title: Senescent NP cells treated with H-151 #2 for p65 CUT&Tag

data_processing:
Sequencing adapters were removed via the Cutadapt (v4.1)
Rimmed fastq files were aligned with Bowtie2 (v2.2.1) (Langmead & Salzberg, 2012) to the human genome assembly GRCh38 (hg38) from Genome Reference Consortium, using the following parameters: --local--very-sensitive--no-mixed--no-discordant--phred33-I 10-X 700.
Bam files containing uniquely mapped reads were created using Samtools v1.15.1 (Li et al., 2009).
CUT&Tag signals were called on using MACS v2.2.7.1 (Zhang et al., 2008) as normalized to control group (No-degenerated group and DMSO group), using the following settings: FDR cutoff of 1e-3, BAMPE format.
The MACS--bdg setting was used to generate control scaled, normalized bigwig files, which were used to visualize normalized binding signals. The same bigwig files were also used to generate profile plots using deepTools plotprofile (RamÄ±Â´rez et al., 2016).
Genes proximal to peaks were annotated against the hg38 genome using annotatePeaks.pl from HOMER v4 (Heinz et al., 2010). DUX4, DUX4-IGH and DUX4-del50 binding motifs were identified using findMotifsGenome.pl from HOMER v4.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Nucleus pulposus tissue #5

growth_protocol: Nucleus pulposus (NP) cells were isolated from human no-degenerated NP tissues and cultured in DMEM:F12 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2.

extract_protocol:
DNA were isolated with p65 (CST, #8242) antibodies. Briefly, collected nucleus pulposus (NP) cells were immobilized on Concanavalin A-coated magnetic beads (ConA), permeabilized with digitonin and incubated with p65 (CST, #8242)  antibody (1st Ab). The following day, ConA-nuclei-1st Ab were spun, and the supernatant was removed, nuclei were resuspended in 100 Î¼l of Wash Buffer 150 and incubated with a secondary antibody (2nd Ab) diluted 1:100 in Wash Buffer 150 for 1 h at room temperature. After removal of the 2nd Ab, nuclei were washed with Wash Buffer 150 and incubated with the protein AG-conjugated-Transposase (pAG-Tn5) preloaded with sequencing adapters, diluted 1:20 in Wash Buffer 300 for 1 h at room temperature. Nuclei were then washed twice in Wash Buffer 300 and tagmentation reaction was performed by addition of 10 mM MgCl2 following incubation at 37 Â°C for 1 h. After a wash with TAPS buffer (10 mM TAPS), tagmented DNA was released by addition of 5 Î¼l 0.1% SDS release buffer following incubation at 58 Â°C for 1 h. Finally, 15 Î¼l  of 0.67% Triton-X-100 were added to neutralize SDS and allow PCR for library preparation.
Libraries were prepared according to instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly, RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer. cDNA was synthed using dNTPs, DNA polymeraseI and RNaseH. Then cDNA was purified using AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols. 2 Î¼l of 10 Î¼M i5 universal adapter primer and 2 Î¼l of 10 Î¼M i7 uniquely barcoded adapter primers were added to released, tagmented DNA, followed by addition of 25 Î¼l of 2X Master Mix. PCR was performed as follows: Cycle 1: 72 Â°C for 3 min (gap filling), Cycle 2: 95 Â°C for 3 min, Cycle 3: 98 Â°C for 10 s, Cycle 4: 60 Â°C for 5 s. 72Â°C for 1 min and hold at 4 Â°C. For p65 CUT&Tag, repeat Cycles 3-4 15 times. Amplified DNA was then recovered through size exclusion purification by addition of VAHTS DNA Clean Beads, followed by two washes in 80% ethanol and elution in 22 Î¼l of 10 mM Tris-HCl (pH8). Quantification and average fragment size of libraries was performed via the 4200 TapeStation system (Agilent), using the D5000 high sensitivity kit (Agilent 5067-5592/5067-5593). 450bp of average library fragment size was selected for library quantification. A 5 nM pool of the libraries was then run with the NovaSeq instrument and sequenced in paired end (PE), generating 2x150 bp reads.

treatment_protocol: Human nucleus pulposus (NP) tissues were digested with 0.2% type II collagenase for 8 hours. Passage 8 NP cells were collected via serial passage and treated with STING pharmacological inhibitor (H-151) or vehicle (DMSO) for 24 hours.

value: Nucleus pulposus tissue #5

value: Nucleus pulposus cells

tag: chip antibody

value: Treated with H-151 for 24 hours


title: Senescent NP cells treated with H-151 #1 for p65 CUT&Tag

status: Public on Mar 20 2024

type: SRA

city: Wuhan

first: Cao

last: Yang

state: Hubei

address: Jiefang average

country: China

institute: Wuhan Union Hospital

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Nucleus pulposus tissue #4

tag: tissue

value: Nucleus pulposus tissue #4

tag: cell type

tag: treatment


title: BV2 vehicle miR-7a 4

city: Kuopio

first: Flavia

last: Scoyni

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

library_source: transcriptomic

data_processing:
Bulk RNA sequences of mRNA (dataset: BV2) have been aligned and quantified to the mouse genome of reference GRCm38 using the nf-core workflow (3.0 version of “rnaseq”).
We filtered out lowly expressed molecules in any condition using the function “filterByExpr” to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for outliers and sample’s features inducing batch effect by performing a principal component analysis and unsupervised consensus clustering with Cola.
We finally created the design matrix for each pair of conditions to compare (contrast) and performed the differential expression analysis using limma/edgeR model controlling for the false discovery rate with Benjamini-Hochberg Procedure.
Assembly: GRCm38

molecule: total RNA

organism: Mus musculus

growth_protocol: Murine glioblastoma cell line (BV2) cells were cultured in RPMI 1640 Medium, GlutaMAX™ Supplemented base medium (Gibco, 31966021), 1% Penicillin-Streptomycin and 10% heat inactivated and filtered FBS (Gibco, 10270106) in temperature controlled humidified incubator (37 °C, 5% CO2).

extract_protocol:
RNA extraction was performed with TRIzol™ Reagent (Invitrogen) following manufacturer's protocol
RNA libraries for RNA-seq were prepared using CORALL total RNA-Seq Library Prep Kit (Lexogen GmbH) after ribosomal RNA depletion with RiboCop rRNA Depletion Kit V1.2 (Lexogen GmbH) following manufacturer's protocols.

treatment_protocol: Cells were treated with 10ng/ml LPS or vehicle for 24h and then transfected with miRNA scramble negative control or miR-7a-5p, miR-29a-3p or miR-146a-5p

tag: cell line

value: Glioblastoma

tag: genotype

value: WT

value: Vehicle overexpressing miR-7a-5p mimic


title: Senescent NP cells treated with DMSO #3 for p65 CUT&Tag

source_name: Nucleus pulposus tissue #6

value: Nucleus pulposus tissue #6

value: Treated with DMSO for 24 hours


title: BV2 vehicle miR-7a 2

tag: time

value: 6 months old mice


title: Senescent NP cells treated with DMSO #1 for p65 CUT&Tag


title: BV2 vehicle miR-7a 1


title: No-degenerated NP cells #3 for p65 CUT&Tag

source_name: No-degenerated nucleus pulposus tissue #3


title: No-degenerated NP cells #2 for p65 CUT&Tag

source_name: No-degenerated nucleus pulposus tissue #2


title: Vdr AF2 kidney 1

city: Leuven

first: Annemieke

last: Verstuyf

address: Herestraat 49 box 902

country: Belgium

institute: KU Leuven

description:
GC106689
raw counts_kidney.csv

data_processing:
Averages of 4.3 x 106 reads/sample (kidney) and 3.8 x 106 reads/sample (duodenum) were obtained
reads were mapped against the mus musculus reference genome (mm10)
Differential gene expression was performed with Limma v3.34.9 (R/Bioconductor software package in Biomex v1.0-5)
Assembly: mus musculus reference genome (mm10).
Supplementary files format and content: tab delimited tekst file includes raw counts for each sample

source_name: kidney cortex

extract_protocol:
Tissues were homogenized (Precellys 24, Bertin technologies, France) in TRIzol Reagent (Invitrogen) and RNA was extracted according to the manufacturer’s instructions.
sequencing libraries of  1µg of total RNA were prepared with the LexoGen QuantSeq Library preparation kit by the Genomics Core (KU Leuven, Belgium).

value: kidney cortex

value: delta AF2

value: Inotiv TD.96348


title: Vdr AF2 kidney 4

description:
GC106692
raw counts_kidney.csv


title: Vdr AF2 kidney 2

description:
GC106690
raw counts_kidney.csv


title: Vdr-/- kidney 3

description:
GC106673
raw counts_kidney.csv

value: knockout


title: Vdr AF2 kidney 3

description:
GC106691
raw counts_kidney.csv


title: Vdr-/- kidney 4

description:
GC106674
raw counts_kidney.csv


title: No-degenerated NP cells #1 for p65 CUT&Tag

source_name: No-degenerated nucleus pulposus tissue #1


title: Degenerated NP cells #3 for p65 CUT&Tag

source_name: Degenerated nucleus pulposus tissue #3

value: Degenerated nucleus pulposus tissue #3


title: Degenerated NP cells #2 for p65 CUT&Tag

source_name: Degenerated nucleus pulposus tissue #2

value: Degenerated nucleus pulposus tissue #2


title: BV2 LPS neg ctrl (scramble) 3

value: LPS 10ng/ml for 24h and overexpressing neg control scramble


title: Vdr-/- kidney 1

description:
GC106671
raw counts_kidney.csv


title: Degenerated NP cells #1 for p65 CUT&Tag

source_name: Degenerated nucleus pulposus tissue #1

value: Degenerated nucleus pulposus tissue #1


title: sts,rep3

city: Guangzhou

first: Xiaotian

last: He

state: Guangdong

address: Dongfeng Road

institute: Sun Yat-sen University Cancer Center (SYSUCC)

data_processing:
FeatureCounts tools in subread Software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Usingthe Rprogram (version 4.1.1, http://www.R-project.org), transcriptional analysis was conducted, and to identify differentially expressed genes (DEGs) in different clusters, the "limma" package was utilized.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

growth_protocol: A549 cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml). Apoptosis was induced by Staurosporine or cisplatin. After co-culture with tumor cells for 96 h, RNA was extracted and mRNA sequencing was performed.

extract_protocol:
Total RNA from the A549 cells treated with PBS or apoEVs for 96h in vitro was extracted using TRIzol reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: lung adenocarcinoma

value: apoEVs (apoptosis induced by staurosporine)


title: Vdr-/- kidney 2

description:
GC106672
raw counts_kidney.csv


title: BV2 LPS neg ctrl (scramble) 4


title: Senescent NP cells treated with H-151 #3 for p65 CUT&Tag

value: Nucleus pulposus cells

value: Treated with H-151 for 24 hours


title: BV2 vehicle miR-7a 3

value: Glioblastoma

value: WT


title: BV2 LPS neg ctrl (scramble) 2


title: sts,rep2


title: BV2 LPS neg ctrl (scramble) 1

value: 2 months old mice


title: sts,rep1


title: ddp,rep3

value: apoEVs (apoptosis induced by cisplatin)


title: Senescent NP cells treated with DMSO #2 for p65 CUT&Tag

value: Nucleus pulposus tissue #5

value: Treated with DMSO for 24 hours


title: BV2 vehicle neg ctrl (scramble) 4

value: Vehicle overexpressing neg control scramble


title: ddp,rep2


title: BV2 vehicle neg ctrl (scramble) 3


title: control,rep3

value: control


title: Vdr+/+ kidney 4

description:
GC106670
raw counts_kidney.csv

value: kidney cortex

value: wildtype

value: Inotiv TD.96348


title: Vdr+/+ kidney 3

description:
GC106669
raw counts_kidney.csv


title: BV2 vehicle neg ctrl (scramble) 2


title: ω- ApoE3Ch/PSEN1 E280A, scRNA-seq

city: Boston

first: Joseph

middle: F

last: Arboleda-Velasquez

state: Massachusetts

address: 20 Staniford St.

country: USA

institute: Schepens Eye Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the standard GRCh38-2020-A human reference transcriptome using the 10X Genomics Cell Ranger Suite (cellranger-6.0.1) with default parameters.
Assembly: GRCh38
Supplementary files format and content: HDF5 (h5) files (filtered_feature_bc_matrix.h5 from 10X Genomics Cell Ranger workflow)

source_name: cerebral organoid

extract_protocol:
Six organoids from each individual cell line (eight lines in total) were pooled and processed using MACS papain neural tissue dissociation kit (Miltenyi Biotec #130-092-628) according to manufacturer’s protocol and resuspended in 0.22μm filter sterilized dPBS 0.04%BSA solution. Cells were serially filtered through a 70μm (Miltenyi Biotec #130-110-916) then 40μm (Bel-Art #H136800040) strainer to remove clumped cells.
Samples were kept on wet ice and assessed at the BioMicroCenter core facility (Massachusetts Institute of Technology) for viability, cell density, and quality. Samples were loaded (target 10,000 cells) on a Chromium Controller (10x Genomics). Library construction and sequencing were performed using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 with cDNA amplified 12 cycles using standard conditions. Libraries were sequenced on 2 lanes of a NovaSeq 6000 (Illumina) S4 flowcell at 150PE.

value: cerebral organoid

value: PSEN1 E280A, APOE3 R136S

value: successful CRISPR-Cas9


title: BV2 LPS miR-146a 3

value: LPS 10ng/ml for 24h and overexpressing miR-146a-5p mimic


title: control,rep2

value: lung adenocarcinoma


title: ω- ApoE3WT/PSEN1 E280A (2), scRNA-seq

description: 10x Genomics

value: PSEN1 E280A, APOE3 wt

value: failed CRISPR-Cas10


title: ω- ApoE3WT/PSEN1 E280A (1), scRNA-seq

description: 10x Genomics

value: failed CRISPR-Cas9


title: Vdr+/+ kidney 1

description:
GC106651
raw counts_kidney.csv


title: Vdr+/+ kidney 2

description:
GC106652
raw counts_kidney.csv


title: Vdr+/+ kidney 6

description:
GC106688
raw counts_kidney.csv


title: ddp,rep1


title: BV2 vehicle neg ctrl (scramble) 1

value: Glioblastoma

value: WT

value: 2 months old mice


title: Vdr AF2 duodenum 4

description:
GC106764
raw counts_duodenum.csv

source_name: duodenum

value: duodenum

value: delta AF2


title: s12: b-glucan-treated LSK cells from Spleen

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

data_processing:
Quality of sequencing was assessed using FastQC software.
Raw reads in fastq format were collected and aligned to the mouse genome using STAR 2.6 algorithm.
Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package (glmFit model) in R.
Assembly: mm10
Supplementary files format and content: csv file include CPM values for each Sample

source_name: b-glucan-treated LSK cells from Spleen

growth_protocol: HSPC were sorted from the F1-L BM and spleen, either treated with β-glucan or PBS.

extract_protocol:
RNA was extracted using the PicoPure kit according to the manufacturer’s instructions.
DNA-free kit was used to remove any DNA traces from  the samples.
mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2.
Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500.

treatment_protocol: Female 3-months-old NZBW/F1 mice were injected i.p. with either 1mg of  β-glucan peptide in 200uL of PBS or 200uL PBS  as control every 15 days, till the age of 6 months old.

value: hematopoietic stem and progenitor cells

value: b-glucan

value: 6 months old

value: Spleen


title: α- ApoE3Ch/PSEN1WT, scRNA-seq

description: 10x Genomics

value: cerebral organoid

value: PSEN1 wt, APOE3 R136S


title: α- ApoE3Ch/PSEN1 E280A (2), scRNA-seq

description: 10x Genomics

value: PSEN1 E280A, APOE3 R136S


title: control,rep1

value: control


title: s11: b-glucan-treated LSK cells from Spleen


title: α- ApoE3Ch/PSEN1 E280A (1), scRNA-seq

description: 10x Genomics


title: Vdr AF2 duodenum 3

description:
GC106763
raw counts_duodenum.csv

value: Inotiv TD.96348


title: s10: b-glucan-treated LSK cells from Spleen


title: α- ApoE3WT/PSEN1 E280A, scRNA-seq

description: 10x Genomics

value: PSEN1 E280A, APOE3 wt

value: successful CRISPR-Cas9


title: Vdr+/+ kidney 5

description:
GC106687
raw counts_kidney.csv

value: kidney cortex

value: wildtype


title: Vdr AF2 duodenum 2

description:
GC106762
raw counts_duodenum.csv


title: s9: PBS-treated LSK cells from Spleen

source_name: PBS-treated LSK cells from Spleen

value: PBS


title: Old_Replicates 2

city: Villigen

first: Shivashankar

last: GV

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institut

data_processing:
Hi-C sequencing reads were mapped to the human genome using the bwa software
The pairtools software (version 0.3.0) was used to filter the Hi-C mapped reads and remove PCR/optical duplicates
The derived .pairs files were converted to the .hic file format using Juicer tools software
For bias correction, the matrix-balancing method INTER_SCALE that is specifically designed for inter-chromosomal contacts from Juicer tools was used to normalize the inter-chromosomal maps. Furthermore, low-confidence regions such as repeats, centromeres, as well as pericentromeric regions (+/- 2 Mb) were filtered out using the annotations from the UCSC table browser.
The filtered Hi-C values were then log(x+1) transformed and z-scored by subtracting the mean and dividing through the standard deviation over all inter-chromosomal contacts
Assembly: GRCh38/hg38

growth_protocol: Cells were cultured in MEM media containing 15%FBS, 1% Penstrep, 1% Non essential amino acids and 1% GlutaMAX in a cell culture incubator with 5% Co2 and 37C.

extract_protocol:
Cells were fixed with formaldehyde followed by quenching using 1M Glycine. Fixed cells were then processed for cell lyses using cell lyses buffer followed by restriction digetion with HindIII ovenight. Digested genome was end repair followed by DNA ligation, purification of HiC DNA using ethanol precepitation.
HiC libraires were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: For Rejuvenation we took the GM08401 cells and cultured on fixed micropattern size 78*190 for 8 days with MEM complete medium and for re-differentiation or rejuvenation we kept thte collagen gel with 1mg/ml concentration on these day 8 spheroid and cultured for 48 hours.

value: Dermal Fibroblast

value: Wild type


title: Old_Replicates 1


title: Rejuvenation Replicate1

value: Reprogrammed and re-differentiaed


title: Vdr AF2 duodenum 1

description:
GC106761
raw counts_duodenum.csv

value: duodenum

value: delta AF2


title: Rejuvenation Replicate2


title: s7: PBS-treated LSK cells from Spleen

value: hematopoietic stem and progenitor cells

value: 6 months old


title: CK-PRE-BM

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing analysis was carried out using 10X Genomics’ CellRanger software. Fastq files were generated using the CellRanger mkfastq pipeline.
Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger count pipeline. The expression matrices from different samples were concatenated.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Bone Marrow

extract_protocol:
FACS-purified live BM MNCs or Lin-CD34+ cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: Bone Marrow Mononuclear cells

value: Baseline


title: Vdr-/- duodenum 3

description:
GC106745
raw counts_duodenum.csv

value: knockout


title: Vdr-/- duodenum 4

description:
GC106746
raw counts_duodenum.csv

value: Inotiv TD.96348


title: s6: b-glucan-treated LSK cells from Bone Marrow

value: b-glucan


title: s8: PBS-treated LSK cells from Spleen

value: Spleen


title: CK-C8-CD34pos

value: Bone Marrow CD34+ cells

value: Canakinumab C14D36


title: CK-C8-BM


title: s5: b-glucan-treated LSK cells from Bone Marrow


title: Vdr-/- duodenum 1

description:
GC106743
raw counts_duodenum.csv


title: CK-82-BM

value: Canakinumab C11D29


title: CK-82-CD34pos


title: s4: b-glucan-treated LSK cells from Bone Marrow


title: CK-70-CD34pos

value: Canakinumab C8D29


title: CK-70-BM


title: Vdr+/+ duodenum 6

description:
GC106760
raw counts_duodenum.csv

value: wildtype


title: s3: PBS-treated LSK cells from Bone Marrow

source_name: PBS-treated LSK cells from Bone Marrow

value: PBS


title: Vdr-/- duodenum 2

description:
GC106744
raw counts_duodenum.csv

value: duodenum


title: CK-58-CD34pos

value: Canakinumab C5D29


title: Vdr+/+ duodenum 5

description:
GC106759
raw counts_duodenum.csv


title: CK-58-BM


title: s2: PBS-treated LSK cells from Bone Marrow

value: hematopoietic stem and progenitor cells


title: ω- ApoE3WT/PSEN1WT, scRNA-seq

description: 10x Genomics

value: cerebral organoid

value: PSEN1 wt, APOE3 wt

value: successful CRISPR-Cas9


title: Vdr+/+ duodenum 4

description:
GC106742
raw counts_duodenum.csv


title: s1: PBS-treated LSK cells from Bone Marrow

value: 6 months old

value: Bone Marrow


title: Young_Replicate1

value: Dermal Fibroblast

value: Wild type


title: CK-51-BM

value: Bone Marrow Mononuclear cells

value: Canakinumab C4D29


title: CK-PRE-CD34pos

value: Bone Marrow CD34+ cells

value: Baseline


title: AM21_AM_TB_Fresh

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

data_processing:
Sequence quality was assessed using FastQC, and sequencing adapters were removed using AdapterRemoval. Reads were aligned to the human genome (GRCh38) using STAR. Alignments were assessed with Picard and filtered to paired, non-PCR duplicate, primary alignments with mapping quality > 30 using samtools. Reads in genes were counted with Rsubread.
Assembly: hg38
Supplementary files format and content: Raw counts in genes. Comma delimited. Libraries are columns. Genes are rows labeled with their ENSEMBL gene ID

source_name: bronchoalveolar lavage

growth_protocol: Cyropreserved PBMCs were differentiated for 5 days in M-CSF and then CD14 negative column isolated to obtain MDMs. Fresh bronchoalveolar lavage samples were treated with streptomycin and penicillin, washed with HBSS to remove non-adherent cells, and rested overnight to obtain AMs. MDMs and AMs were cultured in RPMI/20% autologous serum.

extract_protocol:
Samples were thawed, mixed with chloroform, and the aqueous layer plus 50% ethanol was processed using miRNeasy Mini Kit with DNA digestion by DNAse I.
AM.MDM.Mtb libraries were prepared using Clontech SMARTer stranded v2 Pico Mammalian kit and sequenced on a NovaSeq6000 SP flow cell. MDM.IFN libraries were prepared usingNEBNext Ultra II Directional RNA Library Prep Kit and sequenced on a NovaSeq6000 S4 flow cell. AM.cryo libraries were prepared using Clontech SMARTer stranded v2 Pico Mammalian kit and sequenced on a NovaSeq6000 S1 flow cell.

treatment_protocol: Mycobacterium tuberculosis H37Rv strain was used in infection experiments at a multiplicity of infection (MOI) 1:1 for 6 hours. Cells were lysed and preserved in TRIzol.

value: bronchoalveolar lavage

value: alveolar macrophage

value: M. tuberculosis

value: Fresh


title: Vdr+/+ duodenum 2

description:
GC106724
raw counts_duodenum.csv

value: duodenum

value: wildtype

value: Inotiv TD.96348


title: CK-42-CD34pos

value: Canakinumab C2D32


title: Vdr+/+ duodenum 3

description:
GC106741
raw counts_duodenum.csv


title: Adult2, periphery, CD70p, rep2

first: Yi-Rong

last: Peng

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

description: 10X Genomics, scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: calJac4
Supplementary files format and content: Tab-separated values files and matrix files

organism: Callithrix jacchus

source_name: Retina

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by antibody staining and beads-enrichment or FACS sorting .
Foveal and peripheral retina tissues were dissected from neonatal and adult marmoset retinas. The foveal piece (~1.5mm in diameter) of the retina containing the whole fovea area was dissected out and dissociated into individual cells for high throughput droplet-based single cell RNA sequencing (scRNA-seq, 10x Genomics). The peripheral area (any area 5mm away from the foveal center) was also dissociated into a single cell suspension and underwent two enrichment procedures. We first used CD73, a photoreceptor marker, to label photoreceptors and used a microbeads-conjugated secondary antibody to deplete all the CD73 labeled cells (1). Second, we enriched RGCs and ACs with CD90 positive selection via fluorescence-activated cell sorting (FACS). The peripheral cells after CD73 depletion or CD90 enrichment were used to generate scRNA-seq libraries (10X Genomics). Libraries were sequenced on the Illumina HiSeq 2500 platform. The peripheral retinal tissues of an adult marmoset were snap frozen with dry ice. Nuclei were isolated with ice-cold Nuclei EZ lysis buffer and resuspended with 1%BSA/1X PBS. Nuclei were stained with anti-NeuN-PE (Millipore) for 30min at 4C. After washing and resuspension, the nuclei solution was additionally stained with Dyecycle Ruby (Thermo Fisher) before sorting. NeuN-positive and Dyecycle-positive nuclei were sorted via FACS. The sorted nuclei were used to generate single nuclei sequencing (snRNA-seq) libraries (10X Genomics) and were sequenced on the Illumina NovaSeq S4 platform.Frozen foveal and peripheral retinas were retrieved from a -80 °C freezer and placed on ice. Nuclei from these frozen samples were separately isolated using Lysis Buffer and Nuclei Isolation Columns from the Chromium Nuclei Isolation Kit (10X Genomics) following the Manufacturer’s User Guide. The isolated nuclei were then resuspended in Resuspension Buffer (10X Genomics). ScATAC-seq libraries were generated from the recovered nuclei using the Chromium Next GEM Single Cell ATAC Reagent v2 Kit (10X Genomics). The quantity and quality of the scATAC-seq libraries were evaluated using Qubit fluorometers (Thermo Fisher) and Tapestation (Agilent). ScATAC-seq libraries were sequenced on the Illumina Novaseq X Plus 10B platform.

value: Retina

value: Retinal cell types


title: CK-42-BM

value: Bone Marrow


title: AM21_AM_TB_Cryo

value: Frozen


title: AM21_AM_Media_Cryo

value: Media


title: AM21_AM_Media_Fresh


title: Mutant 3 [BL121]

first: Mingyi

last: Zhang

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
Upper quartile was used to normalize the data and differential expression was calculated by selecting transcripts that changed with FDR<0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: incisor

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
The mouse incisor samples from control and Gli1-CreER;Arid1bfl/fl (mutant) mice were collected at 4 days post-tamoxifen induction for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
cDNA library preparation and sequencing were performed at the Molecular Genomics Core at the University of Southern California.

value: incisor

value: TMX induction


title: Adult2, periphery, CD73dp, rep1

description: 10X Genomics, scRNA-seq


title: Mutant 2 [BL116]


title: AM18_AM_Media_Cryo


title: AM18_AM_TB_Cryo


title: Adult2, fovea, rep2

description: 10X Genomics, scRNA-seq


title: TRIMA22_MDM_untreated

source_name: blood

value: blood

value: monocyte-derived macrophage


title: Young_Replicate2

value: Dermal Fibroblast

value: Wild type


title: Adult2, fovea, rep1

description: 10X Genomics, scRNA-seq


title: TRIMA22_MDM_IFNg

value: IFNg


title: Mutant 1 [BL57]


title: TRIMA22_MDM_IFNb

value: IFNb


title: TRIMA22_MDM_IFNA8


title: Adult1, fovea, rep3

description: 10X Genomics, scRNA-seq


title: CK-51-CD34pos

value: Bone Marrow CD34+ cells

value: Canakinumab C4D29


title: Control 3 [BL53]

value: wild type


title: Adult2, periphery, CD73dp, rep2

description: 10X Genomics, scRNA-seq


title: Adult1, fovea, rep2

description: 10X Genomics, scRNA-seq


title: Control 2 [BL52]


title: Adult1, fovea, rep1

description: 10X Genomics, scRNA-seq


title: Control 1 [BL18]


title: TRIMA21_MDM_IFNA8


title: TRIMA21_MDM_IFNe

value: IFNe


title: Vdr+/+ duodenum 1

description:
GC106723
raw counts_duodenum.csv

value: duodenum

value: wildtype

value: Inotiv TD.96348


title: TRIMA21_MDM_IFNg

value: Frozen


title: TRIMA21_MDM_untreated

value: Media


title: Neonate2, periphery, CD73dp, rep4

description: 10X Genomics, scRNA-seq

value: Retina

value: Retinal cell types


title: TRIMA21_MDM_IFNb

value: blood


title: C352_MDM_untreated

value: monocyte-derived macrophage


title: Neonate2, periphery, CD73dp, rep3

description: 10X Genomics, scRNA-seq


title: C352_MDM_IFNA8


title: Hippocampus, BL6129, Veh treated, rep4

city: Rochester

first: Cheng

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
paired-end RNA-seq reads were aligned with STAR using 2-pass mode.
Gene level counts were obtained using the subRead featureCounts program.
Assembly: mm10
Supplementary files format and content: tab-delimited gene-level count

source_name: Hippocampus

extract_protocol:
Crushed frozen hippocampi were homogenized through QIAshredder (Qiagen #79656), and RNA was extracted using the RNeasy Mini Kit (Qiagen #74104), using their standard protocol. Quality of extracted RNA was assessed using an RNA Integrity Number (RIN) and a DV200 value generated by the Agilent Fragment Analyzer. Qualitative concentration was determined using a Qubit Fluorometer.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at 50 million fragment reads per sample following Illumina’s standard protocol Illumina’s standard protocol using the Illumina NovaSeq™ 6000 and S1 flow cell. The flow cells were sequenced as 100 X 2 paired end reads using NovaSeq S1 sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed using Illumina’s RTA version 3.4.4.

value: Hippocampus

tag: Sex

value: female

value: Veh


title: Hippocampus, BL6129, Veh treated, rep3


title: TRIMA22_MDM_IFNe


title: C352_MDM_IFNg

value: IFNg


title: C352_MDM_IFNb

value: IFNb


title: Neonate2, periphery, CD90 rep1

description: 10X Genomics, scRNA-seq


title: Neonate2, fovea, rep2

description: 10X Genomics, scRNA-seq


title: Hippocampus, BL6129, Veh treated, rep1


title: Neonate2, fovea, rep1

description: 10X Genomics, scRNA-seq


title: BB2_MDM_IFNg


title: Hippocampus, BL6129, NAVI treated, rep4

value: NAVI


title: IMM cells, 120 minute LPS Stimulation Rep 3

type: RNA

city: Bethesda

first: Matthew

middle: James

last: Marino

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

hyb_protocol: Hybridization was carried out according to the NanoString manufacturer Guidelines.

scan_protocol: Scanning was carried out by the NCI CCR Genomics core according to the NanoString manufacturer Guidelines.

data_processing: Raw files and the RLF were imported into nSolver Analysis 4.0. Normalization was performed relative to the unstimulated 0 minute timepoint using the Normalize function provided in the software.

label: Nanostring

source_name: IMM, 120 minute LPS Stimulation

growth_protocol: IMM cells maintained in cDMEM. DMEM supplemented with heat inactivated 10% FBS and 0.02M HEPES in a humidified atmosphere with 5% CO2 and 37C.

extract_protocol: RNA was harvested with the miRNeasy mini plus kit (Qiagen)

treatment_protocol: After 5 passages following thaw from -80C in cDMEM, LPS (Enzo Life Sciences) was used to stimulate the cells (100 ng / mL in cDMEM) at the 0, 30, 60, and 120 minute timepoints. After stimulation the plates (10 cm treated dishes) had the LPS containing media aspirated off the top and were immediately placed on ice. 2 washes with ice cold PBS were performed before the addition of lysis buffer.

value: IMM


title: BB2_MDM_IFNe

value: IFNe


title: BB2_MDM_IFNb


title: IMM cells, 120 minute LPS Stimulation Rep 1


title: C352_MDM_IFNe


title: IMM cells, 60 minute LPS Stimulation Rep 3

source_name: IMM, 60 minute LPS Stimulation


title: Neonate1, periphery, CD73dp, rep1

description: 10X Genomics, scRNA-seq


title: Hippocampus, BL6129, NAVI treated, rep1


title: Hippocampus, BL6129, Veh treated, rep2


title: Hippocampus, BL6129, DQ treated, rep3

value: DQ


title: Neonate1, fovea, rep2, tech rep1

description: 10X Genomics, scRNA-seq


title: BB2_MDM_untreated


title: Neonate1, fovea, rep2, tech rep2

description: 10X Genomics, scRNA-seq


title: Hippocampus, BL6129, DQ treated, rep4


title: IMM cells, 30 minute LPS Stimulation Rep 3

source_name: IMM, 30 minute LPS Stimulation


title: IMM cells, 60 minute LPS Stimulation Rep 1


title: Neonate1, fovea, rep1

description: 10X Genomics, scRNA-seq


title: IMM cells, 30 minute LPS Stimulation Rep 2


title: IMM cells, 120 minute LPS Stimulation Rep 2


title: Hippocampus, BL6129, DQ treated, rep2


title: BB1_MDM_IFNe


title: Neonate1, fovea, rep2, tech rep3

description: 10X Genomics, scRNA-seq


title: BB2_MDM_IFNA8


title: 5_Monozyten_unstim

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

description:
215_27_TTAGGC_L002_R1_001
215_27

data_processing:
Mapped filtered reads against GRCh38 reference genome using STAR (v2.5.2b) aligner allowing for soft clipping of adapter  sequences. For quantification, we used transcript annotation files from Ensembl version 86.
Quantify gene expression levels based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For quality control use FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.2.2).
Assembly: GRCh38
Supplementary files format and content: MoMF_counts.csv: comma separated csv file containing raw counts
Supplementary files format and content: MoMF_tpm.csv: comma separated csv file containing raw transcripts per million (tpm)

source_name: blood (PBMC)

growth_protocol: Monocytes were cultured in X-VivoTM 15 media (Lonza) containing 1 % PenStrep (Gibco) and 2 % HSA (Gibco).

extract_protocol:
To extract RNA, cells were harvested, washed with PBS and lysed in RLT Plus Buffer (Qiagen) followed by extraction of RNA using Rneasy® Mini Kit (Qiagen), according to the manufacturers’ protocol. Extracted RNA samples were quantified by NanoDrop™ 8000 Spectrophotometer (Thermo Fisher Scientific) or NanoPhotometer® N120 (Implen).
For sequencing library preparation, 100ng of total RNA was used as input for the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122–2002, Illumina Inc, San Diego, CA) producing a 275 bp fragment including adapters in average size. Eight libraries were normalized and pooled together on a single lane and sequenced as 52 bp, single reads and 7 bases index read on an Illumina HiSeq2000 instrument using the TruSeq SBS Kit HS- v3 (50-cycle) (FC-401–3002, Illumina Inc, San Diego, CA).

treatment_protocol: For differentiation into macrophages 100 ng/ml rhM-CSF (Macrophage Colony-stimulating Factor) (R&D) was added for 7 days

value: blood (PBMC)

value: Monocyte/Macrophages

value: Untreated control

tag: donor id


title: IMM cells, 30 minute LPS Stimulation Rep 1


title: Hippocampus, BL6129, DQ treated, rep1


title: IMM cells, 60 minute LPS Stimulation Rep 2


title: 3_Monozyten_unstim

description:
215_16_ACTTGA_L004_R1_001
215_26


title: BB1_MDM_untreated

value: Media

value: Frozen


title: BB1_MDM_IFNA8


title: BB1_MDM_IFNg


title: Hippocampus, BL6129, NAVI treated, rep3


title: 4_M_CSF_unstim

description:
215_19_TTAGGC_L005_R1_001
215_24

value: M-CSF


title: Hippocampus, 3xTg, VehD treated, rep3

value: VehD


title: 5_M_CSF_unstim

description:
215_24_ACTTGA_L008_R1_001
215_25


title: AM19_MDM_Media

value: blood

value: monocyte-derived macrophage


title: AM19_MDM_TB

value: M. tuberculosis


title: Hippocampus, 3xTg, VehD treated, rep2

value: Hippocampus

value: female


title: IMM cells, 0 minute LPS stimulation Rep 2

source_name: IMM, 0 minute LPS Stimulation


title: IMM cells, 0 minute LPS stimulation Rep 3


title: 3_M_CSF_unstim

description:
215_13_ACAGTG_L004_R1_001
215_21


title: IMM cells, 0 minute LPS stimulation Rep 1


title: Hippocampus, 3xTg, VehD treated, rep1


title: 2_M_CSF_unstim

description:
215_7_CAGATC_L003_R1_001
215_20


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (10 uM)_rep3 [3-5]

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the mouse reference genome GRCm38 (mm10) using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCm38.86.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days.

extract_protocol:
Total RNA was isolated from cells using Maxwell (Promega) based method.
One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.  The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

treatment_protocol: We obtained gRc and dexamethasone from Sigma (St Louis, MO, USA). gRc was dissolved in 100% dimethyl sulfoxide (DMSO; Sigma) to a final concentration of 20 mM and 200 mM, respectively, filtered, and stored at -20°C until use. Myotubes were treated with vehicle (0.1% DMSO), 10 µM and 20 µM gRc, or 200 µM dexamethasone for indicated times.

value: dexamethasone 200 uM, ginsenoside Rc 10 uM

value: 36 hr (gRc 10 uM), Pre-treatment 12 h) + (DEX 24 h)


title: AM19_AM_Media

value: bronchoalveolar lavage

value: alveolar macrophage

value: Fresh


title: Hippocampus, 3xTg, VehD treated, rep4


title: Batch1_dexamethasone (200 uM)_rep3 [3-4]

value: dexamethasone 200 uM

value: 36 hr (0.1% DMSO, Pre-treatment 12 h) + (DEX 24 h)


title: AM18_MDM_TB


title: Hippocampus, 3xTg, VehN treated, rep3

value: VehN


title: 1_M_CSF_unstim

description:
215_3_TTAGGC_L003_R1_001
215_19

value: blood (PBMC)

value: Monocyte/Macrophages


title: Hippocampus, 3xTg, VehN treated, rep4


title: AM18_MDM_Media

value: Media

value: Frozen


title: 5_M_CSF_LPS_IFN_gamma

description:
215_26_CGATGT_L008_R1_001
215_16

value: M-CSF+LPS+IFN-gamma


title: Batch1_ginsenoside Rc (20 uM)_rep3 [3-3]

value: ginsenoside Rc 20 uM

value: 36 hr


title: 4_M_CSF_LPS_IFN_gamma

description:
215_21_ACAGTG_L005_R1_001
215_15


title: Hippocampus, 3xTg, VehN treated, rep1

value: Hippocampus


title: Batch1_control_rep3 [3-1]

value: 0.1% DMSO


title: 3_M_CSF_LPS_IFN_gamma

description:
215_15_CAGATC_L004_R1_001
215_14


title: Batch1_ginsenoside Rc (10 uM)_rep3 [3-2]

value: ginsenoside Rc 10 uM


title: AM18_AM_TB

value: M. tuberculosis


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (20 uM)_rep2 [2-6]

value: dexamethasone 200 uM, ginsenoside Rc 20 uM

value: 36 hr (gRc 20 uM), Pre-treatment 12 h) + (DEX 24 h)


title: AM18_AM_Media

value: bronchoalveolar lavage

value: alveolar macrophage

value: Fresh


title: Hippocampus, 3xTg, VehN treated, rep2

value: female

value: VehN


title: 2_M_CSF_LPS_IFN_gamma

description:
215_9_ATCACG_L004_R1_001
215_13

value: blood (PBMC)

value: Monocyte/Macrophages


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (20 uM)_rep3 [3-6]


title: AM19_AM_TB


title: AM17_MDM_TB

value: blood

value: monocyte-derived macrophage

value: Frozen


title: Neonate1, periphery, CD73dp, rep2

description: 10X Genomics, scRNA-seq

value: Retina

value: Retinal cell types


title: 5_M_CSF_IL_4_ IL_13

description:
215_25_ATCACG_L002_R1_001
215_9


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (10 uM)_rep2 [2-5]

value: dexamethasone 200 uM, ginsenoside Rc 10 uM

value: 36 hr (gRc 10 uM), Pre-treatment 12 h) + (DEX 24 h)


title: AM17_MDM_Media

value: Media


title: Hippocampus, 3xTg, NAVI treated, rep2

value: Hippocampus

value: NAVI


title: Batch1_dexamethasone (200 uM)_rep2 [2-4]

value: dexamethasone 200 uM

value: 36 hr (0.1% DMSO, Pre-treatment 12 h) + (DEX 24 h)


title: AM17_AM_TB

value: bronchoalveolar lavage

value: alveolar macrophage

value: M. tuberculosis

value: Fresh


title: Hippocampus, 3xTg, NAVI treated, rep1

value: female


title: Batch1_ginsenoside Rc (20 uM)_rep2 [2-3]

value: ginsenoside Rc 20 uM

value: 36 hr


title: AM17_AM_Media


title: Hippocampus, BL6129, NAVI treated, rep2


title: Hippocampus, 3xTg, DQ treated, rep4

value: DQ


title: Hippocampus, 3xTg, NAVI treated, rep4


title: 2_M_CSF_IL_4_ IL_13

description:
215_8_ACTTGA_L003_R1_001
215_4

value: blood (PBMC)

value: Monocyte/Macrophages


title: Batch1_ginsenoside Rc (10 uM)_rep2 [2-2]

value: ginsenoside Rc 10 uM


title: Hippocampus, 3xTg, DQ treated, rep2


title: AM15_MDM_Media

value: blood

value: monocyte-derived macrophage

value: Frozen


title: 3_M_CSF_IL_4_ IL_13

description:
215_14_GCCAAT_L004_R1_001
215_7


title: 1_M_CSF_IL_4_ IL_13

description:
215_4_TGACCA_L003_R1_001
215_3


title: 3_Hepatic_Stellate_Cell_TNFA_20ng_per_ml_72h

data_processing:
Mapped filtered reads against GRCh38 reference genome using STAR (v2.5.2b) aligner allowing for soft clipping of adapter  sequences. For quantification, we used transcript annotation files from Ensembl version 86.
Quantify gene expression levels based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For quality control use FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.2.2).
Assembly: GRCh38
Supplementary files format and content: HSC_counts.csv: comma separated csv file containing raw counts
Supplementary files format and content: HSC_tpm.csv: comma separated csv file containing raw transcripts per million (tpm)

source_name: liver

growth_protocol: Primary human HSC, purchased from Zenio, were used for supernatant transfer assay between passage 2 and 5. Cells were cultured in SteCM Stellate Cell Medium (ScienCell™) containing 2 % FBS (ScienCell™), 1 % P/S Solution (ScienCell™) and 1 % SteCGS (ScienCell™). Primary HHStecs were seeded in 24 well plates at 60,000 cells per well density. After 2h, medium was replaced for starvation (w/o FBS, SteCGS) for additional 22h.

treatment_protocol: Supernatant of stimulated immune cells was added in 1:6 dilution and incubated for 48 h. As positive control rhTGF-β1 (R&D) was used in different concentrations (0.1, 1, 2 and 10 ng/ml).

value: liver

value: Hepatic stellate cell


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (20 uM)_rep1 [1-6]

value: dexamethasone 200 uM, ginsenoside Rc 20 uM

value: 36 hr (gRc 20 uM), Pre-treatment 12 h) + (DEX 24 h)


title: Hippocampus, 3xTg, DQ treated, rep3

value: Hippocampus


title: Hippocampus, 3xTg, DQ treated, rep1


title: Hippocampus, 3xTg, NAVI treated, rep3

value: NAVI


title: AM15_AM_Media

value: bronchoalveolar lavage

value: alveolar macrophage

value: Media

value: Fresh


title: AM15_AM_TB

value: M. tuberculosis


title: Batch1_dexamethasone (200 uM)_ginsenoside Rc (10 uM)_rep1 [1-5]

value: dexamethasone 200 uM, ginsenoside Rc 10 uM

value: 36 hr (gRc 10 uM), Pre-treatment 12 h) + (DEX 24 h)


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep4

city: COLUMBUS

first: Deqiang

last: Li

state: Ohio

address: 575 Children’s Crossroad, WB4321

institute: Nationwide Children's Hospital

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
For the samples with biological replicates:  Differential expression analysis of two conditions/groups was performed using  the DESeq R package (1.6.3). The padj<0.05 was set as the threshold for significantly differential expression by default
Assembly: mm10

source_name: Mouse Cardiac Endothelial Cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of RNA was used for the construction of sequencing libraries.
llumina standard protocols

value: Mouse Cardiac Endothelial Cell

value: Mouse Cardiac Endothelial Cells

value: Hdac3 knockout

value: Hdac3 sgRNA lentivirus transduction


title: Batch1_dexamethasone (200 uM)_rep1 [1-4]

value: dexamethasone 200 uM

value: 36 hr (0.1% DMSO, Pre-treatment 12 h) + (DEX 24 h)


title: 1_Hepatic_Stellate_Cell_TNFA_20ng_per_ml_72h

value: liver

value: Hepatic stellate cell


title: Batch1_control_rep2 [2-1]

value: 0.1% DMSO

value: 36 hr


title: AM12_MDM_TB

value: blood

value: monocyte-derived macrophage

value: Frozen


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep3


title: Batch1_ginsenoside Rc (20 uM)_rep1 [1-3]

value: ginsenoside Rc 20 uM


title: AM15_MDM_TB

value: M. tuberculosis


title: 3_Hepatic_Stellate_Cell_TGFB1_5ng_per_ml_72h


title: AM12_MDM_Media

value: Media


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep2


title: Batch1_ginsenoside Rc (10 uM)_rep1 [1-2]

value: ginsenoside Rc 10 uM


title: 2_Hepatic_Stellate_Cell_TGFB1_5ng_per_ml_72h


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep1

value: Mouse Cardiac Endothelial Cell


title: 1_Hepatic_Stellate_Cell_TGFB1_5ng_per_ml_72h


title: AM12_AM_TB

value: bronchoalveolar lavage

value: alveolar macrophage

value: Fresh


title: 2_Hepatic_Stellate_Cell_TNFA_20ng_per_ml_72h


title: Batch1_control_rep1 [1-1]


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep4

value: Mouse Cardiac Endothelial Cells

value: CTL

value: Empty vector lentivirus transduction


title: Cardiac ventricle, cox7a1-/-, replicate 4

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

institute: University of Bern

description:
NextSeq P2 100 cycles Flowcell (400 M)
KO_10

data_processing:
Data were quality checked with Fastqc and Multiqc
Sequences were trimmed with fastp
2 pass alignment was performed with STAR Aligner
reads were dounted using featurecounts
Normalization and downstream analysis including differential expression analysis was performed in R
Assembly: GRCz11 v109 Ensembl
Supplementary files format and content: feature counts, tab seprated values

organism: Danio rerio

source_name: Cardiac Ventricle

extract_protocol:
4 pools each comprising 5 ventricles were sequenced per condition.
Libraries for RNA-seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol

value: Cardiac Ventricle


title: 2_Hepatic_Stellate_Cell_IL13_10ng_per_ml_72h

value: liver

value: Hepatic stellate cell


title: AM12_AM_Media


title: 3_Hepatic_Stellate_Cell_IL13_10ng_per_ml_72h


title: BB1_MDM_IFNb

value: blood

value: IFNb


title: Cardiac ventricle, cox7a1-/-, replicate 3

description:
NextSeq P2 100 cycles Flowcell (400 M)
KO_9


title: 1_Hepatic_Stellate_Cell_IL13_10ng_per_ml_72h


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep3


title: Cardiac ventricle, cox7a1-/-, replicate 2

description:
NextSeq P2 100 cycles Flowcell (400 M)
KO_8


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep2


title: AM10_MDM_Media

value: monocyte-derived macrophage

value: Frozen


title: 3_Hepatic_Stellate_Cell_Control_72h

value: Unstimulated control


title: AM10_AM_TB

value: M. tuberculosis


title: Cardiac ventricle, cox7a1-/-, replicate 1

description:
NextSeq P2 100 cycles Flowcell (400 M)
KO_7


title: Bulk RNA_Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep1


title: AM10_AM_Media

value: Media


title: Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep3

data_processing:
Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality. Each read has four descriptive sentences in as follow:
For the samples with biological replicates:  Differential expression analysis of two conditions/groups was performed using  the DESeq R package (1.6.3). The padj<0.05 was set as the threshold for significantly differential expression by default
Assembly: mm10

extract_protocol:
Total RNA was harvested using miRNeasy Micro kit (Qiagen). 3 ug of total RNA was used for the construction of sequencing libraries.
llumina standard protocols

value: Mouse Cardiac Endothelial Cell

value: Hdac3 knockout

value: Hdac3 sgRNA lentivirus transduction


title: 2_Hepatic_Stellate_Cell_Control_72h


title: AM10_MDM_TB


title: Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep2


title: Cardiac ventricle, wt sibling, replicate 4

description:
NextSeq P2 100 cycles Flowcell (400 M)
WT_5

value: WT


title: Cardiac ventricle, wt sibling, replicate 3

description:
NextSeq P2 100 cycles Flowcell (400 M)
WT_3


title: Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep1

value: Mouse Cardiac Endothelial Cells


title: CMV CSP, 10 donors, scRNAseq

city: New Delhi

first: Veena

middle: S.

last: Patil

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description:
Expt2_10donors_CSP
10X Genomics
e2_barcodes.tsv.gz
e2_features.tsv
e2_matrix.mtx.gz

data_processing:
Sequenced reads from the 5ʹ single-cell gene expression and associated V(D)J library were mapped to the GRCh38 reference genome using 10X genomics’ cellranger multi (v6.1.1).
count (Cell Ranger 6.1.1) was used to generate the filtered UMI matrix with default parameters
The cell surface protein quantification was run as part of the same pipeline.
The Seurat package (v4.3) in R (v4.2.2) was used to filter, normalize and scale the UMI matrix.
The Seurat package (v4.3) in R (v4.2.2) was used to perform all further downstream analyses.
Assembly: refdata-gex-GRCh38-2020-A from Cell Ranger
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 from Cell Ranger
Supplementary files format and content: e1_barcodes.tsv.gz barcodes data captured for 2,578 cells from 3 donors for virus-reactive cells
Supplementary files format and content: e1_features.tsv meta data captured for 2,578 cells from 3 donors for virus-reactive cells
Supplementary files format and content: e1_matrix.mtx.gz count data captured for 2,578 cells from 3 donors for virus-reactive cells
Supplementary files format and content: e2_barcodes.tsv.gz barcodes data captured for 7,161 cells from 10 donors for CMV-reactive cells
Supplementary files format and content: e2_features.tsv meta data captured for 7,161 cells from 10 donors for CMV-reactive cells
Supplementary files format and content: e2_matrix.mtx.gz count data captured for 7,161 cells from 10 donors for CMV-reactive cells
Supplementary files format and content: e1_clonotypes.csv clonotype information captured from 2,578 cells from 3 donors for virus-reactive cells
Supplementary files format and content: e1_filtered_contig_annotations.csv clonotype meta data captured from 2,578 cells from 3 donors for virus-reactive cells
Supplementary files format and content: e2_clonotypes.csv clonotype information captured from 7,161 cells from 10 donors for CMV-reactive cells
Supplementary files format and content: e2_filtered_contig_annotations.csv clonotype meta data captured from 7,161 cells from 10 donors for CMV-reactive cells

molecule: polyA RNA

source_name: Blood

extract_protocol:
For single-cell RNA-seq using 10X genomics, PBMCs from 10 donors that showed highest response to peptide stimulation in preliminary experiments, were stimulated with pp65 and IE-1 PepTivators for 6 and 24 hrs. The stimulated cells from each donor were washed and individually stained with Cell-hashtag (HTO:Hash Tag Oligo; D1-D10) TotalSeq C antibody (Biolegend) (0.5 µg/condition) as per manufacturer’s recommendations for 30 minutes on ice. The stained and washed PBMCs from all 10 donors were then pooled and stained with oligo-tagged TotalSeq C antibody for cell surface proteins for T cell memory markers (CD45RA, CCR7, CD95 and IL7Rα) (Biolegend) (0.5 µg/condition) for 30 minutes on ice. Following washing, the pooled cells were further stained with fluorescence-conjugated surface antibodies to enable FACS sorting of antigen-specific cells. Cells were sorted using FACSAria Fusion Cell Sorter (Becton Dickinson) in LoBind 1.5 mL microcentrifuge (Eppendorf) tubes with 50% FBS supplemented with recombinant RNase inhibitor (1:100, Takara). Cells were then centrifuged for 5 minutes (500 g at 4 C) and the supernatant was carefully removed leaving 5 to 10 µl. 25 µl of resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04 %, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 µl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer's instructions (10x Genomics).
scRNA-Seq with 10x Genomics 5' v1.1; The sorted antigen-specific cells from various memory compartments were pooled in desired ratios and used for single-cell RNA-Seq and TCR-Seq assay using 10X Genomics kit, 5ʹ V(D)J with gene expression and cell surface protein expression v1.1 as per the manufacturer’s recommendations. Initial amplification of cDNA libraries and final libraries were performed for 15 cycles and 14 cycles respectively for gene expression library. V(D)J and cell surface protein libraries were generated corresponding to each 5ʹ gene expression library using 9 cycles of amplification. Libraries were sequenced on Illumina NovaSeq6000 sequencing platform for PE150 reads.

value: Blood

value: CMV-antigen-reactive T cells


title: 1_Hepatic_Stellate_Cell_Control_72h


title: CMV VDJ, 10 donors, scRNAseq

description:
Expt2_10donors_VDJ
10X Genomics


title: Cardiac ventricle, wt sibling, replicate 2

description:
NextSeq P2 100 cycles Flowcell (400 M)
WT_2

value: Cardiac Ventricle


title: Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep3

value: CTL

value: Empty vector lentivirus transduction


title: CMV GEX, 10 donors, scRNAseq

description:
Expt2_10donors_GEX
10X Genomics


title: Cardiac ventricle, wt sibling, replicate 1

description:
NextSeq P2 100 cycles Flowcell (400 M)
WT_1


title: Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep2


title: Mouse Cardiac Endothelial Cell - Empty vector (EV) - rep1


title: 4virus VDJ, 3 donors, scRNAseq

description:
Expt1_3donors_VDJ
10X Genomics

value: CMV, EBV, DENV, Flu-antigen-reactive T cells


title: 4virus CSP, 3 donors, scRNAseq

description:
Expt1_3donors_CSP
10X Genomics
e1_barcodes.tsv.gz
e1_features.tsv
e1_matrix.mtx.gz


title: hPSCs derived-day8 Msx1+Pdgfralow cells with Mock treatment, biol rep 2

city: Chengdu

first: Zhonghan

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: In the all.counts.txt file, the data for this Sample is in column "Mock-Msx1+Pdgfralow, biol rep 2".

data_processing:
Quanlity filtering using fastqc (version 0.11.8) with default parameters.
Trimmed sequence reads were mapped to GRCh38 using HISAT2 software (version 2.1.0).
Read counts for each gene were based on sense-strand data obtained using the featureCounts (version 2.0.3) software from the Subread package.
Assembly: GRCh38
Supplementary files format and content: all.counts.txt: Tab-separated values file including read counts for each Sample.

source_name: human pluripotent stem cell-derived Msx1+Pdgfralow cells

extract_protocol:
RNA was harvested using TRI Reagent (Sigma).
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
The Msx1-P2A-tdTomato-hPSCs were digested by Accutase (STEM CELL, Cat# 07920) for 4 min to form single cells. After counting, cells were suspended with PGM1 medium containing Y27632 and seeded in a new matrigel-coated culture dish with a density of 10,000 cells per square centimeter. The medium containing Y27632 was removed and replaced with PGM1 medium the next day. The cells were washed with a wash medium (DMEM/F12 containing 3 mg/mL BSA and 1% Pen-Strep) to remove the residual PGM1 medium. Then cells were washed with CDMi basic medium (50% F12 (Gibco, Cat# 31765-035) + 50% IMDM (Gibco, Cat# 31980-030) + 1 mg/mL Poly(vinyl alcohol) (Sigma, Cat# P8136) + 450 μM Monothioglycerol (Sigma, Cat# M6145) + 0.7 μg/mL Insulin (Solarbio, Cat# I8830) + 15 μg/ml transferrin (Sigma, Cat# T0665) + 1% Pen-Strep + 1% Lipids concentrate (Gibco, Cat# 11905-031)). The MPS medium (CDMi medium + 50 ng/mL Activin A (Solarbio, Cat# P00101) + 6 μM CHIR99021 (MCE, Cat# HY-10182A) + 40 ng/mL BMP4 (R&D systems, Cat# 314-BP/CF) + 10 ng/mL FGF2 (Peprotech, Cat# 100-18B)) was added at day 0. On day 1, the MPS medium was replaced by LPM medium (CDMi medium + 60 ng/mL BMP4 + 1 μM CHIR99021). This process lasted for 3 days. The day 4 LPM was in an immature state and needed to continue differentiation in the LM medium (CDMi medium + 500 ng/mL FGF8 (MCE, Cat# HY-P70533) + 500 ng/mL FGF10 (MCE, Cat# HY-P4088). When the day 4 cells had been digested with TryPLE for 2 min, the wash medium was added to terminate the digestion. After centrifugation at 450g for 3 min, the cells were resuspended in the LM medium and inoculated into Poly(2-hydroxyethyl methacrylate) (Sigma, Cat# P3932)-treated low-adhesion U-bottom 96-well plates with 25000 cells per well. Cells were centrifuged 300g for 6 min and incubated at 37 ℃ for 24 h to promote pellets formation. On day 5 of collection, the pellets were placed on a low-adhesion 60mm plate treated with Poly(2-hydroxyethyl methacrylate) and cultured for 3 days using the LM medium.
The Msx1-P2A-tdTomato-hPSCs were digested by Accutase (STEM CELL, Cat# 07920) for 4 min to form single cells. After counting, cells were suspended with PGM1 medium containing Y27632 and seeded in a new matrigel-coated culture dish with a density of 10,000 cells per square centimeter. The medium containing Y27632 was removed and replaced with PGM1 medium the next day. The cells were washed with a wash medium (DMEM/F12 containing 3 mg/mL BSA and 1% Pen-Strep) to remove the residual PGM1 medium. Then cells were washed with CDMi basic medium (50% F12 (Gibco, Cat# 31765-035) + 50% IMDM (Gibco, Cat# 31980-030) + 1 mg/mL Poly(vinyl alcohol) (Sigma, Cat# P8136) + 450 μM Monothioglycerol (Sigma, Cat# M6145) + 0.7 μg/mL Insulin (Solarbio, Cat# I8830) + 15 μg/ml transferrin (Sigma, Cat# T0665) + 1% Pen-Strep + 1% Lipids concentrate (Gibco, Cat# 11905-031)). The MPS medium (CDMi medium + 50 ng/mL Activin A (Solarbio, Cat# P00101) + 6 μM CHIR99021 (MCE, Cat# HY-10182A) + 40 ng/mL BMP4 (R&D systems, Cat# 314-BP/CF) + 10 ng/mL FGF2 (Peprotech, Cat# 100-18B)) was added at day 0. On day 1, the MPS medium was replaced by LPM medium (CDMi medium + 60 ng/mL BMP4 + 1 μM CHIR99021). This process lasted for 3 days. The day 4 LPM was then differentiated into LM in the CDMi medium (Mock medium). When the day 4 cells had been digested with TryPLE for 2 min, the wash medium was added to terminate the digestion. After centrifugation at 450g for 3 min, the cells were resuspended in the Mock medium and inoculated into Poly(2-hydroxyethyl methacrylate) (Sigma, Cat# P3932)-treated low-adhesion U-bottom 96-well plates with 25000 cells per well. Cells were centrifuged 300g for 6 min and incubated at 37 ℃ for 24 h to promote pellets formation. On day 5 of collection, the pellets were placed on a low-adhesion 60mm plate treated with Poly(2-hydroxyethyl methacrylate) and cultured for 6 days using the Mock medium.

value: Mock

value: Day 8


title: 4virus GEX, 3 donors, scRNAseq

description:
Expt1_3donors_GEX
10X Genomics


title: hPSCs derived-day8 Msx1+Pdgfralow cells with Mock treatment, biol rep 1

description: In the all.counts.txt file, the data for this Sample is in column "Mock-Msx1+Pdgfralow, biol rep 1".

value: human pluripotent stem cell-derived Msx1+Pdgfralow cells


title: EV, Suicide male, MDD20

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
Data trimmed with cutadapt
Extracellular RNA Communication Consortium’s (ERCC) exceRpt small RNA-Seq pipeline (v.4.6.3)
no mismatch allowed during alignment
filter: excluded miRNAs with less than 10 counts in 70% of subjects per group
Assembly: hg38
Supplementary files format and content: csv file contains filtered raw read counts

source_name: Anterior cingulate cortex-derived Evs

extract_protocol:
QIAzol lysis reagent was added at 5X to each sample, which were then incubated at room temperature for 5 min. 1X of chloroform was added, and the samples were incubated at room temperature for 3 min. They were centrifuged at 12000g at 4 °C for 15 min, and the aqueous phase was collected. 1.5 volumes of 100 % ethanol were added and mixed gently. The mixture was then added to QIAGEN MinElute columns, and the MiRNeasy Micro Kit was used according to the manufacturer’s protocol (QIAGEN).
Libraries were constructed follwing the Galas Lab - 4N library prep - Version 1.0 protocol

treatment_protocol: For each subject, 200-400 mg of brain tissue were cut into very fine pieces while still partially frozen. The tissue was then incubated in Hibernate E medium (800 µL / 100 mg of tissue) in the presence of 75 U/mL of collagenase type III at 37 oC for 20 min with gentle shaking. The reaction was then halted using protease (PI) and phosphatase (PS) inhibitors (1X) , and the sample was centrifuged at 300g for 5 min. The pellet was homogenized in phosphate buffered saline (PBS) with 1X PI/PS, while the supernatant was collected and centrifuged at 2,000g for 10 min. The supernatant was collected again and centrifuged at 10,000g for 30 min. The supernatant was overlaid on a size exclusion column for extracellular vesicle (EV) separation according to the manufacturer’s protocol. Samples were then concentrated using Amicon centrifugal filters. EVs were treated with Proteinase K at 37 °C for 30 min, then with PureLink RNAseA at room temperature for 2 min.

value: Anterior cingulate cortex-derived Evs

tag: gender

value: male

tag: sample type

value: MDD


title: EV, Control male, CTRL20

value: control


title: EV, Suicide male, MDD19


title: KYSE-150_NSUN6_KD_rnc

city: guangzhou

first: hui

last: han

state: guangdong

address: yuexiu

institute: the first affiliated hospital，sun yat-sen university

data_processing:
Reads were aligned to hg19 using tophat
High quality reads were mapped to UCSC human reference genome(GRCh37/hg19). The gene expression level (Columns 2 to 4 in the txt file)  was normalized by using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method. Translational efficiency (TE Column 5 in the txt file) were calculated using the following formula: TE = (FPKM in RNC)/(FPKM in input).
Assembly: hg19
Supplementary files format and content: txt

source_name: esophagus

growth_protocol: KYSE-150 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
Cells were treated with 100μg/ml cycloheximide and then incubated with 1ml cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer) [20mM HEPES-KOH (pH 7.4), 15mM MgCl2, 200mM KCl, 100μg/ml cycloheximide and 2mM dithiothreitol] on ice. 30 minutes later, cell lysates were collected and centrifuged at 16,200g for 10 minutes at 4℃. 10% of the supernatants was used as input control.The remaining supernatants was layered onto 35ml sucrose buffer (30% sucrose in RB buffer) and then subjected to after ultra-centrifugation at 174,900g for 5 hours at 4℃ in a SW32 rotor (Beckman Coulter, USA) to collect the mRNAs. Purified RNA samples were isolated from the input and polyribosome-bound mRNAs using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions for subsequent library construction and RNA-seq.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit.
Polyribosome-bound mRNAs sequencing (polyribosome-seq)

treatment_protocol: KYSE-150 cells were  transfected with shRNA for stable knockdown of NSUN6. KYSE-150 cells with normal expression of NSUN6 were used as control.

value: esophagus

value: esophageal epithelial cells


title: KYSE-150_NSUN6_KD_input


title: EV, Suicide male, MDD18


title: hPSCs derived-day8 Msx1+Pdgfra+ cells with Mock treatment, biol rep 2

description: In the all.counts.txt file, the data for this Sample is in column "Mock-Msx1+Pdgfra+, biol rep 2".

source_name: human pluripotent stem cell-derived Msx1+Pdgfra+ cells


title: KYSE-150_ctrl_rnc

value: normal


title: hPSCs derived-day8 Msx1+Pdgfralow cells with FGF8+10 treatment, biol rep 2

description: In the all.counts.txt file, the data for this Sample is in column "FGF8+10-Msx1+Pdgfralow, biol rep 2".


title: EV, Suicide male, MDD17


title: KYSE-150_ctrl_input


title: mouse CD4Tcells KLRG1lo spleen isotype rep3

city: Cambridge

first: Jonathan

last: Hill

state: MA

address: 50 Hampshire St 8th floor

department: Immunobiology

institute: Surface Oncology

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 2.0ST for 16–18 h in GeneChip® Hybridization oven 640 at 45 °C with rotation (60 r.p.m.). The hybridized samples were washed and stained using Affymetrix fluidics station 450 as per manufacturer’s instruction (Hybridization, Washing and Staining kit, Affymetrix).

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Data were processed with RMA expressing (GC-RMA) using brainarray cdfs

label: biotin

label_protocol: All procedures were performed as described in the GeneChip® Whole Transcript (WT) Plus Reagent Kit Manual (Affymetrix, Santa Clara, CA). Briefly, the total RNA was isolated using an RNeasy kit (Qiagen), and the sample integrity was verified using RNA 6000 Pico Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies). The total RNA (200 ng) was reverse transcribed using GeneChip® WT PLUS Reagent Kit (Affymetrix). The obtained cDNA was used as a template for in vitro transcription using GeneChip® WT Expression Kit (Life Technologies). The obtained antisense cRNA was purified using Nucleic Acid Binding Beads (GeneChip® WT PLUS Reagent Kit, Affymetrix) and used as a template for reverse transcription to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. The DNA was then fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) and labeled with DNA labeling reagent covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Mouse splenocytes were prepared by mechanical dissociation of whole spleens, followed by ACK lysis of red blood cells. After staining with antibody cocktails, total CD45+ cells (day 5; n=5 per treatment) and tetramer positive T-cells (day 10; n=5 per treatment) were sorted by FACS directly into lysis buffer.

extract_protocol: Total RNA was extracted from sorted cells with the RNeasy®  Mini Kit (Qiagen, Cat. No: 74104)

treatment_protocol: Female C57BL/6 mice were purchased (~6 weeks old) from Taconic labs. Mice were infected i.p. with 20 cysts of Me49 strain of T. gondii . Anti-IL-27p28 antibody was injected i.p. (1mg/mouse) at day 0, 4, 7, 10 or with same dose of isotype IgG

tag: strain

tag: time point

value: IgG


title: mouse CD4Tcells KLRG1lo spleen anti-p28 rep3

value: Anti-IL-27p28 antibody


title: mouse CD4Tcells KLRG1lo spleen isotype rep2


title: mouse CD4Tcells KLRG1lo spleen isotype rep1


title: mouse CD4Tcells KLRG1lo spleen anti-p28 rep2


title: mouse CD4Tcells KLRG1hi spleen anti-p28 rep1


title: mouse CD4Tcells KLRG1hi spleen anti-p28 rep2


title: hPSCs derived-day8 Msx1+Pdgfralow cells with FGF8+10 treatment, biol rep 1

description: In the all.counts.txt file, the data for this Sample is in column "FGF8+10-Msx1+Pdgfralow, biol rep 1".


title: EV, Suicide male, MDD16


title: RNA samples from monocyte of PsA patients 1

city: Kaohsiung

first: Sung-Chou

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description:
RMA expression value derived from Expression Console software; core-exon analysis
PsA1.sst-rma-combined-dabg.chp Signal

hyb_protocol: Samples were hybridized with GeneChip Human Clariom D Arrays (Affymetrix) and scanned at the Kaohsiung Chang Gung Memorial Hospital Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis was conducted with Partek.

source_name: monocyte

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Monocyte cells were collected from PsA patients or healthy control subjects.

extract_protocol: Blood samples from patients were processed to eliminate red blood cells, yielding buffy coats enriched with peripheral blood mononuclear cells (PBMCs). CD14+ monocytes were then isolated from PBMCs using CD14+ MicroBeads. The collected RNA samples were first subjected to quality control by measuring the RNA integrity number (RIN) values with TapeStation 4200 (G2291BA, Agilent). Only the RNA samples with RIN value≥7 were further prepared with the WT PLUS reagent kit (902280, Thermo Fisher), followed by measuring gene expression level with Clariom D Human microarray chip (902927, Thermo Fisher)

treatment_protocol: Not applicable

tag: subject status

value: PsA patient

value: monocyte


title: RNA samples from monocyte of PsA patients 2

description:
RMA expression value derived from Expression Console software; core-exon analysis
PsA2.sst-rma-combined-dabg.chp Signal


title: mouse CD4Tcells KLRG1lo spleen anti-p28 rep1


title: RNA samples from monocyte of healthy control subjects 1

description:
RMA expression value derived from Expression Console software; core-exon analysis
HC1.sst-rma-combined-dabg.chp Signal

value: healthy control


title: RNA samples from monocyte of healthy control subjects 2

description:
RMA expression value derived from Expression Console software; core-exon analysis
HC2.sst-rma-combined-dabg.chp Signal


title: hPSCs derived-day8 Msx1+Pdgfra+ cells with Mock treatment, biol rep 1

description: In the all.counts.txt file, the data for this Sample is in column "Mock-Msx1+Pdgfra+, biol rep 1".

value: human pluripotent stem cell-derived Msx1+Pdgfra+ cells


title: mouse CD4Tcells KLRG1hi spleen anti-p28 rep3


title: hPSCs derived-day8 Msx1+Pdgfra+ cells with FGF8+10 treatment, biol rep 1

description: In the all.counts.txt file, the data for this Sample is in column "FGF8+10-Msx1+Pdgfra+, biol rep 1".


title: hPSCs derived-day8 Msx1+Pdgfra+ cells with FGF8+10 treatment, biol rep 2

description: In the all.counts.txt file, the data for this Sample is in column "FGF8+10-Msx1+Pdgfra+, biol rep 2".


title: EV, Control male, CTRL17


title: p22086-s008_4-Cell-Surface

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: *features.tsv.gz files are available on the series record.

library_source: other

data_processing:
Composite host/virus references were created by concatenating sequence and annotation files for the host and virus and running cellranger mkref
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline
Further processing was done with Seurat v4.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: KU501215.1 Zika virus strain PRVABC59
Assembly: ChlSab1.1.104
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: other

source_name: PBMC

growth_protocol: CD14+ monocytes were isolated from PMBCs of healthy human blood using the MojosortTM Human CD14 Selection Kit (BioLegend, Cat# 480026) To generate monocyte derived dendritic cells (moDCs), CD14+ monocytes were stimulated in non-tissue culture treated plates with 100ng/mL GM-CSF (R&D Systems, Cat# 7954-GM-020/CF) and IL-4 (R&D Systems, Cat# 6507-IL-025/CF) in complete RPMI. Complete RPMI was prepared as follows: RPMI 1640 (Corning, Cat# 10-040-CI) supplemented with 10% FBS, 2mM L-glutamine (Corning, Cat# 25-005-CI), 1mM HEPES (Corning, Cat# 25-060-CI), 1mM Sodium Pyruvate (Corning, Cat# 25-000-CI), 1x NEAA (Corning, Cat# 25-025-CI), and 1x Penicillin-Streptomycin. The next day, the media was replaced with fresh cytokines, removing un-adherent cells. After 4 more days in culture, differentiated moDCs consistently expressing CD14− CD11c+ HLA-DR+ DC-SIGN+ were harvested in the supernatant. For experiments, moDCs were cultured in complete RPMI in U-bottom 96-well plates at 1e5 cells per well.

extract_protocol:
Cells were washed with 0.04% w/v bovine serum albumin (BSA) in PBS and counted.
Feature Barcoding was performed on moDCs prior to single cell RNAseq to label mock and ZIKV treated cells. Cells were blocked with Human TruStain FcX on ice for 10 minutes and then surface stained with BioLegend antibodies (TotalSeq™-C0253 anti-human Hashtag 3 Antibody and TotalSeq™-C0252 anti-human Hashtag 2 Antibody) on ice for 20 minutes.
The 10X Genomics Chromium Next GEM Single Cell 5’ v2 assay protocol (PN-1000264) was modified to be ZIKV-inclusive by adding a ZIKV-specific primer to the reverse transcription reaction mixture (Fig 1). All other steps were followed according to the manufacturer’s protocol. The ZIKV-specific primer (5’-AAGCAGTGGTATCAACGCAGAGTACCCTTCCACAAAGTCCCTATTGC-3’) was previously published by Lanciotti et al. (49) and modified to contain the non-poly-dT tag (underlined sequence) for cDNA amplification. After bead cleanup, cDNA was amplified 13 cycles, and gene expression (5’ GEX) and feature barcoded libraries were generated using the 5’ v2 Library Construction Kit (PN-1000190). 5’ GEX libraries were constructed using cDNA that was first fragmented at 32ºC for 5 min. Each sample was indexed with the Dual Index Kit TT Set A plate (PN-1000215) for 14 cycles of 98ºC for 20s, 54ºC for 30s, 72ºC for 20s, with a final extension of 72ºC for 1 min. Amplified feature barcoded libraries were constructed using DNA from supernatant cleanup. Each sample was indexed with the Dual Index Kit TN Set A plates (PN-1000250) for cycles of 98ºC for 20s, 54ºC for 30s, and 72ºC for 20s, with a final extension of 72ºC for 1 min. For QC, final libraries un on a HS DNA chip on an Agilent Bioanalyzer 2100. The 5’GEX and feature barcoded libraries were pooled separately and then combined at an appropriate ratio in order to obtain the targeted read depth of 50,000/cell and 5,000/cell for the 5’ GEX and feature barcoded libraries, respectively.

treatment_protocol: soluble human IFN-β treatment for 23 hrs

value: PBMC

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD298 Anti Beta2M :Mock/TotalSeq-C0252 ; Infected/TotalSeq-C0253

tag: infection

value: ZIKV

tag: primer concentration


title: afterPRI-724 [30b]

city: Tokyo

first: Juntaro

last: Matsuzaki

address: 1-5-30 Shibakoen, Minato-ku

country: Japan

institute: Keio University Faculty of Pharmacy

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using 3D-Gene Extraction software(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: LiverTissue

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from tissue using miRNesy mini kit (Qiagen).

value: M

tag: age

tag: virus

value: HCV

tag: child-pugh

value: A

tag: lsm

tag: tissue

value: Liver

tag: disease

value: Cirrhosis


title: EV, Control male, CTRL16

value: Anterior cingulate cortex-derived Evs

value: male

value: control


title: afterPRI-724 [28b]

value: HBV


title: mouse CD4Tcells KLRG1hi spleen isotype rep2

tag: treatment

value: IgG


title: mouse CD4Tcells KLRG1hi spleen isotype rep1


title: EV, Suicide male, MDD15

value: MDD


title: p22086-s004_4-5-GEX

data_processing:
Composite host/virus references were created by concatenating sequence and annotation files for the host and virus and running cellranger mkref
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline
Further processing was done with Seurat v4.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: KU501215.1 Zika virus strain PRVABC59
Assembly: ChlSab1.1.104
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

tag: cell type

value: monocyte derived dendritic cells (moDCs)

value: mRNA


title: mouse CD4Tcells KLRG1hi spleen isotype rep3


title: EV, Control male, CTRL15

tag: gender


title: p22086-s007_3-Cell-Surface

value: PBMC

value: IFN-Beta


title: mouse splenocytes anti-p28 rep4

value: Anti-IL-27p28 antibody


title: p22086-s003_3-5-GEX

value: ZIKV


title: EV, Suicide male, MDD14

tag: sample type


title: EV, Suicide male, MDD13


title: p22086-s006_2-Cell-Surface

value: HTO

value: Anti CD298 Anti Beta2M :Mock/TotalSeq-C0252 ; Infected/TotalSeq-C0253


title: beforePRI-724 [26a]

value: M

value: HCV

value: A


title: beforePRI-724 [28a]

value: Liver

value: Cirrhosis


title: afterPRI-724 [26b]


title: afterPRI-724 [23b]


title: EV, Suicide male, MDD12

value: Anterior cingulate cortex-derived Evs

value: male


title: p22086-s002_2-5-GEX


title: p22086-s005_1-Cell-Surface

value: Mock


title: mouse splenocytes anti-p28 rep2

tag: strain


title: EV, Control male, CTRL14

value: control


title: beforePRI-724 [23a]

value: HBV


title: mouse splenocytes anti-p28 rep3

tag: time point


title: p22086-s001_1-5-GEX

value: monocyte derived dendritic cells (moDCs)

value: mRNA


title: beforePRI-724 [30a]


title: EV, Suicide male, MDD11

value: MDD


title: mouse splenocytes isotype rep5

value: IgG


title: afterPRI-724 [22b]


title: beforePRI-724 [22a]


title: mouse splenocytes anti-p28 rep1

value: Anti-IL-27p28 antibody


title: EV, Control male, CTRL13


title: afterPRI-724 [21b]

value: B


title: 4_M_CSF_IL_4_ IL_13

description:
215_20_TGACCA_L005_R1_001
215_8

value: blood (PBMC)

value: Monocyte/Macrophages

tag: donor id


title: Spleen from TMEV-infected mice on day 35_5

city: Osakasayama

first: Ijaz

last: Ahmad

state: Osak/Kansai

address: 377-2 Onohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

data_processing:
Basecalls were performed, using CASAVA on Linux
The raw sequence data were aligned to reference genome, Mus musculus GRCm38.75, downloaded from ENSEMBLE, using the Spliced Transcripts Alignment to a Reference (STAR).
The read count data were normalized by DEG elimination strategy (DEGES), using “R” and the package “tag count comparison (TCC).”
Assembly: mm10
Supplementary files format and content: An Excel file includes the read count data normalized with DEGES.

source_name: Spleen

extract_protocol:
Total RNA was isolated from the platelets, using the RNeasy Mini Kit (Qiagen, Valencia, CA) and TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA), according to the manufacturer’s instruction. The Quality of RNA was examined using NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Female SJL/J mice (5 wk old, 15–17 g) were inoculated intracerebrally with 2 × 10^5 PFUs of TMEV (Daniels' strain). As a control, age-matched female SJL/J mice were injected with 20 μL PBS intracerebrally. We collected the spleens on 4, 7, and 35 days post infection. We also collected blood from the carotid artery, using the syringes prefilled with 0.1 mL ACD buffer (Sigma-Aldrich, St Louis, MO), centrifuged the blood at 118 g for 8 min and obtained platelet-rich plasma, followed by platelet isolation with centrifugation at 735 g for 10 min. Platelets were resuspended to PBS (pH 7.37–7.38) very slowly and gently.

value: SJL/J

tag: Sex

value: Female

value: Spleen

tag: genotype

value: Wild type

value: Intracerebral TMEV infection

tag: time

value: 35 days post infection


title: ExpTcell_NA_T_24hrs_3_rep1

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Fastqc
Trimming of reads using trimmomatic and fastp
Hisat2 alignment using Ensemble Grch38
Raw Gene ocunt generation using htseq-count program
Assembly: Grch38
Supplementary files format and content: htseq-Count text fiile

source_name: Expanded T cells

growth_protocol: T cell expansion was done by activating PBMCs with PHA and IL2 in T cell media for 12 days. T cells were sustained with IL2 throughout the expansion. Experiment was performed on day 13.

extract_protocol: Advanta™ RNA-Seq NGS Library Prep Kit and 48.Atlas™ IFC (Fluidigm)

treatment_protocol: On day 13, expanded T cells were either non-activated or activated with CD3/CD28 DynaBeads (Gibco) for 24 hours. This was followed by treatment (or not) with 200 µM of pregnenolone for 2 or 24 hours.

value: PBMC-derived expanded T cells

tag: t cell activation

value: No

tag: pregnenolone (200 µm) treatment

value: Yes

tag: biological replicate

tag: technical replicate


title: EV, Control male, CTRL19

value: Anterior cingulate cortex-derived Evs

value: male

value: control


title: EV, Control male, CTRL11


title: ExpTcell_NA_UT_2hrs_4


title: Spleen from TMEV-infected mice on day 35_4


title: beforePRI-724 [21a]

value: M

tag: age

tag: virus

value: HBV

tag: child-pugh

tag: lsm

value: Liver

value: Cirrhosis


title: EV, Suicide male, MDD10

tag: tissue

value: MDD


title: Spleen from TMEV-infected mice on day 35_3

value: SJL/J

tag: treatment


title: mouse splenocytes isotype rep3

value: IgG


title: Spleen from TMEV-infected mice on day 35_2

value: Female

value: Spleen


title: ExpTcell_Act_UT_24hrs_2

tag: cell type


title: mouse splenocytes isotype rep1

tag: strain


title: EV, Control male, CTRL10

tag: gender

tag: sample type


title: mouse splenocytes isotype rep2

tag: time point


title: Spleen from TMEV-infected mice on day 35_1

tag: Sex

tag: genotype

value: Wild type

value: Intracerebral TMEV infection


title: afterPRI-724 [18b]

value: HCV

value: B

tag: disease


title: beforePRI-724 [18a]


title: mouse splenocytes isotype rep4


title: ExpTcell_NA_UT_0hrs_2_rep2

value: PBMC-derived expanded T cells

tag: t cell activation

value: No

tag: pregnenolone (200 µm) treatment


title: afterPRI-724 [17b]

value: A


title: EV, Control male, CTRL12

value: Anterior cingulate cortex-derived Evs

value: male

value: control


title: Spleen from control mice on day 35_4

value: Intracerebral PBS injection

tag: time

value: 35 days post injection


title: beforePRI-724 [17a]

value: M

tag: age

value: Liver

value: Cirrhosis


title: Spleen from control mice on day 35_5

value: SJL/J

value: Female


title: EV, Control male, CTRL9


title: EV, Control male, CTRL8


title: ExpTcell_Act_UT_24hrs_3_rep2

value: Yes

tag: biological replicate

tag: technical replicate


title: afterPRI-724 [15b]

tag: virus

value: HBV

tag: child-pugh

tag: lsm


title: beforePRI-724 [15a]

tag: tissue


title: ExpTcell_NA_T_24hrs_3_rep2

tag: cell type


title: ExpTcell_Act_UT_2hrs_3_rep2


title: EV, Control male, CTRL7

tag: gender


title: afterPRI-724 [14b]


title: ExpTcell_NA_UT_0hrs_3


title: EV, Control male, CTRL6

tag: sample type


title: EV, Suicide male, MDD9

value: MDD


title: Spleen from control mice on day 35_1

tag: strain

value: Spleen

value: Wild type

tag: treatment


title: ExpTcell_Act_T_24hrs_1

value: PBMC-derived expanded T cells

tag: time point


title: ExpTcell_Act_T_24hrs_2_rep2


title: EV, Suicide male, MDD8


title: Spleen from TMEV-infected mice on day 7_5

tag: Sex

tag: genotype

value: Intracerebral TMEV infection

value: 7 days post infection


title: EV, Control male, CTRL5

value: Anterior cingulate cortex-derived Evs

value: male


title: beforePRI-724 [11a]

value: HCV

value: A

tag: disease


title: EV, Suicide male, MDD7


title: Spleen from TMEV-infected mice on day 7_4

tag: time


title: ExpTcell_NA_T_2hrs_1

tag: t cell activation

value: No

tag: pregnenolone (200 µm) treatment


title: Spleen from control mice on day 35_3

value: Intracerebral PBS injection

value: 35 days post injection


title: afterPRI-724 [10b]

value: M

tag: age

value: Liver

value: Cirrhosis


title: Spleen from TMEV-infected mice on day 7_3

value: SJL/J

value: Female


title: ExpTcell_Act_T_2hrs_3_rep1

value: Yes

tag: biological replicate

tag: technical replicate


title: Spleen from TMEV-infected mice on day 7_2

value: Spleen

value: Wild type


title: beforePRI-724 [10a]

tag: virus

tag: child-pugh

tag: lsm


title: Spleen from control mice on day 35_2

tag: tissue


title: ExpTcell_Act_T_24hrs_2_rep1

tag: cell type

value: PBMC-derived expanded T cells


title: EV, Suicide male, MDD5

tag: gender

tag: sample type

value: MDD


title: ExpTcell_Act_UT_24hrs_3_rep1

tag: time point


title: EV, Suicide male, MDD6

value: Anterior cingulate cortex-derived Evs


title: Spleen from TMEV-infected mice on day 7_1

tag: strain

tag: Sex

tag: treatment

value: Intracerebral TMEV infection

value: 7 days post infection


title: ExpTcell_Act_T_2hrs_1


title: EV, Suicide male, MDD4

value: male


title: Spleen from control mice on day 7_5

tag: genotype

tag: time

value: 7 days post injection


title: beforePRI-724 [14a]

value: HBV

value: A

tag: disease


title: afterPRI-724 [11b]

value: M

tag: age

value: HCV


title: afterPRI-724 [02b]

value: F

value: Liver

value: Cirrhosis


title: ExpTcell_NA_T_24hrs_2_rep2

tag: t cell activation

value: No

tag: pregnenolone (200 µm) treatment

value: Yes

tag: biological replicate


title: beforePRI-724 [02a]

tag: virus

tag: child-pugh


title: ExpTcell_NA_T_24hrs_2_rep1

tag: technical replicate


title: EV, Suicide male, MDD3

tag: tissue


title: Spleen from control mice on day 7_4

value: SJL/J

value: Female

value: Spleen

value: Wild type

value: Intracerebral PBS injection


title: 33b_afterPRI-724

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner 3000 (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale. Experimental batch effect was removed using Partek Genomics Suite 7.19.1125.

source_name: Plasma

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from EVs suspended in 300uL PBS using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

treatment_protocol: Plasma EVs were isolated from 1 mL of plasma via the TIM4-affinity method, using the MagCapture Exosome Isolation Kit PS (Wako, Osaka, Japan), according to the manufacturer's instruction.

tag: gender

value: B

tag: lsm

tag: molecule type

value: miRNA


title: EV, Suicide male, MDD1

value: Anterior cingulate cortex-derived Evs

value: male

tag: sample type

value: MDD


title: Spleen from control mice on day 7_3

tag: strain

tag: Sex

value: 7 days post injection


title: ExpTcell_NA_UT_24hrs_4

tag: cell type

value: PBMC-derived expanded T cells

tag: time point


title: Spleen from control mice on day 7_2

tag: genotype

tag: treatment

tag: time


title: 33a_beforePRI-724

value: M

tag: age

value: HBV


title: Spleen from control mice on day 7_1


title: ExpTcell_NA_T_2hrs_2_rep2

tag: t cell activation

tag: pregnenolone (200 µm) treatment

tag: biological replicate


title: ExpTcell_NA_T_2hrs_4

tag: technical replicate


title: 28b_afterPRI-724

tag: virus

tag: child-pugh

value: A


title: 30b_afterPRI-724

tag: gender

value: HCV

tag: lsm


title: EV, Suicide male, MDD2

tag: tissue

tag: sample type


title: ExpTcell_Act_T_2hrs_2

value: Yes


title: EV, Control male, CTRL3

value: control


title: Spleen from TMEV-infected mice on day 4_4

tag: strain

value: SJL/J

tag: Sex

value: Female

value: Intracerebral TMEV infection

value: 4 days post infection


title: EV, Control male, CTRL2


title: ExpTcell_NA_T_2hrs_3

tag: cell type

value: No

tag: time point


title: EV, Control male, CTRL1


title: 30a_beforePRI-724

tag: molecule type

value: miRNA


title: Spleen from TMEV-infected mice on day 4_3

value: Spleen

tag: genotype

value: Wild type

tag: treatment

tag: time


title: Spleen from TMEV-infected mice on day 4_2


title: EV, Control male, CTRL4

value: Anterior cingulate cortex-derived Evs

value: male


title: EV, Control male, CTRL18


title: shNR4A3_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

data_processing:
Raw data quality was evaluated with Fast QC, and per base quality score distribution plotted
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: .txt file format of raw counts

source_name: Human monocytic leukaemia_ THP1

growth_protocol: The appropriate number of shNT, shNR4A2 and shNR4A3 THP-1 cells were counted, centrifuged at 1,200rpm (290xg) and the supernatant was removed. Cells were transferred to an environmental gas chamber (37℃, 5%/10% CO2) and resuspended in buffered DMEM media supplemented with 10% FBS, 1% P/S. at a concentration of 750,000 cells/ml (3 million cells/ 4 mls media on 60mm plastic petri dishes). Cells were incubated for 2 hours. LPS-stimulated cells were treated with 2.5ug/ml LPS  for a further 2 hours before lysis.

extract_protocol:
Cells were collected and total mRNA was extracted using the Omega EZNA Total RNA Kit I, as per the manufacturer’s instructions.
cDNA library preparation was performed with polyA selection using Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane. Library preparation and sequencing were performed by Genewiz (Germany).

treatment_protocol: Cells were treated +/- LPS for 2hrs in their respective CO2 chamber

tag: cell line

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle_transduction

value: NR4A3 targeting shRNA

value: 10% CO2 + LPS


title: 26b_afterPRI-724

value: M

tag: age

value: A


title: 28a_beforePRI-724

tag: virus

value: HBV


title: shNR4A3_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep2