title: HC_4

city: Bethesda

first: Lu

state: Maryland

address: 4721 Rosedale Avenue, Apt 407

department: Department of Dermatology

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: LC_1480
10X Genomics

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (v5.0.1). By using CellRanger (v8.0.1), the filtered FASTQ files were aligned to the GRCh38-2020-A human reference genome to generate the raw gene expression matrices. The output gene expression matrices were imported for filtering in Seurat (v5.1.0).
Assembly: GRCh38
Supplementary files format and content: Matrix tabble with raw gene counts for every gene and every cell

source_name: peripheral blood

extract_protocol:
The human blood samples were centrifuged at 3,000 rpm for 15 minutes to separate plasma and cellular components. Plasma was aliquoted and stored at -80°C until further analysis. The cellular fraction was treated with RBC lysis buffer (Solarbio, China) to remove erythrocytes. The prepared human blood cells were washed with phosphate buffered saline (PBS) containing 0.04% bovine serum albumin (Sigma-Aldrich, USA). Cell viability was assessed by trypan blue staining with a threshold of >85%. Cell numbers were counted using an automated cell counter (Countess II FL, ThermoFisher) to achieve a final concentration of 700-1200 cells/μl.
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an IlluminaNovaSeq6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: peripheral blood

value: peripheral blood cells


title: P4O2 COVID-19, study visit 1, patient 34

status: Public on Nov 21 2025

type: SRA

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: nasal epithelial cells

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

tag: cell type

value: nasal epithelial cells

tag: time

value: 3-6 months post-COVID

tag: visit

value: study visit 1

tag: individual

value: patient 34

tag: disease state

value: long COVID


title: HC_3

last: Zhang

country: USA

description:
Library name: LC_1479
10X Genomics

library_source: transcriptomic single cell

tag: tissue


title: IFA_Tamiflu_12_2

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

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

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

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

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

value: Lung

tag: virus

value: IFA

tag: genotype

tag: treatment

value: Tamiflu


title: P4O2 COVID-19, study visit 1, patient 33

value: patient 33


title: CPUO_4

description:
Library name: LC_1414
10X Genomics


title: Kidney_HFD-SHAM_2

city: Indianapolis

first: Wenjun

state: IN

address: 1044 W. Walnut Street, R4 W116

institute: Indiana University School of Medicine

description: Library name: KC408Kidney_HFD-SHAM

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

source_name: Kidney

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

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

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

value: Kidney

value: WT

value: HFD+Sham

tag: batch


title: IFA_Tamiflu_12_1


title: P4O2 COVID-19, study visit 1, patient 32

value: patient 32


title: HC_2

description:
Library name: LC_11052
10X Genomics


title: Kidney_HFD-SHAM_1

description: Library name: KC407Kidney_HFD-SHAM


title: IFA_Tamiflu-IFNAR_8_4

value: Tamiflu-IFNAR


title: P4O2 COVID-19, study visit 1, patient 31

value: patient 31


title: HC_1

description:
Library name: LC_11051
10X Genomics

value: peripheral blood


title: Kidney_ND-IRI_3

description: Library name: KC424Kidney_ND-IRI

value: ND+hIRI


title: IFA_Tamiflu-IFNAR_8_2


title: IFA_Tamiflu-IFNAR_8_3


title: CPUO_3

description:
Library name: LC_1277
10X Genomics

value: peripheral blood cells


title: Kidney_ND-IRI_2

description: Library name: KC420Kidney_ND-IRI


title: P4O2 COVID-19, study visit 1, patient 29

value: nasal epithelial cells

value: 3-6 months post-COVID

value: patient 29


title: P4O2 COVID-19, study visit 1, patient 28

value: study visit 1

value: patient 28

value: long COVID


title: Kidney_ND-IRI_1

description: Library name: KC404Kidney_ND-IRI


title: Kidney_ND-SHAM_3

description: Library name: KC422Kidney_ND-SHAM

value: ND+Sham


title: IFA_Tamiflu-IFNAR_8_1

value: Lung

value: IFA


title: Kidney_HFD-SHAM_3

description: Library name: KC419Kidney_HFD-SHAM

value: Kidney

value: WT


title: CPUO_1

description:
Library name: LC_1027
10X Genomics


title: IFA_Tamiflu-CD8_8_4


title: P4O2 COVID-19, study visit 1, patient 27

value: patient 27


title: Kidney_ND-SHAM_2

description: Library name: KC421Kidney_ND-SHAM


title: human iPSc-derived CD205+ TEPs - Replicate 6

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

description: Library name: TEP_CD205_NP9

data_processing:
Reads were aligned to the human reference genome (hg19) using TopHat2/Bowtie2 with default parameters. Fpkm quantification was performed using HTSeq-count
Assembly: Hg19
Supplementary files format and content: Tab-delimited text file with count quantification

source_name: Thymic epithelial progenitor cells

extract_protocol:
CD205+ cells were isolated from iPSc-derived TEPs by FACS sorting
Libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA kit and Illumina Nextera XT DNA Library Preparation Kit following manufacturer's protocols.

value: Thymic epithelial progenitor cells


title: IFA_Tamiflu-CD8_8_2


title: Kidney_ND-SHAM_1

description: Library name: KC406Kidney_ND-SHAM


title: human iPSc-derived CD205+ TEPs - Replicate 5

description: Library name: TEP_CD205_NP8


title: IFA_Tamiflu-CD8_8_1


title: P4O2 COVID-19, study visit 1, patient 30

value: patient 30


title: P4O2 COVID-19, study visit 1, patient 25

value: patient 25


title: human iPSc-derived CD205+ TEPs - Replicate 4

description: Library name: TEP_CD205_NP7


title: mESCs, Hmgn1-/-Hmgn2-/-, rep 3

city: Chapel Hill

first: Riya

last: Gohil

state: NC

address: 250 Bell Tower Drive, 3314 Genome Sciences Building

institute: University of North Carolina at Chapel Hill

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, rep 3

data_processing:
Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 12 -c SortedByCoordinate
Differentially expressed genes were identified using DESeq2 from Bioconductor (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: For each sample, a text file with reads per gene (gene count) is given.

source_name: v6.5 mESC

growth_protocol: Mouse embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA was extracted and purified using the Zymo Direct-zol RNA MiniPrep kit (Zymo).
Libraries were prepared by Novogene, with poly-A transcript enrichment and sequenced by Novogene.

treatment_protocol: Cells were grown and counted (10 million cells per IP condition) prior to crosslinking. Cells were collected via trypsin treatment for 5 minutes at 37˚C. Cell were harvested after 48 hours for RNA collection.

tag: cell line

value: v6.5 mESC


title: CPUO_2

description:
Library name: LC_1040
10X Genomics

value: peripheral blood

value: peripheral blood cells


title: human iPSc-derived CD205+ TEPs - Replicate 3

description: Library name: TEP_CD205_NP6


title: IFA_Tamiflu_8_3

value: Tamiflu


title: IFA_Tamiflu_8_2


title: mESCs, Hmgn1-/-Hmgn2-/-, rep 2

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, rep 2


title: P4O2 COVID-19, study visit 1, patient 24

value: nasal epithelial cells

value: 3-6 months post-COVID

value: patient 24


title: human iPSc-derived CD205+ TEPs - Replicate 2

description: Library name: TEP_CD205_NP2


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

city: Austin

first: Frances

middle: Anne

last: Champagne

state: Texas

address: 108 E Dean Keeton St

department: Psychology

institute: University of Texas at Austin

description: Library name: 88M1

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

organism: Rattus norvegicus

source_name: Medial preoptic area

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

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

value: Medial preoptic area

tag: age

value: Postnatal day 10

value: 150 ug/kg Mixed BP

tag: Sex

value: Male

tag: nest attendance

tag: licking/grooming


title: mESCs, Hmgn1-/-Hmgn2-/-, rep 1

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, rep 1


title: IFA_Tamiflu_8_1

value: Lung

value: IFA


title: P4O2 COVID-19, study visit 1, patient 22

value: study visit 1

value: patient 22

value: long COVID


title: mESCs, Hmgn2-/-, rep 2

description: Library name: Hmgn2-/- mESCs, rep 2


title: human iPSc-derived CD205+ TEPs - Replicate 1

description: Library name: TEP_CD205_NP1

value: Thymic epithelial progenitor cells


title: P4O2 COVID-19, study visit 1, patient 21

value: patient 21


title: mESCs, Hmgn2-/-, rep 3

description: Library name: Hmgn2-/- mESCs, rep 3

value: v6.5 mESC


title: IFA_PBS_8_4

value: PBS


title: IFA_PBS_8_3


title: P4O2 COVID-19, study visit 1, patient 20

value: patient 20


title: P4O2 COVID-19, study visit 1, patient 26

value: nasal epithelial cells

value: patient 26


title: Isolated DCs from D28 hTOs - Replicate 2

description: Library name: DC2

data_processing:
Reads were aligned to the human reference genome (hg19) using TopHat2/Bowtie2 with default parameters. Fpkm quantification was performed using Cufflinks,
Assembly: Hg19
Supplementary files format and content: Tab-delimited text files with fpkm quantification for each sample

source_name: thymic organoid

extract_protocol:
Cells were isolated from hTOs seeded with primary early thymic progenitors (ETPs) at the late phase of maturation (D28) by FACS sorting with CD45-EPCAM+HLA-DRhigh phenotype (TEChigh), CD45-EPCAM+HLA-DRlow (TEClow) and CD45+EPCAMlo (DC)
Libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA kit and Illumina Nextera XT DNA Library Preparation Kit following manufacturer's protocols.

value: thymic organoid

value: Dendritic cells


title: Isolated DCs from D28 hTOs - Replicate 1

description: Library name: DC1


title: mESCs, Hmgn2-/-, rep 1

description: Library name: Hmgn2-/- mESCs, rep 1


title: IFA_PBS_8_2


title: mESCs, Hmgn1-/-, rep 3

description: Library name: Hmgn1-/- mESCs, rep 3


title: HLA-DRlow isolated TECs from D28 hTOs

description: Library name: TEClo

value: Thymic epithelial cells


title: P4O2 COVID-19, study visit 1, patient 23

value: 3-6 months post-COVID

value: patient 23


title: IFA_PBS_8_1

value: Lung


title: P4O2 COVID-19, study visit 1, patient 17

value: patient 17


title: mESCs, Hmgn1-/-, rep 2

description: Library name: Hmgn1-/- mESCs, rep 2


title: IFA_Tamiflu-IFNAR_6_4

value: IFA

value: Tamiflu-IFNAR


title: HLA-DRhigh isolated TECs from D28 hTOs

description: Library name: TEChi


title: IFA_Tamiflu-IFNAR_6_3


title: mESCs, Hmgn1-/-, rep 1

description: Library name: Hmgn1-/- mESCs, rep 1


title: Mock-24-GFPp replicate 3

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package FASTX-toolkit [http://hannonlab.cshl.edu/fastx_toolkit/].
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.7.11a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Assembly: GRCh38.p14 (GenCode release 46)
Supplementary files format and content: In excel file format, Raw read counts data

source_name: HEK293 cell

extract_protocol:
RNA extraction was based on a method described by Phan[7] and his colleagues. The cells were washed twice before being resuspended in a 1:1 mixture of PBS and Drop-seq lysis buffer (Ficoll PM-400 6%, Sarkosyl 0.2%, EDTA 10 mM, Tris pH 7.5 200 mM, DTT 50 mM), supplemented with proteinase K. Samples were heat to 56°C for an hour (cross-link heat reversal) followed by incubation for 10 mins at RT followed by incubation on ice for at least 5 mins. The lysate was then combined with 350 uL of RLT plus buffer from RNeasy kit and processed according to the manufacturer’s protocol. The RNA samples thus obtained were quantified and assessed for integrity using the 4200 TapeStation system (Agilent, Santa Clara, CA). RNA quality and concentration were assessed with a BioAnalyzer
RNA-Seq Libraries were generated by using the NEBNext rRNA Depletion kit v2(Human/Mouse/Rat) followed by section 2 of the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB). RNA-Seq libraries were quantified by qPCR according to the Illumina Sequencing Library qPCR Quantification Guide and the quality of the libraries was evaluated on Agilent Bioanalyzer 2100 using the Agilent DNA-1000 chip. The RNA-Seq library sequencing was performed using Illumina Next-Seq500

value: HEK293 cell

value: HEK293 cell line

value: cell line

value: WT

value: Transfected paraformaldehyde fixed, sorted, virus gene removed

value: 24 hours


title: Mock-24-GFPp replicate 2


title: mESCs, WT, rep 3

description: Library name: WT mESCs, rep 3

value: v6.5 mESC

value: Wildtype


title: IFA_Tamiflu-IFNAR_6_1


title: Mock-24-GFPp replicate 1


title: P4O2 COVID-19, study visit 1, patient 15

value: nasal epithelial cells

value: study visit 1

value: patient 15

value: long COVID


title: mESCs, WT, rep 2

description: Library name: WT mESCs, rep 2


title: P4O2 COVID-19, study visit 1, patient 14

value: 3-6 months post-COVID

value: patient 14


title: IFA_Tamiflu-CD8_6_4

value: Lung


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

value: patient 19


title: mESCs, WT, rep 1

description: Library name: WT mESCs, rep 1


title: P4O2 COVID-19, study visit 1, patient 13

value: patient 13


title: AAV24-GFPpAFp replicate 2

value: HEK293 cell

value: Transfected paraformaldehyde fixed, sorted, virus producer


title: IFA_Tamiflu-CD8_6_2

value: IFA


title: mESCs, Hmgn1-/-Hmgn2-/-, CTCF, rep 2

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, CTCF, rep 2

library_source: genomic

data_processing:
Alignment: reads were aligned to a hybrid mm10+hg38 genome with  bowtie (v1.3.1) with parameters -v 2 -p 24 -S -m 1 -best -strata
PCR Duplicate Removal: duplicates removed with samtools (v1.17) fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v2.1.2) with parameters -f BED -g mm -q 0.01
Spike-in Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = (5/(# human reads / # mouse reads))*100
Coverage File Generation: bigwig files were generated using bedtools (v2.25.0) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normaliztion Factor) followed by ucsctools (v320) bedGraphToBigWig
Assembly: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary files format and content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in a genome browser.

molecule: genomic DNA

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
mESCs were treated with 1% formaldehyde for 5 minutes to crosslink the chromatin, followed by quenching with 2.5M glycine. After chromatin extraction, 5% of HEK293T chromatin was added to the mESC samples as a spike-in control for normalization. The crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2, washed, and resuspended in Shearing Buffer. Nuclei were sonicated using a Covaris E220 with the following parameters: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes, resulting in chromatin fragments ranging from 200 to 1000 base pairs.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: Cells were grown and counted (10 million cells per IP condition) prior to crosslinking. Cells were collected via trypsin treatment for 5 minutes at 37˚C.

tag: chip antibody

value: CTCF (Active Motif, 61311)


title: IFA_Tamiflu-CD8_6_3


title: AAV24-GFPpAFp replicate 1

value: HEK293 cell line

value: cell line

value: WT


title: P4O2 COVID-19, study visit 1, patient 12

value: patient 12


title: mESCs, Hmgn1-/-Hmgn2-/-, CTCF, rep 1

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, CTCF, rep 1

value: v6.5 mESC


title: P4O2 COVID-19, study visit 1, patient 18

value: nasal epithelial cells

value: study visit 1

value: patient 18


title: mESCs, Hmgn1-/-Hmgn2-/-, RAD21, rep 2

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, RAD21, rep 2

value: RAD21 (abcam, ab992)


title: AAV24-GFPpAFn replicate 3

value: Transfected paraformaldehyde fixed, sorted, non virus producer

value: 24 hours


title: IFA_Tamiflu_6_4

value: Lung

value: Tamiflu


title: P4O2 COVID-19, study visit 1, patient 16

value: 3-6 months post-COVID

value: patient 16

value: long COVID


title: P4O2 COVID-19, study visit 1, patient 11

value: patient 11


title: P4O2 COVID-19, study visit 1, patient 10

value: patient 10


title: AAV24-GFPpAFn replicate 2

value: HEK293 cell

value: HEK293 cell line

value: cell line


title: mESCs, Hmgn1-/-Hmgn2-/-, RAD21, rep 1

description: Library name: Hmgn1-/-Hmgn2-/- mESCs, RAD21, rep 1

value: v6.5 mESC


title: IFA_Tamiflu_6_3

value: IFA


title: AAV24-GFPpAFn replicate 1

value: WT


title: P4O2 COVID-19, study visit 1, patient 9

value: nasal epithelial cells

value: study visit 1

value: patient 9


title: AAV24-GFPpAFp replicate 3

value: Transfected paraformaldehyde fixed, sorted, virus producer

value: 24 hours


title: P4O2 COVID-19, study visit 1, patient 8

value: patient 8


title: IFA_Tamiflu_6_1

value: Lung

value: Tamiflu


title: 293SF-fixed replicate 2

value: paraformaldehyde fixed


title: IFA_Tamiflu_6_2


title: FRBplusPD1-Vax

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (mm10) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v7.2.0)
Subsequent filtering and downstream analyses were performed using Seurat (v5). Genes expressed in less than 3 cells and cells that express less than 300 genes were excluded from further analyses. Additional filtering of cells was determined based on the overall distributions of total RNA counts (< 80,000) and the proportion of mitochondrial genes (< 10%) detected to eliminate potential doublets and dying cells, respectively. Additional detection of doublets was performed using Scrublet.  Thresholding for doublet detection was set based on total distribution of doublet scores (doublet threshold = 0.2). Quantification of mitochondrial and ribosomal gene expression was calculated using the PercentageFeatureSet function, using gene sets compiled from the Mouse Genome Informatics database. Cell cycle phase scoring was accomplished against normalized expression via the CellCycleScoring function using mouse genes orthologous to known cell cycle phase marker genes. Raw counts were normalized by dividing gene counts to total counts per sample and multiplying by scaling factor of 10,000 and then applying log transformation. Principle component analysis was performed on normalized and scaled features (top 3000 variable features defined after variance stabilization transformation) and optimal dimensionality of the dataset was decided by examination of the Elbow plot, as the total number of PCs where gain in cumulative variation explained was greater than 0.1% (PCs = 41). UMAP was applied for non-linear dimensional reduction to obtain a low dimensional representation of cellular states. The FindNeighbors function was utilized that implements a graph based nearest neighbor clustering approach, and then the FindClusters function was used to identify unsupervised cell clusters using the leiden method at a resolution of 0.08.
Assembly: mm10
Supplementary files format and content: 10x Genomics cellragner output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: .rds object containing quality filtered total cells and associated metadata

source_name: Ascites/Peritoneal fluid

growth_protocol: 5x106 IE9-mp1-hFRa cells (IP in 500µl PBS) were injected to establish tumors. IP tumor progression was monitored based on increased abdominal distension (measured as changes in circumference) due to accumulation of peritoneal ascites, which closely correlates with solid tumor growth in this model, with mice considered endpoint and euthanized when abdominal circumference reached 10cm (or at earlier measurements if mice developed decreasing health status due to peritoneal disease progression).

extract_protocol:
), mice were injected IP with 5ml PBS and the peritoneal wash (corresponding to the OC TME) collected from 4 mice/group. Recovered cells were washed in PBS and immediately stained with Zombie NIR, prepared in PBS for sorting of viable cells. Stained cells were sorted using a BD FACSAria II, collecting 30,000 live cells per mouse, which were then pooled within cohorts (120,000 live cells/group). For later time points, mice receiving  FR-B T cell + anti-PD-1 treated mice were categorized as having Progressive Disease (PD; defined as animals with ascites accumulation and abdominal circumference ≥ 8.0 cm) or Durable Response (DR; defined as mice having no ascites accumulation) on Day 38. Ascites and/or peritoneal washes were collected from PD and DR animals (n=4/group), subjected to ACK lysis to remove red blood cells, counted and pooled equally within each cohort (50,000 cells/mouse) to reach 200,000 total live cells/group.  Similarly, ascites or peritoneal wash from mice treated with FR-B T cells + aPD1 or FR-B T cells+ aPD1+ Ad-OVA Vax were collected 14 days post vaccination (day 28) were collected from 4 mice/group, subjected to ACK lysis, counted, and equally pooled to reach 120,000 live cells/group. Immediately following preparation, cells were provided to the Roswell Park Genomics Shared Resource (GSR) for further processing and single cell sequencing (10x Genomics).
Single Cell 5' Reagent Kits v2 (Dual Index)
10x Genomics 5'GEX

treatment_protocol: Mice received 1.0x106 FR-B T cells or an equivalent number of Control T cells delivered by loco-regional IP infusion (200µl PBS injection volume). 2 days post ACT, mice received 200µg of anti-PD1 (Clone RMP1-14, Bio X cell) or IgGa2 isotype control (Bio X cell) by IP injection, which was delivered every 3rd day (5 or 6 total doses). For vaccination studies, a E1/E3-deleted human adenovirus serotype 5 expressing full-length ovalbumin (Ad-OVA)   (kindly provided by Dr. Brian Lichty, McMaster University) was used to elicit OVA-specific T cell responses. 108 PFU Ad-OVA was delivered by intramuscular injection into both rear limbs 2 weeks post ACT.

value: Ascites/Peritoneal fluid

value: total live cells

tag: library type

tag: timepoint

value: d28 post ACT

value: FR-B T cells + aPD1 + Ad-OVA Vax

tag: response

value: Late Response


title: P4O2 COVID-19, study visit 1, patient 7

tag: cell type

tag: time

value: 3-6 months post-COVID

tag: visit

value: patient 7

value: long COVID


title: FRBplusPD1-last

tag: tissue

value: FR-B T cells + aPD1


title: IFA_PBS_6_4

tag: virus

value: IFA

value: PBS


title: IFA_Tamiflu-CD8_6_1

tag: genotype


title: 293SF-fixed replicate 1

value: HEK293 cell

value: HEK293 cell line

value: cell line

value: WT

tag: treatment


title: PD

value: d33 post ACT

value: Progressive Disease (PD/NR)


title: IFA_PBS_6_3

value: Lung


title: P4O2 COVID-19, study visit 1, patient 5

value: nasal epithelial cells

value: study visit 1

tag: individual

value: patient 5

tag: disease state


title: EZH2-ΔSBD-AEBP2-ChIP-mESC

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

state: New York

address: 1230 York ave

institute: Rockefeller University

description:
Library name: EZH2-ΔSBD-AEBP2-ChIP
ChIP-seq

data_processing:
ChIP-seq reads were aligned using the Rsubread R Bioconductor package (v1.30.6) and predicted fragment lengths calculated by the ChIPQC R Bioconductor package (v1.16.2). Normalized, fragment-extended signal bigWigs were created using the rtracklayer R Bioconductor package (v1.40.6), and peaks called using MACS2 (v2.1.1)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: mouse embryonic stem cells

growth_protocol: ES cells (C57BL/6 × 129S4/SvJae F1) were maintained on gelatin-coated plates in KnockOut DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life Technologies) and LIF. 293T cells (ATCC) were cultured in DMEM supplemented with 4.5 g/l glucose (Corning), 10% FBS (Atlanta Biologicals), 2 mM L-glutamine (Life Technologies) and 1:100 penicilin/streptomycin (Corning).

extract_protocol:
Cross-linking ChIP in mESCs was done using ~2 × 107 cells per immunoprecipitation. Before fixation, medium was aspirated, cells were collected by TrypLE Express Enzyme (Gibco), and cells washed once with PBS. Cells were cross-linked (1% paraformaldehyde for 5 min at room temperature (RTo)) with gentle shaking. Glycine was added to quench (final concentration 125 mM, incubated for 5 min at RTo), then cells washed once with cold PBS and pelleted. To obtain a soluble chromatin extract, cells were resuspended in 1 ml LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× Complete protease inhibitor) and incubated rotating at 4 °C for 10 min. Samples were centrifuged, resuspended in 1 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1× Compete protease inhibitor), and incubated rotating at 4 °C for 10 min. Finally, samples were centrifuged, resuspended in 1 ml LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100 and 1× Complete protease inhibitor) and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 14 min using a Covaris E220 focused ultrasonicator at peak power 140, duty factor 5, and cycles/burst 200.
ChIP and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. All libraries were analyzed by TapeStation prior to sequencing. Single-end sequencing was performed on the Illumina NextSeq 500 sequencer.

value: mouse embryonic stem cells

tag: batch


title: DR

value: Ascites/Peritoneal fluid

value: total live cells

value: Durable Response (DR/R)


title: P4O2 COVID-19, study visit 1, patient 6

value: 3-6 months post-COVID

value: patient 6

value: long COVID


title: EZH2-ΔSBD-EPOP-ChIP-mESC

description:
Library name: EZH2-ΔSBD-EPOP-ChIP
ChIP-seq


title: IFA_PBS_6_2

value: IFA

value: PBS


title: P4O2 COVID-19, study visit 1, patient 4

value: patient 4


title: FRB-PD1

value: d7 post ACT

value: FR-B T cells + aPD1

value: Early Response


title: IFA_PBS_6_1

value: Lung


title: P4O2 COVID-19, study visit 1, patient 3

value: nasal epithelial cells

value: patient 3


title: EZH2-KO-AEBP2-ChIP-mESC

description:
Library name: EZH2-KO-AEBP2-ChIP
ChIP-seq

value: EZH2 KO


title: EZH2-KO-EPOP-ChIP-mESC

description:
Library name: EZH2-KO-EPOP-ChIP
ChIP-seq

value: mouse embryonic stem cells


title: FRB-IgG

value: Ascites/Peritoneal fluid

value: FR-B T cells + IgG


title: IFA_none_4_4


title: A1-AEBP2-ChIP-mESC

description:
Library name: A1-AEBP2-ChIP
ChIP-seq

value: WT


title: IFA_none_4_3


title: UTD-IgG

value: total live cells

value: UTD T cells + IgG


title: IFA_none_4_2


title: UTD-PD1

value: UTD T cells + aPD1


title: A1-EPOP-ChIP-mESC

description:
Library name: A1-EPOP-ChIP
ChIP-seq


title: P4O2 COVID-19, study visit 2, patient 48

value: 12-18 months post-COVID

value: study visit 2

value: patient 48

value: long COVID


title: P4O2 COVID-19, study visit 2, patient 47

value: patient 47


title: P4O2 COVID-19, study visit 1, patient 2

value: 3-6 months post-COVID

value: study visit 1

value: patient 2


title: EZH2-ΔSBD-H3K27ac-ChIP-mESC

description:
Library name: EZH2-ΔSBD-H3K27ac-ChIP
ChIP-seq

extract_protocol:
Cross-linking ChIP in mESCs was done using ~2 × 107 cells per immunoprecipitation. Before fixation, medium was aspirated, cells were collected by TrypLE Express Enzyme (Gibco), and cells washed once with PBS. Cells were cross-linked (1% paraformaldehyde for 5 min at room temperature (RTo)) with gentle shaking. Glycine was added to quench (final concentration 125 mM, incubated for 5 min at RTo), then cells washed once with cold PBS and pelleted. To obtain a soluble chromatin extract, cells were resuspended in 1 ml LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× Complete protease inhibitor) and incubated rotating at 4 °C for 10 min. Samples were centrifuged, resuspended in 1 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1× Compete protease inhibitor), and incubated rotating at 4 °C for 10 min. Finally, samples were centrifuged, resuspended in 1 ml LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100 and 1× Complete protease inhibitor) and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 14 min using a Covaris E220 focused ultrasonicator at peak power 140, duty factor 5, and cycles/burst 200. For ChIP-Rx of histone post-translational modifications, after centrifugation, samples were spiked with soluble chromatin from Drosophila S2 cells to comprise 2–5% of total chromatin in the lysate.
ChIP and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. All libraries were analyzed by TapeStation prior to sequencing. Single-end sequencing was performed on the Illumina NextSeq 500 sequencer.


title: IFA_none_4_1

value: Lung

value: IFA


title: JuPa02_Mo_WT_CD8_3H_CITE

city: LA JOLLA, SAN DIEGO

first: Pandurangan

last: Vijayanand

state: CALIFORNIA

address: 9420 ATHENA CIRCLE

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

library_source: other

data_processing:
bcl2fastq (v2.20.0.422) to demultiplex UMIs
count and aggr Cell Ranger (3.1.0) was used to generate filtered and aggregate UMI matrix, respectively
Seurat (4.1.1). Was used to filter, normalize and scale UMI matrix
Tissue identities were inferred by MULTIseqDemux (autoThresh = TRUE and maxiter = 10) from Seurat (v4.1.1 ) using the UMI matrix
Assembly: mm10 (v3.0.0)

molecule: protein

source_name: Liver

growth_protocol: Both Gpr25 WT and Gpr25 KO OT-I cells were transferred at a 1:1 ratio intravenously or intratracheally into congenic recipient mice.

extract_protocol:
Complementary DNA libraries were constructed using the standard 10x Genomics sequencing protocol.
To facilitate the integration of single-cell RNA-seq from the sorted CD8+ T cell subsets, 10x Genomics 3′TAG v3.1 chemistry was used.
Transferred OT-I memory CD8+ T cells were sorted into a low-retention 1.5-ml collection tube, containing 500 μl of a solution of phosphate-buffered saline (PBS):fetal bovine serum (1:1) supplemented with ribonuclease inhibitor (1:100). After sorting, ice-cold PBS was added to make up to a volume of 1400 μl. Cells were then spun down (5 min at 600g and 4°C), and the supernatant was carefully aspirated, leaving 5 to 10 μl. The cell pellet was gently resuspended in 25 μl of resuspension buffer (0.22-μm filtered ice-cold PBS supplemented with ultrapure bovine serum albumin; 0.04%; Sigma-Aldrich). After that, 33 μl of the cell suspension was transferred to a PCR tube and single-cell libraries prepared as per the manufacturer’s instructions (10x Genomics).

treatment_protocol: Mice that received both Gpr25 WT and KO cells were then infected with LCMV-OVA intraperitoneally and intratracheally to induce liver TRM and lung TRM cells, respectively.

value: Liver

tag: cell line

value: ex vivo FACS-sorted

value: T cells

tag: age

value: 12 days after T cell transfer, host 8-12 weeks

tag: strain

value: Gpr25 WT, Gpr25 KO, CD45.1 (recipient)

value: LCMV-OVA infection

value: Hashtag derived oligonucleotide (HTO)

tag: antibodies/tags

value: B0302 anti-mouse Hashtag 2


title: JuPa02_Mo_WT_CD8_3H_Gex


title: EZH2-H3K27ac-ChIP-mESC

description:
Library name: EZH2-KO-H3K27ac-ChIP
ChIP-seq

value: mouse embryonic stem cells

value: EZH2 KO


title: PBS_none_4_4


title: A1-H3K27ac-ChIP-mESC

description:
Library name: A1-H3K27ac-ChIP
ChIP-seq

value: WT


title: JuPa02_Mo_KO_CD8_3H_Gex


title: P4O2 COVID-19, study visit 2, patient 45

value: nasal epithelial cells

value: 12-18 months post-COVID

value: study visit 2

value: patient 45

value: long COVID


title: P4O2 COVID-19, study visit 2, patient 46

value: patient 46


title: JuPa02_Mo_KO_CD8_3H_CITE

value: Liver

tag: library type


title: P4O2 COVID-19, study visit 2, patient 36

value: patient 36


title: PBS_none_4_2

value: Lung


title: Vancomycin and BAP Single cell RNA-seq - LSK cells

city: Toronto

first: Wilder

last: Scott

address: 2075 Bayview Ave

institute: SRI

description: Library name: LSK VANC + BAP

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate was used to aggregate multiple samples for combined analysis
Assembly: mm10
Supplementary files format and content: gene matrices, cell barcode and gene list are included as .mtx, .tsv and .tsv files, respectively

source_name: Bone marrow

growth_protocol: Mice were bred and raised using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2

treatment_protocol: Breeding pairs and nursing dams were administered vancomycin (200 mg/L; Sigma-Aldrich, MO) in drinking water beginning at the time of mating. Offspring were continuously exposed via maternal consumption and direct intake until adulthood (lifelong). The SCFA cocktail (referred to as BAP) consisted of 40 mM butyrate, 67.5 mM acetate, and 25.9 mM propionate (all from Sigma-Aldrich), prepared fresh weekly and delivered via drinking water, as described previously (Smith et al., 2013). SCFAs solutions were prepared and changed weekly. Offspring were maintained of vancomycin+BAP until adulhood (lifelong).

value: Bone marrow

value: LSK

value: Vancomycin + BAP


title: JuPa01_Mo_WT_CD8_3H_Gex

value: ex vivo FACS-sorted

value: T cells

value: 5 days after T cell transfer, host 8-12 weeks

value: Gpr25 WT, Gpr25 KO, CD45.1 (recipient)

value: LCMV-OVA infection


title: P4O2 COVID-19, study visit 2, patient 35

value: nasal epithelial cells

value: patient 35


title: JuPa01_Mo_WT_CD8_3H_CITE

value: Hashtag derived oligonucleotide (HTO)

value: B0302 anti-mouse Hashtag 2


title: P4O2 COVID-19, study visit 2, patient 44

value: 12-18 months post-COVID

value: study visit 2

value: patient 44

value: long COVID


title: JuPa01_Mo_KO_CD8_3H_Gex

value: Liver


title: 60 min conjugation, S. meliloti, replicate 2

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

institute: CNRS

description: Library name: SM60B

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

organism: Sinorhizobium meliloti

source_name: prokaryotic cell

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

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

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

value: prokaryotic cell


title: P4O2 COVID-19, study visit 2, patient 12

value: patient 12


title: P4O2 COVID-19, study visit 2, patient 43

value: patient 43


title: JuPa01_Mo_KO_CD8_3H_CITE

value: ex vivo FACS-sorted


title: Control Single cell RNA-seq - LSK cells

description: Library name: LSK control

value: Bone marrow

value: LSK

value: Control (Regular water)


title: 60 min conjugation, S. meliloti, replicate 1

description: Library name: SM60A


title: 30 min conjugation, S. meliloti, replicate 2

description: Library name: SM30B


title: mES LaminB b2

city: Philadelphia

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: mES.LaminB.b2
zscores.1kb.mES.LaminB.b2.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed

data_processing:
For CUT&RUN samples, adapters were trimmed from fastq files using TrimGalore with default parameters (ver. 0.6.4 using Cutadapt 4.2). The resulting reads were mapped with bowtie2 (ver. 2.5.0) with the parameters -X 2000 -N 1 --local --dovetail to the mm10 assembly. Only reads mapping to the 19 autosomal chromosomes were retained, and any reads mapping to the mm10 CUT&RUN blacklist or the first 3 Mb were removed to eliminate repetitive sequences near centromeres. Duplicates were marked using Picard.
Normalized bw files were produced for each Lamin B1 or H3K9me2 sample, normalizing against a merged bam file of all IgG samples from the corresponding tissue, using deeptools bamCoverage with the parameters --operation log2 --extendReads  --binSize 50. To minimize the impact of LTR/LINE regions on window-based scores, any regions overlapping LTR or LINE elements detected by RepeatMasker and downloaded from the UCSC Table Browser were set to a minimum of 0. From these bw files, counts in tiled bins of 1kb or 10kb were calculated using deeptools multiBigwigSummary.
Z-scores for each bin were calculated from count files produced as above, ignoring any window with 0 counts in any sample, and rolling means incorporating the 5 windows flanking each window to each side were calculated from the z-scores.
Assembly: mm10
Supplementary files format and content: z-score bedgraphs contain rolling means of z-scores from 1kb bins
Supplementary files format and content: coordinates of LAD, KOD, and open regions for mES, heart, and forebrain
Library strategy: CUT&Run

source_name: mES

growth_protocol: mouse tissues: Wildtype pregnant C57BL6J dames were dissected, and embryos were staged to confirm they were E11.5. Any embryos not matching the exact stage were discarded. Cell lines: Murine C57BL/6 embryonic pluripotent stem cells were obtained from American Type Culture Collection (ATCC, cat# SCRC-1002). These cells were thawed and initially plated on 0.1% bovine gelatin coated plates with mitotically inactivated murine embryonic fibroblasts (ATCC, cat# SCRC-1040.2a) before transitioning them to LIF + 2i media. LIF + 2i media consists of DMEM with 15% Hyclone FBS (Fisher Scientific, cat# SH30070.03), 1% NEAA (Gibco, cat#11140-050), 1% Glutamax (Gibco, cat# 35050-061), 1% Pen/Strep (Gibco, cat# 15140-122), 1% Sodium Pyruvate (Gibco, cat# 11360), and 0.0007% B-mercaptoethanol (Gibco, cat# 21985-023), supplemented with LIF (1:10,000, Millipore-Sigma, cat# ESG1106), 1uM PD0325901 (Millipore-Sigma cat# PZ0162), and 3uM CHIR99021 (Millipore-Sigma, cat# SML1046).

extract_protocol:
Whole hearts and right forebrain lobes were collected and pooled by tissue type from the remaining embryos. Each tissue or cell type consisted of 3 biological replicates (tissues from 3 separate pooled litters or 3 separate culture vessels). Mouse embryonic stem cells (mESCs) or freshly isolated tissues were dissociated into single cell suspensions (via TrypLE (Gibco, cat# 12605-010) for mESCs or papain (Worthington, cat# LK003150) for tissues).
CUT&RUN was then performed per the instructions included in the CUTANA ChIC/CUT&RUN Kit (EpiCypher, cat# 14-1048, v1.0-v3.0). In brief, cells were washed and then allowed to bind to activated ConA beads. Samples were then incubated overnight at 4C on a nutator with the appropriate antibody. The following day samples were washed again and then incubated with pAG-MNase for 10 minutes at room temperature. Samples were washed again, and targeted chromatin digestion was initiated with 100mM calcium chloride and allowed to proceed for 2 hours at 4C on a nutator. The reactions were then stopped, and DNA fragments were collected via incubation in a thermocycler set to 37C for 10 minutes. Finally, DNA fragments were purified via the NucleoSpin Gel and PCR Clean-up kit (Takara Bio USA, Inc, cat# 740609). DNA libraries for Next-Generation sequencing were prepared utilizing the KAPA HyperPrep Kit (Kapa Biosystems, cat# KK8502 07962347001) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, cat# E6440S). To begin, samples were end repaired & A-tailed via incubation in a thermocycler for 30 minutes at 20C followed by a 58C incubation for 60 minutes. Next adapters were ligated per kit instructions with a 15-minute incubation at 20C with ligation buffer & DNA ligase, followed by a 37C incubation for 15 minutes with NEB USER enzyme for an additional 15 minutes. Post-ligation cleanup was performed using 1.1x AngenCourt AMPure XP Beads (Beckman Coulter, cat# A63880). Next, the libraries were amplified per kit instructions with the following thermocycler conditions: 1 cycle of initial denaturation at 98C for 45 seconds, 14 cycles of denaturation at 98C for 15 seconds and annealing and extension at 60C for 10 seconds, and 1 final extension cycle at 72C for 1 minute. Amplification was followed by an additional cleanup step with the 1.1x AngenCourt AMPure XP Beads and library quantification using the NEBNext Library Quantification Kit (cat# E7630) as per kit instructions. Library quality and fragment size was then determined via Agilent Technologies TapeStation using the High Sensitivity D1000 ScreenTape (cat# 5067-5584) and reagents (cat# 5067-5585). Libraries were then pooled and denatured via the standard Illumina protocol. Finally, samples were paired-end sequenced on an Illumina NextSeq 500 with a high-throughput flow cell (cat# 20022408).

value: mES

tag: cut&run antibody

value: Lamin B1 (Abcam, cat #ab16048, lot #GR195923)


title: P4O2 COVID-19, study visit 2, patient 42

value: nasal epithelial cells

value: patient 42


title: PBS_none_4_3

value: Lung


title: mES IgG b3

description: Library name: mES.IgG.b3

value: IgG (Cell Signaling, cat #2729S, lot #10)


title: mES LaminB b1

description:
Library name: mES.LaminB.b1
zscores.1kb.mES.LaminB.b1.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed


title: P4O2 COVID-19, study visit 2, patient 31

value: 12-18 months post-COVID

value: study visit 2

value: patient 31


title: 30 min conjugation, S. meliloti, replicate 1

description: Library name: SM30A


title: C1_Heart_d19

city: Kraków

first: Monika

middle: Marta

last: Stefanska

state: malopolska

address: Medical College, Wielicka 265

department: Department of Clinical Immunology

country: Poland

institute: Jagiellonian University

description: Fresh Frozen Spatial Transcriptome

data_processing:
*library strategy: Spatial Transcriptomics
Output fastq files were uploaded to 10x Genomics Space Ranger Software (spaceranger-2.0.1). Data were demultiplexed, pre-analyzed and mapped to the mouse reference genome (mm10-3.0.0) with a provided by 10x Genomics cellranger mkref pipeline.
Assembly: mm10-3.0.0
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: aligned_fiducials.jpg.gz
Supplementary files format and content: detected_tissue_image.jpg.gz
Supplementary files format and content: scalefactors_json.json.gz
Supplementary files format and content: tissue_hires_image.png.gz
Supplementary files format and content: tissue_lowres_image.png.gz
Supplementary files format and content: tissue_position_list_csv.gz

source_name: Heart

extract_protocol:
Fresh frozen tissues were OCT embedded, and 10 µm sections were cut with cryostat.
Spatial transcriptome sequencing libraries were prepared using 10x Genomics Visium Spatial Gene Expression Slides.

value: Heart

tag: Stage

value: BALB/c wt


title: JuPa08_WT_CD8_Gex

description:
10X Genomics_5v2_0
sc_gpr25_lung_day30_umi.txt.gz
sc_gpr25_lung_day30_annotation.txt.gz

data_processing:
bcl2fastq (v2.20.0.422) to demultiplex UMIs
count and aggr Cell Ranger (3.1.0)  was used to generate filtered and aggregate UMI matrix, respectively
Seurat (4.1.1). Was used to filter, normalize and scale UMI matrix
Tissue identities were inferred by MULTIseqDemux (autoThresh = TRUE and maxiter = 10) from Seurat (v4.1.1) using the UMI matrix
Assembly: mm10 (v3.0.0)
Supplementary files format and content: sc_gpr25_liver_day30_annotation.txt.gz for 2745 cells in TAB delimited TXT
Supplementary files format and content: sc_gpr25_liver_day30_umi.txt.gz for 2745  cells in TAB delimited TXT
Supplementary files format and content: sc_gpr25_lung_day30_annotation.txt.gz for 2102 cells in TAB delimited TXT
Supplementary files format and content: sc_gpr25_lung_day30_umi.txt.gz for 2102 cells in TAB delimited TXT
Library strategy: CITE-Seq

tag: cell type

value: T cells

value: 30 days after T cell transfer, host 8-12 weeks

value: Gpr25 WT, Gpr25 KO, CD45.1 (recipient)

value: LCMV-OVA infection

value: GEX


title: A1_Heart_d0

description: Fresh Frozen Spatial Transcriptome


title: P4O2 COVID-19, study visit 2, patient 41

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

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

tag: time

value: patient 41

value: long COVID


title: Vancomycin Single cell RNA-seq - LSK cells

description: Library name: LSK VANC

value: Bone marrow

value: LSK

value: Vancomycin


title: JuPa08_KO_CD8_Gex

value: Lung

value: ex vivo FACS-sorted


title: P4O2 COVID-19, study visit 2, patient 18

value: nasal epithelial cells

value: 12-18 months post-COVID

tag: visit

value: patient 18


title: mES IgG b1

description: Library name: mES.IgG.b1

tag: tissue

value: mES

value: IgG (Cell Signaling, cat #2729S, lot #10)


title: Infected DblGATA1 4 w.p.i 5

type: RNA

city: Stanford

first: Daniel

last: Arve-Butler

state: CA

address: 299 Campus Drive, FAIRCHILD BUILDING D33

institute: Stanford University

description:
GATA5
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 5, 4 w.p.i.)

hyb_protocol: Xenium probe hybridization, ligation and RCA per 10x protocols.

scan_protocol: Imaging on 10x Genomics Xenium Analyzer; onboard processing.

data_processing:
Xenium Onboard Analysis generated per-cell transcript counts and spatial coordinates; data exported as cell_feature_matrix.zarr.zip, cells.csv.gz, and transcripts.parquet with Xenium Explorer v1.7. Downstream analysis in R/Seurat v5 with SCTransform, PCA/UMAP, clustering, integration across samples; outputs: xenium_integrated_final.rds, clusters_per_cell.csv, marker_genes_per_cluster.csv.
Processed files contain: clusters_per_cell.csv: per-cell metadata (sample/group/batch/cluster) and UMAP (numeric); marker_genes_per_cluster.csv: per-cluster differential expression (gene, cluster, avg_log2FC, pct.1, pct.2, p_val, p_val_adj); xenium_integrated_final.rds: Seurat object with normalized counts, reductions, clusters.

source_name: Mesenteric lymph node

label_protocol: Not applicable (imaging-based in situ assay).

growth_protocol: Salmonella Typhimurium SL1344 was grown overnight in LB at 37 °C with agitation.

extract_protocol: Mesenteic lymph nodes harvested 4 wpi, embedded in OCT, cryosectioned (10 µm), placed on Xenium slides.

treatment_protocol: Mice (7–10 weeks) were orally inoculated with 1×10^8 CFU in 20 µl; controls received no treatment.

value: MLN

value: 129X1/SvJ DblGATA1

value: STm SL1344 1e8 CFU oral


title: Infected DblGATA1 4 w.p.i 6

description:
GATA6
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 6, 4 w.p.i.)


title: PBS_none_4_1

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

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

tag: virus


title: mES LaminB b3

description:
Library name: mES.LaminB.b3
zscores.1kb.mES.LaminB.b3.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed

tag: genotype

value: Lamin B1 (Abcam, cat #ab16048, lot #GR195923)


title: JuPa03_WT_CD8_CITE

description:
10X Genomics_5v2_0
sc_gpr25_liver_day30_annotation.txt.gz

value: Liver

value: T cells

value: 30 days after T cell transfer, host 8-12 weeks

value: Gpr25 WT, Gpr25 KO, CD45.1 (recipient)

tag: treatment

value: LCMV-OVA infection

value: Hashtag derived oligonucleotide (HTO)

value: B0302 anti-mouse Hashtag 2:GGTCGAGAGCATTCA


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

value: 3-6 months post-COVID

value: study visit 1

tag: individual

value: patient 1

value: long COVID


title: Infected DblGATA1 4 w.p.i 3

description:
GATA3
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 3, 4 w.p.i.)


title: JuPa03_KO_CD8_CITE

value: ex vivo FACS-sorted


title: mES H3K9me2 b2

description:
Library name: mES.H3K9me2.b2
zscores.1kb.mES.H3K9me2.b2.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed

value: mES


title: mES H3K9me2 b3

description:
Library name: mES.H3K9me2.b3
zscores.1kb.mES.H3K9me2.b3.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed


title: KO Sample 2_late

first: Bo

last: Yu

address: 1291 Welch Road, Biomedical Innovations Building Room 2700 Room 2700

department: OB/GYN

description: Library name: A14_95_P10

data_processing:
. Each DNA sequencing library was run at 1X coverage and resulting in an average of 24 million raw reads. Sequencing quality was assessed using Novogene’s internal platform and FastQC v0.12.0
Assembly: GRCh38
Supplementary files format and content: bam

source_name: Fallopian tube , distal

growth_protocol: Fresh distal FT tissues were minced and digested with collagenase type I (Sigma) for 45 min at 37°C. Dissociated mucosal cells were cultured in 2D culture media until 70-80% confluent, then digested with TrypLE (Gibco), seeded in Matrigel (Corning), and cultured as previously described17,18. Organoids were passaged by digestion with TrypLE (Gibco) + 10 μM Y-27632 (SelleckChem) for 5 min at 37°C, followed by pipetting, washing with Advanced DMEM/F12, and replating in Matrigel. The culture medium was changed every 3–5 days. Cultures were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
DNA was extracted with DNA micro kit (Zymo) from control or TP53-/- FTOs simultaneously after 17 ± 1 weeks (mean ± SD) of culture.
DNA was submitted to Novogene for quality control, library preparation and 150 bp paired-end sequencing on NovaSeq X Plus.

treatment_protocol: Dissociated single cells were electroporated using a Neon Next electroporator to introduce CRISPR-Cas and TP53 gRNA via plasmid Addgene_85559

value: Fallopian tube , distal

value: Primary patient-derived organoids

value: Fallopian tube epithelial cells


title: Infected DblGATA1 4 w.p.i 2

description:
GATA2
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 2, 4 w.p.i.)

value: MLN

value: 129X1/SvJ DblGATA1

value: STm SL1344 1e8 CFU oral


title: KO Sample 1_late

description: Library name: A13_86P12


title: JuPa03_WT_CD8_Gex

description:
10X Genomics_5v2_0
sc_gpr25_liver_day30_umi.txt.gz
sc_gpr25_liver_day30_annotation.txt.gz

value: Liver

value: T cells

value: 30 days after T cell transfer, host 8-12 weeks

value: GEX


title: mES IgG b2

description: Library name: mES.IgG.b2

value: IgG (Cell Signaling, cat #2729S, lot #10)


title: Ctrl Sample 2_late

description: Library name: A12_97P11

value: Wild-type


title: heart LaminB b3

description:
Library name: heart.LaminB.b3
zscores.1kb.heart.LaminB.b3.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed

source_name: heart

value: heart

value: Lamin B1 (Abcam, cat #ab16048, lot #GR195923)


title: JuPa03_KO_CD8_Gex

value: Gpr25 WT, Gpr25 KO, CD45.1 (recipient)

value: LCMV-OVA infection


title: Ctrl Sample 1_late

description: Library name: A11_45P12


title: heart LaminB b2

description:
Library name: heart.LaminB.b2
zscores.1kb.heart.LaminB.b2.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed


title: Infected WT 4 w.p.i 8

description:
WT8
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 8, 4 w.p.i.)

value: 129X1/SvJ WT


title: Infected WT 4 w.p.i 7

description:
WT7
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 7, 4 w.p.i.)


title: mES H3K9me2 b1

description:
Library name: mES.H3K9me2.b1
zscores.1kb.mES.H3K9me2.b1.bedGraph.gz
mES.open.bed
mES.KODs.bed
mES.LADs.bed

value: mES


title: KO Sample 4_late

description: Library name: Fot89_late

value: Fallopian tube , distal

value: Primary patient-derived organoids


title: Infected WT 4 w.p.i 6

description:
WT6
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 6, 4 w.p.i.)

value: MLN


title: heart LaminB b1

description:
Library name: heart.LaminB.b1
zscores.1kb.heart.LaminB.b1.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed


title: KO Sample 3_late

description: Library name: Fot35_late

value: Fallopian tube epithelial cells


title: NB-30kPa-2

city: Beijing

first: Miao

last: Chen

address: 37 Xueyuan Road, Haidian District

country: China

institute: Beihang University

description: Library name: Sample 10

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: SK-N-SH

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent followed by purification with an RNA miniprep kit according to manufacturer’s instructions. RNA was qualified and quantified using a Nanodrop One Spectorphotometer (Thermo Fisher).
cells RNA was harvested using Trizol reagent. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.

value: SK-N-SH

value: tumor cell


title: Infected DblGATA1 4 w.p.i 4

description:
GATA4
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 4, 4 w.p.i.)

value: 129X1/SvJ DblGATA1

value: STm SL1344 1e8 CFU oral


title: NB-30kPa-3

description: Library name: Sample 11


title: NB-30kPa-4

description: Library name: Sample 12


title: NB-30kPa-1

description: Library name: Sample 9


title: heart IgG b6

description: Library name: heart.IgG.b6


title: Infected WT 4 w.p.i 5

description:
WT5
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 5, 4 w.p.i.)


title: KO Sample 3

description: Library name: A8_35P5


title: NB-8kPa-4

description: Library name: Sample 8


title: Infected WT 4 w.p.i 4

description:
WT4
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 4, 4 w.p.i.)


title: heart IgG b4

description: Library name: heart.IgG.b4


title: KO Sample 2

description: Library name: A7_95P6


title: Infected DblGATA1 4 w.p.i 1

description:
GATA1
Xenium in situ spatial transcriptomics of MLN (DblGATA1 infected replicate 1, 4 w.p.i.)


title: Infected WT 4 w.p.i 3

description:
WT3
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 3, 4 w.p.i.)


title: KO Sample 4

description: Library name: A6_89P4


title: heart IgG b3

description: Library name: heart.IgG.b3


title: KO Sample 5

description: Library name: A5_36P9


title: Infected WT 4 w.p.i 2

description:
WT2
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 2, 4 w.p.i.)


title: heart IgG b2

description: Library name: heart.IgG.b2


title: KO Sample 1

description: Library name: A4_86P9


title: heart IgG b1

description: Library name: heart.IgG.b1


title: Uninfected control 2

description:
UI2
Xenium in situ spatial transcriptomics of MLN (uninfected control replicate 2)

value: No treatment


title: Uninfected control 1

description:
UI1
Xenium in situ spatial transcriptomics of MLN (uninfected control replicate 1)


title: NB-1kPa-4

description: Library name: Sample 4


title: Ctrl Sample 2

description: Library name: A3_WT97P5


title: NB-1kPa-3

description: Library name: Sample 3


title: heart H3K9me2 b3

description:
Library name: heart.H3K9me2.b3
zscores.1kb.heart.H3K9me2.b3.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed


title: heart H3K9me2 b2

description:
Library name: heart.H3K9me2.b2
zscores.1kb.heart.H3K9me2.b2.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed


title: heart IgG b5

description: Library name: heart.IgG.b5

value: IgG (Cell Signaling, cat #2729S, lot #10)


title: NB-1kPa-2

description: Library name: Sample 2


title: Ctrl Sample 1

description: Library name: A2_WT45P9

value: Wild-type


title: NB-8kPa-3

description: Library name: Sample 7


title: heart H3K9me2 b1

description:
Library name: heart.H3K9me2.b1
zscores.1kb.heart.H3K9me2.b1.bedGraph.gz
heart.open.bed
heart.KODs.bed
heart.LADs.bed

value: heart


title: NB-1kPa-1

description: Library name: Sample 1


title: forebrain LaminB b3

description:
Library name: forebrain.LaminB.b3
zscores.1kb.forebrain.LaminB.b3.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed

source_name: forebrain

value: forebrain

value: Lamin B1 (Abcam, cat #ab16048, lot #GR195923)


title: Xenium spatial transcriptomics data from mouse kidney transplantation C57BL/6 to BALB/c specimen 2

type: other

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

data_processing: Xenium: Raw data was analyzed using the xenium ranger v2.0 import-segmentation tool with parameter –expansion-distance=5. Results from this were directly imported into Seurat and clustered. In brief, data from all samples were normalized scaled and PCA was performed using highly variable genes. Harmony analysis was run on which basis clustering was performed with resolution 0.3. The so-generated clusters were inspected on the spatial histological images and for marker gene expression. Based on this, broad cell types were determined. All cells from the leukocyte, interstitial cell or endothelial cell compartment were first labeled as non-tubular cells. Non-tubular cells were further separated into endothelial cells, interstitial cells and leukocytes using the Robust Cell Type Decomposition tool40 and the snRNA-seq data from our mouse experiments. Additionally, cell types (Prolif, CD-IC-A, CD-IC-B and PEC) were also determined by using RCTD and mouse snRNA-seq. RCTD was also used for sub cell type annotation (e.g. PT Injury h1 etc.).

molecule: other

source_name: mouse kidney

treatment_protocol: In situ single cell RNA expression analysis was performed using the Xenium system (10X Genomics). 5μm thick FFPE tissue sections were placed on a Xenium slide according to the Xenium Tissue Preparation Guide (CG000578). Sections were dried at 37°C for 2 hours and placed overnight in a desiccator at room temperature, followed by deparaffinization and decrosslinking (CG000580). The Probe Hybridization Mix was prepared using a pre-designed 379 gene panel (Mouse Tissue Atlassing v1) and 100 gene custom add-on panel. Probe Hybridization, Ligation & Amplification were performed according to the Xenium In Situ Gene Expression user guide (CG000582)

tag: mode of transplantation


title: NB-8kPa-1

description: Library name: Sample 5


title: forebrain LaminB b2

description:
Library name: forebrain.LaminB.b2
zscores.1kb.forebrain.LaminB.b2.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed


title: Xenium spatial transcriptomics data from mouse kidney transplantation BALB/c to C57BL/6 specimen 3

extract_protocol: Probe Hybridization, Ligation & Amplification were performed according to the Xenium In Situ Gene Expression user guide (CG000582)


title: Infected WT 4 w.p.i 1

description:
WT1
Xenium in situ spatial transcriptomics of MLN (WT infected replicate 1, 4 w.p.i.)

tag: batch


title: KO 2

description: Library name: R6_35_ko

data_processing:
RNA-seq reads were processed using the RNA sequencing analysis pipeline (v3.17.0) established by nf-core.
Samples were aligned to GRCh38 using the STAR-RSEM method.
Assembly: GRCh38
Supplementary files format and content: rsem.merged.transcript_counts.tsv

source_name: Fallopian tube, distal

extract_protocol:
Total RNA was extracted using the Direct-ZOL extraction kit (Zymo) from control or TP53-/- FTOs simultaneously after 14 ± 1 weeks (mean ± SD) of culture.
RNA was submitted to Novogene for quality control, library preparation with poly-A enrichment and 150 bp paired-end sequencing on NovaSeq X Plus.

value: Fallopian tube, distal

tag: cell line


title: KO 3

description: Library name: R7_89_ko


title: KO 1

description: Library name: R5_86_ko


title: forebrain LaminB b1

description:
Library name: forebrain.LaminB.b1
zscores.1kb.forebrain.LaminB.b1.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed


title: small extracellular vesicles from myotubes of normal glucose tolerance donor, biological rep5

city: Oslo

first: Stian

last: Christiansen

address: Folke Bernadottes Vei 13D

country: Norway

institute: OsloMet

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with normal glucose tolerance
NGT_EO52

hyb_protocol: Samples were hybridized for 18 h at 48 °C on the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G30007.

data_processing: Normalization of signal intensities and quality control were done using the Affymetrix® GeneChip™ Command Console software

label: biotin

source_name: small extracellular vesicles from cultured human myotubes of a donor with normal glucose tolerance

label_protocol: A total of 5 ng RNA was subjected to poly-A tailing, and biotin labelling using FlashTag Biotin HSR RNA Labeling kit (Thermo Fisher Scientific, Waltham, USA) following the manufacturer’s instructions.

growth_protocol: Human skeletal muscle cells were differentiated for 7 days in DMEM (5.5 mM glucose) containing 2% fetal bovine serum, 25 pM insulin, 50 µg/mL gentamicin, and 1.25 µg/mL amphotericin B in a humidified CO2 (5%) atmosphere at 37°C, with medium changed every two to three days.

extract_protocol: RNA was isolated from sEV samples using the miRNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

treatment_protocol: On day 6 of differentiation, cell medium was changed to serum free DMEM (5.5 mM glucose) with 25 pM insulin, gentamicin (50 µg/mL) and amphotericin B (1.25 µg/mL). The cells were incubated for another 24 h for synthesis and secretion of EVs, before media were collected, remnant cells and cell debris were removed by centrifugation at 450 g for 5 min. Next, the media underwent an initial centrifugation at 17 000 g for 30 min, before the supernatant was filtered through a 0.22 µm filter. The supernatant was transferred to Centricon-70 Plus 100 kDa Centrifugal Filter Columns and centrifuged at 3 500 g for 15 min. The filters were washed with phosphate buffered saline and further centrifuged at 3 500 g for 10 min. Finally, the filters were turned upside down, centrifuged at 1 000 g for 2 min, and the sEV filtrates were collected.

value: small extracellular vesicles from human myotubes

value: normal glucose tolerance

tag: age


title: Wildtype 4

description: Library name: R4_97_wt


title: Xenium spatial transcriptomics data from mouse kidney transplantation C57BL/6 to BALB/c specimen 3


title: forebrain IgG b6

first: Emily

description: Library name: forebrain.IgG.b6


title: Xenium spatial transcriptomics data from mouse kidney transplantation BALB/c to C57BL/6 specimen 1


title: KO 4

description: Library name: R8_95_ko


title: Wildtype 3

description: Library name: R3_33_wt


title: Xenium spatial transcriptomics data from mouse kidney transplantation C57BL/6 to BALB/c specimen 1


title: Xenium spatial transcriptomics data from mouse kidney transplantation BALB/c to BALB/c specimen 1


title: forebrain IgG b5

description: Library name: forebrain.IgG.b5


title: small extracellular vesicles from myotubes of normal glucose tolerance donor, biological rep4

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with normal glucose tolerance
NGT_EO35


title: Wildtype 2

description: Library name: R2_32_wt


title: small extracellular vesicles from myotubes of normal glucose tolerance donor, biological rep3

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with normal glucose tolerance
NGT_EO34


title: forebrain IgG b4

description: Library name: forebrain.IgG.b4


title: small extracellular vesicles from myotubes of normal glucose tolerance donor, biological rep2

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with normal glucose tolerance
NGT_EO32


title: small extracellular vesicles from myotubes of normal glucose tolerance donor, biological rep1

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with normal glucose tolerance
NGT_EO29


title: Wildtype 1

description: Library name: R1_45_wt


title: EMu_C3_1_ATAC

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

data_processing:
For ATAC-seq, Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). Q20 and Q30 of the raw data and clean data were calculated. These reads were aligned to a reference genome downloaded from NCBI BioProject database (accession number PRJNA555707) using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with MACS2 using ‘MACS2 call-peak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
For RNA-seq, The original image data were transferred into sequencing data by base calling, which were defined as raw reads. Clean data (clean reads) were obtained by removing reads containing an adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, and GC contents of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Then, E. sinensis genome was downloaded from NCBI BioProject database (accession number PRJNA555707) and used as reference genome. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: accession number reference genome is PRJNA555707
Supplementary files format and content: .narrowPeak files inlcude peak information
Supplementary files format and content: excel file include FPKM of genes

organism: Eriocheir sinensis

source_name: muscle

growth_protocol: The healthy river crabs obtained from aquatic farm were cultured in a plastic incubator (70×40×50 cm) at 20±1◦C with natural light.

extract_protocol:
nuclei were extracted from muscle samples for ATAC-seq anlysis. The total RNA was extracted using the TRIzol method (Invitrogen) for RNA-seq analysis.
For ATAC-seq analysis, the nuclei pellet was re-suspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition. PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated. For RNA-seq analysis, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations. Library quality was assessed on the Agilent Bioanalyzer 2100 system and 150 bp paired-end reads were generated.

treatment_protocol: During collection of the samples, crabs with average weight of 8.41±1.47 g were put on the ice plate for low-temperature anesthesia. Muscle of each crab were quickly collected and put in liquid nitrogen immediately, and then transferred to −80◦C refrigerator for preservation.

value: muscle

value: WT

value: untreated


title: NB-8kPa-2

description: Library name: Sample 6


title: forebrain IgG b3

description: Library name: forebrain.IgG.b3


title: EMu_C3_1_RNA


title: forebrain IgG b2

description: Library name: forebrain.IgG.b2


title: P9- Drug-resistant_HTB24-0248_P53_AML

city: Monrovia

first: Ling

last: Li

address: 1218 S 5TH AVE, MONROVIA

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

description: polyA enriched single cell RNA-seq libraries

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using CellRanger's default settings
Gene expression level of Ensembl coding genes were quantified using CellRanger's default settings
Assembly: GRCh38
Supplementary files format and content: text files containing the raw gene expression count

source_name: bone marrow

extract_protocol:
single cell suspension were prepare from primary AML blasts(P9), and the single cell emulsion were generated on 10xGenomics Chromium with 5' Solution V3.1 kit
single cell RNA-seq libraries were generated by using 10xGenomics Chromium GEM-X SINGLE CELL 5' v3 gene expression kit

value: bone marrow

value: PDX cells

value: P9- Drug-resistant


title: EMu_C2_1_ATAC


title: P9- Drug-naive_HTB24_VR

value: P9- Drug-naïve


title: forebrain IgG b1

description: Library name: forebrain.IgG.b1


title: Xenium spatial transcriptomics data from mouse kidney transplantation C57BL/6 to C57BL/6 specimen 1


title: EMu_C2_1_RNA


title: scg5_RNAi_scRNA-seq

city: Shanghai

first: Yuxiaofei

last: Wang

address: 320 Yue-Yang Road

institute: University of Chinese academy of sciences

description: SeekOne

data_processing:
Read counts for each transcripts are generated using CellRanger (v7.0.0);
data was normalized and scaled by SCTransform implemented in Seurat (V4.1.0)
Assembly: Schmidtea mediterranea transcriptome is available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389
Supplementary files format and content: filtered_feature_bc_matrix through CellRanger

organism: Schmidtea mediterranea

source_name: tail

growth_protocol: Asexual S. mediterranea (strain CIW4) anamials were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
planarians were chopped and dissociated in CMFB (CMF+1% FBS) on a cold plate (4 °C). Cells were strained through a 40um strainer and stained with DAPI (1:1000; Beyotime) and DRAQ5 (1:1000; BioStatus). Flow cytometry and sorting were conducted on a Sony MA900 cell sorter.
Around 20,000 cells were loaded into SeekOne' Microwell & Magnetic Beads platform for making single-cell libraries.

treatment_protocol: Animals were fed every 3 days for a total of two RNAi feeding and EGFP dsRNA was used for control.

value: tail

tag: strain

value: scg5 RNAi

value: 3dpa planarian after scg5 RNAi


title: nsf_RNAi_scRNA-seq

description: SeekOne

value: nsf RNAi

value: 3dpa planarian after nsf RNAi


title: EMu_C1_1_ATAC


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep6

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO57

source_name: small extracellular vesicles from cultured human myotubes of a donor with type 2 diabetes

value: type 2 diabetes


title: forebrain H3K9me2 b3

description:
Library name: forebrain.H3K9me2.b3
zscores.1kb.forebrain.H3K9me2.b3.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed

value: forebrain


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep5

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO56


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep4

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO47


title: EGFP_RNAi_scRNA-seq

description: SeekOne

value: EGFP RNAi

value: 3dpa planarian after EGFP RNAi


title: EMu_C1_1_RNA


title: marmoset 11years,2months female MO, rep 11-301 rep2

status: Public on Nov 20 2025

city: Cambridge

first: Margaret

last: Schroeder

state: MA

address: 77 Massachusetts Avenue

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

description:
Library name: Exp091_cjaged_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

data_processing:
Demultiplexed fastq files were generated by the Broad Institute Genomics Platform using Illumina software. 10x Genomics Cell Ranger software version 7.1 was used for alignment and counting via the 10x Genomics Cloud Analysis platform. For samples that were sequenced across several library pools, fastq files were grouped prior to alignment to create one cell-by-gene (cell x gene) counts matrix per sample. CellBender (v0.2.0) remove-background (Fleming et al., 2023) was used to remove ambient RNA and call nuclei with default parameters and expected_cells = 10,000, total-droplets-included = 40,000 and the –cuda flag. CellBender-cleaned cell x gene matrix .h5 files were read into Python in the anndata format using a custom function written by Stephen Fleming (https://github.com/broadinstitute/CellBender/issues/57).
Assembly: Reads were aligned to an optimized mouse reference genome based on the mouse GRCm38 primary sequence assembly (version 2, Pool et al. 2024) or or a modified marmoset mCalja1.2.pat.X assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) provided courtesy of Michael DeBerardine and Fenna Krienen (Princeton Neuroscience Institute) in which mitochondrial genes from CM021961.1 (https://www.ncbi.nlm.nih.gov/nuccore/1820101357/) were annotated using MITOS2113. The marmoset reference genome was generated from the .fasta and .gtf files using Cell Ranger “mkref” v7.1.0 using default parameters without filtering for any gene/transcript biotype and is available at: https://doi.org/10.5281/zenodo.16915694.
Supplementary files format and content: Processed data files are cell x gene count matrices in .h5 format without ambient RNA removal.

organism: Callithrix jacchus

source_name: MO

growth_protocol: Common marmosets were housed in AAALAC-accredited facilities at MIT, in spacious holding rooms with a 12 hour light/dark cycle, temperature 74.0 ± 2.0°F (23.3 ± 1.1°C), relative humidity of 50 ± 20 %, and unrestricted access to food and water. Cages contained a variety of perches and enrichment devices. Procedures were conducted with prior approval by the MIT Committee for Animal Care (CAC) and following veterinary guidelines. Animal work was performed in accordance with protocols approved by MIT’s Committee on Animal Care and NIH guidelines. All postnatal mice were wild-type C57BL/6J originally obtained from Jackson Laboratories and bred in-house. Timed pregnant C57BL/6J females were either obtained from Jackson Laboratories to arrive between gestation day 11 and 15 or were impregnated in house by setting up overnight mating pairs with females in proestrus or estrus phase. Embryos were harvested at E18.5 (18 days after the plug date). Mice were housed in a facility with a light cycle running from 07:00 to 19:00,  temperature 20-22.2°C, humidity 30-70%, and food and water available ad libitum. Postnatal mice were not derived from timed pregnant females. Instead, age was determined during regular pup checks by experienced researchers based on the Jax Mice Pup Appearance Chart.

extract_protocol:
Nuclei were extracted from frozen tissue using the 10x Genomics Chromium Nuclei Isolation Kit (Protocol CG000505, Rev A).
snRNAseq libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Protocol CG000315 Rev C or Rev D) following manufacturer instructions.

treatment_protocol: None; animals were wild-type and allowed to develop normally.

value: MO

value: nuclei


title: marmoset 11years,2months female thalamus, rep 11-301 rep2

description:
Library name: Exp091_cjaged_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: thalamus

value: thalamus


title: marmoset 11years,2months female MO, rep 11-301 rep1

description:
Library name: Exp091_cjaged_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 11years,2months female striatum, rep 11-301 rep2

description:
Library name: Exp091_cjaged_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: striatum

value: striatum


title: marmoset 11years,2months female thalamus, rep 11-301 rep1

description:
Library name: Exp091_cjaged_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 11years,2months female PFC, rep 11-301 rep2

description:
Library name: Exp091_cjaged_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: PFC

value: PFC


title: marmoset 11years,2months female striatum, rep 11-301 rep1

description:
Library name: Exp091_cjaged_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 11years,2months female PFC, rep 11-301 rep1

description:
Library name: Exp091_cjaged_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate male thalamus, rep 22-201 rep2

description:
Library name: Exp082_cjneo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep2

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO14

value: small extracellular vesicles from human myotubes


title: marmoset neonate male striatum, rep 22-201 rep2

description:
Library name: Exp082_cjneo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep1

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO11


title: marmoset neonate male PFC, rep 22-201 rep2

description:
Library name: Exp082_cjneo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate male MO, rep 22-201 rep2

description:
Library name: Exp082_cjneo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: forebrain H3K9me2 b2

description:
Library name: forebrain.H3K9me2.b2
zscores.1kb.forebrain.H3K9me2.b2.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed


title: marmoset neonate male thalamus, rep 22-201 rep1

description:
Library name: Exp082_cjneo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: forebrain H3K9me2 b1

description:
Library name: forebrain.H3K9me2.b1
zscores.1kb.forebrain.H3K9me2.b1.bedGraph.gz
forebrain.open.bed
forebrain.KODs.bed
forebrain.LADs.bed


title: marmoset neonate male striatum, rep 22-201 rep1

description:
Library name: Exp082_cjneo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate male MO, rep 22-201 rep1

description:
Library name: Exp082_cjneo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male striatum, rep 09-34 rep2

description:
Library name: Exp080_cjaged_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male thalamus, rep 09-34 rep2

description:
Library name: Exp080_cjaged_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate male PFC, rep 22-201 rep1

description:
Library name: Exp082_cjneo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male thalamus, rep 09-34 rep1

description:
Library name: Exp080_cjaged_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male MO, rep 09-34 rep1

description:
Library name: Exp080_cjaged_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male PFC, rep 09-34 rep1

description:
Library name: Exp080_cjaged_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male striatum, rep 09-34 rep1

description:
Library name: Exp080_cjaged_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male PFC, rep 09-34 rep2

description:
Library name: Exp080_cjaged_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female MO, rep 21-164 rep2

description:
Library name: Exp078_cj14mo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female thalamus, rep 21-164 rep1

description:
Library name: Exp078_cj14mo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female thalamus, rep 21-164 rep2

description:
Library name: Exp078_cj14mo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female MO, rep 21-164 rep1

description:
Library name: Exp078_cj14mo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female striatum, rep 21-164 rep1

description:
Library name: Exp078_cj14mo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female striatum, rep 21-164 rep2

description:
Library name: Exp078_cj14mo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female striatum, rep 22-110 rep2

description:
Library name: Exp077_cj7mo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female MO, rep 22-110 rep2

description:
Library name: Exp077_cj7mo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female PFC, rep 22-110 rep2

description:
Library name: Exp077_cj7mo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female thalamus, rep 22-110 rep1

description:
Library name: Exp077_cj7mo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female thalamus, rep 22-110 rep2

description:
Library name: Exp077_cj7mo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female striatum, rep 22-110 rep1

description:
Library name: Exp077_cj7mo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 13years,7months male MO, rep 09-34 rep2

description:
Library name: Exp080_cjaged_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male thalamus, rep 21-181 rep2

description:
Library name: Exp076_cj7mo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female MO, rep 22-110 rep1

description:
Library name: Exp077_cj7mo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 7mo,4wks female PFC, rep 22-110 rep1

description:
Library name: Exp077_cj7mo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male PFC, rep 21-181 rep2

description:
Library name: Exp076_cj7mo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male MO, rep 21-181 rep2

description:
Library name: Exp076_cj7mo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male striatum, rep 21-181 rep2

description:
Library name: Exp076_cj7mo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male striatum, rep 21-181 rep1

description:
Library name: Exp076_cj7mo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male PFC, rep 21-181 rep1

description:
Library name: Exp076_cj7mo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male thalamus, rep 21-181 rep1

description:
Library name: Exp076_cj7mo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 6mo,3wks male MO, rep 21-181 rep1

description:
Library name: Exp076_cj7mo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male MO, rep 21-108 rep2

description:
Library name: Exp060_cj14mo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male thalamus, rep 21-108 rep2

description:
Library name: Exp060_cj14mo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female PFC, rep 21-164 rep2

description:
Library name: Exp078_cj14mo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months, 4wks female PFC, rep 21-164 rep1

description:
Library name: Exp078_cj14mo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male striatum, rep 21-108 rep1

description:
Library name: Exp060_cj14mo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male thalamus, rep 21-108 rep1

description:
Library name: Exp060_cj14mo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male PFC, rep 21-108 rep2

description:
Library name: Exp060_cj14mo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male MO, rep 21-108 rep1

description:
Library name: Exp060_cj14mo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female striatum, rep 21-197 rep2

description:
Library name: Exp057_cjneo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset 14months,1wks male PFC, rep 21-108 rep1

description:
Library name: Exp060_cj14mo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female PFC, rep 21-197 rep2

description:
Library name: Exp057_cjneo_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female thalamus, rep 21-197 rep2

description:
Library name: Exp057_cjneo_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female striatum, rep 21-197 rep1

description:
Library name: Exp057_cjneo_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female thalamus, rep 21-197 rep1

description:
Library name: Exp057_cjneo_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: ESC_Cbs_OE_H3K27ac_r2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: 07ESC_Cbs_OE_H3K27ac_r2

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010) was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of millon reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Assembly: Assembly: mm10 from UCSC genome
Supplementary files format and content: Supplementary files format and content: BigWig files and normalized DESEQ2 excel file

source_name: mouse embryonic stem cells

growth_protocol: ESCs were maintained on 0.2% gelatin coated plate in Knockout DMEM medium (Thermo Fisher Scientific, 10829018) containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement (Thermo Fisher Scientific, 10828028), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
RNA libraries for RNA-seq were preced using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mouse embryonic stem cells

value: CBS_OE viral transfection

tag: antibody

value: Active motif, 39135


title: ESC_Cbs_OE_input_r1

description: Library name: 11ESC_Cbs_OE_input_r1


title: marmoset 14months,1wks male striatum, rep 21-108 rep2

description:
Library name: Exp060_cj14mo_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: marmoset neonate female MO, rep 21-197 rep1

description:
Library name: Exp057_cjneo_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: ESC_Cth_OE_input_r2

data_processing:
trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
mapped bam files were merged with bamtools merge (default settings)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome version
Supplementary files format and content: bigWig files

growth_protocol: Control , Lmna KO and CTH OE Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF for 2 days. mESC were preplated for 50min and collected for RNA extraction.

extract_protocol:
ESCs were dissociated by 0.05% trypsin-EDTA followed by preplating for 50min to obtain single mESCs and 1million mESCs were collected for H3K9ac and H3k27ac chip-seq
Libraries were constructed with the NEB Ultra DNA II Library Kit for Illumina (#E7103S/L)


title: ESC_Cbs_OE_H3k9ac_r2

description: Library name: 03ESC_Cbs_OE_H3k9ac_r2

value: Cell Signaling Technology, 9649S