title: TECs in hTOs at D7

description:
Library name: Orga3D_early_D7
10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the cellranger v4 software
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
D7 dissociated hTOs were sorted using a FACS ARIA (BD Biosciences) to purify epithelial cell population (EPCAM+ CD45-) and remove dead cells and debris
Libraries were prepared with Chromium Single-Cell 3′ Reagent v2 Kit (10× Genomics) as per the manufacturer’s protocol. Illumina adapters were incorporated during library preparation.

value: Thymic Epithelial Cells


title: mRNA_Melanoma_rep54

status: Public on Nov 21 2025

type: SRA

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

library_source: transcriptomic

data_processing:
Read count extraction and calculation of TPM and FPKM were performed by RSEM 1.3.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM, FPKM and expected count values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
RNA was extracted from FF tumour specimens using RNeasy Micro Kit (Qiagen).
mRNA libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

tag: tissue

value: Melanoma

tag: age

tag: Sex

value: male


title: Human control bladder, biol rep 2

city: Chengdu

first: Lede

last: Lin

state: Sichuan

address: No.37 Guoxue Lane, Wuhou District, Chengdu, Sichuan, P. R. China

country: China

institute: West China Hospital of Sichuan University

description: Library name: Control_2

library_source: transcriptomic single cell

data_processing:
The FASTQ files were aligned to the human GRCh38 reference genome using the Cell Ranger toolkit from 10X Genomics. Following this, the scRNA-seq data underwent quality control (QC) analysis using the Seurat package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Bladder

extract_protocol:
The procedure initiated with the fastidious creation of a single-cell suspension, succeeded by a rigorous assessment of its viability. It was ascertained that the cells exhibited a remarkable degree of activity, surpassing the 85% threshold, and were distinguished by their excellent uniformity and minimal impurities. To augment the efficiency of isolating individual cells, the cell concentration was carefully fine-tuned to an exact range of 700 to 1200 cells per microliter.
During the construction of the single-cell RNA sequencing (scRNA-seq) library, each cell, along with its associated cellular enzymes, was attached to a gel bead. This assembly was subsequently encapsulated within an oil droplet, forming a single-cell gel bead-in-emulsion (GEM). Each gel bead was uniquely labeled with a distinct barcode, incorporated a unique molecular identifier (UMI) sequence, and was equipped with a poly-dT primer sequence designed to initiate reverse transcription. The GEM droplets were then collected in Eppendorf tubes, where cell membranes were lysed using specifically designed recovery reagents, releasing the mRNA. The liberated mRNA interacted with the enzymes, dNTP substrates, and the poly-dT primer sequence within the droplets. Under precisely controlled conditions in a polymerase chain reaction (PCR) apparatus, reverse transcription was initiated, resulting in the synthesis of complementary DNA (cDNA). In the final step, the cDNA underwent PCR amplification, thereby completing the construction of the scRNA-seq library.

value: Bladder


title: mRNA_Melanoma_rep55


title: healthy donor 2_Control-FB

city: Incheon

first: Hye-Yeon

last: Ju

address: 119 Academy-ro Yeonsu-gu, Incheon Republic of Korea

country: South Korea

institute: Incheon National University

description:
Library name: 8674-TK-2-Control-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

data_processing:
Library quality was assessed using a bioanalyzer and quantified using a qPCR-based method equipped with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument. The prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, in accordance with the manufacturer’s protocols. 150-bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50,000 reads per cell. Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 were subjected to quality control analysis, including read quality assessment. Real Time Analysis Software and NovaSeq Control Software v1.8.0 (Illumina, San Diego, CA, USA) were used for base calling. MultiQC v1.7 (Illumina, San Diego, CA, USA) was used for data quality assessments.
10x Genomics Cell Ranger v5.0.0 was used to perform single-cell gene counting based on the human genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes, features.tsv.gz: list of gene IDs, matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) of female mTNBC were obtained from a clinical study approved by the institutional review board of the Korea University Medical Center Anam Hospital, Seoul, the Republic of Korea (no. ED17183). PBMCs of two healthy donors with no known medical history of cancer or other general conditions such as hypertension, diabetes, hyperlipidemia, and cardiovascular and inflammatory diseases were collected for comparison. In brief, whole blood samples were collected, and PBMCs were isolated by Ficoll–Paque™ density-gradient centrifugation.
ScRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 platform (10X Genomics) according to the manufacturer’s protocol. In brief, 10,000 cells were loaded into each channel of the Chromium X controller to achieve the target cell recovery of 5,000 cells. The cells were partitioned into gel bead emulsions, where cell lysis and barcoded reverse transcription of RNA were performed, followed by cDNA amplification. The amplified cDNA was purified using SPRI beads, and dual-indexed libraries were constructed by fragmentation, end repair, A-tailing, adapter ligation, and PCR amplification.

value: Blood

tag: subject status

value: healthy donor

tag: cell type

value: Peripheral blood mononuclear cells


title: 24289R-01-08

city: New Brunswick

first: Chadni

last: Patel

state: NJ

address: 195 Little Albany Street

country: USA

institute: Rutgers Cancer Institute

description: Library name: Sample 8

data_processing:
Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus 10B (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction).
Reads were aligned to the reference genome using the STAR Aligner (version 2.7.10b), a highly efficient RNA-Seq aligner that performs well with large genomes.
Differential gene expression analysis was performed using DESeq2 (version 1.40.2), a widely used package for RNA-Seq data analysis. DESeq2 normalizes read counts and identifies differentially expressed genes based on statistical models that account for variations between samples.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Differential expression analysis table was generated as a csv file by DESeq2
Supplementary files format and content: Normalized counts table as csv file for each sample in that comparison

extract_protocol:
Total RNA was extracted from the samples using Qiagen RNeasy mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).

tag: cell line

value: brain endothelial cells

tag: treatment

value: Doxorubicin (DOXO)


title: Human control bladder, biol rep 1

description: Library name: Control_1


title: crtl-4

city: Hefei

first: Chenyang

last: He

address: 443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: sample4

data_processing:
Raw reads were processed using fastp v0.18.0 to remove adapter-containing reads, reads with >10% unknown bases (N), and reads with >50% low-quality bases (Q ≤ 20).
Clean reads were aligned to an rRNA database using Bowtie2 v2.2.8. Reads mapping to rRNA were removed.
Remaining reads were aligned to the reference genome using HISAT2 v2.1.0 with default parameters.
Aligned reads were assembled using StringTie v1.3.1, and gene expression levels (FPKM and TPM) were quantified using RSEM.
Assembly: mm10
Supplementary files format and content: Processed data files include gene-level and transcript-level expression matrices generated by RSEM, reported as  TPM values. Differential expression result tables include log2 fold change, p-value, and FDR values generated by DESeq2 or edgeR.

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from samples using standard procedures. mRNA was enriched with Oligo(dT) beads (mRNA Capture Beads), followed by bead-based purification. The enriched mRNA was fragmented at high temperature and used as the template for first-strand cDNA synthesis using a reverse transcription enzyme mix.
After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the MGI DNBSEQ-T7 or Illumina Novaseq X Plus.

value: Liver


title: mRNA_Melanoma_rep52

value: UNKNOWN


title: healthy donor 1_Control-FB

description:
Library name: 8674-TK-1-Control-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: mRNA_Melanoma_rep53


title: crtl-3

description: Library name: sample3


title: 24289R-01-06

description: Library name: Sample 6


title: healthy donor 2_Control

description:
Library name: 8674-TK-2-Control
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: 24289R-01-07

description: Library name: Sample 7


title: crtl-2

description: Library name: sample2


title: healthy donor 1_Control

description:
Library name: 8674-TK-1-Control
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: mRNA_Melanoma_rep51


title: mRNA_Melanoma_rep50


title: SPOP_d6_3_1

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

description:
Library name: SPOP_d6_3_1
SPOP_normalized_expression.tsv

data_processing:
After pre-processing with prinseq-lite (v0.20.4), raw sequencing files (FASTQ format) were aligned to the human or mouse reference genome (GRCh38 and GRCm38) using STAR (v2.7.9a) with default settings.
Final processing was performed using SAMtools (v1.4) and counts per gene were obtained utilizing featureCounts (v2.0.3).
Differential expression analysis was done using R package DESeq2 (v1.46.0) and time-series plots illustrating dynamic expression changes over time were generated using the maSigPro R library (v1.76.0).
Assembly: HEK293T cells: GRCh38, murine GFP-NUP98::KDM5A AML cells: GRCm38
Supplementary files format and content: For HEK293T cells: tab-delimited file with normalized counts per gene
Supplementary files format and content: For murine GFP-NUP98::KDM5A-driven AML cells: tab-delimited file with normalized counts per gene

growth_protocol:
All HEK293T cell lines were cultured in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, at 37°C, 5% CO2, and 95% humidity.
All NUP98::KDM5A cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, 1 mM Sodium pyruvate, 50 µM 2-Mercaptoethanol and 20 mM HEPES at 37°C, 5% CO2, and 95% humidity.

extract_protocol:
RNA was isolated using the NEB Monarch Total RNA Miniprep Kit (NEB).
For HEK293T cells: Sequencing libraries were generated using the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina.
For murine GFP-NUP98::KDM5A-driven AML cells: Sequencing libraries were generated by Novogene.

treatment_protocol: murine GFP-NUP98::KDM5A cells were cultured with doxycycline (1 ug/mL) to induce SPOP-bioPROTAC or empty vector expression.

value: acute myeloid leukemia cells

tag: genotype

value: SPOP-bioPROTAC

value: doxycycline


title: 24289R-01-04

description: Library name: Sample 4

value: PBS


title: SPOP_d6_2_1

description:
Library name: SPOP_d6_2_1
SPOP_normalized_expression.tsv


title: 24289R-01-05

description: Library name: Sample 5


title: mTNBC patient 2_Case

description:
Library name: 8674-TK-2-Case
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: mTNBC patient

value: chemo, radiation therapy


title: mRNA_Melanoma_rep49

value: female


title: mTNBC patient 1_Case-FB

description:
Library name: 8674-TK-1-Case-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.


title: 24289R-01-03

description: Library name: Sample 3


title: 24289R-01-02

description: Library name: Sample 2


title: mRNA_Melanoma_rep48

value: Melanoma


title: mRNA_Melanoma_rep47


title: SPOP_d3_3_1

description:
Library name: SPOP_d3_3_1
SPOP_normalized_expression.tsv


title: mRNA_Melanoma_rep46


title: NHC-0010, NHC

city: Nashville

first: Matthew

middle: Tyler

last: Stier

state: TN

address: 1161 21st Avenue South

department: Internal Medicine

institute: Vanderbilt University Medical Center

description: Library name: 10069-MS-0048

data_processing:
Raw sequencing data were processed using Cell Ranger software (v7.1.0), aligning reads to the GRCh38-2020-A transcriptome reference with the intron inclusion option enabled.
Assembly: GRCh38-2020-A
Supplementary files format and content: HDF5 (.h5); AnnData (.h5ad)

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs (0.5–1.0 mL, 2 million cells/mL) were rapidly thawed at 37°C for 3 minutes, then diluted dropwise into 7 mL of HPLM supplemented with 10% dialyzed fetal bovine serum (dFBS). Cells were centrifuged at 300 × g for 5 minutes at room temperature, washed with 2 mL of HPLM + 10% dFBS, and subsequently washed with 2 mL of cold PBS containing 0.04% bovine serum albumin (BSA). The final wash step included filtration through a 35-μm cell strainer (Falcon, Cat. #352235) during centrifugation. Cells for single-cell RNA-seq library generation were resuspended in cold PBS + 0.04% BSA at a concentration of 1,000 cells/μL.
Single-cell RNA-seq libraries were generated using the Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics) targeting 20,000 cells per sample for capture. Libraries were sequenced on an Illumina NovaSeq 6000 system (S4 flow cell, PE150) targeting 50,000 reads per cell.

value: PBMC

tag: group

value: NHC

tag: source

value: HC

value: Female

tag: location

value: Outpatient

tag: batch


title: NHC-0009, NHC

description: Library name: 10069-MS-0047

value: Male


title: 24289R-01-01

description: Library name: Sample 1

value: brain endothelial cells


title: crtl-1

description: Library name: sample1

value: Liver


title: mRNA_Melanoma_rep45

value: male


title: SPOP_d3_1_1

description:
Library name: SPOP_d3_1_1
SPOP_normalized_expression.tsv

value: acute myeloid leukemia cells


title: SPOP_d3_2_1

description:
Library name: SPOP_d3_2_1
SPOP_normalized_expression.tsv

value: SPOP-bioPROTAC


title: MCF7PR_C3

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

description: Library name: MCF7PR_C3

data_processing:
The paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.9
Illumina TruSeq adapters and low-quality bases at the 3 prime end were trimmed from the reads using cutadapt 4.1 and read quality was checked again using FastQC 0.11.9
The trimmed reads were aligned to the Gencode GRCh38 human reference genome using STAR 2.7.10b
The sorted BAM file with mapped reads for each sample was then used as an input for featureCounts (Subread 2.0.6) in order to generate read count data on gene/feature level (parameters: -p --countReadPairs -t exon -g gene_id -s 0)
Genes/features were annotated using the GTF file from Gencode human GRCh38 reference
Assembly: GRCh38
Supplementary files format and content: Read count data generated by featureCounts (Subread 2.0.6) for each sample

growth_protocol: All the cells lines (MB231, BT549, MCF7, MCF7PR) were maintained in and maintained in α-Media, consisting of α-MEM (Corning) supplemented with 10% fetal calf serum (HyClone), 10 µM sodium pyruvate, 10 µg/mL insulin, 0.5 µg/mL hydrocortisone, 1X MEM non-essential amino acids (Corning), 2 mM glutamine, and 25 ng/mL EGF

extract_protocol:
Total RNA was isolated from cell lysates using PureLink RNA Mini Kit (Invitrogen) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

treatment_protocol: Cells were treated with vehicle (DMSO), 30nM RP-6306, 10 nM RP-3500 or combination for 48 hours.

value: Breast Cancer Cells

value: COMB

tag: time

value: May

tag: experiment


title: V-0089.2, CI-Sep

description: Library name: 10069-MS-0046

value: CI-Sep

value: Abdominal

value: MICU


title: mTNBC patient 2_Case-FB

description:
Library name: 8674-TK-2-Case-FB
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: Blood

value: mTNBC patient

value: Peripheral blood mononuclear cells

value: chemo, radiation therapy


title: EV_3_1

description:
Library name: EV_3_1
SPOP_normalized_expression.tsv

value: empty vector

value: doxycycline


title: MCF7PR_C2

description: Library name: MCF7PR_C2


title: mRNA_Melanoma_rep43

value: Melanoma

value: female


title: V-0085.2, CI-NS

description: Library name: 10069-MS-0044

value: PBMC

value: CI-NS

value: NS

value: Female

value: SICU


title: MCF7PR_C1

description: Library name: MCF7PR_C1

value: Breast Cancer Cells

value: COMB

value: May


title: MCF7PR_Ai3

description: Library name: MCF7PR_Ai3

value: ATRi


title: EV_1_1

description:
Library name: EV_1_1
SPOP_normalized_expression.tsv

value: acute myeloid leukemia cells


title: mRNA_Melanoma_rep42


title: V-0086.2, CI-Sep

description: Library name: 10069-MS-0045

value: CI-Sep

value: Abdominal

value: Male


title: EV_2_1

description:
Library name: EV_2_1
SPOP_normalized_expression.tsv

value: empty vector


title: mTNBC patient 1_Case

description:
Library name: 8674-TK-1-Case
10X Genomics Chromium Single Cell 3′ v3.1 platform, Raw files are gene expression files and feature barcode (FB) files.

value: Blood

value: mTNBC patient

value: Peripheral blood mononuclear cells

value: chemo, radiation therapy


title: SPOP_d6_1_1

description:
Library name: SPOP_d6_1_1
SPOP_normalized_expression.tsv

value: SPOP-bioPROTAC

value: doxycycline


title: V-0084.2, CI-NS

description: Library name: 10069-MS-0043

value: PBMC

value: CI-NS

value: NS


title: mRNA_Melanoma_rep41

value: Melanoma

value: female


title: MCF7PR_Ai2

description: Library name: MCF7PR_Ai2

value: Breast Cancer Cells

value: ATRi

value: May


title: MCF7PR_Ai1

description: Library name: MCF7PR_Ai1


title: mRNA_Melanoma_rep40


title: V-0079.2, CI-Sep

description: Library name: 10069-MS-0041

value: CI-Sep

value: Respiratory

value: SICU


title: MCF7PR_Mi3

description: Library name: MCF7PR_Mi3

value: MYTi


title: V-0078.2, CI-NS

description: Library name: 10069-MS-0040

value: Female

value: MICU


title: MCF7PR_Mi2

description: Library name: MCF7PR_Mi2


title: mRNA_Melanoma_rep44


title: mRNA_Melanoma_rep38

value: male


title: Medial preoptic area, Corn Oil, Male, rep6

city: Austin

first: Frances

middle: Anne

last: Champagne

address: 108 E Dean Keeton St

department: Psychology

institute: University of Texas at Austin

description: Library name: 9M1

library_source: genomic

data_processing:
Adaptor sequences and low-quality reads (q < 30) were trimmed using trim galore (version 0.6.10) and cutadapt (version 4.6). Diversity sequences and reads without the MspI site (CGG) were removed using a custom python script provided by the manufacturer of the oxRRBS kit (https://github.com/nugentechnologies/NuMetRRBS).
Paired-end reads were mapped to the rat genome (mRatBN7.2; RefSeq) using bismark (version 0.22.3) and bowtie2 (version 2.5.2) with the default settings.
PCR duplicates were removed based on the genomic coordinates of the reads and a 6-bp unique molecular identifier found in the read index using a custom python script provided by the manufacturer of the oxRRBS kit (https://github.com/tecangenomics/nudup).
An average of about 8.5 million uniquely aligned, de-duplicated reads per sample were analyzed for DNA methylation levels using the bismark methylation extractor.
Assembly: mRatBN7.2 (RefSeq)
Supplementary files format and content: Counts of methylated and unmethylated cytosines per CpG site using the bismark methylation extractor

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Medial preoptic area

extract_protocol:
DNA was extracted using the MagMAX FFPE DNA/RNA Ultra Kit (#A31881, ThermoFisher Scientific). For unfixed frozen tissue, 210 μl of protease solution was pipetted onto each MPOA sample and allowed to incubate at 55C at 900 rpm for at least one hour. The homogenate was immediately processed for RNA and DNA extraction using the Kingfisher Flex System following the manufacturer’s instructions. Some DNA samples were extracted using the MagMAX DNA Multi-Sample Ultra 2.0 Kit following the manufacturer’s instructions for tissue samples (#A45721, ThermoFisher Scientific).
Library preparation for oxRRBS was done using the Ovation RRBS Methyl-Seq System with the TrueMethyl oxBS module (Tecan) using 55 ng of input DNA. Between 12-20 samples were processed per batch of library preparation with a total of 5 batches, balanced by prenatal treatment group and sex. The oxidation of DNA prior to bisulfite conversion converts 5hmC to 5fC and allows for discrimination between 5mC and 5hmC at single base-pair resolution. For this study, oxidative bisulfite conversion was used to remove 5hmC and detect only 5mC in the samples.

treatment_protocol: From gestation day 8 until parturition (gestational day 21-22), cage-pairs of dams were randomly assigned to receive control Corn Oil, 50 μg/kg BPA, 50 μg/kg Mixed Bisphenols (BP), or 150 μg/kg Mixed BP. Equal parts BPA, BPS, and BPF were used for both Mixed BP treatment groups.

value: Medial preoptic area

value: Postnatal day 10

value: Corn Oil

value: Male

tag: licking/grooming


title: Medial preoptic area, Corn Oil, Female, rep6

description: Library name: 9F1


title: Medial preoptic area, 50 ug/kg BPA, Male, rep5

description: Library name: 93M1

value: 50 ug/kg BPA


title: Medial preoptic area, 50 ug/kg BPA, Female, rep4

description: Library name: 93F1


title: MCF7PR_Mi1

description: Library name: MCF7PR_Mi1


title: V-0076.2, CI-Sep

description: Library name: 10069-MS-0038

value: PBMC

value: SSTI


title: mRNA_Melanoma_rep37

value: Melanoma


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep6

description: Library name: 89F1

value: 150 ug/kg Mixed BP


title: mRNA_Melanoma_rep36

value: female


title: MCF7PR_D6

description: Library name: MCF7PR_D_3

value: Breast Cancer Cells

value: DMSO

value: Apr


title: MCF7PR_D5

description: Library name: MCF7PR_D_2


title: mRNA_Melanoma_rep35


title: V-0081.2, CI-Sep

description: Library name: 10069-MS-0042

value: CI-Sep

value: Respiratory

value: SICU


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep5

description: Library name: 88F1

value: Female


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep5

description: Library name: 87M1

value: Medial preoptic area


title: MCF7PR_D4

description: Library name: MCF7PR_D_1


title: NHC-0007, NHC

description: Library name: 10069-MS-0035

value: NHC

value: HC

value: Outpatient


title: NHC-0006, NHC

description: Library name: 10069-MS-0034

value: Male


title: mRNA_Melanoma_rep39


title: MCF7PR_D3

description: Library name: MCF7PR_D3

value: May


title: V-0072.2, CI-Sep

description: Library name: 10069-MS-0033

value: PBMC

value: Urinary

value: MICU


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep4

description: Library name: 87F1

value: Postnatal day 10

value: 150 ug/kg Mixed BP


title: mRNA_Melanoma_rep33

value: Melanoma

value: male


title: V-0077.2, CI-NS

description: Library name: 10069-MS-0039

value: CI-NS

value: NS


title: MCF7PR_D2

description: Library name: MCF7PR_D2

value: Breast Cancer Cells

value: DMSO


title: Medial preoptic area, Corn Oil, Male, rep5

description: Library name: 84M1

value: Medial preoptic area

value: Corn Oil


title: mRNA_Melanoma_rep32

value: female


title: V-0068.2, CI-Sep

description: Library name: 10069-MS-0032

value: CI-Sep

value: Abdominal

value: SICU


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep6

description: Library name: 91M1

value: Male


title: Medial preoptic area, Corn Oil, Female, rep5

description: Library name: 84F1

value: Female


title: mRNA_Melanoma_rep31


title: V-0073.2, CI-NS

description: Library name: 10069-MS-0037

value: PBMC

value: MICU


title: MCF7_C3

description: Library name: MCF7_C3

value: COMB

value: May


title: V-0064.2, CI-Sep

description: Library name: 10069-MS-0030

value: Respiratory


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep3

description: Library name: 77F1

value: Postnatal day 10

value: 150 ug/kg Mixed BP


title: mRNA_Melanoma_rep29

value: Melanoma


title: MCF7_C2

description: Library name: MCF7_C2

value: Breast Cancer Cells


title: Medial preoptic area, 50 ug/kg BPA, Male, rep4

description: Library name: 73M1

value: Medial preoptic area

value: 50 ug/kg BPA


title: mRNA_Melanoma_rep34

value: male


title: mRNA_Melanoma_rep28


title: V-0063.2, CI-NS

description: Library name: 10069-MS-0029

value: CI-NS

value: NS


title: V-0060.2, CI-Sep

description: Library name: 10069-MS-0028

value: CI-Sep

value: Abdominal

value: SICU


title: MCF7_Ai3

description: Library name: MCF7_Ai3

value: ATRi


title: Medial preoptic area, 50 ug/kg BPA, Male, rep3

description: Library name: 69M1

value: Male


title: V-0058.2, CI-NS

description: Library name: 10069-MS-0027

value: PBMC

value: Female


title: mRNA_Melanoma_rep26

value: female


title: mRNA_Melanoma_rep27


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep4

description: Library name: 63M1

value: Postnatal day 10


title: MCF7PR_D1

description: Library name: MCF7PR_D1

value: DMSO

value: May


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep3

description: Library name: 62M1

value: 150 ug/kg Mixed BP


title: V-0067.2, CI-NS

description: Library name: 10069-MS-0031

value: MICU


title: mRNA_Melanoma_rep25

value: Melanoma


title: MCF7_Mi3

description: Library name: MCF7_Mi3

value: Breast Cancer Cells

value: MYTi


title: V-0053.2, CI-Sep

description: Library name: 10069-MS-0025

value: SSTI


title: V-0055.2, CI-Sep

description: Library name: 10069-MS-0026

value: CI-Sep


title: mRNA_Melanoma_rep24

value: male


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep2

description: Library name: 62F1

value: Medial preoptic area


title: NHC-0005, NHC

description: Library name: 10069-MS-0024

value: NHC

value: HC

value: Outpatient


title: MCF7_Ai1

description: Library name: MCF7_Ai1

value: ATRi


title: Medial preoptic area, 50 ug/kg BPA, Female, rep3

description: Library name: 73F1

value: 50 ug/kg BPA

value: Female


title: mRNA_Melanoma_rep23


title: mRNA_Melanoma_rep30

value: female


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep2

description: Library name: 61M1

value: Postnatal day 10

value: Male


title: MCF7_Mi2

description: Library name: MCF7_Mi2

value: May


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep1

description: Library name: 61F1

value: 150 ug/kg Mixed BP


title: mRNA_Melanoma_rep22

value: Melanoma


title: MCF7_Mi1

description: Library name: MCF7_Mi1

value: Breast Cancer Cells

value: MYTi


title: NHC-0004, NHC

description: Library name: 10069-MS-0023

value: PBMC


title: MCF7_C1

description: Library name: MCF7_C1

value: COMB


title: MCF7_Ai2

description: Library name: MCF7_Ai2


title: V-0043.2, CI-NS

description: Library name: 10069-MS-0022

value: CI-NS

value: NS

value: MICU


title: Medial preoptic area, 50 ug/kg BPA, Male, rep2

description: Library name: 5M1

value: Medial preoptic area


title: V-0042.2, CI-NS

description: Library name: 10069-MS-0021


title: mRNA_Melanoma_rep20


title: mRNA_Melanoma_rep21

value: male


title: MCF7_D6

description: Library name: MCF7_D_3

value: DMSO

value: Apr


title: MCF7_D5

description: Library name: MCF7_D_2


title: V-0041.2, CI-Sep

description: Library name: 10069-MS-0020

value: CI-Sep

value: Respiratory

value: SICU


title: Medial preoptic area, 50 ug/kg BPA, Female, rep2

description: Library name: 5F1

value: Postnatal day 10

value: 50 ug/kg BPA

value: Female


title: MCF7_D4

description: Library name: MCF7_D_1

value: Breast Cancer Cells


title: mRNA_Melanoma_rep19

value: Melanoma

value: female


title: MCF7_D3

description: Library name: MCF7_D3

value: May


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep4

description: Library name: 53M1

value: 50 ug/kg Mixed BP

value: Male


title: V-0036.2, CI-NS

description: Library name: 10069-MS-0017

value: PBMC

value: CI-NS

value: NS

value: MICU


title: mRNA_Melanoma_rep18


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep5

description: Library name: 53F1

value: Medial preoptic area


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep6

description: Library name: 55F1


title: mRNA_Melanoma_rep16

value: male


title: V-0035.2, CI-NS

description: Library name: 10069-MS-0016


title: V-0038.2, CI-Sep

description: Library name: 10069-MS-0018

value: CI-Sep

value: Respiratory


title: MCF7_D1

description: Library name: MCF7_D1

value: DMSO


title: V-0034.2, CI-Sep

description: Library name: 10069-MS-0015

value: Urinary

value: SICU


title: Medial preoptic area, Corn Oil, Male, rep3

description: Library name: 50M1

value: Postnatal day 10

value: Corn Oil


title: BT549_C3

description: Library name: BT549_C3

value: Breast Cancer Cells

value: COMB


title: MCF7_D2

description: Library name: MCF7_D2

value: May


title: mRNA_Melanoma_rep14

value: Melanoma


title: Medial preoptic area, Corn Oil, Female, rep4

description: Library name: 50F1

value: Female


title: mRNA_Melanoma_rep15


title: BT549_C2

description: Library name: BT549_C2


title: V-0033.2, CI-Sep

description: Library name: 10069-MS-0014

value: PBMC

value: Abdominal


title: V-0040.2, CI-Sep

description: Library name: 10069-MS-0019

value: Male

value: MICU


title: BT549_C1

description: Library name: BT549_C1


title: Medial preoptic area, Corn Oil, Male, rep2

description: Library name: 49M1

value: Medial preoptic area


title: mRNA_Melanoma_rep13

value: male


title: mRNA_Melanoma_rep12

value: female


title: BT549_Ai3

description: Library name: BT549_Ai3

value: ATRi


title: mRNA_Melanoma_rep17


title: Medial preoptic area, Corn Oil, Female, rep3

description: Library name: 49F1


title: Medial preoptic area, Corn Oil, Male, rep4

description: Library name: 52M1


title: NHC-0003, NHC

description: Library name: 10069-MS-0012

value: NHC

value: HC

value: Outpatient


title: V-0031.2, CI-NS

description: Library name: 10069-MS-0013

value: CI-NS

value: NS


title: BT549_Ai2

description: Library name: BT549_Ai2

value: Breast Cancer Cells


title: mRNA_Melanoma_rep11


title: NHC-0002, NHC

description: Library name: 10069-MS-0011


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep1

description: Library name: 46M1

value: Postnatal day 10

value: 150 ug/kg Mixed BP


title: BT549_Ai1

description: Library name: BT549_Ai1

value: May


title: mRNA_Melanoma_rep10

value: Melanoma


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep3

description: Library name: 39M1

value: 50 ug/kg Mixed BP


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep4

description: Library name: 39F1

value: Female


title: V-0029.2, CI-NS

description: Library name: 10069-MS-0009

value: PBMC

value: MICU


title: mRNA_Melanoma_rep9

value: male


title: BT549_Mi3

description: Library name: BT549_Mi3

value: MYTi


title: BT549_Mi2

description: Library name: BT549_Mi2


title: mRNA_Melanoma_rep8

value: female


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep2

description: Library name: 38M1

value: Medial preoptic area

value: Male


title: V-0027.2, CI-Sep

description: Library name: 10069-MS-0008

value: CI-Sep

value: Bloodstream


title: mRNA_Melanoma_rep7


title: V-0026.2, CI-NS

description: Library name: 10069-MS-0007

value: CI-NS

value: NS


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep3

description: Library name: 38F1

value: Postnatal day 10


title: BT549_D6

description: Library name: BT549_D_3

value: Breast Cancer Cells

value: DMSO

value: Jan


title: BT549_Mi1

description: Library name: BT549_Mi1

value: May


title: mRNA_Melanoma_rep6

value: Melanoma


title: V-0023.2, CI-NS

description: Library name: 10069-MS-0006

value: PBMC


title: V-0022.2, CI-NS

description: Library name: 10069-MS-0005

value: SICU


title: Medial preoptic area, Corn Oil, Female, rep2

description: Library name: 33F1

value: Corn Oil

value: Female


title: BT549_D5

description: Library name: BT549_D_2


title: mRNA_Melanoma_rep5

value: male


title: NHC-0001, NHC

description: Library name: 10069-MS-0010

value: NHC

value: HC

value: Outpatient


title: mRNA_Melanoma_rep4


title: V-0021.2, CI-Sep

description: Library name: 10069-MS-0004

value: CI-Sep

value: SSTI

value: MICU


title: V-0020.2, CI-NS

description: Library name: 10069-MS-0003

value: CI-NS

value: NS

value: Male


title: Medial preoptic area, 50 ug/kg BPA, Male, rep1

description: Library name: 14M1

value: Medial preoptic area

value: Postnatal day 10

value: 50 ug/kg BPA


title: BT549_D3

description: Library name: BT549_D3

value: Breast Cancer Cells

value: DMSO

value: May


title: mRNA_Melanoma_rep3

value: Melanoma


title: V-0019.2, CI-NS

description: Library name: 10069-MS-0002

value: PBMC

value: Female


title: mRNA_Melanoma_rep2

value: male


title: Medial preoptic area, 50 ug/kg BPA, Female, rep1

description: Library name: 14F1


title: mRNA_Melanoma_rep1

value: female


title: BT549_D2

description: Library name: BT549_D2


title: BT549_D1

description: Library name: BT549_D1


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep1

description: Library name: 103M1

value: 50 ug/kg Mixed BP


title: MB231_C3

description: Library name: MB231_C3

value: COMB


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep2

description: Library name: 103F1


title: V-0018.2, CI-Sep

description: Library name: 10069-MS-0001

value: CI-Sep

value: Abdominal

value: SICU


title: Medial preoptic area, Corn Oil, Male, rep1

description: Library name: 33M1

value: Corn Oil

value: Male


title: iETV2 EBs, PDGFRalpha-FLK1+, Rep3

city: St. Louis

first: Dereck

last: Alleyne

state: MO

address: 425 South Euclid Avenue

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

description: Library name: iETV2-SP3-RNA

data_processing:
RNA sequencing data were aligned to the mm10 reference genome using Rsubread, version 2.20.0, and gene-level counts were obtained using the featureCounts algorithm packaged in Rsubread.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: All ES cells were maintained on irradiated mouse embryonic fibroblast (MEF) feeders in ES-DMEM media containing 15% FBS, 1% L-glutamine, 1% non-essential amino acids, 2% LIF conditioned media (generated in house) and 150μM 1-thioglycerol in DMEM). Cultures were passaged every 2 days, and prior to differentiation the cells were cultured in feeder-free conditions on gelatin-coated plates in ES-IMDM (DMEM, replaced with Iscove’s modified Dulbecco’s Media). For differentiation, single ES cells (0.4-1×105) were seeded in polyHema-coated Petri dishes in differentiation media (15% FBS, 50μg/ml ascorbic acid and 450μM 1-thioglycerol in IMDM) to generate embryoid bodies.

extract_protocol:
Total RNA was extracted from sorted EB cells using the Qiagen RNeasy mini kit and quality control was performed using the Bioanalyzer 2100 instrument (Agilent). Samples with an RNA integrity score > 10 were selected to generate bulk RNA sequencing libraries.
TruSeq Stranded Total RNA library prep kit (Illumina) was used to generate sequencing libraries

value: mouse embryonic stem cells

value: Doxycycline-inducible Etv2

value: Doxycyline, 2ug/ml


title: UCB_NI_Donor4_LIB1

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

description: Library name: UCB_NI_Donor4_LIB1

data_processing:
The raw scRNA-seq data were analyzed using subcommand multi in the 10× Genomics software CellRanger (version: 8.0.0). The sequencing reads were mapped to the human reference genome (GRCh38). Upon acquiring the processed scRNA-seq data, we utilized R package Seurat 38 (version: 5.0.2) to isolate non-empty droplets, ensuring that the detected genes numbered over 200 and were expressed in a minimum of three cells. Subsequently, cells were filtered based on three criteria: 1) the count of detected genes had to exceed 200 but remain below 10,000, 2) the count of detected UMIs had to exceed 1,000 but remain below 75,000, and 3) mitochondrial transcripts had to constitute less than 10% of the total. To eliminate potential doublets, we employed Python package scrublet 39, identifying doublets with an expected rate of 6% per library and excluding cells with a doubletScore above the 90th percentile. Following these steps, we retained high-quality single cells that exhibited more than 500 detected genes but fewer than 60,000 UMIs for further analysis. Gene expression levels were quantified using UMI counts per million mapped reads (CPM), calculated by dividing the UMI count of a specific gene in a single cell by the total UMI count in that cell, then multiplying by 100,000. For this study, the gene expression levels were transformed into log2(CPM + 1).
Assembly: Homo sapiens
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features and "matrix.mtx" files include scRNA-seq gene expression.

molecule: cytoplasmic RNA

source_name: Umbilical cord blood (UCB) cell

extract_protocol:
BD Vacutainer K2 EDTA tube (10ml) was used for blood collection. We obtained peripheral venous blood samples by venipunction from six participants. And then used Ficoll density gradient centrifugation (TBD, China) to separate PBMCs. We pre-added 4 mL Ficoll to each 15 mL centrifuge tube. For each participant, equal volumes of blood were carefully layered onto Ficoll and centrifuged at 800 g and RT for 25 min (3 acceleration and 1 brake). After centrifugation, we collected PBMCs with a pipette into a 15-ml tube and diluted up to 15 ml with pre-warmed PBS (TBD, China). After centrifuging for 10 min, at 250 g and RT, PBMC were resuspended in a 2 mL Red Blood Cell Lysis Buffer (Solarbio, China). After incubating the cells on ice for 10 min, 8 mL PBS was added, gently mixed, and centrifuged at 4℃ 300 g for 10 min. We resuspended the centrifuged cells in 10 ml of pre-prepared washing buffer (1× PBS with 0.04% BSA). The cleaning step was performed at 250 g and 4℃ for 10 min. The second time the cells were resuspended by the cleaning buffer and counted with the Dual Fluorescence Cell Counter (LunaTM fl). After centrifugation, the cells were resuspended in the cell cryopreservation system recommended by 10× Genomics. With about 2×106 cells per milliliter, one-milliliter aliquots were gradually frozen in a freezing box over the course of 24 h at -80℃ before being kept in a vapor-phase liquid nitrogen tank.
We selected samples before vaccination and at days 7, 14, 37, and 60 after vaccination for scRNA-seq. The cells were first thawed according to the 10× Genomics protocol (Demonstrated Protocol, CG00039). The thawed cells were then stained with trypan blue and placed under a light microscope to observe the cell state and background. The cells were counted using the Dual Fluorescence Cell Counter (LunaTM fl), and subsequent procedures were performed after confirming that the survival rate was not less than 90%. The ChromiumTM Single cell 5’ Reagent Kit, Chromium Single Cell Human BCR Amplification Kit, and Chromium Single Cell Human TCR Amplification Kit of the Chromium platform (10× Genomics, California, USA) were used to create the scRNA-seq and paired single-cell BCR and TCR libraries following the Chromium Single Cell 5’ Reagent Kits User Guide (v2 Chemistry Dual Index). On the Illumina HiSeq X Ten platform, generated scRNA-seq libraries were sequenced. The preprocessing of the PE150 Illumina sequencing reads was done using the 10× Genomics software CellRanger (version: 6.1.2).

value: Umbilical cord blood (UCB) cell

tag: donor

value: Non-infected (NI)

tag: library number

value: Library 1


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep1

description: Library name: 100F1

tag: tissue

value: Medial preoptic area

value: Postnatal day 10


title: BT549_D4

description: Library name: BT549_D_1

value: Breast Cancer Cells

value: DMSO

value: Jan


title: iETV2 EBs, PDGFRalpha-FLK1+, Rep2

description: Library name: iETV2-SP2-RNA


title: UCB_NI_Donor3_LIB1

description: Library name: UCB_NI_Donor3_LIB1


title: Medial preoptic area, Corn Oil, Female, rep1

description: Library name: 2F1

tag: age

value: Female


title: MB231_C1

description: Library name: MB231_C1

value: COMB

value: May


title: iETV2 EBs, PDGFRalpha-FLK1+, Rep1

description: Library name: iETV2-SP1-RNA


title: Medial preoptic area, Corn Oil, Male, rep6

description: Library name: 33M1

data_processing:
Adaptor sequences, poly-A tails (> 8 base-pairs long), and low-quality reads were trimmed using a custom script for tag-seq processing (https://github.com/z0on/tag-based_RNAseq) followed by cutadapt (version 1.18).
Trimmed reads were mapped to the rat genome (mRatBN7.2; RefSeq) using STAR (version 2.7.3a) with the default settings (output files were unsorted BAM) and sorted using samtools (version 1.10).
Gene counts were calculated for each sample using the bedtools (version 2.27.1) multicov function.
Assembly: mRatBN7.2 (RefSeq)
Supplementary files format and content: Raw counts for each sample

extract_protocol:
RNA was extracted using the MagMAX FFPE DNA/RNA Ultra Kit (#A31881, ThermoFisher Scientific). For unfixed frozen tissue, 210 μl of protease solution was pipetted onto each MPOA sample and allowed to incubate at 55C at 900 rpm for at least one hour. The homogenate was immediately processed for RNA and DNA extraction using the Kingfisher Flex System following the manufacturer’s instructions.
All RNA samples were diluted to 20 ng/μl before submission for library preparation and tag-seq at the Genome Sequence and Analysis Facility at the University of Texas at Austin.

tag: Sex

tag: nest attendance


title: UCB_NI_Donor2_LIB1

description: Library name: UCB_NI_Donor2_LIB1


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep6

description: Library name: 63M1

value: 150 ug/kg Mixed BP


title: MB231_Ai3

description: Library name: MB231_Ai3

tag: cell type

value: ATRi


title: UCB_NI_Donor1_LIB2

description: Library name: UCB_NI_Donor1_LIB2

value: Library 2


title: MB231_Ai2

description: Library name: MB231_Ai2

tag: cell line


title: Medial preoptic area, Corn Oil, Male, rep5

description: Library name: 50M1

tag: treatment

value: Corn Oil

value: Male


title: Wildtype EBs, PDGFRalpha-FLK1+, Rep3

description: Library name: WT-SP3-RNA

value: mouse embryonic stem cells

tag: genotype

value: Wildtype


title: Wildtype EBs, PDGFRalpha-FLK1+, Rep2

description: Library name: WT-SP2-RNA


title: MB231_Ai1

description: Library name: MB231_Ai1


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep6

description: Library name: 103F1

value: 50 ug/kg Mixed BP


title: MB231_C2

description: Library name: MB231_C2


title: Wildtype EBs, PDGFRalpha-FLK1+, Rep1

description: Library name: WT-SP1-RNA


title: UCB_IS_Donor4_LIB1

description: Library name: UCB_IS_Donor4_LIB1

value: Umbilical cord blood (UCB) cell

tag: group

value: Infected SARS-CoV-2 (IS)

value: Library 1


title: MB231_Mi3

description: Library name: MB231_Mi3

value: Breast Cancer Cells

value: MYTi


title: UCB_IS_Donor3_LIB1

description: Library name: UCB_IS_Donor3_LIB1


title: Medial preoptic area, 50 ug/kg BPA, Male, rep5

description: Library name: 93M1

value: Medial preoptic area

value: Postnatal day 10

value: 50 ug/kg BPA


title: MB231_Mi2

description: Library name: MB231_Mi2

value: May


title: MB231_Mi1

description: Library name: MB231_Mi1


description: Library name: 55F1

value: Female


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep5

description: Library name: 53F1


title: UCB_NI_Donor1_LIB1

description: Library name: UCB_NI_Donor1_LIB1

value: Non-infected (NI)


title: UCB_IS_Donor1_LIB2

description: Library name: UCB_IS_Donor1_LIB2

value: Library 2


title: Wildtype EBs, PDGFRalpha+FLK1+, Rep1

description: Library name: WT-DP1-RNA


title: MB231_D3

description: Library name: MB231_D3

value: DMSO


title: Medial preoptic area, Corn Oil, Male, rep4

description: Library name: 9M1

value: Corn Oil

value: Male


title: Wildtype EBs, PDGFRalpha+FLK1+, Rep3

description: Library name: WT-DP3-RNA

value: mouse embryonic stem cells

value: Wildtype


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato positive-Rep3

description: Library name: TGET_SP_EP_R3

source_name: T-GFP; Etv2-tdTomato

value: T-GFP; Etv2-tdTomato

value: SP Etv2 positive


title: MB231_D2

description: Library name: MB231_D2


title: UCB_IS_Donor1_LIB1

description: Library name: UCB_IS_Donor1_LIB1

value: Umbilical cord blood (UCB) cell

value: Infected SARS-CoV-2 (IS)

value: Library 1


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep6

description: Library name: 55M1

value: Medial preoptic area

value: 50 ug/kg Mixed BP


title: Patient_4_Baseline

city: Zürich

first: Ana Maria

last: Florescu

address: Wagistrasse 14

country: Switzerland

institute: Molecular Partners

description: Library name: Patient_4_Baseline

data_processing:
he RNASeq data was treated with the following 5 step process to generate a TPM matrix from the source bcl file. Step 1 : software bcl-convert (version 00.000.000.3.9.3) was used to convert *.bcl files for each sample to *.fastq.gz file. Step 2 : software STAR (version 2.7.3a) was used to convert the *.fastq.gz files, using human genome version hg38, to alignment files *.bam, sorted with duplicates removed. Step3 : software TPMCalculator (version 0.0.3) was used to convert *.bam, using hg38.ensGene.gtf annotation, to read count and TPM files with suffix _gene.out. Step 4 : software samtools index (version 1.1) was used to create *.bai files from .bam files for use in the QC steps
Assembly: hg38
Supplementary files format and content: quantile normalized TPM matrix

source_name: tumor

extract_protocol:
Maxwell® RSC simplyRNA Blood Kit
Novaseq 6000

value: tumor


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato positive-Rep2

description: Library name: TGET_SP_EP_R2


title: MB231_D1

description: Library name: MB231_D1

value: Breast Cancer Cells

value: May


title: Wildtype EBs, PDGFRalpha+FLK1+, Rep2

description: Library name: WT-DP2-RNA


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato positive-Rep1

description: Library name: TGET_SP_EP_R1


title: Patient_18_C2D8

description: Library name: Patient_18_C2D8


title: single- nuclei RNA sequencing data from human kidney transplants TCMR specimen 4

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

description: Library name: sn.r4

data_processing:
Single nuclei RNA sequencing: Digital expression matrices were generated with the 10x Genomics Cell Ranger software (version 3.0.2 for mice and version 8.0.0 for human samples) using the parameter `–expect-cells 10000` against the mouse mm10 or human GRCh38-3.0.0 genome. Human samples were further filtered using cellbender remove-background with fpr 0.01 to remove ambient RNA. Data integration and clustering were performed using the following workflow: NormalizeData -> FindVariableFeatures -> SelectIntegrationFeatures -> FindIntegrationAnchors -> IntegrateData -> ScaleData -> RunPCA(npcs=30) -> harmony::RunHarmony(group.by.vars = c("group"), lambda = 2, tau = 1000, theta = 1, assay.use = "integrated", kmeans_init_nstart = 60, kmeans_init_iter_max=2000, max.iter.harmony = 30) -> ScaleData -> FindNeighbors(reduction=”harmony”, dims=1:15) -> FindClusters(resolution=0.5)  Cell types were assigned based on marker gene expression as published previously.
Assembly: Mouse single nuclei RNA sequencing: mm10
Assembly: Human single nuclei RNA sequencing: GRCh38
Supplementary files format and content: output files from cellranger

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Mouse and human single nuclei RNA sequencing: For single-nucleus RNA sequencing (snRNA-seq), kidneys from 10–12-week-old male mice were dissected and rinsed with ice-cold PBS. A 1–2 mm middle slice was extracted, and the cortex was trimmed to enrich for medullary cell types. Specimens were preserved in pre-cooled RNAlater (Invitrogen #AM7020) at 4°C for 24 hours before being stored at -80°C until nuclei isolation, following the protocol described by Leiz, Hinze et al. (2021). All samples underwent single-cell sequencing using the 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 chemistry protocol (#CG000204 Rev D), targeting 9,000–10,000 nuclei per sample. Libraries were sequenced on Illumina HiSeq 4000 platforms (paired-end), and digital expression matrices were generated with the 10x Genomics Cell Ranger software (version 3.0.2) using the parameter `–force-cells 10000` against the mouse mm10 genome. Archived human kidney biopsy samples were prepared similarly, stored at -80°C in RNAlater, and included from the archive of the Hannover Medical School protocol biopsy program. All subsequent steps, starting from the -80°C storage in RNAlater, were identical to those used for mouse tissue.
For single nuclei RNA sequencing: library preparation were performed according to the 10x Genomics single cell protocol (10X Genomics toolkit version v3.1, Pleasanton, CA)

value: kidney


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato negative-Rep3

description: Library name: TGET_SP_EN_R3

value: SP Etv2 negative


title: Medial preoptic area, Corn Oil, Female, rep5

description: Library name: 9F1

value: Postnatal day 10

value: Female


title: UCB_IS_Donor2_LIB1

description: Library name: UCB_IS_Donor2_LIB1


title: Patient_4_C2D8

description: Library name: Patient_4_C2D8


title: Medial preoptic area, 50 ug/kg BPA, Female, rep6

description: Library name: 5F1

value: 50 ug/kg BPA


title: single- nuclei RNA sequencing data from human kidney transplants TCMR specimen 1

description: Library name: sn.r1


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato negative-Rep2

description: Library name: TGET_SP_EN_R2

value: mouse embryonic stem cells


title: Medial preoptic area, 50 ug/kg BPA, Male, rep4

description: Library name: 5M1

value: Male


title: TGET EBs, PDGFRalpha-FLK1+, Etv2-tdTomato negative-Rep1

description: Library name: TGET_SP_EN_R1

value: T-GFP; Etv2-tdTomato


title: Patient_16_Baseline

description: Library name: Patient_16_Baseline


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep4

description: Library name: 91M1

value: 150 ug/kg Mixed BP


title: single- nuclei RNA sequencing data from human kidney transplants stable allograft specimen 2

description: Library name: sn.c2


title: Patient_16_C2D8

description: Library name: Patient_16_C2D8


title: single- nuclei RNA sequencing data from human kidney transplants stable allograft specimen 4

description: Library name: sn.c4


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep5

description: Library name: 46M1


title: Medial preoptic area, 50 ug/kg BPA, Male, rep2

description: Library name: 73M1


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato positive-Rep2

description: Library name: TGET_DP_EP_R2

value: DP Etv2 positive


title: Patient_8_Baseline

description: Library name: Patient_8_Baseline


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato positive-Rep3

description: Library name: TGET_DP_EP_R3


title: single- nuclei RNA sequencing data from human kidney transplants stable allograft specimen 1

description: Library name: sn.c1


title: Medial preoptic area, 50 ug/kg BPA, Male, rep3

description: Library name: 68M1


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato positive-Rep1

description: Library name: TGET_DP_EP_R1


title: Medial preoptic area, Corn Oil, Male, rep3

description: Library name: 52M1

value: Corn Oil


title: Patient_8_C2D8

description: Library name: Patient_8_C2D8


title: 60 min conjugation, ΔuvrD, replicate 2

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

country: France

institute: CNRS

description: Library name: UD60B

data_processing:
Sequence reads were mapped to references genomes and pESBL using Bowtie2.
.bam fileswere used to measure the read counts of each gene with featureCounts, followed by differential gene expression (DGE) analysis done by DESeq2 package in SARTools.
Assembly: E. coli chromosome (NC_000913.2)
Assembly: S. meliloti genome (NC_003047.1; NC_003037.1; NC_003078.1)
Supplementary files format and content: tab-delimited text file containing raw count per sample, Padj and log2 fold change (I2FC) of fragments per kilobase of gene per million reads  (FPKM)

organism: Escherichia coli

source_name: prokaryotic cell

growth_protocol: Cells were grown in LB media with agitation (180 rpm) at 37 ᵒC and 30 ᵒC for E. coli and S. meliloti, respectively.

extract_protocol:
Total RNA was extracted with Monarch Total RNA Miniprep Kit (New England Biolabs, NEB), following manufacturer’s protocol.
Library construction was performed by Novogene.

treatment_protocol: Donor and recipient growing cells were mixed and placed in a filter membrane in a LB plate supplemented with 1 mM MgCl2. Cells were incubated at 37 ᵒC for 30 and 60 minutes.  After incubation, cells were recovered and washed twice with 2 mM Ethylenediaminetetraacetic acid solution (EDTA). Pellet was resuspended in 1 ml of EDTA.

tag: strain

value: prokaryotic cell


title: Medial preoptic area, Corn Oil, Female, rep4

description: Library name: 50F1

value: Medial preoptic area


title: single- nuclei RNA sequencing data from human kidney transplants TCMR specimen 3

description: Library name: sn.r3


title: Patient_7_C2D8

description: Library name: Patient_7_C2D8


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato negative-Rep2

description: Library name: TGET_DP_EN_R2

value: DP Etv2 negative


title: 60 min conjugation, ΔuvrD, replicate 1

description: Library name: UD60A


title: Patient_7_Baseline

description: Library name: Patient_7_Baseline

value: tumor


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato negative-Rep1

description: Library name: TGET_DP_EN_R1


title: 30 min conjugation, ΔuvrD, replicate 1

description: Library name: UD30A


title: Patient_14_C2D8

description: Library name: Patient_14_C2D8


title: 30 min conjugation, ΔuvrD, replicate 2

description: Library name: UD30B


title: Patient_14_Baseline

description: Library name: Patient_14_Baseline


title: Medial preoptic area, Corn Oil, Male, rep2

description: Library name: 49M1


title: TGET EBs, PDGFRalpha+FLK1+, Etv2-tdTomato negative-Rep3

description: Library name: TGET_DP_EN_R3


title: Day 4 iETV2 EBs, PDGFRalpha-FLK1+, Rep1

description: Library name: Etv2OE-SP1-ATAC

data_processing:
ATAC sequencing data were pre-processed using the ATAC-seq Integrative Analysis Package (AIPAC), version 1.1 using default settings. Briefly, sequencing reads were aligned to the mm10 reference genome using bowtie2. Quality control and filtering of low-quality reads was performed before peak calling. Peaks were called using MACS2 software using default settings and a consensus peak matrix was obtained using DiffBind version 3.14.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: norm_counts_atac.txt

extract_protocol:
FACS-sorted EB cells were washed in cold PBS, counted and aliquoted (50,000 live cells). For the Tn5 transposition reaction, the Omni-ATAC protocol was used with some modifications. Briefly, cells were lysed and then resuspended in transposition reaction buffer (50% TD Tagment DNA buffer and 5% TDE1 Tagment DNA enzyme in PBS) for 30 minutes.
ATAC-sequencing libraries were generated using the Nextera Index kit (Illumina) and sequenced (75 base pairs, paired end)

value: Etv2 overexpressing SP

value: Doxycyline, 2ug/ml


title: Day 4 iETV2 EBs, PDGFRalpha-FLK1+, Rep2

description: Library name: Etv2OE-SP2-ATAC


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep5

description: Library name: 88F1


title: Patient_19_C2D8

description: Library name: Patient_19_C2D8


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep5

description: Library name: 103M1

value: 50 ug/kg Mixed BP


title: 60 min conjugation, replicate 2

description: Library name: p60m2


title: 60 min conjugation, replicate 1

description: Library name: p60m1


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep4

description: Library name: 62F1


title: Medial preoptic area, Corn Oil, Female, rep3

description: Library name: 84F1


title: Day 4 Etv2KO EBs, PDGFRalpha+FLK1+, Rep2

description: Library name: Etv2KO-DP4-ATAC

source_name: Etv2 knockout

value: Etv2 knockout

value: Etv2 knockout DP


title: Patient_19_Baseline

description: Library name: Patient_19_Baseline


title: Day 4 Etv2KO EBs, PDGFRalpha+FLK1+, Rep1

description: Library name: Etv2KO-DP3-ATAC


title: Patient_9_C2D8

description: Library name: Patient_9_C2D8


title: 30 min conjugation, replicate 2

description: Library name: p30m2


title: 30 min conjugation, replicate 1

description: Library name: p30m1


title: Patient_9_Baseline

description: Library name: Patient_9_Baseline


title: Day 4 Wildtype EBs, PDGFRalpha-FLK1+, Rep2

description: Library name: WT-SP2-ATAC

value: wildtype


title: Medial preoptic area, 50 ug/kg BPA, Male, rep1

description: Library name: 14M1

value: Postnatal day 10

value: 50 ug/kg BPA


title: Mock conjugation, replicate 2

description: Library name: pmock2


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep3

description: Library name: 46F1

value: Female


title: Patient_10_Baseline

description: Library name: Patient_10_Baseline


title: Mock conjutagion, replicate 1

description: Library name: pmock1


title: Day 4 Wildtype EBs, PDGFRalpha-FLK1+, Rep1

description: Library name: WT-SP1-ATAC

value: mouse embryonic stem cells


title: Patient_18_Baseline

description: Library name: Patient_18_Baseline


title: Day 4 Wildtype EBs, PDGFRalpha+FLK1+, Rep2

description: Library name: WT-DP2-ATAC


title: Patient_10_C2D8

description: Library name: Patient_10_C2D8


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep2

description: Library name: 100F1


title: Hypo_d6_replicate3

city: Boston

first: Nikolaos

last: Tsopoulidis

state: MA

address: 185 Cambridge Street, CPZN 4100

institute: MGH Molecular Biology

data_processing:
Transcriptome mapping was performed with STAR using the UCSC annotation of the mm10 reference genome.
Read counts for individual genes were generated using featureCounts. Only genes with CPM > 2 for at least two samples were included in the analyses.
Assembly: mm10
Supplementary files format and content: Table with CPM values for each sample

source_name: Esophagus

growth_protocol: Complete SAGM medium, supplemented with 10 μM Y-27632 (Tocris), 1 μM CHIR99021 (Tocris), 1 μM A83-01, and 1 μM DMH-1, was used for culture. Cells were kept in the exponential growth phase (maximum 8,000 cells/cm²). Media changes were performed every 48 hours. Cells were dissociated from the flasks and dishes either by scraping or treatment with TrypLE (Gibco) for 10 minutes. Epithelial cells were collected in 1% BSA/PBS (Invitrogen) and spun down at 300 g.

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen).
RNA-seq libraries were constructed from polyadenosine (polyA)-selected RNA using NEBNext Ultra Directional RNA library prep kit for Illumina (New England BioLabs). Libraries were amplified for 14 cycles. Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit. Libraries were quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument. Each lane of sequencing was pooled with unique barcodes. Pooled libraries are also quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument.

treatment_protocol: ETOH or 4OHT(0.05 µM) or 4OHT+DOX(50ng/ml)

value: Esophagus

value: Esophageal basal cells

value: Nudt21 Hypomorph

value: 4OHT+DOX for 6 days


title: Day 4 Wildtype EBs, PDGFRalpha+FLK1+, Rep1

description: Library name: WT-DP1-ATAC


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep3

description: Library name: 38F1

value: Medial preoptic area


title: Patient_6_Baseline

description: Library name: Patient_6_Baseline


title: Hypo_d6_replicate2


title: Hypo_d6_replicate1


title: Patient_1_Baseline

description: Library name: Patient_1_Baseline


title: Patient_2_C2D8

description: Library name: Patient_2_C2D8


title: single- nuclei RNA sequencing data from mouse kidney transplantation BALB/c to C57BL/6 specimen 3

description: Library name: sn.BALB/c to C57BL/6 3

value: kidney


title: single- nuclei RNA sequencing data from mouse kidney transplantation C57BL/6 to BALB/c specimen 3

description: Library name: sn.C57BL/6 to BALB/c 3


title: Hypo_d4_replicate1

value: 4OHT+DOX for 4 days


title: Patient_1_C2D8

description: Library name: Patient_1_C2D8

value: tumor


title: single- nuclei RNA sequencing data from mouse kidney transplantation C57BL/6 to BALB/c specimen 1

description: Library name: sn.C57BL/6 to BALB/c 1


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep4

description: Library name: 39M1

value: Male


title: Hypo_d4_replicate3


title: Patient_6_C2D8

description: Library name: Patient_6_C2D8


title: Medial preoptic area, 50 ug/kg BPA, Female, rep4

description: Library name: 14F1


title: Hypo_d4_replicate2


title: single- nuclei RNA sequencing data from mouse kidney transplantation BALB/c to BALB/c specimen 1

description: Library name: sn.BALB/c to BALB/c 1

value: BALB/c


title: Medial preoptic area, 50 ug/kg BPA, Female, rep5

description: Library name: 73F1


title: KO_d6_replicate2

value: Nudt21 KO

value: 4OHT for 6 days


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep3

description: Library name: 62M1

value: 150 ug/kg Mixed BP


title: Medial preoptic area, 50 ug/kg BPA, Female, rep3

description: Library name: 58F1

value: Postnatal day 10


title: Patient_15_Baseline

description: Library name: Patient_15_Baseline


title: Medial preoptic area, Corn Oil, Female, rep2

description: Library name: 49F1

value: Corn Oil


title: single- nuclei RNA sequencing data from mouse kidney transplantation C57BL/6 to C57BL/6 specimen 1

description: Library name: sn.C57BL/6 to C57BL/6 1


title: single- nuclei RNA sequencing data from mouse kidney transplantation BALB/c to BALB/c specimen 2

description: Library name: sn.BALB/c to BALB/c 2


title: Patient_15_C2D8

description: Library name: Patient_15_C2D8


title: Patient_11_C2D8

description: Library name: Patient_11_C2D8


title: single- nuclei RNA sequencing data from mouse kidney transplantation BALB/c to C57BL/6 specimen 1

description: Library name: sn.BALB/c to C57BL/6 1


title: Patient_2_Baseline

description: Library name: Patient_2_Baseline


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep3

description: Library name: 53M1

value: 50 ug/kg Mixed BP


title: Patient_11_Baseline

description: Library name: Patient_11_Baseline


title: single- nuclei RNA sequencing data from mouse kidney transplantation C57BL/6 to BALB/c specimen 2

description: Library name: sn.C57BL/6 to BALB/c 2


title: Patient_12_C2D8

description: Library name: Patient_12_C2D8


title: Medial preoptic area, Corn Oil, Male, rep1

description: Library name: 84M1


title: KO_d6_replicate1


title: Medial preoptic area, 150 ug/kg Mixed BP, Male, rep2

description: Library name: 61M1


title: KO_d6_replicate3


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep2

description: Library name: 61F1

value: Female


title: KO_d4_replicate2

value: Esophagus

value: 4OHT for 4 days


title: KO_d4_replicate1

value: Esophageal basal cells


title: cd3

type: RNA

first: Jin

last: Zhang

address: Anhui Medical University, No. 81 Meishan Road, Shushan District, Hefei City, Anhui Province, China

institute: public health

description: Biological replicate 3 of 3. Cd-treated sperm, harvested at 15 week old after 10 weeks of Cd exposure

hyb_protocol: The labeled RNA samples underwent hybridization on an Arraystar Human mRNA & lncRNA Epitranscriptomic Microarray platform (8×60K format).

scan_protocol: Data acquisition was performed with an Agilent G2505C Scanner, followed by feature extraction using Agilent Feature Extraction software (v11.0.1.1).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: The use of the arraystar super RNA labeling kit resulted in the labeling of “IP” and “Sup” RNAs with Cy5 and Cy3, respectively.

growth_protocol: All mice were raised in standard conditions (20–25 ℃ environment temperature, 50–60% air humidity and 12-h light/dark cycle)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Male C57 mice at 5 weeks of age were randomly assigned to two groups. One group was supplied with control drinking water for 10 weeks, while the other group was exposed to 100 mg/L CdCl2 via drinking water for 10 weeks. Sperm were subsequently collected for analysis when the mice reached 15 weeks of age.

tag: gender

value: 15 weeks old

tag: fraction

value: IP

value: Sup

value: Sperm


title: Patient_12_Baseline

description: Library name: Patient_12_Baseline

value: tumor


title: Patient_13_Baseline

description: Library name: Patient_13_Baseline


title: cd2

description: Biological replicate 2 of 3. Cd-treated sperm, harvested at 15 week old after 10 weeks of Cd exposure

value: Male


title: KO_d2_replicate2

value: 4OHT for 2 days


title: cd1

description: Biological replicate 1 of 3. Cd-treated sperm, harvested at 15 week old after 10 weeks of Cd exposure


title: Medial preoptic area, 50 ug/kg Mixed BP, Female, rep1

description: Library name: 39F1

value: Medial preoptic area


title: KO_d4_replicate3

value: Nudt21 KO


title: Patient_13_C2D8

description: Library name: Patient_13_C2D8


title: Patient_17_C2D8

description: Library name: Patient_17_C2D8


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep2

description: Library name: 38M1


title: C3

description: Biological replicate 3 of 3. Control sperm, untreated, harvested at 15 week old.


title: Medial preoptic area, Corn Oil, Female, rep1

description: Library name: 33F1


title: RNA-seq NRDE2 KD replicate 3

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

institute: UMR9002 CNRS-UM

description:
Library name: NRDE2 replicate3
rep3

data_processing:
Raw reads were aligned to the human genome (GRCh38, Ensembl v84) using STAR aligner.
PCR duplicates were removed using SAMtools rmdup.
Intronic retention analysis was performed using IRFinder.
Read counts were quantified with featureCounts (GTF annotation: GRCh38 v84).
Differential gene expression analysis performed using DESeq2 (R/Bioconductor).
Differential intron retention analysis between NRDE2 and Control conditions performed using IRFinder/DESeq2.
Assembly: Homo sapiens GRCh38, Ensembl annotation release 84.
Supplementary files format and content: BAM files (sorted by genomic coordinates)
Supplementary files format and content: gene count tables (CSV)
Supplementary files format and content: differential expression results (TSV)
Supplementary files format and content: intron retention metrics and statistical comparisons  (IRFinder output TXT, DESeq2 TSV)

source_name: HeLa Cells

growth_protocol: HeLa cells were grown in DMEM + 10% FCS and antibiotics at 37°C + 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol. Paired end sequencing of polyA+ selected mRNA (20M clean reads per sample, 125 bp reads) was carried out.
Libraries were prepared by Beijing Genome Institute.

treatment_protocol: Cells were treated with lentiviral particles expressing shCon or shNRDE2. Samples were comllected 5 days post-transduction.

value: HeLa Cells

value: epithelial cell

value: NRDE2 KD


title: Floxed_d0_replicate3

value: Nudt21 floxed

value: Etoh for 4 days


title: C1

description: Biological replicate 1 of 3. Control sperm, untreated, harvested at 15 week old.


title: Medial preoptic area, 150 ug/kg Mixed BP, Female, rep1

description: Library name: 63F1

value: Postnatal day 10

value: 150 ug/kg Mixed BP

value: Female


title: RNA-seq NRDE2 KD replicate 2

description:
Library name: NRDE2 replicate2
rep2


title: Medial preoptic area, 50 ug/kg BPA, Female, rep2

description: Library name: 93F1

value: 50 ug/kg BPA


title: Floxed_d0_replicate2

value: Esophagus

value: Esophageal basal cells


title: C2

description: Biological replicate 2 of 3. Control sperm, untreated, harvested at 15 week old.

value: 15 weeks old

value: IP

value: Sup

value: Sperm


title: Patient_3_C2D8

description: Library name: Patient_3_C2D8

value: tumor


title: Floxed_d0_replicate1


title: RNA-seq NRDE2 KD replicate 1

description:
Library name: NRDE2 replicate1
rep1


title: Patient_3_Baseline

description: Library name: Patient_3_Baseline


title: KO_d2_replicate3

value: Nudt21 KO

value: 4OHT for 2 days


title: Medial preoptic area, 50 ug/kg BPA, Female, rep1

description: Library name: 68F1

value: Medial preoptic area


title: B15_sorted monocytes, S. aureus cell free supernatants

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Library name: B15_cfs

data_processing:
Basecalling and demultiplexing were performed using Illumina bcl2fastq (v2.20.0).
Sequence data quality was assessed using FastQC (v0.11.8).
Counts for each gene were estimated using featureCounts (v1.5.1).
Reads were aligned to the Ensembl GRCm38 reference genome using STAR (v2.7.9a).
Assembly: GRCh38/hg38
Supplementary files format and content: Two tab-delimited text files together contain raw counts for all samples.

source_name: blood

extract_protocol:
total RNA was extracted using mirVanaTM Isolation kit
RNA library followed the Illumina Stranded mRNA Prep Ligation protocol by Illumina: mRNA isolation, cDNA synthesis, anchor ligation, library amplification, indexing. Library yield and quality were checked with Qubit (Thermo Fisher Scientific) and the Agilent TapeStation

value: blood

value: monocytes

value: CFS


title: KO_d2_replicate1


title: Patient_5_C2D8

description: Library name: Patient_5_C2D8


title: Patient_5_Baseline

description: Library name: Patient_5_Baseline


title: RNA-seq Control replicate 2

description:
Library name: Control replicate2
rep2

value: HeLa Cells

value: epithelial cell

value: Control


title: Δyjbl-30´zinc-R3

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
Pipeline for RNAseq analysis CLC Genomics Workbench 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics Workbench 22.0.2 (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to NC_011916.1 using CLC Genomics Workbench 22.0.2 (parameters-mismatch cost:2 insertion cost:3 deletion cost:3 lenght fraction: 0.8 similarity fraction: 0.8 strand specific:rev)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NCBI Reference Sequence: NC_011916.1
Supplementary files format and content: xlsx file including TPM from each sample

organism: Caulobacter vibrioides

source_name: bacterial cell

growth_protocol: Growth in PYE-Medium, 200 rpm shaking, 30 °C until OD 0.4

extract_protocol:
RNA extraction using the Hot Phenol methode, following DNase treatment/Pci extraction, rRNAdepletion and mRNA purification
RNA libraries for RNAseq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer´s protocol

treatment_protocol: 80 µM ZnSo4/Mock 30´

value: {delta}yjbl

value: bacterial cell

value: 80 µM ZnSo4


title: Patient_17_Baseline

description: Library name: Patient_17_Baseline


title: B15_sorted monocytes, unstimulated

description: Library name: B15_uns

value: Unstimulated


title: Δyjbl-30´zinc-R2


title: OS02-shControl-2

city: Beijing

first: hanyuchen

last: han

address: 27 Taiping Rd

institute: Beijing Institute of biotechnology

description: Library name: SAMPLE4

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level feature: Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: bone

value: osteosarcoma cells


title: B14_sorted monocytes, S. aureus cell free supernatants

description: Library name: B14_cfs


title: Medial preoptic area, 50 ug/kg Mixed BP, Male, rep1

description: Library name: 100M1

value: Postnatal day 10

value: 50 ug/kg Mixed BP

value: Male


title: Δyjbl-30´zinc-R1


title: OS01-shControl-1

description: Library name: SAMPLE3


title: RML Vx, S4 challenge d8 not protected

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

description:
Library name: 16054
10x Genomics

data_processing:
cellranger mkfastq v. 3.0.2
cellranger count v. 3.0.2
Assembly: refdata-cellranger-mm10-1.2.0
Supplementary files format and content: filtered tab delimited values and matrix files

source_name: Lung

extract_protocol:
10X Genomics v3.1 3' Kit
10X Genomics v3.1 3' Kit

value: Lung

value: LVS Vx + Ftt d8 not protected


title: B14_sorted monocytes, unstimulated

description: Library name: B14_uns

value: blood


title: B14_sorted monocytes, SEA

description: Library name: B14_sea

value: monocytes

value: SEA


title: Δyjbl-30´control-R2

value: mock


title: Δyjbl-30´control-R3


title: RML Vx, S4 challenge d8 protected

description:
Library name: 16053
10x Genomics

value: LVS Vx + Ftt d8 protected


title: OS91-shGREM1-1

description: Library name: SAMPLE1


title: RNA-seq Control replicate 3

description:
Library name: Control replicate3
rep3

value: HeLa Cells

value: epithelial cell

value: Control


title: B15_sorted monocytes, SEA

description: Library name: B15_sea


title: B11_sorted monocytes, S. aureus cell free supernatants

description: Library name: B11_cfs

value: CFS


title: Naïve, Bp challenge d8

description:
Library name: 16051
10x Genomics

value: Naïve + Bp d8


title: B11_sorted monocytes, SEA

description: Library name: B11_sea


title: B11_sorted monocytes, unstimulated

description: Library name: B11_uns

value: Unstimulated


title: hMAN co-transplantation 1

city: Piscataway

first: Ziyuan

last: Ma

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description: 10x Genomics 3' Gex v3.1

data_processing:
The demuiltiplexing, barcoded processing, gene counting were made using the Cell Ranger (version v7.1.0) using the Human (GRCh38) and mouse (mm10) reference - 2020-A (10x Genomics).
Assembly: Human (GRCh38) and mouse (mm10) reference - 2020-A
Supplementary files format and content: Filtered cell-associated barcodes in MEX format (feature-barcode matrices).

source_name: Brain

growth_protocol: Human primitive macrophage progenitors (PMPs) were generated from the control hiPSC and hESC lines using a previously established protocol. Yolk sac embryoid bodies (YS-EBs) were generated by treating them with mTeSR 1 medium (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To induce myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). Four to six weeks after plating, human PMPs emerged in the supernatant and continued to be produced for more than three months. Human primitive neural progenitor cells (pNPCs) were generated from hiPSCs and hESCs. The pNPCs were cultured in a medium consisting of a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) plus GlutaMax (Gibco) and DMEM/F12 (Hyclone), supplemented with 1x N2, 1x B27-RA (Thermo Fisher Scientific), FGF2 (20 ng/ml, Peprotech), CHIR99021 (3 µM, Biogems), human leukemia inhibitory factor (hLIF, 10 ng/ml, Millipore), SB431542 (2 µM), and ROCK inhibitor Y-27632 (10 µM, Tocris). The pNPCs were passaged with TrypLE Express (Thermo Fisher Scientific) once per week. PMPs and pNPCs were collected from the supernatant and suspended at a concentration of 100,000 cells/µl in PBS. Cells were then injected into the brains of P0 Rag2−/− IL2rγ−/− hCSF1KI immunodeficient mice. The transplantation sites were bilateral from the midline = ±1.0 mm, posterior from bregma = −2.0 mm, and dorsoventral depths = −1.5 and −1.2 mm. The pups were placed in ice for 4-5 mins to anesthetize and then injected with 0.5 μl of cells into each site (four sites total) using a digital stereotaxic device (David KOPF Instruments) that was equipped with a neonatal mouse adapter (Stoelting).

extract_protocol:
Chimeric mice were anesthetized and perfused with cold DPBS (1x). Brains were dissected and dissociated using Adult Brain Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. Human cells were isolated by mouse cell depletion kit (Miltenyi) following the manufacturer’s protocols. Isolated cell suspension then loaded to the Chromium controller for mRNA barcoding and reverse transcription using Chromium Next GEM Single Cell 3' Kit v3.1.
scRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3' Kit v3.1 and Dual Index Kit TT Set A, following the manufacturer’s protocols. Quality control of the scRNA-seq libraries were performed by Agilent 2100 Bioanalyzer, and libraries were sequenced in Novaseq 6000 S4 flow cells.

value: Brain

value: Control WT

value: PMP + pNPC


title: hMAN co-transplantation 2

description: 10x Genomics 3' Gex v3.1


title: Naïve, S4 challenge d2

description:
Library name: 16049
10x Genomics

value: Naïve + Ftt d2


title: Wt-30´zinc-R2

value: wt

value: bacterial cell

value: 80 µM ZnSo4


title: RNA-seq Control replicate 1

description:
Library name: Control replicate1
rep1


title: RML Vx, S4 challenge d2

description:
Library name: 16050
10x Genomics

value: Lung

value: LVS Vx + Ftt d2


title: pNPC_WT_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (version 0.6.10)
Trimmed sequence reads were mapped to GRCh38 reference genome and GENCODE v44 primary assembly using STAR (version 2.7.11a).
Read count extraction and normalization were performed using RSEM (version 1.3.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts, fragments per kilobase per million (FPKM), and transcripts per kilobase million (TPM) for each sample from RSEM output.

source_name: Human ESC differentiated pNPC cells

growth_protocol: Human primitive neural progenitor cells (pNPCs) were generated from hiPSCs and hESCs. The pNPCs were cultured in a medium consisting of a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) plus GlutaMax (Gibco) and DMEM/F12 (Hyclone), supplemented with 1x N2, 1x B27-RA (Thermo Fisher Scientific), FGF2 (20 ng/ml, Peprotech), CHIR99021 (3 µM, Biogems), human leukemia inhibitory factor (hLIF, 10 ng/ml, Millipore), SB431542 (2 µM), and ROCK inhibitor Y-27632 (10 µM, Tocris). The pNPCs were passaged with TrypLE Express (Thermo Fisher Scientific) once per week.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocols.

value: Human ESC differentiated pNPC cells

value: H1 ESC line

value: Primitive Neural Progenitor Cells


title: B93_isolated monocytes, S. aureus cell-free supernatants

description: Library name: B93_cfs

value: blood

value: monocytes


title: Wt-30´zinc-R1


title: RML Vx, no challenge d2

description:
Library name: 16048
10x Genomics

value: LVS Vx d0


title: B93_isolated monocytes, SEA

description: Library name: B93_sea

value: SEA


title: pNPC_WT_rep2


title: Bp Vx, Bp challenge d8

description:
Library name: 16052
10x Genomics

value: Bp Vx + Bp d8


title: OS92-shGREM1-2

description: Library name: SAMPLE2

value: bone

value: osteosarcoma cells


title: B93_isolated monocytes, unstimulated

description: Library name: B93_uns

value: Unstimulated


title: Bp Vx, Bp challenge d2

description:
Library name: 16047
10x Genomics

value: Bp Vx + Bp d2


title: Wt-30´control-R3

value: wt

value: mock


title: Wt-30´control-R2

value: bacterial cell


title: pNPC_WT_rep1


title: Δyjbl-30´control-R1

value: {delta}yjbl


title: 53098

city: Monrovia

first: Ling

last: Li

state: CA

address: 1218 S 5TH AVE, MONROVIA

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

data_processing:
Real-Time Analysis (RTA) v3.4.4 software was used for base calling and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.
Sequences were aligned to GRCh38 using STAR with default settings
Gene expression level of Ensembl coding genes were quantified using in-house R scripts
Assembly: GRCh38
Supplementary files format and content: tab delimited text file gene expression counts

source_name: bone marrow

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from tissue following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
KAPA RNA HyperPrep with RiboErase protocol to generate sequencing libraries
stranded ribosomal RNA depletion RNA-seq

value: bone marrow

value: PDX cells


title: Wt-30´control-R1


title: Naïve, Bp challenge d2

description:
Library name: 16046
10x Genomics

value: Lung

value: Naïve + Bp d2


title: B92_isolated monocytes, S. aureus cell-free supernatants

description: Library name: B92_cfs

value: blood

value: CFS


title: Bp Vx, no challenge d2

description:
Library name: 16045
10x Genomics

value: Bp Vx d0


title: Wt-30´zinc-R3

value: 80 µM ZnSo4


title: B92_isolated monocytes, SEA

description: Library name: B92_sea

value: monocytes

value: SEA


title: 53097


title: Tgfa KO 22mo-39016bl

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

description: Library name: 39016bl

data_processing:
Raw sequence reads were trimmed to remove possible adapter sequences and low-quality reads using Trimmomatic v.0.36 (PMID: 24695404). The trimmed reads were mapped to the mouse GRCh38 reference genome using the STAR aligner v.2.5.2b (PMID: 23104886). Reads mapping to annotated genes were quantified using featureCounts from the Subread package v.1.5.2 (PMID: 23558742).
Assembly: GRCm38
Supplementary files format and content: counts.txt: Tab-delimited text files include raw read counts

source_name: epidermis

extract_protocol:
Total RNA was isolated with Trizol reagent and then with Zymo Direct-zol RNA Mini Prep Plus and DNase treatment
RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA), and loaded to Illumina NovaSeq 6000 system for 150bp paired-end sequencing.

value: epidermis

value: keratinocytes

value: Tgfa KO


title: Tgfa KO 22mo-39017bl

description: Library name: 39017bl


title: 53094

value: WT


title: IFA_Tamiflu-IFNAR_12_4

data_processing:
Aligned to the mouse (GRcm39) plus influenza A (GCF_000865725.1) genome using STAR aligner
Read counting was perfromed using featureCounts
Assembly: GRcm39 + GCF_000865725.1
Supplementary files format and content: Tab deliminated text file with raw counts table with rows as genes and columns as samples.

extract_protocol:
Right inferior lobes of the lungs were collected into Trizol and snap frozen. After thawing, RNA was extracted using Qiagen Nucleic Acid Isolation Service
Libraries were constructed with 1ug of RNA using the Illumina Tru-Seq Stranded mRNA kit.

treatment_protocol: Animals were treated with PBS (control), Tamiflu, Tamiflu plus anti-IFNAR, or Tamiflu plus anti-CD8a at 4 days post infection

tag: virus

value: IFA

value: Tamiflu-IFNAR


title: Naïve d2

description:
Library name: 16044
10x Genomics

value: Naïve d0


title: 53093

value: bone marrow


title: B92_isolated monocytes, unstimulated

description: Library name: B92_uns

value: Unstimulated


title: HEK_c3_5_4

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

institute: University of Veterinary Medicine, Vienna

description:
Library name: HEK_c3_5_4
HEK_normalized_expression.tsv

data_processing:
After pre-processing with prinseq-lite (v0.20.4), raw sequencing files (FASTQ format) were aligned to the human or mouse reference genome (GRCh38 and GRCm38) using STAR (v2.7.9a) with default settings.
Final processing was performed using SAMtools (v1.4) and counts per gene were obtained utilizing featureCounts (v2.0.3).
Differential expression analysis was done using R package DESeq2 (v1.46.0) and time-series plots illustrating dynamic expression changes over time were generated using the maSigPro R library (v1.76.0).
Assembly: HEK293T cells: GRCh38, murine GFP-NUP98::KDM5A AML cells: GRCm38
Supplementary files format and content: For HEK293T cells: tab-delimited file with normalized counts per gene
Supplementary files format and content: For murine GFP-NUP98::KDM5A-driven AML cells: tab-delimited file with normalized counts per gene

source_name: HEK293T NUP98::KDM5A Cas9

extract_protocol:
RNA was isolated using the NEB Monarch Total RNA Miniprep Kit (NEB).
For HEK293T cells: Sequencing libraries were generated using the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina.
For murine GFP-NUP98::KDM5A-driven AML cells: Sequencing libraries were generated by Novogene.

value: HEK293T NUP98::KDM5A Cas9


title: Tgfa KO 22mo-39015bl

description: Library name: 39015bl


title: IFA_Tamiflu-IFNAR_12_3

value: Lung


title: HEK_c3_5_3

description:
Library name: HEK_c3_5_3
HEK_normalized_expression.tsv


title: Tgfa KO 22mo-38505br

description: Library name: 38505br


title: IFA_Tamiflu-IFNAR_12_2


title: Tgfa KO 22mo-38504br

description: Library name: 38504br


title: IFA_Tamiflu-CD8_12_4


title: HEK_c3_5_1

description:
Library name: HEK_c3_5_1
HEK_normalized_expression.tsv


title: IFA_Tamiflu-IFNAR_12_1


title: P4O2 COVID-19, study visit 1, patient 40

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
S4.300 (PE150)
To remove low quality reads/read-ends and sequencing adapters, readouts were trimmed using Trim-Galore v0.6.10, which acts as a wrapper around FastQC v0.12.1 and cutadapt v4.3
Transcripts were aligned against the human genome (GRCh38.p14) using Salmon v1.10.1
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: nasal epithelial cells

extract_protocol:
RNA was harvested using the Bioline ISOLATE II mini kit.
KAPA mRNA Hyperprep capture according to the manufacturer's protocol

value: nasal epithelial cells

tag: time

value: 3-6 months post-COVID

tag: visit

value: study visit 1

tag: individual

value: patient 40

tag: disease state

value: long COVID


title: WT 22mo-38382br

description: Library name: 38382br

tag: tissue


title: P4O2 COVID-19, study visit 1, patient 39

value: patient 39


title: IFA_Tamiflu-CD8_12_3


title: HEK_WT_A1061_4

description:
Library name: HEK_WT_A1061_4
HEK_normalized_expression.tsv

source_name: HEK293T Cas9

value: HEK293T Cas9


title: WT 22mo-38380br

description: Library name: 38380br

value: epidermis

value: keratinocytes


title: P4O2 COVID-19, study visit 1, patient 38

value: patient 38


title: HEK_WT_A1061_3

description:
Library name: HEK_WT_A1061_3
HEK_normalized_expression.tsv

value: WT


title: IFA_Tamiflu-CD8_12_2

value: IFA


title: WT 22mo-38205br

description: Library name: 38205br


title: HEK_WT_A1061_2

description:
Library name: HEK_WT_A1061_2
HEK_normalized_expression.tsv


title: HEK_WT_A1061_1

description:
Library name: HEK_WT_A1061_1
HEK_normalized_expression.tsv


title: P4O2 COVID-19, study visit 2, patient 16

value: 12-18 months post-COVID

value: study visit 2

value: patient 16


title: P4O2 COVID-19, study visit 1, patient 37

value: patient 37


title: IFA_Tamiflu-CD8_12_1

value: Lung


title: P4O2 COVID-19, study visit 2, patient 49

value: nasal epithelial cells

value: patient 49


title: P4O2 COVID-19, study visit 1, patient 36

value: 3-6 months post-COVID

value: study visit 1

value: patient 36


title: HEK_c3_5_2

description:
Library name: HEK_c3_5_2
HEK_normalized_expression.tsv

value: HEK293T NUP98::KDM5A Cas9


title: IFA_Tamiflu_12_4

value: Tamiflu


title: IFA_Tamiflu_12_3


title: Kidney_HFD-IRI_2

city: Indianapolis

first: Wenjun

state: IN

address: 1044 W. Walnut Street, R4 W116

institute: Indiana University School of Medicine

description: Library name: KC416Kidney_HFD-IRI

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.42.4) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: UCSC mm10
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: Kidney

growth_protocol: 10-week-old C57BL/6 mice (n=3, each group) were housed in sterile, individual ventilated cages under a 12-hour light/dark cycle with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Thermo Science) according to manufacturer’s instruction.
Illumina mRNA

treatment_protocol: The mice were fed with either control diet (ND: 20% protein, 10% fat, 70% carbohydrates) or high fat diet (HFD: 12.6% protein, 29% fat, 46.2% carbohydrates; TD 160785, Envigo) for 12 weeks before subjected to the hepatic ischemia-reperfusion injury (IRI) by occluding the  segment of hepatic pedicle supplying the left lateral and right median liver lobes using a non-traumatic micro-aneurysm clamp  for 60 minutes or Sham procedure.  Total 4 groups of: HFD_IRI, HFD_sham, ND_IRI, ND_sham. The mouse liver and kidney tissue were harvested in 6hrs after ischemia injury.

value: Kidney

value: HFD+hIRI

tag: batch


title: Kidney_HFD-IRI_1

description: Library name: KC415Kidney_HFD-IRI


title: P4O2 COVID-19, study visit 1, patient 35

value: patient 35

value: long COVID


title: Kidney_HFD-IRI_3

description: Library name: KC418Kidney_HFD-IRI

value: WT