title: 906_Lem

description: Library name: 906


title: 859_Lem

status: Public on Feb 25 2025

type: SRA

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

country: USA

institute: Washington University in St. Louis School of Medicine

description: Library name: 859

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned and quantitated with Illumina DRAGEN version 3.9.3-8 Bio-IT platform
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and TPM in tab-delimitted text format

molecule: total RNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Frozen cortical tissue was weighed and homogenized in RNAase-free beaded tubes (REDE, Next Advance) in chloroform with TRIzol™. Samples were centrifuged for 15 minutes at 12’000xg at 4°C and the aqueous upper supernatant transferred for RNA isolation with the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.
Takara Clontech SMARTer Ultra Low RNA

treatment_protocol: Mice were gavaged daily with a single 30mg/kg dose of lemborexant or 0.5% methylcellulose vehicle at ZT13, starting at 7.5M of age until euthanizing at 9.5M of age.

tag: tissue

value: Cortex

tag: Sex

value: male

tag: age

tag: genotype

tag: treatment

value: Lem


title: 1596_Veh

description: Library name: 1596

value: Veh


title: 1601_Veh

description: Library name: 1601


title: 1574_Veh

description: Library name: 1574


title: 1597_Veh

description: Library name: 1597


title: 1425_Lem

description: Library name: 1425


title: 1600_Veh

description: Library name: 1600


title: 1374_Lem

description: Library name: 1374


title: 1064_Lem

description: Library name: 1064


title: 1602_Veh

description: Library name: 1602


title: 1525_Lem

description: Library name: 1525


title: 1419_Lem

description: Library name: 1419


title: 1594_Veh

description: Library name: 1594


title: RA_LV_4

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - fastp 0.20.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.6a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3 - salmon-1.3.0, --seqBias --gcBias --posBias
Assembly: GRCm38.p6 + Gencode-M25 Annotation
Supplementary files format and content: gene counts

source_name: Left ventricles

growth_protocol: Neonatal mice were nursed by dams who were rotated between room air and hyperoxia every 24 hours.

extract_protocol:
Samples were isolated using the Direct-zol DNA/RNA isolation kit (Zymo) and gDNA elimination columns (Qiagen).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols

treatment_protocol: Neonatal mice were exposed to room air (21% oxygen) or hyperoxia (100% oxygen)

value: Left ventricles

tag: strain

value: Room air


title: RA_LV_3


title: RA_LV_5


title: RA_LV_1


title: RA_LA_4

source_name: Left atria

value: Left atria


title: RA_LV_2


title: RA_LA_2


title: RA_LA_5


title: RA_LA_3


title: RA_LA_1


title: O2_LV_6

value: Hyperoxia


title: O2_LV_5


title: O2_LV_2


title: O2_LV_1


title: O2_LV_4


title: PE_barcodeLibrary

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCh38.p13
Supplementary files format and content: feature matrix .h5 file and Scanpy python processing notebook
Supplementary files format and content: GP.h5
Supplementary files format and content: Barcode_GP.ipynb
Supplementary files format and content: PE.h5
Supplementary files format and content: Barcode_PE.ipynb

organism: Homo sapiens

source_name: Periosteum long bone

extract_protocol:
Graft tissue generated by skeletal stem cells was mechanically and enzymatically digested, stained with antibodies, and living Venus-expressing populations purified via FACS. cDNA was prepared according to 10X Genomics manufacturer instructions for 3' v3.1.
25% (10ul) of cDNA was used for standard 10X Genomics library preparation protocol. Another 25% was used for clonal barcode amplification. The extra 10 µL of cDNA were amplified using a combination of Partial Read 1 primer  (5’-CTACACGACGCTCTTCCGATCT-3’) and an adaptor-FBP1 (Read 2 primer + barcode recognition site) primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCGACCACCGAACGCAACGCACGCA-3’). Barcode amplification was run as recommended for cDNA reaction (10X protocol step 2.2) plus 4 extra cycles. From there the product was handled as per standard protocol starting from the index primer reaction without any fragmentation or ligation steps.

treatment_protocol:
n/a
n/a

tag: cell type

value: skeletal stem cells

value: Periosteum long bone

value: 17 weeks gestation


title: 1333_Lem

description: Library name: 1333


title: O2_LA_4


title: GP_barcodeLibrary

description: 10x Genomics

source_name: Growth plate long bone

value: Growth plate long bone


title: 1370_Lem

description: Library name: 1370


title: O2_LA_3


title: O2_LA_1


title: O2_LA_2


title: O2_LA_5


title: human PBMCs from recovered adults_003

city: Shanghai

first: yangdian

last: lai

address: South Chongqing Road 281

country: China

institute: Shanghai Jiaotong University School of Medicine

description: Library name: Adult_003

data_processing:
scRNA sequencing reads were subjected to quality control based on FastQC software v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Then, we used Cell Ranger software (version 3.1.0) to process, align, and summarize sequencing data. Demultiplex FASTQ reads were aligned to the human genome reference (GRCh38-3.0.0). Reads with low base-calling quality scores and assigned cell barcodes were filtered. Unique molecular identifier (UMI) counts of each transcript were quantified. UMI matrix was converted to Seurat objects by the R package Seurat v3. Further analysis was performed by R package. Raw UMI count matrices were filtered to remove the genes expressed in fewer than three cells and the cells with either fewer than 200 genes, or more than 6000 genes, or high percentages of mitochondrial genes (more than 15%). To account for the differences in sequencing depth across the cells, UMI count was then normalized by a global-scaling method, converted with a scaling factor (10,000 by the default) and log-transformed with the LogNormalize function in Seurat for downstream analysis.
Assembly: GRCh38-3.0.0
Supplementary files format and content: FASTQ Files

source_name: blood

extract_protocol:
Whole blood was collected in a tube containing ethylene diamine tetraacetic acid (EDTA). PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation with LymphoprepTM solution (AXIS-SHIELD Poc AS, Oslo, Norway) according to the manufacturer’s recommendations. The mononuclear cell layer was carefully transferred to a new 15 mL conical tube and washed twice with RPMI 1640 medium (Hyclone, Logan, UT, USA) by centrifuging at 486 × g for 10 min at room temperature. PBMCs were resuspended in RPMI 1640 culture medium containing 10% fetal bovine serum (FBS) (Millipore, Danvers, MA, USA), 100 units/mL penicillin, and 100 μg/mL streptomycin (GIBCO, Grand Island, NY, USA).
Single cell RNA (sc-RNA) libraries of PBMCs were prepared according to the guideline from the Chromium Single Cell 5' v3 chemistry (10x Genomics, Cat No. 120237) based on the Drop-seq methodology. The libraries were sequenced using Illumina nova S6000 device by Genergy Biotechnology (Shanghai, China).

value: blood

tag: cell line

value: PBMCs


title: Ctbp1/2dKO 4h 0.25 mM4-Cl-HIPP  rep2

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

data_processing:
NGS data quality was assessed with FastQC (RRID: SCR 014583, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Gene-level quantification was performed with Salmon version 1.9.0 (RRID: SCR_0170361). Settings were: -libType A, -gcBias, -biasSpeedSamp 5 using the mm39 (M28, GRCm39) reference transcriptome provided by Gencode.
Gene count normalization and differential expression analysis were performed with DESeq2 version 1.44.0 (RRID: SCR_015687) after import of gene-level estimates with “tximport” version 1.32.0 (RRID: SCR_016752) in R (RRID: SCR_00190, R version 4.1.15).
Assembly: mm39
Supplementary files format and content: unfiltered tab-delimited text file (txt) with length-scaled TPMs for each sample, log2Foldchanges and adjusted p-value for the comparison of inhibitor treatment )MTOB or 4Cl-HIPP) over DMSO (vehicle control) for either wildtype (wt) of Ctbp1,2 double knockout (dKO) cells

molecule: polyA RNA

growth_protocol: J774.1 cells were grown on tissue culture treated dishes in full growth medium (DMEM high glucose (Sigma Aldrich #D6429) supplemented with 1% Penicillin/Streptomycin (Sigma Aldrich #P4333) and 10% FBS superior (Sigma Aldrich #S0615)). Cells were passaged at ~70-80% confluency by scraping and resuspending in fresh medium.

extract_protocol:
RNA was extracted using the ReliaPrep RNA Miniprep System (Promega #Z6012) according to the manufacturers instructions. In brief samples were mixed with 2-propanol and nucleic acids were bound to a silica membrane by column centrifugation. To remove DNA, DNAseI was added to the membrane and incubated for 15 min before the membrane was washed thrice and dried. RNA was eluted in 30 µl nuclease-free water.
1 ug of RNA was quality controled using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit and libraries prepared using Illumina's TruSeq unstranded mRNA Library Preperation kit.

treatment_protocol: Cells were seeded at 250,000 cells/well in wells of a 24-well plate in 1 mL full growth medium (DMEM high glucose + 1% P/S + 10% FBS) and incubated at 37°C and 5% CO2 overnight. The next day, cells were treated with MTOB (2 M stock in PBS; final concentration 1.5 mM), 4-Cl-HIPP (500 mM stock in DMSO, final concentration 250 µM) or a vehicle control (PBS/DMSO) for 4 h before lysing the cells in 200 µl RNA lysis buffer (Promega #Z6012).

value: macrophage


title: Ctbp1/2dKO 4h 0.25 mM4-Cl-HIPP  rep1


title: Ctbp1/2dKO 4h 1.5 mM MTOB  rep3

value: MTOB


title: human PBMCs from recovered adults_002

description: Library name: Adult_002


title: Ctbp1/2dKO 4h 1.5 mM MTOB  rep2


title: human PBMCs from recovered adults_001

description: Library name: Adult_001


title: Ctbp1/2dKO 4h 1.5 mM MTOB  rep1


title: human PBMCs from recovered adolescents_003

description: Library name: Ado_003


title: ESV con-1

city: Beijing

first: Xiaoli

last: Zhang

address: 119 Xincun Road, Fengtai District

institute: Beijing Neurosurgical Institute

description:
Library name: Sample 4
ESV_1

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: processed.data.xlsx

source_name: xenografts

extract_protocol:
RNA was harvested using Trizol (Invitrogen) . 1.0ug 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.

value: xenografts

value: colorectal cancer

value: WT

value: ESV

tag: batch


title: HT-29 con-2

description:
Library name: Sample 2
Con_2

value: no


title: ESV con-2

description:
Library name: Sample 5
ESV_2


title: HT-29 con-1

description:
Library name: Sample 1
Con_1


title: HT-29 con-3

description:
Library name: Sample 3
Con_3


title: ESV con-3

description:
Library name: Sample 6
ESV_3


title: human PBMCs from recovered adolescents_002

description: Library name: Ado_002


title: Ctbp1/2dKO vehicle rep3

value: vehicle


title: Ctbp1/2dKO vehicle rep2


title: human PBMCs from recovered adolescents_001

description: Library name: Ado_001


title: Ctbp1/2dKO vehicle rep1


title: Ctbp1/2dKO 4h 0.25 mM4-Cl-HIPP  rep3


title: Rank4, rep3

city: Chongqing

first: Ruijing

last: Yang

address: yuzhong

institute: Chongqing medical university

description: Library name: F30

library_source: genomic

data_processing:
16S rRNA gene amplicon library preparation and sequencing were performed. Quality control of the raw sequences was conducted using fastq software, followed by merging with FLASH software. Based on recommended parameters, noise reduction was applied to the optimized sequences post-quality control and assembly using the DADA2 plugin within the Qiime2 pipeline. Amplicon Sequence Variant (ASV) is a unit used to represent microbial species or populations. Utilizing DADA2 denoising processing, DNA sequences devoid of chimeras and sequencing errors were obtained. DNA sequences within microbiome are measured and analyzed to calculate their differences and similarities. Similar DNA sequences are clustered into the same ASVs, thereby obtaining an ASV number for each microorganism. To minimize the effects of sequencing depth on alpha and beta diversity measure, the number of sequences from each sample was rarefied to 20,000, which still yielded an average Good’s coverage of 99.09%. Utilizing the Silva 16S rRNA gene database (version 138), taxonomic analysis of ASVs was conducted using the Naïve Bayes classifier implemented within Qiime2.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values fles and matrix files
Library strategy: 16S rRNA-seq

molecule: genomic DNA

source_name: colon contents

extract_protocol:
The colon contents were immediately removed and dispensed into sterile tubes. The colon contents from the upper segment were rapidly frozen in liquid nitrogen and stored at -80°C. Total microbial genomic DNA was extracted using the FastPure Stool DNA Isolation Kit (MJYH,shanghai, China) according tomanufacturer’s instructions. The quality and concentration of DNA were determined by 1.0% agarose gel electrophoresis and a NanoDrop® ND-2000 spectrophotometer (Thermo Scientific Inc., USA) and kept at-80 ℃ priortofurther use. DNA was amplified by PCR.
Purified amplicons were pooled in equimolar amounts and paired-end sequenced on an Illumina NextSeq 2000 PE300 platform (Illumina, San Diego,USA) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China).

value: colon contents

value: 6-8 weeks old

value: male


title: Rank4, rep4

description: Library name: F31


title: Rank4, rep2

description: Library name: F29


title: Rank4, rep1

description: Library name: F28


title: Rank3, rep6

description: Library name: E27


title: wildtype 4h 0.25 mM4-Cl-HIPP  rep3

value: wildtype


title: 10194_IPF_LL_replicate_5

city: Columbus

first: Jhonny

last: Rodriguez Lopez

state: Ohio

address: Holly Ave 1383 203A

department: Internal medicine

institute: The Ohio State University

description:
Library name: 10194_IPF_LL_replicate_5
10x genomics

data_processing:
Raw sequencing reads were processed using the Cell Ranger pipeline (v7.1.0, 10x Genomics) for quality assessment and alignment to the human reference genome.
The reference datasets used were refdata-gex-GRCh38-2020-A and Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A provided by 10x Genomics.
A unique molecular identifier (UMI) count matrix was generated as the output of Cell Ranger, which was then used to create a Seurat object for downstream analysis.
Quality control metrics included filtering cells based on gene expression counts and mitochondrial RNA content.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, which contain information on cell barcodes, feature annotations, and expression matrices, respectively.
Supplementary files format and content: The single cell was further analyzed for normalization, scaling, and identification of highly variable genes to create clusters of cells based on expression profiles.

source_name: Human lung

extract_protocol:
From FFPE lung tissue, two 50-µm scrolls were obtained and dissociated into a single-cell suspension according to demonstrated Protocol CG000632, Rev B by 10x Genomics. The cell suspension was counted to determine the single cell reaction input between 5x10^5 and 2x10^6 cells.
From isolated cells, fixed RNA profiling and library preparation (Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples, User Guide CG000527, Rev E. 10x Genomics) were conducted with the Chromium X platform.

treatment_protocol: Lungs were obtained from human subjects with IPF or healthy controls. Samples were not subjected to any additional treatment before processing.

value: Human lung

value: Lung cell types


title: wildtype 4h 0.25 mM4-Cl-HIPP  rep2


title: Rank3, rep4

description: Library name: E25


title: 10172_IPF_LL_replicate_3

description:
Library name: 10172_IPF_LL_replicate_3
10x genomics


title: Rank4, rep6

description: Library name: F33


title: Rank3, rep3

description: Library name: E24


title: 10183_IPF_LL_replicate_4

description:
Library name: 10183_IPF_LL_replicate_4
10x genomics


title: 101601_IPF_LL_replicate_2

description:
Library name: 101601_IPF_LL_replicate_2
10x genomics


title: Rank2, rep6

description: Library name: D20


title: Rank3, rep1

description: Library name: E22


title: 10160_IPF_LL_replicate_1

description:
Library name: 10160_IPF_LL_replicate_1
10x genomics


title: wildtype 4h 1.5 mM MTOB  rep3


title: Rank2, rep4

description: Library name: D18


title: Rank4, rep5

description: Library name: F32


title: Rank2, rep5

description: Library name: D19


title: Rank2, rep3

description: Library name: D17


title: wildtype 4h 1.5 mM MTOB  rep2


title: Rank2, rep7

description: Library name: D21


title: 20166_Healthy_replicate_9

description:
Library name: 20166_Healthy_replicate_9
10x genomics


title: wildtype 4h 1.5 mM MTOB  rep1


title: Rank2, rep2

description: Library name: D16


title: Rank3, rep5

description: Library name: E26


title: wildtype vehicle rep2


title: 2020_10_IPF_LL_replicate_6

description:
Library name: 2020_10_IPF_LL_replicate_6
10x genomics


title: Rank2, rep1

description: Library name: D15


title: 20150_Healthy_replicate_8

description:
Library name: 20150_Healthy_replicate_8
10x genomics


title: Go-through-tube, Rank1, rep5

description: Library name: C13


title: wildtype vehicle rep3


title: Go-through-tube, Rank1, rep6

description: Library name: C14


title: 20141_Healthy_replicate_7

description:
Library name: 20141_Healthy_replicate_7
10x genomics


title: wildtype 4h 0.25 mM4-Cl-HIPP  rep1


title: Rank3, rep2

description: Library name: E23


title: Go-through-tube, Rank1, rep4

description: Library name: C12


title: wildtype vehicle rep1


title: Go-through-tube, Rank1, rep3

description: Library name: C11


title: 20126_Healthy_replicate_6

description:
Library name: 20126_Healthy_replicate_6
10x genomics


title: Go-through-tube, Rank1, rep1

description: Library name: C8


title: Go-through-tube, Rank1, rep2

description: Library name: C9


title: 20116_Healthy_replicate_5

description:
Library name: 20116_Healthy_replicate_5
10x genomics


title: long_RNA_Saline_nonM2MC_Deficient_4

city: Boston

first: Matthew

middle: Robert

last: Jones

state: MA

address: 72 East Concord Street

department: Medicine

institute: Boston University School of Medicine

data_processing:
For RNA-Seq data, the raw data was aligned to a composite reference genome of mouse, influrenza A and antibiotic resistance plasmid containing TdTomato using HISAT2 (version 2.1.0) aligner.  DIfferential expression analysis were than performed on the output using R and DESeq2 package.
For small RNA, raw sequencing data is first processed using a custom pipeline and script to remove adaptor sequence, remove invalid and consolidate UMI, and remove reads that are shorter than 15 bases.  The processed reads are then use as input for COMPSRA analysis.  DIfferential expression analysis were than performed on the output using R and DESeq2 package.
Assembly: mm10, IVA (CY046986.1), Tdtomato (LC311026.1), default COMPSRA small RNA database (v1.03)
Supplementary files format and content: tab-delimited text files containing raw read count for both RNA-Seq and small RNASeq

source_name: Lung

extract_protocol:
Cells were sorted from Miwi2+/tom and Miwi2tom/tom mice into Qiagen buffer RLT supplemented with 1% beta-mercaptoethanol. RNA  was isolated on the Qiagen QIASymphony SP/AS using the QIAshymphony RNA kit and the miRNA CT 400 protoocol.
The RNA-Seq libraries were prepared using Illumina Stranded Total RNA with RiboZero Plus kit per the manufacturer instruction.  The small RNA-Seq libraries were prepared using Qiagen QIASeq small RNA kit per the manufacturer instruction.

value: Lung

value: deficient

value: Saline


title: long_RNA_Saline_M2MC_Deficient_4


title: 20108_Healthy_replicate_4

description:
Library name: 20108_Healthy_replicate_4
10x genomics


title: Forced loss, Rank1, rep5

description: Library name: A6


title: long_RNA_Saline_M2MC_Deficient_3


title: Forced loss, Rank1, rep3

description: Library name: A3


title: Forced loss, Rank1, rep2

description: Library name: A2


title: Forced loss, Rank1, rep1

description: Library name: A1


title: 20132_Healthy_replicate_2

description:
Library name: 20132_Healthy_replicate_2
10x genomics


title: ESCCO39_Tumor-Org

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

country: Japan

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

data_processing:
The reads were aligned to the reference human genome (hg38) with STAR (ver.2.7.5a) software.
The reads aligned to rRNA and transfer RNA (tRNA) regions were removed.
The mapped reads were assigned to genes (Ensembl database annotation version GRCh38.105) using FeatureCounts from the Bioconductor package Rsubread (ver.2.0.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each samples

source_name: Tumor

extract_protocol:
Total RNA was isolated from ESCCOs and ENOs using an RNeasy mini kit (Qiagen)
The RNA sequencing library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: Esophageal

value: Tumor

value: Oragnoid


title: long_RNA_Saline_nonM2MC_Deficient_3


title: long_RNA_Saline_nonM2MC_Deficient_2


title: ESCCO37_Tumor-Org


title: 20095_Healthy_replicate_1

description:
Library name: 20095_Healthy_replicate_1
10x genomics


title: long_RNA_Saline_M2MC_Deficient_2


title: WCMC37 2HE-5NMe replicate 2

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
In order to remove reads that originate from mouse feeder cells, sequencing reads were first aligned to the mouse genome (GRCm38) using hisat2 (2.2.1) with default settings. Reads that did not align to the mouse genome were then aligned to the human genome (GRCh38). The number of reads that aligned to each gene were calculated using HTSeq with -a set to 0 and all other settings set to default. Genes with low median expression (<10 reads per million) were removed from the analysis.
Assembly: GRCh38.p13
Supplementary files format and content: csv file with reads per million of genes with >10 reads per million

growth_protocol: hESC were cultured on a MEF layer in hESC medium (DMEM/F12 [Invitrogen], 20% knockout serum replacement [Invitrogen], 0.1 mM 2-mercaptothanol, 1x MEM non-essential amino acids [Gibco], 200 mM L-Glutamine) supplemented with 10 ng/ml FGF-2 [StemBeads, StemCulture]. Human embryonic stem cells were dissociated into single cells using Accutase (Stem Cell Tech) and plated at high density on Matrigel (Corning) in hESC medium supplemented with Y-27632 to improve cell survival. Cells were cultured for 10 days in the presence of LDN193189 (#72142, Stem Cell Technologies), SB431542 (#1614, Tocris) and XAV939 (#3748, Tocris) (until day 4). Afterward cells were maintained inN2-supplemented DMEM/F12 until day 20. Neurons were replated following dissociation with Accuatase onto PLO/laminin/fibronectin-coated plates in neuronal media (Neurobasal media, B27–vitamin A, Glutamax) supplemented with DAPT, BDNF, GDNF, ascorbic acid, and cAMP. Neuronal media was replaced every 4-5 days. On day 21 of neuronal differentiation, neurons were plated at 150K/cm2. Cells were incubated in neuronal media with 5-aza-dC (1 µM) for two weeks and then either DMSO or 2HE-5NMe as indicated.

extract_protocol:
RNA was extracted from the cells using Trizol (Invitrogen, 15596026) following the manufacturer’s instructions. The RNA was precipitated using isopropanol, washed with 70% ethanol and resuspended in water.
The RNA (100 ng) was then converted into a cDNA library using the SMART-seq mRNA LP (with UMIs) kit (Takara, 634762) following the manufacturer’s instructions. The quality of the library was assessed using a High Sensitivity D5000 ScreenTape assay (Agilent) and then the cDNAs were sequenced using a NovaSeq 6000 with S1 Flow Cells (paired end, 2x50 bp).

treatment_protocol: Cells were treated with 2HE-5NMe or vehicle after washout of 5-aza-dC

value: human embryonic stem cell line differentiated to neurons

value: FXS

value: 1 week 5-daza-dC then 2 weeks 2HE-5NMe


title: ESCCO37_Normal-Org

source_name: Normal

value: Normal


title: ESCCO36_Tumor-Org


title: long_RNA_Saline_M2MC_Deficient_1


title: ESCCO34_Tumor-Org


title: long_RNA_Saline_nonM2MC_Deficient_1


title: WCMC37 2HE-5NMe replicate 1


title: long_RNA_Saline_M2MC_Haplosufficient_4

value: haplosufficient


title: long_RNA_Saline_nonM2MC_Haplosufficient_4


title: Forced loss, Rank1, rep4

description: Library name: A4

value: colon contents


title: WCMC37 vehicle replicate 1

value: 1 week 5-daza-dC then 2 weeks vehicle


title: 20160_Healthy_replicate_3

description:
Library name: 20160_Healthy_replicate_3
10x genomics


title: Saline_Vehi4

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Hypothalamus

extract_protocol:
Mice were scarified at 90 min after administration of LPS or saline, and daridorexant or vehicle (each n=4) and intracardially perfused with ice-cold diethylpyrocarbonate (DEPC)-treated PBS to washout blood cells in the brain and. The mouse brain was quickly dissected to remove the cortex, cerebellum, and olfactory bulbs and homogenized in ISOGEN (Fujifilm, Japan), and total RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The LPS was derived from Escherichia coli 055: B5 (Sigma) and dissolved in 0.9 % saline (Otsuka). A mouse model of LPS-induced systemic inflammation was established by peritoneal administration of LPS at 2.5 mg/kg. Daridorexant (Idorsia co. Ltd) was suspended in 0.5 w/v % methyl cellulose 400 solution and sterilized (Fujifilm Wako Pure Chemical Corporation). Mice were orally administered daridorexant-HCl (108 mg/kg, equivalent of 100 mg/kg free base) or vehicle. Daridorexant was administered for three days prior to LPS-induced inflammation. In LPS-injected group, LPS + vehicle (LPS/Vehicle) or LPS + daridorexant (LPS/Daridorexnant) group was prepared, respectively. As saline-injected group instead of LPS injection, Saline/Daridorexantor Saline/Vehicle group was arranged, respectively.

value: Hypothalamus

value: male


title: SI-214 2HE-5NMe replicate 2


title: Forced loss, Rank1, rep6

description: Library name: A7

value: 6-8 weeks old


title: Saline_Dari3

value: Saline, daridorexant


title: Saline_Vehi3


title: Saline_Dari1


title: Saline_Dari4


title: WCMC37 vehicle replicate 2


title: SI-214 vehicle replicate 2


title: long_RNA_Saline_M2MC_Haplosufficient_3

value: Lung


title: LPS_Dari4

value: LPS, daridorexant


title: Saline_Vehi2

value: Saline


title: Saline_Vehi1


title: ESCCO35_Tumor-Org

value: Esophageal


title: long_RNA_Saline_nonM2MC_Haplosufficient_3


title: SI-214 2HE-5NMe replicate 1


title: LPS_Dari3


title: SI-214 vehicle replicate 1


title: ESCCO29_Normal-Org


title: Saline_Dari2


title: LPS_Dari2


title: LPS_Dari1


title: long_RNA_Saline_nonM2MC_Haplosufficient_2


title: LPS_Vehi4

value: LPS


title: long_RNA_Saline_M2MC_Haplosufficient_1


title: non-diabetic wound [SC_W5]

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger with default paramaters (cellranger)
Gene-barcode matrices were determined using 10X Genomics Cellranger  with default parameters (cellranger run)
Aligned reads were examined for read quality metrics and stored as Seurat objects using Seurat v4.0 package in R.
Assembly: hg:38
Supplementary files format and content: barcode files
Supplementary files format and content: gene names file
Supplementary files format and content: count matrix file

source_name: skin

extract_protocol:
Single-cell suspensions were generated from the diabetic and non-diabetic wounds using 10x genomics platform. Briefly, the tissue was chopped into small pieces and subjected to enzymatic dissociation using a whole-skin dissociation kit (cat. no. 130-101-540) in MACS C Tubes (cat. no. 130-093-237; Miltenyi Biotec, San Diego, CA). The samples were incubated in a water bath at 37°C for 3 h. After incubation, the samples were diluted by adding 0.5 mL of cold complete cell culture medium to stop the enzymatic reaction. The C Tubes were then tightly closed and attached upside down onto the sleeve of the gentle- MACS Octo Dissociator, and a UW human skin dissociation program was performed. The cell suspension was subjected to a 70-µm filter and placed on a 15-mL tube to remove the debris. RBCs were lysed using 10X RBC lysis buffer (cat. no. 420301; BioLegend, San Diego, CA).
library construction was done according to the manufacturer’s recommendations  (10X Genomics)

value: skin

tag: tissue type

value: non-diabetic wound

value: Male


title: ESCCO29_Tumor-Org

value: Tumor

value: Oragnoid


title: LPS_Vehi3


title: LPS_Vehi2


title: long_RNA_Saline_M2MC_Haplosufficient_2

value: haplosufficient


title: LPS_Vehi1


title: long_RNA_PR8_M2MC_Deficient_4

value: deficient


title: long_RNA_Saline_nonM2MC_Haplosufficient_1


title: ESCCO20_Tumor-Org


title: mESC, Nsd1, HA ChIP

first: Jie

last: Li

address: 413 E 69th Street, Belfer Building, BB-1462

data_processing:
Raw sequencing reads were aligned to mm10 mouse genome using STAR 2.7.10b with splicing alignment disabled (--alignIntronMax 1 --alignEndsType EndToEnd). Non-primary aligned, duplicated reads and reads mapping to ENCODE blacklisted regions were filtered out before downstream analysis. The MACS2 software 2.2.7.1 was employed for peak calling using the default parameters (q<0.05 as significance cut off) and input as control.
Peak annotation and TF motif enrichment analysis with peak summit bed file as input and a specified region size of 200 was carried out using the Homer 4.11 functions ‘annotatePeaks.pl’ and ‘findMotifsGenome.pl’, respectively.
Alignment bam files were also transformed into read coverage bigWig files using the deepTools 3.5.4 function ‘bamCoverage’ with options [-bs 10 --centerReads -e 250] and normalized to reads per genome coverage (RPGC).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mouse blastocyst

growth_protocol: E14 mouse ES cells were cultured in DMEM supplemented with 15% heat-inactivated FBS, 1% NEAA (nonessential amino acids), 0.1mM β-mercaptoethanol, 1% antibiotics, and 1000 U/mL recombinant mouse LIF (leukemia inhibitory factor, Sigma: ESG1107) on top of mitotically inactivated mouse embryonic fibroblast (MEF, Thermo Fisher: A34963) feeder layer in TC-treated dish or plate pre-coated by 0.1% gelatin.

extract_protocol:
E14 single cell suspension was subject to a dual cross-linking protocol: initial fixation under 2mM DSG (Thermo Fisher: 20593) in PBS for 45min at RT, followed by fixation in 1% formaldehyde in PBS (Thermo Fisher: 28908) for 10min, and then quenched by addition of 125mM glycine for 5min. The cross-linked cells were sequentially lysed or washed in LB1, LB2, and LB3, followed by sonication for 60 cycles on Bioruptor sonicator at high energy with 30s on and 30s off (Diagenode: B01020001). The cleared sonication supernatant was then incubated with Flag (Sigma: F1804) or HA (abcam: ab9110) antibody-bound dynabeads (Thermo Fisher: 11202D,11204D) overnight at 4 °C. After sequential washes with low-salt buffer, high-salt buffer, LiCl buffer, and TE buffer, the ChIP product was eluted and subject to overnight reverse crosslink at 65 °C, followed by RNase (Roche: 11119915001) and Protease K (Roche: 03115828001) digestion, and DNA recovery by Qiagen PCR purification kit (Qiagen: 28106).
The ChIP-seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit (NEB: E7645L)

value: mouse blastocyst

tag: developmental stage

value: mouse embryonic stem cell

tag: antibody

value: HA


title: mESC, Nsd1, Flag ChIP-input


title: ESCCO25_Tumor-Org


title: long_RNA_PR8_nonM2MC_Deficient_4


title: R1_WT_HA_experiment1_rep2

city: Nijmegen

first: Michiel

last: Vermeulen

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

data_processing:
ChIP-seq data was processed using seq2science v0.7.1 using default options. Paired-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCm39 was downloaded with genomepy v0.11.1. The effective genome size was estimated per sample by khmer v2.0 by calculating the number of unique kmers with k being the average read length per sample. Reads were aligned with bwa-mem2 v2.2.1 with options '-M'. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.14. Mapped reads were removed if they did not have a minimum mapping quality of 30, were a (secondary) multimapper, were a PCR/optical duplicate or aligned inside the ENCODE blacklist. Afterwards samples were downsampled to -1 reads. Peaks were called with macs2 v2.2.7 with options '--buffer-size 10000' in BAMPE mode. For H3K27me3, macs2 was used with broad-peak setting. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample. The fraction reads in peak score (frips) was calculated by featurecounts v1.6.4. A consensus set of summits was made with gimmemotifs combine_peaks v0.15.1. A peak feature distribution plot and peak localization plot relative to TSS were made with chipseeker. All summits were extended with 100 bp to get a consensus peakset. Genome browser snapshots and heatmaps were generated using Easeq. Motif analyses were performed using the SeqPos motif tool (http://cistrome.org/ap/) with default settings (region width: 600 bp; p-value cutoff: 0.001). Genomic region enrichment analysis was performed with CEAS. Diffbind R package was used to perform differential binding analyses and to generate consensus peak lists by selecting peaks that are present in both replicates.
Assembly: GRCm39
Supplementary files format and content: bigWig

source_name: R1 mESCs

growth_protocol: R1 and E14 dTAG-SUZ12 mouse embryonic stem cells (mESCs) were cultured on 0.15% (w/v) gelatin-coated dishes in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 1x non-essential amino acids, 50 U/mL penicillin-streptomycin, 15% fetal bovine serum, leukemia inhibitory factor (LIF; produced in-house) and 100 μM β-mercaptoethanol.

extract_protocol:
Samples were fixed and lysed as described before (Schmidt et al., 2009). The chromatin extracts were sonicated for 6 cycles of 30 sec on, 30 sec off using a Diagenode Bioruptor Pico.
Immunoprecipitated DNA was processed for library preparation KAPA HyperPrep Kit (KAPA Biosystems) using 5ng DNA starting material. Sequencing was performed using an Illumina NextSeq 500, 42-bp paired-end reads were generated.

value: R1 mESCs

value: mouse embryonic stem cells

value: wild-type


title: R1_WT_experiment1_input


title: ESCCO18_Tumor-Org


title: long_RNA_PR8_M2MC_Deficient_3

value: Lung


title: long_RNA_PR8_M2MC_Deficient_2


title: ESCCO19_Tumor-Org


title: R1_WT_HA_experiment1_rep1


title: ESCCO17_Tumor-Org


title: R1_WT_H3K27me3_experiment1_rep2


title: mESC, Nsd1, Flag ChIP

value: Flag


title: long_RNA_PR8_nonM2MC_Deficient_3


title: R1_WT_Ezh2_experiment1_rep2


title: mESC, Nsd1, HA ChIP-input


title: Caki-YAPs127a_2

city: boston

first: Jiyuan

last: Liu

state: Massachusetts

address: 55 fruit st.

institute: Mass Gen Hospital

description:
Library name: Caki-YAPs127a_2
Caki-YAPs127a_2

data_processing:
reads were aligned with HISAT2 and assembled and quantified with Cufflinks using reference genome GRCm39 .The reads then were pseudo-aligned and quantified by Salmon 1.9.0.
Assembly: GRCm39
Supplementary files format and content: excel sheet with raw count matix

source_name: Caki

growth_protocol: cells were cultured in DMEM/F12 medium with FBS

extract_protocol:
Total RNA was extracted by combining the TRIzol protocol (Invitrogen; Carlsbad, CA) with the QIAGEN RNeasy mini kit (QIAGEN, Carlsbad, CA). Briefly, 1x107 cells were lysed with 0.65ml TRIzol reagent for 10 minutes at room temperature before adding 300ul chloroform. The mixture was vortexed for 15 seconds, kept static for 3 minutes, and then centrifuged samples at 12,000 rpm for 3 min at room temperature. The supernatant was carefully transferred into another DNase/RNase-free centrifuge tube, mixed well with an equal volume of 70% ethanol by pipetting, and loaded to the RNeasy Mini spin column provided in the QIAGEN RNeasy mini kit. The column with samples was kept static for 2 minutes before centrifuging for 15 s at 12,000rpm. Discard the flow-through. After washing, the spin column was placed in a new 2 ml collection tube and dried by spinning at 15,000 rpm for 5 min. RNA on the membrane will be eluted with 40μl RNase-free water (supplied in kit).
High-quality libraries were prepared following Illumina Stranded mRNA Prep Manual

treatment_protocol: Caki cells were cultured to 40% confluent and then transfected with retrovirus-based empty control vector (MXIV), or vectors expressing wild type of YAP1 (YAP), or constitutively active YAP1 (YAPS127A, a replacement of Serine at residue 127 with Alanine resulting in the constitutive activation of YAP1 protein [66]). All transfected cells were selected with G418 (200-400μg/ml). YAP1 expression in these cells was confirmed by RT-PCR and Western blot.

value: Caki

value: a cell line that was isolated from the kidney of a male clear cell carcinoma patient

value: YAP1s127a overexpression

value: transfection


title: long_RNA_PR8_M2MC_Deficient_1


title: Caki-YAPs127a_1

description:
Library name: Caki-YAPs127a_1
Caki-YAPs127a_1


title: Caki-YAP_3

description:
Library name: Caki-YAP_3
Caki-YAP_3

value: YAP1 overexpression


title: R1_WT_Ezh2_experiment1_rep1


title: ESCCO12_Tumor-Org

value: Esophageal

value: Tumor


title: ESCCO15_Normal-Org

value: Normal

value: Oragnoid


title: Caki-YAPs127a_3

description:
Library name: Caki-YAPs127a_3
Caki-YAPs127a_3


title: EmT_cl2_experiment1_input

value: Ezh2-miniTurboID clone 2


title: EmT_cl2_HA_experiment1_rep2


title: Caki-YAP_2

description:
Library name: Caki-YAP_2
Caki-YAP_2


title: Caki-YAP_1

description:
Library name: Caki-YAP_1
Caki-YAP_1


title: long_RNA_PR8_M2MC_Haplosufficient_4

value: haplosufficient


title: ESCCO11_Tumor-Org


title: long_RNA_PR8_nonM2MC_Haplosufficient_4


title: long_RNA_PR8_nonM2MC_Deficient_1

value: deficient


title: Caki-MX_2

description:
Library name: Caki-MX_2
Caki-MX_2

value: MX


title: EmT_cl2_H3K27me3_experiment1_rep2

value: R1 mESCs

value: mouse embryonic stem cells


title: ESCCO15_Tumor-Org


title: ESCCO7_Normal-Org


title: ESCCO11_Normal-Org


title: Caki-MX_3

description:
Library name: Caki-MX_3
Caki-MX_3


title: EmT_cl2_H3K27me3_experiment1_rep1


title: ESCCO7_Tumor-Org


title: long_RNA_PR8_nonM2MC_Deficient_2

value: Lung


title: long_RNA_PR8_M2MC_Haplosufficient_3


title: long_RNA_PR8_nonM2MC_Haplosufficient_3


title: R1_WT_H3K27me3_experiment2_rep2

value: wild-type


title: Caki-MX_1

description:
Library name: Caki-MX_1
Caki-MX_1

value: Caki


title: Untreated IgG cnt

description:
Cut&run fragments
WCMC37_untreated_IgG

data_processing:
We used an alignment strategy that eliminates reads that align to any mouse transcripts, since some mouse feeder cells may have remained in the sample used for CUT&RUN.  Paired-end reads were aligned to human genome version GRCh38.p13 using Bowtie2. Reads were normalized for sizes of libraries. Reads were then mapped onto a list of all protein-coding gene promoters (-1000 to +1000 of MANE Select transcription start sites from GRCh38.p13).
Assembly: GRCh38.p13
Supplementary files format and content: Bedgraph contains reads per million at regions across the genome
Library strategy: CUT&RUN

growth_protocol: hESC were cultured on a MEF layer in hESC medium (DMEM/F12 [Invitrogen], 20% knockout serum replacement [Invitrogen], 0.1 mM 2-mercaptothanol, 1x MEM non-essential amino acids [Gibco], 200 mM L-Glutamine) supplemented with 10 ng/ml FGF-2 [StemBeads, StemCulture]. Human embryonic stem cells were dissociated into single cells using Accutase (Stem Cell Tech) and plated at high density on Matrigel (Corning) in hESC medium supplemented with Y-27632 to improve cell survival. Cells were cultured for 10 days in the presence of LDN193189 (#72142, Stem Cell Technologies), SB431542 (#1614, Tocris) and XAV939 (#3748, Tocris) (until day 4). Afterward cells were maintained inN2-supplemented DMEM/F12 until day 20. Neurons were replated following dissociation with Accuatase onto PLO/laminin/fibronectin-coated plates in neuronal media (Neurobasal media, B27–vitamin A, Glutamax) supplemented with DAPT, BDNF, GDNF, ascorbic acid, and cAMP. Neuronal media was replaced every 4-5 days. On day 21 of neuronal differentiation, neurons were plated at 150K/cm2. Cells were incubated in neuronal media with 5-aza-dC (1 µM), DMSO, or 2HE-5NMe if indicated.

extract_protocol:
300,000 FXS neurons were harvested, washed and bound to beads. Neurons-beads were divided into three aliquots for determining binding locations of IgG control, H3K4me3, and H3K27me3. Neurons were permeabilized and the appropriate primary antibodies were utilized on each aliquot separately. Protein A-MNase fusion protein (gifted by the Henikoff lab) was then added to bind to primary antibody locations. Targeted digestion was activated with addition of calcium and occurred for 5 minutes. Cut fragments were then released from insoluble nuclear chromatin and extracted using NucleoSpin columns (Takara) following manufacturer’s instructions.
Size selection was performed using AMPure XP beads (Agencourt) before library preparation with the Kapa Hyper Prep Kit (Roche) following manufacturer’s instructions. End repair and A-tailing were performed before adapter ligation with TruSeq (Illumina) indices. The libraries were amplified and then quality control was performed to ensure that primer dimers were negligible.

value: human embryonic stem cell line differentiated to neurons

value: FXS

value: Untreated

tag: cut&run antibody

value: IgG


title: long_RNA_PR8_M2MC_Haplosufficient_2


title: diabetic wound [SC_W11]

value: skin

value: diabetic wound

value: Male


title: diabetic wound [SC_W10]


title: R1_WT_H3K27me3_experiment2_rep1


title: Untreated H3K27me3

description:
Cut&run fragments
WCMC37_untreated_H3K27me3


title: R1_WT_experiment2_input


title: diabetic wound [SC_W9]


title: long_RNA_PR8_M2MC_Haplosufficient_1


title: Untreated H3K4me3

description:
Cut&run fragments
WCMC37_untreated_H3K4me3


title: diabetic wound [SC_W8]


title: EmT_cl2_HA_experiment1_rep1


title: ETT5C2_H3K27me3_experiment2_rep2

value: Ezh2-TurboID clone T5C2


title: diabetic wound [SC_W7]


title: ETT5C2_H3K27me3_experiment2_rep1


title: ETT5C2_experiment2_input


title: 5-aza-dC H3K4me3

description:
Cut&run fragments
WCMC37_5azadC_H3K4me3

value: 1 week 5-daza-dC


title: non-diabetic wound [SC_W6]

value: non-diabetic wound

value: missing

value: unknown


title: aged, 5days, hematoma, ADT

city: Berlin

first: Christian

last: Bucher

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
aged_5days_hematoma.h5

library_source: other

data_processing:
Cellranger count (10X Genomics, v7.1.0) was used to process the raw sequencing reads, which included alignment to the mouse genome (mm10) and generation of count matrices with mRNA, ADT and HTO read counts.
The count data was then processed according to standard Seurat (v4.1.1) processing. Demultiplexing was carried out within Seurat using the HTODemux() function. This allowed us to remove doublets. In total, 14810 (58.55%) of all droplets were single cells with a median of 2100 expressed mRNAs. Next, we estimated cell cycle scores for the cells. These genes were then regressed using the difference between the G2M and S scores. We complete the pre-processing step of the RNA assay by filtering cells based on the number of mRNAs per cell (cells with >6500 genes were removed), the percentages of mitochondrial (cells with <10% were removed) and ribosomal (cells with <25%) genes. This resulted in the loss of 12.81% of cells, i.e. 87.19% (n = 12913) of cells were preserved.
In addition, the protein expression (ADT) data was filtered and normalized using Seurat's centered log ratio method.
Assembly: mm10
Supplementary files format and content: Cellranger output files: h5 files in HDF5 archive format, filtered feature barcode matrix files.

molecule: other

source_name: hematoma

growth_protocol: C57BL/6N mice were purchased from Charles River Laboratories with an age of 6 weeks and were used at an age of 12 and 26 weeks. Mice were housed in individually ventilated cages (non-experienced immune status) or in conventional cages (experienced immune status).

extract_protocol:
Animals were intraperitoneally injected with a mixture of medetomidine and ketamine to induce a deep anesthesia. Thereafter, animals were euthanized by cervical dislocation. The osteotomized femur was extracted and stored for transportation in ice cold phosphate-buffered saline (PBS). The fracture gap and proximal and distal regions from the osteotomy were separated and a single cell suspension was achieved by flushing and filtering through meshes. Cells were stained with fluorescently labeled sorting antibodies, oligonucleotide labeled hashtag antibodies and oligonucleotide labeled surface protein antibodies (Totalseq, BioLegend, San Diego, USA) before pooling sample of three animals. An enrichment sort for low abundant cells was performed by decreasing highly abundant cells by multi-layer sorting (staining: Ly6G, CD45R/B220, CD11c, Live/Dead, Ter119, CD41)  before cell encapsulation according the 10X Genomics protocol.
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (CG000317 Rev C) was used according the manufacturer's protocol to construct the libraries.
Chromium Single Cell 3’ v3.1 Gene Expression Library, Chromium Single Cell 3’ v3.1 Cell Surface Protein Library

treatment_protocol: Bone regeneration was studied by introducing an osteotomy on the left femur with an external rigid fixation system (MouseExFix, RISystem, Davos, Switzerland).  Following fixation, a 0.70 mm osteotomy was introduced between the medial pins using a Gigli wire  (RISystem, Davos, Switzerland). Mice were anesthetized with a mixture of isoflurane and oxygen. First line analgesia was done with Bubrenorphine pre surgery, antibiotics with clindamycine. Post-surgery, tramadol was added to the drinking water for 3 days.

value: hematoma

tag: gender

value: female

tag: mouse strain

tag: fracture region

tag: mouse age

tag: immune status

value: non-experienced

tag: time post_osteotomy

tag: library type

value: ADT

tag: adt

value: CD335, CD3, CD4, CD8a, CD19, aged_5days_hematoma_HTO4, aged_5days_hematoma_HTO5, aged_5days_hematoma_HTO6


title: ETT5C1_H3K27me3_experiment2_rep2

value: R1 mESCs

value: mouse embryonic stem cells

tag: genotype

value: Ezh2-TurboID clone T5C1

tag: treatment


title: 5-aza-dC H3K27me3

description:
Cut&run fragments
WCMC37_5azadC_H3K27me3

tag: cell type

value: human embryonic stem cell line differentiated to neurons

value: FXS


title: non-diabetic wound [SC_W4]

tag: tissue

value: skin

tag: Sex

tag: age


title: aged, 5days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
aged_5days_hematoma.h5

value: mRNA


title: aged, 5days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
aged_5days_proximal_distal.h5

source_name: bone marrow

value: bone marrow

value: CD335, CD3, CD4, CD8a, CD19, aged_5days_proximal_distal_HTO1, aged_5days_proximal_distal_HTO2, aged_5days_proximal_distal_HTO3, aged_5days_proximal_distal_HTO4, aged_5days_proximal_distal_HTO5, aged_5days_proximal_distal_HTO6


title: 5-aza-dC DMSO IgG cnt

description:
Cut&run fragments
WCMC37_5azadC_DMSO_IgG

tag: cell line

value: 1 week 5-daza-dC then 2 weeks DMSO

value: IgG


title: long_RNA_PR8_nonM2MC_Haplosufficient_2

value: Lung

value: haplosufficient


title: PD423

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

country: Switzerland

institute: ETH Zurich

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
PD423_S10_L001_R1_001

data_processing:
Bulk samples were mapped using STAR, followed by SNP calling. For this we used BCFFtools (v1.11,). We performed a pileup using the common loci of the 1000 Genomes project  on the Hg38 iGenomes genome (-d 8000, -Ou), calling SNPs with the bcftools call function (-mv, -Ob). Using the reheader function we then updated the bcf file to make it compatible with demuxlet. We detected 146,848 SNPs, ranging between 25K and 51K per genotype (see table). Next, the bcf file was sorted in the same order as the bam files and bcftools +fill-tags was used to add frequencies.
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger RNA (version 4.0.0) count pipeline.
Demuxlet was run on all samples to assign every cell to a genotype using SNPs called on the bulk RNA samples.
UMI count matrices were then loaded into Scanpy, doubles were removed and standard processing procedures were followed.
Assembly: hg38 (introns used as exons)
Supplementary files format and content: h5ad
Supplementary files format and content: counts (tsv)
Supplementary files format and content: vcf

source_name: Nucleus Basalis of Meynert

extract_protocol: SMARTer stranded total RNA library prep kit

value: Brain

tag: developmental stage

value: Adult


title: aged, 5days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
aged_5days_proximal_distal.h5

value: female

value: non-experienced


title: PD348

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
PD348_S9_L001_R1_001


title: 5-aza-dC DMSO H3K27me3

description:
Cut&run fragments
WCMC37_5azadC_DMSO_H3K27me3

tag: cut&run antibody


title: ETT5C1_H3K27me3_experiment2_rep1

value: R1 mESCs


title: aged, 2days, hematoma, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
aged_2days_hematoma.h5

value: hematoma

tag: gender

value: ADT

value: CD335, CD3, CD4, CD8a, CD19, aged_2days_hematoma_HTO1, aged_2days_hematoma_HTO2, aged_2days_hematoma_HTO3


title: ETT5C1_experiment2_input

value: mouse embryonic stem cells

value: Ezh2-TurboID clone T5C1


title: 5-aza-dC DMSO H3K4me3

description:
Cut&run fragments
WCMC37_5azadC_DMSO_H3K4me3

value: human embryonic stem cell line differentiated to neurons

value: FXS


title: long_RNA_PR8_nonM2MC_Haplosufficient_1


title: 5-aza-dC IgG cnt

description:
Cut&run fragments
WCMC37_5azadC_IgG

value: 1 week 5-daza-dC


title: EmT_cl14_H3K27me3_experiment2_rep2

value: Ezh2-miniTurboID clone 14


title: PD188

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
PD188_S7_L001_R1_001


title: PD194

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
PD194_S8_L001_R1_001


title: EmT_cl14_H3K27me3_experiment2_rep1


title: aged, 2days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
aged_2days_hematoma.h5

tag: mouse strain

value: mRNA


title: EmT_cl14_experiment2_input


title: aged, 2days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
aged_2days_proximal_distal.h5

value: bone marrow

tag: fracture region

value: CD335, CD3, CD4, CD8a, CD19, aged_2days_proximal_distal_HTO1, aged_2days_proximal_distal_HTO2, aged_2days_proximal_distal_HTO3, aged_2days_proximal_distal_HTO4, aged_2days_proximal_distal_HTO5, aged_2days_proximal_distal_HTO6


title: aged, 2days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
aged_2days_proximal_distal.h5

tag: mouse age


title: 5-aza-dC 2HE-5NMe H3K4me3

description:
Cut&run fragments
WCMC37_5azadC_2H_H3K4me3

value: 1 week 5-daza-dC then 2 weeks 2HE-5NMe


title: 2HE-5NMe IgG cnt

description:
Cut&run fragments
WCMC37_2H_IgG

value: 2 weeks 2HE-5NMe without 5-daza-dC

value: IgG


title: EmT_cl2_H3K27me3_experiment2_rep2

value: Ezh2-miniTurboID clone 2


title: immune aged, 5days, hematoma, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
immune_aged_5days_hematoma.h5

value: female

tag: immune status

value: experienced

value: CD335, CD3, CD4, CD8a, CD19, immune_aged_5days_hematoma_HTO4, immune_aged_5days_hematoma_HTO5, immune_aged_5days_hematoma_HTO6


title: 5-aza-dC 2HE-5NMe H3K27me3

description:
Cut&run fragments
WCMC37_5azadC_2H_H3K27me3


title: immune aged, 5days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
immune_aged_5days_hematoma.h5

value: hematoma

tag: time post_osteotomy


title: 2HE-5NMe H3K27me3

description:
Cut&run fragments
WCMC37_2H_H3K27me3


title: EmT_cl2_H3K27me3_experiment2_rep1

value: R1 mESCs

value: mouse embryonic stem cells


title: immune aged, 5days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
immune_aged_5days_proximal_distal.h5

tag: library type

value: ADT

value: CD335, CD3, CD4, CD8a, CD19, immune_aged_5days_proximal_distal_HTO1, immune_aged_5days_proximal_distal_HTO2, immune_aged_5days_proximal_distal_HTO3, immune_aged_5days_proximal_distal_HTO4, immune_aged_5days_proximal_distal_HTO5, immune_aged_5days_proximal_distal_HTO6


title: C72

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
C72_S3_L001_R1_001

value: Brain

value: Adult


title: C23

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
C23_S1_L001_R1_001


title: immune aged, 5days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
immune_aged_5days_proximal_distal.h5

value: mRNA


title: EmT_cl14_experiment1_input

value: Ezh2-miniTurboID clone 14


title: 2HE-5NMe H3K4me3

description:
Cut&run fragments
WCMC37_2H_H3K4me3

value: human embryonic stem cell line differentiated to neurons

value: FXS


title: C45

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
C45_S2_L001_R1_001


title: 5-aza-dC 2HE-5NMe IgG cnt

description:
Cut&run fragments
WCMC37_5azadC_2H_IgG

value: 1 week 5-daza-dC then 2 weeks 2HE-5NMe


title: H2R5-ATEV

city: Buffalo

first: Stelios

middle: T.

last: Andreadis

address: 908 Furnas Hall

department: Chemical and Biological Engineering

institute: University at Buffalo

description:
Library name: Sheep H2R5 ATEV (Graft)
10x Genomics

data_processing:
Following library generation and sequencing on an illumina SP NovaSeq flowcell, reads were demultiplexed using the 10x Genomics Cell Ranger (v7.2.0) mkfastq command with bcl2fastq2 version 2.20.0.422. Once demultiplexed, individual samples were analyzed using Cell Ranger v.7.2.0 count against a Custom reference genome from the Ensembl database (ARS-UI_Ramb_v2.0) that was built using the Cell Ranger mkref command. The resulting counts matrix served as input for subsequent downstream analysis.
Utilizing the filtered counts matrix from Cell Ranger, further preprocessing and downstream analysis was performed using R (v4.3.3). First, potential doublets were removed using scDblFinder (v1.16.0) package [40]. The data was then processed using the standard Seurat (v5.0.0) workflow i.e., SCTransform, RunPCA, FindNeighbors, FindClusters and RunUMAP. Appropriate cutoffs (ATEV - Genes > 600, UMI > 1200, Mitochondrial transcripts > 15%, NATIVE – Genes > 800, UMI > 1000, Mitochondrial transcripts > 10%) were applied to the samples. Clustering of the cells was done with an initial resolution of 1 for ATEV and 0.2 for NATIVE. Cell types were determined by the expression of canonical genes, and clusters with similar cell type were merged and processed accordingly. This resulted in 6 unique populations in both ATEV and NATIVE. Subsequent differential expression testing was performed using the FindAllMarkers (Wilcoxon Rank Sum test) function in Seurat.
Assembly: ARS-UI_Ramb_v2.0
Supplementary files format and content: Tab separated valiue files and matrix files

organism: Ovis aries

source_name: Carotid artery

extract_protocol:
ATEV and native carotid artery were explanted after 12 weeks and transported to the laboratory in Endothelial Growth Medium (EBM2 + Supplements containing 10% FBS). The native artery and ATEV were washed by perfusion with PBS to remove, blood stains, processed and trimmed to remove surrounding fat tissue. The ATEVs and the native artery were then clamped at one end and perfused with the Digestion Buffer (PBS containing 200 U/mL collagenase 1, 0.05 U/ml elastase, 5 U/ml neutral protease, and 0.3 U/ml deoxyribonuclease I, 5 mg/ml collagenase type II and 0.5 mg/ml elastase. The neovessels were then clamped at the other end and incubated in 35mm dishes containing PBS at 37°C and 5% CO2 atmosphere for 20 minutes. The digested neovessels were then perfused and washed with FBS to neutralize the enzymatic digestion and the cells detached from the ATEVs were collected into 5ml conical tubes. The isolated cells were then passed through cell strainer to remove clumps and obtain a homogenous population of single cells. The isolated cells were counted, resuspended in EBM2 growth medium and processed for scRNA sequencing.
Library construction was performed using the 10X Genomics Chromium Platform with reagents from the Single Cell NextGEM v3.1 kit according to the manufacturer’s recommendations in the University at Buffalo Genomics Core (UBGBC) for scRNA sequencing. To remove red blood cells from cell capture, the dissociated sheep cells were treated with red blood cell lysis buffer (10X volume RBC lysis buffer, 10 minutes incubation at room temperature, spin 5 minutes at 500 g in swinging bucket rotor, resuspend cell pellet in 200 ul RBC lysis buffer). After lysis treatment, the cells were counted on a Logos Biosystems LUNA II in bright field mode using 0.4% Trypan blue exclusion for viability. The cells were captured (~10,000 cells per capture) using the 10X Genomics Chromium Platform with reagents from the Single Cell NextGEM v3.1 kit according to the manufacturer’s recommendations. After drop-seq capture, cDNA from captured transcripts was used as input to generate double stranded Illumina sequencing libraries. Following final cleanup, qPCR (QuantaBio library quantification kit) was used determine final concentration of the libraries. The single cell RNA libraries were diluted and denatured to 250 pM for sequencing on the NovaSeq 6000 (28x91 paired end read length). Data generated from the NovaSeq were transferred to the Center for Computational Research at UB for data analysis.

value: 1-2 years

value: Carotid artery

value: Macrophages, Endothelial Cells, Smooth muscle cells


title: C87

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
C87_S5_L001_R1_001


title: EmT_cl14_HA_experiment1_rep1


title: EmT_cl14_HA_experiment1_rep2


title: PD106

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
PD106_S6_L001_R1_001


title: immune aged, 2days, hematoma, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
immune_aged_2days_hematoma.h5

value: female

value: experienced

tag: adt

value: CD335, CD3, CD4, CD8a, CD19, immune_aged_2days_hematoma_HTO1, immune_aged_2days_hematoma_HTO2, immune_aged_2days_hematoma_HTO3


title: Native Aorta

description:
Library name: Sheep Native Aorta (carotid artery)
10x Genomics

value: Endothelial Cells, Smooth muscle cells, Fibroblasts, macrophages


title: C5

description:
PD_atlas_human_final.h5ad
PD_atlas_human_final_genotyped.h5ad

source_name: Adult Brain

extract_protocol: 10x Genomics CHROMIUM Single Cell RNA Library 7 Gel Bead kit v3


title: C73

description:
called_vcf.vcf.gz
PD_bulk_human.tsv
C73_S4_L001_R1_001


title: small_RNA_Saline_M2MC_Deficient_4

value: Lung

tag: genotype

value: deficient

value: Saline


title: C1

value: Brain


title: immune aged, 2days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
immune_aged_2days_proximal_distal.h5

value: bone marrow

value: ADT

value: CD335, CD3, CD4, CD8a, CD19, immune_aged_2days_proximal_distal_HTO1, immune_aged_2days_proximal_distal_HTO2, immune_aged_2days_proximal_distal_HTO3, immune_aged_2days_proximal_distal_HTO4, immune_aged_2days_proximal_distal_HTO5, immune_aged_2days_proximal_distal_HTO6


title: C10

value: Adult


title: small_RNA_Saline_nonM2MC_Deficient_4

tag: treatment


title: EmT_cl14_H3K27me3_experiment1_rep1

value: R1 mESCs

tag: cell type

value: mouse embryonic stem cells

value: Ezh2-miniTurboID clone 14


title: immune aged, 2days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
immune_aged_2days_proximal_distal.h5

tag: tissue

value: mRNA


title: small_RNA_Saline_M2MC_Deficient_3


title: EmT_cl2_experiment2_input

value: Ezh2-miniTurboID clone 2


title: C9


title: Trim24_untreated_rep2

source_name: E14 mESCs

value: E14 mESCs


title: young, 2days, hematoma, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
young_2days_hematoma.h5

value: hematoma

value: female

value: non-experienced

value: CD335, CD3, CD4, CD8a, CD19, young_2days_hematoma_HTO1, young_2days_hematoma_HTO2, young_2days_hematoma_HTO3


title: small_RNA_Saline_nonM2MC_Deficient_3

value: Lung

value: deficient


title: Trim24_untreated_rep1


title: immune aged, 2days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
immune_aged_2days_hematoma.h5

value: experienced


title: small_RNA_Saline_M2MC_Deficient_2

value: Saline


title: young, 2days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
young_2days_hematoma.h5


title: Sall4_untreated_rep2


title: C7

value: Brain


title: small_RNA_Saline_nonM2MC_Deficient_2


title: young, 2days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
young_2days_proximal_distal.h5

value: bone marrow


title: young, 5days, hematoma, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
young_5days_hematoma.h5

value: ADT

value: CD335, CD3, CD4, CD8a, CD19, young_5days_hematoma_HTO4, young_5days_hematoma_HTO5, young_5days_hematoma_HTO6


title: Sall4_untreated_rep1

value: mouse embryonic stem cells


title: C11

value: Adult


title: C3


title: C6


title: Sall1_untreated_rep1


title: young, 5days, hematoma, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
young_5days_hematoma.h5

value: mRNA


title: small_RNA_Saline_M2MC_Haplosufficient_4

value: haplosufficient


title: C4


title: Input_untreated_sall1_4_trim24

value: E14 mESCs


title: small_RNA_Saline_nonM2MC_Haplosufficient_4


title: Nanog_untreated_rep2


title: young, 5days, proximal, distal, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
young_5days_proximal_distal.h5


title: C2


title: young, 2days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
young_2days_proximal_distal.h5

value: CD335, CD3, CD4, CD8a, CD19, young_2days_proximal_distal_HTO1, young_2days_proximal_distal_HTO2, young_2days_proximal_distal_HTO3, young_2days_proximal_distal_HTO4, young_2days_proximal_distal_HTO5, young_2days_proximal_distal_HTO6


title: small_RNA_Saline_nonM2MC_Deficient_1


title: EmT_cl14_H3K27me3_experiment1_rep2

value: R1 mESCs

value: Ezh2-miniTurboID clone 14


title: Sall1_untreated_rep2


title: SSC FetalTendon

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome GRCh38.p13 using STAR 2.4 (Dobin et al., 2013)
When aligning female data the entire Y chromosome was masked, while only the PAR regions on the Y chromosome were masked for male data. If sex was unknown PAR-masking was used.
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Assembly: hg38
Supplementary files format and content: RSM_gRDS_hSSC.csv = raw gene counts
Supplementary files format and content: Fetal.h5ad = raw gene counts for fetal hSSC analysis
Supplementary files format and content: LineageTree.h5ad = raw gene counts for fetal hSSC lineage tree analysis
Supplementary files format and content: GPPE.h5ad = raw gene counts for growth plate versus periosteal hSSC analysis
Supplementary files format and content: Aging.h5ad = raw gene counts for patient hSSC analysis

source_name: Tendon

growth_protocol: freshly purified cells without prior in vitro culture

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and cell populations purified via FACS.
SmartSeq2 pipeline (Picelli et al.)
SmartSeq2 single cell RNA sequencing

treatment_protocol: no treatment

value: SSC

value: Tendon

tag: Sex

value: not provided

value: fetal


title: small_RNA_Saline_M2MC_Deficient_1

value: Lung

value: deficient

value: Saline


title: small_RNA_Saline_M2MC_Haplosufficient_3


title: small_RNA_Saline_nonM2MC_Haplosufficient_3


title: Nanog_untreated_rep1


title: C8

value: Brain


title: Freshly-isolated Nrf2:p65 DKO hepatocytes 3

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

data_processing:
Alignment  - Salmon version 1.10.3 quant -l SF –fldMean 170 -fldSD 50 --seqBias --validateMappings Differential expression - DESeq2 version 1.42.1
Assembly: GRCm39 M33
Supplementary files format and content: normalized counts

source_name: Liver

growth_protocol: Adult male mice (8-9 weeks old)

extract_protocol:
Column (Qiagen)
Illumina TruSeq stranded mRNA

treatment_protocol: Control (C57BL6/j), Nrf2 flox/flox, p65 flox/flox and Nrf2:p65 double floxed mice were injected with AAV8Cre to induce a hepatocyte-specific knockout of the respective genes. 12 days after injection, mice were euthanized and the liver was perfused with Liberase TM solution followed by low speed centrifugation of the cell suspension and additional centrifugation in Percoll density media. Total RNA was isolated from freshly isolated hepatocytes and subjected to library preparation using TrueSeq stranded protcol.

value: Liver

value: Hepatocytes

value: Nrf2:p65 DKO


title: SSC FetalSuture

city: Sacramento

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: Suture

value: Suture

tag: age


title: Freshly-isolated Nrf2:p65 DKO hepatocytes 2


title: Nanog_72hr_rep1

tag: cell line

value: mouse embryonic stem cells

value: dTAG-13 for 72 hours


title: SSC FetalVertebraDisc

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: SpineDisc

value: SpineDisc


title: SSC FetalVertebraBone

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: SpineBone

value: SpineBone


title: small_RNA_Saline_nonM2MC_Haplosufficient_2

source_name: Lung

value: haplosufficient


title: small_RNA_Saline_M2MC_Haplosufficient_2


title: Nanog_72hr_rep2

value: E14 mESCs


title: Nanog_1hr_rep2

value: dTAG-13 for 1 hour


title: small_RNA_Saline_M2MC_Haplosufficient_1


title: Freshly-isolated Nrf2:p65 DKO hepatocytes 1


title: Freshly-isolated p65KO hepatocytes 2

value: p65 KO


title: SSC FetalPhalange

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: Phalange

value: SSC

value: Phalange

value: not provided

value: fetal


title: Nanog_1hr_rep1


title: Freshly-isolated p65KO hepatocytes 1


title: small_RNA_PR8_M2MC_Deficient_4

value: Lung

value: deficient


title: Input_untreated_nanog


title: Freshly-isolated Nrf2KO hepatocytes 2

value: Liver

value: Hepatocytes

value: Nrf2 KO


title: SSC FetalPelvis

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: Pelvis

value: Pelvis


title: SSC FetalParietalSkull

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: ParietalSkull

value: ParietalSkull


title: small_RNA_PR8_nonM2MC_Deficient_4


title: Input_72h_nanog

value: mouse embryonic stem cells

value: dTAG-13 for 72 hours


title: Freshly-isolated Nrf2KO hepatocytes 1


title: small_RNA_PR8_M2MC_Deficient_3


title: SSC AgingNU62yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

source_name: Nonunion

value: Nonunion

value: F


title: Input_1h_nanog

value: E14 mESCs

value: dTAG-13 for 1 hour


title: Freshly-isolated hepatocytes from the control mice 3

value: Control


title: sci_L3_Strand_seq_yi293

city: Los Angeles

first: Yi

last: Yin

state: CA

address: 695 Charles E. Young Dr. S.

department: Human Genetics

institute: University of California, Los Angeles

data_processing:
*library strategy: sci-L3
Reads were aligned to hs37d5 or a hybrid reference of hs37d5 and mm10. For sci-L3-HiC pairs files were using the 4DN Docker image (v43; https://github.com/4dn-dcic/docker-4dn-hic) that contains wrapper scripts for running pairtools, pairix, and cooler. The filtered BAMs were converted to the pairsam format and sorted (run-pairsam-parse-sort.sh). PCR duplicates were marked (DD) within the pairsam files (run-pairsam-markasdup.sh) and subsequently filtered out by only retaining valid pairs (UU - unique-unique, UR - unique-rescued, RU - rescued-unique) (run-pairsam-filter.sh). For sci-L3-RNA/ATAC, DNA reads were isolated based on the reverse transcription UMI (rt_UMI) filtered for proper read pairs (FR), a maximum insert size of 2000, and a maximum soft-clipping ratio of 0.5. A CB tag was added to the BAM files based on the cell barcodes present in the read name. Using the CB tag, BAMs were converted into fragment files using sinto (0.10.0).
Aligned reads were filtered for proper read pairs (FR), a maximum insert size of 2000, and a maximum soft-clipping ratio of 0.5 (defined as the number of soft-clipped bases over the number of matched bases) to remove excessively soft-clipped reads. Following filtering, reads were split by species of origin (hs37d5 or mm10) and cell barcodes. For each cell, strand breakpoints and background estimates were obtained using breakpointR (1.18.0) using blacklisted regions for hg19 and mm10 (version 2). BreakpointR breakpoints were filtered to eliminate false calls using a set of distance and strand state based criteria using sciStrandR (0.1.0).
Assembly: mm10, hs37d5
Supplementary files format and content: Gzipped fragment files provided for the ATAC portion of sci-L3-RNA/ATAC
Supplementary files format and content: Gzipped pairs files provided for sci-L3-HiC

source_name: cell line

growth_protocol: BJ-5ta (CRL-4001, ATCC), HEK239T (CRL-3216, ATCC), and NIH/3T3 (CRL-1658, ATCC), and Patski (gift from Disteche lab) cells were cultured in DMEM medium supplemented with 10% FBS and 1x Pen-Strep. HAP1 cells were cultured in IMDM medium supplemented 10% FBS and 1x Pen-Strep. GM12878 cells were cultured in RPMI-1640 medium supplemented with 15% FBS and 1x Pen-Strep. All cells were cultured at 37°C, 5% CO2. For sci-L3-Strand-seq, cells were cultured with BrdU at 40 µM final concentration for 24 hours prior to fixation.

extract_protocol: sci-L3-Strand-seq. Fixation and nucleosome depletion was performed as previously described in ‘Methods and molecular design of sci-L3-WGS and sci-L3-target-seq’, subsections ‘Single Cell Preparation and Nucleosome Depletion’ and ‘Tagmentation (first-round barcodes) and ligation (second-round barcodes)’ (Yin, Yi et.al. 2019 PMID: 31495564). Notably, cells were trypsinized and fixed with 37% formaldehyde (final 1-1.5% concentration) in 1x PBS at a cell density of 1 million/mL for 10 minutes at room temperature with gentle tube inversion. For first round barcoding, Patski nuclei were distributed into wells with barcodes 1-12, while HAP1 nuclei were distributed into wells with barcodes 13-24. The remaining nuclei were stained with DAPI at a final concentration of 5 mg/mL and used for FACS as described in Fig2A. After the ligation reaction was stopped by the addition of the stop solution (lysis buffer (LB: 60 mM Tris-Ac pH 8.3, 2 mM EDTA pH 8.0, 15 mM DTT) with 0.1% Triton-X100 (LBT)), nuclei were pooled and stained with Hoechst-33258 to a final concentration of 10ng/µL and the quenched population was sorted (100-300 nuclei per well) into a 96-well plate containing 3 µL of LB. The major differences of sci-L3-Strand-seq arise in the ‘Cell lysis, gap extension and linear amplification by in vitro transcription’ subsection of the protocol (1). Right after gap extension with the Bst WarmStart 2.0 polymerase at 68°C for 5 minutes and its inactivation with 80°C for 10 minutes, Hoechst-33258 was added at a final concentration of 10ng/µL and incubated at room temperature for 10 minutes in the dark. A 1 or 5 minute exposure in a Bio-Rad Gel Doc with a 365nm UV bulb, or a dose of 27-4000 mJ/cm2 was administered with a UVP crosslinker (CL-3000L). Note, we did not observe any differences in library quality between 1 or 5 minute exposures, or in doses above 270 mJ/cm2. At this stage, each well had a volume of around 7.7 µL, to which 0.3uL of USER enzyme (a mix of uracil DNA glycosylase and endonuclease VIII, referred to as UDG+EndoVIII in the text, NEB) was added and incubated at 37°C for 15 minutes. Next, 0.9 µL of its inhibitor UGI (NEB) was added with a further incubation at 37°C for 10 minutes. Finally, the T7 in vitro transcription system was assembled as previously described by adding 2 µL H2O, 2 µL T7 Pol mix and 10 µL rNMP mix (NEB, HiScribe T7 Quick High Yield RNA Synthesis Kit) and incubated at 37°C for 10-16 hours. The remaining section, ‘RNA purification, RT and SSS’, was performed exactly as previously described (Yin, Yi et.al. 2019 PMID: 31495564).  sci-L3-Hi-C. The major differences of sci-L3-Hi-C arise in the first ‘Single Cell Preparation and Nucleosome Depletion’ subsection of the protocol (1). After 2% formaldehyde fixation and quenching as done for sci-L3-Strand-seq, the proximity ligation was performed largely as previously described for Dip-C (18). The pelleted cells after fixation were washed with ice-cold 1x PBS, resuspended in 500 µL Hi-C lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% IGEPAL with 100uL Protease inhibitors (“PI”, Sigma P8340) and incubated on ice for at least 15 minutes. The nuclei were pelleted at 2500g for 5 minutes at 4°C and washed with ice-cold Hi-C lysis buffer. The pellet was resuspended in 50 µL of 0.5% SDS (diluted with H2O) and incubated for 10 minutes at 62°C. The SDS was quenched with the addition of Triton X-100 (145 µL H2O, 25 µL 10% Triton X-100) and with a further incubation of 15 minutes at 37°C. Next, 25 µL of NEBuffer2 was added, followed by 20 µL of 25U/µL MboI (NEB, R0147M) and left overnight at 37°C. The nuclei were pelleted at 2500g for 5 minutes at 4°C and washed with 1 mL of ligation buffer (1x T4 DNA ligase buffer, NEB B0202S with 0.1mg/mL BSA, NEB B9000S). Ligation was performed with 1 mL ligation buffer and 10 µL of 1U/µL T4 DNA ligase (Life Tech 15224-025) at 16°C for 4 hours. Nuclei were passed through a 35 µM cell strainer, pelleted at 2500g for 5 minutes at 4°C, washed with 1 mL lysis buffer (LB: 60 mM Tris-Ac pH 8.3, 2 mM EDTA pH 8.0, 15 mM DTT) and resuspended with LB at a concentration of 20,000 nuclei per µL. The remaining steps were performed exactly as previously described in subsection ‘Tagmentation (first-round barcodes) and ligation (second-round barcodes)’  onwards (Yin, Yi et.al. 2019 PMID: 31495564).  sci-L3-RNA/ATAC. The major differences of sci-L3-RNA/ATAC arise in the nucleosome depletion step previously described in the ’Methods and molecular design of sci-L3-RNA/DNA co-assay’ subsection of the protocol (Yin, Yi et.al. 2019 PMID: 31495564). Cells were trypsinized, combined together (HEK293T, BJ-5ta, NIH/3T3), and fixed with 2% PFA in 1x PBS at room temperature for 10 minutes at a density of 1 million/mL. The subsequent quenching (with glycine), washing, and nuclei isolation (with 0.1% IGEPAL) steps are identical with sci-L3-WGS, except the addition of 1% Superase-In to all the LB and 1xNEBuffer2.1 buffers. After the isolation of nuclei, the pellet was split in half. One half subjected to nucleosome depletion with the addition of 776 µL of 1x NEBuffer2.1, 24 µL of 10% SDS and an incubation at 42°C for 15 minutes. The SDS was quenched with 180 µL of 10% Triton-X100 with 10 µL Superase-In, and further incubated at 42°C for 10 minute. The depleted nuclei were pelleted, washed with 1 mL LB with 1% Superase-In, and resuspended in LB with 1% Superase-In at a 20,000 nuclei per µL concentration. These nuclei represent the sci-L3-RNA/DNA sample. For the other half, the nuclei were washed with 200 µL of LB with 1% Superase-In and 0.1% Triton-X100 and resuspended in LB with 1% Superase-In at a 20,000 nuclei per µL concentration. These nuclei represent the sci-L3-RNA/ATAC sample. For the first round barcoding, the nucleosome depleted nuclei were distributed into wells with barcodes 1-5, while the non-nucleosome depleted nuclei were distributed into wells with barcodes 6-10. The subsequent steps were performed exactly as previously described in the sci-L3-RNA/DNA co-assay subsections ‘RT and Tagmentation, Ligation, FACS, and Cell Lysis’, ‘Gap Extension and Linear Amplification by In Vitro Transcription’, and ‘RNA Purification, RT, and SSS’ (Yin, Yi et.al. 2019 PMID: 31495564).

value: cell line

value: Patski, HAP1

value: Combination of 2 cell lines


title: SSC AgingNU59yo

institute: UC Davis

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: SSC

value: M


title: small_RNA_PR8_nonM2MC_Deficient_3

value: Lung

value: deficient


title: Freshly-isolated hepatocytes from the control mice 2

value: Liver

value: Hepatocytes


title: SSC AgingNU60yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: sci_L3_RNA/ATAC/DNA_yi261_2

description: Combination of multiple libraries: lib261, lib262, lib263, lib273, lib274, lib275, lib276, lib277, lib278, lib279

value: HEK293T, BJ-5ta, NIH/3T3

value: Combination of 3 cell lines


title: Freshly-isolated hepatocytes from the control mice 1


title: small_RNA_PR8_M2MC_Deficient_2


title: mESC, Nsd1-KO-2, day 4, biol rep 2

data_processing:
The fastq files were trimmed using trim-galore 0.6.7 and then aligned to mm39 mouse genome using STAR 2.7.11a. Primary aligned, non-duplicated reads were supplied to featureCounts 2.0.6 for counting read fragments aligned to exons. Raw gene expression counts were further processed with DESeq2 1.42.0. Low-count genes with an average count < 1 were filtered out before downstream analysis.
Differentially expressed genes were defined with a significance cut off of padj<0.01 and |log2FC|>0.58. PCA clustering was performed on VST normalized expression values for top 500 most variable genes. MA plots were generated using the shrunken log2 fold changes, which removed noises associated with low-count genes.
Fuzzy c-means clustering was performed to assign genes to distinct clusters displaying differential gene expression trajectories along differentiation.
Gene Set Enrichment Analysis (GSEA) with H/C2/C5 gene set collections and Gene Ontology (GO) pathway enrichment analysis with the Biological Process annotations was done using the R package clusterProfiler 4.10.0 using a significance cut off of BH-adjusted p values<0.01.
Assembly: mm39
Supplementary files format and content: VST normalized count table

source_name: mouse blastocyst

extract_protocol:
Total RNAs were extracted using RNeasy Plus kit (Qiagen: 74136), followed by removal of residual DNAs using Turbo DNA-free kit (Thermo Fisher: AM1907) to ensure purity of RNA sample.
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit v2 following the kit's protocol.

treatment_protocol: LIF and MEF were removed to induce mESC in vitro differentiation

value: mouse blastocyst

tag: developmental stage

value: mouse embryonic stem cell

value: LIF and MEF withdrawal

tag: time point

value: 4 days


title: small_RNA_PR8_nonM2MC_Deficient_2

extract_protocol:
Cells were sorted from Miwi2+/tom and Miwi2tom/tom mice into Qiagen buffer RLT supplemented with 1% beta-mercaptoethanol. RNA  was isolated on the Qiagen QIASymphony SP/AS using the QIAshymphony RNA kit and the miRNA CT 400 protoocol.
The RNA-Seq libraries were prepared using Illumina Stranded Total RNA with RiboZero Plus kit per the manufacturer instruction.  The small RNA-Seq libraries were prepared using Qiagen QIASeq small RNA kit per the manufacturer instruction.


title: SSC GrowthPlateSSC

description:
SmartSeq2
RSM_gRDS_hSSC.csv
LineageTree.h5ad

source_name: GrowthPlate

value: GrowthPlate

value: not provided

value: fetal


title: sci_L3_RNA/ATAC/DNA_yi261_3

value: cell line


title: SSC AgingNU51yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: Nonunion


title: sci_L3_RNA/ATAC/DNA_yi261_1


title: small_RNA_PR8_M2MC_Deficient_1


title: small_RNA_Saline_nonM2MC_Haplosufficient_1

value: haplosufficient

value: Saline


title: SSC GrowthPlateOP

value: OP


title: sci_L3_HiC_yi239

description: Low depth

source_name: blood, cell line

value: blood, cell line

value: Lymphoblastoid cell line


title: SSC GrowthPlateBCSP

value: BCSP


title: mESC, Nsd1-KO-1, day 4, biol rep 2


title: small_RNA_PR8_nonM2MC_Deficient_1

value: Lung

value: deficient


title: young, 5days, proximal, distal, ADT

description:
Antibody derived olignoucleotide and Hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads
young_5days_proximal_distal.h5

source_name: bone marrow

value: bone marrow

tag: gender

value: female

value: non-experienced

value: ADT

value: CD335, CD3, CD4, CD8a, CD19, young_5days_proximal_distal_HTO1, young_5days_proximal_distal_HTO2, young_5days_proximal_distal_HTO3, young_5days_proximal_distal_HTO4, young_5days_proximal_distal_HTO5, young_5days_proximal_distal_HTO6


title: sci_L3_HiC_yi238

description: Medium depth


title: mESC, Nsd1-KO-1, day 4, biol rep 1

value: mouse blastocyst

value: mouse embryonic stem cell

value: LIF and MEF withdrawal

value: 4 days


title: small_RNA_PR8_M2MC_Haplosufficient_4

value: haplosufficient


title: SSC FetalFrontralSkull

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: FrontalSkull

value: SSC

value: FrontalSkull

value: not provided

value: fetal


title: small_RNA_PR8_nonM2MC_Haplosufficient_4


title: mESC, WT, day 4, biol rep 2

value: WT


title: control_Habib

source_name: Adult Brain

value: Brain

value: Adult


title: SSC AgingFX77yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

source_name: Fracture

value: Fracture

value: F


title: SSC AgingFX72yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: M


title: small_RNA_PR8_M2MC_Haplosufficient_3

value: Lung


title: mESC, Nsd1-KO-2, day 4, biol rep 1


title: mESC, WT, day 4, biol rep 1


title: control_TST


title: mESC, Nsd1-KO-2, day 2, biol rep 1

value: 2 days


title: small_RNA_PR8_M2MC_Haplosufficient_2


title: small_RNA_PR8_nonM2MC_Haplosufficient_3


title: SSC AgingFX65yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: SSC AgingFX61yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: small_RNA_PR8_M2MC_Haplosufficient_1


title: mESC, Nsd1-KO-1, day 2, biol rep 2

value: mouse blastocyst


title: SSC AgingFX63yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: sci_L3_HiC_yi237

description: High depth

value: blood, cell line

value: Lymphoblastoid cell line


title: SSC AgingFX53yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: control_Soma


title: mESC, WT, day 2, biol rep 2

value: mouse embryonic stem cell

value: LIF and MEF withdrawal


title: mESC, Nsd1-KO-1, day 2, biol rep 1


title: mESC, Nsd1-KO-2, day 2, biol rep 2


title: SSC AgingFX67yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: SSC


title: day4_noLif, Nsd1, HA Cut&Run

data_processing:
Raw sequencing reads were aligned to mm10 mouse genome using STAR 2.7.10b with splicing alignment disabled (--alignIntronMax 1 --alignEndsType EndToEnd). Non-primary aligned, duplicated reads and reads mapping to ENCODE blacklisted regions were filtered out before downstream analysis.
The MACS2 software 2.2.7.1 was employed for peak calling using q<0.1 as significance cut-off.
Peak annotation and TF motif enrichment analysis with peak summit bed file as input and a specified region size of 200 was carried out using the Homer 4.11 functions ‘annotatePeaks.pl’ and ‘findMotifsGenome.pl’, respectively. Alignment bam files were also transformed into read coverage bigWig files using the deepTools 3.5.4 function ‘bamCoverage’ with options [-bs 10 --centerReads -e 250] and normalized to reads per genome coverage (RPGC).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

extract_protocol:
Cut&Run was performed following the EpiCypher CUTANA CUT&RUN Protocol. Briefly, one million live cells were washed and immobilized onto activated ConA magnetic beads (Bangs Laboratories: BP531) by incubation at RT for 10min, followed by permeabilization and incubation with HA antibody (1:100 dilution) on nutator overnight at 4 °C. On the next day, the cell-bead slurry was washed twice and incubated with pAG-MNase (1:20 dilution, EpiCypher: 15-1116) for 10min at RT, followed by addition of CaCl2 and 2h incubation at 4 °C for targeted chromatin cleavage by activated MNase. After chromatin digestion, stop buffer was added and chromatin fragments released into supernatant were purified using the Monarch DNA Cleanup Kit (NEB: T1030) per manufacturer’s instruction.
Cut&Run library was prepared using the NEB Ultra II DNA Library Prep Kit (NEB: E7645).

value: LIF and MEF withdrawal for 4 days


title: SSC AgingFX39yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: mESC, Nsd1-KO-2, day 0, biol rep 2

value: 0 day


title: WT VSMC, repeat #2

city: La Jolla

first: Ming

last: He

address: 9500 Gilman Dr.

institute: UCSD

description: Library name: WT2

data_processing:
Trimmomatic was used to process the fastq files to remove poor-quality and adapter reads. RNA reads were aligned by using HISAT2 with a prebuilt reference mouse UCSC mm10 transcriptome index. To evaluate gene expression, gene information was obtained from GENCODE, and count per gene was calculated by featureCount.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file contains raw read counts, gene IDs, and gene symbols for each sample.

source_name: Aorta

growth_protocol: Isolated mouse vascular smooth muscle cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics, under a humidified atmosphere containing 10% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Kit according to the manufacturer's protocols.

treatment_protocol: The diabetic condition medium consisted of basal growth medium supplemented with 4.5 g/L glucose and 0.3 mM H2O2.

value: Aorta

value: Primary vascular smooth muscle cells

value: myocyte

value: Diabetic condition medium

tag: batch


title: Bmal1 KO VSMC, repeat #2

description: Library name: BKO2

value: Bmal1 KO


title: Bmal1 KO VSMC, repeat #3

description: Library name: BKO3


title: mESC, WT, day 2, biol rep 1

value: WT


title: Bmal1 KO VSMC, repeat #1

description: Library name: BKO1


title: SSC AgingFX34yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: Fracture

value: F


title: WT VSMC, repeat #3

description: Library name: WT3


title: small_RNA_PR8_nonM2MC_Haplosufficient_1

data_processing:
For RNA-Seq data, the raw data was aligned to a composite reference genome of mouse, influrenza A and antibiotic resistance plasmid containing TdTomato using HISAT2 (version 2.1.0) aligner.  DIfferential expression analysis were than performed on the output using R and DESeq2 package.
For small RNA, raw sequencing data is first processed using a custom pipeline and script to remove adaptor sequence, remove invalid and consolidate UMI, and remove reads that are shorter than 15 bases.  The processed reads are then use as input for COMPSRA analysis.  DIfferential expression analysis were than performed on the output using R and DESeq2 package.
Assembly: mm10, IVA (CY046986.1), Tdtomato (LC311026.1), default COMPSRA small RNA database (v1.03)
Supplementary files format and content: tab-delimited text files containing raw read count for both RNA-Seq and small RNASeq

value: Lung

value: haplosufficient


title: small_RNA_PR8_nonM2MC_Haplosufficient_2


title: mESC, Nsd1-KO-2, day 0, biol rep 1

value: mouse blastocyst


title: WT VSMC, repeat #1

description: Library name: WT1