title: UAD022_Granulocytes

description:
granulocyte sample from AD patient
203219730117_R06C01


title: maternal placenta, LPS, 13.11 h, replicate 26

status: Public on Feb 01 2024

type: SRA

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

source_name: maternal placenta

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

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

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

tag: tissue

value: maternal placenta

tag: genotype

value: WT

tag: treatment

value: LPS


title: maternal placenta, H2O, 13.11 h, replicate 26


title: WT_SHAM_2.ZT0

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
14500 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Assembly: GRCm38, release 81
Supplementary files format and content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

molecule: total RNA

source_name: tibialis anterior muscle

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

treatment_protocol: Tibialis anterior muscle was collected and snap frozen with liquid nitrogen at two different time point intervals during 24hr period (ZT0 and ZT12).

tag: strain

tag: Sex

value: female

value: wild-type

tag: age

value: 13 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

value: whole muscle

value: Sham


title: A2,liver,WT,WD diet+hUC-MSCs cell

city: Shanghai

first: lan

last: Zhong

address: Jimo Road 150

country: China

institute: Shanghai East hospital

data_processing:
Reads were filtered by Cutadapt-1.9 and verified using FastQC-0.11.9.
Filtered reads were aligned to the mus musculus reference genome using HISAT2-2.2.1.
The mapped reads were assembled using StringTie-2.1.6
All transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare-0.9.8.
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM.
Assembly: GRCm38/mm10

source_name: Liver

growth_protocol: Five-week-old male C57BL/6j mice were fed a WD diet (fat, 40%; Fructose,20%; Cholesterol,2%; Nutrition).

extract_protocol:
After 40 weeks, the mice were sacrificed and liver, serum and visceral adipose tissue (VAT) were collected.
Total RNA was extracted using Trizolreagent(thermofisher,15596018)following the manufacturer's procedure.

treatment_protocol: After 32 weeks of WD feeding, all mice received 1 injection of PBS or MSCs via the tail vein.

tag: model

value: WD-induced NASH

value: Liver

value: WD diet+hUC-MSCs cell


title: maternal placenta, TiO2, 13.11 h, replicate 8


title: maternal placenta, LPS, 13.11 h, replicate 28


title: UAD001_Granulocytes

type: genomic

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

description:
granulocyte sample from AD patient
203219730200_R04C01

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Illumina iScan System as per manufacturer’s protocol

data_processing:
Illumina® GenomeStudio, normalized with R package wateRmelon (QN + BMIQ)
Processed data files include: Average M value

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Granulocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from granulocytes and monocytes using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: Granulocytes

tag: gender

value: Male

tag: donor id

tag: loy status

value: non-LOY

tag: sample type

value: genomic DNA

tag: disease state

value: Alzheimer's disease


title: Akata BCR 1

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

country: USA

institute: Tulane Health Sciences Center

library_source: genomic

data_processing:
Aligned using bowtie2
Duplicates marked and removed using Picard
Bam files converted to bigwig using DeepTools
Assembly: hg38 and chrEBV_Akata_inverted
Supplementary files format and content: bigWig

source_name: B cell lymphoma

extract_protocol:
The ATAC-seq protocol from Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21.29.1-21.29-9.
Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030)

value: B cell lymphoma

tag: cell line

value: Akata

value: anti-IgG


title: maternal placenta, LPS, 13.11 h, replicate 25

value: maternal placenta

value: WT

value: LPS


title: A1,liver,WT,WD diet+hUC-MSCs cell


title: Akata Ctl 6


title: UAD001_Monocytes

description:
monocyte sample from AD patient
203219730200_R03C01

source_name: Monocytes

value: Monocytes


title: maternal placenta, H2O, 13.11 h, replicate 25


title: KAD056_Monocytes

description:
monocyte sample from AD patient
203219760033_R07C01

value: LOY


title: Akata Ctl 5


title: A0,liver,WT,WD diet+hUC-MSCs cell


title: maternal placenta, LPS, 13.11 h, replicate 24


title: maternal placenta, H2O, 13.11 h, replicate 27


title: KAD056_Granulocytes

description:
granulocyte sample from AD patient
203219760033_R06C01


title: D1,liver,WT,WD diet+Vehicle

value: WD diet+Vehicle


title: maternal placenta, H2O, 13.11 h, replicate 24


title: HP_C57BL6JxBXD65_14m_5XFAD Carrier

city: BAR HARBOR

first: Niran

last: Hadad

state: Maine

address: 5 Bloomfield Rd, Unit A

institute: The Jackson Laboratory

description:
10x Genomics
CK19120

library_source: transcriptomic single cell

data_processing:
Base call files were converted to FASTQ files using bcl2fastq v2.20.0.422 and were aligned to the mouse mm10 pre mRNA reference transcriptome (GRCh38.93, 10x Genomics mm10 reference 3.0.0) using Cell Ranger count pipeline V3.1.0 (10x Genomics) to obtain gene x cell count matrix for each sample.
Assembly: GRCh38.93, 10x Genomics mm10 reference 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
Nuclei were isolated from frozen left hippocampal hemisphere from 6 mo and 14 mo Ntg-BXDs and AD-BXDs females (n=12-14 per group) using manual dissociation with lysis buffer following 10x guidelines and recommendations for nuclei isolation from frozen brain tissue.  Nuclei were resuspended and filtered through a 40 μm Flowmi Cell Strainer to remove cell debris and viability was assessed using Countess II FL Automated cell counters (Thermo Fisher Scientific). Nuclei suspensions were loaded onto independent single channels of a Chromium Controller.
Library construction were performed according the manufacter's instructions using Single Cell 3’ Reagent kit, v3 Chemistry (10x Genomics). Libraries were quality checked using Agilent 4200 Tapestation, quantified using KAPA qPCR kit, pooled and loaded onto an Illumina NovaSeq 6000 S2 flow cells for sequencing targeting 600M reads per library.

value: Hippocampus

value: 14 months

value: 5XFAD Carrier

value: Female


title: Akata Ctl 3


title: maternal placenta, LPS, 13.11 h, replicate 23


title: KAD054_Monocytes

description:
monocyte sample from AD patient
203219760033_R05C01

value: Male


title: HP_C57BL6J_14m_5XFAD Carrier

description:
10x Genomics
CK19119


title: KAD054_Granulocytes

description:
granulocyte sample from AD patient
203219760033_R04C01

value: Granulocytes


title: Akata Ctl 2


title: HP_C57BL6JxBXD33_14m_5XFAD Carrier

description:
10x Genomics
CK19107


title: KAD052_Monocytes

description:
monocyte sample from AD patient
203219760033_R02C01

value: non-LOY

value: genomic DNA


title: Akata Ctl 1

value: B cell lymphoma


title: HP_C57BL6JxBXD124_14m_5XFAD Carrier

description:
10x Genomics
CK19078


title: HP_C57BL6JxBXD28_14m_5XFAD Carrier

description:
10x Genomics
CK19093


title: maternal placenta, H2O, 13.11 h, replicate 22


title: KAD052_Granulocytes

description:
granulocyte sample from AD patient
203219760033_R01C01

value: Alzheimer's disease


title: maternal placenta, H2O, 13.11 h, replicate 23


title: maternal placenta, LPS, 13.11 h, replicate 22


title: HP_C57BL6JxBXD99_14m_5XFAD Carrier

description:
10x Genomics
CK19068


title: Mutu Zta 3

value: Mutu

value: Zta


title: Akata Ctl 4

value: Akata


title: KAD051_Monocytes

description:
monocyte sample from AD patient
203219760006_R08C01


title: maternal placenta, H2O, 13.11 h, replicate 21

value: maternal placenta

value: WT


title: Mutu Zta 1


title: maternal placenta, LPS, 13.11 h, replicate 21

value: LPS


title: HP_C57BL6JxBXD39_14m_5XFAD Carrier

description:
10x Genomics
CK19051


title: Mutu Zta 2


title: KAD046_Monocytes

description:
monocyte sample from AD patient
203219760006_R04C01

value: Monocytes


title: KAD046_Granulocytes

description:
granulocyte sample from AD patient
203219760006_R03C01


title: HP_C57BL6JxBXD83_14m_5XFAD Carrier

description:
10x Genomics
CK19044

value: Hippocampus


title: maternal placenta, LPS, 12.11 h, replicate 12


title: maternal placenta, H2O, 12.11 h, replicate 12


title: HP_C57BL6JxBXD161_14m_5XFAD Carrier

description:
10x Genomics
CK19021

value: 14 months


title: maternal placenta, LPS, 12.11 h, replicate 11


title: Mutu Ctl 1

value: Ctl


title: HP_C57BL6JxBXD50_14m_5XFAD Carrier

description:
10x Genomics
CK19014

value: 5XFAD Carrier

value: Female


title: KAD051_Granulocytes

description:
granulocyte sample from AD patient
203219760006_R07C01

value: Granulocytes

value: Male

value: LOY


title: KAD041_Granulocytes

description:
granulocyte sample from AD patient
203219760207_R07C01

value: non-LOY

value: genomic DNA


title: KAD041_Monocytes

description:
monocyte sample from AD patient
203219760207_R08C01

value: Alzheimer's disease


title: iWAT_old_Rep5

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads were aligned  with STAR Mapper v2.7.8a using Ensembl gene annotations.
Count files were created using STAR counts.
Assembly: Monodelphis domestica reference genome (ASM229v1) using Ensembl gene annotations.
Supplementary files format and content: csv countfiles, raw reads, Ensembl Gene Annotation

organism: Monodelphis domestica

source_name: inguinal adipose tissue

extract_protocol:
RNA was extracted from three different adipose tissue depots (anterior subcutanous, inguinal, interscapular) using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
Paired-end: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Single-end: Libraries were prepared by isolating total RNA from fat tissue homogenized in TRIzol reagent. Total RNA was converted to cDNA and then to sequencing-ready barcoded Illumina libraries with the NUGEN complete RNAseq kit

value: inguinal adipose tissue

value: 10 weeks

value: f

tag: animal id

tag: developmental stage

value: old


title: iWAT_old_Rep4

tag: tissue

value: m


title: iWAT_old_Rep3


title: maternal placenta, LPS, 12.11 h, replicate 10

value: maternal placenta

tag: genotype

value: WT

tag: treatment

value: LPS


title: HP_C57BL6JxD2Gpnmb_14m_5XFAD Carrier

description:
10x Genomics
CK19012

value: Hippocampus

tag: strain

value: 14 months

tag: Sex


title: HP_C57BL6JxBXD33_14m_Ntg

description:
10x Genomics
CK19121

tag: age

value: Ntg

value: Female


title: HP_C57BL6JxBXD113_14m_5XFAD Carrier

description:
10x Genomics
CK19059

value: 5XFAD Carrier


title: KAD037_Granulocytes

description:
granulocyte sample from AD patient
203219760207_R05C01

value: Granulocytes

value: Male

value: LOY


title: Mutu Ctl 3

value: B cell lymphoma

value: Mutu

value: Ctl


title: HP_C57BL6JxBXD39_14m_Ntg

description:
10x Genomics
CK19108


title: maternal placenta, H2O, 12.11 h, replicate 10


title: KAD036_Granulocytes

description:
granulocyte sample from AD patient
203219760207_R03C01

value: non-LOY

value: genomic DNA

value: Alzheimer's disease


title: Mutu Ctl 2


title: maternal placenta, LPS, 12.11 h, replicate 9

value: maternal placenta


title: HP_C57BL6JxBXD28_14m_Ntg

description:
10x Genomics
CK19102


title: KAD027_Granulocytes

description:
granulocyte sample from AD patient
203219640144_R08C01


title: maternal placenta, H2O, 12.11 h, replicate 9

value: WT


title: iWAT_old_Rep1

value: inguinal adipose tissue

value: 10 weeks

value: f

value: old


title: HP_C57BL6JxBXD124_14m_Ntg

description:
10x Genomics
CK19101

value: Hippocampus

value: 14 months

value: Ntg

value: Female


title: iWAT_old_Rep2


title: HP_C57BL6J_14m_Ntg

description:
10x Genomics
CK19091


title: iWAT_young_Rep5

value: 6 weeks

value: m

value: young


title: KAD025_Monocytes

description:
monocyte sample from AD patient
203219640144_R04C01

value: Monocytes

value: Male

value: LOY


title: maternal placenta, TiO2, 15.11 h, replicate 5


title: maternal placenta, TiO2, 15.11 h, replicate 6


title: HP_C57BL6JxBXD99_14m_Ntg

description:
10x Genomics
CK19083


title: iWAT_young_Rep4


title: iWAT_young_Rep3


title: KAD025_Granulocytes

description:
granulocyte sample from AD patient
203219640144_R03C01

value: Granulocytes

value: genomic DNA

value: Alzheimer's disease


title: KAD034_Granulocytes

description:
granulocyte sample from AD patient
203219760207_R01C01

value: non-LOY


title: iWAT_young_Rep2

value: inguinal adipose tissue


title: maternal placenta, H2O, 15.11 h, replicate 25

value: maternal placenta

value: WT


title: HP_C57BL6JxBXD113_14m_Ntg

description:
10x Genomics
CK19069

value: Hippocampus


title: KAD019_Granulocytes

description:
granulocyte sample from AD patient
203219650051_R08C01


title: maternal placenta, H2O, 12.11 h, replicate 11


title: HP_C57BL6JxBXD66_14m_Ntg

description:
10x Genomics
CK19061

value: 14 months


title: maternal placenta, LPS, 15.11 h, replicate 20

value: LPS


title: HP_C57BL6JxD2Gpnmb_14m_Ntg

description:
10x Genomics
CK19046

value: Ntg

value: Female


title: KAD010_Granulocytes

description:
granulocyte sample from AD patient
203219650051_R06C01


title: iWAT_young_Rep1

value: 6 weeks

value: f


title: KAD026_Granulocytes

description:
granulocyte sample from AD patient
203219640144_R06C01


title: maternal placenta, LPS, 15.11 h, replicate 21


title: axWAT_old_Rep4

source_name: anterior subcutaneous adipose tissue

value: anterior subcutaneous adipose tissue

value: 10 weeks

value: old


title: KAD007_Granulocytes

description:
granulocyte sample from AD patient
203219650051_R05C01

value: Granulocytes

value: Male


title: KAD019_Monocytes

description:
monocyte sample from AD patient
203219640144_R01C01

value: Monocytes

value: genomic DNA

value: Alzheimer's disease


title: maternal placenta, LPS, 15.11 h, replicate 19

value: maternal placenta


title: HP_C57BL6JxBXD50_14m_Ntg

description:
10x Genomics
CK19035


title: KAD004_Monocytes

description:
monocyte sample from AD patient
203219650051_R03C01

value: non-LOY


title: axWAT_old_Rep2


title: maternal placenta, H2O, 15.11 h, replicate 23

value: WT


title: HP_C57BL6JxBXD161_14m_Ntg

description:
10x Genomics
CK19029

value: Hippocampus

value: 14 months


title: axWAT_old_Rep1


title: KAD002_Granulocytes

description:
granulocyte sample from AD patient
203219650051_R01C01


title: axWAT_old_Rep3

value: m


title: axWAT_young_Rep5

value: young


title: maternal placenta, H2O, 15.11 h, replicate 22


title: HP_C57BL6JxBXD83_14m_Ntg

description:
10x Genomics
CK19003

value: Ntg

value: Female


title: HP_C57BL6JxBXD65_14m_Ntg'

description:
10x Genomics
CK19019


title: maternal placenta, LPS, 15.11 h, replicate 18

value: LPS


title: axWAT_young_Rep4

value: anterior subcutaneous adipose tissue

value: 6 weeks


title: maternal placenta, H2O, 15.11 h, replicate 21


title: HP_C57BL6JxBXD113_6m_5XFAD Carrier

description:
10x Genomics
CK19109

value: 6 months

value: 5XFAD Carrier


title: axWAT_young_Rep3

value: f


title: axWAT_young_Rep2


title: maternal placenta, H2O, 15.11 h, replicate 24


title: HP_C57BL6JxBXD53_14m_Ntg

description:
10x Genomics
CK19020


title: HP_C57BL6JxBXD99_6m_5XFAD Carrier

description:
10x Genomics
CK19092


title: maternal placenta, LPS, 5.11 h, replicate 27


title: maternal placenta, H2O, 5.11 h, replicate 27


title: KAD004_Granulocytes

description:
granulocyte sample from AD patient
203219650051_R02C01

value: Granulocytes

value: Male

value: genomic DNA


title: maternal placenta, LPS, 15.11 h, replicate 17

value: maternal placenta


title: HP_C57BL6JxBXD124_6m_5XFAD Carrier

description:
10x Genomics
CK19085


title: brain, Del exposure group, rep3

city: Changsha

first: Hao

last: Wu

address: Shuanghe Road 728, Kaifu District, Changsha

institute: Hunan Fisheries Science Institute

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.
Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Assembly: crucian carp reference genome (NCBI: GCF_003368295.1, Carassius auratus)
Supplementary files format and content: execl files include FPKM values for each sample

organism: Carassius carassius

source_name: crucian carp

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: brain

value: WT

value: 0.6 ug/L Del


title: HP_C57BL6JxD2Gpnmb_6m_5XFAD Carrier

description:
10x Genomics
CK19094

value: Hippocampus


title: sham-treated rat peritoneal tissue, biological rep 2

type: RNA

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

description: Gene expression data from sham-treated control peritoneal tissue

hyb_protocol: Biotinylated fragmented aRNA  (10 µg ) was hybridized onto the GeneChip® Rat Genome 230 2.0 array. Hybridization was performed for 16 h at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0), using Affymetrix default settings, QC metrics, and PLIER normalization.

label: biotin

organism: Rattus norvegicus

source_name: sham-treated control peritoneal tissue

label_protocol: The synthesis of double-stranded cDNA, the in vitro transcription, the cleanup of  aRNA and biotin-labeling  were undertaken with the 3´IVT Plus Kit (Thermo Fisher Scientific).

growth_protocol: Tumors were collected from study animals. About half of the material was flash-frozen and stored in -80°C, while the remaining material was subjected to histopathological  and immunohistochemical analyses.

extract_protocol: Total RNA from tumors and control peritoneal tissues was isolated using the ‘AllPrep DNA/RNA Mini Kit’ (Qiagen), following manufacturer’s protocol.

treatment_protocol: Malignant mesotheliomas were induced in Wistar rats by single peritoneal injection with MWCNTs and amosite asbestos suspended in artificial lung medium.

value: Wistar

value: male

value: peritoneal tissue


title: maternal placenta, H2O, 15.11 h, replicate 20


title: HP_C57BL6JxBXD66_6m_5XFAD Carrier

description:
10x Genomics
CK19076

value: Female


title: brain, Del exposure group, rep2


title: brain, Del exposure group, rep1


title: maternal placenta, LPS, 15.11 h, replicate 16

value: LPS


title: HP_C57BL6JxBXD33_6m_5XFAD Carrier

description:
10x Genomics
CK19062


title: sham-treated rat peritoneal tissue, biological rep 1


title: axWAT_young_Rep1

value: anterior subcutaneous adipose tissue

value: 6 weeks

value: m

value: young


title: maternal placenta, TiO2, 5.11 h, replicate 6


title: brain, control group, rep3

value: control


title: HP_C57BL6J_6m_5XFAD Carrier

description:
10x Genomics
CK19054

value: 6 months

value: 5XFAD Carrier


title: Amosite-induced  rat mesothelioma, biological rep 2

description: Gene expression data from amosite asbestos-induced malignant peritoneal mesothelioma

value: malignant biphasic peritoneal mesothelioma


title: brain, control group, rep2

value: brain


title: maternal placenta, H2O, 15.11 h, replicate 19

value: maternal placenta

value: WT


title: maternal placenta, TiO2, 5.11 h, replicate 5


title: HP_C57BL6JxBXD39_6m_5XFAD Carrier

description:
10x Genomics
CK19045

value: Hippocampus


title: HP_C57BL6JxBXD161_6m_5XFAD Carrier

description:
10x Genomics
CK19053


title: MWCNT B-induced rat mesothelioma, biological rep 2

description: Gene expression data from MWCNT B-induced malignant peritoneal mesothelioma

value: Wistar

value: malignant peritoneal sarcomatoid mesothelioma


title: brain, control group, rep1


title: sham-treated rat peritoneal tissue, biological rep 3

value: male

value: peritoneal tissue


title: HP_C57BL6JxBXD65_6m_5XFAD Carrier

description:
10x Genomics
CK19037

value: Female


title: scRNAseq_CD31_P8MI_2

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: snRNA

data_processing:
scRNA-seq: The 10x Genomics Cell Ranger software (cellranger 3.0.1,www.10xgenomics.com) was used to handle raw sequencing data. Fastq files were aligned to the mouse mm10 genome. A pre-mRNA version of the reference genome was provided for gene count quantification with the Cellranger count function.
CellBender v0.1.0 was used to remove background from the Cellranger output with the remove-background module in default settings.
The h5 expression matrices from each data source were then imported into Seurat 3 for downstream processing and annotation to account for source-specific quality differences (Stuart et al, 2019).
Single cells were filtered for UMI (unique molecular identifiers) counts with a minimum of 500 and a maximum of 25,000 per cell. We also imposed a cutoff of 0.5% for mitochondrial reads and a cutoff of 0.25% for doublet score.
Seurat toolkit version v.4.0 in R v.3.8 was used to perform downstream analyses. The processed UMI count matrices of filtered cells were normalized with the Seurat function SCTransform to regress out additional variation.
The FindVariableFeatures function was used to calculate the top 5,000 most variable features for each sequenced library. The Seurat function FindIntegrationAnchors was used to find mutual nearest neighbors across subsets. Seurat’s IntegrateData function was used to construct an integrated matrix for each cell with a correction vector (based on anchor and similarity scores). The integrated data were scaled and the principal components were calculated (n = 50). Dimensional reduction (UMAP) and clustering were used to identify clusters (dimensions = 20, cluster resolution = 1.5).
Assembly: mm10
Supplementary files format and content: 10x output

source_name: Heart

extract_protocol:
Atria and aorta were removed from the heart, and the remaining tissue was used for single cell digestion. Cells were harvested at either P5 or P12, from pools of 5 hearts subjected to MI at P1 or P8, respectively. Tissues were minced into small pieces in digestion buffer (HBSS, 1 mg/mL collagenase A) and incubated at 37ºC with agitation for 30 minutes. The suspension was triturated with a 5 mL pipette every 10 minutes. Proper digestion was verified by appearance of single cells under a microscope. The digestion was then diluted 1:1 with HBSS, and the resulting cell suspension was centrifuged at 300 rpm for 6 minutes to remove cardiomyocytes. Supernatant was passed through a 40-micron filter to remove tissue fragments and cardiomyocytes, and then centrifuged at 500 x g for 6 minutes. The cell pellet was resuspended in 1 mL of MACs buffer (PBS, 0.5 % BSA, 2 mM EDTA). The resuspended cells were centrifuged at 500 x g for 6 minutes to remove residual buffer and resuspended in a final volume of 80 uL for incubation with 20 uL of CD31 MACs beads (Miltenyi Biotech). MACs enrichment for CD31+ cells was performed according to the Miltenyi enrichment protocol. Live cells were quantified with Trypan Blue and inCyto C-Chip DHC-F01. For single-nuclei ATAC sequencing, nuclei were isolated from cells according to the 10x protocol. Live nuclei were quantified with DAPI and inCyto C-Chip DHC-F01.
scRNA-seq libraries were generated using the 10x Chromium Single Cell 3′ Library Kit v3 (10x Genomics) according to the manufacturer’s instructions. snATAC-seq libraries were generated using the 10x Chromium Single Cell ATAC Library Kit v1 according to the manufacturer’s instructions.

treatment_protocol: Mouse were subjected to MI at P1 or P8

value: Heart

tag: time

tag: enrichment

value: CD31+ enrichment

value: left anterior descending artery occlusion


title: maternal placenta, H2O, 5.11 h, replicate 26


title: maternal placenta, LPS, 5.11 h, replicate 26

value: LPS


title: Amosite-induced  rat mesothelioma, biological rep 1

source_name: amosite asbestos-induced malignant peritoneal mesothelioma

value: malignant peritoneal epithelioid mesothelioma


title: MWCNT B-inducedd rat mesothelioma, biological rep 1

source_name: MWCNT B-induced malignant peritoneal mesothelioma

value: malignant peritoneal epitheloid mesothelioma


title: HP_C57BL6JxBXD28_6m_5XFAD Carrier

description:
10x Genomics
CK19030

value: 6 months

value: 5XFAD Carrier


title: Amosite-induced  rat mesothelioma, biological rep 3


title: HP_C57BL6JxBXD50_6m_5XFAD Carrier

description:
10x Genomics
CK19028


title: maternal placenta, LPS, 5.11 h, replicate 25


title: MWCNT C-induced rat mesothelioma, biological rep 3

description: Gene expression data from MWCNT C-induced malignant peritoneal mesothelioma

value: malignant peritoneal biphasic mesothelioma


title: MWCNT C-induced  rat mesothelioma, biological rep 1

source_name: MWCNT C-induced malignant peritoneal mesothelioma


title: X7,Mus musculus,Liver,sf,57

city: San Rafael

first: Evan

last: Witt

state: California

address: 791 Lindaro Street

institute: Biomarin Pharmaceutical

description: PE42 protocol

data_processing:
BWA-mem
MACS2
Assembly: GRCm38.p6
Supplementary files format and content: bam- aligned reads
Supplementary files format and content: narrowPeak- MACS2 output from bam files

extract_protocol:
Flash-Frozen mouse liver tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

value: Liver

tag: vector treatment

value: sf

tag: timepoint _(weeks)


title: MWCNT C-induced rat mesothelioma, biological rep 2

tag: gender


title: maternal placenta, H2O, 5.11 h, replicate 25

value: maternal placenta

value: WT


title: maternal placenta, LPS, 5.11 h, replicate 24


title: X10,Mus musculus,Liver,sf,57

description: PE42 protocol


title: CYP1544

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: mm10
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)

source_name: Lung

extract_protocol:
RNEasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: M

value: Cyp1b1 KO

value: High fat diet for 10 weeks


title: HP_C57BL6JxBXD53_6m_5XFAD Carrier

description:
10x Genomics
CK19004

value: Hippocampus

value: Female


title: MWCNT D-induced rat mesothelioma, biological rep 3

description: Gene expression data from MWCNT D-induced malignant peritoneal mesothelioma

value: Wistar

value: male


title: HP_C57BL6J_6m_Ntg

description:
10x Genomics
CK19100

value: Ntg


title: HP_C57BL6JxBXD83_6m_5XFAD Carrier

description:
10x Genomics
CK19027


title: CYP1546

value: F


title: X3,Mus musculus,Liver,sf,57

description: PE42 protocol


title: maternal placenta, H2O, 5.11 h, replicate 24


title: maternal placenta, LPS, 5.11 h, replicate 23

value: LPS


title: HP_C57BL6JxD2Gpnmb_6m_Ntg

description:
10x Genomics
CK19099

value: 6 months


title: CYP1734


title: MWCNT D-induced rat mesothelioma, biological rep 2

source_name: MWCNT D-induced malignant peritoneal mesothelioma

value: malignant peritoneal sarcomatoid mesothelioma


title: MWCNT D-induced rat mesothelioma, biological rep 1

value: malignant peritoneal epithelioid mesothelioma


title: maternal placenta, LPS, 5.11 h, replicate 22

source_name: maternal placenta


title: HP_C57BL6JxBXD65_6m_Ntg

description:
10x Genomics
CK19086


title: CYP1564

value: Wild Type


title: X5,Mus musculus,Liver,sf,57

description: PE42 protocol

value: Liver

value: sf


title: X1,Mus musculus,Liver,sf,57

description: PE42 protocol


title: maternal placenta, H2O, 5.11 h, replicate 23

value: maternal placenta

value: WT


title: W7,Mus musculus,Liver,293,57

description: PE42 protocol


title: W6,Mus musculus,Liver,293,57

description: PE42 protocol


title: HP_C57BL6JxBXD39_6m_Ntg

description:
10x Genomics
CK19075


title: CYP1445

value: Lung


title: maternal placenta, H2O, 5.11 h, replicate 22


title: X4,Mus musculus,Liver,sf,57

description: PE42 protocol


title: CYP1443

value: High fat diet for 10 weeks


title: W5,Mus musculus,Liver,293,57

description: PE42 protocol


title: HP_C57BL6JxBXD113_6m_Ntg

description:
10x Genomics
CK19070

value: Hippocampus


title: maternal placenta, H2O, 5.11 h, replicate 21


title: HP_C57BL6JxBXD124_6m_Ntg

description:
10x Genomics
CK19060

value: Female


title: X2,Mus musculus,Liver,sf,57

description: PE42 protocol


title: W4,Mus musculus,Liver,293,57

description: PE42 protocol


title: HP_C57BL6JxBXD28_6m_Ntg

description:
10x Genomics
CK19052


title: CYP18RNA

data_processing:
Partek Flow platform used for data processing
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Genome_build: mm10
Supplementary_files_format_and_content: Text file including CPM for each sample (in columns) and gene (in rows)

source_name: Pulmonary microvascular endothelial cells

growth_protocol: 60 mm dishes seeded w 1.6x10^6 cells, cultured in EGM-2+5% FBS

treatment_protocol: Transfected with 5 ul of 10 uM stock scrambled or CYP1B1 siRNA using Lipofectamine 2000 in Optimem media (media changed 2 hours before transfection). 24 hours after transfection, 1uM E2 or 1uM 16aOHE added for 24 hours in 5% serum

tag: sirna

tag: estrogen

value: 1 uM 16aOHE


title: maternal placenta, H2O, 5.11 h, replicate 20


title: maternal placenta, LPS, 5.11 h, replicate 20


title: CYP17RNA


title: W3,Mus musculus,Liver,293,57

description: PE42 protocol

source_name: Liver


title: HP_C57BL6JxBXD161_6m_Ntg

description:
10x Genomics
CK19043


title: HP_C57BL6JxBXD53_6m_Ntg

description:
10x Genomics
CK19084


title: CYP15RNA

value: 1 uM E2


title: CYP14RNA


title: maternal placenta, LPS, 5.11 h, replicate 21


title: W1,Mus musculus,Liver,293,57

description: PE42 protocol


title: HP_C57BL6JxBXD99_6m_Ntg

description:
10x Genomics
CK19038

value: Ntg


title: CYP13RNA


title: HP_C57BL6JxBXD83_6m_Ntg

description:
10x Genomics
CK19036


title: maternal placenta, H2O, 5.11 h, replicate 19


title: S7,Mus musculus,Liver,sf,24

description: PE42 protocol


title: maternal liver, H2O, 13.11 h, replicate 20

source_name: maternal liver

value: maternal liver


title: HP_C57BL6JxBXD33_6m_Ntg

description:
10x Genomics
CK19022


title: maternal liver, TiO2, 13.11 h, replicate 7


title: S6,Mus musculus,Liver,sf,24

description: PE42 protocol


title: CYP12RNA

value: vehicle


title: S5,Mus musculus,Liver,sf,24

description: PE42 protocol


title: Old_96w_TRF_24.ZT20

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

source_name: tibialis anterior muscle

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

value: female

value: wild-type

tag: feeding

value: time-restricted

tag: zeitgeber time

value: whole muscle


title: maternal liver, TiO2, 13.11 h, replicate 6


title: CYP16RNA


title: CYP9RNA

value: scrambled


title: Old_96w_TRF_23.ZT20


title: maternal liver, LPS, 15.11 h, replicate 15

value: LPS


title: W2,Mus musculus,Liver,293,57

description: PE42 protocol

value: Liver


title: S3,Mus musculus,Liver,sf,24

description: PE42 protocol

value: sf


title: CYP11RNA


title: S4,Mus musculus,Liver,sf,24

description: PE42 protocol


title: Old_96w_TRF_22.ZT20

value: male


title: CYP10RNA


title: maternal placenta, LPS, 5.11 h, replicate 19

value: maternal placenta

value: WT


title: maternal liver, H2O, 15.11 h, replicate 18


title: S2,Mus musculus,Liver,sf,24

description: PE42 protocol


title: maternal liver, TiO2, 19.11 h, replicate 2


title: CYP8RNA


title: HP_C57BL6JxBXD50_6m_Ntg

description:
10x Genomics
CK19011

value: Hippocampus

value: 6 months

value: Female


title: Old_96w_TRF_21.ZT20


title: maternal liver, LPS, 19.11 h, replicate 12


title: CYP7RNA

value: 1 uM 16aOHE


title: R7,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_TRF_19.ZT16


title: CYP6RNA

value: 1 uM E2


title: CYP5RNA


title: maternal liver, H2O, 19.11 h, replicate 10

value: maternal liver


title: maternal liver, LPS, 19.11 h, replicate 11


title: R5,Mus musculus,Liver,293,24

description: PE42 protocol


title: CYP4RNA


title: maternal liver, H2O, 19.11 h, replicate 9


title: CYP3RNA

value: vehicle


title: Old_96w_TRF_16.ZT12

value: female

value: wild-type


title: R4,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_TRF_17.ZT16

value: time-restricted

value: whole muscle


title: R6,Mus musculus,Liver,293,24

description: PE42 protocol


title: maternal liver, LPS, 19.11 h, replicate 10

value: LPS


title: CYP2RNA

value: scrambled


title: R3,Mus musculus,Liver,293,24

description: PE42 protocol

value: Liver


title: maternal liver, H2O, 19.11 h, replicate 8


title: Old_96w_TRF_15.ZT12

value: male


title: Old_96w_TRF_20.ZT16


title: S1,Mus musculus,Liver,sf,24

description: PE42 protocol

value: sf


title: maternal liver, LPS, 19.11 h, replicate 9

value: WT


title: Periapical lesion of DTA mice, pulp exposure, 14 days, rep3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse build mm9) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

source_name: Periapical lesion

growth_protocol: Mice were housed in light/temperature-controlled environment at the UT Health San Antonio with 2-5 animals per cage where food and water were available ad libitum. Breeding was completed withing our facility, and 8-12-week-old female mice were used for all experiments.

extract_protocol:
After tissue grinding and homogenization in RNA lysis buffer, total RNA was isolated from harvested periapical lesions using the RNAeasy Kit (Qiagen; Valencia, CA) according to the manufacturer’s recommendation. After quantification with Nanodrop (Thermo Scientific; Rockford, IL), RNA was stored at -80ºC.
Total RNA was used for RNA-Seq library preparation by following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. #, KR1151, KAPA Biosystems)

treatment_protocol: Apical periodontitis was modelled in mice by performing pulp exposure procedures and allowing infections to occur for either 0, 7, or 14 days. Briefly, an intraperitoneal injection of ketamine (75 mg/kg)/dexdomitor (1mg/kg) was given to anesthetize mice, as described previously (Austah et al. 2016). The mice were then mounted on a custom jaw retraction apparatus, and pulp exposures were created in all four first molars, and an intraperitoneal injection of Antisedan (1 mg/kg) was given to reverse the anesthesia for Day 7 and 14 mice. Day 0 mice were immediately euthanized via cervical dislocation following pulp exposure, and Day 7 and 14 mice were returned to the housing facility. At the appropriate time point, mice were briefly anesthetized with isoflurane and euthanized via cervical dislocation. Then the first molars were dissected, pooling 3-4 teeth per mouse, and immediately snap frozen in liquid nitrogen and stored at -80ºC.

value: Periapical lesion

value: Nav1.8cre+/- DTA+/-

value: pulp exposure, 14 days


title: R1,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_TRF_13.ZT12


title: N7,Mus musculus,Liver,sf,12

description: PE42 protocol


title: maternal liver, LPS, 19.11 h, replicate 8


title: maternal liver, H2O, 19.11 h, replicate 7


title: Periapical lesion of DTA mice, pulp exposure, 14 days, rep2


title: Old_96w_TRF_18.ZT16


title: N6,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pulp exposure, 14 days, rep1


title: maternal liver, LPS, 19.11 h, replicate 7


title: Old_96w_TRF_11.ZT8


title: N5,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pulp exposure, 7 days, rep4

value: pulp exposure, 7days


title: maternal liver, H2O, 19.11 h, replicate 6


title: Old_96w_TRF_14.ZT12


title: maternal liver, LPS, 13.11 h, replicate 20


title: Old_96w_TRF_10.ZT8


title: N4,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pulp exposure, 7 days, rep2


title: Old_96w_TRF_8.ZT4


title: R2,Mus musculus,Liver,293,24

description: PE42 protocol


title: N3,Mus musculus,Liver,sf,12

description: PE42 protocol


title: N2,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pulp exposure, 7 days, rep3


title: Old_96w_TRF_9.ZT8


title: Periapical lesion of DTA mice, pulp exposure, 7 days, rep1


title: maternal liver, H2O, 15.11 h, replicate 17


title: Old_96w_TRF_7.ZT4


title: maternal liver, LPS, 15.11 h, replicate 14


title: M7,Mus musculus,Liver,293,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pre_exposure, 0hr, rep3


title: maternal liver, TiO2, 13.11 h, replicate 5


title: Old_96w_TRF_12.ZT8


title: Old_96w_TRF_5.ZT4


title: M6,Mus musculus,Liver,293,12

description: PE42 protocol


title: Periapical lesion of DTA mice, pre_exposure, 0hr, rep2


title: Periapical lesion of DTA mice, pre_exposure, 0hr, rep1


title: maternal liver, LPS, 13.11 h, replicate 19


title: maternal liver, H2O, 13.11 h, replicate 19


title: Old_96w_TRF_4.ZT0


title: Periapical lesion of control mice, pulp exposure, 14 days, rep3

value: Nav1.8 cre+/-


title: M5,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, H2O, 13.11 h, replicate 18

value: maternal liver


title: Periapical lesion of control mice, pulp exposure, 14 days, rep2


title: Old_96w_TRF_3.ZT0


title: maternal liver, LPS, 13.11 h, replicate 18


title: Old_96w_TRF_2.ZT0


title: Periapical lesion of control mice, pulp exposure, 14 days, rep1


title: maternal liver, LPS, 13.11 h, replicate 17


title: Old_96w_TRF_1.ZT0


title: Periapical lesion of control mice, pulp exposure, 7 days, rep4


title: N1,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Old_96w_TRF_6.ZT4


title: M2,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, H2O, 13.11 h, replicate 17


title: Periapical lesion of control mice, pulp exposure, 7 days, rep3


title: Old_96w_ALF_24.ZT20

value: ad libitum


title: Old_96w_ALF_23.ZT20


title: maternal liver, LPS, 13.11 h, replicate 16


title: V2,Mus musculus,Liver,sf,57

description: PE42 protocol


title: Periapical lesion of control mice, pulp exposure, 7 days, rep2

value: female


title: Old_96w_ALF_22.ZT20

value: wild-type


title: maternal liver, H2O, 13.11 h, replicate 16


title: M3,Mus musculus,Liver,293,12

description: PE42 protocol


title: U5,Mus musculus,Liver,293,57

description: PE42 protocol


title: Old_96w_ALF_21.ZT20


title: M4,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, LPS, 13.11 h, replicate 15


title: Periapical lesion of control mice, pulp exposure, 7 days, rep1


title: maternal liver, H2O, 13.11 h, replicate 15


title: Periapical lesion of control mice, pre_exposure, 0hr, rep3


title: U4,Mus musculus,Liver,293,57

description: PE42 protocol


title: U3,Mus musculus,Liver,293,57

description: PE42 protocol


title: Periapical lesion of control mice, pre_exposure, 0hr, rep2


title: maternal liver, LPS, 13.11 h, replicate 14


title: Old_96w_ALF_18.ZT16


title: P6,Mus musculus,Liver,293,24

description: PE42 protocol


title: P7,Mus musculus,Liver,293,24

description: PE42 protocol


title: maternal liver, LPS, 13.11 h, replicate 13


title: Periapical lesion of control mice, pre_exposure, 0hr, rep1


title: Old_96w_ALF_17.ZT16


title: Old_96w_ALF_19.ZT16


title: maternal liver, LPS, 13.11 h, replicate 12


title: Old_96w_ALF_14.ZT12


title: maternal liver, H2O, 13.11 h, replicate 14


title: M1,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, H2O, 13.11 h, replicate 13


title: U2,Mus musculus,Liver,293,57

description: PE42 protocol


title: P5,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_ALF_15.ZT12


title: P4,Mus musculus,Liver,293,24

description: PE42 protocol


title: CD11c+CD206+ Pool3

city: Bangkok

first: Rangsima

last: Reantragoon

address: 1873 Rama 4 Road

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

hyb_protocol: 10 mg of total cDNA was subsequently hybridized to a reporter and capture probe sets of the nCounter Myeloid Innate Immunity Gene Expression Panel (NanoString Technologies) at 65C for 18 hours using a thermal cycler.

scan_protocol: none provided

data_processing: Raw data from the digital analyzer were evaluated for the quality and normalized to internal positive and negative controls and geometric mean of 38 housekeeping genes. Expression values of genes were calculated as log2 fold-change from the mean of internal negative control and were considered as upregulated and downregulated when the log2 fold-change expression value was greater than 0.5 and lower than -0.5, respectively.

label: NanoString

source_name: Infrapatellar fat pad

extract_protocol: Total RNA was extracted from sorted macrophage using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions and total RNA concentration was measured by Nanodrop and Qubit. Fluorometer. Total RNA was converted to cDNA and amplified with a multiplex low input primer pool using the nCounter Low RNA Input Kit (NanoString Technologies)

tag: tissue source

value: Infrapatellar fat pad

tag: cell type

tag: pool


title: Old_96w_ALF_16.ZT12

tag: genotype

tag: tissue

value: whole muscle


title: CD11c+CD206- Pool3


title: CD11c-CD206- Pool3


title: maternal liver, H2O, 13.11 h, replicate 12

tag: treatment


title: P3,Mus musculus,Liver,293,24

description: PE42 protocol


title: maternal liver, LPS, 13.11 h, replicate 11

value: LPS


title: Old_96w_ALF_20.ZT16

tag: strain

tag: Sex


title: CD11c-CD206+ Pool3


title: P2,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_ALF_12.ZT8

tag: age


title: P1,Mus musculus,Liver,293,24

description: PE42 protocol


title: Old_96w_ALF_11.ZT8


title: CD11c+CD206+ Pool2


title: maternal liver, H2O, 13.11 h, replicate 11


title: L7,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Old_96w_ALF_13.ZT12


title: CD11c-CD206+ Pool2


title: maternal liver, LPS, 12.11 h, replicate 7


title: L6,Mus musculus,Liver,sf,12

description: PE42 protocol


title: maternal liver, TiO2, 12.11 h, replicate 2


title: L4,Mus musculus,Liver,sf,12

description: PE42 protocol


title: Old_96w_ALF_10.ZT8


title: maternal liver, LPS, 12.11 h, replicate 8


title: maternal liver, H2O, 12.11 h, replicate 8


title: CD11c+CD206- Pool2


title: Old_96w_ALF_9.ZT8


title: Old_96w_ALF_7.ZT4


title: Old_96w_ALF_8.ZT4


title: CD11c-CD206- Pool2


title: CD11c-CD206+ Pool1


title: maternal liver, H2O, 12.11 h, replicate 7


title: maternal liver, LPS, 12.11 h, replicate 6


title: Old_96w_ALF_6.ZT4


title: MAC2A_DMSO_IgG_MWZ7564

city: Memphis

first: Brian

middle: J

last: Abraham

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequencing reads were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in paired-end mode with parameters -k 2 -m 2 --best -X 600
Read alignments were converted into fragments using samtools view, samtools sort, and bedtools bamtobed
Fragment coverage was calculated in 50bp bins genome-wide using bedtools makewindows and bedtools intersect and were normalized to the millions of mapped reads
Assembly: hg19
Supplementary files format and content: bigWig files contain reads-per-million-normalized coverage of fragments in 50bp bins
Library strategy: CUT&RUN-Seq

source_name: ALCL

growth_protocol: Cells were grown in T75 flasks in RPMI media containing 10% FBS and 1% pen-strep

extract_protocol:
Live cells were washed and incubated with activated concanavalin A beads for 10 min at room temperature. Cells were then resuspended in antibody buffer containing 0.01% digitonin, 1 ml of each antibody was added to individual cell aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ml of Cutana pA/G-MNase and 100 mM CaCl2. Retrieved genomic DNA was purified with a MinElute PCR purification kit and eluted in 10 ml of buffer EB.
Swift 2S automated library prep (manufacturer's instructions)

value: ALCL


title: Old_96w_ALF_5.ZT4


title: Old_96w_ALF_4.ZT0


title: K6,Mus musculus,Liver,293,12

description: PE42 protocol

value: Liver


title: CD11c+CD206- Pool1


title: maternal liver, H2O, 12.11 h, replicate 5

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


title: JB6_DMSO_IgG_MWZ9803


title: CYP1RNA

value: scrambled

value: vehicle


title: Old_96w_ALF_2.ZT0


title: L2,Mus musculus,Liver,sf,12

description: PE42 protocol

value: sf


title: CD11c-CD206- Pool1


title: maternal liver, TiO2, 15.11 h, replicate 3

value: WT


title: maternal liver, H2O, 12.11 h, replicate 6


title: D+Q treated, old bladder, rep6

city: Farmington

first: Dylan

last: Baker

state: CT

address: 10 Discovery Dr

data_processing:
Fastq files were aligned to mouse mm10-2020-A reference using STAR 2.7.3
Gene counts were generated from post alignment sam files quantitated with Subread featureCounts1.6.4
Raw counts data was gene length scaled and normalized by library size (TPM)
Assembly: mm10
Supplementary files format and content: comma-delimited file of raw gene counts for each sample
Supplementary files format and content: comma-delimited file of normalized gene expression for each sample

source_name: bladder

extract_protocol:
Nucleospin RNA isolation kit (Clonetech)
Illumina TruSeq Stranded Total RNA library preparation kit
v2.5 150 cycle reagent kit

value: bladder

value: 26-months old

value: D+Q-gavaged


title: L5,Mus musculus,Liver,sf,12

description: PE42 protocol


title: KO_26w_TRF_24.ZT20

value: male

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

value: 26 weeks

value: time-restricted


title: CD11c+CD206+ Pool1


title: MAC2A_IgG_MWZ10054


title: K5,Mus musculus,Liver,293,12

description: PE42 protocol


title: D+Q treated, old bladder, rep5

value: female


title: maternal liver, LPS, 12.11 h, replicate 5

value: maternal liver


title: KO_26w_TRF_23.ZT20

value: whole muscle


title: maternal liver, H2O, 15.11 h, replicate 16


title: JB6_IgG_MWZ10054


title: Old_96w_ALF_3.ZT0

value: wild-type

value: ad libitum


title: D+Q treated, old bladder, rep4


title: L3,Mus musculus,Liver,sf,12

description: PE42 protocol

value: Liver


title: K3,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, TiO2, 15.11 h, replicate 4


title: K1,Mus musculus,Liver,293,12

description: PE42 protocol


title: maternal liver, LPS, 15.11 h, replicate 13

value: LPS


title: Old_96w_ALF_1.ZT0


title: KO_26w_TRF_21.ZT20


title: MV4:11 RNA-seq Venetoclax_C10 rep3

first: Jing

last: Wang

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 or mm10 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
SLAM-seq was processed using SLAMdunk.
Assembly: hg19, mm10
Supplementary files format and content: ChIP-seq: one peak file per Sample
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: SLAM-seq: tab-delimited text file include raw counts for each Sample

growth_protocol: Media for all cell lines was supplemented with 100 IU/ml Penicillin and 100μg/ml streptomycin.

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single-end sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

treatment_protocol: Treatment that occurred is noted in SAMPLES section.

tag: cell line

value: 50 nM venetoclax and 100 nM C10


title: D+Q treated, old bladder, rep2


title: KO_26w_TRF_19.ZT16


title: maternal liver, LPS, 15.11 h, replicate 11

first: Albin

last: Sandelin

address: Markvangen 26

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


title: MV4:11 RNA-seq C10 rep2


title: Vehicle treated, old bladder, rep4

value: Vehicle-gavaged


title: MV4:11 RNA-seq Venetoclax_C10 rep1


title: maternal liver, H2O, 15.11 h, replicate 14

value: WT


title: KO_26w_TRF_17.ZT16

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

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


title: MV4:11 RNA-seq Venetoclax rep4

value: 50 nM venetoclax


title: KO_26w_TRF_22.ZT20


title: D+Q treated, old bladder, rep3

value: bladder

value: 26-months old


title: MV4:11 RNA-seq Venetoclax_C10 rep4


title: maternal liver, H2O, 15.11 h, replicate 15


title: MV4:11 RNA-seq Venetoclax_C10 rep2


title: MV4:11 RNA-seq Venetoclax rep3


title: MV4:11 RNA-seq C10 rep3


title: D+Q treated, old bladder, rep1

value: D+Q-gavaged


title: KO_26w_TRF_18.ZT16

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


title: MV4:11 RNA-seq Venetoclax rep1


title: MV4:11 RNA-seq C10 rep1


title: Vehicle treated, old bladder, rep3


title: maternal liver, LPS, 15.11 h, replicate 12


title: maternal liver, LPS, 15.11 h, replicate 10


title: KO_26w_TRF_14.ZT12

value: male

value: 26 weeks


title: maternal liver, H2O, 15.11 h, replicate 13


title: KO_26w_TRF_25.ZT12

value: time-restricted


title: KO_26w_TRF_13.ZT12

value: female


title: MV4:11 RNA-seq C10 rep4


title: Vehicle treated, old bladder, rep2


title: MV4:11 RNA-seq DMSO rep4

value: DMSO


title: maternal liver, H2O, 15.11 h, replicate 12

value: maternal liver


title: Vehicle treated, old bladder, rep1


title: maternal liver, H2O, 15.11 h, replicate 11


title: Water treated, old bladder, rep2

value: Water-gavaged


title: MV4:11 RNA-seq Venetoclax rep2


title: KO_26w_TRF_16.ZT12

value: whole muscle


title: MV4:11 RNA-seq DMSO rep3


title: maternal liver, LPS, 5.11 h, replicate 18

value: LPS


title: Water treated, old bladder, rep5


title: maternal liver, LPS, 15.11 h, replicate 9


title: Water treated, old bladder, rep3


title: Water treated, old bladder, rep4


title: maternal liver, LPS, 15.11 h, replicate 8


title: maternal liver, H2O, 5.11 h, replicate 18


title: KO_26w_TRF_12.ZT8


title: Water treated, old bladder, rep1


title: KO_26w_TRF_11.ZT8


title: MV4:11 RNA-seq DMSO rep1


title: Untreated, old bladder, rep6

value: Untreated


title: KO_26w_TRF_10.ZT8


title: KO_26w_TRF_9.ZT8


title: maternal liver, H2O, 15.11 h, replicate 10


title: Untreated, old bladder, rep5


title: iPSC-BMELCs, No Virus, 24h

city: Kawasaki

first: Yasunari

last: Kanda

state: Kanagawa

address: 3-25-26 Tonomachi, Kawasaki-ku

department: Division of Pharmacology

country: Japan

institute: National Institute of Health Science

data_processing:
NovaSeq Control Software v 1.7.5, Real Time Analysis (RTA) v 3.4.4, bcl2fastq2 v 2.20
Sequence reads were trimmed for adaptor sequence/low-quality sequence using NovaSeq software
Trimmed sequence reads were mapped to GRCh38 using NovaSeq software
Read count extraction and normalization were performed using NovaSeq software
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: brain microvascular endothelial like cells

growth_protocol: iPSC-BMELCs were maintained in Human Endothelial-SFM-based medium supplemented with 1% platelet-poor plasma derived bovine serum, 1 μM A83-01, and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using miRNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA kit (Takara).

treatment_protocol: SARS-CoV-2 original strain JPN/TY/WK-521 was infected to iPSC-BMELCs at a multiplicity of infection (MOI) of 1 for 24 h.

value: No infection


title: maternal liver, TiO2, 5.11 h, replicate 3

city: Gentofte

institute: University of Copenhagen

value: WT


title: maternal liver, TiO2, 5.11 h, replicate 4


title: Untreated, old bladder, rep4


title: KO_26w_TRF_8.ZT4

city: Barcelona

institute: UPF


title: Untreated, old bladder, rep3


title: KO_26w_TRF_6.ZT4


title: maternal liver, LPS, 5.11 h, replicate 17


title: MV4:11 RNA-seq DMSO rep2


title: maternal liver, LPS, 5.11 h, replicate 16


title: APOE3/3 iMG LD Negative21 [ATAC-seq]

city: Stanford

first: Tony

last: Wyss-Coray

state: CA

address: 290 Jane Stanford Way

department: Neurology

institute: Stanford University

data_processing:
Bowtie2 with default parameters was used to map ATAC-seq.
HOMER was used to convert aligned reads into ‘‘tag directories’’ for further analysis
assembly: hg38

source_name: iMG

extract_protocol:
Approximately 100,000 iMG were pelleted at 300 xg and 4 oC. Next, pellets were gently resuspended in ice-cold 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spun down at 500 xg for 10 min and 4 oC. The supernatants were discarded, and pellets gently resuspended in 50 μL of transposition reaction mix (25 μL tagment DNA buffer (Nextera, Illumina), 2.5 μL tagment DNA enzyme (Nextera, Illumina), 22.5 μL nuclease free water) and incubated at 37 oC for 30 minutes. Tagmented DNA was purified using MinElute PCR purification kit (Qiagen) and size selected for 70 – 500 bp using AmpureXP beads (Beckman Coulter).
Libraries were constructed and amplified using 1.25 μM Nextera index primers and NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs). A quantitative PCR was run to determine the optimal number of cycles. Libraries were gel size selected for 165-300 bp fragments and single-end sequenced for 100 cycles (PE100) on an Illumina NovaSeq6000.

value: iMG

value: iMicroglia

value: APOE 3/3

value: APOE3/3 iMG LD Negative


title: Untreated, old bladder, rep2

value: bladder

value: 26-months old


title: maternal liver, H2O, 5.11 h, replicate 17


title: APOE3/3 iMG LD Negative12 [ATAC-seq]


title: Untreated, old bladder, rep1


title: iPSC-BMELCs, SARS-CoV-2, 24h

value: brain microvascular endothelial like cells

value: SARS-CoV-2 infection


title: KO_26w_TRF_5.ZT4

value: male

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

value: 26 weeks

value: time-restricted


title: maternal liver, H2O, 5.11 h, replicate 16

value: maternal liver


title: APOE3/3 iMG LD Positive22 [ATAC-seq]

value: APOE3/3 iMG LD Positive


title: KO_26w_TRF_4.ZT0

value: female

value: whole muscle


title: KO_26w_TRF_2.ZT0


title: Middle aged, bladder, rep4

value: 10-months old

value: Untreated


title: APOE3/3 iMG LD Negative11 [ATAC-seq]

value: iMG

value: iMicroglia


title: maternal liver, LPS, 5.11 h, replicate 15

value: WT

value: LPS


title: APOE3/3 iMG LD Positive12 [ATAC-seq]

value: APOE 3/3


title: APOE3/3 iMG LD Negative22 [ATAC-seq]

value: APOE3/3 iMG LD Negative


title: KO_26w_TRF_1.ZT0


title: Middle aged, bladder, rep3

value: bladder


title: maternal liver, LPS, 5.11 h, replicate 14


title: APOE3/3 iMG LD Positive21 [ATAC-seq]


title: Mu-RE_26w_TRF_24.ZT20

value: male

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


title: maternal liver, H2O, 5.11 h, replicate 15


title: Middle aged, bladder, rep2


title: maternal liver, H2O, 5.11 h, replicate 14


title: Middle aged, bladder, rep1


title: Young bladder rep6

value: 2-months old


title: Mu-RE_26w_TRF_22.ZT20

value: 26 weeks

value: time-restricted


title: Mu-RE_26w_TRF_23.ZT20


title: maternal liver, LPS, 5.11 h, replicate 13

value: maternal liver


title: Sample 99-15-L003 [snRNA-seq]

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

source_name: brain (frontal cortex)

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

value: brain (frontal cortex)

tag: disease status

value: AD

value: APOE 4/4

value: Male

value: ad apoe 44


title: Sample 99-15-L004 [snRNA-seq]


title: KO_26w_TRF_3.ZT0

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

value: whole muscle


title: Mu-RE_26w_TRF_21.ZT20


title: maternal liver, H2O, 5.11 h, replicate 13

value: WT


title: Middle aged, bladder, rep5

value: 10-months old

value: female

value: Untreated


title: Sample 99-15-L002 [snRNA-seq]


title: Young, bladder, rep5

value: bladder


title: Young, bladder, rep4


title: Sample 18-75-L004 [snRNA-seq]

value: Healthy

value: APOE 3/3

value: Female

value: nd apoe 33


title: Mu-RE_26w_TRF_20.ZT16

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

value: 26 weeks

value: time-restricted


title: Young bladder rep3

value: 2-months old


title: Sample 99-15-L001 [snRNA-seq]

value: brain (frontal cortex)

value: AD

value: APOE 4/4

value: Male


title: maternal liver, LPS, 5.11 h, replicate 12

value: maternal liver

value: WT

value: LPS


title: Mu-RE_26w_TRF_19.ZT16

value: male

value: whole muscle


title: APOE3/3 iMG LD Positive11 [ATAC-seq]

value: iMG

value: iMicroglia

value: APOE3/3 iMG LD Positive


title: Young, bladder, rep2

value: bladder

value: female

value: Untreated


title: Sample 18-68-L004 [snRNA-seq]

value: Healthy

value: APOE 3/3

value: nd apoe 33


title: Mu-RE_26w_TRF_18.ZT16

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

value: 26 weeks

value: time-restricted


title: maternal liver, H2O, 5.11 h, replicate 11

value: maternal liver


title: maternal liver, H2O, 5.11 h, replicate 12

value: WT


title: Young, bladder, rep1

value: 2-months old


title: Ing4+/+ Ing5+/+ replicate 4

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm10 using Rsubread version 1.28.1
Read counts were summarized using the Rsubread featureCounts function and NCBI RefSeq annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Ensembl ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Embryonic heart

extract_protocol:
Total RNA was isolated from E10.5 hearts using an RNA isolation kit (Qiagen RNeasy Micro Kit; Qiagen 74004) according to manufacturer’s instructions.
Sequencing libraries were prepared using Illumina’s TruSeq stranded library kit.

treatment_protocol: Embryonic hearts were isolated from 4 genotypes that were either wild-type or had lost one, two or three of the combined four alleles of the Ing4 and Ing5 gene (Ing4+/-Ing5-/-, Ing4+/+Ing5-/-, Ing4+/-Ing5+/+, Ing4+/+Ing5+/+)

value: Embryonic heart

tag: litter


title: Sample 18-68-L002 [snRNA-seq]

value: brain (frontal cortex)

value: Male


title: Mu-RE_26w_TRF_15.ZT12

value: whole muscle


title: Sample 18-68-L003 [snRNA-seq]


title: maternal liver, LPS, 5.11 h, replicate 10

value: LPS


title: Mu-RE_26w_TRF_14.ZT12

value: male


title: maternal liver, H2O, 5.11 h, replicate 10


title: maternal lung, TiO2, 13.11 h, replicate 4

source_name: maternal lung

value: maternal lung


title: Ing4+/+ Ing5+/+ replicate 3


title: Sample 18-28-L004 [snRNA-seq]

value: AD

value: APOE 4/4

value: Female

value: ad apoe 44


title: Ing4+/+ Ing5+/+ replicate 2


title: maternal lung, TiO2, 13.11 h, replicate 3


title: maternal liver, LPS, 5.11 h, replicate 11


title: Ing4+/+ Ing5+/+ replicate 1


title: maternal lung, H2O, 13.11 h, replicate 10


title: Sample 18-28-L003 [snRNA-seq]


title: Mu-RE_26w_TRF_17.ZT16

value: female

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


title: Ing4+/+ Ing5-/- replicate 4


title: maternal lung, TiO2, 13.11 h, replicate 2


title: Mu-RE_26w_TRF_12.ZT8

value: 26 weeks

value: time-restricted


title: Mu-RE_26w_TRF_10.ZT8


title: Sample 18-28-L002 [snRNA-seq]


title: KO_26w_TRF_15.ZT12

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


title: Mu-RE_26w_TRF_13.ZT12


title: Ing4+/+ Ing5-/- replicate 3


title: Sample 18-20-L004 [snRNA-seq]

value: Healthy

value: APOE 3/3

value: nd apoe 33


title: Sample 18-28-L001 [snRNA-seq]

value: brain (frontal cortex)


title: Mu-RE_26w_TRF_9.ZT8

value: whole muscle


title: Ing4+/+ Ing5-/- replicate 2

value: Embryonic heart


title: Sample 18-68-L001 [snRNA-seq]

value: Male


title: maternal lung, TiO2, 19.11 h, replicate 1

value: maternal lung

value: WT


title: Ing4+/+ Ing5-/- replicate 1


title: Mu-RE_26w_TRF_8.ZT4

value: male


title: maternal lung, LPS, 19.11 h, replicate 6

value: LPS


title: Sample 18-20-L003 [snRNA-seq]


title: Mu-RE_26w_TRF_7.ZT4


title: Ing4+/- Ing5+/+ replicate 4


title: maternal lung, H2O, 19.11 h, replicate 5


title: Mu-RE_26w_TRF_11.ZT8


title: Mu-RE_26w_TRF_6.ZT4


title: Ing4+/- Ing5+/+ replicate 3


title: maternal lung, LPS, 19.11 h, replicate 5


title: Mu-RE_26w_TRF_5.ZT4


title: Mu-RE_26w_TRF_4.ZT0


title: Ing4+/- Ing5+/+ replicate 2


title: maternal lung, H2O, 19.11 h, replicate 4


title: maternal lung, H2O, 15.11 h, replicate 9


title: Ing4+/- Ing5+/+ replicate 1


title: maternal lung, LPS, 19.11 h, replicate 4


title: Mu-RE_26w_TRF_3.ZT0


title: Sample 16-29-L004 [snRNA-seq]


title: Ing4+/- Ing5-/- replicate 4


title: Sample 16-29-L003 [snRNA-seq]


title: Mu-RE_26w_TRF_2.ZT0


title: Sample 16-29-L002 [snRNA-seq]


title: maternal lung, LPS, 19.11 h, replicate 3


title: Ing4+/- Ing5-/- replicate 2


title: Sample 18-20-L002 [snRNA-seq]


title: Sample 16-29-L001 [snRNA-seq]


title: maternal lung, LPS, 19.11 h, replicate 2


title: WT_26w_TRF_24.ZT20

value: wild-type


title: Ing4+/- Ing5-/- replicate 1


title: MOZ WT, replicate 5

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm10 using Rsubread version 1.30.8
Read counts were summarized using the Rsubread featureCounts function and NCBI RefSeq annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Ensembl ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

treatment_protocol: Embryonic hearts were isolated from 2 genotypes that were either wild-type or had lost both alleles of the Kat6a (Moz) gene (Kat6a-/- and 5 Kat6a+/+)

value: MOZ WT


title: maternal lung, H2O, 19.11 h, replicate 2


title: Sample 15-27-L003 [snRNA-seq]

value: AD

value: Female

value: ad apoe 33


title: maternal lung, LPS, 19.11 h, replicate 1


title: WT_26w_TRF_23.ZT20

value: female

value: 26 weeks

value: time-restricted


title: MOZ KO, replicate 3

value: MOZ KO


title: Sample 15-27-L002 [snRNA-seq]

value: brain (frontal cortex)

value: APOE 3/3


title: WT_26w_TRF_21.ZT20

value: whole muscle


title: maternal lung, H2O, 19.11 h, replicate 1


title: Sample 15-27-L001 [snRNA-seq]


title: maternal lung, LPS, 13.11 h, replicate 10


title: MOZ WT, replicate 4

value: Embryonic heart


title: Ing4+/- Ing5-/- replicate 3


title: Sample 14-20-L004 [snRNA-seq]

value: Healthy

value: nd apoe 33


title: maternal lung, LPS, 15.11 h, replicate 7

value: maternal lung

value: WT


title: maternal lung, H2O, 19.11 h, replicate 3


title: MOZ KO, replicate 2


title: Sample 14-20-L003 [snRNA-seq]


title: Sample 18-20-L001 [snRNA-seq]

value: Male


title: WT_26w_TRF_20.ZT16

value: male

value: wild-type


title: maternal lung, H2O, 15.11 h, replicate 8


title: MOZ WT, replicate 3

value: MOZ WT


title: WT_26w_TRF_19.ZT16


title: MOZ KO, replicate 1


title: Sample 15-27-L004 [snRNA-seq]

value: AD

value: Female

value: ad apoe 33


title: Sample 14-20-L002 [snRNA-seq]


title: maternal lung, TiO2, 13.11 h, replicate 1


title: WT_26w_TRF_22.ZT20

value: 26 weeks

value: time-restricted


title: WT_26w_TRF_17.ZT16

value: female


title: MOZ WT, replicate 2


title: Sample 14-20-L001 [snRNA-seq]

value: brain (frontal cortex)

value: APOE 3/3


title: maternal lung, H2O, 13.11 h, replicate 9


title: WT_26w_TRF_16.ZT12

value: whole muscle


title: MOZ WT, replicate 1

value: Embryonic heart


title: NHDF cells,UV, 0.06% Osmoter treatment, biol rep 3

city: Shanghai

first: Xiaojuan

last: Yan

address: Guiping Road

institute: Fosun Jinmei Cosmetics

data_processing:
Sequece reads were trimmed for adaptor sequence/low-quality sequence using trim_galore software
Trimmed sequence reads were mapped with GRCh37/hg19 using STAR software, and the BAM files were qualified using qualimap software
Read count statistic were performed using featurecouns software
Assembly: Homo Sapiens(GRCh37/hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: normal human dermal fibroblasts

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

extract_protocol:
Total RNA were extracted using Trisol reagent
After extraction of total RNA from the sample and digestion of DNA with DNase I, eukaryotic mRNA with poly-A tail was enriched by magnetic beads with Oligo (dT), the bound mRNA was eluted, and interrupted by divalent cations and high temperature conditions in interruption buffer. The first strand of cDNA was synthesized by reverse transcription using random primers. The mRNA in the heterozygous duplex was digested by RNase H to synthesize the complementary cDNA strand, and the second cDNA strand was synthesized. After purification, the cDNA was repaired at the end, the base "A" was added to the 3 'end, and the linker was attached. Finally, PCR amplification was performed

treatment_protocol: Cells were treated with 0.02% Osmoter or 0.06% Osmoter for 24 hours. UV treated group were exposured under UVA at 6J and furthur treated with 0.02% or 0.06% Osmoter

value: normal human dermal fibroblasts

value: UV+0.06% Osmoter treatment


title: Sample 14-14-L003 [snRNA-seq]


title: WT_26w_TRF_15.ZT12


title: maternal lung, LPS, 13.11 h, replicate 8

value: maternal lung

value: WT

value: LPS


title: maternal lung, H2O, 13.11 h, replicate 8


title: Sample 14-14-L002 [snRNA-seq]

value: Male


title: WT_26w_TRF_13.ZT12

value: male

value: wild-type


title: NHDF cells,UV, 0.06% Osmoter treatment, biol rep 1


title: WT_26w_TRF_18.ZT16


title: Sample 16-30-L003 [snRNA-seq]

value: Healthy

value: nd apoe 33


title: WT_26w_TRF_14.ZT12

value: 26 weeks


title: NHDF cells,UV, 0.06% Osmoter treatment, biol rep 2


title: Sample 14-02-L004 [snRNA-seq]

value: Female


title: WT_26w_TRF_12.ZT8

value: time-restricted


title: maternal lung, H2O, 13.11 h, replicate 7


title: Sample 14-14-L001 [snRNA-seq]

value: brain (frontal cortex)

value: AD

value: ad apoe 33


title: maternal lung, LPS, 13.11 h, replicate 7


title: WT_26w_TRF_11.ZT8

value: whole muscle


title: NHDF cells,UV, 0.02% Osmoter treatment, biol rep 2

value: normal human dermal fibroblasts

value: UV+0.02% Osmoter treatment


title: maternal lung, LPS, 13.11 h, replicate 6

value: maternal lung


title: maternal lung, LPS, 13.11 h, replicate 9

value: WT


title: NHDF cells,UV, 0.02% Osmoter treatment, biol rep 3


title: Sample 13-72-L004 [snRNA-seq]

value: APOE 4/4

value: ad apoe 44


title: WT_26w_TRF_10.ZT8

value: female


title: NHDF cells,UV, 0.02% Osmoter treatment, biol rep 1


title: Sample 14-14-L004 [snRNA-seq]

value: APOE 3/3

value: Male


title: NHDF cells,UV, biol rep 3

value: UV


title: WT_26w_TRF_9.ZT8

value: male

value: wild-type

value: 26 weeks


title: maternal lung, H2O, 13.11 h, replicate 6


title: maternal lung, LPS, 13.11 h, replicate 5

value: LPS


title: WT_26w_TRF_8.ZT4

value: time-restricted


title: Sample 13-72-L003 [snRNA-seq]

value: brain (frontal cortex)

value: AD

value: Female


title: WT_26w_TRF_7.ZT4

value: whole muscle


title: NHDF cells,UV, biol rep 1

value: normal human dermal fibroblasts


title: Sample 13-69-L004 [snRNA-seq]


title: maternal lung, H2O, 13.11 h, replicate 5

value: maternal lung

value: WT


title: Sample 13-69-L002 [snRNA-seq]

value: APOE 4/4

value: ad apoe 44


title: NHDF cells,0.06% Osmoter treatment, biol rep 2

value: 0.06% Osmoter treatment


title: maternal lung, LPS, 13.11 h, replicate 3


title: maternal lung, H2O, 13.11 h, replicate 4


title: NHDF cells,UV, biol rep 2


title: Sample 13-72-L001 [snRNA-seq]


title: WT_26w_TRF_6.ZT4


title: NHDF cells,0.06% Osmoter treatment, biol rep 3


title: NHDF cells,0.02% Osmoter treatment, biol rep 3

value: 0.02% Osmoter treatment


title: Sample 13-72-L002 [snRNA-seq]


title: NHDF cells,0.06% Osmoter treatment, biol rep 1


title: Sample 13-54-L004 [snRNA-seq]

value: APOE 3/3

value: ad apoe 33


title: maternal lung, H2O, 13.11 h, replicate 3


title: Sample 13-54-L003 [snRNA-seq]


title: WT_26w_TRF_4.ZT0

value: female

value: wild-type


title: Sample 13-69-L003 [snRNA-seq]


title: NHDF cells,0.02% Osmoter treatment, biol rep 2


title: maternal lung, LPS, 13.11 h, replicate 2

value: LPS


title: WT_26w_TRF_2.ZT0

value: male

value: 26 weeks

value: time-restricted


title: Sample 13-69-L001 [snRNA-seq]

value: brain (frontal cortex)

value: AD

value: Female


title: WT_26w_TRF_1.ZT0

value: whole muscle


title: maternal lung, LPS, 13.11 h, replicate 4

value: maternal lung

value: WT


title: NHDF cells,0.02% Osmoter treatment, biol rep 1

value: normal human dermal fibroblasts


title: WT_26w_TRF_5.ZT4


title: maternal lung, H2O, 13.11 h, replicate 2


title: maternal lung, LPS, 13.11 h, replicate 1


title: KO_26w_ALF_23.ZT20

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

value: ad libitum


title: Sample 13-54-L002 [snRNA-seq]

value: APOE 3/3


title: WT_26w_TRF_3.ZT0


title: NHDF cells,Control, biol rep 3

value: Control


title: Mu-RE_26w_TRF_1.ZT0

value: female

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


title: Sample 13-42-L004 [snRNA-seq]

value: APOE 4/4

value: Male

value: ad apoe 44


title: maternal lung, H2O, 13.11 h, replicate 1


title: maternal lung, TiO2, 12.11 h, replicate 1


title: KO_26w_ALF_22.ZT20

value: 26 weeks


title: KO_26w_ALF_21.ZT20


title: KO_26w_ALF_25.ZT16


title: maternal lung, LPS, 12.11 h, replicate 4

value: LPS


title: NHDF cells,Control, biol rep 1


title: Sample 12-44-L004 [snRNA-seq]

value: brain (frontal cortex)

value: Healthy

value: nd apoe 33


title: Patient 20, BCR-derived cDNA

city: OULLINS

first: Pierre

last: Sujobert

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

country: France

institute: CIRI - Centre International de Recherche en Infectiologie

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

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

source_name: Lymph node

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

value: Lymph node

value: Immune cells

tag: library type

value: BCR

tag: antibodies/tags


title: Sample 12-44-L003 [snRNA-seq]

value: Female


title: maternal lung, H2O, 12.11 h, replicate 4

value: maternal lung

value: WT


title: Patient 20, HTO-derived cDNA

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

library_source: other

molecule: protein

value: HTO

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


title: Sample 12-44-L002 [snRNA-seq]

value: APOE 3/3


title: KO_26w_ALF_19.ZT16

value: female

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

value: ad libitum

value: whole muscle


title: Patient 20, mRNA-derived cDNA

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

value: mRNA


title: KO_26w_ALF_20.ZT16

value: 26 weeks


title: Sample 12-44-L001 [snRNA-seq]

value: brain (frontal cortex)

value: Healthy


title: maternal lung, H2O, 12.11 h, replicate 3


title: maternal lung, LPS, 12.11 h, replicate 2

value: LPS


title: Patient 18, BCR-derived cDNA

value: Lymph node

value: Immune cells


title: KO_26w_ALF_18.ZT16

value: male


title: Sample 12-37-L004 [snRNA-seq]

value: AD

value: APOE 4/4

value: Male

value: ad apoe 44


title: Sample 13-54-L001 [snRNA-seq]

value: APOE 3/3

value: Female

value: ad apoe 33


title: KO_26w_ALF_17.ZT16

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

value: ad libitum


title: Patient 18, HTO-derived cDNA

value: HTO

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


title: Sample 12-37-L003 [snRNA-seq]

value: brain (frontal cortex)


title: NHDF cells,Control, biol rep 2

value: normal human dermal fibroblasts

value: WT

value: Control


title: maternal lung, H2O, 12.11 h, replicate 2

value: maternal lung


title: KO_26w_ALF_16.ZT12

value: female

value: 26 weeks

value: whole muscle


title: Sample 12-37-L002 [snRNA-seq]

value: AD

value: APOE 4/4

value: Male


title: Patient 18, mRNA-derived cDNA

value: Lymph node

value: Immune cells

value: mRNA


title: KO_26w_ALF_15.ZT12

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

value: ad libitum


title: maternal lung, LPS, 12.11 h, replicate 1

value: LPS


title: KO_26w_ALF_14.ZT12

value: male


title: Sample 12-37-L001 [snRNA-seq]

value: brain (frontal cortex)

value: ad apoe 44


title: maternal lung, H2O, 12.11 h, replicate 1

value: WT


title: Patient 16, HTO-derived cDNA

value: HTO

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


title: Patient 16, BCR-derived cDNA

value: BCR


title: maternal lung, LPS, 12.11 h, replicate 3

value: maternal lung


title: Sample 12-27-L004 [snRNA-seq]

value: AD

value: APOE 3/3

value: Female

value: ad apoe 33


title: maternal lung, TiO2, 15.11 h, replicate 2


title: Patient 16, mRNA-derived cDNA

value: Lymph node

value: Immune cells


title: KO_26w_ALF_13.ZT12

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

value: 26 weeks

value: whole muscle


title: maternal lung, TiO2, 15.11 h, replicate 1


title: Sample 12-27-L002 [snRNA-seq]


title: Sample 12-27-L001 [snRNA-seq]


title: Patient 15, HTO-derived cDNA

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


title: KO_26w_ALF_11.ZT8

value: male

value: ad libitum


title: maternal lung, LPS, 15.11 h, replicate 6

value: WT

value: LPS


title: KO_26w_ALF_10.ZT8

value: female


title: maternal lung, LPS, 15.11 h, replicate 5


title: Patient 12, BCR-derived cDNA

value: BCR


title: maternal lung, H2O, 15.11 h, replicate 7

value: maternal lung


title: maternal lung, H2O, 15.11 h, replicate 6


title: Patient 15, mRNA-derived cDNA

value: mRNA


title: Patient 15, BCR-derived cDNA


title: KO_26w_ALF_8.ZT4


title: Patient 12, HTO-derived cDNA

value: HTO


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


title: Sample 11-59-L002 [snRNA-seq]

value: brain (frontal cortex)

value: AD

value: APOE 4/4

value: Male

value: ad apoe 44


title: Sample 11-59-L001 [snRNA-seq]


title: Patient 12, mRNA-derived cDNA

value: Lymph node

value: Immune cells


title: KO_26w_ALF_7.ZT4

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

value: 26 weeks

value: whole muscle


title: KO_26w_ALF_6.ZT4

value: male

value: ad libitum


title: maternal lung, H2O, 15.11 h, replicate 5

value: WT


title: KO_26w_ALF_12.ZT8


title: Sample 12-27-L003 [snRNA-seq]

value: APOE 3/3

value: Female

value: ad apoe 33


title: Sample 11-59-L004 [snRNA-seq]


title: Sample 11-14-L003 [snRNA-seq]


title: Sample 11-59-L003 [snRNA-seq]