title: Patient_073_During [PAT_073_D_IgA]


title: P2_PNEU_Day8_K1

status: Public on Aug 15 2024

type: SRA

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

country: Germany

institute: University of Bielefeld

library_source: genomic

data_processing:
The ATAC-seq reads of each sample were mapped to the human reference genome GRCh38 using Bowtie2 v2.5.0 with default settings. Samtools v1.16.1 was used for formatting, quality filtering, and removing duplicates to guarantee unique mapping; the MAPQ (mapping quality, 0=non-unique, >10 probably unique) was set to a sophisticated value of 30.
After examining each replicate separately, replicates of respected groups were combined to maximize the peak calling strength using the samtools merge function. MACS3 v3.0.0b1 was used for peak calling with the parameters “–nomodel –nolambda –keep-dup auto –call summits” the peaks were filtered by a q-value cutoff of 0.05. The sequences of peaks from 250 bp upstream and 250 bp downstream of the peaks were extracted with R v4.2.2 and Bedtools v2.30.0 (R-Citation). In R v4.2.2 GenomicRanges v1.42.0 linked the ATAC-Seq peaks with the nearest genes. The promoter was defined as the region within 2 kb of the reference transcript start site. Enriched motifs in the peak sequences were analyzed with MEME-ChIP v5.5.1 and default settings. Gene ontology analysis of the identified motifs was done with GOMo v5.5.1. The differential peak analysis of the ATAC-seq was performed using HOMER2 v4.11 with a replicate FDR cutoff of 0.05 for peak identification calculated by DESeq2 v1.24.0. The genomic annotation of the peaks was determined using ChIPSeeker v1.34.1. The genomic distribution of peaks was visualized using Adobe Illustrator 2023 (Adobe Inc., San Jose, USA).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file

molecule: genomic DNA

organism: Homo sapiens

source_name: Tongue base

extract_protocol:
ATAC-seq analysis was performed with technical replicates (n=3). ATAC-seq was performed according to Buenrostro et al. with harvested P1 and P2 cells, including isolation of intact nuclei and tagging with Tn5 transposase.
After cell preparation, transposition reaction, library preparation, and purification, the quality of libraries was assessed using an Agilent Bioanalyzer High Sensitivity DNA Analysis kit. Sequencing was performed first on an Illumina MiSeq system in paired-end mode 2 x 50 bp and finally on the Illumina NextSeq 2000 system in paired-end mode 2 x 50 bp with P3 chemistry

tag: tissue

value: Tongue base

tag: cell line

tag: cell type

value: epithelial cancer cells

tag: treatment

value: undifferentiated


title: Patient_072_After [PAT_072_A_IgA]

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:
PT_IgA_Slide_4.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

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

source_name: Gonococcal infection

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 with confirmed infection

value: Blood

tag: tissue subtype

value: Serum


title: Patient_065_During [PAT_065_D_IgA]

description:
PT_IgA_Slide_3.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

label: Goat Anti-Human IgA alpha chain (DyLight® 650) pre-adsorbed secondary antibody


title: P2_CFM_Day8_C2

value: differentiated


title: Patient_065_Before [PAT_065_B_IgA]

description:
PT_IgA_Slide_2.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: P1_CFM_Day8_C3

source_name: Oropharynx / Tonsil

value: Oropharynx / Tonsil


title: Patient_064_During [PAT_064_D_IgA]


title: P1_CFM_Day8_C2


title: Patient_069_During [PAT_069_D_IgA]


title: Patient_063_During [PAT_063_D_IgA]


title: Patient_064_Before [PAT_064_B_IgA]


title: Patient_067_Before [PAT_067_B_IgA]


title: P1_CFM_Day8_C1


title: P1_PNEU_Day8_K3


title: P1_PNEU_Day8_K1


title: P1_PNEU_Day8_K2


title: ISE18SB-B1_S15

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
The sequence reads were mapped to Ixodes scapularis GCF_016920785.2 using default settings of STAR (version 2.7.9a).
Gene count extraction was performed using default settings of featureCounts (version 2.0.1)
Normalization and conversion to FPKM were performed using DEseq2 (version 1.40.2)
Assembly: GCF_016920785.2
Supplementary files format and content: comma-separated text file include raw count of each samples

molecule: total RNA

organism: Ixodes scapularis

growth_protocol: Cells were seeded to fresh media, grown in standard conditions, and collected for RNA prep on day 4 (60% confluency)

extract_protocol:
Trizol was added to each cell pellet of approximately 5.5 x 10^6 cells and RNA extracted using the Zymo Research Direct-zol RNA Miniprep Kit
Libraries were constructed using the KAPA mRNA HyperPrep kit


title: ISE18-SB-A2_S14


title: Patient_065_After [PAT_065_A_IgA]

description:
PT_IgA_Slide_15.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: P2_CFM_Day8_C3


title: Patient_062_During [PAT_062_D_IgA]


title: Patient_062_Before [PAT_062_B_IgA]


title: ISE18SB-A1_S13


title: ISE18-B1_S11


title: Patient_059_After [PAT_059_A_IgA]

description:
PT_IgA_Slide_13.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_061_Before [PAT_061_B_IgA]


title: Patient_060_Before [PAT_060_B_IgA]


title: ISE18-A1_S9


title: ISE18-A2_S10


title: ISE18-B2_S12


title: ISE6-B1_S7


title: Patient_057_After [PAT_057_A_IgA]


title: Patient_058_Before [PAT_058_B_IgA]


title: Patient_056_During [PAT_056_D_IgA]

description:
PT_IgA_Slide_14.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: ISE6-A2_S6


title: Patient_055_Before [PAT_055_B_IgA]


title: Patient_055_During [PAT_055_D_IgA]


title: Patient_054_Before [PAT_054_B_IgA]

description:
PT_IgA_Slide_12.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_053_After [PAT_053_A_IgA]


title: ISE6-A1_S5


title: Patient_053_During [PAT_053_D_IgA]


title: IDE2-B1_S3


title: Patient_053_Before [PAT_053_B_IgA]


title: IDE2-A1_S1


title: Patient_058_During [PAT_058_D_IgA]


title: IDE2-A2_S2


title: Patient_052_After [PAT_052_A_IgA]


title: Patient_052_Before [PAT_052_B_IgA]

description:
PT_IgA_Slide_9.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Ifnar1KO_IFNzVADNecrostatin_treated_r2

type: RNA

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

hyb_protocol: For each sample labeled cRNA was hybridized on SurePrint G3 Mouse GE 8x60K microarray (Design ID # 028005, Agilent Technologies, Santa Clara, CA, USA) at 65°C for at least 16 hours followed by washing steps.

scan_protocol: The microarrays were read on the Agilent DNA Microarray SureScan Scanner using the FeatureExtraction program (Agilent Technologies, Santa Clara, CA, USA).

data_processing:
Green median fluorescence signal exported by FeatureExtraction was analyzed in R/Bioconductor and the limma package. Median background signal was subtracted and the datasets were normalized by the quantiles method. Data points with outlier flags from FeatureExtraction were assigned null weights and marked 'null'. Probes representing control spots and those with signal below threshold (10% brighter than the 95th percentile of negative controls) in 4 of the 12 arrays were filtered out and marked 'null'.
Background-subtracted, quantile-normalized median green signal

organism: Mus musculus

source_name: bone marrow-derived macrophages

label_protocol: cDNA synthesis was prepared, amplified with T7 RNA polymerase and labeled with Cyanine-3 (LowInput quickAmp Labeling Kit One-Color)

growth_protocol: Mouse bone marrow were used as a source of cells to generate primary murine bone marrow derived macrophages (BMDMs) from WT (C57BL/6) and IFNAR1 knockout mice. Bones were extracted and flushed with ice-cold R8+gentamycin using small gauge needle and the harvested cells were passed through 70-100 nm strainer in a 50 mL falcon tube. Cells were pelleted at 1600 RPM for 8 minutes. 50 mm non-tissue culture petri dishes were coated evenly with macrophages colony stimulating factor (M-CSF) at final concentration 5 ng/mL. Following centrifugation, the cell pellet was resuspended in R8 with gentamycin and around 10E6 to 17E6 cells were added carefully to the coated petri dish. R8+ gentamycin was added to the cells for a final volume of 10 mL. Cells were incubated at 37°C for 6 days to allow macrophages differentiation.

extract_protocol: Total RNA was prepared using RNeasy kit (74104, QIAGEN)

treatment_protocol: In general, on day 6 the differentiated bone marrow derived macrophages (BMDMs) were seeded in 6-well flat bottom tissue culture plate at 8E5 cell/well overnight at 37°C to ensure the adherence to the plate before treatments. On day 7, BMDMs were treated with appropriate concentrations of inhibitors and left for 6-hours before extracting RNA and measuring viability. Cells were treated with the following: LPS: 100 ng/mL and IFNβ: 1000U/mL.

tag: genotype

value: IFN, zVAD and Necrostatin-1


title: Patient_051_During [PAT_051_D_IgA]


title: Patient_061_During [PAT_061_D_IgA]


title: Ifnar1KO_IFNzVADNecrostatin_treated_r1


title: Patient_052_During [PAT_052_D_IgA]


title: Ifnar1KO_LPSzVADNecrostatin_treated_r2

value: LPS, zVAD and Necrostatin-1


title: WT_IFNzVADNecrostatin_treated_r1

value: WT


title: IDE2-B2_S4


title: WT_LPSzVADNecrostatin_treated_r1


title: WT_IFNzVADNecrostatin_treated_r2


title: WT_LPSzVADNecrostatin_treated_r2


title: Ifnar1KO_LPSzVADNecrostatin_treated_r1


title: Ifnar1KO_IFNzVAD_treated_r2

value: IFN and zVAD


title: WT_IFNzVAD_treated_r2


title: Patient_048_During [PAT_048_D_IgA]

description:
PT_IgA_Slide_1.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_051_After [PAT_051_A_IgA]


title: Patient_048_Before [PAT_048_B_IgA]


title: WT_IFNzVAD_treated_r1


title: Patient_048_After [PAT_048_A_IgA]


title: Patient_049_Before [PAT_049_B_IgA]


title: Ifnar1KO_IFNzVAD_treated_r1


title: Patient_050_During [PAT_050_D_IgA]

description:
PT_IgA_Slide_11.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_049_After [PAT_049_A_IgA]


title: Patient_046_During [PAT_046_D_IgA]


title: Patient_047_During [PAT_047_D_IgA]

description:
PT_IgA_Slide_7.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Ifnar1KO_LPSzVAD_treated_r2

value: LPS and zVAD


title: Ifnar1KO_LPSzVAD_treated_r1


title: WT_LPSzVAD_treated_r1


title: WT_LPSzVAD_treated_r2


title: Patient_046_Before [PAT_046_B_IgA]

description:
PT_IgA_Slide_10.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_044_During [PAT_044_D_IgA]


title: Patient_045_After [PAT_045_A_IgA]


title: Patient_045_Before [PAT_045_B_IgA]


title: Patient_043_Before [PAT_043_B_IgA]


title: Patient_044_After [PAT_044_A_IgA]


title: Ifnar1KO_zVAD_treated_r1

value: zVAD


title: Ifnar1KO_zVAD_treated_r2


title: WT_zVAD_treated_r1


title: WT_zVAD_treated_r2


title: Patient_043_During [PAT_043_D_IgA]


title: Patient_042_After [PAT_042_A_IgA]

description:
PT_IgA_Slide_8.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_041_During [PAT_041_D_IgA]


title: Patient_041_Before [PAT_041_B_IgA]


title: Ifnar1KO_IFN_treated_rep2

value: IFN

value: Bone marrow derived macrophages

value: IFN-treated


title: Ifnar1KO_IFN_treated_rep1


title: WT_IFN_treated_rep2


title: WT_IFN_treated_rep1


title: WT_LPS_treated_rep2

value: LPS

value: LPS-treated


title: Ifnar1KO_LPS_treated_rep1


title: WT_LPS_treated_rep1


title: Patient_040_After [PAT_040_A_IgA]

value: Male


title: Patient_039_During [PAT_039_D_IgA]

value: Individual with confirmed infection


title: Patient_039_Before [PAT_039_B_IgA]

value: Blood


title: Ifnar1KO_no_treatment_rep2

value: notreat


title: Patient_040_Before [PAT_040_B_IgA]

value: Serum


title: Ifnar1KO_no_treatment_rep1


title: WT_no_treatment_rep2


title: Patient_038_During [PAT_038_D_IgA]


title: Patient_037_During [PAT_037_D_IgA]


title: Patient_039_After [PAT_039_A_IgA]


title: WT_no_treatment_rep1


title: Patient_034_After [PAT_034_A_IgA]


title: Patient_040_During [PAT_040_D_IgA]


title: Patient_035_After [PAT_035_A_IgA]


title: Ifnar1KO_LPS_treated_rep2


title: X2075.3_2D_LSB

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 iPSC

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 LDN193189 (100 nM, 04-0074, Stemgent) and SB431542 (2 μM, S4317, Sigma-Aldrich) for another 4 days for neuroectodermal differentiation (LSB), 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: iPSC

tag: subject id

tag: iPSclinerep

tag: condition

value: LSB

tag: days of selfrenewal or differentiation


title: Patient_035_Before [PAT_035_B_IgA]


title: X2075.3_4DC

value: SR


title: Patient_034_Before [PAT_034_B_IgA]


title: X2075.3_6D_LSB


title: X2075.3_2DC


title: Patient_033_After [PAT_033_A_IgA]

description:
PT_IgA_Slide_6.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_033_During [PAT_033_D_IgA]


title: X2075.1_6D_LSB


title: X2075.1_2D_LSB


title: Patient_031_Before [PAT_031_B_IgA]


title: Patient_032_Before [PAT_032_B_IgA]


title: X2063.2_6D_LSB


title: X2075.1_2DC


title: X2063.2_4D_LSB


title: Patient_036_During [PAT_036_D_IgA]


title: X2063.2_6DC


title: X2075.3_4D_LSB


title: Patient_027_During [PAT_027_D_IgA]


title: Patient_030_After [PAT_030_A_IgA]


title: Patient_029_After [PAT_029_A_IgA]


title: X2075.3_6DC


title: Patient_027_After [PAT_027_A_IgA]


title: X2063.2_4DC


title: Patient_028_After [PAT_028_A_IgA]


title: X2063.2_2DC


title: Patient_026_After [PAT_026_A_IgA]


title: X2063.1_4DC


title: Patient_032_During [PAT_032_D_IgA]


title: X2063.1_6DC


title: Patient_026_During [PAT_026_D_IgA]


title: 2053-6_4D_LSB


title: 2053-6_6D_LSB


title: Patient_025_Before [PAT_025_B_IgA]


title: Patient_026_Before [PAT_026_B_IgA]


title: Patient_025_During [PAT_025_D_IgA]


title: Patient_029_Before [PAT_029_B_IgA]


title: Patient_024_Before [PAT_024_B_IgA]


title: 2053-6_6DC


title: 2053-6_2D_LSB


title: Patient_025_After [PAT_025_A_IgA]


title: 2053-6_D4C


title: Patient_024_After [PAT_024_A_IgA]


title: 2053-6_D2C


title: Patient_024_During [PAT_024_D_IgA]


title: Patient_023_After [PAT_023_A_IgA]


title: 2053-2_6D_LSB


title: X2063.1_2DC


title: 2053-2_4D_LSB


title: Patient_022_Before [PAT_022_B_IgA]


title: Patient_021_After [PAT_021_A_IgA]


title: Patient_022_After [PAT_022_A_IgA]


title: 2053-2_D4C


title: 2053-2_6DC


title: Patient_023_During [PAT_023_D_IgA]


title: Patient_021_Before [PAT_021_B_IgA]


title: Patient_020_During [PAT_020_D_IgA]


title: Patient_020_Before [PAT_020_B_IgA]

description:
PT_IgA_Slide_5.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_020_After [PAT_020_A_IgA]


title: UC06_NogSB_6_days

molecule: polyA RNA

source_name: human pluipotent stem cell

treatment_protocol: For differentiation, cells were plated at a density of 18 X 103 cells/cm2 in a Matrigel-coated plate and Noggin (500 ng/ml, 719-NG, R&D Systems) and SB431542 (2 μM, S4317, Sigma-Aldrich) were added to mTeSR1 medium for neurectodermal 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.

tag: pluripotent cell type

value: ESC

tag: treatment condition

value: NSB


title: UC06_NogSB_4_days


title: 2053-2_2D_LSB


title: SA01_NogSB_4_days


title: Patient_018_During [PAT_018_D_IgA]


title: Patient_018_After [PAT_018_A_IgA]


title: i13_NogSB_6_days


title: Patient_019_During [PAT_019_D_IgA]


title: 2053-2_D2C


title: SA01_NogSB_6_days


title: Patient_017_After [PAT_017_A_IgA]


title: Patient_017_Before [PAT_017_B_IgA]


title: i07_NogSB_6_days


title: i13_NogSB_4_days


title: Patient_017_During [PAT_017_D_IgA]


title: i13_NogSB_2_days


title: Patient_016_After [PAT_016_A_IgA]

value: Female


title: Patient_016_Before [PAT_016_B_IgA]


title: i07_NogSB_4_days


title: i07_NogSB_2_days


title: Patient_015_During [PAT_015_D_IgA]


title: i04_NogSB_6_days


title: UC06_NogSB_2_days


title: Patient_015_Before [PAT_015_B_IgA]


title: Patient_015_After [PAT_015_A_IgA]


title: Patient_014_Before [PAT_014_B_IgA]


title: i04_NogSB_4_days


title: SA01_NogSB_2_days


title: i04_NogSB_2_days


title: H9_NogSB_4_days


title: H9_NogSB_6_days


title: Patient_013_During [PAT_013_D_IgA]


title: UC06_Con_6_days


title: Patient_014_During [PAT_014_D_IgA]


title: H9_NogSB_2_days


title: Patient_013_Before [PAT_013_B_IgA]


title: UC06_Con_4_days


title: UC06_Con_2_days


title: SA01_Con_6_days


title: Patient_012_During [PAT_012_D_IgA]


title: Patient_011_Before [PAT_011_B_IgA]


title: SA01_Con_4_days


title: Patient_010_Before [PAT_010_B_IgA]


title: Patient_011_During [PAT_011_D_IgA]


title: SA01_Con_2_days


title: i13_Con_6_days


title: Patient_014_After [PAT_014_A_IgA]


title: i07_Con_6_days


title: i13_Con_4_days


title: Patient_010_During [PAT_010_D_IgA]


title: i13_Con_2_days


title: i07_Con_4_days


title: Patient_008_During [PAT_008_D_IgA]


title: Patient_009_After [PAT_009_A_IgA]


title: Patient_009_During [PAT_009_D_IgA]


title: Patient_012_After [PAT_012_A_IgA]


title: Patient_008_Before [PAT_008_B_IgA]


title: i04_Con_6_days


title: i07_Con_2_days


title: i04_Con_4_days


title: i04_Con_2_days


title: Patient_008_After [PAT_008_A_IgA]


title: Patient_006_During [PAT_006_D_IgA]


title: Patient_007_After [PAT_007_A_IgA]


title: H9_Con_6_days


title: Patient_007_During [PAT_007_D_IgA]


title: H9_Con_4_days


title: Patient_004_Before [PAT_004_B_IgA]


title: UC06_BMP_6_days


title: Patient_005_After [PAT_005_A_IgA]


title: H9_Con_2_days


title: Patient_003_Before [PAT_003_B_IgA]


title: Patient_003_During [PAT_003_D_IgA]


title: UC06_BMP_4_days


title: UC06_BMP_2_days


title: SA01_BMP_6_days


title: SA01_BMP_4_days


title: Patient_002_After [PAT_002_A_IgA]


title: Patient_002_During [PAT_002_D_IgA]


title: i13_BMP_4_days


title: i13_BMP_6_days


title: Patient_001_Before [PAT_001_B_IgA]


title: i13_BMP_2_days


title: Patient_006_Before [PAT_006_B_IgA]


title: Patient_004_During [PAT_004_D_IgA]


title: i07_BMP_4_days


title: Patient_082_Before [PAT_082_B_IgG]

description:
PT_IgG_Slide_1.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

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


title: Patient_080_After [PAT_080_A_IgG]

description:
PT_IgG_Slide_5.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: SA01_BMP_2_days


title: i07_BMP_2_days


title: Patient_081_During [PAT_081_D_IgG]


title: i04_BMP_6_days


title: i04_BMP_4_days


title: Patient_082_During [PAT_082_D_IgG]


title: Patient_079_During [PAT_079_D_IgG]


title: Patient_080_During [PAT_080_D_IgG]


title: Patient_078_After [PAT_078_A_IgG]


title: Patient_077_During [PAT_077_D_IgG]

description:
PT_IgG_Slide_4.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: i04_BMP_2_days


title: H9_BMP_4_days


title: H9_BMP_6_days


title: i07_BMP_6_days


title: H9_BMP_2_days


title: Patient_075_After [PAT_075_A_IgG]


title: Patient_076_Before [PAT_076_B_IgG]


title: Patient_076_During [PAT_076_D_IgG]


title: T169A (F) unstimulated

city: Medford

first: rebecca

last: batorsky

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

data_processing:
Raw reads were trimmed using Trim Galore
Trimmed reads were aligned using STAR
Gene count matrix was produced using featurecounts and gencode M32
Assembly: GRCm39
Supplementary files format and content: Raw count matrix in csv format

source_name: BMDM

growth_protocol: BMDMs were grown in complete RPMI supplemented with L-glutamine 20% FBS and 30% conditioned L929 cell supernatant for 7 days on non TC treated dishes.

extract_protocol:
RNA was isolated from TRIzol as recommended by the manufacturer.
A TrueSeq kit was used to make a directional cDNA library.

treatment_protocol: 5x105 BMDMs were plated on 24-well TC treated plates and total RNA was isolated from unstimulated, LPS, and LPS/5z7 stimulated B6 BMDMs using TRIzol as recommended by the manufacturer

value: BMDM

value: RIPK1 T169A

value: Unstitm


title: Patient_079_Before [PAT_079_B_IgG]


title: T169A (F) LPS 2 hours


title: T169A (E) unstimulated


title: Patient_075_Before [PAT_075_B_IgG]


title: Patient_074_During [PAT_074_D_IgG]


title: Patient_074_Before [PAT_074_B_IgG]


title: Patient_073_During [PAT_073_D_IgG]


title: T169A (D) LPS 2 hours


title: Patient_078_During [PAT_078_D_IgG]


title: Patient_074_After [PAT_074_A_IgG]


title: T169A (D) unstimulated


title: Patient_075_During [PAT_075_D_IgG]


title: T169A (E) LPS 2 hours


title: T169A (F) LPS/5z7 2 hours


title: Patient_073_Before [PAT_073_B_IgG]


title: Patient_077_After [PAT_077_A_IgG]


title: B6 (C) LPS/5z7 2 hours


title: B6 (C) LPS 2 hours


title: Patient_072_Before [PAT_072_B_IgG]

description:
PT_IgG_Slide_3.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_072_During [PAT_072_D_IgG]


title: B6 (C) unstimulated


title: Patient_071_Before [PAT_071_B_IgG]


title: T169A (E) LPS/5z7 2 hours


title: B6 (B) LPS 2 hours


title: Patient_070_During [PAT_070_D_IgG]


title: B6 (B) LPS/5z7 2 hours


title: T169A (D) LPS/5z7 2 hours


title: B6 (B) unstimulated


title: Patient_072_After [PAT_072_A_IgG]


title: B6 (A) unstimulated


title: NOVA1-CLIP, P21, diencephalon/ mesencephalon, rep3

city: New York

first: Yoko

last: Tajima

state: NY

address: 1230 York avenue

institute: The Rockefeller University

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping on mm10)
collapsing of PCR duplicates
clustering of unique reads
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: brain

extract_protocol:
Brain tissue was UV irradiated and subjected to NOVA1 HITS-CLIP
Partial RNAse digestion, RNA linker ligation and PCR amplification. NOVA1 bound fragments were ligated to a degenerate 5'linker and a 3'linker.

tag: strain background

value: brain

tag: tissue compartment

value: diencephalon/ mesencephalon

value: wild-type

tag: developmental stage


title: Patient_069_During [PAT_069_D_IgG]

value: Male

tag: tissue


title: Patient_070_Before [PAT_070_B_IgG]

value: Individual with confirmed infection


title: Patient_068_During [PAT_068_D_IgG]

value: Blood


title: NOVA1-CLIP, P21, diencephalon/ mesencephalon, rep1


title: Tumor3

city: Chengdu

first: Chunyan

last: Yu

state: Sichuan

address: 37 Guoxue street

country: China

institute: Sichuan University

description:
Tumor tissue
2018jz21_S21

data_processing:
The Cell Ranger software pipeline(version 3.1.0) provided by 10xGenomics was used to demutiplex cellular barcodes, map reads to the genome
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Lung cancer tissues

growth_protocol: Human lung tissue samples were obtained from patients at the department of thoracic surgery between 2017 to 2019, at the west china hospital of Sichuan University (Chengdu, china).

extract_protocol:
single-cell suspensions of the collected samples were prepared through mechanical dissociation and enzymatic degradation within 2-3h after surgery. Each cell suspension was performed to 3’ single-cell RNA sequencing using Single Cell A Chip Kit, Single Cell 3’ Library and Gel Bead Kit V2, and i7 Multiplex Kit (10× genomics, Pleasanton, CA, USA) with a cell recovery target of 10000, following the manufacturer’s instructions.
After generation of GEMs, reverse transcription reactions used barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with Dyna-Beads Myone Silane Beads (Beads, 10× genomics, Cat# 2000048). Then, the cDNA was amplified by PCR with appropriate cycles, which depended on the recovery of cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, Index adapter ligated, and library amplification.
Qualitative and quantitative assessments of the final libraries were performed on a 12-channel Fragment Analyzer with the High Sensitivity NGS Fragment 1-6000 bp assay (Agilent, Santa Clara, CA), and the Qubit 3.0 Fluorometer with the 1× dsDNA High Sensitivity kit (Life Technologies, Carlsbad, CA). Finally, these libraries with an average final concentration of ~30nM and fragment size of ~450bp were then normalized, pooled and sequenced on the NextSeq 500 using a 150 cycle NextSeq 500 high Output Kit v2.5 (Illumina, San Diego, CA). In addition, 150bp paired-end reads were generated.

value: Non-Small Cell Lung Cancer

tag: copd status

tag: sample collection

value: tissue samples during surgery

value: untreated


title: Tumor4

description:
Tumor tissue
2018jz46_S46

tag: treatment


title: Patient_067_During [PAT_067_D_IgG]

tag: Sex

value: Serum


title: Tumor2

description:
Tumor tissue
2018jz37_S37


title: Patient_065_During [PAT_065_D_IgG]

tag: subject group


title: Patient_065_After [PAT_065_A_IgG]

tag: tissue subtype


title: Patient_066_Before [PAT_066_B_IgG]


title: Patient_065_Before [PAT_065_B_IgG]

description:
PT_IgG_Slide_2.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_066_During [PAT_066_D_IgG]


title: Patient_067_Before [PAT_067_B_IgG]


title: CTumor4

description:
Tumor tissue
2018jz54_S54

value: COPD


title: CTumor3

description:
Tumor tissue
2018jz38_S38


title: B6 (A) LPS/5z7 2 hours

tag: cell type

tag: genotype


title: CTumor2

description:
Tumor tissue
2018jz12_S12


title: Patient_064_Before [PAT_064_B_IgG]


title: Patient_064_During [PAT_064_D_IgG]


title: Tumor1

description:
Tumor tissue
2018jz23_S23


title: B6 (A) LPS 2 hours

value: LPS


title: Patient_068_After [PAT_068_A_IgG]


title: Patient_063_During [PAT_063_D_IgG]


title: NOVA1-CLIP, P21, diencephalon/ mesencephalon, rep2


title: CTumor1

description:
Tumor tissue
2018jz11_S11


title: Patient_062_During [PAT_062_D_IgG]


title: COPD4

description:
Non-tumor tissue
2018jz39_S39

value: Non-tumorous lung


title: COPD3

description:
Non-tumor tissue
2018jz14_S14


title: Patient_062_Before [PAT_062_B_IgG]


title: Patient_061_During [PAT_061_D_IgG]


title: Patient_061_Before [PAT_061_B_IgG]


title: Control4

description:
Non-tumor tissue
2018jz13_S13


title: Patient_060_Before [PAT_060_B_IgG]

description:
PT_IgG_Slide_13.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: COPD1

description:
Non-tumor tissue
2018jz61_S60


title: Control2

description:
Non-tumor tissue
2018jz47_S47


title: Patient_058_Before [PAT_058_B_IgG]


title: Control3

description:
Non-tumor tissue
2018jz36_S36


title: Patient_057_After [PAT_057_A_IgG]


title: Control1

description:
Non-tumor tissue
2018jz60_S59


title: Patient_053_After [PAT_053_A_IgG]


title: Patient_056_During [PAT_056_D_IgG]

description:
PT_IgG_Slide_14.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_054_Before [PAT_054_B_IgG]

description:
PT_IgG_Slide_12.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_055_During [PAT_055_D_IgG]

description:
PT_IgG_Slide_15.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_055_Before [PAT_055_B_IgG]


title: Patient_053_Before [PAT_053_B_IgG]


title: COPD2

description:
Non-tumor tissue
2018jz63_S62


title: Patient_053_During [PAT_053_D_IgG]


title: VRgermcellsday14 CBR, rep2

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

country: Japan

institute: Tohoku University

data_processing:
Sequenced reads then were trimmed using fastp software.
For gene expression analysis, reads were mapped to the mouse genome (UCSC mm10 genome assembly and NCBI RefSeq database) using kallisto software with an estimated average fragment length of 50, followed by calculation of read counts and TPM (transcripts per million).
For analyses of differentially expressed genes (DEGs), only genes with a mean TPM exceeding 1 were analyzed.
Functional enrichment analysis of DEGs was performed using the Metascape (https://metascape.org/gp/index.html#/main/step1) (Zhou et al, 2019).
Calculation and drawing of Venn diagrams were performed on the website of Bioinformatics & Evolutionary Genomics (https://bioinformatics.psb.ugent.be/webtools/Venn/).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing TPM value for each sample.

source_name: germ cells

extract_protocol:
RNA was harvested using with Rneasy micro kit (QIAGEN). 100ng of total RNA was used for the construction of sequence libraries.
Each library was constructed using a TruSeq RNA Library Preparation Kit (Illumina).

value: germ cells

value: WT


title: VRgermcellsday14 CBR, rep1


title: Patient_052_During [PAT_052_D_IgG]

description:
PT_IgG_Slide_9.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_058_During [PAT_058_D_IgG]


title: Patient_059_After [PAT_059_A_IgG]


title: VRgermcellsday14 DMSO, rep2

value: DMSO


title: VRgermcellsday14 DMSO, rep1


title: Patient_052_Before [PAT_052_B_IgG]


title: Patient_052_After [PAT_052_A_IgG]


title: Patient_051_During [PAT_051_D_IgG]


title: Patient_051_After [PAT_051_A_IgG]


title: Patient_049_After [PAT_049_A_IgG]


title: Patient_050_During [PAT_050_D_IgG]

description:
PT_IgG_Slide_11.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_048_After [PAT_048_A_IgG]


title: Patient_048_During [PAT_048_D_IgG]


title: CD19+CD24loCD27- B cells_Healthy Donor

city: Shanghai

first: Luman

last: Wang

address: 130 Dong'an Road

department: Immunology

institute: Fudan University

description: mRNA expression profiles from purified CD19+ B cells of  healthy individuals.

hyb_protocol: Following fragmentation, samples were hybridized for 16 hr at 45oC on GeneChip® Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by Affymetrix GeneChip® Scanner 3000.

data_processing: Command Console Software was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized with gene level sst-RMA using Expression Console.

label: biotin

source_name: Purified CD19+CD24loCD27- B cells fromHealthy Donor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA by using Affymetrix  WT PLUS Reagent Kit.

growth_protocol: Human CD19+CD24hiCD27+ B cells and CD19+CD24loCD27- B cells were isolated from PBMCs by positive selection using FACS(BeckmanCoulter, moflo,Miami, FL, USA), and the purity was confirmed to be 90%-98% as judged by flow cytometry analysis.

extract_protocol: Total RNA was extracted from the purified CD19+CD24hiCD27+ B cells and CD19+CD24loCD27- B cells using TRIZOL Reagent  following the manufacturer’s protocol.

treatment_protocol: The cell populations were collected and preserved  as cell pellets in  -80oC.

tag: disease

value: Healthy Donor

tag: cell subtype

value: CD19+CD24loCD27- B cells


title: CD19+CD24hiCD27+ B cells_Healthy Donor

source_name: Purified CD19+CD24hiCD27+ B cells_Healthy Donor

value: CD19+CD24hiCD27+ B cells


title: Patient_046_During [PAT_046_D_IgG]


title: Patient_047_During [PAT_047_D_IgG]

description:
PT_IgG_Slide_7.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: CD19+CD24loCD27- B cells_HT patients-1

description: mRNA expression profiles from purified CD19+ B cells of GD patients

source_name: Purified CD19+CD24loCD27- B cells from HT patients NO.1

value: Hashimoto Disease


title: Patient_048_Before [PAT_048_B_IgG]

value: Male


title: Patient_046_Before [PAT_046_B_IgG]

description:
PT_IgG_Slide_10.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

value: Individual with confirmed infection


title: Patient_049_Before [PAT_049_B_IgG]

value: Blood


title: ExVivoBlood_patient_6_rep1

city: Harbin

first: Jianjian

address: No. 246 Xuefu Road, Nangang District, Harbin, China

institute: The Second Affiliated Hospital of Harbin Medical University

description: lncRNA expression level in PBMCs

hyb_protocol: 1 μg of each Cy3-labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.     50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.     The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.   After hybridization, microarrays were washed with 1 minute at room temperature GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: Peripheral Blood

label_protocol: Each RNA sample was amplified and transcribed into cyanine-3 (Cy3) labeled cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).  The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).  The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated with TRIzol® Reagent (Invitrogen life technologies) from PBMCs following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: female

tag: age

tag: condition

value: myasthenia gravis

value: PBMCs


title: CD19+CD24hiCD27+ B cells_HT patients-1

source_name: Purified CD19+CD24hiCD27+ B cells from HT patients NO.1


title: ExVivoBlood_patient_4_rep1

description: lncRNA expression level in PBMCs


title: ExVivoBlood_patient_2_rep1

description: lncRNA expression level in PBMCs

value: male


title: Patient_045_Before [PAT_045_B_IgG]

value: Serum


title: Patient_044_During [PAT_044_D_IgG]


title: ExVivoBlood_patient_7_rep1

description: lncRNA expression level in PBMCs


title: Patient_045_After [PAT_045_A_IgG]


title: ExVivoBlood_control_8_rep1

description: lncRNA expression level in PBMCs

value: normal


title: ExVivoBlood_patient_8_rep1

description: lncRNA expression level in PBMCs


title: CD19+CD24hiCD27+ B cells_HT patients-2

source_name: Purified CD19+CD24hiCD27+ B cells from HT patients NO.2


title: ExVivoBlood_patient_3_rep1

description: lncRNA expression level in PBMCs


title: ExVivoBlood_patient_5_rep1

description: lncRNA expression level in PBMCs


title: Patient_044_After [PAT_044_A_IgG]


title: ExVivoBlood_control_6_rep1

description: lncRNA expression level in PBMCs


title: ExVivoBlood_control_7_rep1

description: lncRNA expression level in PBMCs


title: Patient_043_Before [PAT_043_B_IgG]


title: ExVivoBlood_patient_1_rep1

description: lncRNA expression level in PBMCs


title: ExVivoBlood_control_5_rep1

description: lncRNA expression level in PBMCs


title: OVF-3

city: shanxi

first: Yiwei

last: wang

address: Taiyuan, Shanxi Province

institute: TYUT

data_processing:
low-quality reads were removed using Trimmomatic (TruSeq3-PE-2.fa:2:30:10)
Hisat2 was used to align the reads to the reference genome
Transcript assembly were performed using StringTie
Differential analysis were performed using DESeq2
Assembly: Triticum aestivum
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: leaf

growth_protocol: Transgenetic wheat were were cultured in a greenhouse at 22 °C with a light/dark cycle of 16/8 hr.

extract_protocol:
RNA was extracted using the MiniBEST Plant RNA Extraction Kit (Takara). 2µg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: leaf

value: TaFAH gene silencing


title: OVF-1


title: ExVivoBlood_control_4_rep1

description: lncRNA expression level in PBMCs


title: OVF-2


title: Patient_040_During [PAT_040_D_IgG]


title: Patient_043_During [PAT_043_D_IgG]


title: RNF-3


title: Patient_042_After [PAT_042_A_IgG]

description:
PT_IgG_Slide_8.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: CD19+CD24loCD27- B cells_HT patients-2

source_name: Purified CD19+CD24loCD27- B cells from HT patients NO.2


title: RNF-2


title: Patient_041_During [PAT_041_D_IgG]

source_name: Gonococcal infection


title: Patient_040_After [PAT_040_A_IgG]


title: Patient_041_Before [PAT_041_B_IgG]


title: Patient_040_Before [PAT_040_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 56

city: Kensington

first: Alexander

last: Richardson

state: NSW

address: Crn Botany and High St

country: Australia

institute: UNSW Sydney

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

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

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.

value: Cornea

value: epithelial cells

value: 60-week old


title: Corneolimbal, 60 week old, Confetti- 57

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


title: Patient_037_During [PAT_037_D_IgG]


title: Patient_039_Before [PAT_039_B_IgG]


title: ExVivoBlood_control_2_rep1

description: lncRNA expression level in PBMCs


title: Patient_035_Before [PAT_035_B_IgG]


title: ExVivoBlood_control_3_rep1

description: lncRNA expression level in PBMCs


title: Corneolimbal, 60 week old, Confetti- 63

description:
SmartSeq-2
60-week old Confetti- 63


title: ExVivoBlood_control_1_rep1

description: lncRNA expression level in PBMCs


title: Corneolimbal, 60 week old, Confetti- 62

description:
SmartSeq-2
60-week old Confetti- 62


title: Corneolimbal, 60 week old, Confetti- 55

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


title: Corneolimbal, 60 week old, Confetti- 54

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


title: Corneolimbal, 60 week old, Confetti- 61

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


title: Patient_034_After [PAT_034_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 52

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


title: Patient_038_During [PAT_038_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 60

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


title: Patient_039_During [PAT_039_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 59

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


title: Corneolimbal, 60 week old, Confetti- 49

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


title: Corneolimbal, 60 week old, Confetti- 48

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


title: Patient_039_After [PAT_039_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 58

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


title: Corneolimbal, 60 week old, Confetti- 53

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


title: Corneolimbal, 60 week old, Confetti- 46

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


title: Patient_030_After [PAT_030_A_IgG]


title: Patient_036_During [PAT_036_D_IgG]


title: Patient_029_After [PAT_029_A_IgG]


title: Patient_035_After [PAT_035_A_IgG]


title: Patient_034_Before [PAT_034_B_IgG]


title: Patient_033_During [PAT_033_D_IgG]

description:
PT_IgG_Slide_6.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_029_Before [PAT_029_B_IgG]


title: Patient_033_After [PAT_033_A_IgG]


title: Patient_032_Before [PAT_032_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 44

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


title: Corneolimbal, 60 week old, Confetti- 47

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


title: Patient_031_Before [PAT_031_B_IgG]


title: Patient_032_During [PAT_032_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 45

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


title: Corneolimbal, 60 week old, Confetti- 43

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


title: Corneolimbal, 60 week old, Confetti- 42

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


title: Patient_026_After [PAT_026_A_IgG]


title: Patient_027_During [PAT_027_D_IgG]


title: Patient_027_After [PAT_027_A_IgG]


title: Patient_028_After [PAT_028_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 40

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


title: Corneolimbal, 60 week old, Confetti- 41

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


title: Corneolimbal, 60 week old, Confetti- 39

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


title: Patient_026_Before [PAT_026_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 38

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


title: Corneolimbal, 60 week old, Confetti- 36

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


title: Patient_025_Before [PAT_025_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 37

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


title: Corneolimbal, 60 week old, Confetti- 35

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


title: Corneolimbal, 60 week old, Confetti- 33

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


title: Patient_024_Before [PAT_024_B_IgG]


title: Patient_024_During [PAT_024_D_IgG]


title: Patient_023_After [PAT_023_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 32

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


title: Corneolimbal, 60 week old, Confetti- 34

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


title: Corneolimbal, 60 week old, Confetti- 50

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


title: Patient_023_During [PAT_023_D_IgG]


title: Patient_026_During [PAT_026_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 51

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


title: Patient_025_After [PAT_025_A_IgG]


title: Patient_022_After [PAT_022_A_IgG]


title: Patient_024_After [PAT_024_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 30

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


title: Corneolimbal, 60 week old, Confetti- 29

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


title: Patient_025_During [PAT_025_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 28

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


title: Patient_021_Before [PAT_021_B_IgG]


title: Patient_022_Before [PAT_022_B_IgG]


title: Patient_021_After [PAT_021_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 27

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


title: RNF-1


title: Corneolimbal, 60 week old, Confetti- 26

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


title: Patient_020_During [PAT_020_D_IgG]


title: Patient_020_Before [PAT_020_B_IgG]


title: Patient_020_After [PAT_020_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 31

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


title: Corneolimbal, 60 week old, Confetti- 23

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


title: Corneolimbal, 60 week old, Confetti- 22

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


title: Patient_019_During [PAT_019_D_IgG]


title: Patient_018_After [PAT_018_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 19

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


title: Corneolimbal, 60 week old, Confetti- 21

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


title: Corneolimbal, 60 week old, Confetti- 20

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


title: Corneolimbal, 60 week old, Confetti- 18

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


title: Patient_016_After [PAT_016_A_IgG]

value: Female


title: Patient_017_Before [PAT_017_B_IgG]


title: Patient_017_After [PAT_017_A_IgG]


title: Patient_016_Before [PAT_016_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 16

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


title: Patient_018_During [PAT_018_D_IgG]


title: Patient_017_During [PAT_017_D_IgG]


title: Patient_015_After [PAT_015_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 14

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


title: Patient_015_Before [PAT_015_B_IgG]


title: Corneolimbal, 60 week old, Confetti- 15

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


title: Corneolimbal, 60 week old, Confetti- 25

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


title: Patient_015_During [PAT_015_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 12

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


title: Patient_014_After [PAT_014_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 24

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


title: Patient_014_Before [PAT_014_B_IgG]


title: Patient_014_During [PAT_014_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 10

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


title: Corneolimbal, 60 week old, Confetti- 11

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


title: Corneolimbal, 60 week old, Confetti- 17

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


title: Patient_013_During [PAT_013_D_IgG]


title: Corneolimbal, 60 week old, Confetti- 9

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


title: Corneolimbal, 60 week old, Confetti- 13

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


title: Patient_012_After [PAT_012_A_IgG]


title: Corneolimbal, 60 week old, Confetti- 5

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


title: Corneolimbal, 60 week old, Confetti- 6

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


title: Corneolimbal, 60 week old, Confetti- 4

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


title: Corneolimbal, 60 week old, Confetti- 3

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


title: Patient_011_Before [PAT_011_B_IgG]

description:
PT_IgG_Slide_1.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Corneolimbal, 60 week old, Confetti- 8

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


title: Corneolimbal, 60 week old, Confetti- 7

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


title: Corneolimbal, 60 week old, Confetti- 2

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


title: Corneolimbal, 60 week old, Confetti+ 62

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


title: Patient_009_During [PAT_009_D_IgG]


title: Patient_013_Before [PAT_013_B_IgG]


title: Patient_008_During [PAT_008_D_IgG]


title: Patient_008_Before [PAT_008_B_IgG]


title: Patient_012_During [PAT_012_D_IgG]


title: Patient_010_During [PAT_010_D_IgG]


title: Patient_011_During [PAT_011_D_IgG]


title: Patient_010_Before [PAT_010_B_IgG]


title: Corneolimbal, 60 week old, Confetti+ 63

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


title: Corneolimbal, 60 week old, Confetti+ 56

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


title: Patient_007_During [PAT_007_D_IgG]


title: Patient_008_After [PAT_008_A_IgG]


title: Corneolimbal, 60 week old, Confetti+ 61

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


title: Corneolimbal, 60 week old, Confetti+ 54

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


title: Patient_007_After [PAT_007_A_IgG]


title: Corneolimbal, 60 week old, Confetti+ 58

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


title: Corneolimbal, 60 week old, Confetti- 1

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


title: Corneolimbal, 60 week old, Confetti+ 59

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


title: Corneolimbal, 60 week old, Confetti+ 52

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


title: Corneolimbal, 60 week old, Confetti+ 55

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


title: Corneolimbal, 60 week old, Confetti+ 53

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


title: Patient_003_Before [PAT_003_B_IgG]


title: Patient_006_During [PAT_006_D_IgG]


title: Corneolimbal, 60 week old, Confetti+ 57

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


title: Corneolimbal, 60 week old, Confetti+ 51

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


title: Patient_006_Before [PAT_006_B_IgG]


title: Patient_005_After [PAT_005_A_IgG]


title: Patient_004_Before [PAT_004_B_IgG]


title: Patient_009_After [PAT_009_A_IgG]


title: Corneolimbal, 60 week old, Confetti+ 50

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


title: Patient_004_During [PAT_004_D_IgG]


title: Corneolimbal, 60 week old, Confetti+ 60

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


title: Corneolimbal, 60 week old, Confetti+ 48

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


title: Patient_001_Before [PAT_001_B_IgG]


title: Patient_002_During [PAT_002_D_IgG]


title: Patient_002_After [PAT_002_A_IgG]


title: Vaccinee_62_24_weeks [BX_62_IgA_v5]

description:
BX_IgA_Slide_003.gpr
Individual participant of clinical trial NCT 04297436

source_name: 4CMenB trial

value: Individual vaccinated with 4CMenB


title: Corneolimbal, 60 week old, Confetti+ 47

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


title: Patient_003_During [PAT_003_D_IgG]


title: Vaccinee_56_24_weeks [BX_56_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 46

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


title: Vaccinee_55_24_weeks [BX_55_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 45

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


title: Corneolimbal, 60 week old, Confetti+ 49

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


title: Corneolimbal, 60 week old, Confetti+ 44

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


title: Vaccinee_54_24_weeks [BX_54_IgA_v5]


title: Vaccinee_52_24_weeks [BX_52_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 42

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


title: Corneolimbal, 60 week old, Confetti+ 41

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


title: Corneolimbal, 60 week old, Confetti+ 39

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


title: Vaccinee_48_24_weeks [BX_48_IgA_v5]

description:
BX_IgA_Slide_002.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 60 week old, Confetti+ 37

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


title: Vaccinee_46_24_weeks [BX_46_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 36

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


title: Vaccinee_50_24_weeks [BX_50_IgA_v5]


title: Vaccinee_39_24_weeks [BX_39_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 38

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


title: Vaccinee_45_24_weeks [BX_45_IgA_v5]


title: Vaccinee_44_24_weeks [BX_44_IgA_v5]


title: Vaccinee_43_24_weeks [BX_43_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 35

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


title: Vaccinee_38_24_weeks [BX_38_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 34

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


title: Vaccinee_37_24_weeks [BX_37_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 33

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


title: Corneolimbal, 60 week old, Confetti+ 32

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


title: Vaccinee_36_24_weeks [BX_36_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 43

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


title: Corneolimbal, 60 week old, Confetti+ 30

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


title: Vaccinee_34_24_weeks [BX_34_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 29

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


title: Vaccinee_32_24_weeks [BX_32_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 40

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


title: Vaccinee_31_24_weeks [BX_31_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 28

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


title: Corneolimbal, 60 week old, Confetti+ 24

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


title: Vaccinee_33_24_weeks [BX_33_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 27

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


title: Corneolimbal, 60 week old, Confetti+ 25

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


title: Vaccinee_30_24_weeks [BX_30_IgA_v5]


title: Vaccinee_42_24_weeks [BX_42_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 23

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


title: Vaccinee_24_24_weeks [BX_24_IgA_v5]


title: Vaccinee_27_24_weeks [BX_27_IgA_v5]


title: Vaccinee_35_24_weeks [BX_35_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 22

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


title: Corneolimbal, 60 week old, Confetti+ 21

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


title: Corneolimbal, 60 week old, Confetti+ 31

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


title: Vaccinee_25_24_weeks [BX_25_IgA_v5]


title: Vaccinee_26_24_weeks [BX_26_IgA_v5]


title: Vaccinee_23_24_weeks [BX_23_IgA_v5]


title: Vaccinee_21_24_weeks [BX_21_IgA_v5]

description:
BX_IgA_Slide_001.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_20_24_weeks [BX_20_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 18

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


title: Corneolimbal, 60 week old, Confetti+ 26

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


title: Vaccinee_19_24_weeks [BX_19_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 16

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


title: Vaccinee_28_24_weeks [BX_28_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 14

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


title: Vaccinee_14_24_weeks [BX_14_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 15

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


title: Corneolimbal, 60 week old, Confetti+ 10

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


title: Corneolimbal, 60 week old, Confetti+ 19

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


title: Vaccinee_17_24_weeks [BX_17_IgA_v5]


title: Vaccinee_12_24_weeks [BX_12_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 9

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


title: Corneolimbal, 60 week old, Confetti+ 11

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


title: Corneolimbal, 60 week old, Confetti+ 17

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


title: Vaccinee_10_24_weeks [BX_10_IgA_v5]


title: Vaccinee_15_24_weeks [BX_15_IgA_v5]


title: Vaccinee_09_24_weeks [BX_09_IgA_v5]


title: Vaccinee_16_24_weeks [BX_16_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 20

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


title: Corneolimbal, 60 week old, Confetti+ 8

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


title: Vaccinee_22_24_weeks [BX_22_IgA_v5]


title: Vaccinee_07_24_weeks [BX_07_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 13

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


title: Vaccinee_11_24_weeks [BX_11_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 5

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


title: Corneolimbal, 60 week old, Confetti+ 12

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


title: Vaccinee_08_24_weeks [BX_08_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 7

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


title: Vaccinee_05_24_weeks [BX_05_IgA_v5]

description:
BX_IgA_Slide_010.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 60 week old, Confetti+ 6

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


title: Corneolimbal, 60 week old, Confetti+ 4

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


title: Vaccinee_04_24_weeks [BX_04_IgA_v5]


title: Vaccinee_13_24_weeks [BX_13_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 3

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


title: Vaccinee_06_24_weeks [BX_06_IgA_v5]


title: Corneolimbal, 60 week old, Confetti+ 2

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


title: Vaccinee_03_24_weeks [BX_03_IgA_v5]


title: Corneolimbal, 18 week old, Confetti- 63

description:
SmartSeq-2
18-week old Confetti- 63

value: 18-week old


title: Corneolimbal, 60 week old, Confetti+ 1

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


title: Corneolimbal, 18 week old, Confetti- 62

description:
SmartSeq-2
18-week old Confetti- 62


title: Corneolimbal, 18 week old, Confetti- 61

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


title: Vaccinee_02_24_weeks [BX_02_IgA_v5]

value: Male


title: Corneolimbal, 18 week old, Confetti- 60

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


title: Vaccinee_55_10_weeks [BX_55_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 59

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


title: Corneolimbal, 18 week old, Confetti- 58

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


title: Corneolimbal, 18 week old, Confetti- 57

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


title: Vaccinee_62_10_weeks [BX_62_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 55

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


title: Corneolimbal, 18 week old, Confetti- 56

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


title: Corneolimbal, 18 week old, Confetti- 54

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


title: Corneolimbal, 18 week old, Confetti- 52

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


title: Corneolimbal, 18 week old, Confetti- 53

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


title: Vaccinee_48_10_weeks [BX_48_IgA_v4]

description:
BX_IgA_Slide_009.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 18 week old, Confetti- 51

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


title: Vaccinee_46_10_weeks [BX_46_IgA_v4]


title: Vaccinee_44_10_weeks [BX_44_IgA_v4]


title: Vaccinee_39_10_weeks [BX_39_IgA_v4]


title: Vaccinee_45_10_weeks [BX_45_IgA_v4]


title: Vaccinee_42_10_weeks [BX_42_IgA_v4]


title: Vaccinee_56_10_weeks [BX_56_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 50

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


title: Corneolimbal, 18 week old, Confetti- 49

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


title: Vaccinee_38_10_weeks [BX_38_IgA_v4]


title: Vaccinee_43_10_weeks [BX_43_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 48

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


title: Corneolimbal, 18 week old, Confetti- 47

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


title: Vaccinee_54_10_weeks [BX_54_IgA_v4]


title: Vaccinee_52_10_weeks [BX_52_IgA_v4]


title: Vaccinee_50_10_weeks [BX_50_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 45

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


title: Vaccinee_34_10_weeks [BX_34_IgA_v4]


title: Vaccinee_37_10_weeks [BX_37_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 46

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


title: Vaccinee_35_10_weeks [BX_35_IgA_v4]


title: Vaccinee_36_10_weeks [BX_36_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 44

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


title: Vaccinee_33_10_weeks [BX_33_IgA_v4]


title: Vaccinee_31_10_weeks [BX_31_IgA_v4]


title: Vaccinee_32_10_weeks [BX_32_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 43

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


title: Corneolimbal, 18 week old, Confetti- 41

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


title: Vaccinee_30_10_weeks [BX_30_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 42

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


title: Vaccinee_28_10_weeks [BX_28_IgA_v4]

description:
BX_IgA_Slide_008.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 18 week old, Confetti- 38

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


title: Vaccinee_26_10_weeks [BX_26_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 39

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


title: Corneolimbal, 18 week old, Confetti- 37

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


title: Corneolimbal, 18 week old, Confetti- 35

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


title: Corneolimbal, 18 week old, Confetti- 36

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


title: Corneolimbal, 18 week old, Confetti- 33

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


title: Corneolimbal, 18 week old, Confetti- 32

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


title: Corneolimbal, 18 week old, Confetti- 34

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


title: Vaccinee_23_10_weeks [BX_23_IgA_v4]


title: Vaccinee_22_10_weeks [BX_22_IgA_v4]


title: Vaccinee_24_10_weeks [BX_24_IgA_v4]


title: Vaccinee_25_10_weeks [BX_25_IgA_v4]


title: Vaccinee_27_10_weeks [BX_27_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 31

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


title: Vaccinee_16_10_weeks [BX_16_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 28

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


title: Vaccinee_17_10_weeks [BX_17_IgA_v4]


title: Vaccinee_20_10_weeks [BX_20_IgA_v4]


title: Vaccinee_15_10_weeks [BX_15_IgA_v4]


title: Vaccinee_21_10_weeks [BX_21_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 40

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


title: Corneolimbal, 18 week old, Confetti- 29

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


title: Vaccinee_13_10_weeks [BX_13_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 27

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


title: Vaccinee_14_10_weeks [BX_14_IgA_v4]


title: Vaccinee_19_10_weeks [BX_19_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 24

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


title: Corneolimbal, 18 week old, Confetti- 23

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


title: Corneolimbal, 18 week old, Confetti- 25

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


title: Vaccinee_10_10_weeks [BX_10_IgA_v4]

description:
BX_IgA_Slide_007.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_11_10_weeks [BX_11_IgA_v4]


title: Vaccinee_12_10_weeks [BX_12_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 20

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


title: Corneolimbal, 18 week old, Confetti- 26

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


title: Vaccinee_05_10_weeks [BX_05_IgA_v4]


title: Vaccinee_09_10_weeks [BX_09_IgA_v4]


title: Vaccinee_06_10_weeks [BX_06_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 17

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


title: Corneolimbal, 18 week old, Confetti- 18

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


title: Corneolimbal, 18 week old, Confetti- 30

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


title: Corneolimbal, 18 week old, Confetti- 21

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


title: Vaccinee_08_10_weeks [BX_08_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 15

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


title: Vaccinee_58_PI [BX_58_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 14

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


title: Corneolimbal, 18 week old, Confetti- 22

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


title: Corneolimbal, 18 week old, Confetti- 16

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


title: Vaccinee_62_PI [BX_62_IgA_v2]


title: Vaccinee_02_10_weeks [BX_02_IgA_v4]


title: Vaccinee_55_PI [BX_55_IgA_v2]

description:
BX_IgA_Slide_006.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_03_10_weeks [BX_03_IgA_v4]


title: Vaccinee_07_10_weeks [BX_07_IgA_v4]


title: Corneolimbal, 18 week old, Confetti- 19

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


title: Vaccinee_56_PI [BX_56_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 13

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


title: Corneolimbal, 18 week old, Confetti- 11

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


title: Vaccinee_54_PI [BX_54_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 12

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


title: Vaccinee_50_PI [BX_50_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 4

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


title: Corneolimbal, 18 week old, Confetti- 10

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


title: Vaccinee_52_PI [BX_52_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 9

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


title: Vaccinee_42_PI [BX_42_IgA_v2]


title: Vaccinee_45_PI [BX_45_IgA_v2]


title: Vaccinee_48_PI [BX_48_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 8

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


title: Corneolimbal, 18 week old, Confetti- 5

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


title: Vaccinee_46_PI [BX_46_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 6

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


title: Corneolimbal, 18 week old, Confetti- 7

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


title: Vaccinee_44_PI [BX_44_IgA_v2]


title: Corneolimbal, 18 week old, Confetti- 3

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


title: Vaccinee_43_PI [BX_43_IgA_v2]


title: Vaccinee_34_PI [BX_34_IgA_v2]

description:
BX_IgA_Slide_005.gpr
Individual participant of clinical trial NCT 04297436


title: Corneolimbal, 18 week old, Confetti- 1

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


title: Corneolimbal, 18 week old, Confetti- 2

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


title: Vaccinee_35_PI [BX_35_IgA_v2]


title: Vaccinee_39_PI [BX_39_IgA_v2]


title: Vaccinee_37_PI [BX_37_IgA_v2]


title: Vaccinee_38_PI [BX_38_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 59

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


title: Corneolimbal, 18 week old, Confetti+ 63

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


title: Vaccinee_32_PI [BX_32_IgA_v2]


title: Vaccinee_36_PI [BX_36_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 62

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


title: Corneolimbal, 18 week old, Confetti+ 57

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


title: Vaccinee_31_PI [BX_31_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 60

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


title: Vaccinee_30_PI [BX_30_IgA_v2]


title: Vaccinee_33_PI [BX_33_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 54

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


title: Vaccinee_29_PI [BX_29_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 58

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


title: Corneolimbal, 18 week old, Confetti+ 56

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


title: Corneolimbal, 18 week old, Confetti+ 61

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


title: Corneolimbal, 18 week old, Confetti+ 52

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


title: Vaccinee_24_PI [BX_24_IgA_v2]


title: Vaccinee_26_PI [BX_26_IgA_v2]


title: Vaccinee_28_PI [BX_28_IgA_v2]


title: Vaccinee_22_PI [BX_22_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 55

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


title: Corneolimbal, 18 week old, Confetti+ 51

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


title: Vaccinee_21_PI [BX_21_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 47

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


title: Corneolimbal, 18 week old, Confetti+ 49

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


title: Corneolimbal, 18 week old, Confetti+ 46

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


title: Vaccinee_25_PI [BX_25_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 53

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


title: Vaccinee_17_PI [BX_17_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 48

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


title: Corneolimbal, 18 week old, Confetti+ 44

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


title: Corneolimbal, 18 week old, Confetti+ 45

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


title: Vaccinee_20_PI [BX_20_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 50

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


title: Vaccinee_27_PI [BX_27_IgA_v2]


title: Vaccinee_19_PI [BX_19_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 41

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


title: Corneolimbal, 18 week old, Confetti+ 43

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


title: Vaccinee_16_PI [BX_16_IgA_v2]

description:
BX_IgA_Slide_004.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_23_PI [BX_23_IgA_v2]


title: Vaccinee_15_PI [BX_15_IgA_v2]


title: Vaccinee_12_PI [BX_12_IgA_v2]


title: Vaccinee_13_PI [BX_13_IgA_v2]


title: Vaccinee_14_PI [BX_14_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 39

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


title: Vaccinee_11_PI [BX_11_IgA_v2]


title: Vaccinee_10_PI [BX_10_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 36

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


title: Corneolimbal, 18 week old, Confetti+ 35

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


title: Corneolimbal, 18 week old, Confetti+ 38

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


title: Corneolimbal, 18 week old, Confetti+ 37

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


title: Vaccinee_07_PI [BX_07_IgA_v2]


title: Vaccinee_09_PI [BX_09_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 34

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


title: Vaccinee_08_PI [BX_08_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 32

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


title: Corneolimbal, 18 week old, Confetti+ 42

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


title: Vaccinee_06_PI [BX_06_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 40

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


title: Corneolimbal, 18 week old, Confetti+ 30

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


title: Corneolimbal, 18 week old, Confetti+ 31

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


title: Vaccinee_04_PI [BX_04_IgA_v2]


title: Vaccinee_05_PI [BX_05_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 29

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


title: Vaccinee_03_PI [BX_03_IgA_v2]


title: Corneolimbal, 18 week old, Confetti+ 28

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


title: Corneolimbal, 18 week old, Confetti+ 26

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


title: Corneolimbal, 18 week old, Confetti+ 27

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


title: Vaccinee_56_24_weeks [BX_56_IgG_v5]

description:
BX_IgG_Slide_008.gpr
Individual participant of clinical trial NCT 04297436


title: Vaccinee_02_PI [BX_02_IgA_v2]


title: Vaccinee_62_24_weeks [BX_62_IgG_v5]

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


title: Corneolimbal, 18 week old, Confetti+ 24

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


title: Corneolimbal, 18 week old, Confetti+ 33

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


title: Corneolimbal, 18 week old, Confetti+ 23

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


title: Vaccinee_54_24_weeks [BX_54_IgG_v5]


title: Vaccinee_50_24_weeks [BX_50_IgG_v5]


title: Vaccinee_55_24_weeks [BX_55_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 25

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


title: Corneolimbal, 18 week old, Confetti+ 22

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


title: Vaccinee_52_24_weeks [BX_52_IgG_v5]


title: Vaccinee_46_24_weeks [BX_46_IgG_v5]

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


title: Corneolimbal, 18 week old, Confetti+ 21

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


title: Vaccinee_48_24_weeks [BX_48_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 20

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


title: Corneolimbal, 18 week old, Confetti+ 19

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


title: Corneolimbal, 18 week old, Confetti+ 17

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


title: Corneolimbal, 18 week old, Confetti+ 18

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


title: Vaccinee_43_24_weeks [BX_43_IgG_v5]


title: Vaccinee_44_24_weeks [BX_44_IgG_v5]


title: Vaccinee_42_24_weeks [BX_42_IgG_v5]


title: Vaccinee_39_24_weeks [BX_39_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 16

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


title: Vaccinee_38_24_weeks [BX_38_IgG_v5]


title: Con, replicate 3, scRNAseq

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were collected and gently rotated to mix thoroughly. Whole blood was first diluted by adding an equal amount of sterile phosphate-buffered saline (PBS), the diluted whole blood was layered onto Ficoll PAQUE, after horizontally centrifuged, the middle mononuclear cell layer was transferred to a new tube, ACK lysis buffer (Miltenyi Biotec) was added to lyse red blood cells. After the last wash, pipet off the supernatant and loosen the pellet by adding PBS with 0.04% BSA.
Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification workflow. In brief, second strand cDNA was synthesized, followed by ligation of the WTA adaptor for universal amplification. Eighteen cycles of PCR were used to amplify the adaptor-ligated cDNA products. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3′ end of the transcripts linked with the cell label and UMI. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: Peripheral blood

tag: cell line

value: 12-13 weeks old

value: Saline intraperitoneal injection


title: T2D, replicate 1, scRNAseq

value: STZ intraperitoneal injection


title: Corneolimbal, 18 week old, Confetti+ 15

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


title: Vaccinee_36_24_weeks [BX_36_IgG_v5]

value: Blood


title: T2D, replicate 2, scRNAseq

value: PBMCs

value: male


title: Vaccinee_37_24_weeks [BX_37_IgG_v5]

value: Serum


title: Con, replicate 2, scRNAseq


title: BMDM,RANKL_4h_3

first: Yijin

last: Hou

address: No. 168, Changhai Road

institute: Department of Traumatic Orthopedics, Changhai Hospital, Naval Medical University

data_processing:
Stringtie（version:1.3.0）
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: FPKM values for each sample

source_name: bone marrow derived macrophage(BMDM)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries
RNA lilbraries for RNA-seg were prepared using SMARTER mRNA-Seg Lilbrary Prep Kit folowing manufacturer's protocols.

value: bone marrow derived macrophage(BMDM)

value: M-CSF;RANKL,4 hours


title: Corneolimbal, 18 week old, Confetti+ 13

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

value: Cornea


title: Corneolimbal, 18 week old, Confetti+ 14

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

value: epithelial cells


title: Con, replicate 1, scRNAseq


title: BMDM,RANKL_4h_1


title: Corneolimbal, 18 week old, Confetti+ 12

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


title: BMDM,RANKL_3d_3

value: M-CSF;RANKL,3 days


title: T2D, replicate 3, scRNAseq


title: Vaccinee_35_24_weeks [BX_35_IgG_v5]

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


title: Vaccinee_34_24_weeks [BX_34_IgG_v5]


title: BMDM,LPS_4h_3

value: M-CSF;LPS,4 hours


title: BMDM,RANKL_3d_2


title: BMDM,RANKL_3d_1


title: Vaccinee_33_24_weeks [BX_33_IgG_v5]

value: Individual vaccinated with 4CMenB


title: Corneolimbal, 18 week old, Confetti+ 10

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

value: 18-week old


title: BMDM,LPS_4h_2


title: BMDM,LPS_4h_1


title: Corneolimbal, 18 week old, Confetti+ 9

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


title: Vaccinee_32_24_weeks [BX_32_IgG_v5]

value: Female


title: Vaccinee_31_24_weeks [BX_31_IgG_v5]


title: BMDM,RANKL_4h_2


title: BMDM,LPS_3d_3

value: M-CSF;LPS,3 days


title: BMDM,LPS_3d_1


title: BMDM,LPS_3d_2


title: Vaccinee_30_24_weeks [BX_30_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 11

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


title: Vaccinee_28_24_weeks [BX_28_IgG_v5]


title: Vaccinee_27_24_weeks [BX_27_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 5

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


title: BMDM,Control_1

value: M-CSF


title: GFP_Ctrl

data_processing:
Trimming using fastp (0.20.0): length_required=50; n_base_limit=6; filtering raw data.QC，fastqc(v0.11.3).Sample correlation using deepTools 3.0.2: --corMethod pearson.
Mapping using BWA (0.7.12-r1039): -T 25 -k 18; aligning with the reference genome.
Sample correlation using deepTools 3.0.2: --corMethod pearson.
Peak calling using MACS2 2.1.0: -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all.
homer findMotifsGenome.pl(v4.9.1);Goseq, topGO, Bioconductor(2.13)(4.10.2);KEGG(KOBAS,3.0.3)
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: α-MEM Culture medium（10%FBS,1%PS）

extract_protocol: CUT&Tag was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Shanghai) according to the product instructions. Briefly, RAW264.7 were stimulated with RANKL and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibody against at 4°C overnight. On next day, samples were incubated with second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted, following by purification for library amplification. The Next Generation Sequencing (second-generation high-throughput sequencing) technique was applied to sequence DNA.

treatment_protocol: 100ng/mL RANKL

value: cell line

tag: chip-antibody

value: Flag-antibody

value: RANKL


title: Corneolimbal, 18 week old, Confetti+ 6

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


title: P2 MGE Fezf2 KO Bax cHET

city: Cambridge

first: Min

last: Dai

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

description: Nuclei suspension preparation and library construction. Brain samples were harvested from mice with specific genotypes and ages, and the cortex was carefully dissected in ice-cold Homogenization Buffer (HB) comprising 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, and 0.5 mM spermidine. The dissected brain tissue was then transferred to a 2 ml Dounce tissue grinder filled with HB supplemented with 0.15-0.25% IGEPAL-CA630 and 0.2 U/µl RNasin. Tissue homogenization was performed with 8-10 strokes of pestle A followed by 9-10 strokes of pestle B. The homogenate was filtered through a 30 μm filter into a 15 ml conical tube and centrifuged at 500 g for 5 min. at 4 °C using a swinging-bucket centrifuge. The resulting pellet was resuspended in 1X PBS containing 1% BSA + 0.2 U/µl RNasin and then passed through a 40 μm filter. DRAQ5 (BioLegend) was added to the nuclei suspension for sorting of GFP+ nuclei on a Sony MA900 cell sorter using a 70 µm nozzle. Nuclei were collected in pre-chilled 0.2 ml PCR tube and counted using a hemocytometer (INCYTO C-Chip). snRNA-seq libraries were prepared using the Chromium Single Cell 3’ Kit v3.1 (10x Genomics), following the manufacturer’s protocol. Pooled libraries were sequenced on NovaSeq 6000 instruments (Illumina).

data_processing:
CellRanger (v7.0.0, 10x Genomics) was used with default parameters to map snRNA-seq data to the mouse reference genome (mm10) provided by 10x Genomics. The gene expression matrices output from CellRanger were then imported into Python v3.9.13 as AnnData objects (anndata v0.8.0). Scanpy v1.9.1 was used as the basic framework for snRNAseq processing. We used Scrublet v.0.2.342 to calculate the potential doublet score for each cell. Unless specified elsewhere, genes expressed in fewer than 3 cells were filtered. Cells were filtered based on the following criteria: n_counts < 15,000, 200 < n_genes < 4,000, ratio_of_mitochondria_genes < 5% (gene symbols beginning with 'mt-'), ratio_of_ribosome_genes < 5% (gene symbols beginning with 'Rpl' or 'Rps') and scrublet_score<0.25. After quality control, the raw counts were normalized using the pp.normalize_total function (counts_per_cell_after = 10,000); the normalized counts were log-transformed using the pp.log1p function. The Pearson residuals were calculated from the raw counts for selecting top 5,000 highly variable genes using experimental.pp.highly_variable_genes function (n_top_genes=5,000). The StandardScaler function (with_mean=False) of scikit-learn v.0.24.0 was then used to scale the Pearson residuals of highly variable genes, followed by the TruncatedSVD function of scikit-learn v.0.24.0 to calculate the Principal Component Analysis (PCA) embeddings for the cells. The unsupervised graph-based Leiden clustering algorithm, pp.neighbors and tl.leiden functions, was used for the clustering based on the PCA embeddings. To sub-cluster specific clusters, the piaso.tl.leiden_local function from our single-cell analysis toolkit PIASO (https://github.com/genecell/PIASO) was used. This function repeats the steps of highly variable gene selection, PCA embedding and Leiden clustering on selected cells while maintaining the clustering results for the remaining cells. After clustering, COSG v1.0.1 was used to identify top marker genes for each cluster, which were cross-compared with well-known marker genes from literature for cell type annotation. For visualization of multiple snRNA-seq datasets across different conditions, we employed the piaso.pl.plot_embeddings_split from PIASO to align cell coordinates from different conditions and scale the gene expression or cell metrics for consistency.
Assembly: mm10
Supplementary files format and content: The .h5 files are the output of CellRanger (v7.0.0), which contains the UMI counts for genes detected among cells.

source_name: Whole cortex

extract_protocol:
Brain samples were harvested from mice with specific genotypes and ages, and the cortex was carefully dissected in ice-cold Homogenization Buffer (HB) comprising 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, and 0.5 mM spermidine. The dissected brain tissue was then transferred to a 2 ml Dounce tissue grinder filled with HB supplemented with 0.15-0.25% IGEPAL-CA630 and 0.2 U/µl RNasin. Tissue homogenization was performed with 8-10 strokes of pestle A followed by 9-10 strokes of pestle B. The homogenate was filtered through a 30 μm filter into a 15 ml conical tube and centrifuged at 500 g for 5 min. at 4 °C using a swinging-bucket centrifuge. The resulting pellet was resuspended in 1X PBS containing 1% BSA + 0.2 U/µl RNasin and then passed through a 40 μm filter. DRAQ5 (BioLegend) was added to the nuclei suspension for sorting of GFP+ nuclei on a Sony MA900 cell sorter using a 70 µm nozzle. Nuclei were collected in pre-chilled 0.2 ml PCR tube and counted using a hemocytometer (INCYTO C-Chip).
snRNA-seq libraries were prepared using the Chromium Single Cell 3’ Kit v3.1 (10x Genomics), following the manufacturer’s protocol. Pooled libraries were sequenced on NovaSeq 6000 instruments (Illumina).
snRNA-seq

value: Whole cortex


title: Vaccinee_26_24_weeks [BX_26_IgG_v5]

value: Blood


title: P2 MGE Fezf2 HET Bax cHET


title: Vaccinee_25_24_weeks [BX_25_IgG_v5]

value: Male

value: Serum


title: P14 MGE Fezf2KO

value: Nkx2.1-Cre;Fezf2 lacZ/lacZ;Sun1-eGFP


title: P14 MGE Fezf2 KO Bax cKO rep2


title: Corneolimbal, 18 week old, Confetti+ 4

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

value: Cornea


title: P14 MGE Fezf2 KO Bax cKO rep1


title: Vaccinee_24_24_weeks [BX_24_IgG_v5]


title: Corneolimbal, 18 week old, Confetti+ 8

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

value: epithelial cells


title: P14 MGE Bax cKO rep2

value: Nkx2.1-Cre;Bax fl/fl;Sun1-eGFP


title: Corneolimbal, 18 week old, Confetti+ 2

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


title: Corneolimbal, 18 week old, Confetti+ 7

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


title: BMDM,Control_3

value: bone marrow derived macrophage(BMDM)


title: BMDM,Control_2


title: P14 MGE Bax cHET

value: Nkx2.1-Cre;Bax fl/+;Sun1-eGFP


title: P14 MGE Bax cKO rep1


title: Zmat1_OE

description: Zmat1 overexpression


title: Corneolimbal, 18 week old, Confetti+ 1

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

value: 18-week old


title: Vaccinee_22_24_weeks [BX_22_IgG_v5]

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

value: Individual vaccinated with 4CMenB


title: P7 cortex interneuron Fezf2 HET

value: Dlx5/6-Cre;Fezf2 lacZ/+;Sun1-eGFP


title: Corneolimbal, 6 week old, Confetti- 63

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

value: 6-week old


title: Vaccinee_21_24_weeks [BX_21_IgG_v5]


title: P7 cortex interneuron Fezf2 KO

value: Dlx5/6-Cre;Fezf2 lacZ/lacZ;Sun1-eGFP


title: P20 cortex interneuron Fezf2 KO


title: P20 cortex interneuron


title: Corneolimbal, 18 week old, Confetti+ 3

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


title: Corneolimbal, 6 week old, Confetti- 62

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


title: RiboTag naive - biol rep 5

city: Bonn

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

institute: University Clinics Bonn

description:
RNA from IP-precipitated HA-tagged ribosomes of Sox10-expressing cells
DE88NGSUKBR140015

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: RiboTag naive - biol rep 4

description:
RNA from IP-precipitated HA-tagged ribosomes of Sox10-expressing cells
DE61NGSUKBR140016

tag: tissue


title: Vaccinee_20_24_weeks [BX_20_IgG_v5]

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

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

value: Male

value: Blood