title: Valid_TFs_RNA_batch3-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Kdm6a-5.0-1

status: Public on Jul 23 2025

type: SRA

city: Shanghai

first: Jincan

last: He

address: siping road 1239

country: China

institute: Tongji university

library_source: transcriptomic

data_processing:
Sequencing reads were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: comma-delimited text files with normalized abundance for every gene and every sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Epi

growth_protocol: Natural mated embryos were dissected from decidua. Peri-implantation stage embryos for 3D in vitro culture were prepared following a previously published protocol (Li et al., Natl Sci Rev.2023).

extract_protocol:
Approximately 10-100 cells per sample were lysed, and cDNA synthesis was performed directly on the cytoplasmic lysate. Three biological replicates were performed per group. The resulting cDNA was amplified for 17 cycles to generated a full-length cDNA library.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

treatment_protocol: Single cells were collected from E3.5 pre-implantation embryos by fist removing zone pellucida with 20mg/ml PE (Pronase E, Sigma). Embryos were then incubated in Ca2+-free CZB medium and gently pipetting with a fire-polished glass tube to obtain single cells. For peri-implantation embryos (E3.5-E5.5), single cells from different lineages (EPI, PE, and EXE) were collected by separating the embryos from decidua either in vivo or from Matrigel in vitro. The embryos were digested with 0.05% TE (Trypsin-EDTA, Gibco, 25300062) to obtain single cells. All cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals, USA) solution before used.

tag: tissue

value: Epi

tag: genotype

value: Kdm6a KO

tag: developmental stage


title: Valid_TFs_RNA_batch3-Epi_Atrx-5.0-1

value: Atrx KO


title: Valid_TFs_RNA_batch2-Epi_Cxxc1-5.0-1

value: Cxxc1 KO


title: Valid_TFs_RNA_batch10-Epi_Mta2-5.0-1

value: Mta2 KO


title: Valid_TFs_RNA_batch2-Epi_Mcrs1-5.0-1

value: Mcrs1 KO


title: Valid_TFs_RNA_batch2-Epi_Ets2-5.0-3

value: Ets2 KO


title: Valid_TFs_RNA_batch2-Epi_Control-5.0-1

value: Wild type


title: Valid_TFs_RNA_batch2-Epi_Ascl2-5.0-2

value: Ascl2 KO


title: Valid_TFs_RNA_batch2-Epi_Lmo2-5.0-2

value: Lmo2 KO


title: Valid_TFs_RNA_batch3-Epi_Atrx-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Ets2-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Elf5-5.0-2

value: Elf5 KO


title: Valid_TFs_RNA_batch10-Epi_Mta2-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Ets2-5.0-1


title: Valid_TFs_RNA_batch2-Epi_Suz12-5.0-2

value: Suz12 KO


title: Valid_TFs_RNA_batch2-Epi_Lmo2-5.0-1


title: Valid_TFs_RNA_batch2-Epi_Elf5-5.0-1


title: Valid_TFs_RNA_batch2-Epi_Mcrs1-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Suz12-5.0-1


title: Valid_TFs_RNA_batch10-Epi_Mta2-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Mcrs1-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Cxxc1-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Suz12-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch2-Epi_Elf5-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Lmo2-5.0-3


title: Valid_TFs_RNA_batch2-Epi_Cxxc1-5.0-3


title: Valid_TFs_RNA_batch10-Epi_Mbd3-5.0-3

value: Mbd3 KO


title: Valid_TFs_RNA_batch2-Epi_Ascl2-5.0-1


title: Valid_TFs_RNA_batch10-Epi_Mbd3-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Junb-5.0-3

value: Junb KO


title: Valid_TFs_RNA_batch10-Epi_Junb-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Hdac13-5.0-1

value: Hdac1 Hdac3 double KO


title: Valid_TFs_RNA_batch10-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch10-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Gtf2b-5.0-1

value: Gtf2b KO


title: Valid_TFs_RNA_batch10-Epi_Hdac13-5.0-3


title: Valid_TFs_RNA_batch10-Epi_Gtf2b-5.0-2


title: Valid_TFs_RNA_batch1-Epi_Ss18-5.0-1

value: Ss18 KO


title: Valid_TFs_RNA_batch10-Epi_Chd4-5.0-1

value: Epi

value: Chd4 KO


title: Valid_TFs_RNA_batch10-Epi_Hsf2-5.0-2

value: Hsf2 KO


title: Valid_TFs_RNA_batch10-Epi_Hdac13-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Fos-5.0-3

value: Fos KO


title: Valid_TFs_RNA_batch1-Epi_Ssrp1-5.0-3

value: Ssrp1 KO


title: Valid_TFs_RNA_batch10-Epi_Fos-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Junb-5.0-1


title: Valid_TFs_RNA_batch10-Epi_Hsf2-5.0-3


title: Valid_TFs_RNA_batch1-Epi_Ssrp1-5.0-1


title: Valid_TFs_RNA_batch10-Epi_Fos-5.0-1


title: Valid_TFs_RNA_batch1-Epi_Ss18-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch10-Epi_Chd4-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Chd4-5.0-3


title: Valid_TFs_RNA_batch1-Epi_Snai1-5.0-3

value: Snai1 KO


title: Valid_TFs_RNA_batch1-Epi_Ss18-5.0-3


title: Valid_TFs_RNA_batch10-Epi_Mbd3-5.0-1


title: Valid_TFs_RNA_batch1-Epi_Snai1-5.0-2


title: Valid_TFs_RNA_batch10-Epi_Gtf2b-5.0-3


title: Valid_TFs_RNA_batch10-Epi_Hsf2-5.0-1


title: Valid_TFs_RNA_batch1-Epi_Ssrp1-5.0-2


title: Valid_TFs_RNA_batch1-Epi_Snai1-5.0-1


title: Valid_TFs_RNA_batch1-Epi_Nelfb-5.0-3

value: Nelfb KO


title: Valid_TFs_RNA_batch1-Epi_Aurkb-5.0-2

value: Aurkb KO


title: Valid_Suz12Eed_RNA-PrE_Suz12EED-5.0-3

source_name: PrE

value: PrE

value: Suz12 Eed double KO


title: Valid_TFs_RNA_batch1-Epi_Control-5.0-1

value: Wild type


title: Valid_TFs_RNA_batch1-Epi_Aurkb-5.0-1


title: Valid_Suz12Eed_RNA-Epi_Suz12EED-5.0-2


title: Valid_TFs_RNA_batch1-Epi_Aurkb-5.0-3


title: Valid_Suz12Eed_RNA-PrE_Control-5.0-3


title: Valid_Suz12Eed_RNA-Epi_Suz12EED-5.0-3


title: Valid_Suz12Eed_RNA-PrE_Control-5.0-1


title: Valid_TFs_RNA_batch1-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch1-Epi_Nelfb-5.0-2


title: Valid_Suz12Eed_RNA-PrE_Suz12EED-5.0-1


title: Valid_Suz12Eed_RNA-Epi_Suz12EED-5.0-1


title: Valid_Suz12Eed_RNA-Epi_Control-5.0-3


title: Valid_Suz12Eed_RNA-Epi_Control-5.0-1


title: Valid_GSK_RNA-Epi_Gsk50-5.0-2

value: GSK treatment


title: Valid_TFs_RNA_batch1-Epi_Nelfb-5.0-1


title: Valid_Suz12Eed_RNA-PrE_Control-5.0-2


title: Valid_GSK_RNA-Epi_Gsk50-5.0-1


title: Valid_Suz12Eed_RNA-Epi_Control-5.0-2


title: Valid_GSK_RNA-Epi_Control-5.0-3


title: Valid_GSK_RNA-Epi_Control-5.0-1


title: Valid_EB_RNA-EB_ZB11-d3-1

source_name: EB

value: EB

value: Zbtb17 KO


title: Valid_EB_RNA-EB_ZB11-d3-2


title: Valid_TFs_RNA_batch1-Epi_Control-5.0-3


title: Valid_Suz12Eed_RNA-PrE_Suz12EED-5.0-2


title: Valid_EB_RNA-EB_ZB11-d2-2


title: Valid_GSK_RNA-Epi_Gsk50-5.0-3


title: Valid_EB_RNA-EB_ZB11-d2-1


title: Valid_EB_RNA-EB_ZB11-d1-2


title: Valid_EB_RNA-EB_ZB11-d0-2


title: Valid_EB_RNA-EB_ZB11-d1-1


title: Valid_EB_RNA-EB_WT-d3-1


title: Valid_EB_RNA-EB_WT-d1-1


title: WT_RNA-VE-5.5_invitro-2

source_name: VE

extract_protocol:
Approximately 10 -100 cells per sample were lysed, and cDNA synthesis was performed directly on the cytoplasmic lysate. Three biological replicates were performed per group. The resulting cDNA was amplified for 17 cycles to generated a full-length cDNA library. Sequencing libraries were prepared using the KAPA Hyper Prep kit according to the manufacturer’s instructions.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

value: VE

value: wild type


title: WT_RNA-VE-5.5_invitro-1


title: Valid_EB_RNA-EB_WT-d3-2


title: Valid_EB_RNA-EB_WT-d0-1


title: Valid_EB_RNA-EB_WT-d1-2


title: WT_RNA-VE_ExE-5.5_invivo-3


title: WT_RNA-VE_ExE-5.5_invivo-1


title: WT_RNA-TGC-5.5_invitro-4

source_name: TGC

value: TGC


title: WT_RNA-VE_Epi-5.5_invivo-1


title: Valid_GSK_RNA-Epi_Control-5.0-2

value: Epi


title: WT_RNA-VE_ExE-5.5_invivo-2


title: WT_RNA-VE_Epi-5.5_invivo-2


title: WT_RNA-TGC-5.5_invitro-3


title: WT_RNA-TGC-5.5_invitro-2


title: WT_RNA-TGC-5.5_invitro-1


title: WT_RNA-TGC-4.75-3


title: WT_RNA-TGC-4.75-2


title: WT_RNA-TE-4.5-3

source_name: TE

value: TE


title: Valid_EB_RNA-EB_WT-d0-2


title: WT_RNA-TGC-4.75-1


title: Valid_EB_RNA-EB_WT-d2-1


title: Valid_EB_RNA-EB_ZB11-d0-1


title: Valid_EB_RNA-EB_WT-d2-2


title: WT_RNA-TE-4.5-2


title: WT_RNA-TE-3.5-2


title: WT_RNA-TE-4.5-1


title: WT_RNA-TE-3.5-3


title: WT_RNA-PrE-5.25-1


title: WT_RNA-TE-3.5-1


title: WT_RNA-PrE-5.25-3


title: WT_RNA-PrE-5.25-2


title: WT_RNA-PrE-5.0-3


title: WT_RNA-PrE-4.75-3


title: WT_RNA-PrE-5.0-1


title: WT_RNA-PrE-4.75-2


title: WT_RNA-PrE-4.75-1


title: WT_RNA-PrE-4.5-2


title: WT_RNA-PrE-4.5-3


title: WT_RNA-PrE-4.5-1


title: WT_RNA-ICM-3.5-2

source_name: ICM

value: ICM


title: WT_RNA-ICM-3.5-3


title: WT_RNA-ExE-5.5_invivo-2

source_name: ExE

value: ExE


title: WT_RNA-ICM-3.5-1


title: WT_RNA-ExE-5.5_invitro-3


title: WT_RNA-ExE-5.5_invivo-1


title: WT_RNA-ExE-5.5_invitro-1


title: WT_RNA-VE-5.5_invitro-3


title: WT_RNA-ExE-4.75-2


title: WT_RNA-ExE-5.5_invitro-2


title: WT_RNA-ExE-4.75-3


title: WT_RNA-ExE-4.75-1


title: WT_RNA-PrE-5.0-2


title: WT_RNA-Epi-5.5_invivo-2


title: WT_RNA-Epi-5.5_invivo-1


title: WT_RNA-Epi-5.5_invitro-3


title: WT_RNA-Epi-5.5_invitro-2


title: WT_RNA-Epi-5.5_invitro-1


title: WT_RNA-Epi-5.0-3


title: WT_RNA-Epi-5.25-3


title: WT_RNA-Epi-5.25_invivo-2


title: WT_RNA-Epi-5.25_invivo-1


title: WT_RNA-Epi-5.25-1


title: WT_RNA-Epi-5.25-2


title: WT_RNA-Epi-5.25_invivo-3


title: WT_RNA-Epi-5.0_invivo-1


title: WT_RNA-Epi-5.0-1


title: WT_RNA-Epi-5.0_invivo-3


title: WT_RNA-Epi-5.0_invivo-2


title: WT_RNA-Epi-4.75-3


title: WT_RNA-Epi-4.75-2


title: WT_RNA-Epi-4.5-3


title: WT_RNA-Epi-4.5-2


title: WT_RNA-Epi-4.75-1


title: Liver_HFHCD_Hete_rep3

first: Yuanwen

last: Chen

state: None Selected

address: No.221 West Yan'an Road

institute: Huadong Hospital

data_processing:
Raw reads in fastq format of RNA-seq were firstly processed using Trimmomatic (v0.36) to remove low-quality reads, then the remaining clean reads were aligned to the mouse genome (GRCm39) using hisat2 (v2.2.1.0) with the default parameter settings.  Reads were quantified using htseq-count (v0.9.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: Liver

extract_protocol:
Total RNA was isolated via TRIzol reagent according to the manufacturer’s protocol and used for subsequent RNA-seq analysis. 500 ng RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were subsequently constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Liver

tag: treatment

value: HFHCD


title: Liver_HFHCD_WT_rep3


title: Liver_HFHCD_Hete_rep1


title: Liver_HFHCD_Hete_rep2


title: Liver_HFHCD_WT_rep1


title: CEBPB_KC_HFHCD

library_source: genomic

data_processing:
To generate aligned BAM files, reads were aligned to mm10 genome using HISAT2 (v2.2.1) with default settings, and PCR duplicates were removed using command rmdup in samtools (v1.10). Deeptools (v3.3.2) was used to generate the read coverage track (command bamCoverage with normalization by RPKM), calculate and visualize of scores per genome regions (command computeMatrix, command plotProfile and plotProfile) and overall similarity between samples (command multiBigwigSummary and plotCorrelation).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Kupffer cell

extract_protocol:
NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, Shanghai, China, N259) was used for tagmented genomic DNA extraction according to the manufacturer’s recommendations.
NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, Shanghai, China, N259) was used for library preparation according to the manufacturer’s recommendations.

tag: cell type

value: Kupffer cell


title: 5xFAD-Dp16

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequence reads were aligned to the mm10 reference genome and gene-level counts obtained using the 10x Genomics Space Ranger pipeline.
Assembly: mm10
Supplementary files format and content: *_tissue_hires_image.png: image of tissue
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market exchange format
Supplementary files format and content: seurat_metadata.csv: Sample and Spot metadata
Library strategy: Spatial Transcriptomics

source_name: whole brain

extract_protocol: Mouse OCT-embedded hemispheres (anteroposterior from bregma: +1 to -2 mm) from each experimental group at 9-months of age, were snap-frozen in isopentane pre-cooled with dry ice and liquid nitrogen. Brains were sectioned on the cryostat at 10 um thickness using a CryoStar NX70 cryostat (ThermoFisher). Sections were prepared according to the Visium Spatial Gene Expression Reagent Kit (10X Genomics, PN-1000187). Sections were fixed in methanol (Sigma) for 30 min at -20 C, then treated for 1 min with isopropanol and air-dried. To stain the tissue, sections were incubated in Mayer s Hematoxylin (Dako) for 7 min at room temperature (RT), then Bluing buffer for 2 min and Eosin (Sigma) for 1 min at RT. After drying, H&E images of sections were taken using an EVOS M7000 Invitrogen microscope (ThermoFisher Scientific).

value: whole brain

tag: Sex

value: male


title: WT_RNA-Epi-4.5-1


title: CEBPB_KC_ND

value: ND


title: 5xFAD


title: Wild-type

value: wild-type C57BL/6J


title: Dp16


title: WT_RNA-Epi-5.0-2


title: HP_5xFAD_Dp16_Tofa_3

description: 5xFAD-Dp16; Tofacitinib-treated; sample 3

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts, normalized fragments-per-kilobase-per-million-mapped (FPKM), or normalized transcripts-per-million-mapped (TPM).

source_name: brain hippocampus

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacture’s protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

treatment_protocol: Tofacitinib = 15mg/kg daily for a month via oral gavage; Sham = 0.5% methylcellulose vehicle daily for a month via oral gavage.

value: brain hippocampus

value: Male

tag: age in_months_post-birth

value: Tofa


title: HP_5xFAD_Dp16_Tofa_4

description: 5xFAD-Dp16; Tofacitinib-treated; sample 4


title: HP_5xFAD_Dp16_Sham_1

description: 5xFAD-Dp16; sham-treated; sample 1

value: Female

value: Sham


title: HP_Dp16_Tofa_4

description: Dp16; Tofacitinib-treated; sample 4


title: HP_Dp16_Tofa_5

description: Dp16; Tofacitinib-treated; sample 5


title: HP_5xFAD_Dp16_Sham_2

description: 5xFAD-Dp16; sham-treated; sample 2


title: HP_5xFAD_Dp16_Tofa_1

description: 5xFAD-Dp16; Tofacitinib-treated; sample 1


title: HP_5xFAD_Dp16_Tofa_2

description: 5xFAD-Dp16; Tofacitinib-treated; sample 2


title: HP_Dp16_Tofa_3

description: Dp16; Tofacitinib-treated; sample 3


title: HP_Dp16_Tofa_2

description: Dp16; Tofacitinib-treated; sample 2


title: HP_Dp16_Sham_2

description: Dp16; sham-treated; sample 2


title: Liver_HFHCD_WT_rep2


title: HP_Dp16_Sham_1

description: Dp16; sham-treated; sample 1


title: HP_Dp16_Sham_3

description: Dp16; sham-treated; sample 3


title: HP_5xFAD_Tofa_4

description: 5xFAD; Tofacitinib-treated; sample 4


title: HP_Dp16_Tofa_1

description: Dp16; Tofacitinib-treated; sample 1


title: HP_5xFAD_Tofa_5

description: 5xFAD; Tofacitinib-treated; sample 5


title: HP_5xFAD_Tofa_6

description: 5xFAD; Tofacitinib-treated; sample 6


title: HP_5xFAD_Sham_3

description: 5xFAD; sham-treated; sample 3


title: HP_5xFAD_Tofa_1

description: 5xFAD; Tofacitinib-treated; sample 1


title: HP_5xFAD_Sham_4

description: 5xFAD; sham-treated; sample 4


title: HP_5xFAD_Sham_2

description: 5xFAD; sham-treated; sample 2


title: HP_WT_Tofa_5

description: Wild-type; Tofacitinib-treated; sample 5


title: HP_WT_Tofa_4

description: Wild-type; Tofacitinib-treated; sample 4


title: HP_WT_Tofa_3

description: Wild-type; Tofacitinib-treated; sample 3


title: HP_WT_Tofa_2

description: Wild-type; Tofacitinib-treated; sample 2


title: HP_WT_Tofa_1

description: Wild-type; Tofacitinib-treated; sample 1


title: HP_WT_Sham_5

description: Wild-type; sham-treated; sample 5


title: HP_WT_Sham_4

description: Wild-type; sham-treated; sample 4


title: HP_WT_Sham_2

description: Wild-type; sham-treated; sample 2


title: HP_WT_Sham_1

description: Wild-type; sham-treated; sample 1


title: HP_5xFAD_Sham_1

description: 5xFAD; sham-treated; sample 1


title: HP_WT_Sham_3

description: Wild-type; sham-treated; sample 3


title: CX_5xFAD_Dp16_Tofa_3

source_name: brain cortex

value: brain cortex


title: HP_5xFAD_Dp16_Sham_4

description: 5xFAD-Dp16; sham-treated; sample 4


title: CX_5xFAD_Dp16_Tofa_4


title: CX_5xFAD_Dp16_Tofa_2


title: CX_5xFAD_Dp16_Tofa_1


title: HP_5xFAD_Tofa_2

description: 5xFAD; Tofacitinib-treated; sample 2


title: CX_5xFAD_Dp16_Sham_4

description: 5xFAD-Dp16; sham-treated; sample 4


title: CX_5xFAD_Dp16_Sham_2

description: 5xFAD-Dp16; sham-treated; sample 2


title: CX_5xFAD_Dp16_Sham_1

description: 5xFAD-Dp16; sham-treated; sample 1


title: CX_Dp16_Tofa_5

description: Dp16; Tofacitinib-treated; sample 5


title: CX_Dp16_Tofa_3

description: Dp16; Tofacitinib-treated; sample 3


title: CX_Dp16_Tofa_2

description: Dp16; Tofacitinib-treated; sample 2


title: CX_Dp16_Tofa_4

description: Dp16; Tofacitinib-treated; sample 4


title: CX_Dp16_Tofa_1

description: Dp16; Tofacitinib-treated; sample 1


title: CX_Dp16_Sham_3

description: Dp16; sham-treated; sample 3


title: CX_Dp16_Sham_2

description: Dp16; sham-treated; sample 2


title: CX_Dp16_Sham_1

description: Dp16; sham-treated; sample 1


title: CX_5xFAD_Tofa_6

description: 5xFAD; Tofacitinib-treated; sample 6


title: CX_5xFAD_Tofa_5

description: 5xFAD; Tofacitinib-treated; sample 5


title: NOVA18_N-Brush_Phase_2_SD7

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of nasal epithelium from influenza infected humans

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

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

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

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from nasal epithlium using Qiagen RNA isolation kit according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Nasal epithelium cells  collected from humans  and stored in RNALater tubes  according to manufacturer's instructions.

value: challenged with influenza

value: Nasal epithelium

tag: study group

value: Vaccinated

tag: study date


title: CX_5xFAD_Tofa_4

description: 5xFAD; Tofacitinib-treated; sample 4


title: NOVA26_N-Brush_Phase_2_SD7


title: NOVA28_N-Brush_Phase_2_SD7


title: NOVA29_N-Brush_Phase_2_SD7


title: NOVA11_N-Brush_Phase_2_SD7


title: CX_5xFAD_Tofa_2

description: 5xFAD; Tofacitinib-treated; sample 2


title: CX_5xFAD_Tofa_1

description: 5xFAD; Tofacitinib-treated; sample 1


title: CX_5xFAD_Sham_4

description: 5xFAD; sham-treated; sample 4


title: NOVA25_N-Brush_Phase_2_SD7


title: CX_5xFAD_Sham_3

description: 5xFAD; sham-treated; sample 3


title: NOVA22_N-Brush_Phase_2_SD7


title: CX_5xFAD_Sham_2

description: 5xFAD; sham-treated; sample 2


title: NOVA21_N-Brush_Phase_2_SD7


title: NOVA44_N-Brush_Phase_2_SD7


title: CX_5xFAD_Sham_1

description: 5xFAD; sham-treated; sample 1


title: CX_WT_Tofa_5


title: NOVA03_N-Brush_Phase_2_SD7


title: NOVA17_N-Brush_Phase_2_SD7


title: CX_WT_Tofa_4


title: CX_WT_Tofa_3


title: NOVA09_N-Brush_Phase_2_SD7


title: CX_WT_Tofa_2


title: NOVA16_N-Brush_Phase_2_SD7


title: CX_WT_Tofa_1


title: CX_WT_Sham_5

description: Wild-type; sham-treated; sample 5


title: NOVA24_N-Brush_Phase_2_SD3


title: NOVA40_N-Brush_Phase_2_SD7


title: NOVA43_N-Brush_Phase_2_SD7


title: NOVA44_N-Brush_Phase_2_SD3


title: NOVA07_N-Brush_Phase_2_SD7


title: NOVA08_N-Brush_Phase_2_SD7


title: NOVA31_N-Brush_Phase_2_SD7


title: NOVA39_N-Brush_Phase_2_SD3


title: NOVA23_N-Brush_Phase_2_SD7


title: NOVA45_N-Brush_Phase_2_SD7


title: NOVA41_N-Brush_Phase_2_SD7


title: NOVA30_N-Brush_Phase_2_SD7


title: NOVA15_N-Brush_Phase_2_SD7


title: CX_WT_Sham_4

description: Wild-type; sham-treated; sample 4


title: NOVA27_N-Brush_Phase_2_SD7


title: NOVA42_N-Brush_Phase_2_SD7


title: NOVA04_N-Brush_Phase_2_SD7


title: NOVA24_N-Brush_Phase_2_SD7


title: NOVA12_N-Brush_Phase_2_SD7


title: NOVA20_N-Brush_Phase_2_SD7


title: NOVA19_N-Brush_Phase_2_SD3


title: NOVA46_N-Brush_Phase_2_SD7


title: NOVA19_N-Brush_Phase_2_SD7


title: CX_WT_Sham_3

description: Wild-type; sham-treated; sample 3


title: NOVA32_N-Brush_Phase_2_SD7


title: CX_WT_Sham_2

description: Wild-type; sham-treated; sample 2


title: CX_WT_Sham_1

description: Wild-type; sham-treated; sample 1


title: NOVA25_N-Brush_Phase_2_SD3


title: NOVA02_N-Brush_Phase_2_SD7


title: HP_5xFAD_15

source_name: 5xFAD; sample 4


title: HP_5xFAD_13

source_name: 5xFAD; sample 3


title: NOVA05_N-Brush_Phase_2_SD7


title: HP_5xFAD_10

source_name: 5xFAD; sample 2


title: NOVA17_N-Brush_Phase_2_SD3


title: NOVA28_N-Brush_Phase_2_SD3


title: NOVA29_N-Brush_Phase_2_SD3


title: NOVA39_N-Brush_Phase_2_SD7


title: NOVA23_N-Brush_Phase_2_SD3


title: HP_5xFAD-Dp16_9

source_name: 5xFAD-Dp16; sample 3


title: NOVA20_N-Brush_Phase_2_SD3


title: NOVA18_N-Brush_Phase_2_SD3


title: HP_5xFAD_6

source_name: 5xFAD; sample 1


title: NOVA01_N-Brush_Phase_2_SD3


title: HP_5xFAD-Dp16_11

source_name: 5xFAD-Dp16; sample 4


title: NOVA30_N-Brush_Phase_2_SD3


title: NOVA31_N-Brush_Phase_2_SD3


title: HP_5xFAD-Dp16_8

source_name: 5xFAD-Dp16; sample 2


title: HP_Dp16_12

source_name: Dp16; sample 3


title: HP_Dp16_14

source_name: Dp16; sample 4


title: HP_Dp16_5

source_name: Dp16; sample 2


title: HP_5xFAD-Dp16_1

source_name: 5xFAD-Dp16; sample 1


title: NOVA07_N-Brush_Phase_2_SD3


title: HP_Dp16_3

source_name: Dp16; sample 1


title: NOVA16_N-Brush_Phase_2_SD3


title: NOVA11_N-Brush_Phase_2_SD3


title: HP_WT_7

source_name: Wild-type; sample 3


title: HP_WT_16

source_name: Wild-type; sample 4


title: NOVA21_N-Brush_Phase_2_SD3


title: NOVA41_N-Brush_Phase_2_SD3


title: NOVA10_N-Brush_Phase_2_SD3


title: NOVA02_N-Brush_Phase_2_SD3


title: NOVA05_N-Brush_Phase_2_SD3


title: HP_WT_4

source_name: Wild-type; sample 2


title: NOVA43_N-Brush_Phase_2_SD3


title: CX_5xFAD_15


title: HP_WT_2

source_name: Wild-type; sample 1


title: CX_5xFAD_13


title: CX_5xFAD_10


title: NOVA04_N-Brush_Phase_2_SD3


title: CX_5xFAD-Dp16_11


title: CX_5xFAD-Dp16_8


title: NOVA42_N-Brush_Phase_2_SD3


title: CX_Dp16_12


title: NOVA26_N-Brush_Phase_2_SD3


title: CX_Dp16_5


title: CX_Dp16_3


title: NOVA08_N-Brush_Phase_2_SD3


title: NOVA40_N-Brush_Phase_2_SD3


title: NOVA15_N-Brush_Phase_2_SD3


title: NOVA45_N-Brush_Phase_2_SD3


title: CX_5xFAD-Dp16_9


title: CX_WT_16


title: NOVA32_N-Brush_Phase_2_SD3


title: NOVA09_N-Brush_Phase_2_SD3


title: CX_WT_7


title: NOVA46_N-Brush_Phase_2_SD3


title: NOVA22_N-Brush_Phase_2_SD3


title: CX_WT_2


title: NOVA27_N-Brush_Phase_2_SD3


title: CX_Dp16_14


title: NOVA29_N-Brush_Phase_2_SD1


title: CX_5xFAD-Dp16_1


title: NOVA02_N-Brush_Phase_2_SD1


title: CX_WT_4


title: NOVA41_N-Brush_Phase_2_SD1


title: NOVA12_N-Brush_Phase_2_SD3


title: NOVA25_N-Brush_Phase_2_SD1


title: NOVA45_N-Brush_Phase_2_SD1


title: NOVA11_N-Brush_Phase_2_SD1


title: 5xFAD; Hippocampus; sample 4

source_name: brain hippocampus

value: M


title: NOVA18_N-Brush_Phase_2_SD1


title: 5xFAD; Hippocampus; sample 3


title: 5xFAD; Hippocampus; sample 1

value: F


title: 5xFAD; Hippocampus; sample 2


title: NOVA31_N-Brush_Phase_2_SD1


title: 5xFAD-Dp16; Hippocampus; sample 4


title: NOVA22_N-Brush_Phase_2_SD1


title: 5xFAD-Dp16; Hippocampus; sample 3


title: 5xFAD-Dp16; Hippocampus; sample 2


title: NOVA23_N-Brush_Phase_2_SD1


title: NOVA30_N-Brush_Phase_2_SD1


title: 5xFAD-Dp16; Hippocampus; sample 1


title: Dp16; Hippocampus; sample 3


title: NOVA24_N-Brush_Phase_2_SD1


title: Dp16; Hippocampus; sample 2


title: NOVA39_N-Brush_Phase_2_SD1


title: Dp16; Hippocampus; sample 1


title: Wild-type; Hippocampus; sample 4


title: Wild-type; Hippocampus; sample 2


title: Wild-type; Hippocampus; sample 3


title: NOVA16_N-Brush_Phase_2_SD1


title: NOVA07_N-Brush_Phase_2_SD1


title: Wild-type; Hippocampus; sample 1


title: NOVA04_N-Brush_Phase_2_SD1


title: 5xFAD; Cortex; sample 4

source_name: brain cortex


title: Dp16; Hippocampus; sample 4


title: 5xFAD; Cortex; sample 1


title: 5xFAD; Cortex; sample 2


title: 5xFAD-Dp16; Cortex; sample 3


title: 5xFAD-Dp16; Cortex; sample 4


title: 5xFAD-Dp16; Cortex; sample 2


title: 5xFAD; Cortex; sample 3


title: Dp16; Cortex; sample 3


title: 5xFAD-Dp16; Cortex; sample 1


title: Dp16; Cortex; sample 2


title: NOVA05_N-Brush_Phase_2_SD1


title: Dp16; Cortex; sample 1


title: Wild-type; Cortex; sample 3


title: Dp16; Cortex; sample 4


title: Wild-type; Cortex; sample 2


title: Wild-type; Cortex; sample 1


title: Wild-type; Cortex; sample 4


title: shHifN23

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

data_processing:
trim_galore
Hisat2
Stringtie
Assembly: GRCm38
Supplementary files format and content: csv files include read counts values for each Sample

source_name: Embryonic stem cells

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

tag: cell line

value: ESC

value: normoxia


title: shHifN22


title: CX_5xFAD_6


title: NOVA01_N-Brush_Phase_2_SD1


title: shHifN21


title: shHifH23

value: hypoxia


title: shHifH22


title: shHifH21


title: ctrlN23

value: scramble shRNA


title: ctrlN22


title: NOVA43_N-Brush_Phase_2_SD1


title: ctrlN21


title: NOVA26_N-Brush_Phase_2_SD1


title: ctrlH23


title: NOVA41_N-Brush_Phase_2_SD_-1

value: SD -1


title: NOVA12_N-Brush_Phase_2_SD1


title: ctrlH22


title: NOVA19_N-Brush_Phase_2_SD_-1


title: NOVA27_N-Brush_Phase_2_SD_-1


title: NOVA39_N-Brush_Phase_2_SD_-1


title: hyperoxia endothelial mutant 2

city: Chicago

first: Lisandra

last: Vila Ellis

state: IL

address: 303 E Superior

department: Cell and Developmental Biology

institute: Northwestern University

description: Endothelial deletion of p53

library_source: transcriptomic single cell

data_processing:
Raw sequencing data (fastq file) was demultiplexed and analyzed using 10X Genomics Cell Ranger ARC software
Further analysis can be achieved using the Cell Ranger ARC-derived analysis files in 10X Genomics Loupe Browser software.
Assembly: mm10
Supplementary files format and content: tsv and mtx files can be opened with Signac (R package) and analyzed.
Supplementary files format and content: filtered_feature_bc_matrix.h5 can be opened with Seurat (R package)

source_name: one male&one female

extract_protocol:
Lung dissociation was performed as described in our previous publication with minor modifications1. Whole lungs were harvested in Leibovitz’s Medium (Gibco, 21-083-027), minced with forceps, and digested in Leibovitz’s with 2 mg/mL Collagenase Type I (Worthington, CLS-1, LS004197), 2 mg/mL Elastase (Worthington, ESL, LS002294), and 0.5 mg/mL DNase I (Worthington, D, LS002007) for 30 minutes at 37 °C. After 15 minutes of digestion, the tissue was mechanically agitated by pipetting. Fetal bovine serum (FBS, Invitrogen, 10082-139) was then added to a final concentration of 20% and the solution was homogenized. Samples were immediately transferred to the 4 °C cold room on ice, where they were filtered with a 70 um cell strainer (Falcon, 352350). Strained samples were centrifuged at 5000 rpm for 1 minute and resuspended in 1 mL of red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) for 3 minutes. Samples were again centrifuged at 5000 rpm for 1 minute, washed with Leibovitz’s + 10% FBS, and filtered into a 5 mL tube with cell strainer cap (Falcon 352235). Cells were then incubated with CD45-PE/Cy7 (BioLegend, 103114), ICAM2-A647 (Invitrogen, A15452), and ECAD-A488 (eBioscience, 53-3249-82) at a concentration of 1:250 for 30 minutes, then centrifuged as above and washed with Leibovitz’s + 10% FBS. Samples were re-filtered and incubated with SYTOX Blue (Invitrogen, S34857), then sorted on a BD FACSAria II Cell Sorter. Excluding dead cells and doublets, four cell populations were collected: CD45+ as the immune lineage, ICAM2+ (from CD45-) as the endothelial lineage, ECAD+ (from CD45- and ICAM2-) as the epithelial lineage, and triple negative representing the mesenchymal lineage.
28 cycles read1, 90 cycles read2, 10 cycles Index1, and 10 cycles Index2

treatment_protocol: Littermates were either maintained in room air (21% O2) or placed in normobaric 80% O2 at P1 until P15.

value: lung

value: epithelial, immune, endothelial, mesenchymal cells

tag: age

value: postnatal day 15

value: p53fl/fl; Tek-Cre


title: ctrlH21


title: hyperoxia endothelial mutant 1

description: Endothelial deletion of p53


title: hyperoxia null mutant

description: Global deletion of p53

source_name: one male

value: p53 null


title: NOVA21_N-Brush_Phase_2_SD1


title: NOVA16_N-Brush_Phase_2_SD_-1


title: NOVA46_N-Brush_Phase_2_SD1


title: NOVA32_N-Brush_Phase_2_SD1


title: hyperoxia null control

description: Global deletion of p53


title: room air null mutant

description: Global deletion of p53


title: NOVA44_N-Brush_Phase_2_SD1


title: room air null control

description: Global deletion of p53


title: NOV_Cre-P8

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Cells were FACS sorted based on CD9 and THY1 to enchrich for SSCs and germ cells

data_processing:
Processed with Cell Ranger v3.0.1 and GENCODE vM17
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Neonatal testis (P8)

extract_protocol:
CD9+/THY1+ testis cells were collected by FACS sorting (see experimental design for details)
scRNA-seq libraries were prepared with 10xGenomics Chromium Single Cell 3' Kit v3.1.

value: Neonatal testis (P8)

value: Tissue

value: Testis cell suspension

value: Cnot3 KO

value: 4OHT injection from P1-P4


title: NOVA03_N-Brush_Phase_2_SD1

value: challenged with influenza

value: Nasal epithelium

value: Vaccinated


title: NOV_WT-P8

value: wild-type

value: 4OHT injection from P1-P2


title: NOVA28_N-Brush_Phase_2_SD1


title: KO_HFD bio rep 3

city: London

first: Hannah

middle: Louise Hoskins

last: Green

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

description:
D3posHFD
KO_HFDvsWT_HFD_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls

data_processing:
Library preparations were sequenced by Novogene on an Illumina platform and paired-end reads were generated. Raw data were firstly processed through in-house perl scripts to generate clean reads by removing reads containing adaptors, reads containing poly-N and low quality reads.
Clean reads were aligned to the reference genome using HISAT2 software and gene expression was quantified using featureCounts software.
Differential gene expression analysis was performed using the DESeq2 R package.
The resulting P-values were adjusted using the Benjamini and Hochberg approach. Genes with an adjusted P-value <0.05 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: .xlsx files of differentially expressed genes

source_name: Lung endothelial cells

growth_protocol: Experimental mice were generated by crossing TET2fl/fl mice to tamoxifen-inducible, endothelial-specific Cre-expressing mice (Cdh5-CreERT2) on a C57Bl/6J background.

extract_protocol:
Mouse lung endothelial cells were isolated by mincing and digesting lung tissue in 1mg/ml collagenase dispase, filtering the suspension through 70um and 30um strainers followed by selection with anti CD31 antibody-conjugated microbeads and MACS separator  (Miltenyi). RNA was isolated using a Promega Reliaprep RNA extraction kit.
Libraries were prepared from 3 biological replicates per group. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. cDNA underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Male Cre+ve TET2fl/fl mice and male Cre-ve TET2fl/fl mice were injected intraperitoneally with 40mg/kg tamoxifen (MP Biomedicals, #0215673894) in peanut oil for 3 consecutive days at 6-8 weeks of age to induce Cre recombination or generate appropriate control animals. One week after tamoxifen injections, mice were fed a high fatdiet(60% kcal from fat, TestDiet 58Y1) orcontinuedastandard chow diet (13% kcal from fat, LabDiet 5053) ad libitum for 20 weeks.

value: Lung endothelial cells

value: Endothelial-specific TET2 knockout

value: 40mg/kg tamoxifen, 3 consecutive days

tag: diet

value: High fat diet (60% kcal from fat) for 20 weeks

value: male


title: KO_HFD bio rep 2

description:
D2posHFD
KO_HFDvsWT_HFD_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls


title: NOVA23_N-Brush_Phase_2_SD_-1

value: SD -1


title: NOVA17_N-Brush_Phase_2_SD1


title: KO_HFD bio rep 1

description:
D1posHFD
KO_HFDvsWT_HFD_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls


title: NOVA19_N-Brush_Phase_2_SD1


title: NOVA18_N-Brush_Phase_2_SD_-1


title: NOVA05_N-Brush_Phase_2_SD_-1


title: NOVA32_N-Brush_Phase_2_SD_-1


title: NOVA29_N-Brush_Phase_2_SD_-1


title: WT_HFD bio rep 3

description:
C3negHFD
KO_HFDvsWT_HFD_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls

value: WT


title: WT_HFD bio rep 1

description:
C1negHFD
KO_HFDvsWT_HFD_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls


title: WT_HFD bio rep 2

description:
C2negHFD
KO_HFDvsWT_HFD_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls


title: NOVA08_N-Brush_Phase_2_SD1


title: KO_CHOW bio rep 3

description:
B3posC
KO_CHOWvsWT_CHOW_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls

value: Standard chow diet


title: NOVA07_N-Brush_Phase_2_SD_-1


title: NOVA27_N-Brush_Phase_2_SD1


title: NOVA15_N-Brush_Phase_2_SD1


title: NOVA40_N-Brush_Phase_2_SD1


title: KO_CHOW bio rep 2

description:
B2posC
KO_CHOWvsWT_CHOW_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls


title: NOVA09_N-Brush_Phase_2_SD1


title: NOVA03_N-Brush_Phase_2_SD_-1


title: NOVA30_N-Brush_Phase_2_SD_-1


title: NOVA31_N-Brush_Phase_2_SD_-1


title: NOVA17_N-Brush_Phase_2_SD_-1


title: NOVA24_N-Brush_Phase_2_SD_-1


title: NOVA12_N-Brush_Phase_2_SD_-1_b


title: NOVA10_N-Brush_Phase_2_SD_-1


title: NOVA04_N-Brush_Phase_2_SD_-1


title: NOVA11_N-Brush_Phase_2_SD_-1


title: NOVA25_N-Brush_Phase_2_SD_-1


title: NOVA46_N-Brush_Phase_2_SD_-1


title: NOVA44_N-Brush_Phase_2_SD_-1


title: WT_CHOW bio rep 3

description:
A3negC
KO_CHOWvsWT_CHOW_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls


title: NOVA06_N-Brush_Phase_2_SD_-1


title: NOVA42_N-Brush_Phase_2_SD1


title: NOVA20_N-Brush_Phase_2_SD1


title: WT_CHOW bio rep 2

description:
A2negC
KO_CHOWvsWT_CHOW_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls


title: WT_CHOW bio rep 1

description:
A1negC
KO_CHOWvsWT_CHOW_deg_all.xls
WT_HFDvsWT_CHOW_deg_all.xls


title: KO_CHOW bio rep 1

description:
B1posC
KO_CHOWvsWT_CHOW_deg_all.xls
KO_HFDvsKO_CHOW_deg_all.xls


title: NOVA09_N-Brush_Phase_2_SD_-1


title: NOVA01_N-Brush_Phase_2_SD_-1


title: WT-BM-M-8M

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8.
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 40% passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 2.3.4, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38 Ensembl92
Supplementary files format and content: MTX files and TSV files contain counts for each barcodes and genes.

source_name: Bone marrow

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10x Genomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols.

value: Bone marrow

value: 8 months

value: Male


title: NOVA40_N-Brush_Phase_2_SD_-1_b


title: NOVA02_N-Brush_Phase_2_SD_-1


title: WT-B-M-8M

description: 10X Genomics

source_name: Brain

value: Brain


title: WT-BM-F-8M

description: 10X Genomics

value: Female


title: NOVA45_N-Brush_Phase_2_SD_-1

value: challenged with influenza

value: Nasal epithelium


title: NOVA26_N-Brush_Phase_2_SD_-1

value: Vaccinated


title: WT-B-F-8M

description: 10X Genomics


title: NOVA42_N-Brush_Phase_2_SD_-1


title: WT-BM-M-2M

description: 10X Genomics

value: 2 months


title: WT-B-M-2M

description: 10X Genomics


title: NOVA43_N-Brush_Phase_2_SD_-1


title: NOVA15_N-Brush_Phase_2_SD_-1


title: WT-B-F-2M

description: 10X Genomics


title: NOVA21_N-Brush_Phase_2_SD_-1


title: NOVA22_N-Brush_Phase_2_SD_-1


title: NOVA69_N-Brush_Phase_2_SD7

value: Unvaccinated


title: NOVA64_N-Brush_Phase_2_SD7


title: FAD4T-BM-F-8M

description: 10X Genomics


title: NOVA52_N-Brush_Phase_2_SD7


title: NOVA20_N-Brush_Phase_2_SD_-1


title: NOVA28_N-Brush_Phase_2_SD_-1


title: NOVA08_N-Brush_Phase_2_SD_-1


title: FAD4T-B-M-8M

description: 10X Genomics


title: NOVA36_N-Brush_Phase_2_SD7


title: NOVA49_N-Brush_Phase_2_SD7


title: WT-BM-F-2M

description: 10X Genomics


title: FAD4T-B-F-8M

description: 10X Genomics


title: FAD4T-B-M-2M

description: 10X Genomics


title: FAD4T-BM-F-2M

description: 10X Genomics


title: NOVA37_N-Brush_Phase_2_SD7


title: FAD4T-BM-M-2M

description: 10X Genomics


title: NOVA71_N-Brush_Phase_2_SD7


title: NOVA47_N-Brush_Phase_2_SD7


title: FAD4T-B-F-2M

description: 10X Genomics


title: Hep3B48H

city: Jinan

first: Rui zhe

last: Li

address: No.104, Wen hua west Road

institute: Shandong University

description: Library name: Sample4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: xlsx files include raw counts and FPKM values

extract_protocol:
RNA was harvested using RNAfast-2000 kit (Fastagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA liberaries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hepatocellular carcinoma cell

value: Hypoxia, MNNG


title: FAD4T-BM-M-8M

description: 10X Genomics


title: Hep3Bcon

description: Library name: Sample3

value: Normoxia, MNNG


title: Huh748H

description: Library name: Sample2


title: NOVA65_N-Brush_Phase_2_SD7


title: NOVA80_N-Brush_Phase_2_SD7


title: NOVA48_N-Brush_Phase_2_SD7


title: Huh7con

description: Library name: Sample1


title: hTERT-HPDE cells, WT, NETs

city: Beijing

first: yuyang

last: wang

address: 5 Dong Dan San Tiao, Beijing

institute: Peking Union Medical College

data_processing:
Quality control: In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the refer: Hisat2 (v2.0.5)
Quantification of gene expression level:
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts for each sample

source_name: hTERT-HPDE

extract_protocol:
RNA was extracted by Trizol Reagent. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. 2ug of total was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman  oulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by  gilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library

value: hTERT-HPDE

value: pancreatic ductal epithelial Cells

value: NETs treatment


title: NOVA56_N-Brush_Phase_2_SD7


title: NOVA66_N-Brush_Phase_2_SD7


title: NOVA50_N-Brush_Phase_2_SD7


title: hTERT-HPDE cells, WT, Ctrl

value: WT

value: Ctrl


title: hTERT-HPDE cells, TLR9, Ctrl

value: pancreatic ductal epithelial cells

value: TLR9 overexperssed


title: NOVA03_N-Brush_Phase_2_SD3


title: hTERT-HPDE cells, TLR9, NETs


title: NOVA34_N-Brush_Phase_2_SD7


title: NOVA01_N-Brush_Phase_2_SD7


title: NOVA81_N-Brush_Phase_2_SD7


title: NOVA75_N-Brush_Phase_2_SD7


title: NOVA33_N-Brush_Phase_2_SD7


title: zebrafish, head removed, phox2bb+, 3dpf

city: Pasadena

first: Yuanyun

last: Huang

state: CA

address: 1200 E.California Blvd MC156-29, Caltech

department: Biology and Biological Engineering

institute: California Institute of Technology

description:
Library name: phox2bb positive bulk ATAC
processd file is after TOBIAS Tn5 correction

data_processing:
Low quality data was removed from the raw data, and the adapter sequence was removed with Cutdapt. Data was then mapped to danio rerio genome (GRCz11) with Bowtie2 (Galaxy version 2.4.2), and duplicates and low mapping quality reads were filtered with MarkDuplicates (Galaxy version 2.18.22). Produced BAM files were then processed with TOBIAS (v0.14.0) for Tn5 correnction, following the instruction, to produce the positive and negative corrected bw. file.
Assembly: GRCz11
Supplementary files format and content: bw files were generated with TOBIAS, ATACorrect function (v0.14.0), where Tn5 bias was corrected in open chromatin.

organism: Danio rerio

source_name: trunk and tail

growth_protocol: Adult zebrafish (Danio rerio) and larvae were maintained at 28 °C, with a 13-h light/11-h dark cycle.

extract_protocol:
About 150 embryos were dissected and separately stored in 6 low-binding microcentrifuge tubes on ice. After dissection, 400 μL Accumax (Invitrogen, Catalog number: 00-4666-56) solution was added into each tube. The tubes were incubated in the Eppendorf ThermoMixer at 30 °C and shaken at 1,000 rpm for about 25 min for cell dissociation. After the dissociation step, the tubes were chilled on ice, and 1 mL of cold HBSS-BSA solution was added to quench the reaction. The solution was passed through a 70 μm cell strainer into a 50 mL conical tube, and an additional 500 μL HBSS-BSA solution was used to rinse the tube and subsequently collected into the conical tube. The solution was then spun down at 4 °C at 1,200 rpm for 11 min. The supernatant was carefully removed and the pellet in each conical tube was resuspended in 1 mL HBSS-BSA solution. We then performed fluorescence-activated cell sorting and sorted out Kaede-positive and Kaede-negative cells.
Around 10, 000 Kaede-positive cells and 50,000 Kaedae-negative cells were sorted. Sorted cells underwent cell lysis, and Tn5 tagmentation. The library was constructed by amplifying the tagmentated DNA with N50x, N70x index, and then purified with magnetic beads. The procedue followed Omni-ATAC protocol.

treatment_protocol: Larvae at 3dpf were anesthetized with tricane and heads were removed.

value: trunk and tail

value: remove head

tag: time


title: NOVA62_N-Brush_Phase_2_SD7

value: challenged with influenza


title: NOVA73_N-Brush_Phase_2_SD7

value: Nasal epithelium


title: zebrafish, head removed, phox2bb-, 3dpf

description:
Library name: phox2bb negative bulk ATAC
processd file is after TOBIAS Tn5 correction


title: miR-1825 mimic control, rep 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: fluorescent labeled cDNA was synthesized and purified using GeneChip Whole Transcript Kit (Affymetrix/Thermo Fisher Scientific, Waltham, MA, USA). Purified cDNA was hybridized to Clariom™ D Assay (Affymetrix/Thermo Fisher Scientific, Waltham, MA, USA) using GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix/Thermo Fisher Scientific, Waltham, MA, USA) on a GeneChip™ Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific, Waltham, MA, USA).

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: The cel files of 8 samples classified in 4 groups (2 replicates for each group) were read and processed using oligo package in R. Robust Multi-array Average (RMA) was used to normalize and summarize the expression values. For the log2 expression data, limma testing was performed to compare inhibitor vs. inhibitor control and mimic vs. mimic control.

source_name: human neck and head cancer cell

label_protocol: Concentration and purities of RNA samples were determined using Multiskan GO UV/Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was evaluated using gel electrophoresis.

growth_protocol: Cells were seeded in 6-well plates at 6 x 10^4 cells/well concentration and then transfected with miR-1825 mimic, inhibitor or control microRNAs.

extract_protocol: Total RNA extraction from cells was carried out using EcoPURE Total RNA Kit (EcoTech Biotechnology, Erzurum, Turkey) as described in manufacturer's instructions.

value: Head and neck squamous cell carcinomas (HNSCCs)

value: transfected with miR-1825 mimic control


title: NOVA76_N-Brush_Phase_2_SD7

value: Unvaccinated


title: NOVA53_N-Brush_Phase_2_SD7


title: miR-1825 mimic control, rep 1


title: NOVA55_N-Brush_Phase_2_SD7


title: miR-1825 mimic, rep 2

value: transfected with miR-1825 mimic


title: NOVA78_N-Brush_Phase_2_SD7


title: inhibitor control, rep 2

value: transfected with inhibitor control


title: NOVA51_N-Brush_Phase_2_SD7


title: NOVA58_N-Brush_Phase_2_SD7


title: miR-1825 mimic, rep 1


title: NOVA77_N-Brush_Phase_2_SD7


title: miR-1825 inhibitor, rep 2

value: transfected with miR-1825 inhibitor


title: NOVA59_N-Brush_Phase_2_SD7


title: NOVA61_N-Brush_Phase_2_SD7


title: NOVA82_N-Brush_Phase_2_SD7


title: kidney biopsy N822

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: ABMR


title: NOVA72_N-Brush_Phase_2_SD7


title: miR-1825 inhibitor, rep 1


title: kidney biopsy N821


title: NOVA68_N-Brush_Phase_2_SD7


title: kidney biopsy N819

value: NR


title: kidney biopsy N820


title: NOVA79_N-Brush_Phase_2_SD7


title: inhibitor control, rep 1


title: kidney biopsy N817


title: NOVA63_N-Brush_Phase_2_SD7


title: kidney biopsy N818

value: Mixed


title: NOVA57_N-Brush_Phase_2_SD7


title: kidney biopsy N814

value: TCMR


title: kidney biopsy N815

value: pTCMR


title: NOVA70_N-Brush_Phase_2_SD7


title: kidney biopsy N813


title: NOVA58_N-Brush_Phase_2_SD3


title: NOVA36_N-Brush_Phase_2_SD3


title: NOVA64_N-Brush_Phase_2_SD3


title: NOVA52_N-Brush_Phase_2_SD3


title: NOVA50_N-Brush_Phase_2_SD3


title: NOVA60_N-Brush_Phase_2_SD7


title: NOVA77_N-Brush_Phase_2_SD3


title: kidney biopsy N809


title: kidney biopsy N811

value: pABMR


title: NOVA49_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_62

city: Bologna

first: Emanuela

last: Palmerini

address: via G.C.Pupilli, 1

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli

hyb_protocol: Once the target-probe complexes are hybridized according to manufacturer’s instructions (NanoString Technologies, Seattle, WA), the complexes are captured on a streptavidin-coated surface using the biotin tag on the capture probe. Here they are aligned and immobilized for imaging, and excess probe is removed.

scan_protocol: The cartridge containing immobilized sample was transferred to the nCounter Digital Analyzer Software and scanned at 555 field of view (FOV).

data_processing:
Quality control (QC) of NanoString nCounter raw data was performed using technical QC flags from nSolver based on four QC assessments: the quality of the data for imaging, binding density, linearity of the positive controls and limit of detection (LOD). Then, RUVSeq-based iterative normalization processwas performed following housekeeping assessment and estimation factors of unwanted variation. We controlled for unwanted technical variation based on a negative binomial-based generalized linear model (GLM) employing the RUVg function from RUVSeq using the final set of 40 endogenous housekeeping genes on the PanCancer Immune Profiling panel.
Normalized count using RUVSeq R package

label: Biotin

source_name: Primary Osteosarcoma cancer

label_protocol: Tumor samples were profiled with the PanCancer Immune Profiling panel, including 730 immune-related target genes, 40 housekeeping genes, and additional positive and negative genes according to manufacturer’s instructions (NanoString Technologies, Seattle, WA).

extract_protocol: Total RNA was extracted from pre-treatment FFPE and non-decalcified tissue by using the RNAstorm FFPE extraction kit (Cell Data Sciences, Fremont, CA). All the samples passed the quality control step with 260/280 and 260/230 ratios ≥1.8 and RNA concentration ≥60 ng/µL.

value: Primary Osteosarcoma cancer

value: F

tag: pgp positive

value: Positive

tag: good response/poor response

value: PR


title: kidney biopsy N810


title: NOVA65_N-Brush_Phase_2_SD3

value: challenged with influenza

value: Nasal epithelium


title: kidney biopsy N808


title: NOVA47_N-Brush_Phase_2_SD3


title: kidney biopsy N807


title: kidney biopsy N805


title: NOVA62_N-Brush_Phase_2_SD3


title: kidney biopsy N806


title: NOVA60_N-Brush_Phase_2_SD3


title: kidney biopsy N812


title: Localized Osteosarcoma Patient, Pt_61

value: GR


title: Localized Osteosarcoma Patient, Pt_59

value: M


title: Localized Osteosarcoma Patient, Pt_60

value: Negative


title: Localized Osteosarcoma Patient, Pt_58


title: kidney biopsy N804


title: Localized Osteosarcoma Patient, Pt_57


title: kidney biopsy N803


title: NOVA48_N-Brush_Phase_2_SD3

value: Unvaccinated


title: Localized Osteosarcoma Patient, Pt_56


title: NOVA81_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_52


title: Localized Osteosarcoma Patient, Pt_55


title: Localized Osteosarcoma Patient, Pt_51


title: Localized Osteosarcoma Patient, Pt_53


title: Localized Osteosarcoma Patient, Pt_54


title: NOVA10_N-Brush_Phase_2_SD1


title: kidney biopsy N802


title: kidney biopsy N800


title: Localized Osteosarcoma Patient, Pt_49


title: Localized Osteosarcoma Patient, Pt_48


title: Localized Osteosarcoma Patient, Pt_47


title: NOVA34_N-Brush_Phase_2_SD3


title: kidney biopsy N799


title: kidney biopsy N798


title: NOVA76_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_45


title: Localized Osteosarcoma Patient, Pt_44


title: Localized Osteosarcoma Patient, Pt_50


title: Localized Osteosarcoma Patient, Pt_42


title: Localized Osteosarcoma Patient, Pt_43


title: NOVA70_N-Brush_Phase_2_SD3


title: NOVA37_N-Brush_Phase_2_SD3


title: kidney biopsy N796


title: Localized Osteosarcoma Patient, Pt_41


title: NOVA73_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_40


title: NOVA72_N-Brush_Phase_2_SD3


title: NOVA33_N-Brush_Phase_2_SD3


title: kidney biopsy N801


title: kidney biopsy N795


title: kidney biopsy N797


title: NOVA71_N-Brush_Phase_2_SD3


title: kidney biopsy N794


title: Localized Osteosarcoma Patient, Pt_39


title: Localized Osteosarcoma Patient, Pt_37


title: Localized Osteosarcoma Patient, Pt_38


title: Localized Osteosarcoma Patient, Pt_36


title: kidney biopsy N792


title: kidney biopsy N793


title: Localized Osteosarcoma Patient, Pt_35


title: Localized Osteosarcoma Patient, Pt_34


title: NOVA53_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_33


title: kidney biopsy N791


title: NOVA57_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_32


title: NOVA55_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_31


title: Localized Osteosarcoma Patient, Pt_30


title: Localized Osteosarcoma Patient, Pt_28


title: NOVA68_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_29


title: kidney biopsy N790


title: Localized Osteosarcoma Patient, Pt_26


title: Localized Osteosarcoma Patient, Pt_27


title: Localized Osteosarcoma Patient, Pt_24


title: Localized Osteosarcoma Patient, Pt_25


title: Localized Osteosarcoma Patient, Pt_23


title: kidney biopsy N789


title: Localized Osteosarcoma Patient, Pt_20


title: Localized Osteosarcoma Patient, Pt_21


title: kidney biopsy N788


title: kidney biopsy N816


title: NOVA59_N-Brush_Phase_2_SD3


title: kidney biopsy N785


title: kidney biopsy N786


title: NOVA56_N-Brush_Phase_2_SD3


title: kidney biopsy N787


title: NOVA63_N-Brush_Phase_2_SD3


title: kidney biopsy N784


title: Localized Osteosarcoma Patient, Pt_19


title: NOVA75_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_18


title: NOVA66_N-Brush_Phase_2_SD3


title: NOVA80_N-Brush_Phase_2_SD3


title: NOVA61_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_17


title: Localized Osteosarcoma Patient, Pt_16


title: Localized Osteosarcoma Patient, Pt_15


title: Localized Osteosarcoma Patient, Pt_14


title: Localized Osteosarcoma Patient, Pt_13


title: NOVA51_N-Brush_Phase_2_SD3


title: NOVA78_N-Brush_Phase_2_SD3


title: kidney biopsy N782


title: Localized Osteosarcoma Patient, Pt_11


title: Localized Osteosarcoma Patient, Pt_22


title: Localized Osteosarcoma Patient, Pt_10


title: Localized Osteosarcoma Patient, Pt_12


title: kidney biopsy N780


title: kidney biopsy N781


title: Localized Osteosarcoma Patient, Pt_7


title: Localized Osteosarcoma Patient, Pt_8


title: Localized Osteosarcoma Patient, Pt_6


title: NOVA82_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_5


title: kidney biopsy N778


title: NOVA79_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_4


title: NOVA69_N-Brush_Phase_2_SD3


title: Localized Osteosarcoma Patient, Pt_9


title: Localized Osteosarcoma Patient, Pt_3


title: NOVA57_N-Brush_Phase_2_SD1


title: kidney biopsy N776


title: kidney biopsy N775


title: kidney biopsy N777


title: Localized Osteosarcoma Patient, Pt_1


title: kidney biopsy N779


title: NOVA47_N-Brush_Phase_2_SD1


title: del11MEFmg115ENDSeq

city: Philadelphia

first: David

last: Glass

state: PA

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description: Library name: del11ENDSeq

data_processing:
trimmomatic-0.36.jar PE -phred33
bwa mem -t 12 -M -k 32
picard.jar MarkDuplicates REMOVE_DUPLICATES=true
bedtools genomecov -bg -scale $rpm
Assembly: mm10
Supplementary files format and content: bigWIg

source_name: Mouse Embryonic Fibroblast (MEF)

extract_protocol:
Live cells were embedded in agarose plugs and lysed using Proteinase K. RNAs were degraded using RNase A. After plug melting and sonication, DNA was ethanol precipitated.
END-Seq (See PMID 32840769 for detailed protocol)

value: Mouse Embryonic Fibroblast (MEF)

value: Brca1 del11 MEF

value: MEF

value: Brca1 del11


title: WTMEFmg115ENDSeq

description: Library name: WTENDSeq

value: WT MEF

value: WT


title: NOVA61_N-Brush_Phase_2_SD1


title: Control_1

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

description:
Library name: 190
10X genomics

data_processing:
Processed data files were generated using CellRanger3.1.0
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values and matrix files

source_name: Heart

extract_protocol:
After euthanasia, hearts were minced with a razor blade and digested with a combination of collagenase I (3.6 mg/ml), DNase I (60 U/ml), and hyaluronidase (60 U/ml) for 1 hour at 37C. Red blood cells were lysed and cells were resuspended in 1 ml PBS containing 1% BSA with Fc blocking solution for 30 minutes on ice. Cells were stained for 30 minutes at room temperature with primary antibodies listed in Supplemental data. After staining for 30 minutes, cells were spun, washed with 1% BSA, and sorted using a Becton–Dickenson FACSAriaII. For scRNA-seq studies, we sorted ~25,000 live, CD45+ cells into individual BSA coated tubes (see Figure 2 for gating strategy used for scRNAseq experiments). Cells were initially counted with trypan blue to ensure quality of cells after sorting. After reaching the core, cells were counted with a BioRad TC20 Automated Cell Counter (PN 1450102) and approximately 5,000 cells from each animal were subjected to bead emulsion and 10X genomics. This was done for N=2-3 animals from each experimental group (Control, HFpEF + sham, HFpEF + tVNS).
10xChromium single cell libraries were prepared according to the standard protocol outlined in the manual. Briefly, sorted single cell suspension, 10x barcoded gel beads, and oil were loaded into Chromium™ Single Cell Chip G to capture single cells in nanoliter-scale oil droplets by Chromium™ Controller and to generate Gel Bead-In-EMulsions (GEMs). We used “Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3.1” and chip G for these experiments.  Full length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction. Sequencing libraries were constructed by following the steps: cDNA fragmentation, end repair & A-tailing, size selection by SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a repeat of SPRIselect beads size selection. The final constructed single cell libraries were sequenced by Illumina Nextseq2000 machine with total reads per cell targeted for a minimum of 25,000.

treatment_protocol: Eight-week-old C57BL/6 CCR2-RFP male mice were exposed to L-NAME, a nitric oxide synthase inhibitor (0.5g/L in drinking water) and high-fat diet (HFD; 60% calories from lard) for 5 weeks in order to induce HFpEF. C57BL/6 CCR2-RFP mice fed a standard chow diet served as controls. We only used male mice because it was previously shown that female mice are protected from HFpEF development in this model. At 13 weeks of age, echocardiography was performed to confirm the development of HFpEF, as previously described . The animals were monitored twice daily for heart failure symptoms, including distress, reduced movement, difficulty in breathing, body edema, and cachexia. The development of heart failure was assessed using a scoring system that integrates these parameters, as previously described, as well as through exercise capacity assessment. None of the mice were excluded because of lack of heart failure symptoms or absence of echocardiographic signs of HFpEF, and the heart failure score was similar between groups.  After 5 weeks of L-NAME and HFD administration, mice were randomly assigned to either sham or tVNS treatment groups. A custom-made electrode was placed on the auricular concha area of each ear for tVNS . Electrical stimulation was delivered daily for 20 minutes over a 4-week period beginning at 13 weeks of age, under 2% isoflurane inhalation anesthesia using a transcutaneous electrical nerve stimulation device (InTENSity Twin Stim; Current Solutions LLC, Austin, TX), with a frequency of 20 Hz, pulse duration of 200μs, and amplitude of 2mA, as in our previous study 18. Electrodes in the active tVNS group were positioned over the auricular concha region with the cathode inside and the anode outside 18, while in the sham group the electrodes were placed at the same area, but no stimulation was delivered. Mice were euthanized at 17 weeks of age (8 weeks after starting HFpEF diet; 4 weeks after starting tVNS) for scRNAseq.

value: Heart

value: Wild type

value: Control

tag: batch

value: October, 2022


title: Control_2

description:
Library name: 192
10X genomics

tag: tissue


title: HFpEF + tVNS_2

description:
Library name: 187
10X genomics

tag: genotype

value: HFpEF + tVNS


title: Localized Osteosarcoma Patient, Pt_2

value: Primary Osteosarcoma cancer

value: Positive

value: PR


title: KEYmg115ENDSeq

description: Library name: KEY(CC)ENDSeq

value: Palb2 KEY (CC) MEF

value: Palb2 KEY (CC)


title: HFpEF + tVNS_3

description:
Library name: 188
10X genomics


title: kidney biopsy N772

value: ABMR


title: HFpEF_3

description:
Library name: 182
10X genomics

value: HFpEF


title: HFpEF_2

description:
Library name: 181
10X genomics


title: kidney biopsy N773

value: NR


title: NOVA34_N-Brush_Phase_2_SD1

value: challenged with influenza

value: Nasal epithelium

value: Unvaccinated


title: kidney biopsy N771

value: pABMR


title: NOVA33_N-Brush_Phase_2_SD1


title: Localized Osteosarcoma Patient, Pt_46

value: M

value: GR


title: NOVA10_N-Brush_Phase_2_SD7


title: kidney biopsy N774


title: control_S7

city: Pittsburgh

first: Tingting

last: Duan

address: 5117 Centre Avenue

institute: University of Pittsburgh

description:
Library name: Sample7
SP230-S7_S31

data_processing:
Raw data is trimmed by trimmomatic
quality is checked by multiQC
sequence is aligned to the mouse genome using Kallisto
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw counts

source_name: spleen and lyphnodes

extract_protocol:
CD8 T cells were collected and  stored in RLT buffer (Qiagen) supplemented with 1% vol/vol β-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen). cDNA synthesis was performed using iScript cDNA Synthesis Kit (Bio-Rad) according  to manufacturer’s instructions.
RNA Sequencing Library Generation RNA was assessed for quality using an Agilent TapeStation 4150/Fragment Analyzer 5300 and RNA concentration was quantified on a Qubit FLEX fluorometer. Libraries were generated with the Illumina Stranded mRNA Library Prep kit (Illumina: 20040534) according to the manufacturer’s instructions. Briefly, 50 ng of input RNA was used for each sample. Following adapter ligation, 14 cycles of indexing PCR were completed, Illumina RNA UD Indexes. Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300. Libraries were normalized and pooled to 2 nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/l) of the libraries.  Library Sequencing Sequencing was performed on an Illumina NextSeq 2000, using a P4 100 flow cell. The pooled library was loaded at 750 pM and sequencing was carried out with read lengths of 2x58 bp, with a target of 40 million reads per sample. Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12).

treatment_protocol: Naïve CD8T cells were stimulated with aCD3 + aCD28 along with IL-12  for 18 hrs. After 18 hrs, stimulate with either vehicle contorl or formate for  24 h

value: spleen and lyphnodes

value: wildtype

value: PBS


title: NOVA59_N-Brush_Phase_2_SD1


title: 2mM formate_S2

description:
Library name: Sample6
SP230-S2_S30

growth_protocol: CD8 T cells were collected and  stored in RLT buffer (Qiagen) supplemented with 1% vol/vol β-mercaptoethanol.

value: 2 mM formate for 24 hrs


title: kidney biopsy N769


title: NOVA48_N-Brush_Phase_2_SD1


title: HFpEF + tVNS_1

description:
Library name: 185
10X genomics

value: Heart

value: Wild type

value: HFpEF + tVNS

value: October, 2022


title: NOVA36_N-Brush_Phase_2_SD1


title: control_S1

description:
Library name: Sample5
SP230-S1_S29


title: control_S13

description:
Library name: Sample3
SP230-S13_S35


title: HFpEF_1

description:
Library name: 179
10X genomics


title: kidney biopsy N768


title: NOVA79_N-Brush_Phase_2_SD1


title: NOVA63_N-Brush_Phase_2_SD1


title: 2mM formate_S11

description:
Library name: Sample2
SP230-S11_S34


title: 2mM formate_S8

description:
Library name: Sample8
SP230-S8_S32


title: kidney biopsy N770


title: kidney biopsy N767


title: NOVA73_N-Brush_Phase_2_SD1


title: 4C_SSBP3-dTAG_control_rep2

first: Xiaokang

last: Wang

address: 315 A  Abramson Research Center, 3615 Civic Center Blvd.

department: Hematology

institute: Children's hospital of Philadelphia

description:
Library name: 4C_SSBP3-dTAG_control_rep2
4C_SSBP3-dTAG_control_merge.bw

data_processing:
4C sequencing data analysis was performed by pipe4C (https://github.com/deLaatLab/pipe4C).
Assembly: mm9
Supplementary files format and content: bw: tracks of 4C signals
Library strategy: 4C-Seq

molecule: nuclear RNA

extract_protocol:
10 million cells were fixed. DpnII and NlaIII were used as first and second restriction enzyme, respectively. Overnight ligation was performed after digestion.
The following 4C primers were used to amplify viewpoints of interest, using 200 ng 4C template input in 4 independent PCR reactions (4 x 50 μl): β-major promoter TACACGACGCTCTTCCGATCTGCAGAGCATATAAGGTGAGGTAGGATC and ACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTTTTCTTTGTTTCTCAGTTTGAGTGCATG Pooled reactions were purified by QIAquick PCR Purification Kit (QIAGEN, 21804) eluting in 50 μl milliQ water. 10 μl purified PCR product was used as input material for a second PCR to obtain full Illumina adapter sequences using a universal forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcoded reverse primer (CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCT) with a 6-nucleotide barcode (XXXXXX). Pooled 4C libraries were purified with Ampure XP beads (Beckman Coulter, A63881) before sequencing on the Illumina NextSeq 2000 platform.

value: Erythroblast


title: kidney biopsy N766


title: 4C_SSBP3-dTAG_control_rep1

description:
Library name: 4C_SSBP3-dTAG_control_rep1
4C_SSBP3-dTAG_control_merge.bw


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep2

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep2
4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_merge.bw

value: 1h dTAGV-2


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep1

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep1
4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_merge.bw

value: 1h dTAGV-1


title: 2mM formate_S14

description:
Library name: Sample4
SP230-S14_S36


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep2

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep2
4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_merge.bw

value: 1h DMSO


title: kidney biopsy N765

value: TCMR


title: control _S10

description:
Library name: Sample1
SP230-S10_S33


title: NOVA49_N-Brush_Phase_2_SD1

description: Gene expression profiling of nasal epithelium from influenza infected humans

value: challenged with influenza

value: Nasal epithelium

value: Unvaccinated


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep1

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep1
4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_merge.bw


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep4

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep4
4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_merge.bw


title: kidney biopsy N764

value: ABMR


title: kidney biopsy N761


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep3

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_rep3
4C_ZF-LDB1-DD_in_SSBP3-dTAG_dTAG_merge.bw

value: 1h dTAGV-3


title: kidney biopsy N763

value: NR


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep1

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep1
4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_merge.bw


title: NOVA53_N-Brush_Phase_2_SD1


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep2

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep2
4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_merge.bw


title: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep3

description:
Library name: 4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_rep3
4C_ZF-LDB1-DD_in_SSBP3-dTAG_DMSO_merge.bw


title: NOVA52_N-Brush_Phase_2_SD1


title: NOVA50_N-Brush_Phase_2_SD1


title: kidney biopsy N762

value: pABMR


title: NOVA55_N-Brush_Phase_2_SD1


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep4

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep4
4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_merge.bw


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep3

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep3
4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_merge.bw


title: NOVA68_N-Brush_Phase_2_SD1


title: kidney biopsy N759


title: kidney biopsy N758


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep2

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep2
4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_merge.bw


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep3

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_rep3
4C_ZF-LDB1-FL_in_SSBP3-dTAG_dTAG_merge.bw


title: NOVA51_N-Brush_Phase_2_SD1


title: 4C_ZF-SSBP3-FL_in_G1E_rep2

description:
Library name: 4C_ZF-SSBP3-FL_in_G1E_rep2
4C_ZF-SSBP3-FL_in_G1E_merge.bw


title: 4C_ZF-SSBP3-FL_in_G1E_rep1

description:
Library name: 4C_ZF-SSBP3-FL_in_G1E_rep1
4C_ZF-SSBP3-FL_in_G1E_merge.bw


title: 4C_ZF-SSBP3-N_in_G1E_rep2

description:
Library name: 4C_ZF-SSBP3-N_in_G1E_rep2
4C_ZF-SSBP3-N_in_G1E_merge.bw


title: 4C_G1E_control_rep2

description:
Library name: 4C_G1E_control_rep2
4C_G1E_control_merge.bw


title: 4C_ZF-SSBP3-N_in_G1E_rep1

description:
Library name: 4C_ZF-SSBP3-N_in_G1E_rep1
4C_ZF-SSBP3-N_in_G1E_merge.bw


title: kidney biopsy N757


title: kidney biopsy N760


title: kidney biopsy N756


title: NOVA37_N-Brush_Phase_2_SD1


description: Library name: SSBP2_4_knockout_clone_2 estradiol_induced

data_processing:
RNA-seq analysis were performed by the nf-core/rnaseq pipleline (version 3.14.0).
Assembly: mm9
Supplementary files format and content: bw: tracks of RNA-seq signals

source_name: cell line

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (QIAGEN, 74104) following manufacturer’s instructions. Genomic DNA was removed by in-column DNase I digestion (Qiagen, 79256) DNAse.
Libraries were constructed using the TruSeq Stranded mRNA kit (Illumina, 20020594)

value: cell line

value: SSBP2_4 knockout clone #2

value: 24h estradiol induced


title: WT_estradiol_induced

description: Library name: WT_estradiol_induced

value: WT


description: Library name: SSBP2_4_knockout_clone_3 estradiol_induced

value: SSBP2_4 knockout clone #3


title: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep1

description:
Library name: 4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_rep1
4C_ZF-LDB1-FL_in_SSBP3-dTAG_DMSO_merge.bw

value: Erythroblast


title: NOVA62_N-Brush_Phase_2_SD1

description: Gene expression profiling of nasal epithelium from influenza infected humans

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

extract_protocol: Total RNA was isolated from nasal epithlium using Qiagen RNA isolation kit according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.


title: kidney biopsy N783

value: Mixed


title: NOVA69_N-Brush_Phase_2_SD1


title: kidney biopsy N754


title: SSBP2_4_knockout_clone_3_uninduced

description: Library name: SSBP2_4_knockout_clone_3_uninduced

value: uninduced


title: kidney biopsy N755


title: SSBP2_4_knockout_clone_2_uninduced

description: Library name: SSBP2_4_knockout_clone_2_uninduced


title: WT_uninduced

description: Library name: WT_uninduced


title: kidney biopsy N753


title: NOVA56_N-Brush_Phase_2_SD1


title: SSBP3_PRO_seq_dTAGV1_rep3

description:
Library name: SSBP3_PRO_seq_dTAGV1_rep3
SSBP3_PRO_seq_dTAGV1_merge_forward.bw
SSBP3_PRO_seq_dTAGV1_merge_reverse.bw

data_processing:
Fastq sequencing files were processed by fastp to remove adaptors and low-quality reads and bases; UMI-tools was used to extract UMI from reads; BWA-MEM was used for reads mapping using mm9 genome build; SAMtools was used to convert SAM filefiles to BAM filefiles and BAM file indexing; UMI-tools was used again for deduplication based on the extracted UMI; CPM was used for normalization to generate bigwig from deeptools bamCoverage. Quantifying differential expression was achieved by HOMER (getDiffExpression.pl) (http://homer.ucsd.edu/homer/ngs/peaksReplicates.html).
Assembly: mm9
Supplementary files format and content: bw: tracks of ChIP-seq signals
Library strategy: PRO-Seq

extract_protocol:
Nuclei were isolated for PRO-seq, followed by run-on reactions, nascent RNA isolation, and cDNA library preparaion as described in a fast PRO-seq version (https://www.biorxiv.org/content/10.1101/2020.05.18.102277v1)
Library preparaion as described in a fast PRO-seq version (https://www.biorxiv.org/content/10.1101/2020.05.18.102277v1)

value: SSBP3-dTAG subline

value: 1h  dTAGV-1


title: 4C_G1E_control_rep1

description:
Library name: 4C_G1E_control_rep1
4C_G1E_control_merge.bw


title: NOVA72_N-Brush_Phase_2_SD1

value: challenged with influenza


title: kidney biopsy N752


title: SSBP3_PRO_seq_DMSO_rep3

description:
Library name: SSBP3_PRO_seq_DMSO_rep3
SSBP3_PRO_seq_DMSO_merge_forward.bw
SSBP3_PRO_seq_DMSO_merge_reverse.bw

value: 1h DMSO


title: NOVA81_N-Brush_Phase_2_SD1

value: Nasal epithelium

value: Unvaccinated


title: G1E_ER4_single_crosslinking_input

description:
Library name: G1E_ER4_single_crosslinking_input
G1E_ER4_single_crosslinking_input_RPKM.bw

data_processing:
The ChIP-seq data was processed by using nf-core/chipseq pipeline 2.0.0.
Assembly: mm9
Supplementary files format and content: bw: tracks of ChIP-seq signals

extract_protocol:
Dual crosslinked DNA from lysed cells was sonicated using the Bioruptor Pico, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106).
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).

treatment_protocol: The cells were either untreated, or treated with 12h estradiol, or 0h/1h/2h DMSO, or 0h/1h/2h dTAGV-1, 0h/4h Auxin.


title: SSBP3_ChIP_single_crosslinking_rep2

description:
Library name: SSBP3_ChIP_single_crosslinking_rep2
SSBP3_ChIP_single_crosslinking_rep2_RPKM.bw


title: SSBP3_ChIP_single_crosslinking_rep1

description:
Library name: SSBP3_ChIP_single_crosslinking_rep1
SSBP3_ChIP_single_crosslinking_rep1_RPKM.bw


title: LDB1_ChIP_single_crosslinking_rep1

description:
Library name: LDB1_ChIP_single_crosslinking_rep1
LDB1_ChIP_single_crosslinking_rep1_RPKM.bw


title: NOVA80_N-Brush_Phase_2_SD1


title: kidney biopsy N750

value: ABMR


title: G1E_ER4_input

description:
Library name: G1E_ER4_input
G1E_ER4_input_RPKM.bw


title: SSBP3_ChIP_2h_dTAG_rep2

description:
Library name: SSBP3_ChIP_2h_dTAG_rep2
SSBP3_ChIP_2h_dTAG_rep2_spike_in_normalized.bw
SSBP3_ChIP_2h_dTAG_merge_spike_in_normalized.bw

value: 2h dTAGV-1


title: LDB1_ChIP_single_crosslinking_rep2

description:
Library name: LDB1_ChIP_single_crosslinking_rep2
LDB1_ChIP_single_crosslinking_rep2_RPKM.bw


title: SSBP3_ChIP_2h_dTAG_rep3

description:
Library name: SSBP3_ChIP_2h_dTAG_rep3
SSBP3_ChIP_2h_dTAG_rep3_spike_in_normalized.bw
SSBP3_ChIP_2h_dTAG_merge_spike_in_normalized.bw


title: SSBP3_ChIP_1h_dTAG_rep3

description:
Library name: SSBP3_ChIP_1h_dTAG_rep3
SSBP3_ChIP_1h_dTAG_rep3_spike_in_normalized.bw
SSBP3_ChIP_1h_dTAG_merge_spike_in_normalized.bw

value: 1h dTAGV-1


title: SSBP3_ChIP_2h_dTAG_rep1

description:
Library name: SSBP3_ChIP_2h_dTAG_rep1
SSBP3_ChIP_2h_dTAG_rep1_spike_in_normalized.bw
SSBP3_ChIP_2h_dTAG_merge_spike_in_normalized.bw

value: cell line


title: SSBP3_ChIP_1h_dTAG_rep2

description:
Library name: SSBP3_ChIP_1h_dTAG_rep2
SSBP3_ChIP_1h_dTAG_rep2_spike_in_normalized.bw
SSBP3_ChIP_1h_dTAG_merge_spike_in_normalized.bw


title: SSBP3_ChIP_0h_dTAG_rep3

description:
Library name: SSBP3_ChIP_0h_dTAG_rep3
SSBP3_ChIP_0h_dTAG_rep3_spike_in_normalized.bw
SSBP3_ChIP_0h_dTAG_merge_spike_in_normalized.bw

value: 0h dTAGV-1


title: kidney biopsy N749

value: NR


title: kidney biopsy N751


title: NOVA60_N-Brush_Phase_2_SD1

description: Gene expression profiling of nasal epithelium from influenza infected humans


title: NOVA78_N-Brush_Phase_2_SD1


title: kidney biopsy N748


title: NOVA58_N-Brush_Phase_2_SD1


title: kidney biopsy N747


title: NOVA65_N-Brush_Phase_2_SD1


title: NOVA75_N-Brush_Phase_2_SD1


title: kidney biopsy N744


title: NOVA64_N-Brush_Phase_2_SD1


title: kidney biopsy N746


title: kidney biopsy N745


title: NOVA66_N-Brush_Phase_2_SD1


title: SSBP3_ChIP_0h_dTAG_rep2

description:
Library name: SSBP3_ChIP_0h_dTAG_rep2
SSBP3_ChIP_0h_dTAG_rep2_spike_in_normalized.bw
SSBP3_ChIP_0h_dTAG_merge_spike_in_normalized.bw


title: SSBP3_ChIP_0h_dTAG_rep1

description:
Library name: SSBP3_ChIP_0h_dTAG_rep1
SSBP3_ChIP_0h_dTAG_rep1_spike_in_normalized.bw
SSBP3_ChIP_0h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_2h_dTAG_rep3

description:
Library name: LDB1_ChIP_2h_dTAG_rep3
LDB1_ChIP_2h_dTAG_rep3_spike_in_normalized.bw
LDB1_ChIP_2h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_2h_dTAG_rep1

description:
Library name: LDB1_ChIP_2h_dTAG_rep1
LDB1_ChIP_2h_dTAG_rep1_spike_in_normalized.bw
LDB1_ChIP_2h_dTAG_merge_spike_in_normalized.bw


title: SSBP3_ChIP_1h_dTAG_rep1

description:
Library name: SSBP3_ChIP_1h_dTAG_rep1
SSBP3_ChIP_1h_dTAG_rep1_spike_in_normalized.bw
SSBP3_ChIP_1h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_1h_dTAG_rep2

description:
Library name: LDB1_ChIP_1h_dTAG_rep2
LDB1_ChIP_1h_dTAG_rep2_spike_in_normalized.bw
LDB1_ChIP_1h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_1h_dTAG_rep1

description:
Library name: LDB1_ChIP_1h_dTAG_rep1
LDB1_ChIP_1h_dTAG_rep1_spike_in_normalized.bw
LDB1_ChIP_1h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_0h_dTAG_rep3

description:
Library name: LDB1_ChIP_0h_dTAG_rep3
LDB1_ChIP_0h_dTAG_rep3_spike_in_normalized.bw
LDB1_ChIP_0h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_0h_dTAG_rep2

description:
Library name: LDB1_ChIP_0h_dTAG_rep2
LDB1_ChIP_0h_dTAG_rep2_spike_in_normalized.bw
LDB1_ChIP_0h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_0h_dTAG_rep1

description:
Library name: LDB1_ChIP_0h_dTAG_rep1
LDB1_ChIP_0h_dTAG_rep1_spike_in_normalized.bw
LDB1_ChIP_0h_dTAG_merge_spike_in_normalized.bw


title: CTCF_ChIP_SSBP2_4_knockout_rep2

description:
Library name: CTCF_ChIP_SSBP2_4_knockout_rep2
CTCF_ChIP_SSBP2_4_knockout_rep2_DESeq2_normalized.bw
CTCF_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw

value: SSBP2/4 knockout clone #3


title: CTCF_ChIP_SSBP2_4_knockout_rep1

description:
Library name: CTCF_ChIP_SSBP2_4_knockout_rep1
CTCF_ChIP_SSBP2_4_knockout_rep1_DESeq2_normalized.bw
CTCF_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: CTCF_ChIP_WT_rep2

description:
Library name: CTCF_ChIP_WT_rep2
CTCF_ChIP_WT_rep2_DESeq2_normalized.bw
CTCF_ChIP_WT_merge_DESeq2_normalized.bw

value: WT


title: CTCF_ChIP_WT_rep1

description:
Library name: CTCF_ChIP_WT_rep1
CTCF_ChIP_WT_rep1_DESeq2_normalized.bw
CTCF_ChIP_WT_merge_DESeq2_normalized.bw

value: Erythroblast


title: SSBP3_ChIP_4h_Auxin_rep1

description:
Library name: SSBP3_ChIP_4h_Auxin_rep1
SSBP3_ChIP_plus_auxin_rep1_RPKM.bw
SSBP3_ChIP_plus_auxin_merge_RPKM.bw

value: 4h Auxin


title: LDB1_ChIP_4h_Auxin_rep2

description:
Library name: LDB1_ChIP_4h_Auxin_rep2
LDB1_ChIP_plus_auxin_rep2_RPKM.bw
LDB1_ChIP_plus_auxin_merge_RPKM.bw


title: LDB1_ChIP_4h_Auxin_rep1

description:
Library name: LDB1_ChIP_4h_Auxin_rep1
LDB1_ChIP_plus_auxin_rep1_RPKM.bw
LDB1_ChIP_plus_auxin_merge_RPKM.bw


title: SSBP3_ChIP_4h_Auxin_rep2

description:
Library name: SSBP3_ChIP_4h_Auxin_rep2
SSBP3_ChIP_plus_auxin_rep2_RPKM.bw
SSBP3_ChIP_plus_auxin_merge_RPKM.bw


title: SSBP3_ChIP_0h_Auxin_rep2

description:
Library name: SSBP3_ChIP_0h_Auxin_rep2
SSBP3_ChIP_minus_auxin_rep2_RPKM.bw
SSBP3_ChIP_minus_auxin_merge_RPKM.bw

value: 0h Auxin


title: LDB1_ChIP_1h_dTAG_rep3

description:
Library name: LDB1_ChIP_1h_dTAG_rep3
LDB1_ChIP_1h_dTAG_rep3_spike_in_normalized.bw
LDB1_ChIP_1h_dTAG_merge_spike_in_normalized.bw


title: SSBP3_ChIP_0h_Auxin_rep1

description:
Library name: SSBP3_ChIP_0h_Auxin_rep1
SSBP3_ChIP_minus_auxin_rep1_RPKM.bw
SSBP3_ChIP_minus_auxin_merge_RPKM.bw


title: LDB1_ChIP_2h_dTAG_rep2

description:
Library name: LDB1_ChIP_2h_dTAG_rep2
LDB1_ChIP_2h_dTAG_rep2_spike_in_normalized.bw
LDB1_ChIP_2h_dTAG_merge_spike_in_normalized.bw


title: LDB1_ChIP_0h_Auxin_rep2

description:
Library name: LDB1_ChIP_0h_Auxin_rep2
LDB1_ChIP_minus_auxin_rep2_RPKM.bw
LDB1_ChIP_minus_auxin_merge_RPKM.bw


title: LDB1_ChIP_0h_Auxin_rep1

description:
Library name: LDB1_ChIP_0h_Auxin_rep1
LDB1_ChIP_minus_auxin_rep1_RPKM.bw
LDB1_ChIP_minus_auxin_merge_RPKM.bw


title: LDB1_ChIP_plus_estradiol_rep3

description:
Library name: LDB1_ChIP_plus_estradiol_rep3
LDB1_ChIP_plus_estradiol_rep3_DESeq2_normalized.bw
LDB1_ChIP_plus_estradiol_merge_DESeq2_normalized.bw

value: 12h Estradiol


title: LDB1_ChIP_plus_estradiol_rep2

description:
Library name: LDB1_ChIP_plus_estradiol_rep2
LDB1_ChIP_plus_estradiol_rep2_DESeq2_normalized.bw
LDB1_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: LDB1_ChIP_plus_estradiol_rep1

description:
Library name: LDB1_ChIP_plus_estradiol_rep1
LDB1_ChIP_plus_estradiol_rep1_DESeq2_normalized.bw
LDB1_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: SSBP3_ChIP_plus_estradiol_rep2

description:
Library name: SSBP3_ChIP_plus_estradiol_rep2
SSBP3_ChIP_plus_estradiol_rep2_DESeq2_normalized.bw
SSBP3_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: SSBP3_ChIP_plus_estradiol_rep1

description:
Library name: SSBP3_ChIP_plus_estradiol_rep1
SSBP3_ChIP_plus_estradiol_rep1_DESeq2_normalized.bw
SSBP3_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: NOVA71_N-Brush_Phase_2_SD1

description: Gene expression profiling of nasal epithelium from influenza infected humans


title: SSBP4_ChIP_plus_estradiol_rep2

description:
Library name: SSBP4_ChIP_plus_estradiol_rep2
SSBP4_ChIP_plus_estradiol_rep2_DESeq2_normalized.bw
SSBP4_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: NOVA77_N-Brush_Phase_2_SD1


title: SSBP4_ChIP_plus_estradiol_rep1

description:
Library name: SSBP4_ChIP_plus_estradiol_rep1
SSBP4_ChIP_plus_estradiol_rep1_DESeq2_normalized.bw
SSBP4_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: kidney biopsy N736

value: Mixed


title: SSBP4_ChIP_rep4

description:
Library name: SSBP4_ChIP_rep4
SSBP4_ChIP_WT_rep4_RPKM.bw
SSBP4_ChIP_WT_merge_RPKM.bw
SSBP4_ChIP_WT_rep4_minus_estradiol_DESeq2_normalized.bw
SSBP4_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N740


title: kidney biopsy N730

value: pABMR


title: SSBP4_ChIP_rep3

description:
Library name: SSBP4_ChIP_rep3
SSBP4_ChIP_WT_rep3_RPKM.bw
SSBP4_ChIP_WT_merge_RPKM.bw
SSBP4_ChIP_WT_rep3_minus_estradiol_DESeq2_normalized.bw
SSBP4_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: SSBP4_ChIP_rep2

description:
Library name: SSBP4_ChIP_rep2
SSBP4_ChIP_WT_rep2_RPKM.bw
SSBP4_ChIP_WT_merge_RPKM.bw
SSBP4_ChIP_WT_rep2_minus_estradiol_DESeq2_normalized.bw
SSBP4_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N738


title: SSBP4_ChIP_rep1

description:
Library name: SSBP4_ChIP_rep1
SSBP4_ChIP_WT_rep1_RPKM.bw
SSBP4_ChIP_WT_merge_RPKM.bw
SSBP4_ChIP_WT_rep1_minus_estradiol_DESeq2_normalized.bw
SSBP4_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: NOVA70_N-Brush_Phase_2_SD1

value: challenged with influenza


title: kidney biopsy N739


title: kidney biopsy N733


title: SSBP2_ChIP_plus_estradiol_rep2

description:
Library name: SSBP2_ChIP_plus_estradiol_rep2
SSBP2_ChIP_plus_estradiol_rep2_DESeq2_normalized.bw
SSBP2_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: SSBP2_ChIP_plus_estradiol_rep1

description:
Library name: SSBP2_ChIP_plus_estradiol_rep1
SSBP2_ChIP_plus_estradiol_rep1_DESeq2_normalized.bw
SSBP2_ChIP_plus_estradiol_merge_DESeq2_normalized.bw


title: SSBP2_ChIP_rep5

description:
Library name: SSBP2_ChIP_rep5
SSBP2_ChIP_WT_rep5_RPKM.bw
SSBP2_ChIP_WT_merge_RPKM.bw
SSBP2_ChIP_WT_rep5_minus_estradiol_DESeq2_normalized.bw
SSBP2_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N735


title: SSBP2_ChIP_rep4

description:
Library name: SSBP2_ChIP_rep4
SSBP2_ChIP_WT_rep4_RPKM.bw
SSBP2_ChIP_WT_merge_RPKM.bw
SSBP2_ChIP_WT_rep4_minus_estradiol_DESeq2_normalized.bw
SSBP2_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N729


title: NOVA47_N-Brush_Phase_2_SD_-1

value: Nasal epithelium

value: SD -1


title: kidney biopsy N737

value: TCMR


title: SSBP2_ChIP_rep3

description:
Library name: SSBP2_ChIP_rep3
SSBP2_ChIP_WT_rep3_RPKM.bw
SSBP2_ChIP_WT_merge_RPKM.bw
SSBP2_ChIP_WT_rep3_minus_estradiol_DESeq2_normalized.bw
SSBP2_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: SSBP2_ChIP_rep2

description:
Library name: SSBP2_ChIP_rep2
SSBP2_ChIP_WT_rep2_RPKM.bw
SSBP2_ChIP_WT_merge_RPKM.bw
SSBP2_ChIP_WT_rep2_minus_estradiol_DESeq2_normalized.bw
SSBP2_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N743

value: ABMR


title: NOVA49_N-Brush_Phase_2_SD_-1

value: Unvaccinated


title: NOVA50_N-Brush_Phase_2_SD_-1


title: NOVA60_N-Brush_Phase_2_SD_-1


title: NOVA66_N-Brush_Phase_2_SD_-1


title: SSBP2_ChIP_rep1

description:
Library name: SSBP2_ChIP_rep1
SSBP2_ChIP_WT_rep1_RPKM.bw
SSBP2_ChIP_WT_merge_RPKM.bw
SSBP2_ChIP_WT_rep1_minus_estradiol_DESeq2_normalized.bw
SSBP2_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw

value: cell line


title: H3K27ac_ChIP_SSBP2_4_knockout_rep2

description:
Library name: H3K27ac_ChIP_SSBP2_4_knockout_rep2
H3K27ac_ChIP_SSBP2_4_knockout_rep2_DESeq2_normalized.bw
H3K27ac_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: H3K27ac_ChIP_SSBP2_4_knockout_rep1

description:
Library name: H3K27ac_ChIP_SSBP2_4_knockout_rep1
H3K27ac_ChIP_SSBP2_4_knockout_rep1_DESeq2_normalized.bw
H3K27ac_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: H3K27ac_ChIP_WT_rep2

description:
Library name: H3K27ac_ChIP_WT_rep2
H3K27ac_ChIP_WT_rep2_RPKM.bw
H3K27ac_ChIP_WT_merge_RPKM.bw
H3K27ac_ChIP_WT_rep2_DESeq2_normalized.bw
H3K27ac_ChIP_WT_merge_DESeq2_normalized.bw


title: H3K27ac_ChIP_WT_rep1

description:
Library name: H3K27ac_ChIP_WT_rep1
H3K27ac_ChIP_WT_rep1_RPKM.bw
H3K27ac_ChIP_WT_merge_RPKM.bw
H3K27ac_ChIP_WT_rep1_DESeq2_normalized.bw
H3K27ac_ChIP_WT_merge_DESeq2_normalized.bw


title: SSBP3_ChIP_SSBP2_4_knockout_rep2

description:
Library name: SSBP3_ChIP_SSBP2_4_knockout_rep2
SSBP3_ChIP_SSBP2_4_knockout_rep2_DESeq2_normalized.bw
SSBP3_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N734


title: NOVA76_N-Brush_Phase_2_SD_-1

description: Gene expression profiling of nasal epithelium from influenza infected humans


title: NOVA69_N-Brush_Phase_2_SD_-1


title: kidney biopsy N742


title: NOVA61_N-Brush_Phase_2_SD_-1


title: kidney biopsy N732


title: NOVA76_N-Brush_Phase_2_SD1


title: NOVA82_N-Brush_Phase_2_SD1


title: kidney biopsy N731


title: NOVA65_N-Brush_Phase_2_SD_-1


title: SSBP3_ChIP_SSBP2_4_knockout_rep1

description:
Library name: SSBP3_ChIP_SSBP2_4_knockout_rep1
SSBP3_ChIP_SSBP2_4_knockout_rep1_DESeq2_normalized.bw
SSBP3_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N725


title: SSBP3_ChIP_WT_rep2

description:
Library name: SSBP3_ChIP_WT_rep2
SSBP3_ChIP_WT_rep2_RPKM.bw
SSBP3_ChIP_WT_merge_RPKM.bw
SSBP3_ChIP_WT_rep2_DESeq2_normalized.bw
SSBP3_ChIP_WT_merge_DESeq2_normalized.bw
SSBP3_ChIP_WT_rep2_minus_estradiol_DESeq2_normalized.bw
SSBP3_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: NOVA34_N-Brush_Phase_2_SD_-1


title: kidney biopsy N724


title: kidney biopsy N728


title: NOVA51_N-Brush_Phase_2_SD_-1_a


title: SSBP3_ChIP_WT_rep1

description:
Library name: SSBP3_ChIP_WT_rep1
SSBP3_ChIP_WT_rep1_RPKM.bw
SSBP3_ChIP_WT_merge_RPKM.bw
SSBP3_ChIP_WT_rep1_DESeq2_normalized.bw
SSBP3_ChIP_WT_merge_DESeq2_normalized.bw
SSBP3_ChIP_WT_rep1_minus_estradiol_DESeq2_normalized.bw
SSBP3_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: kidney biopsy N741


title: NOVA53_N-Brush_Phase_2_SD_-1


title: NOVA79_N-Brush_Phase_2_SD_-1


title: kidney biopsy N722


title: LMO2_ChIP_SSBP2_4_knockout_rep3

description:
Library name: LMO2_ChIP_SSBP2_4_knockout_rep3
LMO2_ChIP_SSBP2_4_knockout_rep3_DESeq2_normalized.bw
LMO2_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N726


title: NOVA52_N-Brush_Phase_2_SD_-1


title: LMO2_ChIP_SSBP2_4_knockout_rep2

description:
Library name: LMO2_ChIP_SSBP2_4_knockout_rep2
LMO2_ChIP_SSBP2_4_knockout_rep2_DESeq2_normalized.bw
LMO2_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N727


title: LMO2_ChIP_SSBP2_4_knockout_rep1

description:
Library name: LMO2_ChIP_SSBP2_4_knockout_rep1
LMO2_ChIP_SSBP2_4_knockout_rep1_DESeq2_normalized.bw
LMO2_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: NOVA56_N-Brush_Phase_2_SD_-1


title: LMO2_ChIP_WT_rep3

description:
Library name: LMO2_ChIP_WT_rep3
LMO2_ChIP_WT_rep2_RPKM.bw
LMO2_ChIP_WT_merge_RPKM.bw
LMO2_ChIP_WT_rep3_DESeq2_normalized.bw
LMO2_ChIP_WT_merge_DESeq2_normalized.bw


title: LMO2_ChIP_WT_rep2

description:
Library name: LMO2_ChIP_WT_rep2
LMO2_ChIP_WT_rep2_RPKM.bw
LMO2_ChIP_WT_merge_RPKM.bw
LMO2_ChIP_WT_rep2_DESeq2_normalized.bw
LMO2_ChIP_WT_merge_DESeq2_normalized.bw


title: NOVA63_N-Brush_Phase_2_SD_-1_b


title: LMO2_ChIP_WT_rep1

description:
Library name: LMO2_ChIP_WT_rep1
LMO2_ChIP_WT_rep1_RPKM.bw
LMO2_ChIP_WT_merge_RPKM.bw
LMO2_ChIP_WT_rep1_DESeq2_normalized.bw
LMO2_ChIP_WT_merge_DESeq2_normalized.bw


title: kidney biopsy N719


title: NOVA33_N-Brush_Phase_2_SD_-1


title: LDB1_ChIP_SSBP2_4_knockout_rep3

description:
Library name: LDB1_ChIP_SSBP2_4_knockout_rep3
LDB1_ChIP_SSBP2_4_knockout_rep3_DESeq2_normalized.bw
LDB1_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N721


title: LDB1_ChIP_SSBP2_4_knockout_rep4

description:
Library name: LDB1_ChIP_SSBP2_4_knockout_rep4
LDB1_ChIP_SSBP2_4_knockout_rep4_DESeq2_normalized.bw
LDB1_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N720


title: LDB1_ChIP_SSBP2_4_knockout_rep2

description:
Library name: LDB1_ChIP_SSBP2_4_knockout_rep2
LDB1_ChIP_SSBP2_4_knockout_rep2_DESeq2_normalized.bw
LDB1_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: LDB1_ChIP_SSBP2_4_knockout_rep1

description:
Library name: LDB1_ChIP_SSBP2_4_knockout_rep1
LDB1_ChIP_SSBP2_4_knockout_rep1_DESeq2_normalized.bw
LDB1_ChIP_SSBP2_4_knockout_merge_DESeq2_normalized.bw


title: kidney biopsy N723


title: LDB1_ChIP_WT_rep4

description:
Library name: LDB1_ChIP_WT_rep4
LDB1_ChIP_WT_rep4_RPKM.bw
LDB1_ChIP_WT_merge_RPKM.bw
LDB1_ChIP_WT_rep4_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_DESeq2_normalized.bw
LDB1_ChIP_WT_rep4_minus_estradiol_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw