title: D_SNI1_G15_1

city: Wuhan

first: Zhen

middle: Zhen

last: Xu

state: Hubei

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: DRG Tissue

growth_protocol: All male rats were randomly divided into groups containing 6¬–8 rats. Drugs were dissolved in 2% DMSO and injected through a catheter for 24 h. Intrathecal catheters were implanted on SNI day 5 as previously described.

extract_protocol:
RNA was extracted from macrophages treated with exosomes using RNeasy Mini Kit (cat. no. 74104, Qiagen, Germany) according to manufacturer’s protocols. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: We excluded animals with postoperative hindlimb paralysis or paresis. Animals without movement disorders received 2% lidocaine through the catheter to verify the intraspinal location. Correct catheterisation was confirmed by immediate bilateral hindlimb paralysis (within 15 s) lasting 20–30 min. We excluded animals that lacked these features. DRGs for patch clamp experiments were incubated with G1, G15, and β-alanine in vitro.

value: DRG Tissue

value: Sprague Dawley


title: U87MG, control, bio_rep2, tech_rep3

status: Public on Jun 29 2022

type: SRA

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: U87MG GBM cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: U87MG cells were subcutaneously or orthotopically implanted in BALB/c nude mice and repeatedly exposed to IR. We then obtained the radioresistant U87MG cells that survived IR (2 Gy each, 30 Gy in total).

tag: cell line

tag: cell type

value: Glioblastoma cell

tag: genotype

value: Luciferase expressing

tag: treatment

value: Non-irradiated


title: D_SNI1_G15_2

country: China

organism: Rattus norvegicus

tag: tissue


title: CKG, Down root, rep1

city: Beijing

first: Chengyu

last: Ye

address: 67 North Forth Ring Road

institute: BGI Genomics

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequenc
Reference genome was built using Hisat2 v2.0.5. Trimmed sequence reads were mapped to Gossypium_hirsutum_v2.1 using Hisat2 v2.0.5
featureCount v1.5.0-p3 was used to count the reads number mapped to each gene
Assembly: Gossypium_hirsutum_v2.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: Down root

extract_protocol:
RNA was extracted using RNAprep Pure Plant Plus Kit (TIANGEN).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X).
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization.
In order to select cDNA fragments of preferentially 370-420 by in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).
Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Down root

value: mixed root cell

tag: time


title: 0hr Soft Rd1 [DS1A11_S1]

city: Berkeley

first: Paola

middle: A

last: Lopez

state: CA

address: Stanley Hall

department: Bioengineering

country: USA

institute: University of California, Berkeley

data_processing:
The reads were initially trimmed using BBDuk to remove Illumina adapters and to filter low quality reads.
The samples were then aligned to ratRibosomal genes using bbmap to remove ribosomal contaminated RNA. Any samples less than 21 bases were removed using BBduk.
Read quality analysis was performed using FastQC to assure there was a Phred score > 28.
The reads were aligned to the rattus norvegicus genome (rn6) using hisat2 v2.1.0.
the aligned reads were converted to counts using htseq.

source_name: hippocampus

extract_protocol:
Phenol-free total RNA was extracted from the cell pellets using RNeasy Plus Micro Kit with gDNA eliminator columns (Quiagen) following the manufacturer’s protocol.
RNA-seq library preparation was carried out by the DNA Technologies and Expression Analysis Core at the University of California, Davis Genome Center using QuantSeq FWD

value: hippocampus

tag: Sex

value: female

tag: developmental stage

value: adult

value: neural stem cell

value: WT

value: mixed differentiation medium (DMEM-F12 with N2 supplemented with 1 uM of retinoic acid and 1% FBS)


title: CKG, Down root, rep3


title: CKN, Down root, rep3


title: CKN, Down root, rep1


title: D_SNI1_G15_3


title: CKG, Down root, rep2


title: D_SNI3 (G15 control)


title: 12hr Soft Rd1 [DS1A23_S3]


title: SW900 2D exosomes-1R

type: RNA

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background and batch corrected using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) implemented in the Transcriptome Analysis Console software version 4.0 (TAC 4.0).

label: biotin

source_name: Exosomes from SW900 cell line grown in adherence conditions (2D) replicate 1

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 13 ngs total RNA (GeneChip Whole Transcript WT Expression Arrays, Affymetrix).

growth_protocol: Primary culture cells were maintained in Dulbecco's Modified Eagle Medium/F12™ supplemented with 1% L-glutamine (Gibco-BRL Life Technologies), 10% fetal bovine serum (Gibco-BRL Life Technologies) and 1% penicillin/streptomycin (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cell lines were maintained in RPMI-1640 medium supplemented with MEM Non-Essential Amino Acids (0.001%) (Gibco-BRL Life Technologies), 10% fetal bovine serum (Gibco-BRL Life Technologies) and 1% penicillin/streptomycin (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.
Exosomes were isolated using ultracentrifugation from cell cultures supernatant and the samples were characterized in size, morphology and specific surface markers determination.
Total RNA was extracted from exosomes using Total RNA Purification Kit (Norgen Biotek, Canada) according to the manufacturer's instructions.

value: Lung cancer cell line

tag: histology

value: LUSC (lung squamous cell carcinoma)


title: SW900 3D exosomes-1R

source_name: Exosomes from SW900 cell line grown in tumorspheres formation (3D) replicate 1


title: D_SNI1 (G15 control)


title: U87MG, control, bio_rep2, tech_rep2


title: CKG, Stem, rep1

source_name: Stem

value: Stem

value: mixed stem cell


title: CKG, Stem, rep2


title: U87MG, control, bio_rep1, tech_rep1


title: CKN, Down root, rep2


title: T cells, HTO-derived cDNA

city: Pittsburgh

first: Khodor

middle: I

last: Abou-Daya

state: PA

address: 200 Lothrop Street

department: Surgery

institute: Starzl Transplantation Institute

description:
Protein
Hashtag-derived oligonucleotide (HTO)

data_processing:
Single cell raw matrix files were obtained using the Cell Ranger's pipeline with alignment to the human reference hg38. The raw matrix was then preprocessed and analyzed using Partek Flow v10.0.21.0801 (Partek). Quality control was done using knee point and EmptyDrops to exclude empty droplets. After centered log ratio (CLR) normalization of the cell hashing count matrix, Hashtag demultiplexing was performed  by using an implementation of the algorithm used in Stoeckius et al. 2018 . Multiplets were excluded based on the cell hashing classification and applying an inclusion filter on counts per cell (600-15000) and detected genes per cell (500-4000). Cells with greater than 10% mitochondrial gene expression were excluded to eliminate dead or apoptotic cells. The resulted gene expression matrix was of 9455 cells by 19,327 genes. Single cell gene expression counts were normalized by log2 (counts per million + 1).
Assembly: hg38
Supplementary files format and content: tab delimited files : Gene Expression and Hashtag-derived oligonucleotide (HTO)

molecule: polyA RNA

source_name: PBMC

extract_protocol:
scRNAseq was performed using 10X Genomics Single Cell 5' solution, version 1, according to the manufacturer’s instructions with 4,000 sorted cells loaded for naïve or activated TCM and 9,000 cells for naïve after co-culture.
mRNA and hashtag oligos cDNA libraries from pooled samples were sequenced on the NovaSeq6000 Platform (Illumina).
scRNAseq and other: Cell hashing

value: PBMC

value: T cells


title: D_sham1 (G15 control)

value: DRG Tissue

value: Sprague Dawley


title: CKN, Stem, rep3


title: D_SNI2 (G15 control)


title: CKN, Stem, rep1


title: 664 day 55

city: Columbia

first: Rocio

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
Reads with low quality bases (Phred score =< 19) were trimmed using the dynamictrim function of SolexaQA++ v3.1.6 with Burrows-Wheeler Aligner algorithm and also only reads with 60 bp length were kept by using lengthsort function of SolexaQA++ v3.1.6
Read quality was confirmed by FastQC and MultiQC
HISAT2 v2.1.0  was used to align trimmed reads to the bovine reference genome assembly ARS-UCD1.2.  To minimize mismatching, --mp 6, 6 –score of HISAT2 v2.1.0 were used and genome aligned paired end reads for each sample were kept for subsequent analysis.  Total read counts for each gene was calculated by using HTseq-count’s default union-counting mode  using NCBI (GCF_002263795.1_ARS-UCD1.2) and Ensembl gene sets (GCA_002263795.2).
Bioconductor packages EdgeR and DESeq2  were used for differential gene expression analyses of day 55 and day 105 maternal blood trasncriptome.  Analysis groups were: 1) AI+ART-Normal vs. ART-LOS, and 2) the two females carrying the two largest LOS (i.e., 604 and 664) vs. all other females.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Abundance measurements files are tab deliminated text files containing name of the gene name (with NCBI and Ensmeble gene name), and raw read counts of annotated gene for each fetus.

organism: Bos taurus

source_name: Day 55 maternal leucocytes

extract_protocol:
Total RNA was isolated from frozen tissues (-80°C) using TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions. RNA samples were stored at -80°C. RNA quality was determined by Agilent anlyzer
For each sample, 2 μg RNA was submitted to the BGI San Diego for library construction. Libraries were sequenced using the DNBSEQ-G400 platform to generate 20 million 100bp paired end reads.

value: maternal blood leucocytes

tag: conception method

value: ART

tag: disease status

value: maternal blood carrying LOS

tag: group of fetuses (ai/artlos/artnormal)

value: ARTLOS


title: CKN, Stem, rep2


title: D_sham3 (G15 control)


title: U87MG, control, bio_rep2, tech_rep1

value: Glioblastoma cell

value: Luciferase expressing

value: Non-irradiated


title: U87MG, control, bio_rep1, tech_rep3


title: D_sham2 (G15 control)


title: CKG, Leaf, rep3

source_name: Leaf

value: Leaf

value: mixed leaf cell


title: 602 day 55


title: T cells, mRNA-derived cDNA

description:
Poly A RNA
poly A RNA


title: CKG, Stem, rep3


title: CKG, Leaf, rep2


title: U87MG, control, bio_rep1, tech_rep2


title: CKG, Leaf, rep1


title: siH_2h_1

city: Kunming

first: Huichun

last: Liang

address: No.17, Longxin Road, Panlong District

institute: Kunming Institute of Zoology. CAS

description:
siCo_2hVSsiH_2h_Gene_differential_expression.txt
siH_0hVSsiH_2h_Gene_differential_expression.txt
siCo_0hVSsiH_0hVSsiCo_2hVSsiH_2h_Gene_differential_expression.txt

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

source_name: Primary HUVEC cells

growth_protocol: We isolated the primary human umbilical vein endothelial cells from neonatal umbilical cord vein.The  informed consent was obtained from the maternal. Expression of CD31 in primary HUVECs was detected by both the flow cytometry and the immunofluorescence staining assays. Primary HUVECs were maintained in EGM-2 BulletKit (CC-3162, Lonza, USA).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary HUVEC cells were transfected with siContral and siHECTD3 by Lipofectamine 20000, and then treated with TNFalpha.

value: primary Human Umbilical Vein Endothelial Cells

tag: passages

tag: transfection

value: Neonatal umbilical cord

tag: agent

value: TNFalpha


title: 512 day 55


title: siH_0h_1

description:
siCo_0hVSsiH_0h_Gene_differential_expression.txt
siH_0hVSsiH_2h_Gene_differential_expression.txt
siCo_0hVSsiH_0hVSsiCo_2hVSsiH_2h_Gene_differential_expression.txt


title: CKN, Leaf, rep3


title: 637 day 55


title: 604 day 55


title: CKN, Leaf, rep2


title: siH_2h_2


title: siCo_2h_1

description:
siCo_0hVSsiCo_2h_Gene_differential_expression.txt
siCo_2hVSsiH_2h_Gene_differential_expression.txt
siCo_0hVSsiH_0hVSsiCo_2hVSsiH_2h_Gene_differential_expression.txt

value: siControl


title: siCo_2h_2


title: siCo_0h_2

description:
siCo_0hVSsiCo_2h_Gene_differential_expression.txt
siCo_0hVSsiH_0h_Gene_differential_expression.txt
siCo_0hVSsiH_0hVSsiCo_2hVSsiH_2h_Gene_differential_expression.txt


title: FIS 343 3D exosomes-1R

source_name: Exosomes from FIS 343 primary culture grown in tumorspheres formation (3D) replicate 1

value: Lung cancer cell line

value: FIS 343

value: LUAD (lung adenocarcinoma)


title: 616 day 55


title: 557 day 55


title: 663 day 55


title: 633 day 55

value: maternal blood carrying normal weighing ART

value: ARTnormal


title: SH1057:2D rec hGREM1 (10% serum)

city: Stockholm

first: Xiangyu

last: Li

address: Tomtebodavägen 23, Solna

department: Science for life laboratory

country: Sweden

institute: KTH-Royal Institute of Technology

data_processing:
Total million reads (or pairs) for a sample
Aggregated percentage of bases that have quality score more the Q30
Kallisto algorithm was used for quantification.
Assembly: Ensembl V102
Supplementary files format and content: tab-delimited text files include TPM and count values for each Sample

source_name: liver

growth_protocol: IHH (immortalized human hepatocytes) cells were cultured in Williams E medium (Life Technologies) and high glucose Dulbecco’s Modified Eagle Medium (DMEM) (Life Technologies), respectively, supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
RNA was isolated from the cells with EZNA total RNA kit (Omega Bio-tek)
RNA sequencing library were prepared with Illumina RNA-Seq with Poly-A selections. Subsequently, the libraries were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RNA v3.4.4) with a 2 × 51 setup using ‘NovaSeqXp’ workflow in ‘S1’ mode flow cell.

treatment_protocol: Cells were treated with recombinant human GREM1 (200 ng/ml) for 24h

value: liver

value: immortalized human hepatocytes (IHH)

value: hepatocytes

value: WT

value: rec hGREM1 (10% serum)


title: siCo_0h_1


title: SH1057:1D Ctrl (10% serum)

value: Ctrl (10% serum)


title: SH1057:2C rec hGREM1 (10% serum)


title: a6: Cardiac fibroblasts,EphrinB2-overexpression, Day7

city: hangzhou

first: wudi

last: li

address: 88 Jiefang Road

institute: Second Affiliated Hospital of Zhejiang University

data_processing:
Illumina Casava software used for basecalling.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Cardiac fibroblasts

extract_protocol:
RNA was harvested using Trizol reagent, 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols

value: Cardiac fibroblasts

value: EphrinB2-overexpression,complete medium

value: Day 7


title: a8: Cardiac fibroblasts,EphrinB2-overexpression,osteogenic differentiation, Day7

description: EphrinB2-overexpression,osteogenic differentiation,Day7


title: a5: Cardiac fibroblasts,EphrinB2-overexpression, Day7


title: 560 day 55

value: maternal blood leucocytes

value: ART


title: a7: Cardiac fibroblasts,EphrinB2-overexpression, osteogenic differentiation,Day7


title: a4: Cardiac fibroblasts,vector, osteogenic differentiation,Day7

description: osteogenic differentiation,Day7

value: osteogenic differentiation


title: siH_0h_2

value: primary Human Umbilical Vein Endothelial Cells

value: Neonatal umbilical cord


title: 628 day 55


title: a3: Cardiac fibroblasts,vector, osteogenic differentiation,Day7

description: osteogenic differentiation,Day7


title: 656 day 55

value: maternal blood carrying LOS

value: ARTLOS


title: SH1057:1C Ctrl (10% serum)


title: a2: Cardiac fibroblasts,vector,Day7

value: complete medium


title: 688 day 55

value: maternal blood carrying normal weighing ART

value: ARTnormal


title: SH1056:2B rec hGREM1 (10% serum)

value: liver

value: immortalized human hepatocytes (IHH)

value: hepatocytes


title: CKN, Leaf, rep1

value: Leaf

value: mixed leaf cell


title: SH1056:1B Ctrl (10% serum)

value: WT

value: Ctrl (10% serum)


title: a1: Cardiac fibroblasts,vector,Day7

value: Cardiac fibroblasts

value: Day 7


title: SH1056:2A rec hGREM1 (10% serum)

value: rec hGREM1 (10% serum)


title: SH1056:1A Ctrl (10% serum)


title: Ang2_antibody_control

city: Helsinki

first: Sawan

middle: KUMAR

last: Jha

state: Haartmaninkatu 8

address: Haartm

department: Research Program Unit

country: Finland

institute: University of Helsinki

data_processing:
Smart-Seq2: Illumina Casava1.8 software was used for basecalling
Smart-Seq2:The sequencing reads were mapped to the mouse reference genome GRCm38 (mm10) with TopHat (version 2.1.1)
Smart-Seq2:Filtering duplicated reads using samtools software (version 0.1.18)
Smart-Seq2:Summarizing gene counts using Subread package (featureCounts function, version 1.4.6-p5)
Smart-Seq2:Raw expression data were processed further in R (version 3.5.1 and version 4.0.3) using Seurat R package (v4.0.6).For QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018).
10X:The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3‚ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
10X:Reads were aligned to mouse reference genome mm10.
10X:Analyses shown in manuscript were performed with Seurat V4.0 (Hao et al., 2021)
10X:Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
10X:Analyses shown in manuscript were performed with Seurat V4.0 (Hao et al., 2021)
Assembly: GRCm38
Supplementary files format and content: Smart-Seq: Matrix table with raw gene counts for every sample/ cell (express_matrix) + gene length and gene title files organized in folders corresponding to the individual plates/samples. 10X: Aggregated matrix files (*matrix.mtx) containing cell counts and tab separated metadata files (*_genes.tsv and *_barcodes.tsv)

source_name: Ear Skin

extract_protocol:
For SMART SEQ experiment: Ear skins of euthanized mice were minced and dissociated by incubation  with 5 mg mL-1 collagenase II, 0.2 mg mL-1 DNase I and 0.2% FBS in PBS for 15 min at 37°C and 750  rpm. Digests were quenched by the addition of 2 mM EDTA f.c., subsequently filtered through a 40 μm  filter and washed for 5 min at 300 g and 4°C with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA). Fcreceptor  binding was blocked by incubation with rat anti-mouse CD16/CD32 (clone 93, 0.5 μg mL-1) for  10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390,  1.0 μg mL-1), anti-PDPN (clone 8.1.1 1 μg mL-1), anti-CD45 (clone 30-F11, 4 μg mL-1), anti-CD11b  (clone M1/70, 4 μg mL-1) and anti-TER-119 (clone TER-119, 4 μg mL-1) antibodies for 20 min on ice.  Prior to sorting of live CD31+ PDPN+ CD45- CD11b- Ter119- lymphatic endothelial cells on a BD FACS  Aria III, samples were filtered through a 40 μm filter and supplemented with 1 μM SytoxBlue to label  dead cells. For 10X experiment: Mouse ear skins minced and dissociated by incubation with 5 mg mL-1 collagenase II, 0.2 mg mL-1 DNase I and 0.2% FBS in PBS for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 70 µm filter and centrifuged at 300g for 5 min at +4C. Cells were resuspended in FACS buffer (PBS, 2% FBS, and 2 mM EDTA) and filtered through a 35 µm cell strainer. Fc-receptor binding was blocked by incubation with rat anti-mouse CD16/CD32 (BD Pharmingen 553142, clone 93, 0.5 µg mL-1) for 10 min on ice followed by incubation with fluorophore-conjugated anti-CD31 (BD Pharmingen 561814, clone MEC 13.3), anti-PDPN (BD 127411 clone 8.1.1 1 µg mL-1), anti-CD45 (BioLegend 103108 clone 30-F11, 4 µg mL-1) and anti-TER-119 (Invitrogen 11-5921-82 clone TER-119, 4 µg mL-1) antibodies on ice for 30 min. Prior to sorting samples were filtered through a 35 µm cell strainer and supplemented with DAPI to label dead cells (0.1 µg mL-1). Live CD31+ PDPN+ CD45- CD11b- Ter119- lymphatic endothelial cells and CD31+ PDPN- CD45- CD11b- Ter119- blood endothelial cells were sorted and pooled. Cell sorting was performed with BD Influx.
Smart-Seq2 library preparation according to Picelli S et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 2014;9(1):171–181. For 10X data, The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 2 chemistry

treatment_protocol: For induction of Cre mediated recombination in Prox1-CreERT2;Tie1fl/fl or Prox1-CreERT2;Tie1;Tie2fl/fl pups, 4-hydroxytamoxifen (4-OHT), dissolved in ethanol (25 mg/ml), was administered to postnatal pups by intragastric injections (2.5 μl, 62.5 μg) at P1-P5.For antibody treatment, Mice were treated with dose of 20 mg/kg of Ang2 blocking antibody (18E5, a gift from Eli Lily) or mouse IgG1 control antibody every three days from P16 to P21.

tag: strain

value: Ang2 antibody

tag: gender

value: male

tag: age

value: skin

value: FACs sorted Ecs

tag: facs sorting

tag: protocol

tag: plate id


title: IgG_antibody_control

tag: genotype

tag: treatment

value: IgG antibody

tag: tissue

tag: cell type

value: FACs sorted ECs


title: 517 day 55

value: maternal blood leucocytes

value: artificial insemination

value: maternal blood carrying healthy fetus

value: AI


title: 606 day 55


title: 519 day 55

value: ART

value: maternal blood carrying normal weighing ART

value: ARTnormal


title: 609 day 55


title: EPS 0h Tug1-KD rep 6

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

data_processing:
Base calling was made with Illumina Real Time Analysis 3 (RTA3) Software.
Reads first underwent adapter trimming and quality check with FastQC v0.11.7.
Raw read quality filtering and adapter trimming were conducted with fastp v0.14.1 (Chen et al., 2018) (auto detect of adapters, trim_tail=1, poly_g_min_len=1, min phred quality 20, min length 36, u 90).
Filtered reads were aligned to the mouse reference genome (Mus musculus, Ensembl version GRCm39.104) using STAR v2.5 (Dobin et al., 2013) in 2-pass mode and expression quantified at the gene level and collated into a m x n matrix.
Genome_build: Mus musculus, Ensembl version GRCm39.104
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw read count values for each sample.
Supplementary_files_format_and_content: AT_raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Myotube

growth_protocol: C2C12 mouse myoblast cells were obtained from a commercial vendor (ATCC Cat# CRL-1772, RRID: CVCL_0188). Myoblasts were seeded in 6-well plates at 37℃ with 5% CO2 in a humidified incubator in proliferation media consisting of Dulbecco’s Modified Eagle Medium (DMEM; Gibco #11995-065) supplemented with 1% v/v penicillin-streptomycin (Gibco #15140-122) and 10% v/v FBS (Gibco #A3161001). Cells were grown to 90% confluence then switched to differentiation media as per proliferation media but 2% v/v horse serum (Gibco #16050-130) instead of FBS. Differentiation media was replaced after 2 days, then on day 3, transfection of Tug1 knockdown or negative control antisense LNAs was performed. Experiments were then conducted 24 h later on day-4 differentiated myotubes.

extract_protocol:
RNA extraction from C2C12 cells: media was aspirated from each well at the end of an experiment, then cells were immediately lysed in TRI-reagent (Ambion 15599018) with homogenisation achieved via pipette mixing. Lysates were then frozen at -80℃ until RNA isolation. TRI-reagent lysates were thawed on ice and centrifuged at 10,000 x g for 10 min at 4℃. An aliquot of the supernatant was taken for RNA purification with on-column DNase-I treatment, as per manufacturer’s directions (Direct-Zol RNA Miniprep #R2052, Zymo Research) followed by additional clean-up step (#R1013, Zymo Research).
RNA concentration was confirmed fluorometrically (Qubit, Thermo Fisher) and RNA integrity number (RIN) determined by electrophoresis (Tapestation, Agilent), all RIN were ≥9.5. Stranded libraries were prepared from 500 ng total RNA input with poly-A+ selection (E7760L, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®) and included an SIRV Spike-In control, isoform E0 (#025.03, Lexogen) diluted in 1:500. Final library size and concentration were assessed (TapeStation, Agilent). Libraries were pre-sequenced (2 x 150 bp paired-end reads) on the MiniSeq Sequencer (Illumina, San Diego, CA) to obtain the read distribution. Each library was then re-pooled to equal molar concentrations, enzymatically treated, denatured and normalized to 2 nM. Finally, the normalized pooled library was sequenced with 150bp paired end reads on the Illumina NovaSeq 6000 platform (Deakin University Genomics Centre), generating at least 40 million reads per sample.

treatment_protocol: Electrical pulse stimulation (EPS) was performed using a commercially available system (C-PACE, IonOptix, MA, USA; Firmware: 139 / PIC v.11, no current leakage mode). Differentiation media volume was increased to 3 mL per well and pre-sterilized carbon electrodes were placed into the 6-well plates which were then returned to the 37℃ humidified incubator. Myotubes underwent EPS for 3 hours. Stimulation parameters were reproduced from a previous report (Tamura et al., 2020) as follows: 13 V, 66 Hz, 2 ms pulse duration in trains of 5 s on and 5 s off. In parallel, plates of cells for the ‘Rest’ condition had the carbon electrodes submerged into the media for the same duration but were not connected to the pulse generator. Immediately after the EPS protocol (EPS 0h) or after 3 hours recovery (EPS 3h), media was removed and cells were harvested in TRI-reagent.

tag: cell line

value: Myotube

tag: treatment (lna)

tag: treatment (eps)

value: EPS 0h


title: AT22-EPS

city: Oslo

first: G. Hege

last: Thoresen

address: Sem Sælands vei 3

department: Section for Pharmacology and Pharmaceutical Biosciences

country: Norway

institute: University of Oslo

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software v2.5
FeatureCounts was used to count the read numbers mapped of each gene and RPKM was then calculated
Differential expression analysis between control and EPS treated cells was performed using DESeq2 R package v2_1.6.3
Assembly: hg38, GRCh38
Supplementary files format and content: excel file include FPKM values for each sample

source_name: Skeletal muscle

extract_protocol:
Total RNA from cultured transduced cells was extracted using QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: Skeletal muscle

value: Primary skeletal muscle cells

value: electrical pulse stimulation


title: AT22-Control

value: unstimulated


title: AT21-EPS


title: AT21-Control


title: EPS 3h Tug1-KD rep 6

value: EPS 3h


title: 669 day 55

tag: conception method

tag: disease status

tag: group of fetuses (ai/artlos/artnormal)


title: 546 day 55


title: 590 day 55


title: EPS 0h Control rep 6

value: Negative control


title: 647 day 55


title: Rest Tug1-KD rep 6

value: Rest


title: AT18-EPS


title: Rest Control rep 6


title: 533 day 55


title: AT18-Control


title: AT10-EPS


title: EPS 3h Tug1-KD rep 5


title: 664 day 105

source_name: Day 105 maternal leucocytes

value: maternal blood carrying LOS

value: ARTLOS


title: 648 day 55

value: maternal blood leucocytes

value: artificial insemination


title: EPS 3h Control rep 5


title: AT10-Control


title: EPS 0h Tug1-KD rep 5


title: 602 day 105


title: AT8-EPS


title: EPS 0h Control rep 5


title: AT8-Control


title: Rest Control rep 5


title: 656 day 105


title: Rest Tug1-KD rep 5


title: AT7-Control


title: AT24-EPS


title: 637 day 105


title: 604 day 105


title: 616 day 105


title: EPS 3h Tug1-KD rep 4


title: EPS 3h Control rep 4


title: AT24-Control


title: 663 day 105


title: 557 day 105


title: EPS 3h Control rep 6


title: 633 day 105


title: BCC5

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: BCC5 (LY021121)

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina).
Raw sequencing data provided as fastq files were processed using the count function of the Cell Ranger pipeline (v. 5.0.1, 10x Genomics).
The count function allowed us to demultiplex reads to individual cells, to align the reads to the human GRCh38 reference (v. GRCh38-2020-A), and to generate filtered matrices of gene counts by cell barcodes.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data files consist of the 3 files generated by Cell Ranger v5.0.1, containing only detected cellular barcodes (filtered_feature_bc_matrix). The file "matrix.mtx.gz" is a sparse matrix containing number of UMIs per gene (in rows) per single cell (in columns). The file "barcodes.tsv.gz" contains the list of detected cellular barcodes (i.e. single cell identities) corresponding to the columns in "matrix.mtx.gz", and the file "features.tsv.gz" contains the genes corresponding to the rows in "matrix.mtx.gz".

source_name: Mohs specimen residual debulking piece of skin

extract_protocol:
Fresh tumor tissue was minced and enzymatically digested to obtain a single cell suspension. Single living cells were then FACS sorted. The cells were resuspended to reach a target final concentration of approximately 1,000 cells/μl.  ScRNA-seq was performed using the Chromium Next GEM single cell 3' reagent kit v3.1 (10xGenomics) following the manufacturer's protocol with a target number of captured cells of 10,000.
Sequencing libraries were prepared after GEM generation and barcoding using the Chromium Next GEM single cell 3'reagent kit v3.1 (10xGenomics) the following manufacturer's protocol.

tag: tumor type

value: infiltrative basal cell carcinoma

tag: location

value: nose

value: skin biopsy


title: BCC4

description: BCC4 (LY261021)


title: EPS 0h Control rep 4


title: 512 day 105

value: ART


title: Rest Tug1-KD rep 4

value: Myotube


title: BCC3

description: BCC3 (LY191021)

value: left cheek


title: B3: A2058 [RSL3+IFN-gamma]

city: Xi'an

first: Weinan

last: Guo

address: No.127, Changle Xi Road

institute: Xijing Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through bcl2fastq
Mapped small RNA tags were used to looking for known miRNA. miRBase22.0 was used as reference, bowtie-1.1.1 were used to obtain the potential miRNA and draw the secondary structures.
MiRNA expression levels were estimated by TPM (transcript per million): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two conditions/groups was performed using the R package edgeR. P-value of 0.05 and |log2(foldchange)|>1 was set as the threshold for significantly differential expression by default.
Predicting the target gene of miRNA was performed by miRanda for animals
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts and TPM for every gene and every sample

source_name: melanoma cell

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) and 1% penicillin–streptomycin (Invitrogen, Carlsbad, CA, USA)

extract_protocol:
Total RNA were extracted with Trizol (Tiangen, Beijing) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). A total amount of 3ug total RNA per sample was used as input material for the small RNA library.
Sequencing libraries were generated using NEB Next®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

treatment_protocol: RSL3 or RSL3+IFN-γ for 24 hours

value: A2058 melanoma cell

tag: time


title: 628 day 105

value: maternal blood carrying normal weighing ART

value: ARTnormal


title: Rest Control rep 4


title: AT7-EPS

value: Skeletal muscle

value: Primary skeletal muscle cells

value: electrical pulse stimulation


title: EPS 3h Tug1-KD rep 3

value: EPS 3h


title: B2: A2058 [RSL3+IFN-gamma]


title: TFAP2E KO CR 021

city: Ithaca

first: Megan

last: Rothstein

state: NY

address: 526 Campus Road Rm 433

institute: Cornell University

description: CUT&RUN library

library_source: genomic

data_processing:
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25
Alignment, bowtie2 v2.4.2, “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Filtering, samtools v1.10 view "-f 2 -F 780 -bh", sort, index
Peak calling, MACS2 v2.2.7.1 "-f BAMPE -g 3e9 -q 0.05 --call-summits"
Generate bigwigs, bamCoverage "--outFileFormat bigwig --binSize 5 --normalizeUsing RPKM"
Assembly: UCSC mm10
Supplementary files format and content: .bigwig files displaying read coverage across the genome
Supplementary files format and content: .bam alignment files
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: mouse P10 VNO dissection

growth_protocol: OMPCre mouse were aged to P10

extract_protocol:
The vomeronasal organs of P10 OMPCre and OMPCreR26AP2 mice were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate. CUT&RUN experiments were performed as previously described(Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext ultra II DNA library prep kit (New England Biolabs E7645) according to the kit's protocol.

tag: developmental stage

tag: target

tag: cre

value: OMPCre

value: vomeronasal organs


title: TFAP2E OMPCre CR 011

description: CUT&RUN library


title: 669 day 105

value: maternal blood leucocytes


title: EPS 3h Control rep 3

value: Negative control


title: 688 day 105


title: A2: A2058 [RSL3]


title: A3: A2058 [RSL3]


title: EPS 3h Tug1-KD rep 2


title: EPS 3h Control rep 2


title: 519 day 105


title: TFAP2E KO CR 020

description: CUT&RUN library


title: EPS 3h Tug1-KD rep 1


title: 648 day 105

value: artificial insemination

value: maternal blood carrying healthy fetus

value: AI


title: 590 day 105


title: EPS 3h Control rep 1


title: 606 day 105


title: A1: A2058 [RSL3]


title: 517 day 105


title: EPS 0h Tug1-KD rep 4

value: EPS 0h


title: lung_AM_S044

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center

data_processing:
Reads were deduplicated based on their UMIs
STAR (version 2.5.3a) was applied for the alignment of reads to the mouse genome (mm9).
Quantification of reads by htseq-count (version 1.0)
DESeq2 (version 1.26.0) was used to identify differentially expressed genes for each group.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

source_name: lung

extract_protocol:
Heart MF: The heart of Cx3cr1Gfp/+ mouse was removed, the organ was chopped into small pieces and digested for 30 min at 37°C in RPMI medium without fetal calf serum supplemented with 1 mg /ml Collagenase IV and 1 mg/ml DNase I. The digestion was stopped by addition of staining buffer (2mM EDTA, 1% FCS in PBS) and the cell suspension was minced through a 100 μm cell strainer. After centrifugation at 1,200 rpm, 4oC for 6 min, supernatant was discarded and cells were blocked with anti-CD16/32 antibodies for 10 min, before anti-F4/80-biotin antibodies were added for 25 min on ice. After washing, the cell pellet was incubated with anti-biotin beads (Miltenyi) for 15min on ice. Cells were washed again (1,200 rpm, 4oC for 6 min) and MACS was performed with LS columns (Miltenyi). After elution and washing of cells, lung cells were stained for CD45, streptavidin, dump (Ly6C, Ly6G), CD11b, MerTK, CD64 and MHCII
Colon MF: Cells from Cx3cr1Gfp/+ mice were isolated as previously described 48. In brief, the intestine was removed and feces were flushed with cold PBS without calcium and magnesium. The intestine was longitudinally opened and cut into 0,5 cm pieces. Intestinal epithelial cells were removed by incubation with the HBSS containing 1mM DTT, 2mM EDTA and 5% of fetal calf serum. The cell suspension was incubated at 37 °C, 125 rpm for 40 min. The cell suspension was shortly vortexed and passed through a 100μm mesh. The intestinal tissue pieces were transferred to a 50 ml Falcon tube containing 5 ml PBS with 5% FBS, 1 mg/ml of collagenase VIII (Sigma) and 0.1 mg/ml DNase I. Samples were incubated at 37 °C, 250 rpm for 40 min. Digested colon tissue was vortexed for 40 sec, passed through a 80μm mesh and cells were collected by centrifugation at 1,200 rpm for 10 min at 4 °C. Cells were stained after CD16/32 block with antibodies against CD45, CD11b, lineage (Ly6C, Ly6G, B220) and MHCII.
Lung AMs: The lung was removed and cut into small pieces. Tissue was collected in RPMI medium without fetal calf serum supplemented with 1 mg/ml Collagenase A and 1 mg/ml DNase I. Tissue was digested for 30 min at 37°C. The suspension was minced and filtered through a 100μm cell strainer. The cell suspension was centrifuged at 1,200 rpm, 4oC for 6 min. The supernatant was removed and cells were blocked with anti-CD16/32 antibodies for 10 min, before anti-CD45-biotin antibodies were added for 25 min on ice. Afterwards, cells were washed with staining buffer (2mM EDTA, 1% FCS in PBS) at 1,200 rpm, 4oC for 6 min, supernatant was discarded and anti-biotin beads (Miltenyi) were added for 15min. Cells were washed again (1,200 rpm, 4oC for 6 min) and MACS was performed with LS columns (Miltenyi). After elution and washing of cells, lung cells were stained for lineage (Ly6C, Ly6G), streptavidin, CD11b, CD64, CD11c and SiglecF.
Spleen RPM: The spleens were removed from Bl6 mice and minced through a 100 μm cell strainer. After washing with staining buffer (2mM EDTA, 1% FCS in PBS) at 1,200 rpm, 4oC for 6 min, supernatant was discarded and cells were blocked with anti-CD16/32 antibodies for 10 min, before anti-F4/80-biotin antibodies were added for 25 min on ice. After washing, the cell pellet was incubated with anti-biotin beads (Miltenyi) for 15 min on ice. Cells were washed again (1,200 rpm, 4oC for 6 min) and MACS was performed with LS columns (Miltenyi). After elution and washing of cells, lung cells were stained for CD45, streptavidin, lineage (Ly6C, Ly6G, B220), CD11b, CD11c and MHCII.
Tongue Langerhans cells: To separate the epithelium from the rest of the tongue and to dislodge Langerhans cells, extracted tongues were injected with 5 U/ml of Dispase II (Sigma) in HEPES buffered saline until completely distended. They were then incubated for 15 min at 37oC and the epithelium layer was peeled off using forceps. The epithelium was minced in 500 μL of PBS with 0.2 mg of DNAse I (Roche), 4.8 mg Collagenase IV (Gibco) and 0.15 mg (60U) hyaluronidase I (Sigma) and incubated for 15 min at 37oC. 10 ml sorting buffer were added to the crude tissue suspension as it was passed through a 100μm cell strainer and centrifuged for 6 min at 1,200 rpm and 4oC. The pellet (enriched for tongue Langerhans cells) was then further processed accordingly.
Tongue macrophages: Tongues were extracted, minced in 500 μL of PBS with 0.2 mg of DNAse I (Roche), 2.4 mg Collagenase IV (Gibco) and 0.15 mg (60U) hyaluronidase I (Sigma) and incubated for 45 min at 37oC. 10 ml sorting buffer were added to the crude tissue suspension as it was passed through a 100 μm cell strainer and centrifuged for 6 min at 1,200 rpm and 14oC. Pellet was resuspended in 3 ml PBS, layered over 3 ml of Ficoll-PaqueTM and centrifuged for 17 min at 2,000 rpm and 14oC with no acceleration nor break. The interface containing leukocytes was collected, 5 ml sorting buffer were added centrifuged for 6 min at 1,200 rpm and 4oC. Leukocyte-containing cell pellets were further processed. All tongue preparations were performed according to this protocol, if not otherwise stated.
Skin Langerhans cells: Ears were dissected and placed over 0.05% Trypsin with EDTA in PBS for 1.5-2 hours at 37oC, until the epidermis could be peeled off using forceps. The epidermis was minced and the crude tissue suspension in sorting buffer was passed through a 100 μm cell strainer and centrifuged for 6 min at 1,200 rpm and 4oC. Cell-pellets were further processed.
Microglia: Brains were dissected, and the olfactory bulb and cerebellum were removed. The remaining brain was minced and filtered through a 70μm cell strainer in ice-cold high-glucose DMEM (Sigma). The cell suspension was centrifuged at 1,200 rpm at 4oC for 6 minutes and the pellet was resuspended in 5 ml of 40% Percoll (GE Healthcare) in PBS and transferred to a 15 ml tube. Tubes were centrifuged at 2,000 rpm for 25 minutes (min) at 14oC with no acceleration nor break. Pellet was resuspended in 10 ml sorting buffer and centrifuged for 6 min at 1,200 rpm and 4oC. Leukocyte-containing cell pellets were further processed.
500-20,000 FACS sorted cells were lysed with 100μl of lysis/binding buffer (Life Technologies), snap-frozen on dry ice and stored at -80°C until further use. mRNA purification was performed with the DynabeadsTM mRNA DIRECTTM Purification Kit (Life Technologies) according to the manufacturer’s guidelines. MARS-seq barcoded RT primers were used for .CC-BY 4.0 International licenseperpetuity. It is made available under apreprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for thisthis version posted February 11, 2022. ; https://doi.org/10.1101/2022.02.09.479699doi: bioRxiv preprint https://doi.org/10.1101/2022.02.09.479699http://creativecommons.org/licenses/by/4.0/19reverse transcription with the Affinity Script cDNA Synthesis Kit (Agilent) in a 10μl reaction volume
The MARS-seq protocol was used for bulk RNA sequencing (Jaitin et al., 2014) After reverse transcription, samples were analyzed by qPCR and samples with similar Ct values were pooled. Samples were treated with Exonuclease I (New England BioLabs (NEB)) for 30min at 37°C and for 10min at 80°C followed by a 1.2X AMPure XP beads (Beckman Coulter) cleanup. The second strand synthesis kit (NEB) at 16°C for 2hours was used for cDNA synthesis followed by a 1.4X AMPure XP bead cleanup. In vitro transcription (IVT) was performed at 37°C for 13-16h with the HiScribe T7 RNA Polymerase kit (NEB). The remaining DNA was digested by Turbo DNase I (Life Technologies) treatment at 37°C for 15min followed by a 1.2X AMPure XP bead cleanup. RNA fragmentation (Invitrogen) was performed at 70°C and the reaction was stopped after 3min with Stop buffer (Invitrogen) followed by a 2X AMPure XP bead cleanup. Ligation of the fragmented RNA to the MARS-seq adapter was performed at 22°C for 2h with T4 RNA ligase (NEB) followed by a 1.5X AMPure XP bead cleanup. A second reverse transcription reaction was performed with MARS-seq RT2 primer and the Affinity Script cDNA Synthesis Kit (Agilent Technologies) followed by 1.5X AMPure XP bead cleanup. Finally, the library was amplified using P5_Rd1 and P7_Rd2 primers and the Kapa HiFi Hotstart ready mix (Kapa Biosystems) followed by a 0.7X AMPure XP bead cleanup. Fragment size was measured using a TapeStation (Agilent Technologies) and library concentrations were measured with a Qubit fluorometer (Life Technologies).

tag: biological replicate

value: biol rep 1

value: lung

value: AMs

tag: Sex

value: female

value: no treatment

tag: facs staining

tag: library protocol

value: MARS-Seq


title: 609 day 105

tag: tissue


title: LHC_S042

source_name: skin

value: biol rep 3

value: skin

tag: cell type

value: sLC

tag: genotype

tag: treatment


title: lung_AM_S047

value: biol rep 2


title: EPS 0h Tug1-KD rep 3

tag: cell line

value: Myotube

tag: treatment (lna)

tag: treatment (eps)


title: lung_AM_S050


title: LHC_S041


title: EPS 0h Control rep 3


title: LHC_S040


title: B1: A2058 [RSL3+IFN-gamma]

value: A2058 melanoma cell


title: 560 day 105

value: maternal blood leucocytes

tag: conception method

value: ART

tag: disease status

value: maternal blood carrying normal weighing ART

tag: group of fetuses (ai/artlos/artnormal)

value: ARTnormal


title: RPM_S039

source_name: spleen

value: spleen

value: spleen RPM


title: EPS 0h Control rep 2

value: Negative control

value: EPS 0h


title: EPS 0h Tug1-KD rep 1


title: EPS 0h Control rep 1


title: EPS 0h Tug1-KD rep 2


title: RPM_S037

value: biol rep 1

value: female


title: RPM_S038

value: no treatment

value: MARS-Seq


title: Rest Control rep 3

value: Rest


title: 533 day 105

value: artificial insemination

value: maternal blood carrying healthy fetus

value: AI


title: MG_S035

source_name: brain

value: biol rep 7

value: brain

value: microglia


title: noCAD_22 [EP00489]

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We mapped all reads to the Human genome version HG38/GRCh38.99, downloaded from the Ensembl database, using a 2-steps approach. First, we aligned reads against the whole genome, by STAR (v.2.7.0f); then, the unmapped reads were locally mapped by Bowtie2 (version 2.3.5). We set the default parameters for both tools, except for --chimSegmentMin 18, --chimScoreMin 12 (STAR) and --local --very-sensitive-local, -q, --mm (Bowtie2).
Gene expression quantification was performed by the featuresCount tool (v. 1.6.4), taking into account genes annotated in the GRCh38.99 release.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample. The header of the files reports gene name,  sample identifiers.

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated using KingFisher Flex Purification system and MagMax for Stabilized Blood Tube RNA Isolation kit (Thermo Fisher Scientific), following manufacturer's instructions, and precipitated through ammonium acetate/ethanol method. α and β-globin mRNAs depletion were performed from precipitated total RNA using the GLOBINclearTM Human kit (Applied Biosystems)
Poly(A)+ RNA enrichment followed the Dynabeads mRNA Purification Kit protocol (Thermo Fisher Scientific). Libraries were prepared and pooled together (6 samples per sequencing run) using multiplex library RNA Barcoding reagents and Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

value: Whole blood

tag: group

value: no coronary artery disease (CAD)

value: F

tag: age

tag: sequencing batch


title: Rest Tug1-KD rep 2

value: Myotube


title: noCAD_25 [EP00519]

value: M


title: Rest Tug1-KD rep 3


title: 647 day 105

value: maternal blood leucocytes


title: Rest Control rep 2

value: Negative control


title: 546 day 105


title: MG_S033

tag: biological replicate

value: biol rep 5

value: female


title: noCAD_23 [EP00504]

tag: Sex


title: noCAD_24 [EP00507]


title: Rest Tug1-KD rep 1


title: noCAD_20 [EP00432]


title: noCAD_21 [EP00470]


title: KO

first: Cornelius

last: Fischer

state: Berlin

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: Cellranger output files (multiple flies)

data_processing:
NovaSeq 6000 data was demultiplexed using bcl2fastq v2.20.0
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and gene-barcode matrix generation was done with Cell Ranger (3.1.0, 10X Genomics).
Cellbender v1 (remove-background)
Seurat version 3 was used for downstream analysis (min cells 5 per gene, min features per cell 300). Non-T-cell contamination removed. SCT regression (cell-cycle and mtRNA)
Genome_build: mm10 (Ensembl, GRCm38.93)
Supplementary_files_format_and_content: *raw_feature_bc_matrix.h5: Unfiltered HDF5 feature-barcode matrix. Contains every barcode from fixed list of known-good barcode sequences. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
Supplementary_files_format_and_content: *filtered_feature_bc_matrix.h5: Filtered HDF5 feature-barcode matrix. Contains only detected cellular barcodes. This includes background and cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
Supplementary_files_format_and_content: *cellbender.h5: Cellbender processed filtered HDF5 feature-barcode matrix
Supplementary_files_format_and_content: *cellbender_filtered.h5: Cellbender processed unfiltered HDF5 feature-barcode matrix

source_name: CD8 T cells

growth_protocol: Ebag9-/- mice were generated as described (Rüder et al.) and backcrossed into C57.BL/6 (B6) mice for 14 generations.

extract_protocol: Splenocytes from immunized mice (pooled from four Ebag9+/+ or -/- mice, respectively) were isolated and living antigen-specific CD8+ T cells were sorted by staining for 7AAD- CD19- CD8+ Dextramer+ T cells.

treatment_protocol: Ebag9+/+ and -/- mice were immunized i.p. with 1.5x10^6 SV40 large T-expressing Co16.113 cells, splenocytes were isolated 7 days after immunization.

tag: strain

value: immune cells

value: CD8 T cells


title: colon_S032

source_name: colon

value: biol rep 2

value: colon

value: colon MF

value: no treatment

tag: facs staining

tag: library protocol

value: MARS-Seq


title: MG_S034

value: biol rep 6

tag: tissue

value: brain

tag: cell type

value: microglia


title: MG_S022

value: biol rep 3

tag: genotype

tag: treatment


title: WT

value: wild type


title: noCAD_18 [EP00352]

value: Whole blood

value: no coronary artery disease (CAD)

value: M


title: Ola 24-48 hpf rep 3

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE (v. 0.36) . Ribosomal RNA sequences were removed using sortmerna (v. 2.1b) and the SILVA rRNA database (version 119). Using Kallisto (v. 0.43.1), the reads were then pseudo-aligned to the published transcriptome of Acipenser baerii (http://publicsturgeon.sigenae.org/ngspipelines/#!/NGSpipelines/Acipenser%20baerii%20-%20publicSiberianSturgeon) and a  count table generated.
Normalized number of reads was generated using DESeq2.
Transcripts were removed that had zero counts in all samples
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.

organism: Acipenser ruthenus

source_name: embryo

extract_protocol:
Total RNA extraction was extracted using TRI reagent (Sigma-Aldrich) following the manufacturer’s protocol, then re-precipitated with LiCl. Total RNA concentration was determined with a NanoDrop 2000 (ThermoScientific), and the quality of RNA was assessed using a Fragment analyzer (Advanced Analytical). In total, three biological replicates (three embryos per condition) were prepared for sequencing.
Libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing (Agilent, G9691) based on the poly-A protocol. The libraries were sequenced on a NextSeq 500 instrument in PE75 high-output mode.

treatment_protocol: Embryos were exposed to either 10 nM camptothecin or 20 µM olaparib for 24 hours during one of three stages: 1) from 2 to 24 hpf (blastula); 2) from 24 to 48 hpf (gastrulation); 3) from 48 to 72 hpf (neurulation). Genotoxicants were replaced with fresh water after 24 hours.Embryos for RNA sequencing were collected at 7 dpf and immediately transferred to a −80°C freezer. Only embryos from the following groups were used for RNA sequencing: CPT 24-48, CPT 48-72, Ola 2-24, Ola 24-48.  In total, three biological replicates (three embryos per condition) were prepared for sequencing.

value: embryo

tag: treatment condition

value: Oolaparib

tag: treatment time

value: 24-48 hpf (gastrulation)

tag: developmental stage used for sequencing

value: 7 dpf

tag: group number

tag: replicate number

value: C


title: Rest Control rep 1

tag: cell line

value: Myotube

tag: treatment (lna)

value: Negative control

tag: treatment (eps)

value: Rest


title: colon_S031

tag: biological replicate

value: biol rep 1

value: colon

value: colon MF

value: female

value: no treatment

value: MARS-Seq


title: MG_S023

value: biol rep 4

value: brain

value: microglia

tag: Sex


title: Ola 24-48 hpf rep 1

value: embryo

value: A


title: MG_S020


title: noCAD_19 [EP00378]

value: Whole blood

tag: group

value: no coronary artery disease (CAD)

value: M

tag: age

tag: sequencing batch


title: Ola 24-48 hpf rep 2

tag: tissue

value: Oolaparib

value: 24-48 hpf (gastrulation)

value: 7 dpf

value: B


title: heart_MHCIIneg_S018

source_name: heart

value: biol rep 3

value: heart

tag: cell type

value: hMHCII- MF

tag: facs staining

tag: library protocol


title: MG_S021

value: biol rep 2

value: female

tag: genotype

tag: treatment

value: no treatment


title: noCAD_16 [EP00309]


title: colon_S043

value: colon

value: colon MF

value: MARS-Seq


title: CPT 48-72 hpf rep3

value: embryo

tag: treatment condition

value: Camptothecin

tag: treatment time

value: 48-72 hpf (neurulation)

tag: developmental stage used for sequencing

value: C


title: Ola 2-24 hpf rep 3

value: Oolaparib

value: 2-24 hpf (blastula)

tag: group number

tag: replicate number


title: CPT 48-72 hpf rep2

value: 7 dpf


title: noCAD_17 [EP00345]

value: Whole blood

value: no coronary artery disease (CAD)

value: M


title: heart_MHCIIneg_S012

value: biol rep 1

value: heart

value: hMHCII- MF


title: heart_MHCIIpos_S017

value: biol rep 3

value: hMHCII+ MF

value: female

value: no treatment


title: heart_MHCIIpos_S014

value: biol rep 2

value: MARS-Seq


title: noCAD_13 [EP00159]


title: noCAD_15 [EP00241]

value: F


title: noCAD_09 [EP00119]


title: Ola 2-24 hpf rep 2

value: embryo

value: B


title: noCAD_12 [EP00157]


title: CPT 48-72 hpf rep1

value: Camptothecin

value: 48-72 hpf (neurulation)

value: A


title: WT_m_our_4_S16

source_name: tongue

value: tongue

value: tCX3CR1+ MF

value: male


title: Ola 2-24 hpf rep 1

value: Oolaparib

value: 2-24 hpf (blastula)

value: 7 dpf


title: noCAD_11 [EP00134]

value: Whole blood

value: no coronary artery disease (CAD)

value: M


title: CPT 24-48 hpf rep 2

value: 24-48 hpf (gastrulation)


title: CPT 24-48 hpf rep 1


title: WT_m_Lyve_3_S11

value: biol rep 3

value: tFOLR2+ MF

value: no treatment

value: MARS-Seq


title: noCAD_14 [EP00209]


title: noCAD_10 [EP00129]

value: F


title: noCAD_04 [EP00055]


title: Ctrl 7 dpf rep 4

value: embryo

value: Control

value: D


title: noCAD_05 [EP00062]


title: noCAD_08 [EP00116]


title: Ctrl 7 dpf rep 2

value: B


title: Ctrl 7 dpf rep 1

value: A


title: heart_MHCIIpos_S011

value: biol rep 1

value: heart

value: hMHCII+ MF

value: female


title: CPT 24-48 hpf rep 3

value: Camptothecin

value: 7 dpf

value: C


title: noCAD_07 [EP00071]

value: Whole blood

value: no coronary artery disease (CAD)

value: M


title: CAD_27 [EP00478]

value: coronary artery disease (CAD)


title: WT_f_our_4_S46

value: biol rep 3

value: tongue

value: tCX3CR1+ MF

value: no treatment

value: MARS-Seq


title: WT_m_our_2_S8

value: male


title: A375-Bottom5

city: Knoxville

first: Rosela

last: Golloshi

state: TN

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

data_processing:
Adapters and reads with a quality score less than 20 were trimmed from the final libraries using Skewer/0.2.2
Trimmed reads were aligned to the hg19 genome using bowtie2 with default parameters
Peaks were called using MACS2 with the following parameters: --nomodel --extsize 300 -g hs --keep-dup all.
Genome_build: hg19

source_name: Skin

extract_protocol:
ATAC-Seq samples were prepared as previously described in Buenrostro et al., 2015
ATAC-Seq libraries were prepared as previously described in Buenrostro et al., 2015.

tag: strain


title: WT_m_Lyve_4_S15

tag: biological replicate

value: biol rep 4

value: tFOLR2+ MF


title: noCAD_06 [EP00068]

tag: Sex


title: Ctrl 7 dpf rep 3

value: embryo

value: Control


title: CAD_26 [EP00461]

tag: group

value: F


title: scRNA-seq-sgTP53-RB1-Enz

city: Dallas

first: Tao

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

description: processed data file: filtered_feature_bc_matrix.h5

data_processing:
Bulk RNAseq:
Adapter trimming and quality trimming was performed with trimgalore (v0.5.0), and ribosomal RNA was removed using SortMeRNA (v4.1.0), using the original FASTQ files.
Trimmed and filtered reads were aligned to reference (GRCh37) with STAR (vSTAR2.6.1d). FeatureCounts (v1.6.4) was used for gene counts, biotype counts, and rRNA estimation.
Reads counts.csv files for genes and transcripts were generated by StringTie (v1.3.5), and RSeQC (v3.0.0) was used for generating RNA quality control metrics.
Reads counts from all samples were normalized using the R package DESeq2 1.26. The vst command in DESeq2 were also used to perform the variance stabilizing transformation.
scRNAseq:
10X scRNA-seq data was preprocessed using the Cellranger v5.0 software. All parameters were set to default.
Used the count command to process the 10x single-cell RNA-seq output into cells by gene expression count matrix
Used the aggr command to pool sequencing runs from 6 samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample; HDF5 Feature Barcode Matrix Format

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol:
For RNAseq samples: LNCaP/AR cells transduced with different CRISPR constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol. For scRNAseq samples: Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 900-1100 cells/μl. Cells were loaded between 10,000 and 17,000 cells/chip position using the Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1 barcoding chemistry).
For RNAseq samples: RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA. For scRNAseq samples: Single-cell gene expression libraries were generated according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols.
For RNAseq samples: RNA-Seq. For scRNAseq samples: Single-cell RNA-seq were performed by the 10x Genomic single cell 5’library platform.

treatment_protocol: For RNAseq samples: When treated with 10 µM enzalutamide and/or 5 µM filgotinib, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 6 days.

tag: cell line

value: LNCaP/AR

value: prostate cancer cells

value: enzalutamide 10µM


title: WT_f_our_3_S42

value: biol rep 2

value: female


title: noCAD_03 [EP00049]

value: Whole blood

value: no coronary artery disease (CAD)

value: M

tag: age

tag: sequencing batch


title: WT_m_Lyve_2_S7

tag: tissue

value: tongue

tag: cell type


title: heart_MHCIIneg_S015

value: heart

value: hMHCII- MF

value: no treatment

tag: facs staining

tag: library protocol


title: WT_f_Lyve_3_S41

tag: genotype

tag: treatment

value: MARS-Seq


title: scRNA-seq-sgTP53-RB1-JAK1-Veh

source_name: LNCaP/AR_Vehicle DMSO

value: Vehicle DMSO


title: WT_m_Lyve_1_S3

value: biol rep 1

value: tFOLR2+ MF

value: male


title: WT_f_tLC_2_S53

value: tLC


title: noCAD_02 [EP00044]


title: noCAD_01 [EP00037]


title: scRNA-seq-sgTP53-RB1-Veh

value: LNCaP/AR

value: prostate cancer cells


title: WT_f_our_1_S19

value: tCX3CR1+ MF


title: A375_Control_R1_HiC

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering
Iterative correction was performed using method described by Imakaev et al and cworld-dekker package avaolable on GitHub.
All processed Hi-C contact maps were scaled to a sum of 1 million using cworld-dekker package on HitHub.
Genome_build: hg19

source_name: Skin epithelium

growth_protocol: Melanoma (A375) cells were grown to confluency under normal conditions. For the transwell experiments, 100000 cells suspended in media with no supplements were pippetted into the transwell and incubated for a 24 hr period. After incubation, migration efficiency was measured and highly migratory (Bottom) and non-migratory (Top) were isolated and grown until confluency. This experiment was repeated in tranwells with 5 and 12μm pore sizes for 10 rounds (Top5, Bottom5, Top12, Bottom12) and 20 rounds (Top20-5, Bottom20-5).

extract_protocol:
Briefly, 5 million of A375 cells subpopulations were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing.
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: A375 subpopulations were grown to confluency and were crosslinked with 1% formaldehyde for subsequent HiC experiments.

tag: condition

value: Control

tag: media

value: DMEM,10%FBS,1% Pen-Strep, 1% L-Glut


title: CAD_25 [EP00442]

value: Whole blood

value: coronary artery disease (CAD)


title: scRNA-seq-sgNT-Veh


title: WT_f_tLC_1_S35

value: tongue

value: female


title: WT_f_Lyve_2_S37


title: CAD_23 [EP00413]

value: M


title: scRNA-seq-sgNT-Enz

value: enzalutamide 10µM


title: scRNA-seq-sgTP53-RB1-JAK1-Enz


title: KOF 1105

city: Atlanta

first: Jason

last: DeBruyne

state: GA

address: 720 Westview Dr, Research Wing 315

department: Pharmacology & Toxicology

institute: Morehouse School of Medicine

description: KOF 1105_S39_L003

data_processing:
sqeuncing and basecalling was done by Illumina HiSeq platform
Analyses were done using Illumina's BaseSpace platform
Adaptor trim (12 nt, 5' end) using FastQ toolkit 2.1.1
RNA Express (combination of STAR aligner and De-Seq) to align, count and perform differential analysis between groups
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing gene ID and transcript counts, input into DeSeq analysis

source_name: Siah2 ko_female_liver

extract_protocol:
Livers were removed, flash frozen in cold Isopentane (2-methylbutane), and RNA harvest using combined Trizol / RNEasy kit(Qiagen, cat#74104) methods. Equal amounts of RNA (determined using nanodrop)  were pooled from livers from 3 mice/time/genotype/sex for RNAseq.
Sequencing was done using the Lexogen Quant-Seq approach
Poly-A selectipon, single sequence/molecule from adaptor added to 5' side.

tag: strain background

value: Siah2 ko

value: liver


title: KOF 1104

description: KOF 1104_S38_L003


title: A375-Top5


title: CAD_24 [EP00425]


title: 6A3_E2_Plus_DOX_Plus_ICI_Non_Invaded_cells_replicate_2

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
Cell line expressing doxycycline inducible constitutively active IKKβ constuct
quant_counts.txt

data_processing:
bulk RNA-seq: Raw reads were mapped to the reference using STAR. Ensembl gene expression was quantified using featureCounts.
scRNA-seq: Raw R2 reads were mapped to the reference transcriptome (hg38  Ensembl gene sequences, exonic only) using BWA MEM. Cell barcodes and UMIs were extracted from R1 using a custom pipeline following OneCellBio adapter design for inDrop. Unique UMI counts were summed for each gene and each unique cell barcode. Only cell barcodes with >500 counts included in the final counts table.
Genome_build: bulk RNA_seq: hg38 (full genome)
Genome_build: scRNA-seq: hg38 Ensembl gene sequences (exonic only)
Supplementary_files_format_and_content: Counts table: Tab-delimited text of counts per gene. Genes down the rows, samples or cells across the columns.
Supplementary_files_format_and_content: Cell list: Tab-delimited text of cell name (matches columns in scRNA-seq counts tables), barcode, number of genes expressed, and UMI counts. All cell barcodes are listed in this file, including those below the 500 count minimum.

source_name: MCF-7 cell line

growth_protocol: Cells were cultured for 3 days in Charcoal depleted RPMI 1640 containing charcoal depleted 5% fetal bovine serum, 1% penicillin–  streptomycin, 1% nonessential amino acids and 2 mmol/L L-glutamine.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Micro Kit
Library prep was carried out using Universal Plus mRNA-Seq Kit, with purification steps done using Agencourt AMPure XP Beads.

treatment_protocol: Cell were treated for 3 days with E2+Doxycycline, then treated +/- ICI during invasion.

tag: library type

value: bulk RNA-seq

value: Breast

value: E2 + Doxycycline + ICI during invasion


title: CAD_22 [EP00410]


title: IRF8_ko, scRNA-seq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Interstitial cells were isolated with collagenase / hyaluronidase  digestion and CD45+ were purified by FACS and analyzed with Chromium™ Single Cell 3’ Reagent Kits v3.1.
scRNA-Seq libraries were prepared according to 10X Chromium manual

value: ex vivo


title: 6A3_E2_Plus_DOX_Plus_ICI_Non_Invaded_cells_replicate_1


title: LPS, scRNA-seq

description: 10x Genomics

extract_protocol:
Interstitial cells were isolated with collagenase / hyaluronidase  digestion and  tongue  Langerhans cells were isolated with dispase digestion. Both preparations were pooled and CD45+ cells were purified by FACS and analyzed with Chromium™ Single Cell 3’ Reagent Kits v3.1.
scRNA-Seq libraries were prepared according to 10X Chromium manual

value: LPS


title: WTF 1091

description: WTF 1091_S36_L003

source_name: wild type_female_liver

value: wild type


title: WTF 1090

description: WTF 1090_S35_L003


title: newborn, scRNA-seq

description: 10x Genomics

value: newborn (p3)


title: WTF 1089

description: WTF 1089_S34_L003


title: 6A3_E2_Plus_DOX_Plus_ICI_Invaded_cells_replicate_2


title: CAD_20 [EP00311]


title: CAD_19 [EP00296]


title: adult, scRNA-seq

description: 10x Genomics

value: adult


title: KOM 1081

description: KOM 1081_S51_L003

source_name: Siah2 ko_male_liver

value: male


title: KOF 1070

description: KOF 1070_S37_L003


title: 6A3_E2_Plus_DOX_Minus_ICI_Invaded_cells_replicate_2

value: E2 + Doxycycline


title: CAD_16 [EP00261]

value: Whole blood

value: coronary artery disease (CAD)


title: TFAP2E CR 017

description: CUT&RUN library

data_processing:
Library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25
Alignment, bowtie2 v2.4.2, “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Filtering, samtools v1.10 view "-f 2 -F 780 -bh", sort, index
Peak calling, MACS2 v2.2.7.1 "-f BAMPE -g 3e9 -q 0.05 --call-summits"
Generate bigwigs, bamCoverage "--outFileFormat bigwig --binSize 5 --normalizeUsing RPKM"
Genome_build: UCSC mm10
Supplementary_files_format_and_content: .bigwig files displaying read coverage across the genome

source_name: mouse P10 VNO dissection

tag: developmental stage

tag: target

tag: cre

value: OMPCre

value: vomeronasal organs


title: KOM 1075

description: KOM 1075_S49_L003

tag: Sex


title: ISCs-VSG ileum [B9 Ile VSG]

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Ile.csv
B9 Ile VSG

data_processing:
The sequencing reads were aligned to the mouse genome (mm10). RNA-sequencing reads were mapped to genome release using STAR (v2.5.3a)
transcript quantification was performed using Salmon (v0.6.0)
Normalization and differential expression analysis were performed using DESeq2. The Benjamini-Hochberg method was used for multiple testing corrections.
To define genes altered by VSG vs. sham, samples from each of the regional segments (duodenum, jejunum, and ileum) were analyzed separately.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2_normalized_counts
Supplementary_files_format_and_content: DESeq2_differential_analysis

source_name: Lgr5+ intestinal epithelial cells

extract_protocol:
Total RNA was isolated from Lgr5+ cells, which were sorted by GFP expression, were using the Total RNA Purification Kit (Norgen Biotek). RNA was quantified with the Nanodrop 2000 (ThermoFisher), and RNA integrity was assessed by the Agilent 4200 Tapestation (Agilent Technologies).
Libraries were prepared using NEBNext Ultra II Directional Library Prep Kit (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on the NextSeq500 platform (Illumina; single end; 85 nt) at the Biotechnology Research Center at the Cornell University (Ithaca, NY, USA).

value: Lgr5+ intestinal epithelial cells

tag: strain

value: Lgr5eGFP mouse

value: ileum

value: VSG


title: CAD_21 [EP00397]

tag: group

value: F

tag: age


title: 6A3_E2_Plus_DOX_Minus_ICI_Non_Invaded_cells_replicate_1

value: bulk RNA-seq

tag: tissue

value: Breast

tag: cell line


title: CAD_14 [EP00191]

value: M

tag: sequencing batch


title: ISCs-Sham ileum [B1 Ile Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Ile.csv
B1 Ile Sham

tag: cell type

value: Sham


title: WTM 1055

description: WTM 1055_S46_L003

source_name: wild type_male_liver

tag: genotype

value: wild type

value: liver


title: TFAP2E CR 016

description: CUT&RUN library


title: WTM 1087

description: WTM 1087_S48_L003

value: male


title: CAD_18 [EP00286]


title: 6A3_E2_Plus_DOX_Minus_ICI_Non_Invaded_cells_replicate_2

tag: treatment

value: E2 + Doxycycline


title: KOM 1076

description: KOM 1076_S50_L003

value: Siah2 ko


title: A375-Bottom5_R2

description:
Bottom-5
Normalized_counts_file_on_Bottom5_vs_Control.tabular.txt

data_processing:
Quality trimming of the reads was performed using BBTools and any reads with a lower than 28 quality score were discarded
Reads were then aligned using STAR alignment with default parameters with an average alignment rate of 89%.
The aligned reads were then sorted by genomic position and feature counts was performed using htseq 0.11.1.  Differential expression of genes was determined by using DESeq through Galaxy
Genome_build: hg19

source_name: Skin Epithelium

extract_protocol:
For Control, Top-5 and Bottom-5, RNA was extracted using Qiagen RNAeasy plus mini kit. RNA libraries were prepared using NebNext Ultra II RNA library prep Kit. For Top20-5, Bottom20-5, Top-12 and Bottom-12, RNA was extracted using the Qiagen RNAeasy plus mini kit as described above. Total RNA was then sent for library preparation and sequencing at GeneWiz.
RNA libraries were prepared using NebNext Ultra II RNA library prep Kit (Cat. No. E7770G). After rRNA depletion, RNA was fragmented (~200 nt) and primed following first and second strand cDNA synthesis. The double stranded cDNA was then purified using AmpureXP beads at a 1.8X concentration. After purification, cDNA libraries were end prepped, ligated adapter and PCR amplified for 7 cycles to enrichment for adaptor ligated DNA using NebNext Multiplex Oligos for illumine (Cat. No. E7335G). cDNA librariers were then purified using AmpureXP beads at a 0.9X concentration and their quality was checked using Agilent Bioanalyzer high sensitivity DNA kit. cDNA samples were then sent to Oklahoma Medical Research Facility (OMRF) for high throughput sequencing.

value: Skin Epithelium


title: ISCs-VSG ileum [B8 Ile VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Ile.csv
B8 Ile VSG


title: WTM 1086

description: WTM 1086_S47_L003


title: A375-Top5_R2

description:
Top-5
Normalized_counts_file_on_Top5_vs_Control.tabular.txt


title: 6A3_E2_Plus_DOX_Plus_ICI_Invaded_cells_replicate_1

value: E2 + Doxycycline + ICI during invasion


title: ISCs-Sham ileum [B10 Ile Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Ile.csv
B10 Ile Sham


title: CAD_17 [EP00262]

source_name: Peripheral blood

value: Whole blood

value: coronary artery disease (CAD)


title: ISCs-Sham jejunum [B1 Jej Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
B1 Jej Sham

value: Lgr5+ intestinal epithelial cells

value: Lgr5eGFP mouse

value: jejunum


title: CAD_15 [EP00226]

value: F


title: MKO-18

description: RNA pooled from livers harvested 3 replicate animals

data_processing:
The reads were mapped to the mouse MGSCv39-mm9 genome using Tophat 2.1.0.
Expression levels were assessed using Cufflinks 2.2.1, which calculates raw counts and the number of fragments per kilobase per million (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Siah2 KO_Male_ZT18_liver

extract_protocol:
Livers were removed, flash frozen in cold Isopentane (2-methylbutane), and RNA harvest using combined Trizol / RNEasy kit(Qiagen, cat#74104) methods. Equal amounts of RNA (determined using nanodrop)  were pooled from livers from 3 mice/time/genotype/sex for RNAseq.
These RNA pools were converted into sequencing libraries by using Illumina TruSeq stranded mRNA Library Prep kits

value: Liver

value: Male

value: Siah2 KO

tag: time point


title: A375-Top5_R1


title: CAD_13 [EP00182]

value: M


title: A375-Bottom5_R1


title: MKO-21

source_name: Siah2 KO_Male_ZT21_liver


title: ISCs-VSG jejunum [B8 Jej VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
B8 Jej VSG

value: VSG


title: 6A3_E2_Plus_DOX_Minus_ICI_Invaded_cells_replicate_1

value: bulk RNA-seq

value: Breast


title: CAD_12 [EP00163]


title: CAD_11 [EP00149]


title: MKO-15

source_name: Siah2 KO_Male_ZT15_liver


title: ISCs-VSG jejunum [B14 Jej VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
B14 Jej VSG


title: A375-Control-R1

description: Control


title: MKO-12

source_name: Siah2 KO_Male_ZT12_liver


title: CAD_10 [EP00144]


title: ISCs-VSG jejunum [B13 Jej VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
B13 Jej VSG


title: A375_Bottom12_R2_HiC

tag: condition

tag: media

value: DMEM,10%FBS,1% Pen-Strep, 1% L-Glut


title: CAD_09 [EP00126]


title: MKO-9

source_name: Siah2 KO_Male_ZT9_liver


title: A375_Bottom12_R1_HiC


title: ISCs-Sham jejunum [B10 Jej Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
B10 Jej Sham

value: Sham


title: ISC-VSG jejunum [A12 Jej VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Jej.csv
A12 Jej VSG


title: MKO-6

source_name: Siah2 KO_Male_ZT6_liver


title: CAD_07 [EP00109]


title: A375_Top12_R2_HiC


title: MKO-3

source_name: Siah2 KO_Male_ZT3_liver


title: ISC_duodenum_VSG replicate #4 [B8 Duo VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
B8 Duo VSG

value: duodenum


title: CAD_06 [EP00101]


title: A375_Top12_R1_HiC

source_name: Skin epithelium


title: MKO-0

source_name: Siah2 KO_Male_ZT0_liver


title: ISC_duodenum_sham replicate #2 [B1 Duo Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
B1 Duo Sham


title: ISC_duodenum_VSG replicate #3 [B14 Duo VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
B14 Duo VSG


title: MWT-21

source_name: wild type_Male_ZT21_liver

value: wild type


title: A375_Top20-5_R1_HiC


title: ISC_duodenum_sham replicate #1 [B10 Duo Sham]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
B10 Duo Sham


title: CAD_03 [EP00050]

value: Whole blood


title: MWT-12

source_name: wild type_Male_ZT12_liver


title: CAD_01 [EP00004]

value: coronary artery disease (CAD)


title: ISC_duodenum_VSG replicate #1 [A12 Duo VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
A12 Duo VSG

value: Lgr5+ intestinal epithelial cells


title: CAD_02 [EP00031]


title: A375_Bottom5_R2_HiC


title: ISC_duodenum_VSG replicate #2 [B13 Duo VSG]

description:
NEBNext Ultra II Directional Library Prep Kit
DESeq2_normalized_counts_Duo.csv
B13 Duo VSG

value: Lgr5eGFP mouse


title: CAD_04 [EP00063]


title: CAD_08 [EP00125]


title: MWT-15

source_name: wild type_Male_ZT15_liver


title: day3_m2e_Tcells_VDJ

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

institute: KTH

data_processing:
Basecalling was performed using Illumina Casava v.1.8 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences.
Read quality was accessed using FASTQC.
UMI counts for both RNA and VDJ were estimated at the transcript level using Cellranger v2.2
Genome_build: mm10
Supplementary_files_format_and_content: We provide individual gene expression matrix files for each sample (output from Cellranger) as well the filtered VDJ annotation table (also output from Cellranger)

extract_protocol:
Lungs were extracted and collected. Single cell suspensions of lung lymphocytes were prepared with the lung dissociation kit from Miltenyi Biotec (ref 130-095-927). Briefly, the harvested lungs were first added into the gentleMACS C tubes containing enzyme mix and broken up into smaller pieces with gentleMAC OctoDissociator (m_lung_01 program). The samples were then incubated at 37°C for 30 minutes before the complete digestion on gentleMAC OctoDissociator (m_lung_02 program), after which, the cell suspensions were washed once with PBS, passed through a mesh and resuspended in appropriate media for further processing. We assessed the CD4+ T cell response in BALB/c mice after immunizations (day 3 and day 8, post infection with influenza A virus) by flow cytometry using the PE-labeled M2e-tetramer, designed and produced by the NIH Tetramer Core Facility.
Sorted lung M2e-teramer+ TCRb+ T cells (CD19-, CD8- F4/80-) from 5 mice at each time point were directly loaded onto a Chromium chip (10X Genomics) and run on the Chromium Controller for droplet generation.
Reverse transcription was conducted in droplets and cDNA recovered through demulsification and bead purification. Pre-amplified cDNA further went through 10X library preparation for quantification of both mRNA and VDJ sequences {10.1038/nprot.2018.021} using 10X genomics v2 Chemistry kit. Libraries were sequenced on an Illumina Nextseq500 (High Output) targeting a minimum depth of 10,000 reads per cell across all samples.

treatment_protocol: Three immunizations with 5μg CTA1-3M2e-DD in sterile PBS were done with 10 days between the doses. Mice were sacrificed 6 months after the final immunization 3 or 8 days after an influenza A virus challenge infection. Influenza A virus challenge experiments were performed using a lethal dose of 4x LD50 of the mouse-adapted X47(H3N2) virus strain (a reassortant between A/Victoria/3/75 (H3N2) and A/Puerto Rico/8/34 (H1N1)) administrated i.n. to mice under light anaesthesia.

value: lung

tag: mouse strain

value: Balb/c

value: M2e+ CD4+ TCRb+ T cells


title: A375_Top5_R1_HiC


title: day8_m2e_Tcells_VDJ


title: A375_Top5_R2_HiC


title: A375_Bottom5_R1_HiC


title: A375_Control_R2_HiC

value: Control


title: MWT-9

source_name: wild type_Male_ZT9_liver

value: Liver

value: Male


title: CAD_05 [EP00085]

value: M


title: day8_m2e_Tcells


title: MWT-3

source_name: wild type_Male_ZT3_liver


title: MWT-18

source_name: wild type_Male_ZT18_liver


title: SG3-R1

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

data_processing:
The CLC Genomics Workbench version 11.01 was used for bioinformatics analyses. All libraries were trimmed from any vector or adapter sequences remaining.  Low quality reads (quality score below 0.05) and reads with more than two ambiguous nucleotides were discarded.
The genome sequence of this species is not available and we used de novo assembly to process this data. The contigs arising from the de novo assembly were used as a reference set of transcripts for RNAseq analysis. Short-read sequence data from the SG of root-exposed and control (starved) larvae was separately mapped against the reference set of assembled transcripts using the CLC Genome Workbench RNAseq function (min. length fraction=0.9, maximum mismatches=2).
The relative expression levels were output as RPKM (Reads Per Kilobase of exon model per Million mapped reads) values, which considers the relative size of the transcripts and only uses the mapped-read datasets (i.e. it excludes the non-mapped reads) to determine relative transcript abundance.
To explore the differential expression profile between two groups of samples in CLC genomic workbench, each gene is modelled by a separate Generalized Linear Model (GLM). The use of the GLM formalism allows the fitting of curves to expression values without assuming that the error on the values is normally distributed. The Wald Test was also used to compare each sample against its control group to test whether a given coefficient is non-zero. We considered genes with more than 2-fold changes and a false discovery rate (FDR) of less than 0.05 as significantly modulated genes.

organism: Inopus flavus

source_name: larval salivary gland

growth_protocol: Soldier fly (Inopus sp. near falvus) larvae were collected from an infested sugarcane field near Hay Point, Queensland (21°18' 5"S, 149 °14' 7"E). In February 2018, stools were dug from the ground and large larvae were manually collected from the roots and associated soil. Larvae were transferred to aerated 480 ml polypropylene containers with soil collected from the same sugarcane field and transported to the laboratory and used in experiments within 2 days.

extract_protocol:
Qiazol (R)  was used for RNA extraction according to manufacture instruction (QIAGEN; Cat No.: 79306). The RNA samples were treated with DNase I for 1 h at 37°C and then their concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel.
The PCR-based cDNA libraries were prepared using the illumine TrueSeq cDNA library construction kit.

treatment_protocol: The larval body surfaces were disinfected by soaking in 75% Ethanol for 30s and then rinsing in phosphate-buffered saline (PBS) before dissecting out the salivary glands. The salivary glands (SG) were extracted by pulling out the head capsule and removing all other tissues, such as fat body droplets. The SG tissue from 20 larvae (representing one biological replicate) were pooled together and transferred to Qiazol lysis reagent for RNA extraction.

value: Exposed to plant root


title: MWT-0

source_name: wild type_Male_ZT0_liver


title: A375_Bottom20-5_R1_HiC


title: MWT-6

source_name: wild type_Male_ZT6_liver


title: day3_m2e_Tcells


title: SG2-R1


title: FKO-21

source_name: Siah2 KO_Female_ZT21_liver

value: Female

value: Siah2 KO


title: CCA1_rep2

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

data_processing:
Paired raw reads were trimmed with Trimmomatic-v.0.36 with default parameters. The remaining reads were aligned to ensemble 1.0 genome using Bowtie v2.3.4 with the following parameters: “bowtie2-X1000–very-sensitive”. Aligned reads were sorted and filtered with MAPQ>10 using SAMtools v1.9 and duplicated reads were removed using Picard version v2.16.0 (http://broadinstitute.github.io/picard/). MACS2 was used to define DNase I hypersensitive site (DHS) regions and DAP-seq peaks with the “--keep-dup all” function. DAP-seq peaks were filtered with “Fold enrichment > 5 and FDR < 1e-5” and DHS peaks with “Fold enrichment > 2 and FDR < 1e-2”. DAP-seq peaks which were overlapped >1bp with DHS (bedtools v2.29.0) were further used.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: peak files

organism: Triticum aestivum

source_name: Triticum aestivum 2-weeks-old seedlings

growth_protocol: 16h light  22°C, 8h dark 19°C

extract_protocol:
genomic DNA
DAP-seq

treatment_protocol: DAP-seq assay was performed with purified MBP fusion protein. Briefly, 10 ug MBP fusion proteins were incubated with 100 ul amylose-coupled agarose resin in 1 X PBS at 4°C for 1h. The beads were collected by centrifugation at 500 g for 2 min. 1 ug sonicated DNA (300 bp-1000 bp) were then co-incubate with the beads in 1 X PBS+0.1% NP40 at 25°C for 30 min. DNA were then purified and library were constricted with Nextera DNA Library Prep Kit (Illumina FC-121-1031).

value: leaves

tag: cultivar

value: Fielder


title: FKO-18

source_name: Siah2 KO_Female_ZT18_liver


title: CCA1_rep1


title: C3-R1

value: Starved


title: FKO-12

source_name: Siah2 KO_Female_ZT12_liver


title: SG1-R1


title: FKO-15

source_name: Siah2 KO_Female_ZT15_liver


title: MHP23Y

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta (release 95) pre-mRNA genome and GRCh38 pre-mRNA genome by Cell Ranger count (v3.0.2).
Alignment results of macaque data and human data were separately aggragated by Cell Ranger aggr (v3.0.2).
Aggragated data of macaque and human were separately read into scanpy.
Genome_build: macaca mulatta release 95
Genome_build: GRCh38
Supplementary_files_format_and_content: The file MHP_year4_11_23_raw.h5ad and HHP_year69_92_raw.h5ad are both formatted by h5ad (created by scanpy), contain the 3 macaque samples and 2 human samples, respectively.

organism: Macaca mulatta

source_name: macaque hippocampus

extract_protocol:
hippocampal formation samples were homogenized in nuclei lysis buffer, isolated nuclei were loaded on 10X Genomics system.
Chromium Single Cell 3' Reagent Kits v3

value: 23 years old

value: hippocampus


title: HSP90a treated mono, biological replicate 7

city: Mannheim

first: Feyza Gul

middle: Ozbay

last: Kurt

address: Theodor-Kutzer-Ufer 1-3

department: Skin Cancer Unit

institute: German Cancer Research Center/ Mannheim University Medical Center

description: Gene expression data from human monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

hyb_protocol: Labeled cRNA is then randomly fragmented and then added to the array for hybridization.

scan_protocol: The entire array is scanned with Agilent Microarray Scanning system with a laser and the information is kept in a computer for quantitative analysis.

data_processing: Two experiments were performed at different times. Samples 1-3 (control) and 8-10 (HSP90α treated) are from the same experiment/array. Samples 4-7 (control) and 11-14 ( HSP90α treated) are from the same experiment/array. Affymetrix CEL files were RMA normalized and expression values log2-transformed. All arrays were normalized together and experiment effect was adjusted. Differentially expressed probesets/genes between groups were identified using the empirical Bayes approach based on moderated t-statistics as implemented in the Bioconductor package limma accounting for batch effects. Gene set enrichment analysis was performed using the camera test. KEGG, Reactome and gene ontology data bases were used in pathways analysis. An enrichment map was used to visualize results from pathway tests. All p-values were adjusted for multiple testing using the Benjamini-Hochberg correction in order to control the false discovery rate. All analyses were performed with statistical software R 4.0 using the add-on package EnhancedVolcano.

label: Biotin

source_name: Human peripheral blood monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human monocytes were isolated from peripheral blood mononuclear cells (PBMC) from buffy coats of healthy donors

extract_protocol: Total RNA from 24h treated monocytes was isolated using Rneasy Kit from Qiagen (Hilden, Germany) according to manufacturer`s instructions. RNA concentration was determined by the microplate reader Tecan Infinite M200 using a Nanoquant plate. The quality of total RNA was confirmed by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Quality and concentration of all samples were checked again on Nanodrop ND-1000, Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany). Microarray experiment were performed at Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ) in Heidelberg, Germany.

treatment_protocol: HSP90a treated monocyte: Human monocytes were treated with recombinant HSP90α (2µg/mL) in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h. Control monocytes: Human monocytes were incubated in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h.

value: Peripheral blood

tag: disease

value: Healthy donor


title: FKO-9

source_name: Siah2 KO_Female_ZT9_liver


title: C1-R1


title: input_rep2


title: HSP90a treated mono, biological replicate 5


title: C2-R1


title: input_rep1


title: HSP90a treated mono, biological replicate 6


title: FKO-6

source_name: Siah2 KO_Female_ZT6_liver


title: MHP11Y

value: 11 years old


title: untreated mono, biological replicate 7

description: Gene expression data from human monocytes incubated in RPMI medium for 24h

source_name: Human peripheral blood monocytes incubated  in RPMI medium for 24h


title: HSP90a treated mono, biological replicate 3


title: untreated mono, biological replicate 6