title: DM1-004_Batch 2_ Urinary Extracellular Vesicles

description:
Library name: DM1-004 Batch 2
Column name in TPM_All Samples.txt. DM1-004 Batch 2


title: Somatosensory cortex cells, cTBS, replicate 3

status: Public on Jan 13 2025

type: SRA

city: Perth

first: Alexander

last: Tang

state: Western Australia

address: 35 Stirling Highway, University of Western Australia

department: School of Biomedical Science

country: Australia

institute: University of Western Australia

library_source: transcriptomic

data_processing:
First 15 base pairs of sequencerd reads were trimmed to remove low-quality sequences using fastp.
Trimmed sequence reads were mapped to GRCm39/mm39 using the STAR RNA-seq aligner. STAR-aligned SAM files were converted into BAM files.
Read counts were generated using GenomicAlignments.
Normalisation of counts was performed using the DESeq2 R package, using a variance stabilising transformation (VST) function.
Assembly: mm39
Supplementary files format and content: Comma-separated values files containing the raw read counts for each sample
Supplementary files format and content: Comma-separated values files containing the read counts that have been normalised using the variance stabilising transformation (VST) for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). A minimum of 50ng total RNA was sent to the Australian Genome Research Facility (Melbourne, Australia) for the construction of sequencing-ready libraries.
RNA libraries for whole transcriptome RNA-seq were prepared using the Illumina Stranded Total RNA Library Preparation Kit with Ribo-Zero Plus, by the technical staff at the Australian Genome Research Facility (Melbourne, Australia).

tag: tissue

value: Brain

tag: strain

tag: treatment

value: cTBS


title: Somatosensory cortex cells, sham, replicate 3

value: sham


title: APAP+HEKSIRP-EV, replicate3

city: Seonbuk-gu

first: Yoon Kyoung

last: Kim

state: Seoul

address: Hwarang-ro 76, Unit102

country: South Korea

institute: SHIFTBIO

data_processing:
Trimmed reads were mapped using HISAT2 (version 2.1.0) to genomic reference (mm10) and aligned reads were generated.
The aligned reads were assembled using SrtingTie (version 2.1.3b).
Assembly: StringTie
Supplementary files format and content: Tab-separted values files for each sample

source_name: Liver

extract_protocol:
The freshly harvested mouse livers were dissociated into single cells, and CD11b+ cells were isolated. RNA from CD11b+ single cells was extracted using Trizol (Sigma). DNA contamination was removed with DNase.
RNA libraries for bulk RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's intruction.

value: Liver

tag: cell type

value: CD11b+ cell

tag: condition

value: APAP induction

value: HEK cell derived SIRP-EV


title: BT549 cells, shADAR1, biol rep 2

city: Saint Louis

first: Che-Pei

last: Kung

state: Missouri

address: 1 Brookings Dr.

department: Medicine

country: USA

institute: Washington University in St. Louis

description: Library name: BT549_ADAR1-Deficient_2

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Homo sapiens

source_name: cell line

growth_protocol: All cancer cell lines were maintained in Dulbecco’s Modification of Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), Sodium Pyruvate, Non-Essential Amino Acids, and L-glutamine in humidified atmosphere in 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated from cells using miRNeasy Mini Kit (Qiagen) including on-column DNase digestion following the manufacturer’s protocol. 1µg of total RNA was used to construct the libraries for sequencing.
RNA libraries for RNA-seq was prepared using KAPA Riboerase kit (Roche) according to manufacturer's instructions.

treatment_protocol: For transduction, one million cells were infected with lentivirus containing shRNA for 24hr in the presence of 10 µg/ml protamine sulfate to facilitate viral entry. Cells transduced with viruses were selected with puromycin (2 µg/ml) for at 72hr.

value: cell line

tag: cell line

value: breast cancer cell

tag: genotype

value: lentiviral shRNA


title: BT549 cells, shNT, biol rep 2

description: Library name: BT549_ADAR1-Intact_2

value: shNT


title: AGEDDox REP2

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
6 totalRNA-Seq samples were pooled and sequenced on NextSeq using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.
The samples have 137 to 159 million pass filter reads with more than 83% of bases above the quality score of Q30.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.  The mapping statistics are calculated using Picard software.  Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
Assembly: hg38
Supplementary files format and content: The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.

source_name: FORESKIN

growth_protocol: BJ human skin fibroblast cells were grown in a humidified 37°C incubator containing 5% CO2 in MEM medium containing glutathione and high concentrations of vitamins (catalog no. 11875093, Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (catalog no. S11050H, Atlanta Biologicals, USA) and 1X penicillin-streptomycin solution (catalog no. 15140122, Gibco, USA)

extract_protocol:
Total RNA was isolated by the trizol method
Total of 3ug of Rna was taken to construct libraries.

treatment_protocol: DMSO/Dox 250nM was treated for 24 hours following 10 days of incubation,

value: FORESKIN

value: BJ SKIN FIBROBLAST

value: FORESKIN FIBROBLAST

value: Dox 250nM


title: Somatosensory cortex cells, iTBS, replicate 3

value: iTBS


title: BT549 cells, shADAR1, biol rep 1

description: Library name: BT549_ADAR1-Deficient_1


title: APAP+HEKSIRP-EV, replicate2


title: BT549 cells, shNT, biol rep 1

description: Library name: BT549_ADAR1-Intact_1


title: DM1-002_Batch 2_ Urinary Extracellular Vesicles

city: Boston

first: Preeti

last: Kumari

state: MA

address: 13 street

department: Neurology

institute: Massachusetts General Hospital

description:
Library name: DM1-002 Batch 2
Column name in TPM_All Samples.txt. DM1-002 Batch 2

data_processing:
Sequencing was performed in two separate batches using an Illumina NextSeq 500 platform at the George Washington University Genomics Core (https://www.gwgenomics.org) and a high output 150-cycle kit to generate more than 83 million paired end reads per sample.
Sequences were trimmed for adaptor sequence/low quality sequence using bbmap with parameters ktrim=r, k=21, mink=11, tbo, tpe, hdist=2, minlen=31, qtrim=r, trimq=10, maq=10, entropy=0.3, entropywindow=50, and entropyk=5.
The trimmed sequence reads were mapped to the human GRCh38 genome using Salmon (v. 1.10.2). The specific mapping procedure involves aligning the reads using the salmon quant function with flags for sequence and GC bias corrections (--seqBias --gcBias), library type specification (-l A), and enhanced statistical modeling (--numBootstraps=20).
Read count extraction and normalization were also performed using Salmon (v. 1.10.2)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Urinary Extracellular Vesicles

extract_protocol:
We extracted RNA using 1ml TRIzol Reagent according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using Takara SMARTer Stranded Total RNA Sequencing kit V2 - pico input mammalian (Takara product number 634412).

value: Urinary Extracellular Vesicles

tag: batch


title: BT549 cells, shADAR1, biol rep 3

description: Library name: BT549_ADAR1-Deficient_3


title: APAP, replicate1

value: PBS


title: APAP, replicate3


title: DM1-001_Batch 1_ Urinary Extracellular Vesicles

description:
Library name: DM1-001 Batch 1
Column name in TPM_All Samples.txt. DM1-001 Batch 1


title: Col_0_22C

city: Grossbeeren

first: Maolin

last: Peng

address: Theodor-Echtermeyer-Weg 1

country: Germany

institute: Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V.

data_processing:
HISAT2 (version 2.2.1) with parameters ‘--dta, --no-mixed, --no-discordant’ was used for aligning raw RNA-seq reads to TAIR10 genome. TPM values for genes were calculated by StringTie (version 2.1.4) with default settings directed by gene annotation file TAIR10 gff3 (https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff). Mean TPM values were calculated from replicates. Differentially expressed genes were identified by edgeR with thresholds q-value < 0.01 and log fold change > 1. To perform clustering of transcriptomic data, identified differentially expressed genes at least in one pairwise comparison (Col-0 37℃ vs 22℃) out of 3 time courses (5min, 15min and 30min) were selected. TPM values were transformed into log2(TPM+1). Genes with the maximum log2(TPM+1) > 2 were kept. Gaussian Mixture Models (GMM), implemented by an R package ClusterR (https://github.com/mlampros/ClusterR), was used for the clustering. The Expectation-Maximization algorithm was used for fitting GMM. The Bayesian information criterion was used for estimating the number of clusters.
Assembly: TAIR10
Supplementary files format and content: raw count

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown 22 ºC and shifted to 37 ºC  or kept at 22 ºC.

extract_protocol:
Samples were homogenizing to powder using Qiagen TissueLyser II (Cat. No. / ID: 85300). Total RNA was extracted MagMAX™ Plant RNA Isolation Kit (Applied Biosystems™A33899) according to the manufacturer's instructions.
Total RNA was quantified using Qubit4 (Thermo Fisher Scientific) according to the manufacturer's instructions and tested for integrity using an RNA screentape in an Agilent2200 tape station (Agilent).

treatment_protocol: Treated using water bath

value: seedling

tag: genotype/treatment


title: Somatosensory cortex cells, sham, replicate 2

value: Brain

value: sham


title: AGEDDox REP1


title: APAP, replicate2

value: Liver

value: CD11b+ cell


title: Control, P3, biol rep 1

city: Pessac

first: Ahmad

last: Sharanek

address: Allée Geoffroy St Hilaire

country: France

institute: BRIC INSERM U1312

description: Library name: P3-1

data_processing:
CBiB (Bordeaux Bioinformatics Center) standard pipeline for quality control, trimming, mapping and generation of raw counts matrix:  The 36 fastq files were received by the CBiB, Bordeaux, France for RNA-seq data analysis. Low quality reads trimming, and quality control, were carried out with fastp version 0.32.2 and MultiQC version 1.9, respectively. For mapping, STAR version 2.7.10a  was used, with the Gencode release 39 reference human genome. The count matrices were generated using the STAR output, retaining only uniquely mapped reads. Downstream analyses were performed in R version 4.1.0.
Quality control with MultiQC version 1.9.
Trimming of low quality reads, with fastp version 0.32.2
Mapping with STAR version 2.7.10a, with the Gencode release 39 reference human genome.
Generation of raw count matrices (only uniquely mapped reads) with R version 4.1.0 and the STAR output.
Assembly: Gencode release 39 reference of the human genome
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: BTSCs were cultured in low attachment flasks as spheres in DMEM/F12 media (Fisher Scientific, #11530566) supplemented with 2 mM GlutaMAX (ThermoFischer, #35050061), 1X B-27 supplement (ThermoFischer, #12587010), 2 μg/ml heparin (Sigma-Aldrich, #H3149), 20 ng/ml EGF (Peprotech, #AF-100-15), 20 ng/ml bFGF (Peprotech, #AF-100-18B), 100 U/ml penicillin-streptomycin (Fisher Scientific, #11548876). All cell lines were tested negative for mycoplasma. All cells were kept in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was extracted at LuxGen facility (Luxembourg Institute of Health) using Rneasy mini kit (Qiagen).  100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared at LuxGen facility, using the Illumina Stranded mRNA Ligation kit according to manufacturer.  All libraries have been quantified using a Qubit HS dsDNA kit (Thermofisher) and the library quality check has been performed using a High Sensitivity NGS Fragment Analysis Kit on a Fragment Analyzer System (Agilent Technologies). Indexed libraries were normalized and pooled to be sequenced on an Illumina  Novaseq 6000 sequencer according to manufacturer’s instructions with targeted conditions of 2 x 75bp and 25M reads/sample.

treatment_protocol: BTSC73 were treated with 500 nM of mubritinib for 24 h.

value: brain tumor stem cells


title: AtHSFA1adelPrDs_in_QK_22C


title: Somatosensory cortex cells, cTBS, replicate 2

value: cTBS


title: YOUNG CONTROL REP2

value: DMSO


title: Somatosensory cortex cells, sham, replicate 1


title: Input_T_rep2

library_source: genomic

data_processing:
BWA (version 0.7.17-r1188) was used to map ChIP-seq raw reads to TAIR10 genome.
Unmapped reads, mate unmapped reads, non-primary alignment and duplicate reads were removed. MACS2 (version 2.2.7.1) was used for peak calling. Identified peaks were filtered by q-value < 0.05.(version 3.5.0) function bamCoverage and normalized using RPKM. HSF binding profiles were generated by deepTools function plotProfile. Enriched known motifs were predicted by HOMER2 (version 4.11), using peaks overlap with high confidence gene locus extend to upstream and downstream 2kb as target sequences and randomly permuted sequences (excluding target sequences) as background.
BigWig files for IGV tracks were generated using deepTools
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
3g of seedlings from each treatment were fixed under vacuum for 20 min in 1 x phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl 10 mM Na2HPO4, and 1.8 mM KH2PO4) containing 1% formaldehyde (sigma, catalogue number F8775). The reaction was stopped by adding glycine to a final concentration of 62 mM. Anti-Flag M2 agarose affinity gel (Sigma, A2220) was used for immunoprecipitation (100 ul of resin suspension was used for each ChIP).
Sequencing libraries were prepared using a TruSeq ChIP sample preparation kit (Illumina) and samples were sequenced using an Illumina NextSeq 550 platform.

tag: chip antibody

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: 11_CD34-Treatment

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

country: Canada

institute: University of Montreal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 32, based on Ensembl 98) using STAR version 2.7.1a
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in TPM values, for these stranded RNA libraries
Assembly: GRCh38
Supplementary files format and content: summary_genes_readcount.stranded.annotated.tsv: table with readcount

source_name: blood

growth_protocol: Cells used for RNA-seq were grown in culture for 16 hours.

extract_protocol:
Total RNA from cells (<5 x10^5) was isolated using Rneasy micro kit as recommended by the manufacturer (Qiagen).
Illumina Kappa Library protocol followed

treatment_protocol: Cells were isolated and placed into media supplemented with FLT3L (50ng/ml), G-CSF (20ng/ml), SCF (100ng/ml), IL-3 (20ng/ml), SR1/UM179 (500 nM) at a denSIty of 0.2x10^6 cells/mL prior to RNA extraction

value: blood

value: Cord blood CD34+

value: Shikonin 0.912 uM


title: Control, P3,  biol rep 3

description: Library name: P3-3


title: 09_CD34-DMSO


title: Input_T_rep1


title: Control, BTSC147, biol rep 1

description: Library name: BTSC147-1


title: Input_R_rep2


title: Control, BTSC53, biol rep 3

description: Library name: BTSC53-3


title: YOUNG CONTROL REP1

value: FORESKIN

value: BJ SKIN FIBROBLAST

value: FORESKIN FIBROBLAST


title: Somatosensory cortex cells, iTBS, replicate 2

value: iTBS


title: 12_CD34-Treatment


title: Somatosensory cortex cells, cTBS, replicate 1


title: Control, BTSC147, biol rep 2

description: Library name: BTSC147-2


title: sorted cells, SAG treatment, rep 2

city: Gothenburg

first: Andrei

middle: S

last: Chagin

state: Västra Götaland

address: Guldhedsgatan 10a

department: Institute of Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Kallisto quant was used to quantify abundances of the transcripts in the fastq files.
Abundance tables were merged, filtered and processing with DESeq2 in Python.
Assembly: GRCm38.96
Supplementary files format and content: Comma-separated text file includes raw counts for each sample

source_name: metaphyseal growth plate

extract_protocol:
Rneasy micro kit (Qiagen #74004)
Takara SMARTer Stranded Total RNA-Seq kit v2 pico input mammalian

value: metaphyseal growth plate

value: SAG


title: Somatosensory cortex cells, iTBS, replicate 1

value: Brain


title: 10_CD34-DMSO


title: Control, BTSC147, biol rep 3

description: Library name: BTSC147-3


title: sorted cells, SAG treatment, rep 3


title: Control, P3, biol rep 2

description: Library name: P3-2


title: Control, BTSC53, biol rep 2

description: Library name: BTSC53-2


title: sorted cells, SAG treatment, rep 4


title: sorted cells, vehicle control, rep 4


title: 8

value: cell line-Primary

value: Shikonin 0.3845 uM


title: Input_R_rep1

value: seedling


title: Input_PT_rep2


title: sorted cells, vehicle control, rep 3


title: AtHSFA1adelPrDs_in_QK_22C_rep2


title: Input_PT_rep1


title: 6


title: Control, BTSC25, biol rep 2

description: Library name: BTSC25-2

value: brain tumor stem cells


title: Control, BTSC25, biol rep 3

description: Library name: BTSC25-3


title: Input_C2_rep2


title: Control, BTSC25, biol rep 1

description: Library name: BTSC25-1


title: Input_C2_rep1


title: 3


title: GPAD-20220124-NMK92M1(snRNA,male,week 92)

first: Li

last: Ding

state: MO

address: 660 S Euclid Ave

institute: Washington University in St Louis

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20220124-NMK92M1_features.tsv.gz
GPAD-20220124-NMK92M1_barcodes.tsv.gz
GPAD-20220124-NMK92M1_matrix.mtx.gz

data_processing:
Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified with the software CellRanger-ARC (v2.0.0) using mouse reference genome (mm10). The resulting gene and fragment count matrices for each sample were treated as input for downstream analysis.
Assembly: mm10
Supplementary files format and content: sparse matrix documenting the gene expression and peak fragments within each cell
Library strategy: 10x multiome

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
C57BL/6J mice were originally purchased from the Jackson Laboratory. Mouse kidneys were collected at embryos (E16.5), newborns (P0), 3 weeks (W3), 12 weeks (W12), 52 weeks (W52), and 92 weeks (W92). To get E16.5 kidneys, 4 female mice and 1 male mouse were grouped for mating on day 1 at 5 pm. Then the male was removed from the females on day 2 at 10 am. Day 2 was designated as E0.5 for any pregnant females. For kidneys collected from other ages, mice were purchased from the Jackson Laboratory. Mice at E16.5 and P0 were euthanized by decapitation. Older mice were euthanized by carbon dioxide asphyxiation. For each mouse, one kidney was embedded in optimal cutting temperature compound (OCT) and the other one was fixed in 10% neutral buffered formalin (Epredia, 5725) then embedded in paraffin. For Visium ST, 10 μm mid-sagittal OCT sections were used on the 10x Genomics Visium platform; for snRNA-Seq and snATAC-Seq, pooled snap-frozen tissues were used for E16.5 and P0 mice, and 300 μm of mid-sagittal OCT sections were used for mice from W3 to W92. All animal experiments were approved by the Washington University in Saint Louis Institutional Animal Care and Use Committee (IACUC) office.
Nuclei lysis buffer was freshly prepared in cold nuclease-free water with a mixture of 10 mM Tris-HCl (pH=7.4) (Thermo; 15567027), 10 mM NaCl (Thermo; AM9759), 3 mM MgCl2 (Thermo; AM9530G), 0.01% NP40 substitute (Sigma, 74385-1L), 1% BSA (MACS, 130-091-376), 1 mM DTT (Sigma, 646563) and 0.4 U/μL Protector RNase inhibitor (Sigma, 3335402001). Cryopreserved tissues were lysed with the cold lysis buffer in the Dounce homogenizer (KONTES, 885300-0002) using pestle B. The homogenate lysate was then filtered through a 40 μm strainer and washed with the wash buffer (2%BSA + 1 x PBS + 0.4 U/μL Protector RNase inhibitor). The filtrate was centrifuged at 500g for 6 minutes at 4°C and resuspended in 500 μL wash buffer for fluorescence-activated cell sorting (FACS). Nuclei were stained with 7-AAD (7-Aminoactinomycin D) dye (Millipore Sigma SML1633-1ML) at a 1:200 dilution. The suspension was FACS sorted for 400,000 positively stained nuclei. After sorting the nuclei suspension was centrifuged at 500g for 6 minutes at 4°C, the pellet was resuspended in 2x Nuclei Dilution Buffer (10x Genomics, 2000153) supplemented with 1 M DTT and 1.2 U/μL Protector RNase inhibitor. Nuclei were stained with Trypan blue 0.4% (Invitrogen, T10282) and quantified using a hemocytometer, 20,000 nuclei were transposed and partitioned into Gel Beads-in-emulsion (GEMs) in the Chromium Controller (10x Genomics, Pleasanton, CA) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol CG000338 Rev A (10x Genomics). The transposed DNA and cDNA of each individual nucleus were separately indexed and then made into libraries following the protocol. All libraries were sequenced on Illumina NovaSeq 6000 system with specific flow cell types (snRNA-Seq: S4; snATAC-Seq: S1). Measurements related to snRNA-Seq and snATAC-Seq were taken from distinct samples.

value: Kidney

tag: age

value: wild-type


title: HSFA1adelPrD2_T_rep2

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: Mubritinib treated, biol rep 3, Hour 24

description: Library name: Mub-3


title: 7

value: blood


title: 1

value: DMSO


title: 2


title: sorted cells, SAG treatment, rep 1


title: sorted cells, vehicle control, rep 1


title: Control, BTSC53, biol rep 1

description: Library name: BTSC53-1


title: 5


title: HSFA1adelPrD2_T_rep1


title: GPAD-20220124-NMK92M1(snATAC,male,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20220124-NMK92M1_features.tsv.gz
GPAD-20220124-NMK92M1_barcodes.tsv.gz
GPAD-20220124-NMK92M1_matrix.mtx.gz


title: Mubritinib treated, biol rep 2, Hour 24

description: Library name: Mub-2


title: GPAD-20220124-NMK92F2(snRNA,female,week 92)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20220124-NMK92F2_features.tsv.gz
GPAD-20220124-NMK92F2_barcodes.tsv.gz
GPAD-20220124-NMK92F2_matrix.mtx.gz


title: 4


title: GPAD-20220124-NMK92F2(snATAC,female,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20220124-NMK92F2_features.tsv.gz
GPAD-20220124-NMK92F2_barcodes.tsv.gz
GPAD-20220124-NMK92F2_matrix.mtx.gz


title: sorted cells, vehicle control, rep 2


title: HSFA1adelPrD2_R_rep1


title: HSFA1adelPrD2_R_rep2


title: Control, biol rep 3, Hour 24

description: Library name: Ctl-3


title: GPAD-20210423-NMK12M2(snRNA,male,week 12)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210423-NMK12M2_features.tsv.gz
GPAD-20210423-NMK12M2_barcodes.tsv.gz
GPAD-20210423-NMK12M2_matrix.mtx.gz


title: ES_EPZ_ED_rep3

type: RNA

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Gene expression in differentiated cells (ADE Day 6) following pretreatment of ESCs with EPZ6438

hyb_protocol: For each sample, 600 ng of Cy3-labelled cRNA was fragmented at 60 °C for 30 min then mixed with an equal volume of 2x Agilent hybridization buffer and hybridised to an Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Agilent; G4852A) for 17 hr at 65 °C.

scan_protocol: Following hybridisations, microarrays were washed and scanned on a Surescan G2600D scanner (serial: SG12524268) using Agilent Scan Control 9.1.7.1 software with default settings. Signal intensity values were extracted from the resulting single channel TIFF images using Agilent feature extraction software (Agilent Feature Extraction 11.0.1.1) with default parameters (AgilentG3_HiSen_GX_1color). All steps were carried out in accordance with manufacturer’s instructions.

data_processing: Data was processed with custom scripts in R. Raw signal quantitation files were read using the ‘read.maimages’ function in the limma package in R with source set to 'agilent' and annotation based on the Agilent annotation file (‘028005_D_20130207.gal’). Control probes were discarded by retaining only those with a 'ControlType' = 0. Processed intensity values per unique probe were produced using the limma package using 'backgroundCorrect' (paramaters = 'normexp' with an offset of 10) followed by quantile normalisation using 'normalizeBetweenArrays' across all samples (R/Bioconductor; (http://www.R-project.org/)).

source_name: ADE Day 6, ESCs treated with EPZ6438 prior to differentiation

label_protocol: 150 ng of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent, 5188–5282) and the mixture labelled with LowInput QuickAmp Labeling Kit One-Color (Agilent 5190-2305).

growth_protocol: Dual reporter ESCs were cultured in ESC medium + LIF as previously described (PMID: 27723457) and differentiated according to our standard ADE differentiation protocol (PMID: 26840225). To generate sufficient cells for Fluorescence Activated Cell Sorting (FACS), ADE differentiation was performed in T75 flasks alongside a 6-well plate that was analysed by flow cytometry at ADE day 6 to monitor differentiation.

extract_protocol: RNA was extracted from 0.1–0.5 M ESCs / ADE cells using an RNeasy Mini kit (Qiagen; 74104). RNA quantification and assessment of integrity was performed using the total RNA nano chip (Agilent; 5067–1511) and measured on an Agilent Bioanalyzer.

treatment_protocol: For FACS sorted ADE populations, no treatment was added to the cultures before or during differentiation. For PRC2 inhibition samples and their controls, cultures were supplemented with either 1:4000 DMSO (control) or 2.5 μM EPZ6438 (EPZ; from 10 mM stock in DMSO) as indicated.

value: ADE Day 6

value: ESCs treated with EPZ6438 prior to differentiation and DMSO during differentiation


title: Mubritinib treated, biol rep 1, Hour 24

description: Library name: Mub-1


title: Control, biol rep 1, Hour 24

description: Library name: Ctl-1


title: ES_EPZ_ED_rep1


title: Control, biol rep 2, Hour 24

description: Library name: Ctl-2


title: HSFA1adelPrD2_PT_rep2


title: HSFA1adelPrD2_C2_rep2


title: GPAD-20210423-NMK12M2(snATAC,male,week 12)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210423-NMK12M2_features.tsv.gz
GPAD-20210423-NMK12M2_barcodes.tsv.gz
GPAD-20210423-NMK12M2_matrix.mtx.gz


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6B

city: La Jolla

first: Jeamin

last: Jung

state: CA

address: 9420 Athena Cir

department: Bioinformatics Core

institute: La Jolla Institute for Immunology

description: 10X Genomics

library_source: other

data_processing:
10x Genomics
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: seurat metadata
Library strategy: CITE-Seq

molecule: protein

source_name: Blood

extract_protocol:
For single cell RNA-seq assays, we used the 10x Genomics platform. Cells were collected in low retention and sterile ice-cold 1.5 mL tubes containing 500 μL of PBS - FBS (1:1 volume) completed with RNase inhibitor (1:100). Approximately 50,000 sorted cells per tube were processed and loaded on the 10X Chromium Controller (10X Genomics). We used a 5’mRNA capture chemistry (5’ 10X v2 chemistry) and performed cDNA amplification and library preparation for gene expression, feature barcoded surface antibodies according to manufacturer's protocol.
Final libraries were quality checked for fragment size by capillary electrophoresis (Fragment analyzer), and quantity by fluorescence assay (Picogreen) before pooling and sequencing on a NovaSeq 6000 (200 cycle S4 kit v1.5; Illumina, San Diego, CA, USA) to a depth of > 25,000 reads/cell for GEX, > 5,000 reads/cell for hashtag oligo libraries.

treatment_protocol: PBMC stimulated with cow milk epitope pool (M111) for 6 hours and then sorted for CD4 memory T cells either positive for  CD154, CD137, both (Positive) or none (Negative)

value: Blood

value: CD4 memory T cells

value: Cow milk epitope pool


title: ADE_EPZ_DE06_rep3

description: Gene expression in differentiated cells (ADE Day 6) following treatment with EPZ6438 during differentiation

source_name: ADE Day 6, treated with EPZ643 during differentiation

value: ESCs treated with DMSO prior to differentiation and EPZ6438 during differentiation


title: HSFA1adelPrD2_PT_rep1


title: ADE_EPZ_DE06_rep2


title: GPAD-20210423-NMK12F2(snRNA,female,week 12)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210423-NMK12F2_features.tsv.gz
GPAD-20210423-NMK12F2_barcodes.tsv.gz
GPAD-20210423-NMK12F2_matrix.mtx.gz


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6A

description: 10X Genomics


title: ADE_EPZ_DE06_rep1


title: HSFA1a_R_rep2


title: HSFA1a_T_rep1


title: ES_EPZ_ED_rep2


title: HSFA1adelPrD2_C2_rep1


title: ADE_d6_Control_rep2

description: Gene expression in differentiated cells (ADE Day 6) following treatment with DMSO

source_name: ADE Day 6, DMSO Treatment


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5B

description: 10X Genomics


title: GPAD-20210423-NMK12F2(snATAC,female,week 12)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210423-NMK12F2_features.tsv.gz
GPAD-20210423-NMK12F2_barcodes.tsv.gz
GPAD-20210423-NMK12F2_matrix.mtx.gz


title: HSFA1a_T_rep2


title: GPAD-20210422-NMK52F1(snATAC,female,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210422-NMK52F1_features.tsv.gz
GPAD-20210422-NMK52F1_barcodes.tsv.gz
GPAD-20210422-NMK52F1_matrix.mtx.gz


title: GPAD-20210422-NMK52M1(snRNA,male,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210422-NMK52M1_features.tsv.gz
GPAD-20210422-NMK52M1_barcodes.tsv.gz
GPAD-20210422-NMK52M1_matrix.mtx.gz


title: GPAD-20210422-NMK52M1(snATAC,male,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210422-NMK52M1_features.tsv.gz
GPAD-20210422-NMK52M1_barcodes.tsv.gz
GPAD-20210422-NMK52M1_matrix.mtx.gz


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5A

description: 10X Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5B

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
10x Genomics
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: seurat metadata

molecule: polyA RNA


title: GPAD-20210419-NMK3M2(snRNA,male,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210419-NMK3M2_features.tsv.gz
GPAD-20210419-NMK3M2_barcodes.tsv.gz
GPAD-20210419-NMK3M2_matrix.mtx.gz


title: GPAD-20210419-NMK3M2(snATAC,male,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210419-NMK3M2_features.tsv.gz
GPAD-20210419-NMK3M2_barcodes.tsv.gz
GPAD-20210419-NMK3M2_matrix.mtx.gz


title: GPAD-20210419-NMK3F2(snRNA,female,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210419-NMK3F2_features.tsv.gz
GPAD-20210419-NMK3F2_barcodes.tsv.gz
GPAD-20210419-NMK3F2_matrix.mtx.gz


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4B

description: 10X Genomics


title: ADE_d6_Control_rep1


title: ADE_d6_Control_rep3


title: GPAD-20210422-NMK52F1(snRNA,female,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210422-NMK52F1_features.tsv.gz
GPAD-20210422-NMK52F1_barcodes.tsv.gz
GPAD-20210422-NMK52F1_matrix.mtx.gz


title: GPAD-20210419-NMK3F2(snATAC,female,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
GPAD-20210419-NMK3F2_features.tsv.gz
GPAD-20210419-NMK3F2_barcodes.tsv.gz
GPAD-20210419-NMK3F2_matrix.mtx.gz


title: Input

value: Input


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6B

description: 10X Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6A

description: 10X Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4A

description: 10X Genomics


title: ADE_d6H-_rep1

description: Gene expression in differentiated cells (ADE Day 6 GSC High HHEX Negative Population)

source_name: ADE Day 6 GSC High HHEX Negative Population, No Treatment


title: ADE_d6H+_rep3

description: Gene expression in differentiated cells (ADE Day 6 GSC High HHEX Positive Population)

source_name: ADE Day 6 GSC High HHEX Positive Population, No Treatment


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5A

description: 10X Genomics


title: HSFA1a_PT_rep2


title: Input_19


title: HSFA1a_C2_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3B

description: 10X Genomics


title: HSFA1a_PT_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3A

description: 10X Genomics


title: 20220130-E16_5F(snATACsnATAC,female,embryonic 16.5)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220130-E16_5F_features.tsv.gz
20220130-E16_5F_barcodes.tsv.gz
20220130-E16_5F_matrix.mtx.gz


title: ADE_d6H+_rep2

value: ADE Day 6 GSC High HHEX Positive Population


title: ADE_d5Ghigh_rep1

description: Gene expression in differentiated cells (ADE Day 5 GSC High Population)

source_name: ADE Day 5 GSC High Population, No Treatment

value: ADE Day 5 GSC High Population


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4B

description: 10X Genomics


title: HSFA1a_C2_rep2


title: ADE_d6H+_rep1


title: ADE_d5Ghigh_rep3


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3A

description: 10X Genomics


title: HSFA1a_R_rep1


title: ADE_d6H-_rep3

value: ADE Day 6 GSC High HHEX Negative Population


title: HSFB4_37C30m

value: seedling


title: Input_12


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4A

description: 10X Genomics


title: 20220130-E16_5M(snRNAsnATAC,male,embryonic 16.5)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220130-E16_5M_features.tsv.gz
20220130-E16_5M_barcodes.tsv.gz
20220130-E16_5M_matrix.mtx.gz


title: ADE_d6H-_rep2


title: HSFC1_37C30m


title: 20220129-NMK0F(snRNA,female,newborn)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220129-NMK0F_features.tsv.gz
20220129-NMK0F_barcodes.tsv.gz
20220129-NMK0F_matrix.mtx.gz

value: newborn


title: HSFB4_22C


title: 20220130-E16_5M(snATACsnATAC,male,embryonic 16.5)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220130-E16_5M_features.tsv.gz
20220130-E16_5M_barcodes.tsv.gz
20220130-E16_5M_matrix.mtx.gz

value: Kidney


title: Input_20


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3B

description: 10X Genomics


title: ADE_d5Glow_rep1

description: Gene expression in differentiated cells (ADE Day 5 GSC Low Population)

source_name: ADE Day 5 GSC Low Population, No Treatment

value: ADE Day 5 GSC Low Population


title: ADE_d5Ghigh_rep2


title: 20210908-NMK92F2(snRNA,female,week 92)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210908-NMK92F2_features.tsv.gz
20210908-NMK92F2_barcodes.tsv.gz
20210908-NMK92F2_matrix.mtx.gz

value: wild-type


title: 20220129-NMK0M(snRNA,male,newborn)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220129-NMK0M_features.tsv.gz
20220129-NMK0M_barcodes.tsv.gz
20220129-NMK0M_matrix.mtx.gz


title: 20220130-E16_5F(snRNAsnATAC,female,embryonic 16.5)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220130-E16_5F_features.tsv.gz
20220130-E16_5F_barcodes.tsv.gz
20220130-E16_5F_matrix.mtx.gz


title: HSFB3_22C

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1B

description: 10X Genomics


title: HSFC1_22C


title: 20210908-NMK92F2(snATAC,female,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210908-NMK92F2_features.tsv.gz
20210908-NMK92F2_barcodes.tsv.gz
20210908-NMK92F2_matrix.mtx.gz


title: HSFB2b_37C30m


title: ADE_d5Glow_rep3


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2B

description: 10X Genomics


title: 20220129-NMK0M(snATAC,male,newborn)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220129-NMK0M_features.tsv.gz
20220129-NMK0M_barcodes.tsv.gz
20220129-NMK0M_matrix.mtx.gz


title: HSFB2b_22C


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2B

description: 10X Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1B

description: 10X Genomics


title: 20220129-NMK0F(snATAC,female,newborn)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20220129-NMK0F_features.tsv.gz
20220129-NMK0F_barcodes.tsv.gz
20220129-NMK0F_matrix.mtx.gz


title: ADE_d5Glow_rep2


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2A

description: 10X Genomics


title: HSFB3_37C30m


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1A

description: 10X Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2A

description: 10X Genomics


title: ADE_d5G-_rep2

description: Gene expression in differentiated cells (ADE Day 5 GSC Negative Population)

source_name: ADE Day 5 GSC Negative Population, No Treatment

value: ADE Day 5 GSC Negative Population


title: ADE_d5G-_rep3


title: 20210907-NMK92M2(snATAC,male,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210907-NMK92M2_features.tsv.gz
20210907-NMK92M2_barcodes.tsv.gz
20210907-NMK92M2_matrix.mtx.gz


title: 20210908-NMK92F1(snRNA,female,week 92)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210908-NMK92F1_features.tsv.gz
20210908-NMK92F1_barcodes.tsv.gz
20210908-NMK92F1_matrix.mtx.gz


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1A

description: 10X Genomics


title: ADE_d5G-_rep1


title: HSFB2a_22C


title: ADE_d4G+_rep3

description: Gene expression in differentiated cells (ADE Day 4 GSC Positive Population)

source_name: ADE Day 4 GSC Positive Population, No Treatment

value: ADE Day 4 GSC Positive Population


title: 20210908-NMK92F1(snATAC,female,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210908-NMK92F1_features.tsv.gz
20210908-NMK92F1_barcodes.tsv.gz
20210908-NMK92F1_matrix.mtx.gz


title: HSFB2a_37C30m


title: HSFB1_37C30m


title: HSFB1_22C


title: ADE_d4G+_rep2


title: ADE_d4G+_rep1


title: 20210907-NMK92M2(snRNA,male,week 92)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210907-NMK92M2_features.tsv.gz
20210907-NMK92M2_barcodes.tsv.gz
20210907-NMK92M2_matrix.mtx.gz


title: HTR8/Svneo cells, miR-455-5p overexpression-NC, rep1

city: Nanjing

first: Hui-zhi

last: Gong

state: JiangSu

address: No. 123, Tianfei Lane, Mo Chou Road

country: China

institute: Nanjing Women and Children’s Healthcare Hospital

data_processing:
Raw Sequenced Reads were analyzed using GLC genomics workbench.
Assembly: hg18
Supplementary files format and content: gene_count_matrix csv file includes all samples raw counts.

source_name: placenta

growth_protocol: HTR-8/SVneo cells were cultured in RPMI-1640 medium with 10% foetal bovine serum and 1% (v/v) penicillin-streptomycin-glutamine mixed Solution, at 37 ℃ and 5% CO2.

extract_protocol:
The total RNA of HTR-8/SVneo cells was isolated using TRIzol (Invitrogen, USA).
VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina was used for the construction of RNA sequencing libraries.

treatment_protocol: HTR8/SVneo cells (5×105 cell/well) were seeded in 6-well plates (2 mL 1% FBS medium/well) and incubated 24 h in hypoxic environments (94% N2, 5% CO2, 1% O2) to simulate the ischaemic–hypoxic state in early pregnancy in vitro. Then H/R group was first cultured in 1% FBS medium in 94% N2, 5% CO2, 1% O2 for 8 h, then placed in 95% air, 5% CO2 with 10% FBS medium for 4 h; this process was performed twice.

value: placenta

value: HTR8/Svneo cells

value: epithelial cells

value: miR-455-5p overexpression-NC

value: hypoxia/reoxygenation


title: HSFA9_37C30m


title: HTR8/Svneo cells, miR-455-5p overexpression-NC, rep3


title: HTR8/Svneo cells, miR-455-5p overexpression-NC, rep2


title: 20210907-NMK92M1(snATAC,male,week 92)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210907-NMK92M1_features.tsv.gz
20210907-NMK92M1_barcodes.tsv.gz
20210907-NMK92M1_matrix.mtx.gz


title: ADE_d4G-_rep3

description: Gene expression in differentiated cells (ADE Day 4 GSC Negative Population)

source_name: ADE Day 4 GSC Negative Population, No Treatment

value: ADE Day 4 GSC Negative Population


title: ADE_d4G-_rep2


title: 20210907-NMK92M1(snRNA,male,week 92)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210907-NMK92M1_features.tsv.gz
20210907-NMK92M1_barcodes.tsv.gz
20210907-NMK92M1_matrix.mtx.gz


title: 20210423-NMK12M1(snRNA,male,week 12)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210423-NMK12M1_features.tsv.gz
20210423-NMK12M1_barcodes.tsv.gz
20210423-NMK12M1_matrix.mtx.gz


title: HTR8/Svneo cells, miR-455-5p overexpression, rep3

value: miR-455-5p overexpression


title: HTR8/Svneo cells, miR-455-5p overexpression, rep2


title: HSFA8_22C


title: HSFA8_37C30m


title: 20210423-NMK12F1(snRNA,female,week 12)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210423-NMK12F1_features.tsv.gz
20210423-NMK12F1_barcodes.tsv.gz
20210423-NMK12F1_matrix.mtx.gz


title: ADE_d3G+_rep3

description: Gene expression in differentiated cells (ADE Day 3 GSC Positive Population)

source_name: ADE Day 3 GSC Positive Population, No Treatment

value: ADE Day 3 GSC Positive Population


title: HTR8/Svneo cells, miR-455-5p overexpression, rep1


title: 20210423-NMK12M1(snATAC,male,week 12)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210423-NMK12M1_features.tsv.gz
20210423-NMK12M1_barcodes.tsv.gz
20210423-NMK12M1_matrix.mtx.gz


title: ADE_d3G+_rep2


title: ADE_d4G-_rep1


title: HSFA7b_37C30m

source_name: seedling


title: 20210423-NMK12F1(snATAC,female,week 12)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210423-NMK12F1_features.tsv.gz
20210423-NMK12F1_barcodes.tsv.gz
20210423-NMK12F1_matrix.mtx.gz


title: SD_01_138_c3_liver

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v4.5 and aligned to the Gencode GRCh38.p13 genome using STAR v2.7.11a. Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping. Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9.  featureCounts v2.0.2 was used to count the number of mapped reads to each gene.
Assembly: GRCh38.p13
Supplementary files format and content: CSV containing raw counts

source_name: Liver

extract_protocol:
The tissue samples were homogenized in the presence of 1ml Trizol and 1; 5mm stainless steel bead, using the Qiagen TissueLyser II instrument for 2min at 25Hz, twice. Homogenized samples were incubated for 5 min at room temperature after which 200ml Chloroform was added, mixed well and incubated for 3min at room temperature. Samples were centrifuged at 10,000 g at 4C after which the aqueous layer was transferred to a new tube and mixed with equal volume of 70%. The samples were loaded to Qiagen RNAeasy column, and the samples were processed according to the protocol, including the optional on column DNAse treatment.  RNA was eluted in 35ml of RNAse free water.
A Quality Control analysis was performed on the RNA samples using the Agilent Bioanalyzer to assess quality and an RNA Qubit assay was used to determine quantity.  Library preparation was completed using the NEBNext® rRNA Depletion kit and protocol (P/N: E7850X, NEB, Ipswich, MA) per manufacturer recommendations. The kit employs an RNaseH-based method to deplete both cytoplasmic and mitochondrial rRNA. After ribosomal depletion, the RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by thermal fragmentation using divalent cations under elevated temperature.  First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument.  Prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturer's protocols. 150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50M reads per sample.  Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment. Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.

value: Liver

tag: kras genotype

value: WT

tag: consensus molecular_subtypes

tag: recist 1.1

value: SD

tag: clinicalbenefit

value: Yes


title: 20210422-NMK52M2(snRNA,male,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210422-NMK52M2_features.tsv.gz
20210422-NMK52M2_barcodes.tsv.gz
20210422-NMK52M2_matrix.mtx.gz

value: Kidney


title: ADE_d3G+_rep1


title: SD_01_133_c3_liver_R2


title: ADE_d3G-_rep2

description: Gene expression in differentiated cells (ADE Day 3 GSC Negative Population)

source_name: ADE Day 3 GSC Negative Population, No Treatment

value: ADE Day 3 GSC Negative Population


title: HSFA9_22C

value: seedling

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: HSFA7b_22C


title: HSFA7a_22C


title: SD_01_133_c3_liver


title: 20210422-NMK52F2(snRNA,female,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210422-NMK52F2_features.tsv.gz
20210422-NMK52F2_barcodes.tsv.gz
20210422-NMK52F2_matrix.mtx.gz

source_name: Kidney

value: wild-type


title: ADE_d3G-_rep3


title: ADE_d3G-_rep1


title: 20210422-NMK52M2(snATAC,male,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210422-NMK52M2_features.tsv.gz
20210422-NMK52M2_barcodes.tsv.gz
20210422-NMK52M2_matrix.mtx.gz


title: ADE_d2_rep3

description: Gene expression in differentiated cells (ADE day 2)

source_name: ADE Day 2, No Treatment

value: ADE Day 2


title: 20210422-NMK52F2(snATAC,female,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210422-NMK52F2_features.tsv.gz
20210422-NMK52F2_barcodes.tsv.gz
20210422-NMK52F2_matrix.mtx.gz


title: SD_01_133_c1_liver


title: SD_01_133_c1_liver_R2


title: HSFA6b_37C30m


title: HSFA6b_22C


title: 20210419-NMK3M(snRNA,male,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210419-NMK3M_features.tsv.gz
20210419-NMK3M_barcodes.tsv.gz
20210419-NMK3M_matrix.mtx.gz


title: SD_01_132_c1_lymph

source_name: Lymph Node

value: Lymph Node


title: ADE_d2_rep1


title: SD_01_126_c3_liver_R2


title: ADE_d2_rep2


title: HSFA6a_37C30m


title: 20210419-NMK3F(snRNA,female,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210419-NMK3F_features.tsv.gz
20210419-NMK3F_barcodes.tsv.gz
20210419-NMK3F_matrix.mtx.gz


title: 20210419-NMK3M(snATAC,male,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210419-NMK3M_features.tsv.gz
20210419-NMK3M_barcodes.tsv.gz
20210419-NMK3M_matrix.mtx.gz


title: SD_01_126_c3_liver


title: HSFA6a_22C


title: HSFA7a_37C30m


title: ESC_rep3

description: Gene expression in mouse ESCs

source_name: ESCs, No Treatment

value: mESCs


title: 20210419-NMK3F(snATAC,female,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210419-NMK3F_features.tsv.gz
20210419-NMK3F_barcodes.tsv.gz
20210419-NMK3F_matrix.mtx.gz


title: HSFA5_37C30m


title: SD_01_126_c1_liver_R2


title: 20210319-NMKE16_5F(snRNA,female,embryonic 16.5)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210319-NMKE16_5F_features.tsv.gz
20210319-NMKE16_5F_barcodes.tsv.gz
20210319-NMKE16_5F_matrix.mtx.gz


title: ESC_rep1

description: Gene expression in mouse ESCs


title: A1-dSBD-EZH2-Y641N-H3K27me2-ChIP-Rx

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

state: New York

address: 1230 York ave

institute: Rockefeller University

description:
Library name: A1-dSBD-EZH2-Y641N-H3K27me2
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. 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.

value: mouse embryonic stem cells


title: HSFA5_22C


title: SD_01_126_c1_liver


title: HSFA4c_37C30m


title: SD_01_124_c3_liver


title: SD_01_124_c1_liver


title: A1-dSBD-EZH2-Y641N-H3K27me3-ChIP-Rx

description:
Library name: A1-dSBD-EZH2-Y641N-H3K27me3
ChIP-seq


title: 20210319-NMKE16_5F(snATAC,female,embryonic 16.5)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210319-NMKE16_5F_features.tsv.gz
20210319-NMKE16_5F_barcodes.tsv.gz
20210319-NMKE16_5F_matrix.mtx.gz


title: 20210218-NMKE16.5M(snRNA,male,embryonic 16.5)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210218-NMKE16.5M_features.tsv.gz
20210218-NMKE16.5M_barcodes.tsv.gz
20210218-NMKE16.5M_matrix.mtx.gz


title: A1-EZH2-Y641N-input-ChIP-Rx

description:
Library name: A1-EZH2-Y641N-input
ChIP-seq


title: 20210228-NMK3F(snATAC,female,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210228-NMK3F_features.tsv.gz
20210228-NMK3F_barcodes.tsv.gz
20210228-NMK3F_matrix.mtx.gz


title: PR_01_129_c6_lymph

value: PR


title: PR_01_120_c1_lymph


title: 20210218-NMKE16.5M(snATAC,male,embryonic 16.5)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210218-NMKE16.5M_features.tsv.gz
20210218-NMKE16.5M_barcodes.tsv.gz
20210218-NMKE16.5M_matrix.mtx.gz


title: HSFA3_37C1h


title: HSFA4a_22C


title: ESC_rep2

description: Gene expression in mouse ESCs


title: HSFA3_37C30m


title: EZH2-ΔSBD-H3K27me2-ChIP, mESC

description:
Library name: EZH2-ΔSBD-H3K27me2-ChIP
ChIP-seq


title: EZH2-ΔSBD-SUZ12-ChIP, mESC

description:
Library name: EZH2-ΔSBD-SUZ12-ChIP
ChIP-seq


title: 20210129-AKICT3M(snRNA,male,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210129-AKICT3M_features.tsv.gz
20210129-AKICT3M_barcodes.tsv.gz
20210129-AKICT3M_matrix.mtx.gz


title: HSFA4c_22C


title: 20210228-NMK3F(snRNA,female,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210228-NMK3F_features.tsv.gz
20210228-NMK3F_barcodes.tsv.gz
20210228-NMK3F_matrix.mtx.gz


title: EZH2-ΔSBD-EZH2-ChIP, mESC

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


title: PD_01_136_c2_liver

value: PD

value: No


title: EZH2-ΔSBD-H3K27me3-ChIP, mESC

description:
Library name: EZH2-ΔSBD-H3K27me3-ChIP
ChIP-seq


title: HSFA3_37C5min


title: 20210129-AKICT3F(snATAC,female,week 12)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210129-AKICT3F_features.tsv.gz
20210129-AKICT3F_barcodes.tsv.gz
20210129-AKICT3F_matrix.mtx.gz


title: PD_01_131_c3_liver


title: PD_01_136_c1_liver


title: PR_01_129_c2_lymph


title: PD_01_131_c1_liver


title: 20210125-NMK0M(snRNA,male,newborn)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210125-NMK0M_features.tsv.gz
20210125-NMK0M_barcodes.tsv.gz
20210125-NMK0M_matrix.mtx.gz

value: newborn


title: A1-EZH2-Y641N-H3K27me2-ChIP-Rx

description:
Library name: A1-EZH2-Y641N-H3K27me2
ChIP-seq


title: 20210129-AKICT3F(snRNA,female,week 12)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210129-AKICT3F_features.tsv.gz
20210129-AKICT3F_barcodes.tsv.gz
20210129-AKICT3F_matrix.mtx.gz


title: A1-dSBD-EZH2-Y641N-input-ChIP-Rx

description:
Library name: A1-dSBD-EZH2-Y641N-input
ChIP-seq


title: HSFA3_22C


title: EZH2-KO-H3K27me32ChIP, mESC

description:
Library name: EZH2-KO-H3K27me32ChIP
ChIP-seq

value: EZH2 KO


title: PD_01_128_c2_liver_R2

value: Liver

value: WT


title: HSFA4a_37C30m


title: A1-EZH2-Y641N-H3K27me3-ChIP-Rx

description:
Library name: A1-EZH2-Y641N-H3K27me3
ChIP-seq


title: HSFA1d_37C30m


title: HSFA1e_37C30m


title: 20210125-NMK0M(snATAC,male,newborn)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210125-NMK0M_features.tsv.gz
20210125-NMK0M_barcodes.tsv.gz
20210125-NMK0M_matrix.mtx.gz


title: HSFA2_37C30m


title: HSFA1e_22C


title: 20210129-AKICT3M(snATAC,male,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210129-AKICT3M_features.tsv.gz
20210129-AKICT3M_barcodes.tsv.gz
20210129-AKICT3M_matrix.mtx.gz


title: PD_01_128_c2_liver


title: 20210125-NMK0F(snRNA,female,newborn)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210125-NMK0F_features.tsv.gz
20210125-NMK0F_barcodes.tsv.gz
20210125-NMK0F_matrix.mtx.gz


title: EZH2-KO-SUZ12-ChIP, mESC

description:
Library name: EZH2-KO-SUZ12-ChIP
ChIP-seq


title: PD_01_128_c1_liver_R2


title: 20210125-NMK0F(snATAC,female,newborn)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20210125-NMK0F_features.tsv.gz
20210125-NMK0F_barcodes.tsv.gz
20210125-NMK0F_matrix.mtx.gz


title: EZH2-KO-EZH2-ChIP, mESC

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


title: EZH2-ΔSBD-input-ChIP, mESC

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


title: HSFA1b_37C30m


title: PD_01_128_c1_liver


title: HSFA1d_22C


title: A1-H3K27me32ChIP, mESC

description:
Library name: A1-H3K27me32ChIP
ChIP-seq


title: HSFA1b_22C


title: A1-H3K27me3-ChIP, mESC

description:
Library name: A1-H3K27me3-ChIP
ChIP-seq


title: EZH2-KO-input-ChIP, mESC

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


title: 20201213-NMK52F(snRNA,female,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201213-NMK52F_features.tsv.gz
20201213-NMK52F_barcodes.tsv.gz
20201213-NMK52F_matrix.mtx.gz


title: 20201213-NMK52M(snATAC,male,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201213-NMK52M_features.tsv.gz
20201213-NMK52M_barcodes.tsv.gz
20201213-NMK52M_matrix.mtx.gz


title: HSFA1a_37C30m


title: PD_01_117_c3_lung

source_name: Lung

value: Lung

value: Mixed


title: EZH2-KO-H3K27me3-ChIP, mESC

description:
Library name: EZH2-KO-H3K27me3-ChIP
ChIP-seq


title: PD_01_123_c1_liver


title: 20201201-NMK3M(snRNA,male,week 3)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201201-NMK3M_features.tsv.gz
20201201-NMK3M_barcodes.tsv.gz
20201201-NMK3M_matrix.mtx.gz

value: Kidney


title: HSFA1a_37C5min

value: seedling


title: PD_01_117_c1_lung


title: HSFA1a_22C

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: PD_01_115_c3_liver_R2


title: A1-JEZH2-ChIP, mESC

description:
Library name: A1-EZH2-ChIP
ChIP-seq


title: 20201201-NMK3M(snATAC,male,week 3)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201201-NMK3M_features.tsv.gz
20201201-NMK3M_barcodes.tsv.gz
20201201-NMK3M_matrix.mtx.gz

value: wild-type


title: TWGBS, AT4G37130 mutant

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

country: Austria

institute: GMI

description: Library name: TWGBS_AT4G37130_mutant

data_processing:
All reads were mapped on TAIR10 reference genome using a Methylpy pipeline v1.2  (https://github.com/yupenghe/methylpy). DNA methylation levels were estimated as weighted methylation levels for each transposon defined in Araport11 annotation. CMT2- and RdDM-targeted transposons were defined as having differential levels of methylation (> 0.1) between wild-type and cmt2 or drm1drm2 in Col-0 as previously described (Kawakatsu et al. 2016). For each line, average DNA methylation was calculated using all transposons for which at least one read was mapped.
Assembly: TAIR10
Supplementary files format and content: methylation ratios provided for all cytosines as wig files

source_name: 9-true-leaf rosette

growth_protocol: grown in soil in long days at 21°C in a climatic chamber

extract_protocol:
genomic DNA was extracted from rosette leaves at 9-true-leaf stage using the GeneJET Plant Genomic DNA Purification Kit (Thermo Scientific) and sheared with an E220 Focused-ultrasonicator (Covaris) to achieve an average fragment size of approximately 350 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) with methylated adapters (New England BioLabs). The adapter-ligated DNA underwent bisulfite conversion using the EZ-96 DNA Methylation-Gold MagPrep Kit (Zymo Research). Bisulfite-treated samples were amplified using EpiMark Hot Start Taq DNA Polymerase and indexed with NEBNext Multiplex Oligos for Illumina (New England BioLabs). All libraries were sequenced on either an Illumina NextSeq 550 or HiSeq 2500 platform.

value: 9-true-leaf rosette


title: A1-SUZ12-ChIP, mESC

description:
Library name: A1-SUZ12-ChIP
ChIP-seq


title: PD_01_115_c3_liver


title: 20201213-NMK52M(snRNA,male,week 52)

description:
snRNA;refer to column "title" for the corresponding snATAC in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201213-NMK52M_features.tsv.gz
20201213-NMK52M_barcodes.tsv.gz
20201213-NMK52M_matrix.mtx.gz


title: TWGBS, AT4G37120 mutant

description: Library name: TWGBS_AT4G37120_mutant


title: A1-input-ChIP, mESC

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


title: choroid plexus, 24M, scRNAseq

city: Shanghai

first: Yidong

last: Shen

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: choroid plexus

extract_protocol:
Whole brains were collected into cold Hanks’ Balanced Salt Solution for dissection after perfusion. For each brain, two lateral ventricle CPs and one fourth ventricle CP were isolated under a dissection microscope into ice-cold Hanks’ Balanced Salt Solution. All CPs isolated from the mice at the same age were pooled together in 1 ml Hanks’ buffer before digestion. The supernatant was discarded after a quick spin-down. CPs were incubated with 600 ml enzyme mix (DMEM with 30 U/ml DNase I,  2 mg/ml Collagenase type I, and 8 mg/ml Collagenase type IV, with shaking at 1,000 rpm for 1 h at 37ºC. During the incubation, the samples were resuspended by finger flicking every 10 min. The suspension was further shaken vigorously. Sample quality was checked by examining 2.5 ml single-cell suspension under a dissection microscope. Undigested tissue fragments were removed by a centrifuge at 600 rpm for 30 sec at 4ºC. Single cells were then resuspended in 500 ml of 0.04% BSA in PBS after centrifuging at 2,500 rpm for 5 min at 4ºC. The quality and number of single cells were examined by mixing 5 ml suspension with an equal volume of Trypan Blue Solution and monitoring the mixture on a hemocytometer under a dissection microscope. The samples for sequencing contained >50,000 single-cells, with <10% multi-cell aggregates and >80% Trypan Blue Solution negative cells.
Single-cell suspension was loaded onto the Chromium Controller (10x Genomics) at 1,000 cell/μl, then subjected to gel beads in emulsions (GEMs) generation, barcoding, GEM-RT clean up, complementary DNA amplification, and 3’ Gene Expression Library construction using Chromium Next GEM Single Cell 3’ Reagent Kits following the manufacturer’s instructions. Invitrogen Qubit assay was used for library quantification before pooling. Sequencing was performed on the Illumina HiSeq instrument with 150 paired-end reads.

value: choroid plexus

value: choroid plexus cells

value: 24 months old

tag: Sex

value: female


title: EZH2-ΔSBD-JARID2-ChIP-mESC

description:
Library name: EZH2-ΔSBD-JARID2-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.
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


title: PD_01_115_c1_liver

value: PD

value: No


title: choroid plexus, 3M, scRNAseq

description: 10x Genomics

value: 3 months old


title: 20201213-NMK52F(snATAC,female,week 52)

description:
snATAC;refer to column "title" for the corresponding snRNA in the same multiome dataset; Reads from Chromium libraries were demultiplexed using bcl2fastq-v2.20 to obtain raw FASTQ files. Then, the raw FASTQ files were aligned and quantified
20201213-NMK52F_features.tsv.gz
20201213-NMK52F_barcodes.tsv.gz
20201213-NMK52F_matrix.mtx.gz


title: PD_01_117_c1_lung_R2


title: EZH2-ΔSBD-MTF2-ChIP-mESC

description:
Library name: EZH2-ΔSBD-MTF2-ChIP
ChIP-seq


title: TWGBS, AT4G37110 mutant

description: Library name: TWGBS_AT4G37110_mutant


title: PD_01_113_c1_liver

value: Liver


title: TWGBS Col_0, rep2

description: Library name: TWGBS_Col_0_rep2


title: chondrocyte, co-culture, IL-1β, 72h, rep3

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiaotong university

description: Library name: FCI372

data_processing:
The constructed libraries underwent quality control (QC), and after passing, they were subjected to sequencing. Sequencing was performed on the DNBSEQ platform with a read length of SE50. The data obtained from sequencing, referred to as raw reads or raw data, underwent QC to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis (PCA), correlation analysis, differential gene selection, etc.) were conducted.
Assembly: GRCm38
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Primary chondrocyte

extract_protocol:
The skin tissue/cartilage tissue was cut into 1 mm diameter pieces with sterilised ophthalmic scissors. Then skin tissue was digested in 0.5 mg/ml collagenase I (Biosharp, China) and DNase I (Roche, Switzerland) for 3 hours, while cartilage tissue was digested in 0.5 mg/ml collagenase II (Biosharp, China) and DNase I (Roche, Switzerland) for 2 hours. The isolated cell suspension was passed through a 100 μm sieve and then centrifuged to remove the supernatant. DFbs were cultured in alpha-MEM with 1% penicillin-streptomycin and 10% fetal bovine serum. Chondrocytes were cultured in DMEM/F12 containing 1% ITS (OriCell, China), 1% penicillin-streptomycin and 10% fetal bovine serum.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing

value: Primary chondrocyte

value: WT


title: EZH2-ΔSBD-input-ChIP-mESC


title: NE_01_135_c1_liver

value: Ineligible


title: NE_01_135_c3_liver


title: chondrocyte, co-culture, IL-1β, 72h, rep2

description: Library name: FCI272


title: EZH2-KO-JARID2-ChIP-mESC

description:
Library name: EZH2-KO-JARID2-ChIP
ChIP-seq

value: EZH2 KO


title: TWGBS Col_0, rep1

description: Library name: TWGBS_Col_0_rep1


title: WT_T_rep2

value: seedling


title: NE_01_122_s2_rectum

source_name: Rectum

value: Rectum

value: Mixed


title: chondrocyte, co-culture, IL-1β, 72h, rep1

description: Library name: FCI172


title: NE_01_122_s1_rectum


title: chondrocyte, co-culture, no IL-1β, 72h, rep3

description: Library name: FC372


title: WT_T_rep1


title: EZH2-KO-MTF2-ChIP-mESC

description:
Library name: EZH2-KO-MTF2-ChIP
ChIP-seq


title: EZH2-KO-input-ChIP-mESC


title: chondrocyte, co-culture, no IL-1β, 72h, rep2

description: Library name: FC272


title: WT_R_rep2


title: chondrocyte, co-culture, no IL-1β, 72h, rep1

description: Library name: FC172


title: P,P-9(Progression), snRNA

city: Seocho-gu

first: Kim

last: Tae-Min

address: Banpo-daero

institute: The Catholic University of Korea

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: Human reference genome(GRCH38)
Supplementary files format and content: rds

source_name: Bladder

extract_protocol:
We utilized the 10X Genomics Chromium Instrument and cDNA synthesis kit (Chromium Next GEM Single Cell 3' Kit v3.1 &Chromium Next GEM Chip G Single Cell Kit) to generate a barcoded cDNA library for single Nuclei RNA-sequencing from sorted nuclei.
Library was performed according to the manufacter's instructions (single cell 3' Reagent Kits v3.1, 10x Genomics), (Read lengths: 28 bp Read1, 10 bp I7 Index, 10 bp I5 Index, and 90 bp Read2)

value: Bladder

tag: patient id

tag: gender

value: Male

tag: histological grade

value: High

tag: Stage

tag: bcg treatment

value: Yes

tag: progression

value: Y

tag: recurrence


title: A1-MTF2-ChIP-mESC

description:
Library name: A1-MTF2-ChIP
ChIP-seq

tag: cell type

value: mouse embryonic stem cells

tag: genotype


title: WT_R_rep1

tag: tissue

tag: genotype/treatment


title: A1-JARID2-ChIP-mESC

description:
Library name: A1-JARID2-ChIP
ChIP-seq

tag: batch


title: chondrocyte, normal culture, IL-1β, 72h, rep3

description: Library name: CI372


title: P,P-9, snRNA

description: 10x Genomics

value: Pre

value: N


title: WT_PT_rep2


title: P,P-8(Progression), snRNA

description: 10x Genomics


title: chondrocyte, normal culture, IL-1β, 72h, rep2

description: Library name: CI272


title: chondrocyte, normal culture, IL-1β, 72h, rep1

description: Library name: CI172


title: WT_P_rep2


title: Effector ex-Treg creERT2 dKO 4

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

description: Library name: Sample 36

data_processing:
Quality of sequencing data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed for adapters and low quality base calls using Trim Galore, with default parameters (v0.6.5; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were then mapped to the GRCm38 mouse reference genome using Hisat2 (v2.1.0; Kim et al., 2019).
BAM files were imported into Seqmonk (v1.47.0; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), excluding those with mapping quality < 30, and reads were quantified over merged mRNA isoforms from the GRCm38 Ensembl release 90 annotation, using the RNA-seq quantitation pipeline.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing gene names and IDs, together with raw read counts over each gene, generated in Seqmonk using merged mRNA isoforms for the GRCm38 Ensembl release 90 annotation

source_name: Spleen + lymph node

extract_protocol:
Single cell suspensions were prepared from pooled spleen and pLN, from an individual mouse of the indicated genotype. CD4+ cells were enriched by negative depletion using biotinylated anti-B220, anti-CD8 and anti-CD11b followed by Streptavidin Dynabeads (Dynal).Naïve or effector Treg and ex-Treg were sorted based on the indicated markers; all samples were sorted to >95% purity. RNA was prepared from sorted cells using the RNeasy Micro Plus kit (Qiagen), and quality was assessed using the Bioanalyzer RNA chip.
cDNA was generated using the SMARTseq v4 ultra low input RNA kit for sequencing, and libraries prepared from the cDNA using the Nextera XT DNA library preparation kit.

treatment_protocol: Mice were fed with tamoxifen for 9 weeks prior to analysis

tag: strain

value: Spleen + lymph node

value: Effector ex-Treg

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hemi Rosa26-flSTOP-tdRFP:hom

tag: age (weeks)

tag: flow markers


title: NP,P-7, snRNA

description: 10x Genomics

value: No


title: Effector ex-Treg creERT2 dKO 3

description: Library name: Sample 35

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hom Rosa26-flSTOP-tdRFP:hom

value: Female


title: P,P-8, snRNA

description: 10x Genomics


title: chondrocyte, normal culture, no IL-1β, 72h, rep3

description: Library name: C372

value: Primary chondrocyte

value: WT


title: Effector ex-Treg creERT2 dKO 2

description: Library name: Sample 34


title: CF,P-6(CF), snRNA

description: 10x Genomics

value: Remission


title: Effector ex-Treg creERT2 dKO 1

description: Library name: Sample 33


title: NP,P-6, snRNA

description: 10x Genomics

value: Bladder

value: CIS


title: WT_P_rep1

data_processing:
HISAT2 (version 2.2.1) with parameters ‘--dta, --no-mixed, --no-discordant’ was used for aligning raw RNA-seq reads to TAIR10 genome. TPM values for genes were calculated by StringTie (version 2.1.4) with default settings directed by gene annotation file TAIR10 gff3 (https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff). Mean TPM values were calculated from replicates. Differentially expressed genes were identified by edgeR with thresholds q-value < 0.01 and log fold change > 1. To perform clustering of transcriptomic data, identified differentially expressed genes at least in one pairwise comparison (Col-0 37℃ vs 22℃) out of 3 time courses (5min, 15min and 30min) were selected. TPM values were transformed into log2(TPM+1). Genes with the maximum log2(TPM+1) > 2 were kept. Gaussian Mixture Models (GMM), implemented by an R package ClusterR (https://github.com/mlampros/ClusterR), was used for the clustering. The Expectation-Maximization algorithm was used for fitting GMM. The Bayesian information criterion was used for estimating the number of clusters.
Assembly: TAIR10
Supplementary files format and content: raw count

extract_protocol:
Samples were homogenizing to powder using Qiagen TissueLyser II (Cat. No. / ID: 85300). Total RNA was extracted MagMAX™ Plant RNA Isolation Kit (Applied Biosystems™A33899) according to the manufacturer's instructions.
Total RNA was quantified using Qubit4 (Thermo Fisher Scientific) according to the manufacturer's instructions and tested for integrity using an RNA screentape in an Agilent2200 tape station (Agilent).

value: seedling


title: chondrocyte, normal culture, no IL-1β, 72h, rep1

description: Library name: C172


title: WT_C2_rep1


title: Effector ex-Treg creERT2 control 5

description: Library name: Sample 32

value: Male


title: WT_C1_rep2


title: chondrocyte, co-culture, IL-1β, 36h, rep3

description: Library name: FCI336


title: NP,P-5, snRNA

description: 10x Genomics

value: High

value: Y


title: Effector ex-Treg creERT2 control 4

description: Library name: Sample 31


title: A1-input-ChIP-mESC

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

value: mouse embryonic stem cells


title: WT_PT_rep1


title: Effector ex-Treg creERT2 control 3

description: Library name: Sample 30


title: NP,P-4, snRNA

description: 10x Genomics

value: Ta

value: N


title: chondrocyte, co-culture, IL-1β, 36h, rep1

description: Library name: FCI136


title: QK_37C5min_rep2


title: P,P-2(Progression), snRNA

description: 10x Genomics

value: Yes

value: P


title: chondrocyte, co-culture, IL-1β, 36h, rep2

description: Library name: FCI236


title: QK_37C5min


title: Effector ex-Treg creERT2 control 2

description: Library name: Sample 29

value: Spleen + lymph node

value: Effector ex-Treg


title: P,P-2(BCG), snRNA

description: 10x Genomics


title: Effector ex-Treg creERT2 control 1

description: Library name: Sample 28


title: WT_C2_rep2


title: chondrocyte, normal culture, no IL-1β, 72h, rep2

description: Library name: C272


title: chondrocyte, co-culture, no IL-1β, 36h, rep3

description: Library name: FC336


title: Effector Treg creERT2 dKO 4

description: Library name: Sample 27

value: Effector Treg

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hemi Rosa26-flSTOP-tdRFP:hom


title: P,P-2, snRNA

description: 10x Genomics

value: No


title: QK_37C15min


title: chondrocyte, co-culture, no IL-1β, 36h, rep1

description: Library name: FC136

value: Primary chondrocyte

value: WT


title: NP,P-1, snRNA

description: 10x Genomics

value: Bladder


title: Effector Treg creERT2 dKO 3

description: Library name: Sample 26

value: Zfp36l1-fl/fl Zfp36l2-fl/fl Foxp3-eGFP-cre-ERT2:hom Rosa26-flSTOP-tdRFP:hom

value: Female


title: chondrocyte, normal culture, IL-1β, 36h, rep3

description: Library name: CI336


title: WT_C1_rep1

value: seedling


title: QK_22C_rep2


title: NP,P-3, snRNA

description: 10x Genomics

value: Low

value: Y


title: Panc-1, AA, rep3-2

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

data_processing:
De-multiplexing, alignment, and gene counting using both lanes was accomplished with CellRanger (7.2.0).
Ambient RNA was removed through CellBender (0.3.1)
Count matrices were imported into R using scCustomize(2.1.2), then quality filtered via Seurat (5.0.1). Cells with less than 1000 genes detected or with mitochondrial RNA% > 10% were filtered out. Non-protein-coding genes were removed before normalization and scaling.
Cell cycle phase score was predicted using the cyclone function from scran package (1.26.2)
Assembly: GRCh38
Supplementary files format and content: rds file containing quality filtered Seurat object.

growth_protocol: Panc-1,  pancreatic cancer cells were cultured in RPMI (Sigma, #R1383) or DMEM (Gibco, #41966-029) adjusted to correct pH at 5% CO2 (7.6 and 6.5 for Ctrl and acid-adapted, respectively) either by titration with hydrochloric acid or by replacing the appropriate amount of NaHCO3- with NaCl. Cell culture media were supplemented with 5-10% Fetal Bovine Serum (FBS, Gibco, #F9665), 1% Penicillin/Streptomycin (P/S, Sigma-Aldrich, #P0781) and for RPMI also 10 mM glucose (Sigma, #G8644). To ensure correct growth conditions, medium pH was measured inside the incubator, after equilibration at 5% CO2, using a mini-pH electrode.

extract_protocol:
Nuclei were isolated from Panc-1 cells using an IgePal-based lysis buffer (protocol optimized from (Krishnaswami et al, 2016)) , see Supplemental Material for further details). Briefly, 4x106 cells were collected in BSA-coated DNA LoBind tubes (Eppendorf Cat. #022431021), lysed over ice (10 min) and centrifuged (350 RCF, 5 min, 4°C). Lysed cells/nuclei were washed in ice-cold PBS supplemented with BSA (3%), Protease and RNAse inhibitors, followed by centrifugation (800 RCF, 10 min, 4°C). This wash step was repeated twice. For optimal removal of cell membrane, nuclei were spun down through a gradient of Iodixanol (50 % over 29%, 14000 RCF, 22 min, “Optiprep”, Stemcell Cat #7820), washed and filtered through 30 µm filters (Miltenyi Biotec Cat. #130-098-458). Nuclei isolation was verified by BF imaging, and a control sample was stained with 4’,6-diamidino-2-phenylindole (DAPI) to assess nuclear membrane integrity. Nuclei were counted and adjusted to a final concentration of 700-1200 nuclei/µL in nuclei storage buffer.
cDNA libraries were prepared using 10X Genomics Chromium technology. Briefly, for each sample, 5-10*104 nuclei along with reagents, and partitioning oil were loaded onto the 10X Chromium chip (3’ V3.1) according to manufacturer's recommendations (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, Document Number CG000204 Rev D, 10x Genomics), and processed in the 10X Chromium controller (10X Genomics). Indexed libraries were pooled, then sequenced in two lanes.

treatment_protocol: isogenic human Panc-1 cells were randomly split into control and acid adaptation groups with three replicates in each group. AA samples were cultured under acidic conditions (pH 6.7) for 4 weeks, while Ctrl samples were maintained at constant physiological pH of 7.6 for the same time. At the end of the adaptation, nuclei from each cell group were extracted and subjected to single cell RNA sequencing using the 10x Genomics snRNA-seq workflow.

tag: cell line

tag: treatment

value: Acid Adaptation


title: Effector Treg creERT2 dKO 2

description: Library name: Sample 25

tag: Sex


title: chondrocyte, normal culture, IL-1β, 36h, rep2

description: Library name: CI236


title: Panc-1, AA, rep3-1


title: Effector Treg creERT2 dKO 1

description: Library name: Sample 24

value: Male


title: QK_22C


title: dPrD2_T_rep2


title: Panc-1, Ctrl, rep3-2

value: Control


title: Effector Treg creERT2 control 5

description: Library name: Sample 23


title: Panc-1, Ctrl, rep3-1


title: dPrD2_T_rep1


title: chondrocyte, co-culture, no IL-1β, 36h, rep2

description: Library name: FC236


title: chondrocyte, normal culture, no IL-1β, 36h, rep3

description: Library name: C336


title: dPrD2_R_rep2


title: chondrocyte, normal culture, no IL-1β, 36h, rep2

description: Library name: C236


title: Effector Treg creERT2 control 4

description: Library name: Sample 22


title: QK_37C15min_rep2


title: Panc-1, AA, rep2


title: chondrocyte, normal culture, no IL-1β, 36h, rep1

description: Library name: C136


title: Panc-1, Ctrl, rep2


title: dPrD2_R_rep1