title: Rat, ADSC-EVs, rep2

city: Shanghai

first: Yanquan

address: 1567#, Jinqian Road, Shanghai, China

institute: International Peace Maternity and Child Health Hospital

description: Library name: ADSC_EV_2

data_processing:
A cDNAlibrary constructed by technology from the pooled RNA from samples of this study was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt  (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing polyA and polyG;  3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value below 20) bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).  including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Assembly: mRatBN7.2
Supplementary files format and content: genes_fpkm_expression.xlsx. Files include FPKM and count values for each Sample.
Supplementary files format and content: genes_fpkm_expression_text.txt The FPKM values and differential expression analysis of genes across all samples were performed.

organism: Rattus norvegicus

source_name: Adipose-derived mesenchymal stem cells

growth_protocol: Adipose-derived mesenchymal stem cells were extracted from the inguinal region of rats. After being cultured in vitro, the extracellular vesicles in the supernatant were collected.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5 ug of total RNA was used for the construction of sequencing libraries.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with DV200 ＞30% or RIN number ＞4.0, and confirmed by electrophoresis with denaturing agarose gel. Using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Kit (Takara Bio USA, Inc.), using 10-50 ng RNA as the starting template, adding SMART Pico Oligos Mix, denaturing at 72℃ for 3 minutes, using Template Switching Oligo Mix (TSO mix) as the reverse transcription primer, the reverse transcription reaction was carried out at a temperature of 42℃ for 90 min. The reverse transcript from the previous step was amplified by the SeqAmp DNA Polymerase system for 5 cycles of PCR, adding sequencing linkers and tag sequences. Then the amplified DNA-seq library is purified by immobilization onto pure beads. Then resuspend using ZapR-Master-Mix to obtain a first round of rough libraries. Add R-Probes v2 for denaturation, followed by ZapR™ v2 for 60 min incubation at 37℃ to remove the cDNA sequence of ribosomal RNA reverse transcription. Amplify the ribosomal removed product with universal two-terminal primers, and select the corresponding number of cycles according to the initial amount and nucleic acid quality. The reference number of cycles is 12-16. The amplified DNA library is purified again using purification beads and resuspended in nuclease-free water to obtain the final library. Finally, we conducted dual-end sequencing on the Illumina Novaseq™ 6000 (LC Bio Technology Co., Ltd., Hangzhou, China) following standard operating procedures, with the sequencing mode set as PE150.

value: Adipose-derived mesenchymal stem cells

value: mesenchymal stem cells

tag: cellular substructure

value: Extracellular vesicle

value: wild type

value: Extracellular vesicle extraction


title: ChIP_anti_SMC_BWX5297_42C_IPTG25min_HPUra10min_T25

status: Public on Jul 07 2025

type: SRA

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

tag: cell line

value: Bacillus subtilis PY79

tag: cell type

value: Bacterial

tag: genotype

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

tag: treatment

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 10min


title: P14 terminal Tex ICOSneg #1

city: New York

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgICOS-1-1

library_source: transcriptomic

data_processing:
Raw reads were quasi-mapped to the Gencode M25 (GRCm38.p6) gene set using salmon v.1.2.1 (Patro et al., 2017).
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: .tar.gz - folder containing table of gene expression counts and TPM generated by salmon in .sf format

molecule: polyA RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Cells were sorted in lysis reagent (QIAGEN). After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).
1 ng RNA from 10,000 sorted cells was used as input for the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB).

tag: tissue

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: terminal Tex

tag: genetic modification

value: Icos KO (Icos sgRNA #1)

tag: biological replicate

value: biol rep 1

tag: disease state

value: LCMV chronic infection (40DPI)


title: Rat, ADSC-EVs, rep1

last: li

country: China

description: Library name: ADSC_EV_1

molecule: total RNA


title: P14 terminal Tex Ctrl #3

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgF8-2-1

value: WT (non-targeting sgRNA #2)


title: PBMCs from NSCLC Patient HD4 RNA (Multiome [RNA + ATAC])

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
10x Genomics
hs_multiome_PBMC_HD4_RNA

library_source: transcriptomic single cell

data_processing:
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).

molecule: nuclear RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Human: PBMCs were subjected to nuclei isolation following 10x  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Human: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol: Human: CD34 positive cells were bead-enriched or sorted (based on surface markers described in Methods section) from isolated PBMCs of patients with NSCLC or healthy donors, and combined with the original isolated PBMCs.

value: Blood

value: healthy donor


title: ChIP_anti_SMC_BWX5297_42C_IPTG20min_HPUra5min_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 5min


title: SFA VMCs, 24 months, replicate 2

city: Bryan

first: Andreea

last: Trache

state: TX

address: 402 John Sharp Pkwy

department: Medical Physiology

institute: Texas A&M University

description:
Library name: Sample 5
SMVC_Old_2

data_processing:
Snakemake workflow manager
FASTQ files were trimmed of any adapter, barcode, or low quality (Phred < 20) sequenced using Cutadapt (v3.5)and FastQC (v0.11.9) with the TrimGalore (v0.6.7) wrapper. MultiQC (v1.27.1) was used to compile FASTQ quality metrics pre- and post-trimming to visually confirm the removal of non-biologically relevant and low-quality scoring bases that could impact mapping and quantification steps
Trimmed reads were then mapped to the R. norvegicus (v6.0) reference genome assembly (RefSeq: GCF_000001895.5) using the STAR (v2.7.10b) aligner. Gene-level counts corresponding to annotated gene models from the R. norvegicus GTF (RefSeq: GCF_000001895.5) file were extracted from the STAR-aligned BAM files using featureCounts form the Subread (v2.0.8) package. Gene-level count tables were used for downstream statistical testing.
DESeq2 (v1.46.0) was used to identify differentially expressed genes between the old and young age groups. First gene-level count tables for each sample were combined into a single count matrix in R. A dds object was created with the gene-level count matrix and the model design “~ Age”.  The young samples were leveled as the reference for all downstream hypothesis testing. To focus DGE testing on genes with a moderate level of detectable expression in at least one of the two age groups, low count genes were filtered from the dds object. These low count level genes were removed if they had a total count of less than 10 in at least three of the six samples tested. After standardization and model fitting, differential expression testing was conducted using the Wald’s test. DEGs were identified as those displaying a Benjamini-Hochberg (BH) corrected p-value (p-adj) < 0.05 and a |log2 Fold change| ≥ 1.
DOSE (v4.0.0), clusterProfiler (v4.14.4) , and org.Rn.eg.db (v3.20.0) R packages were used to perform annotated pathway enrichment from the DEGs identified in the RNA-sequencing data. Significantly enriched terms were identified as having a Benjamini-Hochberg (BH) corrected p-value (p-adj) < 0.05 and a fold enrichment of > 0.
Assembly: GCF_000001895.5
Supplementary files format and content: raw counts of STAR mapped reads extracted with featureCounts for all samples in a single csv file.

source_name: soleus feed arteries

extract_protocol:
Total RNA was extracted from cultured VSM cells isolated from both young and old SFA using TRIzol (15596026, Thermo Fisher, Waltham, MA) according to the manufacturer’s protocol. RNA concentration was determined using a Qubit fluorometer (Thermo Fisher, Waltham, MA), and RNA integrity was assessed with an Agilent TapeStation using RNA ScreenTape (5067-5579, Agilent, Lexington, MA). Samples with sufficient quality were normalized to a final concentration of 20 ng/µL for library preparation.
Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (20020594, Illumina, San Diego, CA) following the manufacturer’s instructions. Libraries were then quantified, normalized, and pooled at equimolar concentrations for sequencing. The RNA libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) platform in a 2x100bp approach. Total sequencing depth ranged from 26.9M – 33.1M reads per sample.

value: soleus feed arteries

value: vascular smooth muscle cells


title: SFA VMCs, 24 months, replicate 3

description:
Library name: Sample 6
SMVC_Old_3


title: PBMCs from NSCLC Patient Lu1032 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1032_RNA

value: lung adenocarcinoma


title: P14 terminal Tex Ctrl #2

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgF8-1-2

value: WT (non-targeting sgRNA #1)

value: biol rep 2


title: P14 terminal Tex Ctrl #4

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgF8-2-2


title: ChIP_anti_SMC_BWX5297_42C_noreplisome_IPTG25min_T25

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 25min


title: SFA VMCs, 24 months, replicate 1

description:
Library name: Sample 4
SMVC_Old_1


title: HiC_BWX5230_30C_T15

value: parSdelta9 no a.b., -27degree parS no a.b., dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: ChIP_anti_SMC_BWX5297_42C_HPUraIPTG25min_T50

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 25min


title: Rat, ADSC-EVs, rep3

description: Library name: ADSC_EV_3

value: Adipose-derived mesenchymal stem cells

value: mesenchymal stem cells

value: Extracellular vesicle

value: wild type

value: Extracellular vesicle extraction


title: PBMCs from NSCLC Patient Lu1027 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1027_RNA

value: Blood


title: P14 terminal Tex Ctrl #1

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgF8-1-1

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: terminal Tex

value: biol rep 1

value: LCMV chronic infection (40DPI)


title: ChIP_anti_SMC_BWX5297_42C_IPTG50min_T50

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 35min


title: SFA VMCs, 4 months, replicate 2

description:
Library name: Sample 2
SMVC_Young_2

value: soleus feed arteries

value: vascular smooth muscle cells


title: ctrl-3

city: nanjing

first: xiaoyun

last: chen

state: nanjing

address: nanjing

institute: xiangya

data_processing:
Rawreads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads.  Clean reads for each sample were retained for subsequent analyses.  Thecleanreads were mapped to the reference genome using HISAT2.  FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.  PCA analysis was performed using R (v 3.2.0) to evaluate the biological duplication of samples.  Differential expression analysis was performed using the DESeq2.  Qvalue  < 0.5 or foldchange ＞2 was the threshold for significantly differential expression genes (DEGs).  Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.  The radar map of the top 30 genes was drawn to show the expression of up-regulated or down-regulated DEGs using an R packet grader.  Based on the hypergeometric distribution, GO, KEGG pathway, Reactome, and WikiPathwaysenrichment analysis of DEGs were performed to screen the significant enriched termusingR(v3.2.0), respectively.  R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: blood

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bp paired-endreadswere generated.

treatment_protocol: Neutrophils were treated with control or conditional medium for 21 hours. The control medium is the culture supernatant collected from untreated fibroblasts, whereas the conditional medium is the supernatant obtained from fibroblasts stimulated with IL-1β.

value: blood

value: Primary neutrophil

value: Neutrophil

value: control


title: SFA VMCs, 4 months, replicate 3

description:
Library name: Sample 3
SMVC_Young_3


title: PBMCs from NSCLC Patient Lu1024 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1024_RNA

value: lung adenocarcinoma


title: ChIP_anti_SMC_BWX5297_42C_IPTG45min_T45

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 30min


title: SFA VMCs, 4 months, replicate 1

description:
Library name: Sample 1
SMVC_Young_1


title: P14 effector-like Tex ICOsneg #4

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgICOS-2-2

value: spleen

value: effector-like Tex

value: Icos KO (Icos sgRNA #2)

value: biol rep 2


title: P14 effector-like Tex ICOsneg #3

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgICOS-2-1

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: biol rep 1

value: LCMV chronic infection (40DPI)


title: ChIP_anti_SMC_BWX5297_42C_IPTG40min_T40

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 25min


title: ctrl-2

value: blood


title: ctrl-1

value: Primary neutrophil


title: P14 effector-like Tex Ctrl #4

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgF8-2-2

value: WT (non-targeting sgRNA #2)


title: ChIP_anti_SMC_BWX5297_42C_IPTG25min_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 10min


title: conditional-culture-2

value: Neutrophil

value: conditional medium


title: he3

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

data_processing:
trim-galore,subread,featurecount
Assembly: hg38
Supplementary files format and content: csv

source_name: skin tumor

extract_protocol:
Trizol
Performed by Sangon

value: skin tumor

value: cancer cell

value: WT

value: DBIC+Hemin


title: he1


title: ChIP_anti_SMC_BWX5297_42C_IPTG30min_T30

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 15min


title: P14 effector-like Tex ICOsneg #1

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgICOS-1-1

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: effector-like Tex

value: Icos KO (Icos sgRNA #1)

value: biol rep 1


title: P14 effector-like Tex ICOsneg #2

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgICOS-1-2

value: biol rep 2

value: LCMV chronic infection (40DPI)


title: ChIP_anti_SMC_BWX5297_42C_IPTG20min_T20

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 5min


title: h3

value: Hemin


title: h2

value: skin tumor


title: he2

value: cancer cell


title: P14 effector-like Tex Ctrl #2

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgF8-1-2

value: WT (non-targeting sgRNA #1)


title: H-fib-control_3-1

source_name: dermis

treatment_protocol: Fibroblasts were treated with control or IL-1β (10 ng/mL) for 24 hours in 6-well plates.

value: dermis

value: Primary Fibroblast

value: Fibroblast

value: control


title: P14 effector-like Tex Ctrl #1

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgF8-1-1

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell


title: ChIP_anti_SMC_BWX5297_30C_IPTG15min_T15

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min


title: h1

value: WT


title: P14 Tpex ICOSneg #4

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgICOS-2-2

value: Tpex

value: Icos KO (Icos sgRNA #2)

value: biol rep 2

value: LCMV chronic infection (40DPI)


title: ChIP_anti_SMC_BWX5297_42C_IPTG35min_T35

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 20min


title: conditional-culture-3

value: blood

value: Primary neutrophil

value: Neutrophil

value: conditional medium


title: ChIP_anti_SMC_BWX5297_30C_IPTG10min_T10

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 10min


title: H-fib-control_2-1

value: dermis

value: Primary Fibroblast

value: Fibroblast

value: control


title: e3

value: skin tumor

value: cancer cell

value: WT

value: DBIC


title: ChIP_anti_SMC_BWX5297_T0

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: H-fib-control_1-1


title: P14 effector-like Tex Ctrl #3

description:
Poly-A purified RNA, stranded
sorted P14 effector-like Tex (CD45.1+ PD-1+ CD39+ CX3CR1+)
CX3CR1-sgF8-2-1

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: effector-like Tex

value: WT (non-targeting sgRNA #2)

value: biol rep 1

value: LCMV chronic infection (40DPI)


title: H-fib-IL1B_3-1


title: e2


title: e1


title: conditional-culture-1

value: blood

value: Primary neutrophil

value: Neutrophil

value: conditional medium


title: WGS_BWX5529_42C_T35

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 20min


title: P14 Tpex ICOSneg #1

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgICOS-1-1

value: Tpex

value: Icos KO (Icos sgRNA #1)


title: P14 Tpex ICOSneg #2

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgICOS-1-2

value: biol rep 2


title: c3

value: skin tumor

value: cancer cell

value: WT

value: Ctrl


title: H-fib-IL1B_1-1

value: dermis

value: Primary Fibroblast

value: Fibroblast


title: H-fib-IL1B_2-1


title: WGS_BWX5529_42C_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 15min


title: WGS_BWX5529_42C_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 10min


title: c2


title: P14 Tpex Ctrl #4

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgF8-2-2

value: spleen

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: WT (non-targeting sgRNA #2)

value: LCMV chronic infection (40DPI)


title: Adjacent normal lung cells from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu979_filtered_feature_bc_matrix.h5

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10; Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).
Library strategy: multiome (RNA + ATAC)

source_name: Lung adjacent normal

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scRNA-seq, cells were encapsulated following 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 protocol. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Human: CD45positive cells after sorting or bead-based enrichment were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC Kit v1.1 or Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. For human NSCLC sample multiome assays, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.
Human: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol:
Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.
Human: CD45 positive cells were bead-enriched from processed tissues (Lung Tumor/Lung adjacent normal/PBMC) of patients with NSCLC. In one patient, viable CD45 positive cells were sorted from respective tissues (Lung Tumor/Lung adjacent normal/PBMC), based on surface markers described in Methods section.

value: Lung adjacent normal


title: c1


title: P14 Tpex Ctrl #3

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgF8-2-1

value: Tpex

value: biol rep 1


title: WGS_BWX5529_42C_T20

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 5min


title: Adjacent normal lung cells from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu954_filtered_feature_bc_matrix.h5


title: WGS_BWX5529_42C_T40

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 25min


title: P14 Tpex ICOSneg #3

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgICOS-2-1

value: Icos KO (Icos sgRNA #2)


title: WGS_BWX5529_30C_T15

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: P14 Tpex Ctrl #1

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgF8-1-1

value: WT (non-targeting sgRNA #1)


title: P14 Tpex Ctrl #2

description:
Poly-A purified RNA, stranded
sorted P14 Tpex (CD45.1+ PD-1+ CD39neg)
Tpex-sgF8-1-2

value: biol rep 2


title: Adjacent normal lung cells from NSCLC Patient Lu952 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu952_filtered_feature_bc_matrix.h5


title: Sample_#6_1121_pre_aGVHD_collected_day_60_post_allo_HSCT

city: Lausanne

first: Evarist

last: Planet

address: Route Cantonale 15

country: Switzerland

institute: EPFL

description:
10x genomics
pre-aGVHD patient #6, Day 60, GVH_at_day_70, scRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: hg19
Supplementary files format and content: tab separated files and matrix files

source_name: Peripheral blood

extract_protocol:
PBMCs were diluted at a concentration of 500-1000 cells/ml in PBS 2% FCS and checked for viability and absence of significant doublets or aggregates. The cells were then loaded into a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA) in a NextGEM chip K (PN-1000286) together with beads, master mix reagents (containing RT enzyme and poly-dt RT primers)and oil to generate single-cell-containing droplets.Single-cell Gene Expression libraries were then prepared using ChromiumNext GEM Single Cell 5’ Kit v2.0 (PN-1000263) following the manufacturer’s instruction (protocol CG000331 Rev A). Quality control was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA high-sensitivity assay (Thermo) following manufacturer instructions.With this procedure, the cDNAs from distinct droplets harbor a distinct and unique 10x “cell barcode”.
The sequencing libraries were loaded onto an Illumina HiSeq 4000 paired-end FlowCell and sequenced at ca 50k reads/cell using read lengths of 26 nt for read1 and 90 nt for read2. The Cell Ranger Single Cell Software v5.0.0 was used to perform sample demultiplexing, barcode processing, and 5’ gene counting using default parameters and the human genome assembly GRCh19.

value: Peripheral blood

value: PBMC

value: allogenic hematopoietic stem cell transplantation (HSCT)


title: Sample_#7_1073_pre_aGVHD_collected_day_30_post_allo_HSCT

description:
10x genomics
pre-aGVHD patient #7, Day 30, GVH_at_day_48, scRNAseq


title: Sample_#8_1063_aGVHD_collected_day_30_post_allo_HSCT

description:
10x genomics
aGVHD patient #8, Day 30, GVH_at_day_18, scRNAseq


title: Adjacent normal lung cells from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu941_filtered_feature_bc_matrix.h5


title: Sample_#5_1052_pre_aGVHD_collected_day_30_post_allo_HSCT

description:
10x genomics
pre-aGVHD patient #5, Day 30, GVH_at_day_41,  scRNAseq


title: Adjacent normal lung cells from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu927_filtered_feature_bc_matrix.h5


title: WGS_BWX5529_T0

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: Tumor cells from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu979_filtered_feature_bc_matrix.h5

source_name: Lung tumor

value: Lung tumor


title: Sample_#4_963_control_collected_day_100_post_allo_HSCT

description:
10x genomics
Healthy control patient #4, Day 100, scRNAseq


title: WGS_BWX5297_42C_IPTG20min_HPUra5min_T20

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 5min


title: Sample_#4_963_control_collected_day_60_post_allo_HSCT

description:
10x genomics
Healthy control patient #4, Day 60, scRNAseq


title: Lung of naive mice (scATAC-seq)

description: 10x Genomics

library_source: genomic single cell

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10; Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).

source_name: Lung naive

value: Lung naive

value: immune

tag: strain

value: Naive

tag: time

value: late


title: WGS_BWX5297_42C_HPUraIPTG25min_T50

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 25min


title: Tumor cells from NSCLC Patient Lu952 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu952_filtered_feature_bc_matrix.h5


title: Bone marrow of tumor-bearing (KP) mice replicate 1 (scATAC-seq)

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow

value: Tumor-bearing


title: Sample_#3_1200_control_collected_day_100_post_allo_HSCT

description:
10x genomics
Healthy control patient #3, Day 100, scRNAseq


title: Blood of tumor-bearing (KP) mice (scATAC-seq)

description: 10x Genomics

value: Blood


title: WGS_BWX5529_30C_T10

value: parSdelta9 no a.b., -59degree parS no a.b, dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 10min


title: Sample_#3_1200_control_collected_day_60_post_allo_HSCT

description:
10x genomics
Healthy control patient #3, Day 60, scRNAseq

value: Peripheral blood

value: PBMC

value: allogenic hematopoietic stem cell transplantation (HSCT)


title: Tumor cells from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu927_filtered_feature_bc_matrix.h5

value: Lung tumor


title: WGS_BWX5297_42C_noreplisome_IPTG20min_T20

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 20min


title: McSCs, DMBA_rep 3

city: Tokyo

first: Yasuaki

last: Mohri

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling and preliminary quality analysis.
Low-quality reads and contaminations were filtered out before data analysis by Cutadapt (version 1.9.1). (1) remove the adapter sequences (2) remove the 5' or 3' end bases that contains N’s or of quality values below 20 (3) remove reads that are less than 75 bp long after trimming
Filtered data were subsequently aligned to the reference genome using Hisat2 (v2.0.1) (Nat Methods. 2015 Apr; Kim D, et al.) with default parameters.
Gene expression was calculated as FPKM (Fragments per kilo bases per million reads) based onread counts from HT-seq (V 0.6.1) (Mortazavi, 2008).
Supplementary files format and content: .xls file includes FPKM values

source_name: Skin

extract_protocol:
Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using SMARTER stranded RNA-Seq Kit

value: Skin

value: FACS-purified

value: Melanocyte stem cells

value: Dct-H2B-GFP KI/+

value: DMBA


title: Sample_#3_1200_control_collected_day_30_post_allo_HSCT

description:
10x genomics
Healthy control patient #3, Day 30, scRNAseq


title: WGS_BWX5297_42C_noreplisome_IPTG15min_T15

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 15min


title: Tumor cells from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu954_filtered_feature_bc_matrix.h5


title: PBMCs from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu954_filtered_feature_bc_matrix.h5

value: Blood


title: Bone marrow of tumor-bearing (KP) mice replicate 2 (scATAC-seq)

description: 10x Genomics

value: Bone marrow

value: immune

value: Tumor-bearing

value: late


title: WGS_BWX4310_42C_HPUraIPTG25min_T40

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 25min


title: PBMCs from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu979_filtered_feature_bc_matrix.h5


title: WGS_BWX5297_42C_IPTG25min_HPUra10min_T25

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 10min


title: Sample_#2_1175_control_collected_day_100_post_allo_HSCT

description:
10x genomics
Healthy control patient #2, Day 100, scRNAseq

value: Peripheral blood

value: PBMC

value: allogenic hematopoietic stem cell transplantation (HSCT)


title: WGS_BWX4310_42C_HPUraIPTG20min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 20min


title: Sample_#2_1175_control_collected_day_60_post_allo_HSCT

description:
10x genomics
Healthy control patient #2, Day 60, scRNAseq


title: McSCs, DMBA_rep 1

value: Skin

value: FACS-purified

value: Melanocyte stem cells

value: Dct-H2B-GFP KI/+

value: DMBA


title: Tumor cells from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu941_filtered_feature_bc_matrix.h5

value: Lung tumor


title: WGS_BWX5297_42C_noreplisome_IPTG25min_T25

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 25min


title: McSCs, IR_rep 2

value: IR


title: PBMCs from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu941_filtered_feature_bc_matrix.h5

value: Blood


title: Sample_#2_1175_control_collected_day_30_post_allo_HSCT

description:
10x genomics
Healthy control patient #2, Day 30, scRNAseq


title: McSCs, IR_rep 3


title: Adjacent normal lung cells from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu979_filtered_feature_bc_matrix.h5

value: Lung adjacent normal


title: WGS_BWX4310_42C_IPTG25min_T40

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 25min


title: Sample_#1_1086_control_collected_day_60_post_allo_HSCT

description:
10x genomics
Healthy control patient #1, Day 60, scRNAseq

value: Peripheral blood

value: PBMC


title: Sample_#1_1086_control_collected_day_100_post_allo_HSCT

description:
10x genomics
Healthy control patient #1, Day 100, scRNAseq

value: allogenic hematopoietic stem cell transplantation (HSCT)


title: PBMCs from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu927_filtered_feature_bc_matrix.h5


title: WGS_BWX4310_42C_IPTG20min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 20min


title: Adjacent normal lung cells from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu954_filtered_feature_bc_matrix.h5


title: McSCs, Vehicle (control)_rep 3

value: Skin

value: FACS-purified

value: Vehicle


title: Human_MSC-4

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of hg38. Exclusions included a minimum RPKM value of 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: .xls

source_name: Adipose derived mesenchymal stem cells (MSC)

growth_protocol: MSCs isolated from Patient fat pads and cultured in advanced MEM supplimented with 5% human platelet lysate as described in methods. Patient age and gender and other details found the above paper.

extract_protocol:
RNA was isolated using miRNeasy kit (qiagen).
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.


title: McSCs, IR_rep 1

value: Melanocyte stem cells

value: Dct-H2B-GFP KI/+


title: WGS_BWX4310_42C_HPUraIPTG15min_T30

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 15min


title: Adjacent normal lung cells from NSCLC Patient Lu952 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu952_filtered_feature_bc_matrix.h5


title: WGS_BWX4310_42C_HPUraIPTG30min_T45

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 30min


title: McSCs, DMBA_rep 2

value: DMBA


title: McSCs, Vehicle (control)_rep 2


title: Human_MSC-2

value: Adipose derived mesenchymal stem cells (MSC)


title: Human_MSC-3


title: WGS_BWX4310_42C_IPTG30min_T45

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 30min


title: Adjacent normal lung cells from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu941_filtered_feature_bc_matrix.h5

value: Lung adjacent normal


title: McSCs, Vehicle (control)_rep 1


title: WGS_BWX4310_42C_IPTG15min_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 15min


title: Human_MSC-1


title: WGS_BWX4310_30C_T15

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: Adjacent normal lung cells from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu927_filtered_feature_bc_matrix.h5


title: 3594_TAF1_KO

city: Miami

first: Stephen

middle: D.

last: Nimer

state: FL

address: 1120 NW 14th Street

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
For the scRNA-seq analysis, sequencing data were preprocessed and aligned with Cellranger v4(Genome: mm10). Genes with extreme low expression, cells with low number of detected genes, cells with high mitochondrial counts were filtered.
After correcting batch effect by using Seurat, tSNE plots were generated with clusters identified by using Pagoda2. Clusters were annotated by using singleR and manually with cell type markers. Pseudo-bulk differential analysis based on the aggregation of cell types were performed using DESeq2, then pathway analysis based on ranking of differential expression was performed with GSEA based on KEGG pathway database.
For differentiation trajectory analysis in scanpy (v 1.9.1), we used the expression levels of Procr, Fgd5, Hoxb5, and Ly6a genes to calculate a “stemness score” using the scanpy.tl.score_genes function. The levels of the stemness score were explored with violin plots per cluster obtained from the Leiden algorithm, and a threshold of cells with a score > 1 was selected to create a list of potential root cells, one among them was randomly selected as a root cell and diffusion pseudo time was calculated in Scanpy with default parameters.
Assembly: mm10
Supplementary files format and content: The processed data files are in HDF5 format generated by the CellRanger and contain multidimensional arrays of the final processed data, including the filtered feature-barcode matrices.

extract_protocol: 10x Genomics Chromium single cell controller

value: Bone marrow

value: hematopoietic stem progenitor cells

value: Taf1 KO


title: Tumor cells from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu979_filtered_feature_bc_matrix.h5

value: Lung tumor


title: Lymphatic endothelial cell, Covid Treatm, rep 3

type: RNA

city: Schlieren

first: Giovanna

last: Azzarito

address: Wagistrasse 14

department: Reproductive endocrinology

institute: University Hospital Zurich

description:
Rags_24_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells treated with SARS-CoV2 spike protein

hyb_protocol: 15 ug of cRNA were subjected to 2nd-cylce ss-cDNA synthesis. 5.5 ug of the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin. Hybridization to Clariom S Assay, human (Applied Biosystems, 902927) is performed for 16 hr at 45°C with rotation at 60 rpm in the GeneChip Hybridization Oven 645 (00-0331, 110/220V). GeneChips were washed and stained in the CheneChip Fluidics Station 450 (00-079).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G System (00-0213).

data_processing:
The data were analyzed with GeneChip Command Console Software (GCC) v5.0. The obtained CEL files were up-loaded to the Transcriptome Analysis Console (TAC, applied biosystems) and analysis was performed by the software (Limma-based, eBayes).
LOG2 TAC signal (software produces only avg normalized values for each triplicate)

label: biotin

source_name: human lymphatic endothelial cell line, Covid Treatment

label_protocol: Biotinylation was prepared according to the protocol (GeneChipTM WT PLUS Reagent Kit) from 5.5 ug total RNA.

growth_protocol: SMCs (Human Coronary Artery Smooth Muscle Cells) in 4th passage were cultured in SMC basal growth medium supplemented with SMC growth supplement (5 % v/v FCS, 2 ng/ml human basic Fibroblast Growth Factor, 0.5 ng/ml human Epidermal Growth Factor, 5 ng/ml Heparin, 5 μg/ml insulin and 0.2 μg/ml BSA),  antibiotic-antimycotic (AA; 100 μg/ml streptomycin, 100 μg/ml penicillin and 0.025 μg/ml amphotericin B) and SMGS).  HUVECs (Human umbilical vein endothelial cells) were cultured in Collagen coated flasks in complete growing media: EBM-2 (Endothelial Basal Medium-2) supplemented with Glutamax (1x), antibiotic-antimycotic (AA: 100 μg/ml streptomycin, 100 μg/ml penicillin and 0.025 μg/ml amphotericin B), LSGS (2% v/v FCS, 1 µg/ml hydrocortisone, 10 ng/ml human Epidermal Growth Factor, 3ng/ml human basic Fibroblast Growth Factor, 10 µg/ml heparin) and 10% FCS (Fetal Calf Serum).  PCs (Human Brain Vascular Pericytes) were cultured in Poly-L-Lysine- (PLL-) coated flasks in growing media consisting of pericyte basal medium, fetal bovine serum, pericyte growth supplement and penicillin/streptomycin solution.  LECs (Lymphatic endothelial cells) were propagated in EGM™-2MV BulletKit™ Growth Medium containing EBM-2 (Endothelial Basal Medium-2) supplemented with human Epidermal Growth Factor (hEGF), Vascular Endothelial Growth Factor (VEGF), R3-Insulin-like Growth Factor-1 (R3-IGF-1), Ascorbic Acid, Hydrocortisone, human Fibroblast Growth Factor-Beta (hFGF-β), Fetal Bovine Serum (FBS) and Gentamicin/Amphotericin-B (GA).  All the cell type were cultured under standard tissue culture conditions (37 °C, 5 % CO2).

extract_protocol: Total RNA was extracted by using the Quick-RNA MiniPrep Kit (ZymoResearch) according to the manufacture’s protocol. RNA integrity was checked by determinig the ratio of absorbance at 260 nm and 280 nm / 230 nm respectively. The samples were frozen at -80 °C and shipped to the Gene expression Affymetrix facility in dry ice.

treatment_protocol: Cells grown to 80% confluence were treated with 10ng/ml recombinant SARS-CoV2 spike protein full length S1 subunit (Val16 - Gln690 region) which contains most of the S1 subunit for 36 hours. Briefly, cells were fed using cell type specific medium containing or lacking S1-SP for 60 min under serum free condition. Subsequently FCS was added to a final concentration of 2.5% and the cells allowed to grow for 36 hrs and RNA for microarray assay extracted.

tag: origin

value: Dermal Microvascular_Pooled

tag: treatment with covid protein

value: yes


title: 3564_WT

value: WT


title: Tumor cells from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu954_filtered_feature_bc_matrix.h5


title: Lymphatic endothelial cell, Covid Treatm, rep 2

description:
Rags_23_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells treated with SARS-CoV2 spike protein


title: Lymphatic endothelial cell, Covid Treatm, rep 1

description:
Rags_22_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells treated with SARS-CoV2 spike protein


title: Tumor cells from NSCLC Patient Lu952 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu952_filtered_feature_bc_matrix.h5


title: 3520_WT


title: WGS_BWX5230_42C_T40

value: Bacillus subtilis PY79

value: parSdelta9 no a.b., -27degree parS no a.b., dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 25min


title: Lymphatic endothelial cell, CTR, rep 3

description:
Rags_21_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells not treated

source_name: human lymphatic endothelial cell line, CTR

value: no


title: Tumor cells from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu941_filtered_feature_bc_matrix.h5


title: Lymphatic endothelial cell, CTR, rep 2

description:
Rags_20_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells not treated


title: 3519_WT


title: 3518_TAF1_KO


title: WGS_BWX5230_42C_T35

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 20min


title: Tumor cells from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu927_filtered_feature_bc_matrix.h5


title: Lymphatic endothelial cell, CTR, rep 1

description:
Rags_19_(Clariom_S_Human)
gene expression data from lymphatic endothelial cells not treated


title: WGS_BWX5230_42C_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 15min


title: Taf1_WT_rep3

library_source: other

data_processing:
Proseq: FASTQ data were trimmed by Cutadapt 1.14 and Trimmomatic v0.32.
Proseq: Reads were aligned on mm10 or dm3 genome by bowtie 1.1.2 26. Strand-specific single nucleotide ends of aligned reads were generated by Bedtools v2.28 with genomecov as bedgraph format. Bedgraph data were normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig files.
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format: Proseq: bigwigs were generated with Bedtools v2.28 with genomecov.
Library strategy: Pro-seq

molecule: other

extract_protocol:
PRO-seq experiments were performed as described previously (Mahat, D. B. et al. 2016). Nuclei were isolated by Dounce homogenizer with loose pestle. 1x107 nuclei were subjected to nuclear run-on (30oC, 3min) in the presence of 25 μM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer). Total RNA was extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min).
PRO-seq  libraries used biotinylated nascent RNAs were purified by Dynabeads M-280 streptavidin (Invitrogen). Following adaptor ligation as described in previously (Mahat, D. B. et al. 2016), cDNA synthesis, and PCR amplification 140–350 bp libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science).


title: WGS_BWX5230_42C_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 10min


title: PBMCs from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu979_filtered_feature_bc_matrix.h5

value: Blood


title: Vascular endothelial cell, Covid Treatm, rep 3

description:
Rags_18_(Clariom_S_Human)
gene expression data from vascular endothelial cells treated with SARS-CoV2 spike protein

source_name: human vascular endothelial cell lines, Covid Treatment

value: Umbilical Vein


title: WGS_BWX4310_T0

source_name: Bacillus subtilis PY79

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: PBMCs from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu954_filtered_feature_bc_matrix.h5


title: Taf1_WT_rep2

value: Bone marrow

value: hematopoietic stem progenitor cells


title: WGS_BWX5230_42C_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 5min


title: PBMCs from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu941_filtered_feature_bc_matrix.h5


title: Taf1_WT_rep1


title: 3562_TAF1_KO

value: Taf1 KO


title: PBMCs from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu927_filtered_feature_bc_matrix.h5


title: Vascular endothelial cell, Covid Treatm, rep 1

description:
Rags_16_(Clariom_S_Human)
gene expression data from vascular endothelial cells treated with SARS-CoV2 spike protein

value: yes


title: WGS_BWX5230_30C_T15

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: WGS_BWX4310_exp

value: Cells were grown in CH medium at 30degreeC


title: Vascular endothelial cell, CTR, rep 3

description:
Rags_15_(Clariom_S_Human)
gene expression data from vascular endothelial cells not treated

source_name: human vascular endothelial cell lines, CTR

value: no


title: WGS_BWX5230_30C_T10

value: Bacterial

value: parSdelta9 no a.b., -27degree parS no a.b., dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 10min


title: Taf1_KO_rep2


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics

value: Lung adjacent normal


title: Taf1_KO_rep1


title: Vascular endothelial cell, CTR, rep 2

description:
Rags_14_(Clariom_S_Human)
gene expression data from vascular endothelial cells not treated


title: WGS_BWX5230_T0


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: WGS_BWX5297_42C_T50

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 35min


title: TAF1_KO_Day7_Granulocyte_3

description:
TAF1_KO_Day7_Granulocyte_3
TPM_Granulocyte_Differentiation.csv

data_processing:
nf-core/rnaseq v 3.6
Sequence reads were processed using the nf-core RNA-seq pipeline with default parameters, for pre-processing, alignment and QC, selecting RSEM as aligner
Reads from RSEM were loaded into DESeq2 v 1.38.3 with tximport v 1.26.1, for time-series analysis
Assembly: mm10
Supplementary files format and content: comma separated (.csv) files include TPM values for each Sample

growth_protocol: HSPCs were cultured in 20% Horse Serum (HS, Sigma-Aldrich, H1138) IMDM supplemented with mouse SCF ( PeproTech, 250-03) and IL-3 (PeproTech, 213-13) to expand myeloid cells for 3 days; then half of these cells were cultured in IMDM with mouse cytokines (SCF, IL-3 and G-CSF (PeproTech, 250-05)) for 2 days, and then G-CSF alone for the last 2 days to granulocyte differentiation; and the other half were forced to differentiate toward macrophages in 20% HS IMDM supplemented with mouse GM-CSF (Biolegend, 576302) and M-CSF (PeproTech, 315-02) for 2 days and M-CSF alone for the last 2 days. All cytokines were used at concentration of 50 ng/ml.

extract_protocol:
Total RNA was purified using RNeasy Plus Mini Kit (Qiagen, 74136).
Libraries were generated with KAPA Stranded RNA-Seq Library Preparation Kit

tag: time point

tag: cell subtype

value: Granulocyte

value: In vitro differentiation


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: Vascular endothelial cell, CTR, rep 1

description:
Rags_13_(Clariom_S_Human)
gene expression data from vascular endothelial cells not treated

value: Umbilical Vein


title: TAF1_KO_Day7_Granulocyte_2

description:
TAF1_KO_Day7_Granulocyte_2
TPM_Granulocyte_Differentiation.csv

value: Bone marrow

value: hematopoietic stem progenitor cells


title: WGS_BWX5297_42C_T45

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 30min


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics


title: TAF1_KO_Day7_Granulocyte_1

description:
TAF1_KO_Day7_Granulocyte_1
TPM_Granulocyte_Differentiation.csv

value: Taf1 KO


title: WGS_BWX5297_42C_T40

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 25min


title: Vascular endothelial cell, Covid Treatm, rep 2

description:
Rags_17_(Clariom_S_Human)
gene expression data from vascular endothelial cells treated with SARS-CoV2 spike protein

value: yes


title: Pericyte Cell, Covid Treatm, rep 2

description:
Rags_11_(Clariom_S_Human)
gene expression data from pericytes treated with SARS-CoV2 spike protein

source_name: human pericyte cell lines, Covid Treatment

value: Brain vascular pericytes


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics


title: Pericyte Cell, Covid Treatm, rep 1

description:
Rags_10_(Clariom_S_Human)
gene expression data from pericytes treated with SARS-CoV2 spike protein


title: WGS_BWX5297_42C_T35

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 20min


title: TAF1_KO_Day7_Macrophage_3

description:
TAF1_KO_Day7_Macrophage_3
TPM_Macrophage_Differentiation.csv

value: Macrophage


title: WGS_BWX5297_42C_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 15min


title: TAF1_KO_Day7_Macrophage_2

description:
TAF1_KO_Day7_Macrophage_2
TPM_Macrophage_Differentiation.csv


title: TAF1_KO_Day7_Macrophage_1

description:
TAF1_KO_Day7_Macrophage_1
TPM_Macrophage_Differentiation.csv


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu885 (scATAC-seq)

description: 10x Genomics

value: Lung adjacent normal


title: Pericyte Cell, CTR, rep 3

description:
Rags_9_(Clariom_S_Human)
gene expression data from pericytes not treated

source_name: human pericyte cell lines, CTR

value: no


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics


title: WGS_BWX5297_42C_T25

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 10min


title: WGS_BWX5297_42C_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 5min


title: Pericyte Cell, CTR, rep 2

description:
Rags_8_(Clariom_S_Human)
gene expression data from pericytes not treated


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics


title: Smooth Muscle Cell, Covid Treatm, rep 3

description:
Rags_6_(Clariom_S_Human)
gene expression data from smooth muscle cells treated with SARS-CoV2 spike protein

source_name: human smooth muscle cell lines, Covid Treatment

value: Aortic smooth muscle cells


title: Control_Day7_Granulocyte_2

description:
Control_Day7_Granulocyte_2
TPM_Granulocyte_Differentiation.csv

value: Bone marrow

value: hematopoietic stem progenitor cells

value: Granulocyte

value: WT

value: In vitro differentiation


title: Tumor cells from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics

value: Lung tumor


title: Control_Day7_Granulocyte_3

description:
Control_Day7_Granulocyte_3
TPM_Granulocyte_Differentiation.csv


title: WGS_BWX5297_30C_T10

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 10min


title: Pericyte Cell, CTR, rep 1

description:
Rags_7_(Clariom_S_Human)
gene expression data from pericytes not treated

value: Brain vascular pericytes


title: Smooth Muscle Cell, Covid Treatm, rep 1

description:
Rags_4_(Clariom_S_Human)
gene expression data from smooth muscle cells treated with SARS-CoV2 spike protein

value: yes


title: Pericyte Cell, Covid Treatm, rep 3

description:
Rags_12_(Clariom_S_Human)
gene expression data from pericytes treated with SARS-CoV2 spike protein


title: Control_Day7_Macrophage_2

description:
Control_Day7_Macrophage_2
TPM_Macrophage_Differentiation.csv

value: Macrophage


title: WGS_BWX5297_30C_T15

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: Control_Day7_Granulocyte_1

description:
Control_Day7_Granulocyte_1
TPM_Granulocyte_Differentiation.csv


title: Smooth Muscle Cell, Covid Treatm, rep 2

description:
Rags_5_(Clariom_S_Human)
gene expression data from smooth muscle cells treated with SARS-CoV2 spike protein


title: Smooth Muscle Cell, CTR, rep 2

description:
Rags_2_(Clariom_S_Human)
gene expression data from smooth muscle cells not treated

source_name: human smooth muscle cell lines, CTR

value: no


title: Tumor cells from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics

value: Lung adjacent normal


title: Tumor cells from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics


title: Control_Day7_Macrophage_3

description:
Control_Day7_Macrophage_3
TPM_Macrophage_Differentiation.csv


title: WGS_BWX5297_42C_IPTG50min_T50

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 35min


title: Tumor cells from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: WGS_BWX5297_42C_IPTG40min_T40

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 25min


title: WGS_BWX5297_42C_IPTG35min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 20min


title: Tumor cells from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics


title: Smooth Muscle Cell, CTR, rep 3

description:
Rags_3_(Clariom_S_Human)
gene expression data from smooth muscle cells not treated

value: Aortic smooth muscle cells


title: WGS_BWX5297_42C_IPTG30min_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 15min


title: WGS_BWX5297_42C_IPTG45min_T45

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 30min


title: Tumor cells from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics

value: Lung tumor


title: TAF1_KO_Day5_Granulocyte_3

description:
TAF1_KO_Day5_Granulocyte_3
TPM_Granulocyte_Differentiation.csv

value: Bone marrow

value: hematopoietic stem progenitor cells

value: Granulocyte

value: Taf1 KO

value: In vitro differentiation


title: Smooth Muscle Cell, CTR, rep 1

description:
Rags_1_(Clariom_S_Human)
gene expression data from smooth muscle cells not treated


title: TAF1_KO_Day5_Granulocyte_2

description:
TAF1_KO_Day5_Granulocyte_2
TPM_Granulocyte_Differentiation.csv


title: TAF1_KO_Day5_Macrophage_3

description:
TAF1_KO_Day5_Macrophage_3
TPM_Macrophage_Differentiation.csv

value: Macrophage


title: TAF1_KO_Day5_Granulocyte_1

description:
TAF1_KO_Day5_Granulocyte_1
TPM_Granulocyte_Differentiation.csv


title: WGS_BWX5297_42C_IPTG25min_T25

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 10min


title: TAF1_KO_Day5_Macrophage_2

description:
TAF1_KO_Day5_Macrophage_2
TPM_Macrophage_Differentiation.csv


title: Tumor cells from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics


title: Male,4wks Saline, Sample 4

first: Ania

middle: K.

last: Majewska

address: 601 Elmwood Ave

department: Department of Neuroscience

institute: University of Rochester Medical Center

description: Library name: 164L

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq v2.19.1
Quality filtering and adapter removal was performed using FastP v.0.23.1.
Processed reads were then mapped to the mouse reference genome (GRCm39 + gencode-M31 annotation) using STAR_2.7.9a.
Read counts were quantified using both Subread-featureCounts v2.0.1 with “-s 0” indicating unstranded reads, and Salmon v1.5.2.
Differential expression analysis was performed using DESeq2 within R v4.2.2.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file includes normalized counts for each sample.

source_name: Brain

extract_protocol:
Microglia were isolated using FACS. Total microglial RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). RNA concentration was determined with the NanopDrop One spectrophotometer (NanoDrop) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent). 500 pg of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluorometer 3.0 (Life Technnologies) and the Agilent Bioanalyzer 2100 (Agilent).
150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina) per manufacturer’s protocols.
The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NovaSeq X sequencer (Illumina) with target depth of ~30 million of 150 nt paired-end reads per sample.

treatment_protocol: Mice were treated for 4 weeks with either 20% ethanol at 3g/kg dosage or saline via i.p. injection daily for 5 days/week, and given a 2-week withdrawal period.

value: Brain

tag: Sex

value: Male

tag: agent

value: Saline


title: Male,4wks Saline, Sample 3

description: Library name: 163L


title: PBMCs from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics

source_name: Blood

value: Blood


title: Male,4wks EtOH, Sample 4

description: Library name: 164R

value: EtOH


title: WGS_BWX5297_42C_IPTG20min_T20

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min, finally shifted up to 42degreeC for 5min


title: WGS_BWX5297_30C_IPTG10min_T10

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 10min


title: Male,4wks EtOH, Sample 2

description: Library name: 165R


title: Tumor cells from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics

value: Lung tumor


title: Control_Day7_Macrophage_1

description:
Control_Day7_Macrophage_1
TPM_Macrophage_Differentiation.csv

value: Bone marrow

value: hematopoietic stem progenitor cells

value: WT


title: PBMCs from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: TAF1_KO_Day5_Macrophage_1

description:
TAF1_KO_Day5_Macrophage_1
TPM_Macrophage_Differentiation.csv

value: Taf1 KO

value: In vitro differentiation


title: WGS_BWX5297_30C_IPTG15min_T15

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC and treated with 1mM ITPG for 15min


title: Control_Day5_Granulocyte_3

description:
Control_Day5_Granulocyte_3
TPM_Granulocyte_Differentiation.csv

value: Granulocyte


title: Control_Day5_Granulocyte_1

description:
Control_Day5_Granulocyte_1
TPM_Granulocyte_Differentiation.csv


title: WGS_BWX5297_T0

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: Male,4wks EtOH, Sample 1

description: Library name: 165RL

value: Brain

value: Male


title: Control_Day5_Granulocyte_2

description:
Control_Day5_Granulocyte_2
TPM_Granulocyte_Differentiation.csv


title: WGS_BWX3381_exp

value: parSdelta9 no a.b., -117degree parS (loxP-kan-loxP)

value: Cells were grown in CH medium at 37degreeC


title: WGS_BWX3212_exp

value: parSdelta9 no a.b.


title: PBMCs from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics

value: Blood


title: Male,4wks Saline, Sample 1

description: Library name: 164O

value: Saline


title: Control_Day5_Macrophage_3

description:
Control_Day5_Macrophage_3
TPM_Macrophage_Differentiation.csv

value: Bone marrow

value: Macrophage


title: PBMCs from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics


title: Male,4wks EtOH, Sample 3

description: Library name: 163R

value: EtOH


title: Control_Day5_Macrophage_2

description:
Control_Day5_Macrophage_2
TPM_Macrophage_Differentiation.csv

value: hematopoietic stem progenitor cells

value: WT


title: Tumor cells from NSCLC Patient Lu885 (scATAC-seq)

description: 10x Genomics

value: Lung tumor


title: PBMCs from NSCLC Patient Lu885 (scATAC-seq)

description: 10x Genomics


title: Control_Day5_Macrophage_1

description:
Control_Day5_Macrophage_1
TPM_Macrophage_Differentiation.csv

value: In vitro differentiation


title: PBMCs from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics


title: Male,4wks Saline, Sample 2

description: Library name: 165O


title: PBMCs from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics


title: TAF1_KO_Day3_3

description:
TAF1_KO_Day3_3
TPM_Macrophage_Differentiation.csv

value: Taf1 KO


title: PBMCs from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: TAF1_KO_Day3_2

description:
TAF1_KO_Day3_2
TPM_Macrophage_Differentiation.csv


title: PBMCs from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics


title: TAF1_KO_Day3_1

description:
TAF1_KO_Day3_1
TPM_Macrophage_Differentiation.csv


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 15 minutes, replicate 2

city: Encinitas

first: Audrey

last: Dickinson

state: California

address: 300 Quail Gardens Dr

department: Science and Conservation

institute: San Diego Botanic Garden

description: Library name: Vhyb_309_19.H.T1.R2

data_processing:
Sequencing runs were basecalled using the Dorado v5.0.0 super-high accuracy model with a quality threshold of Q9 and a 200 base pair cutoff.
Reads were aligned using minimap2 v2.28-r1209 against Helixer-generated (v0.3.2) coding sequences (CDS) from either V. macrocarpon, V. oxycoccos, or a concatenated hybrid reference, as appropriate. Only primary alignments were retained.
Transcript abundance was quantified using Salmon v1.6.0.
Assembly: V. macrocarpon, V. oxycoccos (Kawash et al., 2022)
Supplementary files format and content: Quantification table output from Salmon. Rows represent genes in each sample. Columns represent length, effective length, TPM, and the number of reads mapping to each transcript.

organism:
Vaccinium macrocarpon
Vaccinium oxycoccos

source_name: Leaf

growth_protocol: All plants were maintained in a greenhouse in Chatsworth, New Jersey, USA, prior to the temperature stress experiments. Each F1 hybrid with the same genotype identifier were clonally propagated from seedling progeny by cuttings. Experimental material consisted of V. macrocarpon, V. oxycoccos, and their F1 hybrids. Experiments were conducted in mid to late September during the growing season, prior to cold acclimation.

extract_protocol:
Approximately 50 mg of leaf tissue was processed per sample. Total nucleic acids were isolated using a CTAB-based method (Daverdin et al., 2017). RNA was precipitated from total nucleic acid using 10M LiCl overnight, pelleted, and resuspended in nuclease-free water. Samples were treated with DNase (Optizyme, Fisherbrand #BP81071), followed by chloroform treatment, sodium acetate precipitation, ethanol washing, and final resuspension in nuclease-free water.
Full-length cDNA was synthesized from 200 ng of total RNA per sample using the Oxford Nanopore cDNA-PCR Sequencing Kit (SQK-PCB111.24). PCR amplification used barcoded primers (16 cycles), and barcoded cDNA from nine samples was pooled per run. ONT Rapid Adapter Kit (EXP-RAA114) was used to prepare libraries for sequencing with R10.4.1 flow cells and V14 chemistry. Sequencing was performed on the PromethION platform for 72 hours.

treatment_protocol: For temperature stress experiments, plants were acclimated for three days at 21 °C under a 12 h day/night cycle. For heat stress, incubators were pre-set to 45 °C and samples were harvested at 0 min (T0), 15 min (T1, 39.7 °C), and 30 min (T2, 47 °C). For cold stress, incubators were set to 2 °C and samples were harvested at T0, 60 min (T1, 10.5 °C), and 95 min (T2, 3 °C). Whole leaves were collected and snap frozen in liquid nitrogen, then stored in RNAlater ICE.

value: Leaf

tag: temperature

tag: cultivar

value: Ben Lear x NJ96-127


title: WGS_PY79_exp

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

tag: cell line

value: Bacillus subtilis PY79

tag: cell type

value: Bacterial

value: wild type


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 15 minutes, replicate 1

description: Library name: Vhyb_309_19.H.T1.R1

tag: treatment

tag: genotype


title: Control_Day3_3

description:
Control_Day3_3
TPM_Macrophage_Differentiation.csv

tag: tissue


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 0 minutes, replicate 3

description: Library name: Vhyb_309_19.H.T0.R3


title: small EVs_90z_HC

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then at 45°C for 5 minutes • Transfer 200 μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using R package oligo and custom made probe annotation. Background subtraction, normalization and summarization was done with RMA algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

source_name: blood serum small exctracellular vesicles

label_protocol: The fragmented cDNA was labeled by TdT using the proprietary DNA labeling reagent that is covalently linked to biotin according to the manufacturer's recommendations.

growth_protocol: not applicable

extract_protocol: Small EVs were isolated from 150 µl of sera. After the sample passed onto the column, 800 μl of 1X PBS was applied to the column. The fraction containing small EVs was eluted by applying 500 μl of 1X PBS to the column and collected. All samples were treated with proteinase K (20 mg/mL, 10 µl) and RNase Cocktail Enzyme Mix (20 000 U/mL, 5 µl) at 37 °C for 10 min. Finally, SUPERase·In RNase Inhibitor (20 U/μL, 4 µl) was added and mixed well. Total RNA including small RNAs was isolated from small EVs using Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s recommendations, treated with DNase I, and eluted with 50 μl of DEPC-treated water.

treatment_protocol: All samples were centrifuged at 1500 × g for 10 min at 4 °C and then at 10000 × g for 20 min at 4 °C.

tag: condition

value: HC

tag: gender

value: male

tag: age

tag: diagnosis

value: not applicable

tag: clinical stage

tag: localization


title: K14-SCF_rep 3

hyb_protocol: 1.69 µg of Cy3-labelled cDNA was hybridized on Agilent SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C . After hybridization, the slides were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer 2 (Agilent).°

scan_protocol: Slides were scanned immediately after washing on the DNA Microarray Scanner (Agilent) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed using Feature Extraction Software ver. 10.7.1.1 (Agilent) with default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Cyamin-3 (Cy3)

source_name: GFP(+)/SSC(low)

label_protocol: 0.5 µg of cDNA was amplified and labeled with Cyanine-3 (Cy3) using the SureTag DNA Labeling Kit.

extract_protocol: Melanocyte stem cells were sorted with FACS AriaII directly into QIAzol Lysis Reagent (Qiagen) for RNA extraction. Chloroform was added to QIAzol and the supernatant was separated. RNA was precipitated by adding 100% EtOH to the supernatant and then purified using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Single cell suspensions were obtained from skin and then GFP(+)/SSC(low) cells were selected as melanocyte stem cells (McSCs).

value: Melanocyte stem cells

value: K14-SCF Tg


title: small EVs_8z_HC

value: female


title: small EVs_94z_HC


title: small EVs_85z_HC


title: small EVs_95z_HC


title: Control_Day3_1

description:
Control_Day3_1
TPM_Macrophage_Differentiation.csv

source_name: Bone marrow

value: Bone marrow

tag: time point


title: WT_rep 1


title: K14-SCF_rep 2


title: TAF1_KO_Day0_3

description:
TAF1_KO_Day0_3
TPM_Macrophage_Differentiation.csv

value: hematopoietic stem progenitor cells


title: small EVs_83z_HC


title: K14-SCF_rep 1


title: TAF1_KO_Day0_2

description:
TAF1_KO_Day0_2
TPM_Macrophage_Differentiation.csv


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 0 minutes, replicate 1

description: Library name: Vhyb_309_19.H.T0.R1

tag: time


title: WT_rep 3

tag: Sex

value: WT


title: small EVs_67z_HC


title: TAF1_KO_Day0_1

description:
TAF1_KO_Day0_1
TPM_Macrophage_Differentiation.csv


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 95 minutes, replicate 2

description: Library name: Vhyb_ST.C.T2.R2

organism: Vaccinium macrocarpon

value: Stevens


title: Control_Day3_2

description:
Control_Day3_2
TPM_Macrophage_Differentiation.csv

value: In vitro differentiation


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 0 minutes, replicate 2

description: Library name: Vhyb_309_19.H.T0.R2


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 95 minutes, replicate 3

description: Library name: Vhyb_ST.C.T2.R3


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 95 minutes, replicate 1

description: Library name: Vhyb_ST.C.T2.R1


title: small EVs_54z_HC


title: Control_Day0_3

description:
Control_Day0_3
TPM_Macrophage_Differentiation.csv


title: small EVs_60z_HC


title: Anbiotics

city: Changchun

first: Tong

last: Chen

state: Jilin

address: No. 5333, Xi'an Road, Lvyuan District

institute: Jilin University

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: serum

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries (N1, N2, N3, P1,P2, P3) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: serum


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 60 minutes, replicate 2

description: Library name: Vhyb_ST.C.T1.R2

value: Leaf


title: WT_rep 2


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 60 minutes, replicate 3

description: Library name: Vhyb_ST.C.T1.R3


title: WT


title: HFSCs/Hg DMBA-2

description: Gene expression after 3days in DMBA-treated HFSCs/Hg

hyb_protocol: 1.69 µg of Cy3-labelled cDNAs were hybridized on Agilent SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65°C . After hybridization, slides were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature and Gene Expression Wash Buffer 2 (Agilent) at37℃, then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), DMBA, 3days, replicate 2

label_protocol: 0.5 µg cDNA  were labeled with Cyanine-3 (Cy3) using Exo-Klenow fragment enzyme.

extract_protocol: HFSCs/HG were sorted with FACS AriaII directly into Buffer RLT (Qiagen) for RNA extraction. Total mRNAs were purified with an RNeasy Micro Kit (Qiagen) following the standard procedures.

treatment_protocol: After the depilation, the mice were topically applied with Vehicle or DMBA. Single epidermal cell suspensions were obtained and K15-EGFP(Hi)/ITGA6(Hi)/Scal(-) cells were selected as HFSCs/HG with FACS AriaII.

value: Hair follicle stem cells/Hair germ

value: DMBA


title: HFSCs/Hg DMBA-3

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), DMBA, 3days, replicate 3