+Dox+TNF


title: 10H_M_96


title: NanogKO (44C6) rep3 S7/1

source_name: N{delta}

value: N{delta}


title: #3_shMfn2+DMSO

value: DMSO


title: NanogKO (44C6) rep2 S4


title: NanogKO:Esrrb (44J) rep1 S2


title: NanogKO (44C6) rep1 S1


title: Exo7T-seq_wt_14dpp_rep2

value: testis

value: 14 days post partum


title: NanogKO:Esrrb:Nanog (44JN), input, rep3, S6

data_processing:
Raw reads where processed with bcl2fastq (v 2.19.1)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.4.1) flags (-b -F4 -q13)
Normalised bigwigs for visualisation was generated with bamCoverage (anaconda2 v 4.4.0) using binsize 5 and RPKM.
Peaks were called using macs2 (anaconda2 v 2.2.0) against condition and replicate specific input samples specifying q ≤ 0.01)
Consensus peaks pr condition was defined as peaks present in all 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak bed (except for Input sample)

extract_protocol:
Chromatin was crosslinked for 10 min in 1% FA (single fixation), or with a subsequent 45 min fixation with 2 mM Di(N-succinimidyl) glutarate (double fixation) and stopped in glycine.
NEBNext Ultra II DNA library kit

tag: chip antibody


title: #2_shMfn2+Dox


title: 10H_M_94

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: 10H_M_93


title: NanogKO:Esrrb (44J), input, rep3, S5


title: #2_shMfn2+TNF


title: NanogKO:Esrrb:Nanog (44JN), input, rep2, S4


title: 10H_M_92


title: NanogKO:Esrrb (44J), input, rep2, S3


title: 10H_M_91


title: NanogKO:Esrrb:Nanog (44JN), input, rep1, S2


title: NanogKO:Esrrb (44J), input, rep1, S1


title: NanogKO:Esrrb (44J) rep3 S8/2


title: NanogKO:Esrrb:Nanog (44JN), Esrrb ChIP, rep3, S6


title: #1_shMfn2+Dox+TNF


title: #1_shMfn2+Dox


title: 10H_M_90


title: NanogKO:Esrrb (44J), Esrrb ChIP, rep3, S5


title: NanogKO:Esrrb:Nanog (44JN), Esrrb ChIP, rep2, S4


title: 10H_M_88


title: NanogKO:Esrrb (44J), Esrrb ChIP, rep2, S3


title: NanogKO:Esrrb (44J), Esrrb ChIP, rep1, S1


title: #1_shMfn2+TNF


title: 10H_M_87


title: #1_shMfn2+DMSO


title: KIT_Day5

city: Worcester

first: William

middle: T

last: Frantz

state: MA

address: 368 Plantation Street

department: Molecular Medicine

institute: UMass Medical School

data_processing:
Base call files were generated from the Illumina NextSeq 500
Fastq files for each sample were generated from base call files using CellRanger's MkFastQ
Alignment, annotation, and counting were performed using CellRanger
Downstream QC, Dimenstion Reduction, UMAP generation, and DEG analysis were performed in Seuratv3
Genome_build: Lawson lab zebrafish annotation V4.3.2
Supplementary_files_format_and_content: txt.gz fiiles saved from Seurat Objects

organism: Danio rerio

source_name: Tg(mitfa:nlsEGFP) FACS enriched cells

growth_protocol: Tg(mitfa:nlsEGFP) animals in either a WT or kita(lf) background were raised to 3-6 months of age

extract_protocol:
Scales were removed, zebrafish skin cut and peeled off underlying musce, enzymatic and mechanical dissociation, and mitfa:nlsEGFP cells were enriched for during FACS, single cell barcoding using the 10X controller
10X 3' v3.1 scRNAseq library prep steps were followed
Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit

treatment_protocol: 750nM Neocuproine applied for 24 hours between Day 0 and Day 1 to ablate mature melanocytes

value: kita(lf)

tag: day


title: KIT_Day3_2


title: #2_shMfn2+DMSO


title: NanogKO:Esrrb:Nanog (44JN), Esrrb ChIP, rep1, S2


title: KIT_Day3_1


title: 10H_M_86

tag: brain region


title: 10H_M_85

tag: age


title: KIT_Day0


title: KIT_Day1


title: WT_Day10


title: KIT_Day2


title: 10H_M_84

tag: strain


title: Rif1_input

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Fastq files for chip-seq samples were generated with bcl2fastq 1.8.3 from Illumina.
ChIP-seq reads were trimmed from 5' end eith at least 6 bp until the final base had a quality score > 30, using Trim Galore , discarding reads left with < 70 bp
ChIP-seq data was aligned to sacCer3 genome from UCSC with bowtie2 (2.2.0) using -k 1
bigWig files were created by using deeptool bamCompare command, normalizing to reads per kilomillion by multiplying by 1 kilomillion and dividing by the total number of alignments for each sample.
Peask were called by using Macs2 callpeak command with -g 1.2e-7 --nomodel AND with the significance cut-off q-value <=0.01
Assembly: sacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against  FLAG (F1804-1MG; Sigma-Aldrich),
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: none (input)


title: WT_input


title: WT_IP

value: FLAG (F1804-1MG; Sigma-Aldrich)


title: Rif1_IP


title: WT_Day5

value: WT


title: WT_Day3


title: WT_Day2


title: 10H_M_89

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: Sex


title: Sen1_YPD_IP


title: KIT_Day10


title: 10H_M_81


title: WT_Day1


title: Sen1_YPD_input


title: WT_Day0_2


title: 10H_M_80


title: WT_Day0_1


title: Sen1_SDC_IP


title: 10H_M_79


title: PD-1+1

city: Shanghai

first: Jun

last: Deng

state: Shanghai

address: No. 25, Lane 2200, Xietu Road, Xuhui District

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw reads were aligned to the mouse reference genome (mm10) using Tophat2 RNASeq alignment software Hisat2.
The raw reads alignment files were processed using Hisat SAMtools and HTSeq to generate read counts for every gene.
The read counts were then normalized using R package DESeq2. The normalized read counts were then centered and scaled for each gene, generating z-scores. The z-scores basically represent how many standard deviations one particular count is from the average count for that gene. P-values obtained from multiple tests were adjusted using Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary immune cells

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell subtype

value: primary immune cells

value: NZB/W F1

value: 20 weeks


title: PD-1+2

tag: cell type


title: Sen1_SDC_input


title: 10H_M_78


title: Glc7_YPD_IP


title: 10H_M_82


title: PD-1-2

tag: treatment


title: 10H_M_77


title: 10H_M_76


title: P60_BL6Retina_5

city: Bethesda

first: Hong

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: CPM of RNAseq is in the columns named by raw file name.

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq2500 Sequencer at NIDDK Genomics Facility
Single-end reads of RNA-seq are aligned to the mm10 genome assembly using STAR.
Output bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM)
Assembly: mm10
Supplementary files format and content: comma delimited files include CPM values for each gene

source_name: whole retina

extract_protocol:
Total RNA was prepared from dissected retinas (n=3 / library) by TRIzol (ThermoFisher) and RNeasy Micro kit (Qiagen) isolation. Quantification using Qubit RNA Broad-range assay Kit (Thermo Fischer Scientific). 200-400 ng of total RNA from each sample was used for constructing RNA-seq libraries with SMARTer total RNA Sample Prep kit (TakaraBio).
Each RNA-seq librariy was constructed from ~250 ng purified RNA samples by SMARTer total RNA Sample Prep kit (TakaraBio).

treatment_protocol: Mice were kept in a 12h light / 12 h dark cycle and tissues taken in the light phase between ~14.00 - 18.00 hours.

value: wild type mice (C57BL/6J)

tag: cells and tissue

value: retina


title: 10H_M_74


title: P60_BL6Retina_4


title: P60_BL6Retina_6


title: Glc7_YPD_input


title: Glc7_SDC_input


title: P60_BL6Retina_3


title: P60_BL6Retina_2


title: P60_BL6Retina_1


title: 10H_M_73


title: P28_BL6Retina_4


title: PD-1+3


title: 10H_M_72


title: MI-OMU01_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.5), Trimmomatic (ver. 0.39) and cutadapt (ver. 2.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.98) using STAR (ver. 2.7.2b).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.4)
Supplementary files format and content: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Bristol N2

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for one day on mNGM plates covered with OP50 (control-fed group) or B. subtilis natto (MI-OMU01-fed group).

tag: agent

tag: cell line

value: Bristol N2

value: wild-type

value: hermaphrodite

value: three-day-old


title: PD-1-1


title: MI-OMU01_rep1


title: P28_BL6Retina_3


title: P28_BL6Retina_2


title: OP50_rep2


title: 10H_M_71

city: La Jolla

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: 10H_M_70


title: PD-1-3


title: SI_TJ_out_4

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description: Social isolated rat after tamoxifen and Jaeumganghwa-tang treatment

data_processing:
All raw data passed FastQC quality check. Adapter trimming was firstly performed on raw data using cutadapt (v2.9)
The reference genome was downloaded from Ensembl (Rattus norvegicus release 99), and the reference genome index was built using STAR (v2.7.9a)
Paired-end trimmed reads alignment and raw read count calculation were both conducted using RSEM (v1.3.1)
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include expected-count values for each sample

organism: Rattus norvegicus

source_name: tumor-free mammary gland

growth_protocol: A total of 80 Sprague Dawley rats were obtained from Envigo and arrived at 6 weeks of age to Georgetown University animal facility located at the Department of Comparative Medicine. Rats were housed in groups of 3 per cage. All rats received semi-purified AIN93G diet. The animals were housed in a temperature- and humidity-controlled room with a 12-hour light-dark cycle

extract_protocol:
RNA from tumor-free mammary gland was extracted using Qiagen RNeasy Mini Kit (Qiagen, MD) according to the manufacturer’s instructions. RNA concentration and purity were analyzed by Nanodrop 1000 spectrophotometer
Paired-end, dual-indexed libraries for RNAseq were constructed from 500ng total RNA using the TruSeq Stranded Total RNA Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: ER+ mammary tumors were induced by administration of 10 mg of 7,12-dimethylbenz[a]anthracene (DMBA, Sigma) diluted in 1 mL of peanut oil by gavage when rats were 50-days of age.  Tumor development was checked weekly and when a first tumor become palpable per an animal, rats were divided into two groups: those kept on group-housed (3 animals per cage, n=40), or those housed singly (social isolation, n=40). When the first tumor per animal reached a size of ~11mm in diameter, group-housed and socially isolated rats were divided into 2 additional groups. At this point forward, the experiment contained four groups: group-housed treated with tamoxifen (n=19), group-housed treated with tamoxifen+JGT (n=17), socially isolated treated with tamoxifen (n=17) and socially isolated treated with tamoxifen+JGT (n=18).

tag: tissue

value: tumor-free mammary gland

value: TAM+JGT


title: P28_BL6Retina_1

tag: genotype


title: Glc7_SDC_IP


title: OP50_rep1


title: 52 hpf mCherry-positive

city: Calgary

first: Peng

last: Huang

state: Alberta

address: 3330 Hospital Drive N.W.

department: Department of Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: FACS mCherry+, 10x Genomics

data_processing:
A custom zebrafish transcriptome was prepared using V4.3.2 GTFs (Lawson et al., 2021) and the GRCz11 Danio rerio reference genome with appended mCherry sequence using standard CellRanger mkgtf and mkref pipelines.
FASTQs were then filtered and aligned to the reference using Cellranger count. All pipelines used 10X GEnomics CellRanger v5.0.0 software.
Downstream quality control, normalization ,dimension reduction, clustering and analysis was performed in R using Seurat v4.0.0.
Assembly: GRCz11
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: zebrafish trunks dissected at the beginning of the yolk extension

growth_protocol: Zebrafish embryos were raised at 28.5 °C. Embryos older than 24 hours were grown in fish water with added 1-phenyl 2-thiourea (PTU) to prevent pigmentation.

extract_protocol:
About 140 52 hpf nkx3.1NTR-mCherry embryos were anesthetized in fish water with 0.4% tricaine and maintained over ice during dissection. Trunks were dissected at the beginning of the yolk extension using a surgical scalpel. Dissected trunk tissues were then 0.25% Trypsin + 1 mM EDTA solution at 28.5°C for 20 minutes with gentle shaking at 300 rpm. Dissociated was then stopped, and dissolved tissue was washed with 1% FBS solution in 1x DPBS (Dulbecco’s phosphate-buffered saline, ThermoFisher Scientific) and strained. Live, mCherry+ cells were collected by fluorescence-activated cell sorting (FACS). Sorted cells were resuspended in 50 μl HBSS (Hank’s Balanced Salt Solution) + 2% BSA (Bovine Serum Albumin).
15,000 live, mCherry+ cells were loaded into the 10X Genomics Chromium Controller for droplet based cell separation. cDNA libraries were generated using the 10X Genomics 3’ gene expression profiling droplet-based scRNA-seq kit (v3.1 chemistry) according to manufacturer’s protocol. cDNA was amplified for 12 cycles and an index primer was added for sequencing using 14 PCR cycles

value: Sclerotome-derived cells

value: 52 hours post fertilization


title: SI_TJ_out_1


title: SI_TJ_out_2


title: SI_TJ_out_3


title: ompR mutant rep1

city: Beijing

first: Lijun

last: Wang

state: Beijing Shi

address: Shuangqing Road 30#

department: Department of Basic Medical Science

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
High quality reads in each sample were mapped to the reference genome using Bowtie2.
RSEM computes maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
TPM method is used to calculated expression level.
We identified differentially expressed genes by using the DESeq2 package.
Genome_build: K. pneumoniae ATCC43816 (CP009208)  as reference genome
Supplementary_files_format_and_content: An excel file include TPM, counts, fold change, P values for each Sample.

organism: Klebsiella pneumoniae ATCC 43816

source_name: bacteria culture

extract_protocol:
Total RNA was extracted from culture grown on BAP overnight using RNAprep pure Cell / Bacteria Kit according the manufacturer’s instructions (Tiangen Biotech, China) and further purified with a RNeasy Mini Kit (QIAGEN, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ompR knockout

tag: medium

value: Columbia blood plate

tag: temperature

tag: condition

value: 5 percent CO2


title: SI_TAM_out_4

description: Social isolated rat after tamoxifen treatment

value: TAM


title: ompR mutant rep2


title: P15_BL6Retina_3


title: 10H_M_66


title: P15_BL6Retina_1


title: P15_BL6Retina_2


title: 10H_M_65


title: SI_TAM_out_3


title: P6_BL6Retina_3


title: 10H_M_68


title: 10H_M_64


title: P6_BL6Retina_2


title: SI_TAM_out_1


title: 10H_M_69


title: Scrambled shRNA treated, PWK 2, senescent, 20 days

city: Novato

first: Taekyu

last: Kang

address: 8001 Redwood Blvd

institute: Buck Institute

description:
P4.SCR.postSEN
Usf2KD_allTPM.txt

data_processing:
Reads were mapped to their corresponding genomes via tophat v2.1.1
Reads were filtered for only those that mapped uniquely via samtools v1.3.1
Gene counts were generated using HTSeq v0.11.2
TPM counts were generated using custom R scripts.
Assembly: GRCm38.96, SPRET_EiJ_v1.96
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Tail

growth_protocol: All cells were cultured in DMEM with 10% FBS and 1% pen-strep in a 3% O2 and 10% CO2 humidified incubator at 37˚C.

extract_protocol:
RNA was extracted from cells using TriZol and chloroform extraction, then cleaned and treated with DNase on RNeasy columns.
Libraries were constructed in the corresponding sequencing facilities.

treatment_protocol: All senescent samples were treated with 15 Gy of ionizing radiation in a X-RAD 320 X-Ray Biological Irradiator. Senescent samples were collected 10 days or 20 days after IR treatment. 6HR samples were collected 6 hours after IR treatment.  All shRNA treated samples were infected with shRNA containing lentiviral particles with 4 µg/mL of polybrene at an MOI of 5. Cells were then cultured with 2 µg/mL of polybrene in complete medium for 10 days to select for infected cells.

value: Tail

value: Primary fibroblast

value: Scrambled control

value: ionizing radiation, 15 Gy


title: M_2_3_B

city: Wageningen

first: Annemarie

last: Castricum

state: Gelderland

address: Droevendaalsesteeg 4

department: Bioscience

country: Netherlands

institute: Wageningen university and research

data_processing:
Mapping and quantification were done using RSEM and Bowtie2 as a mapper
Differential expression analysis was done in R using DESeq2, performing the nbinomWaldTest and only focusing on genes with a maximum 0.01 padj value
Assembly: V1_clustered_reference.fasta -> Reference sequences used for mapping the reads were constructed using Trinity de novo assembly of all read pairs of V1 using default settings. Reference sequences used for mapping the reads were constructed using Trinity de novo   assembly of all read pairs of V1 using default settings.
Supplementary files format and content: csv file with per sample read counts

organism: Chrysanthemum x morifolium

source_name: Inflorescence (flower bud)

growth_protocol: Plants were grown under greenhouse conditions

extract_protocol:
flower buds were sampled, put in liquid nitrogen and RNA was isolated using CTAB/LiCl
Illumina TruSeq® Stranded mRNA sample preparation kit for low-input with an imput of 2,5 µg RNA per sample. Elution 2 for three minutes instead of eight and enrichment PCR for 13 cycles instead of 15.

treatment_protocol: Diameter sizes per stage: stage 0, 0.5–2   mm; stage 1, 2-3 mm; stage 2, 3–5 mm; stage 3, 5–6 mm; stage 4, 7–10 mm; and stage 5, 10–  25 mm

value: Inflorescence (flower bud)

value: stage 3


title: M_2_3_A


title: P15_BL6Retina_4

value: wild type mice (C57BL/6J)

value: retina


title: Scrambed shRNA treated, PWK 1, senescent, 20 days

description:
P1.SCR.postSEN
Usf2KD_allTPM.txt


title: P1_BL6Retina_4


title: M_2_2_C

value: stage 2


title: WT rep2

value: wide type


title: Usf2 shRNA 2 treated, PWK 2, senescent, 20 days

description:
P4.U5.postSEN
Usf2KD_allTPM.txt

value: Usf2 knockdown


title: Usf2 shRNA 1 treated, PWK 2, senescent, 20 days

description:
P1.U5.postSEN
Usf2KD_allTPM.txt


title: G_TJ_out_3

description: Group housed rat after tamoxifen and Jaeumganghwa-tang treatment

value: tumor-free mammary gland

value: TAM+JGT


title: P1_BL6Retina_2


title: G_TJ_out_1


title: G_TJ_out_2


title: P1_BL6Retina_3


title: Usf2 shRNA 2 treated, PWK 1, senescent, 20 days

description:
P4.U4.postSEN
Usf2KD_allTPM.txt


title: M_2_2_A


title: M_2_1_C

value: stage 1


title: M_2_2_B


title: SI_TAM_out_2


title: M_2_3_C


title: P6_BL6Retina_1


title: G_TJ_in_4

description: Group housed rat during tamoxifen and Jaeumganghwa-tang treatment


title: M_2_1_B


title: E17_BL6Retina_3


title: G_TJ_in_3


title: E17_BL6Retina_2


title: Scrambled shRNA treated, PWK 2, senescent, 10 days

description:
P4.SCR.SEN
Usf2KD_allTPM.txt


title: M_2_0_C

value: stage 0


title: M_2_1_A


title: G_TJ_in_2


title: Scrambed shRNA treated, PWK 1, senescent, 10 days

description:
P1.SCR.SEN
Usf2KD_allTPM.txt


title: P1_BL6Retina_1


title: M_2_0_B


title: E14_BL6Retina_3


title: G_TJ_in_1


title: Usf2 shRNA 1 treated, PWK 2, senescent, 10 days

description:
P1.U5.SEN
Usf2KD_allTPM.txt


title: E14_BL6Retina_2


title: V_2_3_C


title: Usf2 shRNA 1 treated, PWK 1, senescent, 20 days

description:
P1.U4.postSEN
Usf2KD_allTPM.txt


title: M_2_0_A


title: E14_BL6Retina_1


title: Usf2 shRNA 2 treated, PWK 1, senescent, 10 days

description:
P4.U4.SEN
Usf2KD_allTPM.txt


title: G_TAM_out_4

description: Group housed rat after tamoxifen treatment


title: G_TAM_out_3


title: Usf2 shRNA 1 treated, PWK 1, senescent, 10 days

description:
P1.U4.SEN
Usf2KD_allTPM.txt


title: G_TAM_out_2


title: NanogKO:Esrrb:Nanog (44JN) rep3 S9

data_processing:
Raw reads where processed with bcl2fastq (v 2.19.1)
STAR (v 2.5.3a) was used to map sequencing reads and generate the count table (Dobin et al. 2013).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter, for PECAM+PDGFRA- cells.
Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by Dnase treatment (Qiagen).
Ribosomal RNA was removed using the NEBNext rRNA depletion kit. Sequencing libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB)

value: ESC


title: V_2_3_B


title: G_TAM_out_1

value: TAM


title: NanogKO:Esrrb:Nanog (44JN) rep2 S6


title: V_2_3_A


title: Scrambled shRNA treated, PWK 2, irradiated, 6 hours

description:
P4.SCR.6HR
Usf2KD_allTPM.txt

value: Tail


title: G_TAM_in_4

description: Group housed rat during tamoxifen treatment


title: Scrambed shRNA treated, PWK 1, irradiated, 6 hours

description:
P1.SCR.6HR
Usf2KD_allTPM.txt

value: Primary fibroblast


title: V_2_2_C


title: Usf2 shRNA 2 treated, PWK 2, senescent, 10 days

description:
P4.U5.SEN
Usf2KD_allTPM.txt


title: E17_BL6Retina_1


title: Usf2 shRNA 2 treated, PWK 2, irradiated, 6 hours

description:
P4.U5.6HR
Usf2KD_allTPM.txt


title: NanogKO:Esrrb:Nanog (44JN) rep1 S3


title: V_2_2_B


title: G_TAM_in_3


title: G_TAM_in_2


title: NanogKO:Esrrb (44J) rep3 S8


title: NanogKO:Esrrb (44J) rep2 S5


title: Usf2 shRNA 1 treated, PWK 2, irradiated, 6 hours

description:
P1.U5.6HR
Usf2KD_allTPM.txt


title: V_2_2_A


title: Usf2 shRNA 2 treated, PWK 1, irradiated, 6 hours

description:
P4.U4.6HR
Usf2KD_allTPM.txt


title: G_TAM_in_1


title: NanogKO:Esrrb (44J) rep1 S2


title: V_2_1_C


title: NanogKO (44C6) rep3 S7

value: N{delta}


title: V_2_1_B


title: Usf2 shRNA 1 treated, PWK 1, irradiated, 6 hours

description:
P1.U4.6HR
Usf2KD_allTPM.txt

value: ionizing radiation, 15 Gy


title: Scrambled shRNA treated, PWK 2, unirradiated control

description:
P4.SCR.CONT
Usf2KD_allTPM.txt

value: Scrambled control


title: panc1, si-METTL16-2

city: Chongqing

first: Fuming

last: Xie

address: Yuzhong District Yixueyuan Road 1#

institute: Chongqing Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Seqtk(https://github.com/lh3/seqtk).
Trimmed sequence reads were mapped to GRCh38 using Hisat2 (version:2.0.4).
Read count extraction and normalization were performed using Stringtie (version:1.3.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Pancreatic duct cell

growth_protocol: PANC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cells using an Ultrapure RNA kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: PANC-1 cells were transfected with siRNA of METTL16 and control siRNA.

value: Pancreatic duct cell

value: pancreatic adenocarcinoma cells

tag: transfection


title: NanogKO (44C6) rep2 S4


title: panc1, si-METTL16-3


title: V_2_1_A

value: Inflorescence (flower bud)


title: panc1, si-METTL16-1


title: Scrambed shRNA treated, PWK 1, unirradiated control

description:
P1.SCR.CONT
Usf2KD_allTPM.txt


title: panc1, si-NC3

value: WT


title: Usf2 shRNA 2 treated, PWK 2, unirradiated control

description:
P4.U5.CONT
Usf2KD_allTPM.txt


title: V_2_0_C


title: NanogKO (44C6) rep1 S1