title: LIHDIIP14 at 24h

description:
column name description
HK257BGXB_P14T1Th2_19s000241-1-1_He_lane119s000241_sequence.txt.gz


title: Cortex Entorhinalis_J20_TG [204027420024_R04C02]

status: Public on Oct 30 2024

type: genomic

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

hyb_protocol: Not provided

scan_protocol: Illumina HiScan

data_processing: Normalized Average Beta calculated using the SeSame package in R

label: Cy3, Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Cortex Entorhinalis

label_protocol: DNA methylation was measured using the the Mammalian Methylation Array (HorvathMammalMethylChip4, GEO: GPL28271)

growth_protocol: Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol: Genomic DNA from all samples was isolated from the entorhinal cortex or hippocampus using the AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent analysis

tag: tissue

value: Cortex Entorhinalis

tag: externalsampleid

tag: Sex

value: F

tag: dob

tag: dod

tag: agedays

tag: mousestrain

tag: genotype

value: TG


title: M12RPF_A1-RPI38_2nd

type: SRA

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

country: China

institute: Peking Union Medical College

library_source: transcriptomic

data_processing:
Sequenced reads were first trimmed for adaptor sequences and low quality bases using trimmomatic. rRNA, tRNA and mitochondrial were trimmed from clean data. Trimmed reads were aligned to the reference genome using STAR (2.7.3a). Aligned reads were deduplicated and sorted.
Assembly: GENCODE (vM22) mouse genome (mm10)
Supplementary files format and content: TXT format data
Library strategy: Ribo-seq

molecule: total RNA

source_name: bone marrow

extract_protocol:
160 cells were sorted and lysed on ice with 22 mM Tris-HCl (pH 7.4), 1% Triton X-100, 100 µg/mL cycloheximide, 165 mM NaCl, 16.5 mM MgCl2, 5.5 mM CaCl2, 2.2 U/µL RNase inhibitor. Exposed RNA was digested by 10500 U/mL micrococcal nuclease at 37°C for 30 min and then ribosome-protected footprints (RPFs) were generated.
The extracted RPFs for subsequent small RNA library construction was performed including end repair, adapter ligation, cDNA synthesis and PCR amplification. The purified library was sequenced with Illumina NovaSeq 6000 platform.

value: bone marrow

tag: cell type

value: B cell

tag: treatment

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIP13 at 24h

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description:
column name description
HK257BGXB_P13T1Th2_19s000240-1-1_He_lane119s000240_sequence.txt.gz

data_processing:
Quality control of the raw sequencing data was conducted using the FastQC software (v0.11.7-Java-1.8.0_162) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human genome 38 (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) and summarized to genes using the R Bioconductor Rsubread package (v1.32.4). In addition to those already failed with RNA extraction steps due to technical issues, one sample was also excluded for further analysis because CD127 Ab was forgotten to add before sorting. Genes that consistently had zero or very low counts were first removed using the Bioconductor edgeR package (v3.24.3). Trimmed Mean of M-values (TMM) normalization was performed on the filtered data with the edgeR package. The normalized data were voom-transformed to enable differential expression analysis with the Bioconductor limma package (v3.38.3).
Assembly: reference human genome 38
Supplementary files format and content: Excel table summary file for all the samples; each row represents one gene (gene name is based on HGNC to avoid Excel conversion errors), while each column represents the normalized read counts of the corresponding gene for the given sample; the column name of each sample is equal to the raw sequence file name.

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Following the PBMC isolation from fresh blood of different participants at various time points/visits, CD4+ T cells were first enriched with human CD4 microbeads (130-045-101, Miltenyl Biotec) following the manufacture’s recommendations while the remaining fractions of PBMC were immediately cryopreserved as described in other sections of the manuscript. The CD4+ T cells were then immediately shipped to our sorting flow-cytometry facility at 4°C. The CD4+ T cells were first stained in Brilliant Stain Buffer (563794, BD) using all the Abs with specified dilution factors listed in Table S4 (of the manuscript). Incubate for 30 min at 4°C in the dark, briefly vortex once after 15 min. Wash the cells twice: centrifuge at 350g, 10 min, 4°C. Re-suspend the cells at a concentration of 10 million per ml. Proceed to aseptic sorting 20 PSI, with 100 um nozzle and Purity mode in a BD Aria III sorter (for the FACS gating strategy, please refer to Figure S6A of the manuscript). After sorting, cells were centrifuged at 350g, 10 min, 4°C, pelleted and lysated in 700 ul of the Qiazol buffer (Qiagen). Transfer the samples into 1.5 ml Eppendorf tubes and immediately freeze at -80°C until RNA extraction. RNA was extracted using RNeasy Micro kit (Qiagen) following the manufacture’s recommendations.
RNA-seq was performed at the EMBL Genomics Core Facility (Heidelberg, Germany) using single-read 75bp by NextSeq 500 with ~ 50 Million reads/sample. The NEBNext Ultra II RNA Library Prep Kit was used and the rRNA depletion step was included.

value: PBMC

value: CD4 Th2 cells

tag: disease state

value: Pollen allergy patients

value: Pollen allergy AIT

tag: time


title: BNIP3-Ctrl-2

city: Tokyo

first: Takao

last: Fujisawa

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (GRCh38) using HISAT2 (version 2.2.1).
The number of mapped reads to each gene was determined by featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

extract_protocol:
RNA was harvested using ISOGEN (Wako). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 4) (NEB, E6446S).

value: siRNA BNIP3


title: M12RPF_A1-RPI37_2nd

value: T cell


title: BNIP3-Ctrl-1


title: M12RPF_A1-RPI48_1st

value: Mat-KO


title: Cortex Entorhinalis_J20_WT [204027420024_R02C02]

value: WT


title: Cortex Entorhinalis_J20_WT [204027420024_R01C02]


title: LIHDIIC05 at 8h

description:
column name description
HK257BGXB_C05T1Th2_19s000248-1-1_He_lane119s000248_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: LIHDIIC07 at 8h

description:
column name description
HK257BGXB_C07T1Th2_19s000250-1-1_He_lane119s000250_sequence.txt.gz


title: M12RPF_A1-RPI46_1st

value: MPP


title: Cortex Entorhinalis_J20_WT [204027420024_R06C01]

value: Cortex Entorhinalis


title: Cortex Entorhinalis_J20_WT [204027420024_R05C01]

value: F


title: Cortex Entorhinalis_J20_TG [204027420024_R04C01]

value: TG


title: M12RPF_A1-RPI47_1st

value: bone marrow


title: NT-Doxo-1

value: siRNA non-targeting, doxorubicin


title: LIHDIIC03 at 8h

description:
column name description
HK257BGXB_C03T1Th2_19s000246-1-1_He_lane119s000246_sequence.txt.gz


title: NT-Ctrl-3

value: siRNA non-targeting


title: M12RPF_A1-RPI45_1st

value: LT-HSC

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIC02 at 8h

description:
column name description
HK257BGXB_C02T1Th2_19s000245-1-1_He_lane119s000245_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: BNIP3-Ctrl-3

value: siRNA BNIP3


title: NT-Ctrl-2


title: TOP1cccross-CAD-seq NutlinETOrep2

city: ROCKVILLE

first: Subhendu kumar

last: Das

state: MD

address: 9000 Rockville pike, Building 10, Bethesda, Maryland

department: Laboratory of Pathology

country: USA

institute: NCI

description: TOP1cccross-CAD-seq NutlinETOrep2

library_source: genomic

data_processing:
library strategy: Covalent Adduct Detection coupled to ChIP-seq
FastQC and MultiQC were used for quality control of the .fastq-files
Adapter and poor quality read trimming was performed with cutadapt
The ChIP-seq data was mapped using bowtie2. Aligned files were sorted, deduplicated and indexes using SortSam, MarkDuplicates and BuildBamIndex from Picard package.
BigWig files were generated with bamCoverage from Deeptools package.Merging of duplicates for visualization was performed using MergeSamFiles from Picard package.
Assembly: Rn6
Supplementary files format and content: Bam coverage BigWig files generated from merged replicas
Supplementary files format and content: Normalized

organism: Rattus norvegicus

source_name: HO15.19 MYC-ER

growth_protocol: The HO15.19-MYC-ER cells were grown with DMEM and 10% of calf serum (Gibco, 26170-043), MEM Nonessential Amino Acids (Corning cellgro, 25-025-Cl) and 50 μg/ml streptomycin sulfate (Gibco, 15070-063).

extract_protocol:
The TOP1 Cross-CAD-seq was performed in the HO15.19-MYC-ER cells were treated (in biological duplicates) with nutlin (10 mM) with or without Eto (25 mM) as indicated in the figure scheme. Cells were processed for harvesting covalent DNA adducts as discussed previously(Kuzin et al., 2022). Briefly, CAD samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments <1 kb on average. 2 µg of anti-TOP1 antibody (ab109374) were mixed with 40 ml Protein A/G magnetic beads (Pierce, 88803) and incubated at 4ºC for 4 hrs with controlled rotation. Eluted CAD samples from 1×107 cells were added to the Protein A/G-antibody complexes and incubated with rotation overnight at 4ºC. Washing was performed as described previously. The beads were then resuspended in 100 μl TE plus 0.5 % SDS supplemented with proteinase K (500 μg/ml, Roche) and incubated for 4 hrs at 65ºC. Samples were then purified by MiniElute PCR purification kit (QIAGEN, 28006).
CAD ChIP-seq libraries were prepared using the ThruPLEX DNA-seq kit (Takara, R400676) following manufacture’s protocol. Next, library size selection was performed using AMPure XP beads (Beckman, A63880) as previously described(Kuzin et al., 2022). Efficiency of size selection of the Cross-CAD libraries was assessed with a Bioanalyzer using an Agilent High Sensitivity DNA Kit (D1000) and sequenced on NextSeq 2000 (100 cycle) in Single End mode with 100 bp reads. NCI sequencing core, (Bethesda, Maryland, USA)

treatment_protocol: To induce p53, Cells (HO15.19 MYC-ER) were treated with Nutlin (final concentration 10 μM in the growth media) for 3 hrs. Cells were treated with 10 µM MG132 for 30 min before addition of 25 µM ETO and further incubation for 30 min to trap TOP2cc respectively.

value: Rat synovial tissues

tag: cell line

value: Fibroblast-like synoviocytes

value: Treated with 10µM nutlin and 25µM Etoposide

tag: chip antibody


title: M12RPF_A1-RPI44_1st

value: CLP


title: LIHDIIC01 at 8h

description:
column name description
HK257BGXB_C01T1Th2_19s000244-1-1_He_lane119s000244_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: TOP1cccross-CAD-seq NutlinETOrep1

description: TOP1cccross-CAD-seq NutlinETOrep1


title: M12RPF_A1-RPI43_1st

value: CMP


title: Cortex Entorhinalis_J20_WT [204027420024_R02C01]

value: Cortex Entorhinalis

value: F

value: WT


title: Cortex Entorhinalis_J20_WT [204027420024_R01C01]


title: NT-Doxo-3

value: siRNA non-targeting, doxorubicin


title: LIHDIIP15 at 6W

description:
column name description
HJNGHBGXB_P15T3Th2_19s000313-1-1_He_lane119s000313_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: LIHDIIC04 at 8h

description:
column name description
HK257BGXB_C04T1Th2_19s000247-1-1_He_lane119s000247_sequence.txt.gz


title: NT-Doxo-2


title: M12RPF_A1-RPI42_1st

value: bone marrow

value: GMP

value: low-input Ribo-seq (160 cells/type)


title: TOP1cccross-CAD-seq Nutlinrep2

description: TOP1cccross-CAD-seq Nutlinrep2

value: Treated with 10µM nutlin


title: shWNK2 replicate 2 CEC

city: Guangzhou

first: Li

middle: Qiong

last: Zhu

address: No.7 Jinsui road

institute: Sun Yat-sen University

data_processing:
base calling by CASAVA, alignment by STAR (version 2.6.1a), abundance measurement by RSEM (version v1.3.0)
Assembly: hg19
Supplementary files format and content: text files include TPM values for each Sample

source_name: corneal epithelial cells

extract_protocol:
RNA was harvested using RNeasy kit (Tiangen).
RNA-seq libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit, according to the manufacturer's protocols.

value: corneal epithelial cells

value: shWNK2-treated differentiated corneal epithelial cells


title: LIHDIIC08 at D7

description:
column name description
HJNGHBGXB_C08T3Th2_19s000322-1-1_He_lane119s000322_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: M12RPF_A1-RPI40_1st

value: Erythoid cell


title: M12RPF_A1-RPI41_1st

value: MEP


title: Cortex Entorhinalis_J20_TG [204027420024_R03C01]

value: TG


title: TOP1cccross-CAD-seq Nutlinrep1

description: TOP1cccross-CAD-seq Nutlinrep1

value: Rat synovial tissues

value: Fibroblast-like synoviocytes


title: TOP1cccross-CAD-seq untrETOrep2

description: TOP1cccross-CAD-seq untrETOrep2

value: Treated with 25µM Etoposide


title: shWNK2 replicate 1 CEC


title: LIHDIIC07 at D7

description:
column name description
HJNGHBGXB_C07T3Th2_19s000321-1-1_He_lane119s000321_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: LIHDIIC06 at D7

description:
column name description
HJNGHBGXB_C06T3Th2_19s000320-1-1_He_lane119s000320_sequence.txt.gz


title: Scramble control replicate 4 CEC (control of shWNK2 CEC)

value: scramble-treated differentiated corneal epithelial cells


title: M12RPF_A1-RPI38_1st

value: bone marrow

value: B cell


title: TOP1cccross-CAD-seq untrrep2

description: TOP1cccross-CAD-seq untrrep2

value: untreated


title: Scramble control replicate 3 CEC (control of shWNK2 CEC)


title: LIHDIIC05 at D7

description:
column name description
HJNGHBGXB_C05T3Th2_19s000319-1-1_He_lane119s000319_sequence.txt.gz


title: TOP1cccross-CAD-seq untrETOrep1

description: TOP1cccross-CAD-seq untrETOrep1


title: M12RPF_A1-RPI39_1st

value: Myeloid cell

value: low-input Ribo-seq (160 cells/type)


title: NT-Ctrl-1

value: siRNA non-targeting


title: LIHDIIC04 at D7

description:
column name description
HJNGHBGXB_C04T3Th2_19s000318-1-1_He_lane119s000318_sequence.txt.gz

value: PBMC


title: shPAX6 replicate 2 CEC

value: corneal epithelial cells

value: shPAX6-treated differentiated corneal epithelial cells


title: M12RPF_A1-RPI37_1st

value: T cell


title: TOP1cccross-CAD-seq untrrep1

description: TOP1cccross-CAD-seq untrrep1


title: shPAX6 replicate 1 CEC


title: LIHDIIC03 at D7

description:
column name description
HJNGHBGXB_C03T3Th2_19s000317-1-1_He_lane119s000317_sequence.txt.gz

value: CD4 Th2 cells


title: LIHDIIC02 at D7

description:
column name description
HJNGHBGXB_C02T3Th2_19s000316-1-1_He_lane119s000316_sequence.txt.gz


title: BM3_F8

city: New York

first: Gurkan

last: Mollaoglu

state: New York

address: Hess Center for Science and Medicine 5th Floor 302

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq files were aligned to reference genome Gex-mm10-2020-A using CellRanger v5.0.1 (10x Genomics). Feature barcode matrix files generated by CellRanger were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Metastatic ovarian tumor

extract_protocol:
Tumor samples were chopped into small pieces with scissors in digest media containing collagenase and DNAase and then incubated in the same media with 500 rpm lateral shaking at 37 C for 45 min. The single-cell suspension was obtained by passaging the digested tumors through a 70 um filter and washing with PBS. Cells were centrifuged at 350 g for 5 minutes at 4 C and then pellets were resuspended with ACK lysis buffer to lyse red blood cells at room temperature for 10 min and washed with cold PBS. The samples were enriched for immune cells with EasySep Mouse CD45 Positive Selection Kit following the manufacturer’s guidelines. The viability of single cells was assessed using Acridine Orange/Propidium Iodide viability staining reagent. Debris-free suspensions of > 70% viability were deemed suitable for the experiments.
scRNA-Seq was performed using the Chromium platform (10x Genomics) with the 5’ gene expression (5’ GEX) V2 kit, with a targeted recovery of 8,000 cells. Briefly, Gel-Bead in Emulsions (GEMs) were generated on the sample chip K in the Chromium X (10x Genomics). Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 13 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10x-specific sample indexing following the manufacturer’s protocols. Libraries were quantified using TapeStation (Agilent) and QuBit (ThermoFisher) analyses.

value: Metastatic ovarian tumor

tag: metastatic site

value: diaphragm

tag: cancer cell_crispr_ko

value: F8 (control)

tag: mouse genotype

value: WT

tag: mouse strain


title: Scramble control replicate 2 CEC (control of shPAX6 CEC)


title: TOP1cccross-CAD-seq input

description: TOP1cccross-CAD-seq input

tag: tissue

value: Rat synovial tissues

value: Fibroblast-like synoviocytes


title: Brain, MI mice

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

data_processing:
Data was processed using cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: Raw cell x gene matrix

molecule: polyA RNA

source_name: Brain, leukocytes enriched

extract_protocol:
Peripheral blood was collected by retro-orbital bleeding and red blood cells were lysed in RBC lysis buffer (Biolegend). Brain and hearts were excised after perfusion with PBS (Thermo Fisher Scientific), minced and digested with 450 U/mL collagenase I, 125 U/mL collagenase XI, 60 U/mL DNase I and 60 U/mL hyaluronidase (Sigma) in PBS for 40 min at 37 °C. Brain samples were passed through a 70-μm cell strainer and mixed with 30% percoll layered on top of 70% percoll. The percoll gradient was centrifuged at 500g for 30 min with the brake off. The cell fraction was collected and washed with PBS before downstream applications. For heart and brain samples, CD45+ cells were selected with a MACS column (Miltenyi). Briefly, cells were incubated with anti-CD45 microbeads (Miltenyi Biotech) then passed through a MACS separation LD column. Viability of single cells was assessed using Acridine Orange/Propidium Iodide viability staining reagent (Nexcelom), and debris-free suspensions of >80% viability were deemed suitable for the experiments.
Library was constructed according to manufacturer's protocol (10X, Single Cell 5' PE)

value: Brain, leukocytes enriched

tag: stain

value: MI


title: BM3_C7

description: 10x Genomics


title: LIHDIIC01 at D7

description:
column name description
HJNGHBGXB_C01T3Th2_19s000315-1-1_He_lane119s000315_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: Scramble control replicate 1 CEC (control of shPAX6 CEC)

value: scramble-treated differentiated corneal epithelial cells


title: Differentiated CEC replicate 1

value: differentiated corneal epithelial cells


title: Brain, sham mice

value: Sham


title: BM2_1

description: 10x Genomics

value: omentum

value: Il4ra-fl/fl (littermate control)


title: LIHDIIV16 at 8h

description:
column name description
HG533BGXB_V16T1Th2_19s000228-1-1_He_lane119s000228_sequence.txt.gz

value: PBMC

value: Venom allergy patients

value: Venom allergy AIT


title: BM2_3

description: 10x Genomics

value: Metastatic ovarian tumor


title: LIHDIIV17 at 8h

description:
column name description
HG533BGXB_V17T1Th2_19s000229-1-1_He_lane119s000229_sequence.txt.gz

value: CD4 Th2 cells


title: Differentiated CEC replicate 2

value: corneal epithelial cells


title: LIHDIIP12 at 24h

description:
column name description
HG533BGXB_P12T1Th2_19s000239-1-1_He_lane119s000239_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: Primary cultured LSC replicate 2

source_name: limbal stem cells

value: limbal stem cells

value: Primary cultured LSC


title: BM1_8

description: 10x Genomics

value: diaphragm

value: WT


title: Heart, MI mice

source_name: Heart, leukocytes enriched

value: Heart, leukocytes enriched

value: MI


title: Blood, MI+SF mice

source_name: Blood leukocytes

value: Blood leukocytes

value: MI+SF


title: Primary cultured LSC replicate 1


title: BM1_6

description: 10x Genomics


title: LIHDIIP11 at 24h

description:
column name description
HG533BGXB_P11T1Th2_19s000238-1-1_He_lane119s000238_sequence.txt.gz


title: BM1_5

description: 10x Genomics


title: RNA temporal neocortex, epileptogenic,replicate4

first: Yingying

last: Liu

address: Tianhe

data_processing:
CellRanger v7.1.0
Assembly: GRCh38-1.2.0
Supplementary files format and content: Tab-seqarated values files and matrix files

molecule: nuclear RNA

source_name: temporal neocortex

extract_protocol:
Each brain tissue sample was cut into small pieces and then transferred to a Dounce homogenizer with 400 μl of lysis buffer (pH 7.4, 10 mM Tris-HCL, 3 mM MgCl2, 10 mM NaCl, 0.1% IGEPAL, 0.1% Tween 20, 2% BSA). To release the nuclei, the tissues were homogenized. After 10 minutes of centrifugation at 4°C, the nuclei were washed in 1 ml of cold nuclei wash and resuspension buffer (1× PBS supplemented with 0.2 U/μl RNase inhibitor and 1% BSA). Trypan blue and Countess II FL Automated Cell Counter/Microscopy were used to evaluate lysis efficiency and viability. A 40 μm filter was used for the elimination of large clumps and cell debris. Another centrifugation step was performed, and the nuclei were collected for direct myelin removal. Then, 500 μl or an appropriate volume of nucleus wash and resuspension buffer was added to the nucleus pellet to reach the desired 700-1,200 nuclei/μl concentration.
We loaded the nucleus suspension into a Chromium microfluidic chip with 3’ (v2 or v3) chemical properties and labelled it with barcodes using a 10xChromium controller (10xGenomics). Following reverse transcription of RNA from the cells labelled with barcodes, sequencing libraries were prepared using reagents from a Chromium Single Cell 3’ v2 or v3 reagent kit (10xGenomics) following the manufacturer's guidelines.

value: temporal neocortex

tag: Sex

value: Male

tag: age(years)


title: LIHDIIP09 at 24h

description:
column name description
HG533BGXB_P09T1Th2_19s000236-1-1_He_lane119s000236_sequence.txt.gz

value: PBMC


title: LIHDIIP06 at 24h

description:
column name description
HG533BGXB_P06T1Th2_19s000234-1-1_He_lane119s000234_sequence.txt.gz


title: Blood, sham mice

value: Sham


title: Heart, MI+SF mice


title: RNA temporal neocortex, epileptogenic,replicate3

value: Female


title: BM1_2

description: 10x Genomics

value: Metastatic ovarian tumor

value: F8 (control)


title: RNA temporal neocortex, epileptogenic,replicate2


title: BM1_1

description: 10x Genomics


title: Blood, MI mice


title: LIHDIIP03 at 24h

description:
column name description
HG533BGXB_P03T1Th2_19s000232-1-1_He_lane119s000232_sequence.txt.gz

value: CD4 Th2 cells

value: Pollen allergy patients


title: RNA temporal neocortex, epileptogenic,replicate1


title: RNA temporal neocortex, nonepileptic,replicate3


title: LIHDIIP01 at 24h

description:
column name description
HG533BGXB_P01T1Th2_19s000230-1-1_He_lane119s000230_sequence.txt.gz

value: Pollen allergy AIT


title: LIHDIIP02 at 24h

description:
column name description
HG533BGXB_P02T1Th2_19s000231-1-1_He_lane119s000231_sequence.txt.gz


title: LIHDIIV17 at 24h

description:
column name description
HG57FBGXB_V17T2Th2_19s000265-1-1_He_lane119s000265_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Adult-Male-14

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

description: Fresh frozen Spatial Transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics SpaceRanger pipeline to generate FASTQ files.
Sequences were mapped to the mm10 reference genome according to SpaceRanger default settings.
Expression levels of RefSeq genes were quantified using SpaceRanger with default settings.
Assembly: mm10
Supplementary files format and content: raw_feature_bc_matrix.h5: aggregated unfiltered SpaceRanger results in .h5 format
Supplementary files format and content: filtered_feature_bc_matrix.h5: aggregated filtered SpaceRanger results in .h5 format

source_name: Heart Aortic Valve with Left ventricle Myocardium

growth_protocol: Hearts from C57BL/6J mice at postnatal day 3 and male and female adults were dissected, and the aortic valve along with a portion of the left ventricle was utilized

extract_protocol:
Fresh frozen tissue were OCT embedded, and 16𝛍m frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides and Reagent kit according to manufacturer’s construction
Spatial Transcriptomics

treatment_protocol: Following embedding in OCT, the hearts underwent strategic cuts to precisely align the section chosen for Spatial Transcriptomics with the level of the aortic valve, enabling clear visualization and detailed analysis of the underlying structure.

tag: aortic valve

value: Adult AoV2

tag: biological replicates

value: Adult Biol rep 2

tag: age

value: 30 days old


title: BM1_4

description: 10x Genomics

value: diaphragm

value: WT


title: RNA temporal neocortex, nonepileptic,replicate1

value: temporal neocortex


title: Adult-Male-16

value: Adult Biol rep 4

value: Male

value: Heart Aortic Valve with Left ventricle Myocardium


title: Multiplexed sublibraries 2 and 6 [ob/ob male; Sample 13,14,19, and 22]

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description:
Parse Biosciences
These raw fastq files of sublibrary 2 and 6 contain uniquely barcoded cells from all four samples (13,14,19 and 22). Samples details are provided in the sample manifest file.

data_processing:
Each sublibrary contains uniquely barcoded cells from all samples.  Raw sequencing data for sub library-2 and sub library-6 were preprocessed and combined using Parse Biosciences’ split-pipe pipeline (v0.9.6p). Expression matrices were imported into Seurat for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: text

source_name: left hippocampus

extract_protocol:
Wild type (C57BL/6J) and ob/ob male mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and fixed using Parse biosciences nuclei isolation and fixation protocol.
Barcoded single cell libraries were prepared from fixed single cell suspensions using Evercode Whole Transcriptome Mega kit (Parse Biosciences) following the manufacturer’s instructions.  Individual transcriptomes from all samples were uniquely labeled by passing fixed nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Using next-generation sequencing, cells from individual samples are identified using the first well (first barcode) placement. Each sublibrary contains uniquely barcoded cells from all samples.  At the end of library prep, cells are distributed into 16 different sublibraries. The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 and TapeStation, respectively. The libraries were quantified by fluorometry on a Qubit instrument and by qPCR with a Kapa Library Quant kit prior to sequencing. The libraries were sequenced with paired-end 100 bp reads.  The sequencing generated approximately 35,000 reads per cell.

value: left hippocampus

value: 4.5 months

tag: cell type

value: All hippocampal cells

tag: genotype

value: ob/ob

tag: strain


title: Adult-Male-15

value: Adult Biol rep 3


title: ATAC temporal neocortex, epileptogenic,replicate4

data_processing:
cellranger-atac-2.0.0
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: Tab-seqarated values files, bed and matrix files

extract_protocol:
Each brain tissue sample was cut into small pieces and then transferred to a Dounce homogenizer with 400 μl of lysis buffer (pH 7.4, 10 mM Tris-HCL, 3 mM MgCl2, 10 mM NaCl, 0.1% IGEPAL, 0.1% Tween 20, 2% BSA). To release the nuclei, the tissues were homogenized. After 10 minutes of centrifugation at 4°C, the nuclei were washed in 1 ml of cold nuclei wash and resuspension buffer (1× PBS supplemented with 0.2 U/μl RNase inhibitor and 1% BSA). Trypan blue and Countess II FL Automated Cell Counter/Microscopy were used to evaluate lysis efficiency and viability. A 40 μm filter was used for the elimination of large clumps and cell debris. Another centrifugation step was performed, and the nuclei were collected for direct myelin removal. Then, 500 μl or an appropriate volume of nucleus wash and resuspension buffer was added to the nucleus pellet to reach the desired 700-1,200 nuclei/μl concentration.
We loaded the nucleus suspension into the Chromium Next GEM Chip H with 10x reagents and labelled it with barcodes using a 10×Chromium Controller (10X Genomics). Following the amplification of DNA fragments from the cells labelled with barcodes, sequencing libraries were prepared using reagents from the Chromium NextGEM Single Cell ATAC Reagent Kit v1.1 (10x Genomics) following the manufacturer's guidelines. The scATAC-seq libraries were constructed following the Chromium NextGEM Single Cell ATAC Reagent Kit v1.1 User Guide RevC (10x Genomics CG000209).


title: LIHDIIV16 at 24h

description:
column name description
HG57FBGXB_V16T2Th2_19s000264-1-1_He_lane119s000264_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

tag: disease state

tag: treatment

tag: time


title: LIHDIIP04 at 24h

description:
column name description
HG533BGXB_P04T1Th2_19s000233-1-1_He_lane119s000233_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: CTR [p86 ME18}

type: RNA

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

country: Italy

institute: University of Brescia

description:
Control
p86 ME18

data_processing: Ct target values were normalized using reference genes values. FC were computed using a right-censored regression on (-Delta Ct) values to account for limit of detection. Results are reported as Fold Changes

source_name: serum

extract_protocol: Total RNA was extracted from 400 ul of serum with the miRNeasy Serum/Plasma advanced Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA was eluted in 22 ul of H2O and quantified using the Qubit microRNA assay kit (Thermo Fisher Scientific, Waltham, MA, USA) by the Qubit 4 Fluorometer (Thermo Fisher Scientific). cDNA templates were prepared using the TaqMan Advanced miRNA cDNA Synthesis Kit (Thermo Fisher Scientific) according to the manufacturer's guidelines, starting from 10 ng of RNA.   The miR-Amp reaction products were thawed on ice and then diluted 1:20 in 0.1x TE buffer pH 8 (10 mM Tris, 1 mM EDTA, Thermo Fisher Scientific). Each RT-qPCR mix was prepared by combining equal quantities of 1:20 diluted sample and 2x TaqMan OpenArray Real-Time PCR Master Mix (Thermo Fisher Scientific) in a final volume of 60 μl. Each sample mix was transferred in 16 wells (6 μl/well) of an OpenArray 384-well Sample Plate (Thermo Fisher Scientific) and then automatically loaded in a Fixed-content TaqMan OpenArray Plate containing the Human Advanced miRNA panel (Cat. N. A32710, Thermo Fisher Scientific) by the QuantStudio 12K Flex Accufill System (Thermo Fisher Scientific). Each open array plate was loaded with three samples and run on the QuantStudio12K Flex Real-Time PCR System (Thermo Fisher Scientific). Quantification cycle (Cq) was automatically calculated using the ThermoFisher Cloud Software (Thermo Fisher Scientific Relative Quantification Analysis Module, available online at https://www.thermofisher.com/de/de/home/cloud.html). Only target values meeting all the following criteria were considered for subsequent analyses: Amplification Score >1, Cq confidence > 0.8, Cq ≥6. MiR-16-5p, spotted 16 times in each sub-array, was used as a quality control of the OpenArray procedure. Each serum sample was evaluated for the presence of hemolysis. The ratio between the expression levels of miR-451a (expressed in red blood cell) and miR-23a-3p (not affected by hemolysis) was calculated and samples with a delta Cq < 8 were considered acceptable. Samples with hemolysis were excluded from the study.

tag: disease

value: ovarian fibroma


title: LIHDIIV15 at 24h

description:
column name description
HG57FBGXB_V15T2Th2_19s000263-1-1_He_lane119s000263_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Adult-Male-13

value: Adult AoV2

value: Adult Biol rep 1

value: 30 days old


title: END [p86 ME170}

description:
Test
p86 ME170

value: endometrioma


title: END [p86 ME8}

description:
Test
p86 ME8


title: END [p86 ME67}

description:
Test
p86 ME67


title: ATAC temporal neocortex, epileptogenic,replicate3

value: temporal neocortex

value: Female


title: CTR [p86 ME176}

description:
Control
p86 ME176

value: leiomyoma


title: RNA temporal neocortex, nonepileptic,replicate2


title: ATAC temporal neocortex, epileptogenic,replicate2

value: Male


title: Adult-Female-12

value: Adult AoV1

value: Adult Biol rep 4

value: Heart Aortic Valve with Left ventricle Myocardium


title: LIHDIIV14 at 24h

description:
column name description
HG57FBGXB_V14T2Th2_19s000262-1-1_He_lane119s000262_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: END [p86 ME159}

description:
Test
p86 ME159


title: Adult-Female-11

value: Adult Biol rep 3


title: LIHDIIV12 at 24h

description:
column name description
HG57FBGXB_V12T2Th2_19s000261-1-1_He_lane119s000261_sequence.txt.gz


title: END [p86 ME155}

description:
Test
p86 ME155


title: Adult-Female-10

value: Adult Biol rep 2


title: ATAC temporal neocortex, epileptogenic,replicate1


title: END [p86 ME152}

description:
Test
p86 ME152

value: Deep Infiltrating Endometriosis


title: ATAC temporal neocortex, nonepileptic,replicate3


title: Adult-Female-9


title: ATAC temporal neocortex, nonepileptic,replicate2


title: LIHDIIP10 at 2W

description:
column name description
HG57FBGXB_P10T2Th2_19s000272-1-1_He_lane119s000272_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: CTR [p86 ME147}

description:
Control
p86 ME147

value: ovarian cystadenoma


title: P3-mouse-8

value: P3 AoV4

value: P3 Biol rep 2

value: Post-natal day 3

value: not determined


title: LIHDIIP09 at 2W

description:
column name description
HG57FBGXB_P09T2Th2_19s000271-1-1_He_lane119s000271_sequence.txt.gz


title: ATAC temporal neocortex, nonepileptic,replicate1

value: temporal neocortex

value: Female


title: P3-mouse-7

value: P3 Biol rep 1


title: LIHDIIP06 at 2W

description:
column name description
HG57FBGXB_P06T2Th2_19s000269-1-1_He_lane119s000269_sequence.txt.gz


title: END [p86 ME140}

description:
Test
p86 ME140

value: endometrioma


title: END [p86 ME141}

description:
Test
p86 ME141


title: LIHDIIP02 at 2W

description:
column name description
HG57FBGXB_P02T2Th2_19s000267-1-1_He_lane119s000267_sequence.txt.gz


title: High salt 2

city: Tezpur

first: Aditya

last: Kumar

state: Assam

address: R107, Dept Of Molecular Biology & Biotechnology

department: Molecular Biology and Biotechnology

country: India

institute: Tezpur University

data_processing:
Quality control and preprocessing of raw reads obtained from sequencing in FASTQ format was performed open-source package fastp (v0.23.4).
Processed reads were aligned to Human genome version 38 using Hisat2 tool (v2.2.1)  to generate BAM files.
Read counts were generated using the Feature Counts tool (v2.0.6).
Differential expression was calculated using the Bioconductor package edgeR R (v4.3) package.
Assembly: hg38
Supplementary files format and content: tab delimited text files containing read counts of each samples

source_name: Breast; Mammary gland

growth_protocol: MDA MB-231 cells were maintained in DMEM with 10% FBS and 1% Penicillin-Streptomycin , under humidified condition at 5 % CO2 and 37 degree.

extract_protocol:
MDA MB-231 cells were seeded and incubated for 12 hours before treatement in 10% FBS containing DMEM with 1% penicilln and streptomycin, Next day, Cells were treated with 50mM NaCl (0.2 micron sterile filtered) for 24 hours. At the end of incubation period , cells were stored in RNA Later and subjected to RNA Sequencing
Library preparation was performed using NEB Next®UltraTM II RNA Library Prep Kit for Illumina® following manufacturer’s instructions. Further quality and quantity were assessed using Agilent 4150 Tape Station system and Qubit 4 Fluorometer

treatment_protocol: MDA MB-231 cells were seeded and treated with 50 mM NaCl for 24 hours at the end of incubation period, RNA was harvested and subjected to RNA Sequencing

value: Breast; Mammary gland

tag: cell line

value: MDA MB-231

value: Triple negative breast epithelial cell

value: Wild type

value: 50 mM NaCl


title: High salt 1


title: P3-mouse-6

value: P3 AoV3

value: Heart Aortic Valve with Left ventricle Myocardium


title: P3-mouse-5


title: END [p86 ME154}

description:
Test
p86 ME154


title: Control

value: Control


title: END [p86 ME136}

description:
Test
p86 ME136

value: Deep Infiltrating Endometriosis


title: LIHDIIP01 at 2W

description:
column name description
HG57FBGXB_P01T2Th2_19s000266-1-1_He_lane119s000266_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Pollen allergy patients

value: Pollen allergy AIT


title: END [p86 ME139}

description:
Test
p86 ME139


title: P3-mouse-3

value: P3 AoV2

value: Post-natal day 3

value: not determined


title: LIHDIIV15 at 8h

description:
column name description
HG55GBGXB_V15T1Th2_19s000227-1-1_He_lane119s000227_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: LIHDIIV13 at 8h

description:
column name description
HG55GBGXB_V13T1Th2_19s000225-1-1_He_lane119s000225_sequence.txt.gz


title: P3-mouse-1

value: P3 AoV1

value: P3 Biol rep 1


title: P3-mouse-2

value: P3 Biol rep 2


title: END [p86 ME126}

description:
Test
p86 ME126

value: endometrioma


title: LIHDIIV14 at 8h

description:
column name description
HG55GBGXB_V14T1Th2_19s000226-1-1_He_lane119s000226_sequence.txt.gz


title: LIHDIIV12 at 8h

description:
column name description
HG55GBGXB_V12T1Th2_19s000224-1-1_He_lane119s000224_sequence.txt.gz


title: END [p86 ME10}

description:
Test
p86 ME10


title: CTR [p86 ME104}

description:
Control
p86 ME104

value: no gynecological abnormality


title: CTR [p86 ME105}

description:
Control
p86 ME105

value: ovarian cystadenoma


title: Pediatric_258_NUP98-NSD1_MI3454_Palbociclib_3

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Fastq files were analyzed for quality using FastQC
Reads were trimmed of adapters and low-quality reads using Cutadapt with the arguments -a AGATCGGAAGAGCACACGTC -A AGATCGGAAGAGCGTCGTGT -g AGATCGGAAGAGCACACGTC -G AGATCGGAAGAGCGTCGTGT -a "A{100}" -a "T{100}" --nextseq-trim=20 --minimum-length 50.
For the adult sample, human alignment indices were generated from genome version GRch38v42 using STAR with the arguments –sjdbOverhang 149. For the pediatric sample amplified in mice, combined human + mouse alignment indices were generated from a concatenated genome containing genome versions GRch38v42 (human) and GRCm39M31 (mouse) using STAR alignment software with the arguments –sjdbOverhang 149. Genome files were downloaded from GENCODE.
Trimmed reads were aligned to the appropriate genome (human or human+mouse combined) using STAR with the arguments --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within.
Adult patient sample libraries and pediatric patient sample libraries were generated with different strategies, therefore the strandedness was treated separately. Aligned reads from the adult sample were assigned to exons and annotated by gene using HTSeq with the arguments -s rev -r pos -f bam. Aligned reads from the pediatric sample were assigned to exons and annotated by gene using HTSeq with the arguments -s no -r pos -f bam.
For the pediatric sample amplified in mice, reads assigned to the mouse genome were removed prior to differential expression analysis so that only reads unambiguously assigned to the human genome were kept for further analysis.
Gene counts were normalized and differential expression was analyzed using DESeq2 R package
Assembly: Human: GRch38v42 (GENCODE); Mouse: GRCm39M31 (GENCODE)
Supplementary files format and content: There is a .counts file for each individual sample containing the unnormalized raw read counts given by HTSeq counting
Supplementary files format and content: There is a .csv for each experiment (adult patient sample and pediatric patient sample) containing the DESeq2 normalized read counts for each sample in a count matrix format

source_name: Human bone marrow amplified in mouse bone marrow and spleen

growth_protocol: All samples were maintained in MethoCult H4423 Enriched methylcellulose media (STEMCELL)

extract_protocol:
RNA was harvested using the Qiagen Rneasy Mini Kit
Adult sample libraries were prepared by the University of Michigan Advanced Genomics Core using the NEBNext rRNA Depletion Kit followed by the xGen Broad Range RNA Library Kit with xGen Normalase UDI Primers
Pediatric sample libraries were prepared using the NEBNext Single Cell/ Low Input RNA Library Prep Kit.

treatment_protocol:
Adult sample was treated with 250nM MI3454, 75nM Gilteritinib, 75nM Palbociclib, 250nM MI3454 + 75nM Gilteritinib, 250nM MI3454 + 75nM Palbociclib, or DMSO control for 7 days.
Pediatric sample was treated with 250nM MI3454, 25nM Palbociclib,  250nM MI3454 + 25nM Palbociclib, or DMSO control for 8 days.

value: Acute myeloid leukemia

value: leukemic

tag: host strain

value: NSG

value: MI3454 + Palbociclib


title: P3-mouse-4

value: Heart Aortic Valve with Left ventricle Myocardium


title: LIHDIIV11 at 8h

description:
column name description
HG55GBGXB_V11T1Th2_19s000223-1-1_He_lane119s000223_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: Pediatric_258_NUP98-NSD1_MI3454_Palbociclib_1

value: Human bone marrow amplified in mouse bone marrow and spleen


title: LIHDIIV10 at 8h

description:
column name description
HG55GBGXB_V10T1Th2_19s000222-1-1_He_lane119s000222_sequence.txt.gz


title: HITMNG2Col6_Opti02

city: Chicago

first: David

middle: A

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago

description: Data analysis published in Reed et al, "NG2/CSPG4 attenuates motility in mandibular fibrochondrocyte under serum starvation conditions" in Frontiers in Cell and Developmental Biology

data_processing:
For bioinformatics analysis, in house scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases (56). Then sequence quality was verified using FastQC
HISAT2 (57) was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie (58). Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie (58) and edgeR (59) was used to estimate the expression levels of all transcripts

source_name: mandiibular condylar cartilage

growth_protocol: Murine mandibular condylar cartilage of 10-14 day old pups, immortalized with hTERT; HITMNG2Col6 cells have a truncated NG2 extracellular domain.

extract_protocol:
QIAGEN RNEasy kit
a Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation proto
RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip
. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system

treatment_protocol: NORMAL - None, normal growth conditions in AMEM, heat inactivated FBS, L-Glut, Pen, and Plasmocin; Serum Starvation - Optimem with L-Glut, Pen, and Plasmocin

value: mandiibular condylar cartilage

value: immortalized with HTERT

value: Crispr Modified NG2/CSPG4 ectodomain

value: Optimem Serum Free


title: HITMNG2Col6_Opti03


title: Pediatric_258_NUP98-NSD1_Palbociclib_3

value: Palbociclib


title: CTR [ME408}

description:
Control
ME408


title: Pediatric_258_NUP98-NSD1_Palbociclib_2


title: HITMNG2Col6_Opti01


title: END [ME404}

description:
Test
ME404

value: Deep Infiltrating Endometriosis


title: CTR [ME402}

description:
Control
ME402

value: ovarian teratoma


title: Pediatric_258_NUP98-NSD1_MI3454_3


title: Pediatric_258_NUP98-NSD1_Palbociclib_1


title: LIHDIIV09 at 8h

description:
column name description
HG55GBGXB_V09T1Th2_19s000221-1-1_He_lane119s000221_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Pediatric_258_NUP98-NSD1_MI3454_Palbociclib_2

value: Acute myeloid leukemia


title: END [ME398}

description:
Test
ME398

value: endometrioma


title: HITMNG2Col6_Norm03

value: Norm AMEM growth conditions


title: LIHDIIV06 at 8h

description:
column name description
HG55GBGXB_V06T1Th2_19s000218-1-1_He_lane119s000218_sequence.txt.gz


title: LIHDIIV07 at 8h

description:
column name description
HG55GBGXB_V07T1Th2_19s000219-1-1_He_lane119s000219_sequence.txt.gz


title: LIHDIIV08 at 8h

description:
column name description
HG55GBGXB_V08T1Th2_19s000220-1-1_He_lane119s000220_sequence.txt.gz


title: END [ME401}

description:
Test
ME401


title: CTR [ME415}

description:
Control
ME415

value: ovarian cystadenoma


title: END [ME397}

description:
Test
ME397


title: LIHDIIP15 at 0h

description:
column name description
HG33LBGXB_P15T0Th2_19s000204-1-1_He_lane119s000204_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: HITMNG2Col6_Norm01


title: LIHDIIP12 at 0h

description:
column name description
HG33LBGXB_P12T0Th2_19s000201-1-1_He_lane119s000201_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: Pediatric_258_NUP98-NSD1_MI3454_1

value: Human bone marrow amplified in mouse bone marrow and spleen

value: leukemic

value: NSG


title: Pediatric_258_NUP98-NSD1_MI3454_2


title: LIHDIIP11 at 0h

description:
column name description
HG33LBGXB_P11T0Th2_19s000200-1-1_He_lane119s000200_sequence.txt.gz


title: HITM_Opti03

value: mandiibular condylar cartilage

value: immortalized with HTERT

value: wild type

value: Optimem Serum Free


title: HITM_Opti01


title: Pediatric_258_NUP98-NSD1_DMSO_3

value: DMSO


title: HITMNG2Col6_Norm02

value: Crispr Modified NG2/CSPG4 ectodomain


title: Pediatric_258_NUP98-NSD1_DMSO_2

value: Acute myeloid leukemia


title: HITM_Norm02


title: CTR [ME388}

description:
Control
ME388


title: END [ME391}

description:
Test
ME391

value: endometrioma


title: LIHDIIP10 at 0h

description:
column name description
HG33LBGXB_P10T0Th2_19s000199-1-1_He_lane119s000199_sequence.txt.gz


title: HITM_Norm01

value: Norm AMEM growth conditions


title: LIHDIIP04 at 0h

description:
column name description
HG33LBGXB_P04T0Th2_19s000195-1-1_He_lane119s000195_sequence.txt.gz


title: HITM_Norm03


title: KO_input_replicate 3_Female

city: London

first: Rinako

last: Nakagawa

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Read processing was carried out using the nf-core/chipseq pipeline version 1.2.2
Read alignment was carried out using bwa
reads were filtered as indicated in the nf-core/atacseq documentation
bigwig files are scaled to 1 million mapped reads using BEDTools and bedGraphToBigWig
peaks called with MACS2 using "--broad"
Assembly: GRCm38
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: Spleen

growth_protocol: RPMI 1640 medium with GlutaMAX supplemented with 10% fetal bovine serum, 500 U/ml penicillin/streptomycin, 50 µM 2-ME, 1 µg/ml anti-CD40, 5 µg/ml F(ab')2 fragment anti-IgM and 4 ng/ml IL-4 was used. Cells were cultured at 37C at 5% CO2, 1% O2 for two days.

extract_protocol:
Cells were fixed with 2 µM EGS (ethylene glycol bis (succinimidyl succinate)) for 1 hour, followed by 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonication device (Diagenode).
ChIP-seq libraries were prepared using the MicroPlex Library Preparation Kit v3 (Diagenode #C05010002), complemented with 24 UDI for MicroPlex vs - Set I and Set II (Diagenode #C05010008/C05010009). 13.5 µg and 1 µg of chromatin per IP were used as starting material for Kdm2a and H3K36me2, respectively. Libraries were amplified using 9-10 and 10-11 cycles on the thermocycler for H3K36me2 and Kdm2a/input, respectively. Post-amplification libraries were purified using AMPure beads, and the purified libraries were quantified using the Qubit ds DNA HS Assay kit (Invitrogen, #Q32851). Libraries were in size between 350-460bp in length.

value: Spleen

value: Primary

value: B cells

value: KO

tag: chip antibody


title: Pediatric_258_NUP98-NSD1_DMSO_1

tag: tissue


title: KO_input_replicate 2_Female


title: CTR [ME381}

description:
Control
ME381

value: ovarian teratoma


title: END [ME374}

description:
Test
ME374


title: END [ME394}

description:
Test
ME394


title: CTR [ME372}

description:
Control
ME372

value: ovarian cystadenoma


title: HITM_Opti02


title: CTR [ME370}

description:
Control
ME370


title: LIHDIIP06 at 0h

description:
column name description
HG33LBGXB_P06T0Th2_19s000196-1-1_He_lane119s000196_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Pollen allergy patients

value: Pollen allergy AIT


title: LIHDIIV17 at 0h

description:
column name description
HG2C2BGXB_V17T0Th2_19s000191-1-1_He_lane119s000191_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Adult_1055_NUP98-HOXA9_MI3454_Gilteritinib_3

source_name: Bone marrow

value: Bone marrow

value: leukemic

value: MI3454 + Gilteritinib


title: CTR [ME378}

description:
Control
ME378

value: serous ovarian cyst


title: Adult_1055_NUP98-HOXA9_Gilteritinib_3

value: Acute myeloid leukemia

value: Gilteritinib


title: Adult_1055_NUP98-HOXA9_MI3454_Gilteritinib_2


title: WT_input_replicate 1_Male

value: Spleen

value: Primary

value: WT


title: END [ME366}

description:
Test
ME366

value: endometrioma


title: LIHDIIP02 at 0h

description:
column name description
HG33LBGXB_P02T0Th2_19s000193-1-1_He_lane119s000193_sequence.txt.gz

source_name: PBMC


title: END [ME373}

description:
Test
ME373


title: LIHDIIP09 at 0h

description:
column name description
HG33LBGXB_P09T0Th2_19s000198-1-1_He_lane119s000198_sequence.txt.gz


title: LIHDIIP01 at 0h

description:
column name description
HG33LBGXB_P01T0Th2_19s000192-1-1_He_lane119s000192_sequence.txt.gz


title: Adult_1055_NUP98-HOXA9_MI3454_Palbociclib_1

value: MI3454 + Palbociclib


title: KO_input_replicate 1_Male

value: B cells

value: KO


title: Adult_1055_NUP98-HOXA9_MI3454_Palbociclib_2


title: LIHDIIC02 at 0h

description:
column name description
HG33LBGXB_C02T0Th2_19s000207-1-1_He_lane119s000207_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Healthy controls

value: no any AIT treatment


title: WT_input_replicate 3_Female


title: LIHDIIV16 at 0h

description:
column name description
HG2C2BGXB_V16T0Th2_19s000190-1-1_He_lane119s000190_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Adult_1055_NUP98-HOXA9_Palbociclib_3

value: Bone marrow

value: leukemic

value: Palbociclib


title: LIHDIIV12 at 0h

description:
column name description
HG2C2BGXB_V12T0Th2_19s000186-1-1_He_lane119s000186_sequence.txt.gz


title: WT_input_replicate 2_Female


title: KO_Kdm2a_replicate 1_Male

value: Kdm2a (non-commercial)


title: CTR [ME367}

description:
Control
ME367

value: ovarian teratoma


title: Adult_1055_NUP98-HOXA9_MI3454_Gilteritinib_1

value: Acute myeloid leukemia

value: MI3454 + Gilteritinib


title: Adult_1055_NUP98-HOXA9_MI3454_Palbociclib_3


title: LIHDIIV11 at 0h

description:
column name description
HG2C2BGXB_V11T0Th2_19s000185-1-1_He_lane119s000185_sequence.txt.gz


title: END [ME351}

description:
Test
ME351

value: endometrioma


title: Adult_1055_NUP98-HOXA9_Gilteritinib_2

value: Gilteritinib


title: LIHDIIV15 at 0h

description:
column name description
HG2C2BGXB_V15T0Th2_19s000189-1-1_He_lane119s000189_sequence.txt.gz


title: CTR [ME364}

description:
Control
ME364

value: no gynecological abnormality


title: LIHDIIV13 at 0h

description:
column name description
HG2C2BGXB_V13T0Th2_19s000187-1-1_He_lane119s000187_sequence.txt.gz


title: Adult_1055_NUP98-HOXA9_Gilteritinib_1


title: KO_Kdm2a_replicate 3_Female

value: Spleen

value: Primary

value: B cells

value: KO


title: CTR [ME363}

description:
Control
ME363

value: serous ovarian cyst


title: WT_Kdm2a_replicate 2_Female

value: WT


title: Adult_1055_NUP98-HOXA9_Palbociclib_2


title: LIHDIIV09 at 0h

description:
column name description
HG2C2BGXB_V09T0Th2_19s000183-1-1_He_lane119s000183_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Venom allergy patients

value: Venom allergy AIT


title: LIHDIIV06 at 0h

description:
column name description
HG2C2BGXB_V06T0Th2_19s000180-1-1_He_lane119s000180_sequence.txt.gz


title: Adult_1055_NUP98-HOXA9_Palbociclib_1

value: Bone marrow

value: leukemic

value: Palbociclib


title: KO_Kdm2a_replicate 2_Female

value: Kdm2a (non-commercial)


title: END [ME337}

description:
Test
ME337

value: endometrioma


title: END [ME361}

description:
Test
ME361


title: WT_Kdm2a_replicate 3_Female


title: CTR [ME336}

description:
Control
ME336


title: Adult_1055_NUP98-HOXA9_MI3454_2

value: Acute myeloid leukemia


title: WT_Kdm2a_replicate 1_Male


title: LIHDIIV04 at 0h

description:
column name description
HG2C2BGXB_V04T0Th2_19s000178-1-1_He_lane119s000178_sequence.txt.gz


title: Adult_1055_NUP98-HOXA9_MI3454_1


title: LIHDIIV05 at 0h

description:
column name description
HG2C2BGXB_V05T0Th2_19s000179-1-1_He_lane119s000179_sequence.txt.gz


title: CTR [ME335}

description:
Control
ME335

value: ovarian cystadenoma


title: Adult_1055_NUP98-HOXA9_DMSO_3

value: DMSO


title: KO_H3K36me2_replicate 2_Female

value: Spleen

value: Primary


title: LIHDIIV05 at 8h

description:
column name description
HFWKGBGXB_V05T1Th2_19s000217-1-1_He_lane119s000217_sequence.txt.gz


title: CTR [ME334}

description:
Control
ME334


title: KO_H3K36me2_replicate 1_Male

value: B cells

value: KO


title: KO_H3K36me2_replicate 3_Female


title: LIHDIIV04 at 8h

description:
column name description
HFWKGBGXB_V04T1Th2_19s000216-1-1_He_lane119s000216_sequence.txt.gz


title: CTR [ME338}

description:
Control
ME338

value: no gynecological abnormality


title: Adult_1055_NUP98-HOXA9_MI3454_3


title: Adult_1055_NUP98-HOXA9_DMSO_2


title: WT_H3K36me2_replicate 3_Female

value: WT


title: END [ME333}

description:
Test
ME333


title: LIHDIIC10 at 0h

description:
column name description
HFWKGBGXB_C10T0Th2_19s000215-1-1_He_lane119s000215_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Healthy controls

value: no any AIT treatment


title: Non-pregnant, COVID severe, patient 223 (VDJ)

city: Boston

first: Alexandra-Chloe

last: Villani

state: MA

institute: MGH, Harvard

description: An AnnData object that contains both normalized counts and raw counts of this sample, in the raw layer. Additional processed file include protein data from CITEseq (ADT), and epertoire data (BCT/ TCR)

data_processing:
Alignment with CellRanger (v6.0.1), genetic demultiplexing using Souporcell (v2.0), count matrices were aggregated using Pegasus (v1.7.1, python).
GEX count matrices were log-normalized, ADT count matrices were CLR normalized.
PCA was calculated, harmony was used for batch-correciton and the harmony-based PCs were used to create a UMAP and clustering using the leiden algorithm (all of these using Pegasus, python)
Assembly: GRCh38
Supplementary files format and content: GEX files include the leiden clustering, sample info, n_genes is the number of genes per cell, n_count is the number of UMIs per cell, percent_mito is the percent of mitochondrial transcript in the cell.
Supplementary files format and content: TCR files include sample info and TCR gene info ('TRA_v_gene', 'TRB_v_gene', 'TRA_j_gene', 'TRB_j_gene'), variable region protein sequneces ('TRA_cdr3', 'TRB_cdr3'), variable region nucleotite sequneces ('TRA_cdr3_nt', 'TRB_cdr3_nt'), whether the cell has a beta and an alpha chain ( 'has_beta', 'has_alpha', 'has_tcr'), whether the cell has J and V gene and alpha and beta sequences ('has_tcr'), the clone sequences ('clone', consists of V and J genes and CDR3 sequences), the clone proportion ('clone_prop') and whether it is expanded ('expanded_t', will be true if the clone is above 1% of the TCRs in the samples and consists of at leaset 5 cells
Supplementary files format and content: BCR files include sample info and BCR gene info ( 'IGL_v_gene', 'IGK_v_gene', 'IGH_v_gene', 'IGL_j_gene', 'IGK_j_gene', 'IGH_j_gene',), variable region protein sequneces ('IGL_cdr3', 'IGK_cdr3', 'IGH_cdr3'), variable region nucleotite sequneces ('IGH_cdr3_nt', 'IGK_cdr3_nt', 'IGL_cdr3_nt'), whether the cell has a lambda,  kappa and a heavy chain (  'has_lam', 'has_kap', 'has_heavy'), whether the cell has J and V genes ahas a lambda or kappa and a heavy chain ('has_bcr'), the clone sequences ('clone', consists of V and J genes and CDR3 sequences), the clone proportion ('clone_prop') and whether it is expanded ('expanded', will be true if the clone is above 1% of the BCRs in the samples and consists of at leaset 5 cells
Supplementary files format and content: B_Plasma_GEX_BCR.h5ad.tar.gz - include GEX data of B cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and BCR data.
Supplementary files format and content: CD4T_GEX_TCR.h5ad.tar.gz - include GEX data of CD4 T cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and TCR data.
Supplementary files format and content: CD8T_GEX_TCR.h5ad.tar.gz - include GEX data of CD8 T cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and TCR data.
Library strategy: VDJ-seq

extract_protocol:
Cryopreserved PBMC samples. Full details are in the manuscript.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pregnancy

value: NonPregnant

tag: covid infection_status

value: Positive

tag: covid severity_status

value: Severe

value: Female


title: Adult_1055_NUP98-HOXA9_DMSO_1

value: Bone marrow

value: Acute myeloid leukemia

value: leukemic


title: LIHDIIC09 at 0h

description:
column name description
HFWKGBGXB_C09T0Th2_19s000214-1-1_He_lane119s000214_sequence.txt.gz


title: WT_H3K36me2_replicate 1_Male

value: Spleen


title: WT_H3K36me2_replicate 2_Female

value: Primary


title: CTR [ME328}

description:
Control
ME328

value: salpingitis


title: LIHDIIC07 at 0h

description:
column name description
HFWKGBGXB_C07T0Th2_19s000212-1-1_He_lane119s000212_sequence.txt.gz


title: Non-pregnant, COVID severe, patient 213 (VDJ)

tag: Sex


title: LIHDIIC08 at 0h

description:
column name description
HFWKGBGXB_C08T0Th2_19s000213-1-1_He_lane119s000213_sequence.txt.gz


title: Non-pregnant, COVID severe, patient 1 (VDJ)


title: PTBP1_MinusTag_CLAP

city: Pasadena

first: Jimmy

middle: K

last: Guo

address: 1200 E California Blvd

institute: Caltech

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8. Read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to a combined genome reference containing the mouse (mm10) and human (hg38) genomes using STAR aligner181. PCR duplicates were removed using the Picard MarkDuplicates function. For mixing experiments, only reads that mapped uniquely in the genome and unambiguously to the human or mouse genomes were kept for further analysis. For experiments done in a single species, the appropriate reference genome and alignments were used (mm10 for mouse and hg38 for human). These reads were then used for downstream analysis.  For computing enrichments, all human (hg38) and mouse (mm10) annotated genes (RefSeq, downloaded from UCSC GRCh38 and GRCm38, respectively) were used as a reference set except for the genes encoding the transfected proteins. We treated exonic regions and intronic regions of each annotated gene as separate reference genes for computing enrichment. For each reference gene, we enumerated 100 nucleotide windows that span across the gene; for each window, we calculated: (i) the number of reads overlapping the window in the protein elution sample (e.g., CLIP or CLAP) and (ii) the maximum of either the number of observed reads over the window or the median read count over all windows within the gene in the input sample. Because all windows overlapping a gene should have the same expression level in the input sample, this approach provides a conservative estimation of the input coverage because it prevents windows from being scored as enriched if the input values over a given window are artificially low due to stochastic fluctuation, while at the same time accounting for any non-random issues that lead to increases in read counts over a given window (i.e., alignment artifacts leading to non-random assignment or pileups). To directly compare the number of reads within each window between sample and input, we normalized each window count by the total number of reads sequenced and the overall complexity within each sample. For example, if one sample was sequenced twice as deeply as another, then we would expect to observe – on average – twice as many reads over a given window for that sample. To account for the differences in the number of mapped (aligned) reads between samples, we scaled the total number of sequenced reads by the proportion of aligned reads within each sample. For each window, we computed enrichment by dividing the normalized sample counts by the normalized input counts. Nominal p-values were calculated for each window using a binomial test where k (number of successes) is defined as the number of reads in the protein elution samples within the window, N (number of trials) is the sum of the number of reads in the protein elution and input samples, and p (probability of success) is the expected number of reads in the elution sample divided by the sum of the expected number of reads per window in elution and input samples. (The expected number of reads is defined as the total number of reads scaled by the proportion of aligned reads within each sample). For plotting and reporting purposes, we considered all regions with a nominal binomial p-value < 10-6 as significant. However, the overall results reported are robust to the precise p-value cutoff used.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes gene window enrichment calculations

organism:
Homo sapiens
Mus

source_name: HEK239T, PSM33

extract_protocol: Cells were lysed in 1 mL lysis buffer (50mM Tris pH 7.5, 100mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 1X Promega PIC). For CLIP samples, RNA was digested with Ambion RNase I (1:3,000 dilution) to achieve a size range of 100-500 nucleotides in length. We used a fixed RNase condition for all experiments to enable comparison between proteins. Lysates were precleared by mixing with Protein G beads (Dynabeads) for 30 minutes at 4°C. Target proteins were immunoprecipitated overnight at 4°C from 10 million cells with 5 μg of antibody coupled to 40 μL of Protein G beads in 100 μL lysis buffer. Antibodies were pre-coupled to beads for 1 hour at room temperature with mixing, followed by 3 washes with lysis buffer to remove unbound protein. After immunoprecipitation, beads were washed four times with high salt wash buffer (50 mM TrisHCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and four times with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20). RNA and protein were eluted by incubating in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsacrosine, 2.5 mM TCEP) supplemented with 100 mM DTT at 50°C for 20 minutes. Samples were then run through an SDS-PAGE gel and transferred to a nitrocellulose membrane using the iBlot transfer system. The region 70 kDa above the molecular weight of the protein of interest was isolated and treated with Proteinase K (NEB), followed by purification with RNA Clean & Concentrate-5 (Zymo). Anti-V5 antibody (Bethyl, A190-120A) was used for all CLIP experiments.  For CLAP samples, cells were resuspended in 1 mL of cold lysis buffer (50 mM HEPES pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1X Protease Inhibitor Cocktail (Promega), 200 U of RiboLock (NEB), 20 U of TURBO DNase (Ambion), and 1X manganese/calcium mix (0.5mM CaCl2, 2.5 mM MnCl2). Samples were incubated on ice for 10 minutes and then at 37°C for 10 minutes at 1150 rpm shaking on a ThermoMixer (Eppendorf). Lysates were cleared by centrifugation at 15000g for 2 minutes and the supernatant was collected for capture to HaloLink Resin (Promega). For each CLAP capture, 200 μL of 25% HaloLink Resin (50 μL of HaloLink Resin total) was used per 10 million cells. Resin was washed three times with 2 mL of 1X TBS (50 mM Tris pH 7.5, 150 mM NaCl) and incubated in 1X Blocking Buffer (50 mM HEPES, pH 7.5, 10 μg/mL Random 9-mer, 100 μg/mL BSA) for 20 minutes at room temperature with continuous rotation. After the incubation, resin was washed three times with 1X TBS. Cleared lysate was mixed with 50 μL of HaloLink Resin and incubated at 4°C overnight with continuous rotation. The captured protein bound to resin was washed three times with lysis buffer at room temperature and then three times at 90°C for 3 minutes while shaking at 1200 rpm with each of the following buffers: 1X ProK/NLS buffer (50 mM HEPES, pH 7.5, 2% NLS, 10 mM EDTA, 0.1% NP-40, 10 mM DTT), high salt buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 1M NaCl), 8M urea buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 8 M Urea), and Tween buffer (50 mM HEPES, pH 7.5, 0.1% Tween 20, 10 mM EDTA). After the last wash, samples were centrifuged at 7500g for 30 seconds and supernatant was discarded. For elution, HaloLink Resin was resuspended in 100 μL of ProK/NLS buffer + 10 μL of Proteinase K (NEB) and incubated at 50°C for 20 minutes while shaking at 1200 rpm. Elutions were then transferred to microspin cups (Pierce, Thermo Fisher), centrifuged at 2000g for 30 seconds, and purified with RNA Clean and Concentrate-5 (Zymo).

treatment_protocol: Cells were washed once with PBS and then crosslinked on ice using 0.25 J cm-2 (UV 2.5k) of UV at 254 nm in a Spectrolinker UV Crosslinker. Cells were then scraped from culture dishes, washed once with PBS, pelleted by centrifugation at 1500g for 4 min, and flash-frozen in liquid nitrogen for storage at -80 °C.

value: HEK239T, PSM33

value: Human embryonic kidney cells, Mouse embryonic stem cells


title: CTR [ME327}

description:
Control
ME327

value: ovarian teratoma


title: END [ME323}

description:
Test
ME323

value: Deep Infiltrating Endometriosis


title: END [ME321}

description:
Test
ME321

value: endometrioma


title: LIHDIIC06 at 0h

description:
column name description
HFWKGBGXB_C06T0Th2_19s000211-1-1_He_lane119s000211_sequence.txt.gz

data_processing:
Quality control of the raw sequencing data was conducted using the FastQC software (v0.11.7-Java-1.8.0_162) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human genome 38 (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) and summarized to genes using the R Bioconductor Rsubread package (v1.32.4). In addition to those already failed with RNA extraction steps due to technical issues, one sample was also excluded for further analysis because CD127 Ab was forgotten to add before sorting. Genes that consistently had zero or very low counts were first removed using the Bioconductor edgeR package (v3.24.3). Trimmed Mean of M-values (TMM) normalization was performed on the filtered data with the edgeR package. The normalized data were voom-transformed to enable differential expression analysis with the Bioconductor limma package (v3.38.3).
Assembly: reference human genome 38
Supplementary files format and content: Excel table summary file for all the samples; each row represents one gene (gene name is based on HGNC to avoid Excel conversion errors), while each column represents the normalized read counts of the corresponding gene for the given sample; the column name of each sample is equal to the raw sequence file name.

extract_protocol:
Following the PBMC isolation from fresh blood of different participants at various time points/visits, CD4+ T cells were first enriched with human CD4 microbeads (130-045-101, Miltenyl Biotec) following the manufacture’s recommendations while the remaining fractions of PBMC were immediately cryopreserved as described in other sections of the manuscript. The CD4+ T cells were then immediately shipped to our sorting flow-cytometry facility at 4°C. The CD4+ T cells were first stained in Brilliant Stain Buffer (563794, BD) using all the Abs with specified dilution factors listed in Table S4 (of the manuscript). Incubate for 30 min at 4°C in the dark, briefly vortex once after 15 min. Wash the cells twice: centrifuge at 350g, 10 min, 4°C. Re-suspend the cells at a concentration of 10 million per ml. Proceed to aseptic sorting 20 PSI, with 100 um nozzle and Purity mode in a BD Aria III sorter (for the FACS gating strategy, please refer to Figure S6A of the manuscript). After sorting, cells were centrifuged at 350g, 10 min, 4°C, pelleted and lysated in 700 ul of the Qiazol buffer (Qiagen). Transfer the samples into 1.5 ml Eppendorf tubes and immediately freeze at -80°C until RNA extraction. RNA was extracted using RNeasy Micro kit (Qiagen) following the manufacture’s recommendations.
RNA-seq was performed at the EMBL Genomics Core Facility (Heidelberg, Germany) using single-read 75bp by NextSeq 500 with ~ 50 Million reads/sample. The NEBNext Ultra II RNA Library Prep Kit was used and the rRNA depletion step was included.

value: PBMC

value: CD4 Th2 cells

value: Healthy controls


title: Non-pregnant, COVID severe, patient 100 (VDJ)

value: NonPregnant

value: Positive


title: SAFA_MinusTag_CLAP


title: LIHDIIC05 at 0h

description:
column name description
HFWKGBGXB_C05T0Th2_19s000210-1-1_He_lane119s000210_sequence.txt.gz

value: no any AIT treatment


title: CTR [ME319}

description:
Control
ME319

value: ovarian cystadenoma


title: Non-pregnant, COVID severe, patient 77 (VDJ)

value: Severe

value: Female


title: Non-pregnant, COVID severe, patient 182 (VDJ)


title: LIHDIIC04 at 0h

description:
column name description
HFWKGBGXB_C04T0Th2_19s000209-1-1_He_lane119s000209_sequence.txt.gz


title: END [ME332}

description:
Test
ME332


title: LIHDIIC03 at 0h

description:
column name description
HFWKGBGXB_C03T0Th2_19s000208-1-1_He_lane119s000208_sequence.txt.gz


title: Non-pregnant, COVID severe, patient 321 (VDJ)


title: Non-pregnant, COVID severe, patient 50 (VDJ)


title: LIHDIIC10 at 2W

description:
column name description
H77Y3BGXB_C10T4Th2_19s000346-1-1_He_lane119s000346_sequence.txt.gz


title: LIHDIIC09 at 2W

description:
column name description
H77Y3BGXB_C09T4Th2_19s000345-1-1_He_lane119s000345_sequence.txt.gz


title: CTR [ME311}

description:
Control
ME311

value: ovarian fibroma


title: END [ME315}

description:
Test
ME315


title: Non-pregnant, COVID severe, patient 325 (VDJ)


title: LIHDIIC07 at 2W

description:
column name description
H77Y3BGXB_C07T4Th2_19s000343-1-1_He_lane119s000343_sequence.txt.gz


title: Non-pregnant, COVID severe, patient 191 (VDJ)


title: END [ME305}

description:
Test
ME305


title: END [ME307}

description:
Test
ME307


title: Non-pregnant, COVID severe, patient 382 (VDJ)


title: LIHDIIC05 at 2W

description:
column name description
H77Y3BGXB_C05T4Th2_19s000341-1-1_He_lane119s000341_sequence.txt.gz


title: Non-pregnant, COVID asymptomatic, patient 47 (VDJ)

value: Asymptomatic


title: Non-pregnant, COVID asymptomatic, patient 78 (VDJ)


title: Non-pregnant, COVID asymptomatic, patient 103 (VDJ)


title: LIHDIIC04 at 2W

description:
column name description
H77Y3BGXB_C04T4Th2_19s000340-1-1_He_lane119s000340_sequence.txt.gz


title: LIHDIIC03 at 6W

description:
column name description
H77Y3BGXB_C03T5Th2_19s000349-1-1_He_lane119s000349_sequence.txt.gz


title: CTR [ME303}

description:
Control
ME303

value: serous ovarian cyst


title: CTR [ME300}

description:
Control
ME300


title: END [ME304}

description:
Test
ME304


title: LIHDIIC03 at 2W

description:
column name description
H77Y3BGXB_C03T4Th2_19s000339-1-1_He_lane119s000339_sequence.txt.gz


title: Non-pregnant, COVID asymptomatic, patient 31 (VDJ)


title: LIHDIIC02 at 6W

description:
column name description
H77Y3BGXB_C02T5Th2_19s000348-1-1_He_lane119s000348_sequence.txt.gz


title: Non-pregnant, COVID asymptomatic, patient 350 (VDJ)


title: END [ME295}

description:
Test
ME295


title: END [ME294}

description:
Test
ME294


title: Pregnant, COVID severe, patient 101607-SEV (VDJ)

value: Pregnant


title: Pregnant, COVID asymptomatic, patient 105199-ASX (VDJ)


title: CTR [ME292}

description:
Control
ME292


title: AtC3H26OX_10DAG_control_rep2

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression in 10-day-old seedlings of AtC3H26 OX grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10.1 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis

source_name: whole seedlings

growth_protocol: Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 2 d at 4℃. The seeds were sown on 0.7% (w/v) agar plates containing on-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22℃ under SD conditions (8-h-light/16-h-dark cycle).

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

treatment_protocol: 10-day-old WT seedlings grown under SD conditions (8-h-light/16-h-dark cycle) were placed on ﬁlter papers soaked in MS solution containing 150 mM NaCl. After 0, 1, 2, and 4 h, the seedlings were harvested and prepared as whole seedlings.

value: whole seedlings

value: AtC3H26 overexpressing (Col-0)

value: no treatment


title: AtC3H3OX_10DAG_control_rep2

description: Gene expression in 10-day-old seedlings of AtC3H3 OX grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

value: AtC3H3 overexpressing (Col-0)


title: END [ME290}

description:
Test
ME290

value: Deep Infiltrating Endometriosis


title: AtC3H26OX_10DAG_control_rep1


title: END [ME291}

description:
Test
ME291

value: endometrioma


title: Non-pregnant, COVID asymptomatic, patient 94 (VDJ)

description: An AnnData object that contains both normalized counts and raw counts of this sample, in the raw layer. Additional processed file include protein data from CITEseq (ADT), and epertoire data (BCT/ TCR)

value: PBMC


title: CTR [ME289}

description:
Control
ME289


title: Pregnant, COVID severe, patient 915348-SEV (VDJ)


title: Pregnant, COVID negative, patient 644394-CTRL (VDJ)

value: Negative

value: Control


title: CTR [ME281}

description:
Control
ME281

value: ovarian teratoma


title: CTR [ME298}

description:
Control
ME298


title: Pregnant, COVID asymptomatic, patient 324058-ASX (VDJ)

value: Positive


title: AtC3H26OX_10DAG_NaCl_rep2

description: Gene expression in 10-day-old seedlings of AtC3H26 OX grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Whole seedlings were sampled and total RNA was analyzed.

value: 150 mM NaCl for 1, 2, and 4 h


title: END [ME280}

description:
Test
ME280


title: Pregnant, COVID asymptomatic, patient 803763-ASX (VDJ)

value: Female


title: AtC3H26OX_10DAG_NaCl_rep1


title: LIHDIIC01 at 6W

first: Feng

last: Hefeng

description:
column name description
H77Y3BGXB_C01T5Th2_19s000347-1-1_He_lane119s000347_sequence.txt.gz

value: CD4 Th2 cells

value: Healthy controls

value: no any AIT treatment


title: Pregnant, COVID severe, patient 705385-SEV (VDJ)

value: Pregnant

value: Severe


title: Pregnant, COVID negative, patient 729106-CTRL (VDJ)


title: CTR [ME275}

description:
Control
ME275

value: ovarian cystadenoma


title: AtC3H3OX_10DAG_NaCl_rep1

description: Gene expression in 10-day-old seedlings of AtC3H3 OX grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Whole seedlings were sampled and total RNA was analyzed.

value: whole seedlings


title: END [ME273}

description:
Test
ME273


title: Pregnant, COVID negative, patient OB7-CTRL (VDJ)


title: WT_10DAG_NaCl_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle) after 1, 2, and 4 h of 150 mM NaCl treatment. Whole seedlings were sampled and total RNA was analyzed.

value: WT (Col-0)


title: END [ME269}

description:
Test
ME269


title: Non-pregnant, COVID severe, patient 223 (GEX)

description: An AnnData object that contains both normalized counts and raw counts of this sample, in the raw layer.

data_processing:
Alignment with CellRanger (v6.0.1), genetic demultiplexing using Souporcell (v2.0), count matrices were aggregated using Pegasus (v1.7.1, python).
GEX count matrices were log-normalized, ADT count matrices were CLR normalized.
PCA was calculated, harmony was used for batch-correciton and the harmony-based PCs were used to create a UMAP and clustering using the leiden algorithm (all of these using Pegasus, python)
Assembly: GRCh38
Supplementary files format and content: GEX files include the leiden clustering, sample info, n_genes is the number of genes per cell, n_count is the number of UMIs per cell, percent_mito is the percent of mitochondrial transcript in the cell.
Supplementary files format and content: AllCells_GEX.h5ad.tar.gz - include GEX data of cells from all samples. This object has clustering information, PCs, UMAP and differential analysis info.
Supplementary files format and content: B_Plasma_GEX_BCR.h5ad.tar.gz - include GEX data of B cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and BCR data.
Supplementary files format and content: CD4T_GEX_TCR.h5ad.tar.gz - include GEX data of CD4 T cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and TCR data.
Supplementary files format and content: CD8T_GEX_TCR.h5ad.tar.gz - include GEX data of CD8 T cells from all samples. This object has clustering information, PCs, UMAP, differential analysis info and TCR data.
Supplementary files format and content: Myeloid.h5ad.tar.gz - include GEX data of MNP cells from all samples. This object has clustering information, PCs, UMAP and differential analysis info.
Supplementary files format and content: T_NK_interim.h5ad.tar.gz - includes GEX data from all MK,  CD4 T and CD8 T cells before splitting to CD4/CD8 T cells. This object includes the UMAP and clustering we based out split on.

value: NonPregnant


title: AtC3H3OX_10DAG_control_rep1

value: AtC3H3 overexpressing (Col-0)

value: no treatment


title: WT_10DAG_NaCl_rep1


title: Non-pregnant, COVID severe, patient 213 (GEX)

value: PBMC


title: WT_10DAG_control_2_rep2

description: Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.


title: CTR [ME267}

description:
Control
ME267


title: END [ME266}

description:
Test
ME266

value: endometrioma


title: Non-pregnant, COVID severe, patient 1 (GEX)


title: CTR [ME251}

description:
Control
ME251

value: ovarian teratoma


title: CTR [ME244}

description:
Control
ME244


title: Non-pregnant, COVID severe, patient 191 (GEX)

value: Positive


title: WT_10DAG_control_2_rep1


title: Non-pregnant, COVID severe, patient 100 (GEX)


title: WT_10DAG_control_1_rep2


title: Non-pregnant, COVID severe, patient 77 (GEX)


title: END [ME241}

description:
Test
ME241

value: Deep Infiltrating Endometriosis


title: AtC3H3OX_10DAG_NaCl_rep2

value: 150 mM NaCl for 1, 2, and 4 h


title: WT_10DAG_control_1_rep1


title: CTR [ME239}

description:
Control
ME239


title: Non-pregnant, COVID severe, patient 182 (GEX)

value: Female


title: CTR [ME314}

description:
Control
ME314


title: Non-pregnant, COVID severe, patient 50 (GEX)


title: Non-pregnant, COVID severe, patient 321 (GEX)


title: END [ME221}

description:
Test
ME221


title: CTR [ME232}

description:
Control
ME232


title: Non-pregnant, COVID severe, patient 325 (GEX)


title: CTR [ME218}

description:
Control
ME218


title: CTR [ME211}

description:
Control
ME211

value: serous ovarian cyst


title: LIHDIIC06 at 2W

description:
column name description
H77Y3BGXB_C06T4Th2_19s000342-1-1_He_lane119s000342_sequence.txt.gz

value: CD4 Th2 cells

value: Healthy controls

value: no any AIT treatment


title: Non-pregnant, COVID asymptomatic, patient 47 (GEX)

value: Asymptomatic


title: Non-pregnant, COVID severe, patient 382 (GEX)

value: Severe


title: Non-pregnant, COVID asymptomatic, patient 103 (GEX)


title: Non-pregnant, COVID asymptomatic, patient 94 (GEX)


title: outer hair cells, tamoxifen p2-5, rep 2

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3 (NextSeq 500).
FASTQ conversion with bcl-convert v.4.0.3.
Unique molecular identifier (UMI) sequences were extracted from the beginning of R2 reads using UMI-tools (1) v1.1.1 (parameters: extract --extract-method=regex --bc-pattern2=^(?P<umi_1>.{8})(?P<discard_1>.{6}).* for all read pairs).
The resulting read pairs were quality- and adapter-trimmed via Cutadapt (2) v2.5 in paired-end mode (parameters: --nextseq-trim=20 -m 1 -a NNNNNNNNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -O 17 -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Only read 1 of processed read pairs was aligned to the mouse genome (GCF_000001635.27/GRCm39) using STAR (3) v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 109 for GRCm39.
This annotation was also used to generate read counts on exon level summarized for each gene via featureCounts v1.6.4 from the Subread package (4) without prior UMI deduplication. Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
The count output was utilized to identify differentially expressed genes using DESeq2 (5) v1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”.
Assembly: GRCm39
Supplementary files format and content: csv; table containing raw read counts

source_name: Organ of Corti

extract_protocol:
The mRNA of Stat3ΔOHC and control  of the organ of Corti was carefully separated from the cochlea and digested with a lysis buffer containing 1mg/mL Collagenase IV , 2mg/mL Papain and 1mg/mL Thermolysin for 10min at 37°C. Subsequently, OHCs were incubated with Slc26a5-antibodyand then with lgG anti-rabbit microbeads for indirect selection of OHCs. The cell suspension was passed through MACS® Separator columns  to enrich magnetically labeled OHCs.
After elution of OHCs, the RNA was extracted using the Arcturus Pico Pure Isolation Kit. The RNA samples were checked using 2100 Bioanalyzer with RNA 6000 Pico kit and DNase treatment was performed. cDNA libraries suitable for sequencing were prepared with SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian according to manufacturer’s instructions. The PCR amplification was performed using 16 PCR cycles. Libraries were quantified by QubitTM dsDNA HS Assay Kit and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit before equimolar pooling. Sequencing of pooled libraries was performed in paired-end mode with 75 nt read length on the NextSeq 500 platform (Illumina).

value: Organ of Corti

value: outer hair cells

value: Slc-26a5-iCre het/ Stat3-fl het

value: Tamoxifen


title: END [ME210}

description:
Test
ME210


title: outer hair cells, tamoxifen p2-5, rep 4


title: outer hair cells, tamoxifen p2-5, rep 3


title: CTR [ME207}

description:
Control
ME207


title: CTR [ME209}

description:
Control
ME209

value: ovarian cystadenoma


title: CTR [ME205}

description:
Control
ME205


title: Foottissue_postop_rep3

city: Nanchang

first: Zhi-Qiang

last: Fan

address: 152 Ai Guo Road, Nanchang

institute: Jiangxi Provincial People's Hospital

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Foottissue, postoperative, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly foot tissue from patients before operative and after ooperative was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Foottissue

tag: gender

value: female


title: END [ME204}

description:
Test
ME204


title: outer hair cells, tamoxifen p2-5, rep 1


title: Non-pregnant, COVID asymptomatic, patient 31 (GEX)

value: PBMC

value: NonPregnant

value: Positive


title: Foottissue_postop_rep2

source_name: Foottissue, postoperative, replicate 2

value: male

tag: age


title: Foottissue_preop_rep3

source_name: Foottissue, preoperative, replicate 3


title: Foottissue_postop_rep1

source_name: Foottissue, postoperative, replicate 1


title: Foottissue_preop_rep2

source_name: Foottissue, preoperative, replicate 2


title: Foottissue_preop_rep1

source_name: Foottissue, preoperative, replicate 1


title: Macaque, female subject2, left hemisphere, sublibrary3

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw sequencing data from individual libraries were processed and mapped to the reference genome and the gene-cell counts matrices from all snRNA-seq libraries of the same species were concatenated using 10X Genomics cellranger-v6.1.2 or cellranger-v7.0.1
Assembly: mouse: mm10, baboon: Panubis1.0, and macaque: Mmul_10
Supplementary files format and content: Gene matrix.rds contains gene-cell counts for all libraries, metadata.csv contains meta data for all libraries

organism: Macaca mulatta

source_name: Ventral pallidum

extract_protocol:
Nuclear extraction for both mice and primates was performed with density gradient centrifugation according to the protocol described previously with modifications to scale down the reaction volume (85). Samples were moved from -80 ̊C and thawed on ice for 2 minutes. Tissues were transferred to a dounce homogenizer (Millipore Sigma, D8938-1SET) in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, pH 8.0, 5 µg/mL actinomycin, 1% BSA, and 0.08 U/µl RNase inhibitor, 0.01% NP40) on ice. Samples were homogenized for 10 strokes with the loose pestle in a total volume of 1 mL, followed by 10 additional strokes with the tight pestle. The tissue homogenate was then passed through a 50 µm filter and diluted 1:1 with working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 10 mM Tris-HCl, pH 8.0). Nuclei were layered onto an iodixanol gradient after homogenization and ultracentrifuged as described previously. After ultracentrifugation, nuclei were collected between the 30 and 40% iodixanol layers and diluted with resuspension buffer (1xPBS with 1% BSA, and 0.08 U/µl RNase inhibitor). Nuclei were centrifuged at 500 g for 10 min at 4°C and resuspended in resuspension buffer with 5 ng/µl of 7-AAD. FACS was carried out to further remove cellular debris. 7-AAD+ events were collected using a 100 µm nozzle on a BD FACSAria III instrument into a 1.5 mL microcentrifuge tube.
Nuclei were processed according to the manufacturer’s manual of 10X Genomics Chromium Single Cell Gene Expression 3’ V3.1 Assay.

value: Ventral pallidum


title: outer hair cells, control, no treatment, rep 4

value: tissue

tag: cell type

value: no


title: Non-pregnant, COVID asymptomatic, patient 78 (GEX)

value: Female


title: Non-pregnant, COVID asymptomatic, patient 350 (GEX)

value: Asymptomatic


title: outer hair cells, control, no treatment, rep 3

tag: genotype


title: Pregnant, COVID asymptomatic, patient 105199-ASX (GEX)

value: Pregnant


title: outer hair cells, control, no treatment, rep 2

value: Organ of Corti


title: outer hair cells, Stat3 ΔOHC, tamoxifen p16-19, rep 3

value: outer hair cells


title: CTR [ME178}

description:
Control
ME178

source_name: serum

value: leiomyoma


title: outer hair cells, Stat3 ΔOHC, tamoxifen p16-19, rep 1

value: Slc-26a5-iCre het/ Stat3-fl het

value: Tamoxifen


title: CTR [ME186}

description:
Control
ME186

value: serous ovarian cyst


title: Macaque, female subject2, right hemisphere, sublibrary1


title: END [ME200}

description:
Test
ME200

value: Deep Infiltrating Endometriosis


title: Pregnant, COVID severe, patient 101607-SEV (GEX)

value: PBMC

value: Severe


title: CTR [ME203}

description:
Control
ME203

value: ovarian teratoma


title: Pregnant, COVID negative, patient 729106-CTRL (GEX)

value: Negative

value: Control


title: END [ME181}

description:
Test
ME181

value: endometrioma


title: Macaque, female subject2, left hemisphere, sublibrary1

value: Ventral pallidum


title: Macaque, female subject2, left hemisphere, sublibrary2


title: Pregnant, COVID negative, patient 644394-CTRL (GEX)

value: Female


title: Macaque, male subject1, left hemisphere, sublibrary1


title: Pregnant, COVID asymptomatic, patient 324058-ASX (GEX)

value: Positive

value: Asymptomatic


title: outer hair cells, control, no treatment, rep 1

value: Organ of Corti

value: tissue

value: no


title: Pregnant, COVID severe, patient 915348-SEV (GEX)

value: Pregnant


title: outer hair cells, Stat3 ΔOHC, tamoxifen p16-19, rep 2

value: outer hair cells

value: Slc-26a5-iCre het/ Stat3-fl het

value: Tamoxifen


title: CTR [408-MM}

description:
Control
408-MM

value: leiomyoma


title: CTR [ME184}

description:
Control
ME184

value: ovarian cystadenoma


title: Macaque, female subject1, left hemisphere, sublibrary1


title: Pregnant, COVID asymptomatic, patient 803763-ASX (GEX)

value: PBMC


title: CTR [425CM}

description:
Control
425CM

value: no gynecological abnormality


title: CD40KO-RANKL Abl

city: Yokohama

first: Taishin

last: Akiyama

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger software v5.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Thymus

extract_protocol:
The thymus of 6-week-old mice was dissected and minced with a razor. Thymic fragments were pipetted up and down in 1 mL of Hepes-RPMI (Wako). The supernatant was used as lymphocytes, and the remaining fragments were digested by incubation in RPMI 1640 medium containing 0.05 U/mL Liberase (Roche) and 0.01% w/v DNase I (Sigma-Aldrich) at 37°C for 12 min x3 times after each incubation and Pipetting. Reactions were stopped by adding an equal volume of FACS buffer containing 1 mM ethylenediaminetetraacetic acid and washing with FACS buffer. Total cell count was calculated as the sum of lymphocytes and digested cells.
Single-cell emulsions were obtained using a 10x Genomics Controller and a v2 Library and Gel Bead kit (10X Genomics). RNA-sequencing libraries were prepared according to the 10x 3′ v2 kit protocol.

value: Thymus

value: Thymic epithelial cells

tag: strain


title: Pregnant, COVID severe, patient 705385-SEV (GEX)

value: Severe


title: Pregnant, COVID negative, patient OB7-CTRL (GEX)

value: Negative

value: Control

value: Female


title: WT-RANKL Ab

description: 10x Genomics


title: WT-Control

description: 10x Genomics


title: CTR [344-MR}

description:
Control
344-MR