title: heart, TAC, scRNAseq

city: Wenzhou

first: Guang

last: Liang

address: Wenzhou medical university of higher education park chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger software (v7.1.0)
Assembly: Ensembl_v105
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Hearts were dissociated into single cells by dissociation solution.
Single-cell libraries were built by using the 10x Chromium platform(10x Genomics) 3-prime kit(V3).

treatment_protocol: Male mice aged 8 weeks were anesthetized and subjected to thoracotomy to expose the aortic arch. 27G needle and 6-0 nylon suture were used to ligate the aortic arch. Mice were subjected TAC for 6 weeks.

value: heart

value: primary

value: mixed

value: TAC


title: Corneolimbal, 6 week old, Confetti- 60

status: Public on Aug 15 2024

type: SRA

city: Kensington

first: Alexander

last: Richardson

state: NSW

address: Crn Botany and High St

country: Australia

institute: UNSW Sydney

description:
SmartSeq-2
6-week old Confetti- 60

library_source: transcriptomic single cell

data_processing:
Reads quantified with Salmon v0.9.1, Seurat v3.1.4 used to filter and normalise data.
Assembly: mouse transcriptome GRCm38
Supplementary files format and content: Tab-separated values files

molecule: total RNA

organism: Mus musculus

source_name: Cornea

extract_protocol:
Male and female Confetti mice, aged 5, 17 and 59-weeks (n=3/age), were administered Tamoxifen (5 mg/mL) (Sigma-Aldrich, St Louis, MI) in 10% ethanol (Sigma-Aldrich) and 90% sunflower seed oil (Sigma-Aldrich) by intraperitoneal injection on three consecutive days to induce expression of the multi-color fluorescent reporter. Seven days after the first injection, mice were euthanized by cervical dislocation, and their eyes immediately enucleated. Corneas, complete with the limbal ring, were dissected under a stereo microscope (Zeiss, Oberkochen, Germany), taking care to remove extraneous tissue. Samples were exposed to 0.5 U/mL Dispase II (Penzberg, Germany) in defined keratinocyte serum-free media (dKSFM) (ThermoFisher Scientific, Waltham, MA) for 2 hrs at 37°C, then trypsin-EDTA (ThermoFisher) for 10 min at 37°C to generate a single-cell suspension of corneolimbal epithelia. Cells underwent FACS for colored Confetti+ (CFP, GFP, YFP, RFP) and non-colored Confetti- populations, taking care to only sort the epithelial population based on cell granularity, size and shape, and minimizing other cell types such as immune cells.
Single-cell libraries were prepared using the SmartSeq-2 protocol, and sequencing was performed on the Illumina NextSeq platform (Ramaciotti Centre for Genomics, UNSW, Sydney, Australia). Mouse corneolimbal epithelia (n=378 total), including Confetti+ and Confetti- cells (n=189/group) were segregated according to three time-points corresponding to mouse age (n=63 cells/time-point) (T1=6, T2=18 and T3=60-weeks), then sequenced and analyzed. Reads were quantified with Salmon (v0.9.1) using the mouse transcriptome GRCm38 to create an index before quantification. Read counts ranged from 288,000-1.4 million/cell with a median of 778,000/cell. The number of genes per cell ranged from 546 - 7,246 with a median of 4,758. Reads were summarized according to gene level using the R package Tximport [103]. The R package Seurat (v3.1.4) [104] was used to filter and normalize data, after which clustering and differential expression analysis were conducted. Cells with >5% mitochondrial content and those with <2000 genes were then removed, and the number of cells analyzed for Confetti+ at T1, T2, and T3, and Confetti- at T1, T2, and T3 were 62, 55, and 41, and 61, 60 and 59, respectively. After filtering and normalization, 14,343 genes were identified across the data set in 338 cells.

tag: tissue

value: Cornea

tag: cell type

value: epithelial cells

tag: genotype

tag: age

value: 6-week old


title: Vaccinee_17_24_weeks [BX_17_IgG_v5]

type: protein

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

country: United Kingdom

institute: The University of Manchester

description:
BX_IgG_Slide_005.gpr
Individual participant of clinical trial NCT 04297436

hyb_protocol: Slides were blocked with 200 µL of SuperG Blocking Buffer (Grace Biolabs, US) per well and incubated for one hour at room temperature (RT). Washes were done three times with 300μL TBS‐T (0.05% Tween‐20) and once in TBS for 10 min, slides were incubated in the dark for 1hr at 20°C with 100μL of Goat Anti-Human IgG Fc (DyLight 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK), using a working dilution of 1:5000 in blocking agent. The arrays were incubated for IgA detection with 100 μL of Goat Anti-Human IgA alpha chain (DyLight 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK), using a working dilution of 1:5000 in blocking agent. Slides were rinsed in de-ionised water and dried by centrifugation at 200 x g for 2 min.

scan_protocol: Slides were scanned in an InnoScan 710 (Innopsys, France) with the photomultiplier tube set to 40% for 635 nm. Image analysis and data quantification was carried out using Mapix v9.1.0 - Microarray image acquisition and analysis software (Innopsys, France).

data_processing: Microarray spot intensities were quantified using Mapix v9.1.0 Microarray Image Analysis software (Innopsys, France), which utilises automatic background subtraction for each spot. The spot intensities for each protein were recorded in quintuplicate; arithmetic means were determined, and spot intensities for buffer-only controls were subtracted

molecule: protein

organism: Homo sapiens

source_name: 4CMenB trial

label_protocol: Secondary antibodies were purchased from Abcam: Goat Anti-Human IgG Fc (DyLight® 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK) and Goat Anti-Human IgA alpha chain (DyLight® 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK)

extract_protocol: Human sera collected from the KEMRI clinics in Mtwapa and Malindi and from clinical trial NCT 04297436

tag: Sex

value: Male

tag: subject group

value: Individual vaccinated with 4CMenB

value: Blood

tag: tissue subtype

value: Serum


title: heart, Sham, scRNAseq

country: China

description: 10x Genomics

treatment_protocol: The sham operation was carried out in the same procedure except for the aortic constriction.

tag: cell line

tag: treatment

value: Sham


title: Vaccinee_19_24_weeks [BX_19_IgG_v5]

label: Goat Anti-Human IgG Fc (DyLight® 650) pre-adsorbed secondary antibody


title: Vaccinee_23_24_weeks [BX_23_IgG_v5]

description:
BX_IgG_Slide_006.gpr
Individual participant of clinical trial NCT 04297436


title: RiboTag naive - biol rep 2

city: Bonn

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

country: Germany

institute: University Clinics Bonn

description:
RNA from IP-precipitated HA-tagged ribosomes of Sox10-expressing cells
DE34NGSUKBR140017

library_source: other

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_4_2 - Version 11.0.24.0102 - Both ends trimmed -Adapter sequences: AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_4_2 - Version 11.0.24.0102 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Trim bases - Version 11.0.24.0102 - Trim on quality score Phred 10 - 3'end trimmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Alignment STAR - 2.5.3a - Version 11.0.24.0102
Partek Flow Software - Post-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 11.0.24.0102
Partek Flow Software - Gene counts were normalized
Partek Flow Software - Normalized counts were subjected to a noise reduction filter (excluding features where maximum ≤ 15)
Partek Flow Software - DESeq2 analysis
Assembly: mm10 Ensembl Transcripts release 102
Supplementary files format and content: Excel with count matrix of DESeq2 results
Library strategy: RiboTag-Seq

molecule: other

source_name: small intestine

growth_protocol: (Samples 1-30) Enteric glial cells  were derived by isolating enteric neurospheres, keeping them in proliferation medium for 7 days and differentiating enteric glia cultures on indicated coating substrates for 3 days. (Samples 31-35) Small intestines of Sox10iCreERT2Rpl22HA/+ mice were harvested and muscularis externa was mechanically separated and lysed in a Qiagen Powerlyzer (2x (2600rpm, 30s, 5 min rest on ice)). Supernatants were incubated with 100 µl HA‑coupled A/G beads at 4°C and 7 rpm overnight. Magnetic separation was performed for 1 minute, and ribosomes containing mRNA were eluted from beads.

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen) for samples 1-30 or Rneasy Micro Kit for samples 31-35
RNA libraries for RNA-seq were prepared using QuantSeq 3'-mRNA Library Prep Kit (Lexogen) following the manufacturer's instructions

treatment_protocol: (Samples 1-30) On day 3, cells were treated with or without IL-1b for 24h and afterwards, cells were lysed with RLT buffer (Qiagen).

value: small intestine

value: enteric glial cells

tag: strain/genotype

value: Sox10iCreERT2Rpl22HA/+ / Cre+

value: naive


title: Corneolimbal, 6 week old, Confetti- 59

description:
SmartSeq-2
6-week old Confetti- 59


title: RiboTag naive - biol rep 3

description:
RNA from IP-precipitated HA-tagged ribosomes of Sox10-expressing cells
DE45NGSUKBR140013


title: RiboTag naive - biol rep 1

description:
RNA from IP-precipitated HA-tagged ribosomes of Sox10-expressing cells
DE07NGSUKBR140018


title: Corneolimbal, 6 week old, Confetti- 58

description:
SmartSeq-2
6-week old Confetti- 58


title: Poly-L-Orntihine IL-1β - biol rep 4

description:
primary enteric glial cell culture on poly-L-orntihine coating substrate treated with IL-1β (10 ng/ml) in SFM
DE62NGSUKBR139998

library_source: transcriptomic

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_4_2 - Version 11.0.24.0102 - Both ends trimmed -Adapter sequences: AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_4_2 - Version 11.0.24.0102 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Trim bases - Version 11.0.24.0102 - Trim on quality score Phred 10 - 3'end trimmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Alignment STAR - 2.5.3a - Version 11.0.24.0102
Partek Flow Software - Post-alignment QA/QC - Version 11.0.24.0102
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 11.0.24.0102
Partek Flow Software - Gene counts were normalized
Partek Flow Software - Normalized counts were subjected to a noise reduction filter (excluding features where maximum ≤ 15)
Partek Flow Software - DESeq2 analysis
Assembly: mm10 Ensembl Transcripts release 102
Supplementary files format and content: Excel with count matrix of DESeq2 results

value: primary enteric glial cells

value: BL6 background / wildtype

tag: ecm substrate

value: Poly-L-Orntihine IL


title: Poly-L-Orntihine IL-1β - biol rep 5

description:
primary enteric glial cell culture on poly-L-orntihine coating substrate treated with IL-1β (10 ng/ml) in SFM
DE78NGSUKBR140001


title: Vaccinee_15_24_weeks [BX_15_IgG_v5]


title: Poly-L-Orntihine IL-1β - biol rep 3

description:
primary enteric glial cell culture on poly-L-orntihine coating substrate treated with IL-1β (10 ng/ml) in SFM
DE51NGSUKBR140002


title: Poly-L-Orntihine IL-1β - biol rep 2

description:
primary enteric glial cell culture on poly-L-orntihine coating substrate treated with IL-1β (10 ng/ml) in SFM
DE35NGSUKBR139999


title: Corneolimbal, 6 week old, Confetti- 61

description:
SmartSeq-2
6-week old Confetti- 61


title: Corneolimbal, 6 week old, Confetti- 56

description:
SmartSeq-2
6-week old Confetti- 56


title: Poly-L-Orntihine IL-1β - biol rep 1

description:
primary enteric glial cell culture on poly-L-orntihine coating substrate treated with IL-1β (10 ng/ml) in SFM
DE08NGSUKBR140000


title: Laminin IL-1β - biol rep 4

description:
primary enteric glial cell culture on laminin coating substrate treated with IL-1β (10 ng/ml) in SFM
DE72NGSUKBR140012

value: Laminin IL


title: Vaccinee_14_24_weeks [BX_14_IgG_v5]


title: Laminin IL-1β - biol rep 3

description:
primary enteric glial cell culture on laminin coating substrate treated with IL-1β (10 ng/ml) in SFM
DE56NGSUKBR140009


title: Vaccinee_13_24_weeks [BX_13_IgG_v5]

description:
BX_IgG_Slide_004.gpr
Individual participant of clinical trial NCT 04297436


title: Laminin IL-1β - biol rep 5

description:
primary enteric glial cell culture on laminin coating substrate treated with IL-1β (10 ng/ml) in SFM
DE83NGSUKBR140008


title: Corneolimbal, 6 week old, Confetti- 54

description:
SmartSeq-2
6-week old Confetti- 54


title: Corneolimbal, 6 week old, Confetti- 57

description:
SmartSeq-2
6-week old Confetti- 57


title: Vaccinee_16_24_weeks [BX_16_IgG_v5]


title: Matrigel IL-1β - biol rep 5

description:
primary enteric glial cell culture on Matrigel coating substrate treated with IL-1β (10 ng/ml) in SFM
DE94NGSUKBR140004

value: Matrigel IL


title: Laminin IL-1β - biol rep 1

description:
primary enteric glial cell culture on laminin coating substrate treated with IL-1β (10 ng/ml) in SFM
DE02NGSUKBR140011


title: Corneolimbal, 6 week old, Confetti- 53

description:
SmartSeq-2
6-week old Confetti- 53

value: Cornea


title: Vaccinee_12_24_weeks [BX_12_IgG_v5]


title: Corneolimbal, 6 week old, Confetti- 55

description:
SmartSeq-2
6-week old Confetti- 55

value: epithelial cells


title: Matrigel IL-1β - biol rep 3

description:
primary enteric glial cell culture on Matrigel coating substrate treated with IL-1β (10 ng/ml) in SFM
DE40NGSUKBR140006


title: Laminin IL-1β - biol rep 2

description:
primary enteric glial cell culture on laminin coating substrate treated with IL-1β (10 ng/ml) in SFM
DE29NGSUKBR140010


title: Corneolimbal, 6 week old, Confetti- 52

description:
SmartSeq-2
6-week old Confetti- 52

value: 6-week old


title: Matrigel IL-1β - biol rep 4

description:
primary enteric glial cell culture on Matrigel coating substrate treated with IL-1β (10 ng/ml) in SFM
DE67NGSUKBR140005


title: Vaccinee_11_24_weeks [BX_11_IgG_v5]

value: Male


title: Vaccinee_09_24_weeks [BX_09_IgG_v5]

value: Individual vaccinated with 4CMenB


title: Vaccinee_10_24_weeks [BX_10_IgG_v5]

value: Blood


title: Matrigel IL-1β - biol rep 2

description:
primary enteric glial cell culture on Matrigel coating substrate treated with IL-1β (10 ng/ml) in SFM
DE24NGSUKBR140003


title: Matrigel IL-1β - biol rep 1

description:
primary enteric glial cell culture on Matrigel coating substrate treated with IL-1β (10 ng/ml) in SFM
DE13NGSUKBR140007


title: Poly-L-Ornithine naive - biol rep 5

description:
primary enteric glial cell culture on poly-L-ornithine coating substrate treated with control SFM (naive)
DE95NGSUKBR139986

value: Poly-L-Ornithine


title: Vaccinee_45_24_weeks [BX_45_IgG_v5]

description:
BX_IgG_Slide_007.gpr
Individual participant of clinical trial NCT 04297436

value: Serum


title: Corneolimbal, 6 week old, Confetti- 51

description:
SmartSeq-2
6-week old Confetti- 51


title: Vaccinee_08_24_weeks [BX_08_IgG_v5]


title: Poly-L-Ornithine naive - biol rep 4

description:
primary enteric glial cell culture on poly-L-ornithine coating substrate treated with control SFM (naive)
DE79NGSUKBR139983

value: small intestine


title: Poly-L-Ornithine naive - biol rep 3

description:
primary enteric glial cell culture on poly-L-ornithine coating substrate treated with control SFM (naive)
DE68NGSUKBR139987


title: Corneolimbal, 6 week old, Confetti- 49

description:
SmartSeq-2
6-week old Confetti- 49


title: Poly-L-Ornithine naive - biol rep 2

description:
primary enteric glial cell culture on poly-L-ornithine coating substrate treated with control SFM (naive)
DE52NGSUKBR139984


title: Corneolimbal, 6 week old, Confetti- 48

description:
SmartSeq-2
6-week old Confetti- 48


title: Laminin naive - biol rep 4

description:
primary enteric glial cell culture on laminin coating substrate treated with control SFM (naive)
DE73NGSUKBR139994

value: Laminin


title: Corneolimbal, 6 week old, Confetti- 47

description:
SmartSeq-2
6-week old Confetti- 47


title: Vaccinee_05_24_weeks [BX_05_IgG_v5]

description:
BX_IgG_Slide_021.gpr
Individual participant of clinical trial NCT 04297436


title: Laminin naive - biol rep 1

description:
primary enteric glial cell culture on laminin coating substrate treated with control SFM (naive)
DE03NGSUKBR139993


title: Laminin naive - biol rep 3

description:
primary enteric glial cell culture on laminin coating substrate treated with control SFM (naive)
DE46NGSUKBR139995


title: Matrigel naive - biol rep 4

description:
primary enteric glial cell culture on Matrigel coating substrate treated with control SFM (naive)
DE57NGSUKBR139991

value: Matrigel


title: Poly-L-Ornithine naive - biol rep 1

description:
primary enteric glial cell culture on poly-L-ornithine coating substrate treated with control SFM (naive)
DE25NGSUKBR139985

value: naive


title: Matrigel naive - biol rep 3

description:
primary enteric glial cell culture on Matrigel coating substrate treated with control SFM (naive)
DE41NGSUKBR139988

value: primary enteric glial cells


title: Matrigel naive - biol rep 5

description:
primary enteric glial cell culture on Matrigel coating substrate treated with control SFM (naive)
DE84NGSUKBR139990

value: BL6 background / wildtype


title: Vaccinee_04_24_weeks [BX_04_IgG_v5]

description:
BX_IgG_Slide_009.gpr
Individual participant of clinical trial NCT 04297436


title: Laminin naive - biol rep 2

description:
primary enteric glial cell culture on laminin coating substrate treated with control SFM (naive)
DE19NGSUKBR139996


title: Matrigel naive - biol rep 1

description:
primary enteric glial cell culture on Matrigel coating substrate treated with control SFM (naive)
DE14NGSUKBR139989


title: Corneolimbal, 6 week old, Confetti- 50

description:
SmartSeq-2
6-week old Confetti- 50


title: Vaccinee_07_24_weeks [BX_07_IgG_v5]

description:
BX_IgG_Slide_004.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 6 week old, Confetti- 45

description:
SmartSeq-2
6-week old Confetti- 45


title: BBR_3

city: hangzhou

first: wu

middle: chang

last: hong

state: zhejiang

address: binwen street num 548

institute: The Second Clinical Medical College, Zhejiang Chinese Medical  University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
genome build: GRCm38
Supplementary files format and content: 1_genes_fpkm_expression.txt include FPKM values for each sample

source_name: colon tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: colon tissue

tag: strain

value: BALB/c

value: Mouse colon

value: 5-fluorouracil+ berberine


title: Corneolimbal, 6 week old, Confetti- 46

description:
SmartSeq-2
6-week old Confetti- 46

value: Cornea

value: epithelial cells


title: Vaccinee_02_24_weeks [BX_02_IgG_v5]

value: Male


title: Vaccinee_03_24_weeks [BX_03_IgG_v5]

value: Individual vaccinated with 4CMenB


title: Corneolimbal, 6 week old, Confetti- 43

description:
SmartSeq-2
6-week old Confetti- 43

value: 6-week old


title: Laminin naive - biol rep 5

description:
primary enteric glial cell culture on laminin coating substrate treated with control SFM (naive)
DE89NGSUKBR139997


title: Vaccinee_62_10_weeks [BX_62_IgG_v4]

value: Blood


title: Corneolimbal, 6 week old, Confetti- 44

description:
SmartSeq-2
6-week old Confetti- 44


title: Vaccinee_06_24_weeks [BX_06_IgG_v5]

value: Serum


title: Fu_5_2


title: Corneolimbal, 6 week old, Confetti- 42

description:
SmartSeq-2
6-week old Confetti- 42


title: Corneolimbal, 6 week old, Confetti- 41

description:
SmartSeq-2
6-week old Confetti- 41


title: BBR_1


title: P0 TRAP, whole brain, cHet, rep6

city: New York

first: Yoko

last: Tajima

state: NY

address: 1230 York avenue

country: USA

institute: The Rockefeller University

description: TRAP-seq

data_processing:
alignment with Olego
RNA abundance analysis (edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

growth_protocol: For the primary neuron culture of diencephalon/ mesencephalon, ventral diencephalon/ mesencephalon were isolated from e13.5 embryos and plated on laminin-coated plates in culture medium (1xDMEM; 5 mM HEPES; 2 mM L-Glutamine; 0.6% glucose) with each hormone (apo-transferrin, insulin, putrescine dihydrochloride, sodium selenite, progesterone) for 14 days.

extract_protocol:
Trizol and RNeasy Mini extraction
Illumina High-throughput TruSeq RNA Sample preparation: polyA selection

treatment_protocol: For the primary neuron, cells were infected with each lentivirus (pUltra-eGFP; WT, pUltra-eGFP-T2A-Cre; Nova1 KO, pUltra-eGFP-T2A-Cre-P2A-Impact; Nova1 KO + Impact) at DIV7 and RNA was extracted at DIV14.

tag: strain background

value: Brain

tag: tissue compartment

value: whole brain

tag: developmental stage

value: cHet


title: Vaccinee_54_10_weeks [BX_54_IgG_v4]

value: Female


title: Vaccinee_55_10_weeks [BX_55_IgG_v4]


title: Matrigel naive - biol rep 2

description:
primary enteric glial cell culture on Matrigel coating substrate treated with control SFM (naive)
DE30NGSUKBR139992

value: small intestine

value: primary enteric glial cells

value: Matrigel

value: naive


title: Vaccinee_52_10_weeks [BX_52_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 39

description:
SmartSeq-2
6-week old Confetti- 39


title: P0 TRAP, whole brain, cHet, rep3

description: TRAP-seq


title: P0 TRAP, whole brain, cHet, rep5

description: TRAP-seq


title: Fu_5_3

value: colon tissue

value: BALB/c

value: Mouse colon


title: BBR_2

value: 5-fluorouracil+ berberine


title: P0 TRAP, whole brain, cHet, rep4

description: TRAP-seq


title: Corneolimbal, 6 week old, Confetti- 40

description:
SmartSeq-2
6-week old Confetti- 40

value: Cornea

value: epithelial cells


title: P0 TRAP, whole brain, cHet, rep1

description: TRAP-seq


title: Corneolimbal, 6 week old, Confetti- 38

description:
SmartSeq-2
6-week old Confetti- 38

value: 6-week old


title: Vaccinee_50_10_weeks [BX_50_IgG_v4]

value: Individual vaccinated with 4CMenB

value: Blood


title: P0 TRAP, whole brain, cHet, rep2

description: TRAP-seq

value: Brain


title: P0 TRAP, whole brain, cKO, rep6

description: TRAP-seq

value: whole brain

value: cKO


title: Vaccinee_48_10_weeks [BX_48_IgG_v4]

description:
BX_IgG_Slide_020.gpr
Individual participant of clinical trial NCT 04297436

value: Female

value: Serum


title: Corneolimbal, 6 week old, Confetti- 37

description:
SmartSeq-2
6-week old Confetti- 37


title: Vaccinee_46_10_weeks [BX_46_IgG_v4]

value: Male


title: P0 TRAP, whole brain, cKO, rep4

description: TRAP-seq


title: Fu_5_1


title: P0 TRAP, whole brain, cKO, rep5

description: TRAP-seq


title: Vaccinee_45_10_weeks [BX_45_IgG_v4]


title: P0 TRAP, whole brain, cKO, rep3

description: TRAP-seq


title: Corneolimbal, 6 week old, Confetti- 36

description:
SmartSeq-2
6-week old Confetti- 36


title: ALDH low LNCaP cells, No2_3

city: Durham

first: Che-Chia

last: Hsu

state: NC

address: 210 Research Drive, GSRB2, Rm#4014

department: Pathology

institute: Duke University

data_processing:
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 with ERCC genes 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. Below are the statistics of mapping the reads to the reference genome.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Supplementary files format and content: csv

source_name: LNCaP cells

growth_protocol: LNCaP ALDH high and ALDH low cells were cultured in RPMI-1640 supplied with 10% FBS.

extract_protocol:
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
mRNA sequencing via polyA selection

value: LNCaP cells

value: prostate cancer cells

tag: group

value: ALDH low


title: Vaccinee_44_10_weeks [BX_44_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 35

description:
SmartSeq-2
6-week old Confetti- 35


title: P0 TRAP, whole brain, cKO, rep1

description: TRAP-seq


title: Corneolimbal, 6 week old, Confetti- 34

description:
SmartSeq-2
6-week old Confetti- 34


title: Corneolimbal, 6 week old, Confetti- 33

description:
SmartSeq-2
6-week old Confetti- 33


title: Primary neuron, DIV14, Nova1 KO + Impact, rep4

description: bulk RNA-seq

value: diencephalon/ mesencephalon

value: Nova1 KO + Impact


title: Vaccinee_43_10_weeks [BX_43_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 32

description:
SmartSeq-2
6-week old Confetti- 32


title: ALDH low LNCaP cells, No2_1


title: Primary neuron, DIV14, Nova1 KO, rep4

description: bulk RNA-seq

value: Nova1 KO


title: ALDH high LNCaP cells, No1_3

value: ALDH high


title: Corneolimbal, 6 week old, Confetti- 31

description:
SmartSeq-2
6-week old Confetti- 31

value: Cornea

value: epithelial cells


title: ALDH high LNCaP cells, No1_1


title: Primary neuron, DIV14, WT, rep4

description: bulk RNA-seq

value: WT


title: Corneolimbal, 6 week old, Confetti- 30

description:
SmartSeq-2
6-week old Confetti- 30

value: 6-week old


title: Vaccinee_38_10_weeks [BX_38_IgG_v4]

value: Individual vaccinated with 4CMenB

value: Blood


title: Vaccinee_39_10_weeks [BX_39_IgG_v4]


title: Vaccinee_37_10_weeks [BX_37_IgG_v4]

description:
BX_IgG_Slide_019.gpr
Individual participant of clinical trial NCT 04297436


title: Primary neuron, DIV14, Nova1 KO + Impact, rep3

description: bulk RNA-seq

value: Brain


title: 22RV1 cells, shIMPDH2 #2

data_processing:
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 with ERCC genes 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. Below are the statistics of mapping the reads to the reference genome.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 (KD_RNAseq 123478_processed data.csv)

growth_protocol: 22RV1 cells stably expressing shLuc, shIMPA1 and shIMPDH2 were cultured in RPMI-1640 supplied with 10% FBS.


title: P0 TRAP, whole brain, cKO, rep2

description: TRAP-seq

value: whole brain

value: cKO


title: Vaccinee_36_10_weeks [BX_36_IgG_v4]

value: Male

value: Serum


title: ALDH low LNCaP cells, No2_2

value: LNCaP cells

value: prostate cancer cells


title: Corneolimbal, 6 week old, Confetti- 29

description:
SmartSeq-2
6-week old Confetti- 29


title: Corneolimbal, 6 week old, Confetti- 28

description:
SmartSeq-2
6-week old Confetti- 28


title: 22RV1 cells, shIMPDH2 #1


title: Primary neuron, DIV14, WT, rep3

description: bulk RNA-seq

value: diencephalon/ mesencephalon


title: Vaccinee_42_10_weeks [BX_42_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 27

description:
SmartSeq-2
6-week old Confetti- 27


title: 22RV1 cells, shIMPA1 #2


title: Corneolimbal, 6 week old, Confetti- 26

description:
SmartSeq-2
6-week old Confetti- 26


title: Primary neuron, DIV14, Nova1 KO, rep2

description: bulk RNA-seq


title: Vaccinee_35_10_weeks [BX_35_IgG_v4]


title: Primary neuron, DIV14, Nova1 KO + Impact, rep2

description: bulk RNA-seq

value: Nova1 KO + Impact


title: Primary neuron, DIV14, Nova1 KO, rep3

description: bulk RNA-seq

value: Nova1 KO


title: 22RV1 cells, shIMPA1 #1


title: Vaccinee_34_10_weeks [BX_34_IgG_v4]


title: Vaccinee_33_10_weeks [BX_33_IgG_v4]


title: 22RV1 cells, shLuc #1

value: shLuc


title: Corneolimbal, 6 week old, Confetti- 24

description:
SmartSeq-2
6-week old Confetti- 24

value: Cornea


title: Primary neuron, DIV14, Nova1 KO, rep1

description: bulk RNA-seq


title: Vaccinee_32_10_weeks [BX_32_IgG_v4]

value: Female


title: ALDH high LNCaP cells, No1_2

value: ALDH high


title: 22RV1 cells, shLuc #2


title: Vaccinee_30_10_weeks [BX_30_IgG_v4]


title: Primary neuron, DIV14, WT, rep2

description: bulk RNA-seq

value: WT


title: Corneolimbal, 6 week old, Confetti- 22

description:
SmartSeq-2
6-week old Confetti- 22

value: epithelial cells

value: 6-week old


title: S9: 120 Day,Control, Female

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

description: 10X Genomics

data_processing:
All single cell sequencing data analysis was performed using Seurat v3.2.
Filtered data were log transformed, scaled, integrated using reverse Principal Component Analysis (rPCA), clustered and represented by Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction.
Assembly: GRCh38
Supplementary files format and content: barcodes, features and matrix files

source_name: Lung

extract_protocol:
From each lung, 400 mg of tissue was weighed out and placed on a clean glass petri dish containing chilled HBSS and minced (1-2 mm sized pieces) using a sterile razor blade. Lung was then further dissociated with the Miltenyi gentleMACs dissociator (Cat: 130-093-235) using the manufacturer-set dissociator program. Cell solution was then passed through prepared 70um cell strainer. C tube was then rinsed with 3mL HBSS and passed through strainer, and strainer was rinsed further with an additional 2mL HBSS. Strained cell suspension was then centrifuged at 500G for 5 minutes followed by decanting. Cell pellet was then incubated in Red Blood Cell Lysis Buffer (3 minutes at room temperature), diluted with HBSS (4 HBSS:1 RBC), and centrifuged at 500G for 5 minutes followed by decanting. Cell pellet was subsequently resuspended in 2mL 1% BSA and centrifuged at 500G for 5 minutes followed by decanting (this step was repeated a second time). Cells were then resuspended in 1%FBS DMEM/F12 at a concentration of 1000 cells/μL for single cell RNA library preparation with all subsequent cells frozen down in 90% FBS/10% DMSO solution.
Single cell capture and library production was performed on the Chromium 10X Genomics system with version 3 chemistry according to the manufacturer’s instructions.
Sequencing was performed on an Illumina NovaSeq, with read alignment to GRCh38.

treatment_protocol: Lungs were received as fresh whole lobes and processed either immediately for single cell suspension or fixed in 4% PFA for immunohistochemical analyses

value: Lung

value: Control


title: S6: 122 Day, T21, Female

description: 10X Genomics

value: Trisomy 21


title: Vaccinee_31_10_weeks [BX_31_IgG_v4]

value: Individual vaccinated with 4CMenB

value: Blood


title: Primary neuron, DIV14, WT, rep1

description: bulk RNA-seq

value: Brain


title: Corneolimbal, 6 week old, Confetti- 23

description:
SmartSeq-2
6-week old Confetti- 23


title: S8: 122 Day, T21, Female

description: 10X Genomics


title: Pituitary, cHet, rep3

description: bulk RNA-seq

source_name: pituitary

value: pituitary

value: cHet


title: Corneolimbal, 6 week old, Confetti- 20

description:
SmartSeq-2
6-week old Confetti- 20


title: Vaccinee_28_10_weeks [BX_28_IgG_v4]

description:
BX_IgG_Slide_018.gpr
Individual participant of clinical trial NCT 04297436

value: Serum


title: Primary neuron, DIV14, Nova1 KO + Impact, rep1

description: bulk RNA-seq

value: diencephalon/ mesencephalon

value: Nova1 KO + Impact


title: Corneolimbal, 6 week old, Confetti- 21

description:
SmartSeq-2
6-week old Confetti- 21

value: Cornea


title: Pituitary, cKO, rep3

description: bulk RNA-seq

value: cKO


title: Pituitary, cKO, rep2

description: bulk RNA-seq


title: S4: 108 Day, Control, Female

description: 10X Genomics


title: Pituitary, cHet, rep2

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 19

description:
SmartSeq-2
6-week old Confetti- 19


title: Vaccinee_25_10_weeks [BX_25_IgG_v4]

value: Male


title: Vaccinee_26_10_weeks [BX_26_IgG_v4]

value: Female


title: Pituitary, cKO, rep1

description: bulk RNA-seq


title: S7: 108 Day, Control, Female

description: 10X Genomics


title: Vaccinee_27_10_weeks [BX_27_IgG_v4]


title: Vaccinee_24_10_weeks [BX_24_IgG_v4]


title: Pituitary, cHet, rep1

description: bulk RNA-seq


title: S1: 106 Day, Control, Male

description: 10X Genomics


title: Corneolimbal, 6 week old, Confetti- 18

description:
SmartSeq-2
6-week old Confetti- 18

value: epithelial cells


title: Vaccinee_23_10_weeks [BX_23_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 16

description:
SmartSeq-2
6-week old Confetti- 16

value: 6-week old


title: S3: 106 Day, T21, Female

description: 10X Genomics

value: Lung


title: S2: 113 Day, T21, Female

description: 10X Genomics


title: Vaccinee_21_10_weeks [BX_21_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 25

description:
SmartSeq-2
6-week old Confetti- 25


title: S5: 108 Day, T21, Male

description: 10X Genomics


title: Vaccinee_22_10_weeks [BX_22_IgG_v4]


title: Corneolimbal, 6 week old, Confetti- 14

description:
SmartSeq-2
6-week old Confetti- 14


title: IPS control cells

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

description:
IPSC CONTROL
10x Genomics
IPSC features.tsv.gz
IPSC matrix.mtx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: IPS cells

growth_protocol: Cells were diffrentiated and maintained at ALI conditions

extract_protocol:
Airway cells were isolated after incubation in trypsin for 5 minutes and mechanical dissociation. The isolated cells were resuspended in tryspin for  and incubated at 37 °C for 5 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (PBS+0.04% BSA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains a primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up, amplified, and the apropiated sized fragments were selected for subsequent library construction.

value: IPS cells


title: Substantia nigra, cHet, rep4

description: bulk RNA-seq

source_name: brain

value: brain

value: substantia nigra


title: Vaccinee_20_10_weeks [BX_20_IgG_v4]

description:
BX_IgG_Slide_017.gpr
Individual participant of clinical trial NCT 04297436

value: Individual vaccinated with 4CMenB

value: Blood


title: Substantia nigra, cKO, rep4

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 17

description:
SmartSeq-2
6-week old Confetti- 17


title: IPS cells subject PCD 1

description:
IPSC111
10x Genomics
IPSC features.tsv.gz
IPSC matrix.mtx

tag: subject status

value: subject PCD


title: Corneolimbal, 6 week old, Confetti- 13

description:
SmartSeq-2
6-week old Confetti- 13

tag: tissue


title: Substantia nigra, cHet, rep3

description: bulk RNA-seq

value: cHet


title: Vaccinee_19_10_weeks [BX_19_IgG_v4]

value: Serum


title: Corneolimbal, 6 week old, Confetti- 12

description:
SmartSeq-2
6-week old Confetti- 12

tag: cell type


title: Mother PCD subject 3, Airway cells, scRNAseq

description:
PCD117M
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx

source_name: Primary airway cells

value: Primary airway cells

value: Mother PCD subject


title: Mother PCD subject 4, Airway cells, scRNAseq

description:
PCD138M
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Corneolimbal, 6 week old, Confetti- 11

description:
SmartSeq-2
6-week old Confetti- 11

value: Cornea

tag: genotype


title: Mother PCD subject 2, Airway cells, scRNAseq

description:
PCD129M
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Corneolimbal, 6 week old, Confetti- 10

description:
SmartSeq-2
6-week old Confetti- 10

tag: age


title: Vaccinee_17_10_weeks [BX_17_IgG_v4]

tag: Sex


title: Substantia nigra, cHet, rep2

description: bulk RNA-seq


title: Vaccinee_15_10_weeks [BX_15_IgG_v4]

tag: subject group


title: Corneolimbal, 6 week old, Confetti- 15

description:
SmartSeq-2
6-week old Confetti- 15


title: substantia nigra, cKO, rep2

description: bulk RNA-seq

value: cKO


title: Substantia nigra, cKO, rep1

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 9

description:
SmartSeq-2
6-week old Confetti- 9


title: Vaccinee_14_10_weeks [BX_14_IgG_v4]

value: Male

tag: tissue subtype


title: Mother PCD subject 1, Airway cells, scRNAseq

description:
PCD111M
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Corneolimbal, 6 week old, Confetti- 7

description:
SmartSeq-2
6-week old Confetti- 7


title: PCD Subject 3, Airway cells, scRNAseq

description:
PCD117
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx

value: PCD Subject


title: PCD Subject 4, Airway cells, scRNAseq

description:
PCD138
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Caudate putamen, cHet, rep4

description: bulk RNA-seq

value: caudate putamen


title: Substantia nigra, cHet, rep1

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 8

description:
SmartSeq-2
6-week old Confetti- 8

value: epithelial cells

value: 6-week old


title: Vaccinee_13_10_weeks [BX_13_IgG_v4]


title: Caudate putamen, cKO, rep4

description: bulk RNA-seq


title: Vaccinee_12_10_weeks [BX_12_IgG_v4]

description:
BX_IgG_Slide_016.gpr
Individual participant of clinical trial NCT 04297436


title: Substantia nigra, cKO, rep3

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 6

description:
SmartSeq-2
6-week old Confetti- 6


title: Corneolimbal, 6 week old, Confetti- 5

description:
SmartSeq-2
6-week old Confetti- 5


title: Vaccinee_11_10_weeks [BX_11_IgG_v4]


title: Caudate putamen, cHet, rep3

description: bulk RNA-seq


title: Vaccinee_16_10_weeks [BX_16_IgG_v4]


title: PCD Subject 1, Airway cells, scRNAseq

description:
PCD111
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Healthy Subject 5,Nasal Airway cells, scRNAseq

description:
HNEC106
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx

value: Healthy Subject


title: Corneolimbal, 6 week old, Confetti- 4

description:
SmartSeq-2
6-week old Confetti- 4


title: Vaccinee_56_10_weeks [BX_56_IgG_v4]

description:
BX_IgG_Slide_021.gpr
Individual participant of clinical trial NCT 04297436

value: Female


title: Caudate putamen, cKO, rep3

description: bulk RNA-seq

value: brain


title: Vaccinee_09_10_weeks [BX_09_IgG_v4]

value: Individual vaccinated with 4CMenB


title: Vaccinee_10_10_weeks [BX_10_IgG_v4]

value: Blood


title: Healthy Subject 4,Nasal Airway cells, scRNAseq

description:
HNEC105
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: PCD Subject 2, Airway cells, scRNAseq

description:
PCD129
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Corneolimbal, 6 week old, Confetti- 3

description:
SmartSeq-2
6-week old Confetti- 3


title: Corneolimbal, 6 week old, Confetti- 2

description:
SmartSeq-2
6-week old Confetti- 2


title: Caudate putamen, cHet, rep2

description: bulk RNA-seq


title: Caudate putamen, cHet, rep1

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti- 1

description:
SmartSeq-2
6-week old Confetti- 1


title: Vaccinee_07_10_weeks [BX_07_IgG_v4]

description:
BX_IgG_Slide_015.gpr
Individual participant of clinical trial NCT 04297436


title: Caudate putamen, cKO, rep2

description: bulk RNA-seq


title: Vaccinee_08_10_weeks [BX_08_IgG_v4]


title: Healthy Subject 2,Nasal Airway cells, scRNAseq

description:
HNEC103
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Healthy Subject 3,Nasal Airway cells, scRNAseq

description:
HNEC104
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Vaccinee_06_10_weeks [BX_06_IgG_v4]


title: Healthy Subject 1,Nasal Airway cells, scRNAseq

description:
HNEC102
10x Genomics
DNAH5 features.tsv.gz
DNAH5 matrix.mtx


title: Vaccinee_05_10_weeks [BX_05_IgG_v4]


title: Corneolimbal, 6 week old, Confetti+ 63

description:
SmartSeq-2
6-week old Confetti+ 63


title: Vaccinee_03_10_weeks [BX_03_IgG_v4]


title: Periaqueductal gray, cKO, rep4

description: bulk RNA-seq

value: periaqueductal gray


title: periaqueductal gray, cKO, rep1

description: bulk RNA-seq


title: DaroR_siLOC_2

city: Houston

first: Tianyi

last: Zhou

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: treated with siRNA LOC730101

data_processing:
fastqc
trim_galore trimed adaptors
bwa mapping
featurecounts
deseq2
Assembly: hg38
Supplementary files format and content: table deliminated txt including raw counts

molecule: polyA RNA

source_name: hormone insensitive prostate cancer

growth_protocol: All cells were grown in RPMI1640 with 10% FBS and antibiotics at 37°C in a humidified atmosphere at 5% CO2

extract_protocol:
RNA were extracted using Qiagen Rneasy plus kit
mRNAlibrarypreparation were done by Novogene
Poly A enrichment

treatment_protocol: DaroR-Ctl-siRNA group were treated with siRNA control, DaroR-siLOC group were treated with siLOC730101 to knockdown LOC730101 expression

value: hormone insensitive prostate cancer

tag: cell line

value: LNCaP-DaroR

value: siRNA knock down


title: Periaqueductal gray, cHet, rep4

description: bulk RNA-seq

value: cHet


title: Corneolimbal, 6 week old, Confetti+ 61

description:
SmartSeq-2
6-week old Confetti+ 61

value: Cornea


title: DaroR_siLOC_1

description: treated with siRNA LOC730101

tag: treatment


title: Corneolimbal, 6 week old, Confetti+ 62

description:
SmartSeq-2
6-week old Confetti+ 62


title: DaroR_siRNA_2

description: treated with siRNA control

value: Control siRNA


title: Periaqueductal gray, cHet, rep3

description: bulk RNA-seq


title: DaroR_siRNA_1

description: treated with siRNA control


title: Corneolimbal, 6 week old, Confetti+ 59

description:
SmartSeq-2
6-week old Confetti+ 59


title: Vaccinee_02_10_weeks [BX_02_IgG_v4]

value: Male

value: Serum


title: Corneolimbal, 6 week old, Confetti+ 58

description:
SmartSeq-2
6-week old Confetti+ 58


title: DaroR

description: treated with 10uM Darolutamide

data_processing:
fastqc
juicer-hic/run-hic
Assembly: hg19
Supplementary files format and content: hic

source_name: Prostate cancer

extract_protocol:
DNA were extracted using Arima Genomics HiC kit
Hi-C-library preparation

treatment_protocol: DMSO group were treated with only the solvant DMSO for 24 hours, R1881 group were treated with 1nM R1881 dissolved in DMSO for 24 hours, Daro group were treated with 10uM darolutamide for 24 hours, DaroR group were treated with 10uM darolutamide for 12 months

value: Prostate cancer

value: hormone non-sensitive prostate cancer

value: Drug treated


title: Vaccinee_56_PI [BX_56_IgG_v2]


title: Periaqueductal gray, cHet, rep2

description: bulk RNA-seq


title: Periaqueductal gray, cKO, rep3

description: bulk RNA-seq

value: cKO


title: Vaccinee_58_PI [BX_58_IgG_v2]

value: Female


title: Corneolimbal, 6 week old, Confetti+ 57

description:
SmartSeq-2
6-week old Confetti+ 57

value: epithelial cells

value: 6-week old


title: R1881

description: treated with 1nM R1881

value: LNCaP

value: hormone sensitive prostate cancer


title: Corneolimbal, 6 week old, Confetti+ 56

description:
SmartSeq-2
6-week old Confetti+ 56


title: Periaqueductal gray, cHet, rep1

description: bulk RNA-seq

value: brain

value: periaqueductal gray


title: Vaccinee_54_PI [BX_54_IgG_v2]

value: Individual vaccinated with 4CMenB

value: Blood


title: Corneolimbal, 6 week old, Confetti+ 60

description:
SmartSeq-2
6-week old Confetti+ 60

value: Cornea


title: Vaccinee_62_PI [BX_62_IgG_v2]


title: Veh

description: treated with the solvant DMSO

value: WT

value: DMSO


title: Vaccinee_52_PI [BX_52_IgG_v2]

value: Serum


title: Corneolimbal, 6 week old, Confetti+ 55

description:
SmartSeq-2
6-week old Confetti+ 55


title: Periaqueductal gray, cKO, rep1

description: bulk RNA-seq


title: Periaqueductal gray, cKO, rep2

description: bulk RNA-seq


title: Hypothalamus, cHet, rep4

description: bulk RNA-seq

value: hypothalamus

value: cHet


title: siBCAT1_3

city: Shanghai

first: Zilu

last: Pan

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

data_processing:
Illumina Casava1.7 software was used for basecalling
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Assembly: GRCh38,p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Lung adenocarcinoma

extract_protocol:
Total RNA was extracted from cells using TRIzol® Reagent according the manufacturer’s instructions.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: Lung adenocarcinoma

value: ASK120067-resistant NCI-H1975 cells

value: NSCLC cells

value: BCAT1 knockdown


title: Daro

description: treated with 10uM Darolutamide

value: Prostate cancer

value: Drug treated


title: Corneolimbal, 6 week old, Confetti+ 54

description:
SmartSeq-2
6-week old Confetti+ 54

value: epithelial cells

value: 6-week old


title: siBCAT1_2


title: Vaccinee_48_PI [BX_48_IgG_v2]

value: Female


title: Vaccinee_55_PI [BX_55_IgG_v2]

value: Male

value: Individual vaccinated with 4CMenB


title: Vaccinee_50_PI [BX_50_IgG_v2]

description:
BX_IgG_Slide_014.gpr
Individual participant of clinical trial NCT 04297436

value: Blood


title: Corneolimbal, 6 week old, Confetti+ 53

description:
SmartSeq-2
6-week old Confetti+ 53

value: Cornea


title: Hypothalamus, cKO, rep4

description: bulk RNA-seq

value: brain

value: cKO


title: Corneolimbal, 6 week old, Confetti+ 52

description:
SmartSeq-2
6-week old Confetti+ 52


title: Hypothalamus, cHet, rep3

description: bulk RNA-seq

value: hypothalamus


title: NC_3

value: NC


title: Hypothalamus, cKO, rep3

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti+ 51

description:
SmartSeq-2
6-week old Confetti+ 51


title: NC_2

value: Lung adenocarcinoma


title: Vaccinee_45_PI [BX_45_IgG_v2]

value: Serum


title: Vaccinee_46_PI [BX_46_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 50

description:
SmartSeq-2
6-week old Confetti+ 50


title: Hypothalamus, cHet, rep2

description: bulk RNA-seq

value: cHet


title: Vaccinee_44_PI [BX_44_IgG_v2]

description:
BX_IgG_Slide_013.gpr
Individual participant of clinical trial NCT 04297436


title: NC_1

value: ASK120067-resistant NCI-H1975 cells

value: NSCLC cells


title: Corneolimbal, 6 week old, Confetti+ 49

description:
SmartSeq-2
6-week old Confetti+ 49


title: siBCAT1_1

value: BCAT1 knockdown


title: Hypothalamus, cHet, rep1

description: bulk RNA-seq


title: Corneolimbal, 6 week old, Confetti+ 48

description:
SmartSeq-2
6-week old Confetti+ 48

value: epithelial cells


title: PBMCs, Sepsis-4

city: Suzhou

first: zigang

last: qiao

address: Chongwen Road

department: Suzhou Institute of Systems Medicine

institute: Chinese Academy of MedicalSciences & Peking Union Medical College

data_processing:
To estimate gene expression changes, the raw RNA-seq data were preprocessed using fastqc to remove reads of low quality and adaptor contamination.
The high-quality reads were further aligned to the human genome (GrCh38) using HISAT2 (v2.2.1) with default parameters.
Only uniquely mapped reads were retained for gene expression quantification at the count level using stringtie (v2.2.1) based on human gene annotation of Ensembl.
Assembly: GRCh38
Supplementary files format and content: gene expression analysis.xlsx includes TPM values for each Sample

source_name: PBMCs

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
Total RNA was prepared into a cDNA library according to the standard Illumina RNA-seq instructions.

value: Peripheral Blood Mononuclear Cells

tag: condition

value: Sepsis


title: Hypothalamus, cKO, rep2

description: bulk RNA-seq


title: Vaccinee_39_PI [BX_39_IgG_v2]

value: Male


title: Corneolimbal, 6 week old, Confetti+ 47

description:
SmartSeq-2
6-week old Confetti+ 47

value: 6-week old


title: Hypothalamus, cKO, rep1

description: bulk RNA-seq


title: PBMCs, Sepsis-2


title: Vaccinee_42_PI [BX_42_IgG_v2]

value: Individual vaccinated with 4CMenB

value: Blood


title: PBMCs, Sepsis-1


title: Corneolimbal, 6 week old, Confetti+ 46

description:
SmartSeq-2
6-week old Confetti+ 46

value: Cornea


title: Corneolimbal, 6 week old, Confetti+ 45

description:
SmartSeq-2
6-week old Confetti+ 45


title: PBMCs, Healthy-4

value: Healthy


title: Vaccinee_36_PI [BX_36_IgG_v2]


title: Vaccinee_37_PI [BX_37_IgG_v2]


title: Eif5-ZcKO-2

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

data_processing:
Sequencing Platform: DNBSEQ
Sequencing length: PE100
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
Assembly: mm9
Supplementary files format and content: clean data
Supplementary files format and content: TPM, FPKM

source_name: ovary

growth_protocol: 21dpp after birth in mice

extract_protocol:
Total RNA was extracted using RNeasy® Micro Kit (Qiagen)
smart-seq2

treatment_protocol: Eif5 was specifically deleted in oocytes

value: ovary

value: oocyte

value: GV-oocyte

value: oocyte development


title: Vaccinee_43_PI [BX_43_IgG_v2]

value: Serum


title: PBMCs, Healthy-3


title: Corneolimbal, 6 week old, Confetti+ 44

description:
SmartSeq-2
6-week old Confetti+ 44


title: Vaccinee_38_PI [BX_38_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 43

description:
SmartSeq-2
6-week old Confetti+ 43


title: Eif5-ZcKO-1


title: PBMCs, Sepsis-3


title: PBMCs, Healthy-2


title: Eif5-GcKO-3


title: Eif5-ZcKO-3


title: Eif5-GcKO-2


title: Vaccinee_35_PI [BX_35_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 42

description:
SmartSeq-2
6-week old Confetti+ 42


title: Vaccinee_34_PI [BX_34_IgG_v2]


title: Eif5-GcKO-1


title: Eif5-WT-3

value: WT


title: Corneolimbal, 6 week old, Confetti+ 40

description:
SmartSeq-2
6-week old Confetti+ 40


title: Vaccinee_33_PI [BX_33_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 41

description:
SmartSeq-2
6-week old Confetti+ 41


title: Corneolimbal, 6 week old, Confetti+ 39

description:
SmartSeq-2
6-week old Confetti+ 39


title: Corneolimbal, 6 week old, Confetti+ 38

description:
SmartSeq-2
6-week old Confetti+ 38


title: Vaccinee_32_PI [BX_32_IgG_v2]

value: Female


title: Eif5-WT-1


title: PBMCs, Healthy-1


title: OCIAML3 Idasanutlin 300nM Treated Replicate 2

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
reads were processed by fastQC for quality control
single end reads were trimmed using Trimmomatic 0.39 with the TruSeq3-SE.fa adapter file and the parameters: 2:30:10 LEADING:3
trimmed reads were aligned to GRCh38.100 using kallisto 0.46.2 with the parameters --single -l 200 -s 30 --bias --plaintext --bootstrap-samples=50
Assembly: GRCh38
Supplementary files format and content: RNA200316HZ_abundances.txt contains gene-level abundances (TPM) in tab delimited format
Supplementary files format and content: RNA200316HZ_abundances.txt contains gene-level lengths in tab delimited format

extract_protocol:
RNA was harvested using Qiagen Rneasy mini kit. 1ug RNAs were used for RNA library preparation.
The RNA library was prepared using the Illumina Stranded mRNA Preparation kit, following the manufacturer's protocol.

treatment_protocol: Samples were treated with Idasanutlin (300nM)

value: Idasanutlin


title: OCIAML3 Untreated Replicate 2

value: control


title: OCIAML3 Untreated Replicate 1


title: Vaccinee_29_PI [BX_29_IgG_v2]

description:
BX_IgG_Slide_012.gpr
Individual participant of clinical trial NCT 04297436


title: MOLM13 Untreated Replicate 2


title: Vaccinee_31_PI [BX_31_IgG_v2]


title: cep-1 OE rep2

city: Buffalo

first: Johnny

last: Cruz Corchado

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

institute: Roswell Park Comprehensive Cancer Institue

data_processing:
The quality of the RNA sequences was assessed with FastQC
Adapters sequences and reads with a quality lower than Q25 were trimmed by using Trimgalore version 0.67.
Sequencing reads were aligned to the C. elegans genome WBcel235  using the Star aligner v2.7.9a2
Alignments were quantified with Salmon using the annotation  (WBCel235 GTF release 111)
DESeq2 was used to do differential expression between the samples
Assembly: WBcel235(ensembl release 111)
Supplementary files format and content: Excel (CSV) file include TPM(transcript per milion) for all samples
Supplementary files format and content: Excel (csv) file include DESeq2 normalized counts for all Samples
Supplementary files format and content: Excel (csv) file include raw counts for all  Samples

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Day-one adult worms grown at 20C (I-36LLVL Incubator) were bleach-hatched, and ~3200 eggs/genotype (~800 eggs/plate and 4 plates/genotype) were seeded on fresh OP50 plates and allowed to grow for 48 hours at 25°C Echotherm incubator IN30-2.

extract_protocol:
Worms were washed with sterile water, and total RNA was extracted from biological triplicates using the Trizol extraction method.
Libraries were prepared using Illumina TruSeq Stranded mRNA kit.

value: Whole Animal

value: Temp 25C


title: MOLM13 Untreated Replicate 1


title: Vaccinee_30_PI [BX_30_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 37

description:
SmartSeq-2
6-week old Confetti+ 37

data_processing:
Reads quantified with Salmon v0.9.1, Seurat v3.1.4 used to filter and normalise data.
Assembly: mouse transcriptome GRCm38
Supplementary files format and content: Tab-separated values files

source_name: Cornea

value: epithelial cells


title: OCIAML3 Idasanutlin 300nM Treated Replicate 1


title: cep-1 OE rep3


title: Eif5-WT-2


title: Corneolimbal, 6 week old, Confetti+ 35

description:
SmartSeq-2
6-week old Confetti+ 35

value: 6-week old


title: Vaccinee_26_PI [BX_26_IgG_v2]

data_processing: Microarray spot intensities were quantified using Mapix v9.1.0 Microarray Image Analysis software (Innopsys, France), which utilises automatic background subtraction for each spot. The spot intensities for each protein were recorded in quintuplicate; arithmetic means were determined, and spot intensities for buffer-only controls were subtracted

source_name: 4CMenB trial

value: Individual vaccinated with 4CMenB


title: Vaccinee_28_PI [BX_28_IgG_v2]

value: Blood


title: Corneolimbal, 6 week old, Confetti+ 36

description:
SmartSeq-2
6-week old Confetti+ 36

value: Cornea


title: MOLM13 Idasanutlin 300nM Treated Replicate 2


title: Vaccinee_25_PI [BX_25_IgG_v2]

value: Male


title: Corneolimbal, 6 week old, Confetti+ 33

description:
SmartSeq-2
6-week old Confetti+ 33


title: cep-1 OE rep1


title: MOLM13 Idasanutlin 300nM Treated Replicate 1


title: Corneolimbal, 6 week old, Confetti+ 34

description:
SmartSeq-2
6-week old Confetti+ 34


title: Vaccinee_27_PI [BX_27_IgG_v2]


title: ilc-17.1 rep2


title: ilc-17.1 rep1


title: daf-7 rep3


title: Corneolimbal, 6 week old, Confetti+ 31

description:
SmartSeq-2
6-week old Confetti+ 31


title: Corneolimbal, 6 week old, Confetti+ 32

description:
SmartSeq-2
6-week old Confetti+ 32


title: Sample 17_human podocytes at permissive (33C) condition, treated with BT503, replica 2

city: Stony Brook

first: Sandeep

last: Mallipattu

address: HSC-T16 Room 80E

department: Division of Nephrology and Hypertension

institute: Stony Brook University School of Medicine

data_processing:
data were align and count using https://maayanlab.cloud/biojupies/
pathway analysis using https://maayanlab.cloud/Enrichr/

source_name: Kidney

growth_protocol: podocytes were grow at 33c and differentiated at 37c for 14 days

extract_protocol:
trizol total RNA extraction protocol
mRNA library preparation (poly A enrichment)

treatment_protocol: podocytes were treated with compounds for 24 hours

value: Kidney

value: immortal podocytes

value: podocytes

value: non-differentiated


title: ilc-17.1 rep3


title: Sample 18_human podocytes at permissive (33C) condition, treated with BT503, replica 3


title: Sample 16_human podocytes at permissive (33C) condition, treated with BT503, replica 1


title: Vaccinee_24_PI [BX_24_IgG_v2]

value: Serum


title: Vaccinee_23_PI [BX_23_IgG_v2]

description:
BX_IgG_Slide_011.gpr
Individual participant of clinical trial NCT 04297436


title: Sample 15_human podocytes at permissive (33C) condition, treated with DMSO, replica 3

value: WT


title: daf-7 rep2


title: Corneolimbal, 6 week old, Confetti+ 30

description:
SmartSeq-2
6-week old Confetti+ 30


title: Corneolimbal, 6 week old, Confetti+ 29

description:
SmartSeq-2
6-week old Confetti+ 29


title: daf-7 rep1


title: Corneolimbal, 6 week old, Confetti+ 28

description:
SmartSeq-2
6-week old Confetti+ 28


title: daf-2 rep3


title: Vaccinee_20_PI [BX_20_IgG_v2]


title: Sample 14_human podocytes at permissive (33C) condition, treated with DMSO, replica 2


title: daf-2 rep2


title: Vaccinee_19_PI [BX_19_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 27

description:
SmartSeq-2
6-week old Confetti+ 27


title: Sample 12_differentiated human podocytes, treated with LPS+BT503, replica 3

value: differentiated


title: Vaccinee_21_PI [BX_21_IgG_v2]


title: Vaccinee_22_PI [BX_22_IgG_v2]


title: Sample 11_differentiated human podocytes, treated with LPS+BT503, replica 2


title: Vaccinee_17_PI [BX_17_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 26

description:
SmartSeq-2
6-week old Confetti+ 26


title: Sample 10_differentiated human podocytes, treated with LPS+BT503, replica 1


title: N2 HID rep3

value: WTwild-type dauers (N2; Bristol)

value: Temp 27C


title: Corneolimbal, 6 week old, Confetti+ 25

description:
SmartSeq-2
6-week old Confetti+ 25


title: Corneolimbal, 6 week old, Confetti+ 24

description:
SmartSeq-2
6-week old Confetti+ 24


title: N2 HID rep1

value: Whole Animal

value: wild-type dauers (N2; Bristol)


title: Vaccinee_16_PI [BX_16_IgG_v2]


title: N2 HID rep2


title: Corneolimbal, 6 week old, Confetti+ 23

description:
SmartSeq-2
6-week old Confetti+ 23

value: epithelial cells


title: Sample 8_differentiated human podocytes, treated with LPS+DMSO, replica 2


title: Sample 13_human podocytes at permissive (33C) condition, treated with DMSO, replica 1


title: Vaccinee_15_PI [BX_15_IgG_v2]


title: Vaccinee_13_PI [BX_13_IgG_v2]

description:
BX_IgG_Slide_010.gpr
Individual participant of clinical trial NCT 04297436


title: PA14_L4_lax188_Exposed_4

city: Los Angeles

first: Sean

middle: Patrick

last: Curran

state: CA

address: 3715 McClintock Ave #350

department: Geronotology

institute: University of Southern California

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining ploy-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using DESeq2 R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package
Assembly: ce11
Supplementary files format and content: csv file contains read count data used for downstream DEG analysis in R using bioconductor DESeq2 package
Supplementary files format and content: MD5_L4.txt is MD5 checksums

growth_protocol: OP50-raised WT and skn-1gf(lax188) worms were egg prepped and allowed to synchronize overnight into L1 population. Worms were dropped on OP50 and raised until L4 (48 hours later).

extract_protocol:
Zymo Direct-zol RNA Miniprep kit (Cat. #R2052) was used. In brief, worms were homogenized in TRI reagent and then run through the kit. Sample concentration was tested via qubit and 1 ug/sample was sent for sequencing.
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: At L4, worms were washed to control (OP50) plates and treatment (PA14) plates and exposed for 4 hours before collection for RNA processing.

value: Pseudomonas aeruginosa/PA14


title: Corneolimbal, 6 week old, Confetti+ 22

description:
SmartSeq-2
6-week old Confetti+ 22

extract_protocol:
Male and female Confetti mice, aged 5, 17 and 59-weeks (n=3/age), were administered Tamoxifen (5 mg/mL) (Sigma-Aldrich, St Louis, MI) in 10% ethanol (Sigma-Aldrich) and 90% sunflower seed oil (Sigma-Aldrich) by intraperitoneal injection on three consecutive days to induce expression of the multi-color fluorescent reporter. Seven days after the first injection, mice were euthanized by cervical dislocation, and their eyes immediately enucleated. Corneas, complete with the limbal ring, were dissected under a stereo microscope (Zeiss, Oberkochen, Germany), taking care to remove extraneous tissue. Samples were exposed to 0.5 U/mL Dispase II (Penzberg, Germany) in defined keratinocyte serum-free media (dKSFM) (ThermoFisher Scientific, Waltham, MA) for 2 hrs at 37°C, then trypsin-EDTA (ThermoFisher) for 10 min at 37°C to generate a single-cell suspension of corneolimbal epithelia. Cells underwent FACS for colored Confetti+ (CFP, GFP, YFP, RFP) and non-colored Confetti- populations, taking care to only sort the epithelial population based on cell granularity, size and shape, and minimizing other cell types such as immune cells.
Single-cell libraries were prepared using the SmartSeq-2 protocol, and sequencing was performed on the Illumina NextSeq platform (Ramaciotti Centre for Genomics, UNSW, Sydney, Australia). Mouse corneolimbal epithelia (n=378 total), including Confetti+ and Confetti- cells (n=189/group) were segregated according to three time-points corresponding to mouse age (n=63 cells/time-point) (T1=6, T2=18 and T3=60-weeks), then sequenced and analyzed. Reads were quantified with Salmon (v0.9.1) using the mouse transcriptome GRCm38 to create an index before quantification. Read counts ranged from 288,000-1.4 million/cell with a median of 778,000/cell. The number of genes per cell ranged from 546 - 7,246 with a median of 4,758. Reads were summarized according to gene level using the R package Tximport [103]. The R package Seurat (v3.1.4) [104] was used to filter and normalize data, after which clustering and differential expression analysis were conducted. Cells with >5% mitochondrial content and those with <2000 genes were then removed, and the number of cells analyzed for Confetti+ at T1, T2, and T3, and Confetti- at T1, T2, and T3 were 62, 55, and 41, and 61, 60 and 59, respectively. After filtering and normalization, 14,343 genes were identified across the data set in 338 cells.

value: 6-week old


title: Corneolimbal, 6 week old, Confetti+ 21

description:
SmartSeq-2
6-week old Confetti+ 21


title: Sample 7_differentiated human podocytes, treated with LPS+DMSO, replica 1


title: daf-2 rep1

value: Temp 25C


title: PA14_L4_lax188_Exposed_3


title: Vaccinee_12_PI [BX_12_IgG_v2]

extract_protocol: Human sera collected from the KEMRI clinics in Mtwapa and Malindi and from clinical trial NCT 04297436

value: Individual vaccinated with 4CMenB

value: Blood


title: Corneolimbal, 6 week old, Confetti+ 20

description:
SmartSeq-2
6-week old Confetti+ 20

value: Cornea


title: Sample 9_differentiated human podocytes, treated with LPS+DMSO, replica 3

value: Kidney

value: immortal podocytes


title: Sample 6_differentiated human podocytes, treated with BT503, replica 3

description:
rawcounts_1.txt
rawcounts_2.txt

value: podocytes


title: Sample 5_differentiated human podocytes, treated with BT503, replica 2

description:
rawcounts_1.txt
rawcounts_2.txt


title: PA14_L4_lax188_Exposed_2


title: PA14_L4_lax188_Exposed_1


title: Corneolimbal, 6 week old, Confetti+ 19

description:
SmartSeq-2
6-week old Confetti+ 19


title: PA14_L4_lax188_Control_4

value: E. coli/OP50


title: Vaccinee_14_PI [BX_14_IgG_v2]

value: Male

value: Serum


title: Vaccinee_10_PI [BX_10_IgG_v2]


title: Vaccinee_11_PI [BX_11_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 18

description:
SmartSeq-2
6-week old Confetti+ 18


title: Sample 4_differentiated human podocytes, treated with BT503, replica 1

description:
rawcounts_1.txt
rawcounts_2.txt

value: WT

value: differentiated


title: PA14_L4_lax188_Control_3

value: Whole Animal


title: Corneolimbal, 6 week old, Confetti+ 17

description:
SmartSeq-2
6-week old Confetti+ 17


title: Vaccinee_09_PI [BX_09_IgG_v2]


title: Vaccinee_08_PI [BX_08_IgG_v2]


title: Sample 2_differentiated human podocytes, treated with DMSO, replica 2

description:
rawcounts_1.txt
rawcounts_2.txt


title: Corneolimbal, 6 week old, Confetti+ 16

description:
SmartSeq-2
6-week old Confetti+ 16


title: Sample 1_differentiated human podocytes, treated with DMSO, replica 1

description:
rawcounts_1.txt
rawcounts_2.txt


title: PA14_L4_lax188_Control_1


title: Vaccinee_06_PI [BX_06_IgG_v2]

description:
BX_IgG_Slide_009.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_07_PI [BX_07_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 14

description:
SmartSeq-2
6-week old Confetti+ 14


title: PA14_L4_N2_Exposed_4

value: Wildtype


title: Corneolimbal, 6 week old, Confetti+ 15

description:
SmartSeq-2
6-week old Confetti+ 15

value: epithelial cells


title: day5_rep2

city: Minneapolis

first: Samira

last: Azarin

state: MN

address: 421 Washington Ave SE, RM151R Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: Sample 4 biol rep 2

data_processing:
Reads were trimmed for low quality and adaptors using Trimmomatic.
Sequences were mapped to the human reference genome (GRCh38.91) using STAR.
Cfflinks was used to obtain fragments per kilobase of transcript per million (FPKM) files which were converted to transcripts per million (TPM) files.
Assembly: GRCh38.91
Supplementary files format and content: comma-separated value file includes TPM values for each sample

source_name: cell line

extract_protocol:
Cell pellets were collected and lysed using QiaShredder columns (Qiagen). RNA was isolated using the RNeasy Mini Kit (Qiagen) as the manufacturer recommends, including incubation with DNase I (RNAse-free DNase Set, Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina).

treatment_protocol: For differentiation, 70% confluent stem cells were rinsed with DPBS (Gibco) and pre-warmed Accutase (STEMCELL Technologies) was added to the wells. Cells were then placed at 37°C for 5-7 min, after which they were added to an equal volume of fresh media and spun down at 200xg for 5 min. The cells were then resuspended and seeded on Matrigel- or Cultrex-coated plates at 6,000 cells/cm2 in TeSR-E8 or mTeSR Plus with 5 µM ROCK inhibitor (Y-27632, STEMCELL Technologies). Cells were maintained in E8 or mTeSR Plus for two more days, and then the medium was changed to unconditioned medium (UM): DMEM/F12 with 20% Knockout serum replacement (KOSR), MEM non-essential amino acids (1x), GlutaMAX (1x, Gibco), and 0.1 mM β-mercaptoethanol (Sigma), containing 1 µM retinoic acid (RA, Sigma) and 8 µM CHIR 99021 (CHIR, Tocris). Cell culture media was changed daily for five days.

value: cell line

value: induced pluripotent stem cells

value: trophectoderm differentiation


title: PA14_L4_N2_Exposed_3

value: Pseudomonas aeruginosa/PA14


title: Corneolimbal, 6 week old, Confetti+ 13

city: Kensington

first: Alexander

last: Richardson

address: Crn Botany and High St

institute: UNSW Sydney

description:
SmartSeq-2
6-week old Confetti+ 13

value: 6-week old


title: day5_rep1

description: Sample 4 biol rep 1


title: PA14_L4_N2_Exposed_2


title: Vaccinee_05_PI [BX_05_IgG_v2]

city: Manchester

first: Fidel

last: Ramirez Bencomo

address: Michael Smith Building

institute: The University of Manchester

value: Individual vaccinated with 4CMenB

value: Blood


title: Sample 3_differentiated human podocytes, treated with DMSO, replica 3

description:
rawcounts_1.txt
rawcounts_2.txt

value: Kidney

value: immortal podocytes


title: Vaccinee_03_PI [BX_03_IgG_v2]


title: MCAO+AS-Exos_4

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GRCm39.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Microglia sorted from MCAO mice treated with  AS-exos

growth_protocol: Experimental atherosclerosis was established by feeding Apoe KO mice a Western, high-fat diet for 12 weeks and experimental cerebral ischemia was established by middle cerebral artery occlusion.

extract_protocol:
Briefly, infarct cortexes of mice were removed and cut into slices with the aid of microscope. Adult Brain Dissociation Kit (Miltenyi Biotec) was then utilized for tissue digestion according to the manufacture’s protocol. After debris removal, the remaining cell suspensions were incubated with blocking buffer and were then stained with antibodies (CD45-APC, CD11b-PE). Flow cytometry was performed and acquired data were analyzed using FlowJo 10.4. Sorted microglia were then processed to cell lysis for cDNA synthesis. After quality control, amplified cDNAs were used for further library construction and sequencing.
Qualified amplified cDNAs use transposon-based method for further library construction. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.

treatment_protocol: MCAO mice were given 150 μg exosomes, isolated from plasma of ApoE KO mice fed with western diet or normal diet, by tail intravenous injection every 3 days from the day of surgery.

value: Microglia

value: MCAO+AS-exos


title: PA14_L4_lax188_Control_2

value: E. coli/OP50


title: PA14_L4_N2_Control_4


title: PA14_L4_N2_Exposed_1


title: day3_rep1

description: Sample 3 biol rep 1

value: WT


title: Corneolimbal, 6 week old, Confetti+ 12

description:
SmartSeq-2
6-week old Confetti+ 12

value: Cornea


title: day1_rep2

description: Sample 2 biol rep 2


title: Vaccinee_02_PI [BX_02_IgG_v2]

value: Male

value: Serum


title: Corneolimbal, 6 week old, Confetti+ 10

description:
SmartSeq-2
6-week old Confetti+ 10

value: epithelial cells


title: day1_rep1

description: Sample 2 biol rep 1

value: cell line


title: Vaccinee_04_PI [BX_04_IgG_v2]


title: Corneolimbal, 6 week old, Confetti+ 9

description:
SmartSeq-2
6-week old Confetti+ 9


title: day0_rep1

description: Sample 1 biol rep 1

value: induced pluripotent stem cells


title: day0_rep2

description: Sample 1 biol rep 2

value: trophectoderm differentiation


title: day3_rep2

description: Sample 3 biol rep 2


title: MCAO+AS-Exos_2


title: PA14_L4_N2_Control_1

value: Whole Animal

value: Wildtype


title: PA14_L4_N2_Control_2


title: MCAO+Ctrl-Exos_4

source_name: Microglia sorted from MCAO mice treated with  Ctrl-exos

value: MCAO+Ctrl-exos


title: MCAO+AS-Exos_1


title: Corneolimbal, 6 week old, Confetti+ 11

description:
SmartSeq-2
6-week old Confetti+ 11

value: 6-week old


title: Corneolimbal, 6 week old, Confetti+ 8

description:
SmartSeq-2
6-week old Confetti+ 8


title: ASC52telo, TP53 KO, RB1 KO, PIK3CA OE, rep3

city: Sacramento

first: Janai

middle: R.

last: Carr-Ascher

department: Department of Internal Medicine

institute: University of California Davis

data_processing:
RNA-seq fastq files were processed through the TOIL pipeline (https://github.com/BD2KGenomics/toil-rnaseq)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw RSEM gene count values for each sample

extract_protocol:
Total RNA was isolated from human sarcoma models and controls using the RNeasy Mini Kit (Qiagen)
Library preparation was performed by the Functional Genomics Laboratory (FGL), a QB3-Berkeley Core Research Facility at UC Berkeley. Total RNA samples were checked on Bioanalyzer (Agilent) for quality. Only high- quality RNA samples (RIN > 8) were used. At the FGL, Oligo (dT)25 magnetic beads (Thermofisher) were used to enrich mRNA. The treated RNAs were rechecked on Bioanalyzer for their integrity. The library preparation for sequencing was done on Biomek FX (Beckman) with the KAPA hyper prep kit for RNA (now Roche). Truncated universal stub adapters were used for ligation, and indexed primers were used during PCR amplification to complete the adapters and enrich the libraries for adapter-ligated fragments. Samples were checked for quality on an AATI (now Agilent) Fragment Analyzer. Samples were then transferred to the Vincent J. Coates Genomics Sequencing Laboratory (GSL), where quantitative PCR was used to calculate sequence-able molarity with the Kapa Biosystems Illumina Quant qPCR Kits. Libraries were pooled evenly by molarity and sequenced on an Illumina NovaSeq6000 150PE S4. Raw sequencing data were converted into fastq format, sample-specific files using the Illumina bcl2fastq2 software.

value: mesenchymal stem cells

value: TP53 KO, RB1 KO, PIK3CA OE


title: ASC52telo, TP53 KO, RB1 KO, PIK3CA OE, rep2


title: Corneolimbal, 6 week old, Confetti+ 7

description:
SmartSeq-2
6-week old Confetti+ 7


title: Corneolimbal, 6 week old, Confetti+ 6

description:
SmartSeq-2
6-week old Confetti+ 6


title: SA01_sox21KO7_BMP4day2_3_days

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

data_processing:
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene-level read count

source_name: human pluripotent stem cell

growth_protocol: Monolayer culture of hPSC in feeder-free condition was done following the previously established protocol (Chen et al., 2012).  The hPSCs were dissociated to single cells with accutase (A11105, Life Technologies), plated at a density of 1 X 105 cells/cm2 in a Matrigel (354277, BD)-coated plate and cultured with mTeSR1 (05850, Stem Cell Technology). Cells were plated in medium containing 5 μM Y27632, ROCK inhibitor (Y0503, Sigma-Aldrich) to increase cell survival upon dissociation. ROCK inhibitor was removed from the medium at 24 hours after plating. All differentiation protocols began 24 hours after ROCK inhibitor removal.

extract_protocol:
mirVana kit (Ambion)
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.

treatment_protocol: Cells were cultured with Aggrewell medium (05893, Stem Cell Technology) for 2 days after ROCK inhibitor removal and then cultured with N2B27 medium supplemented with Noggin (500 ng/ml, 719-NG, R&D Systems) and SB431542 (2 μM, S4317, Sigma-Aldrich) for another 4 days for neuroectodermal differentiation (NSB) while BMP4 (100 ng/ml, 314-BP, R&D Systems) was added for mesendodermal differentiation upon ROCK inhibitor removal and cultured for 6 days. SR = mTeSR1 only. All differentiation protocols were carried out for 6 days. RNA collected for RNA-seq at 2,4,6 days of differentiation.

value: pluripotent stem cell

tag: subject id

tag: linerep

tag: days of selfrenewal or differentiation


title: SA01_sox21WT8_BMP4day2_3_days


title: ASC52telo, TP53 KO, RB1 KO, PIK3CA OE, rep1


title: MCAO+AS-Exos_3

value: Microglia

tag: strain

value: MCAO+AS-exos


title: Corneolimbal, 6 week old, Confetti+ 5

description:
SmartSeq-2
6-week old Confetti+ 5


title: Corneolimbal, 6 week old, Confetti+ 4

description:
SmartSeq-2
6-week old Confetti+ 4


title: MCAO+Ctrl-Exos_3


title: ASC52telo, TP53 KO, RB1 KO, CDK4 OE, rep3

value: TP53 KO, RB1 KO, CDK4 OE


title: MCAO+Ctrl-Exos_2


title: SA01_sox21WT8_NSB_6_days

value: WT

value: NSB


title: PA14_L4_N2_Control_3

value: E. coli/OP50


title: SA01_sox21WT8_NSB_4_days


title: ASC52telo, TP53 KO, RB1 KO, CDK4 OE, rep2


title: MCAO+Ctrl-Exos_1


title: Corneolimbal, 6 week old, Confetti+ 3

description:
SmartSeq-2
6-week old Confetti+ 3

value: Cornea

value: epithelial cells


title: MCAO_3

source_name: Microglia sorted from MCAO mice

value: MCAO


title: Corneolimbal, 6 week old, Confetti+ 2

description:
SmartSeq-2
6-week old Confetti+ 2


title: ASC52telo, TP53 KO, RB1 KO, CDK4 OE, rep1


title: SA01_sox21WT8_NSB_2_days


title: Corneolimbal, 6 week old, Confetti+ 1

description:
SmartSeq-2
6-week old Confetti+ 1


title: MCAO_2


title: ASC52telo, TP53 KO, RB1 KO, KRAS OE, rep3

value: TP53 KO, RB1 KO, KRAS OE


title: SA01_sox21KO7_NSB_6_days


title: MCAO_1


title: ASC52telo, TP53 KO, RB1 KO, KRAS OE, rep2


title: SA01_sox21KO7_NSB_2_days


title: SA01_sox21KO7_SR_3_days

value: SR


title: MCAO_4


title: ASC52telo, TP53 KO, RB1 KO, YAP1 OE, rep3

value: TP53 KO, RB1 KO, YAP1 OE


title: Sham_4

source_name: Microglia sorted from Sham mice

value: untreated


title: ASC52telo, TP53 KO, RB1 KO, YAP1 OE, rep2


title: SA01_sox21WT8_SR_2_days.1


title: M2c Wild-type Rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al, 2014).
. Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.7a.(Dobin et al, 2013) Aligned reads were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al, 2014). The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al, 2014).
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
The Ensemble annotation was enriched with UniProt data (UniProt Consortium, 2014).
Assembly: mm10
Supplementary files format and content: count table

source_name: Macrophage

extract_protocol:
Total RNA was isolated from macrophages by using RNeasy Micro kit (Qiagen, Hilden, Germany) based on manufacturer’s instructions and as described (Li et al, 2023). Thereafter, RNA concentrations were determined (NanoDrop ND-1000, Thermo Fisher Scientific, Dreieich, Germany;  260 nm)
1.5 µg RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

value: Macrophage


title: M2c sEH-/- Rep3

value: sEH-/-


title: ASC52telo, TP53 KO, RB1 KO, YAP1 OE, rep1

value: mesenchymal stem cells


title: Sham_3


title: M2c sEH-/- Rep2


title: SA01_sox21WT8_SR_3_days

value: pluripotent stem cell


title: M2c Wild-type Rep2


title: Sham_1

value: Microglia


title: Sham_2


title: SA01_sox21KO7_SR_2_days.1


title: ASC52telo, TP53 KO, RB1 KO, rep3

value: TP53 KO, RB1 KO


title: ASC52telo, TP53 KO, RB1 KO, rep2


title: ASC52telo, TP53 KO, RB1 KO, KRAS OE, rep1


title: M2c sEH-/- Rep1


title: SA01_sox21KO7_NSB_4_days


title: Young 1, HTO-derived cDNA

city: Boston

first: Amy

last: Huang

state: MA

address: 25 Shattuck St

department: Immunology

institute: Harvard Medical School

description:
10x Genomics Cell Hashing library
Y1_barcodes.tsv.gz
Y1_features.tsv.gz
Y1_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (v.4.0.0) pipeline with feature barcoding (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis)
Downstream analysis (including log normalization) was performed using Seurat (v.3.2.2) in R (v.4.0.3 "Bunny-Wunnies Freak Out")
Assembly: mm10
Supplementary files format and content: Gzipped tab-separated values files and matrix files
Supplementary files format and content: tab-delimited text file including log normalized counts for each cell

source_name: tumor

extract_protocol: Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: tumor

value: immune

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC class I:TotalSeq-B0301 anti-mouse Hashtag1 Antibody; TotalSeq-B0302 anti-mouse Hashtag2 Antibody; TotalSeq-B0303 anti-mouse Hashtag3 Antibody; TotalSeq-B0304 anti-mouse Hashtag4 Antibody

value: 3-4 months


title: Young 2, HTO-derived cDNA

description:
10x Genomics Cell Hashing library
Y2_barcodes.tsv.gz
Y2_features.tsv.gz
Y2_matrix.mtx.gz


title: SA01_sox21WT8_SR_6_days

value: WT


title: M2c Wild-type Rep1


title: Sorted mouse lung cells, corn oil-treated control biol rep 3

city: Pittsburgh

first: John

last: Alcorn

state: Pennsylvania

address: 4401 Penn Avenue

institute: University of Pittsburgh

data_processing:
STAR v2.7.3a
Sequences were trimmed for unwanted sequences using Bowtie2 v2.5.1, and quality control was performed with RNA-SeQC v1.1.8, RSeQC v3.0.1, and MultiQC v1.7
Paired-end reads were aligned and mapped to reference genome GRCm38 using STAR 2.7.3a
Read count extraction and normalization was performed using DESeq2 and expression was estimated using HTSeq v0.11.2
Assembly: GRCm38.p6
Supplementary files format and content: .xlsx includes raw normalized counts for all samples
Supplementary files format and content: .txt files include splicing annotations for all samples
Supplementary files format and content: .xlsx file includes FPKM values for all samples

source_name: lung

extract_protocol:
RNA was isolated using the Rneasy Mini Kit (Qiagen) per manufacturer instructions.
RNA libraries for RNAseq were prepared using the Takara SMART-Seq v4 Ultra low Input RNA kit per manufacturer instructions.

treatment_protocol: Mice were treated with 1.5mg Tamoxifen in corn oil or corn oil alone intraperitoneally on d-14, -7, 0, and 5. Mice were infected with 900 PFU PR8 on d0 and sacrificed on d6.

value: lung

value: corn oil


title: SA01_sox21WT8_SR_2_days

value: SR


title: Sorted mouse lung cells, corn oil-treated control biol rep 4


title: Sorted mouse lung cells, corn oil-treated control biol rep 1


title: Aged 2, HTO-derived cDNA

description:
10x Genomics Cell Hashing library
O2_barcodes.tsv.gz
O2_features.tsv.gz
O2_matrix.mtx.gz

value: 20-22 months


title: SA01_sox21WT8_SR_4_days


title: SA01_sox21KO7_SR_6_days


title: SA01_sox21KO7_SR_4_days


title: Aged 1, HTO-derived cDNA

description:
10x Genomics Cell Hashing library
O1_barcodes.tsv.gz
O1_features.tsv.gz
O1_matrix.mtx.gz


title: ASC52telo, TP53 KO, RB1 KO, rep1


title: Young 1, mRNA-derived cDNA

description:
10x Genomics 3'v3 library
Y1_barcodes.tsv.gz
Y1_features.tsv.gz
Y1_matrix.mtx.gz

value: mRNA


title: Sorted mouse lung cells, tamoxifen-treated biol rep 4

value: Tamoxifen


title: Sorted mouse lung cells, tamoxifen-treated biol rep 5


title: ASC52telo, rep1


title: ASC52telo, rep3


title: Sorted mouse lung cells, corn oil-treated control biol rep 2


title: SA01_sox21KO7_SR_2_days


title: PTENα_Input

city: Beijing

first: Zeliang

last: Yang

address: No.38 Xueyuan Road,Haidian

institute: Peking University Health Science Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software.
The clean reads were mapped to the VSV reference sequence (https://www.ncbi.nlm.nih.gov/nuccore/J02428.1) using Hisat2 (http://daehwankimlab.github.io/hisat2/, v2.2.1).
A step-wise mapping procedure was applied: (1) Reads that not aligned to the VSV reference sequence were discarded. (2) Reads with low alignment quality were removed. (3) Reads that aligned to the mitochondrial sequence were discarded. Peaks were identified using MACS2 (https://pypi.org/project/MACS2/, v2.2.7.1).
Visualization of peak distribution along genomic regions of interested genes was performed with the Integrative Genomics Viewer (IGV).
Assembly: Vesicular stomatitis Indiana virus, complete genome (J02428.1)
Supplementary files format and content: bigWig, narrowPeak

organism:
Homo sapiens
Vesicular stomatitis Indiana virus

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).

treatment_protocol: Cells were treated with VSV for 14h in the presence of 4-thiouridine

value: Human embryonic kidney

value: VSV infection


title: Aged 2, mRNA-derived cDNA

description:
10x Genomics 3'v3 library
O2_barcodes.tsv.gz
O2_features.tsv.gz
O2_matrix.mtx.gz


title: PTENα_IP


title: SYN, replicate 1, scRNAseq

city: Seoul

first: Hanbi

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Division of Nephrology, Department of Internal Medicine

country: South Korea

institute: Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea

description: 10X Genomics

data_processing:
The quality and basic statistics of raw sequencing data (FASTQ) were assessed using FastQC. After the quality control process, the sequencing data were processed through 10x Genomics Cell Ranger v6.0.2 using mouse reference genome (mm10). The Cell Ranger count pipeline produces gene expression matrices containing the UMI counts per gene, per barcode, and per cluster information.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
The spleens were dissociated into single-cell splenocytes using fully frosted glass slides. The splenocytes were filtered through a 40 µm cell strainer (Falcon, Durham, NC), and preserved in cryomedia (90 % FBS + 10 % DMSO) for scRNA-seq analysis. Cell stocks were thawed in 37℃ 10% FBS/DMEM. The cells were washed twice with cold Ca2+- and Mg2+-free 0.04 % BSA/PBS at 300g for 5min at 4°C. Samples were gently resuspended in cold Ca2+- and Mg2+-free 0.04% BSA/PBS and then counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos biosystems) with AO/PI staining. Cell viability was further assessed using the Dead Cells Removal Kit (Miltenyi biotech, Cat no 130-090-101) and MS columns (Miltenyi biotech, cat no. 130-042-201) according to the manufacturer’s instructions.
According to the 10x Chromium Single Cell 5’ v2 protocol (10x Genomics, document no. CG000331), the scRNA-seq libraries were prepared using the 10x Chromium controller and Next Gem Single Cell 5’ Reagent v2 kits (10x Genomics, PN-1000244).

value: spleen

value: wildtype

value: splenocytes

value: received skin transplants from wild-type C57BL/6 mouse


title: Sorted mouse lung cells, tamoxifen-treated biol rep 2


title: Sorted mouse lung cells, tamoxifen-treated biol rep 1


title: ASC52telo, rep2

value: mesenchymal stem cells


title: Young 2, mRNA-derived cDNA

description:
10x Genomics 3'v3 library
Y2_barcodes.tsv.gz
Y2_features.tsv.gz
Y2_matrix.mtx.gz

value: tumor

value: immune


title: ALLO, replicate 1, scRNAseq

description: 10X Genomics

value: received skin transplants from C57BL/6-Tg(HLAA2.1)1Enge/J mouse twice


title: Aged 1, mRNA-derived cDNA

description:
10x Genomics 3'v3 library
O1_barcodes.tsv.gz
O1_features.tsv.gz
O1_matrix.mtx.gz


title: amniotic fluid fetal cells 56

status: Public on Aug 14 2024

type: genomic

city: Fuzhou

first: Yanting

last: Que

address: No. 88, Jiaotong Road, Taijiang District, Fuzhou City, Fujian Province

institute: Fujian Medical University

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).

label: Biotin

molecule: genomic DNA

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

value: amniotic fluid fetal cells

tag: diagnosis

value: microdeletion of Xp22.33 or Yp11.32


title: amniotic fluid fetal cells 55

description: Hybridized to CytoScan 750K

tag: tissue