title: Mus musculus, oocyte, wildtype, MII, biol repl 4

description:
Library name: Sample 12
Column name fpkm-RNAseq.xls: WM24

value: wildtype


title: 242-PBMC-14-12mo-LPS

status: Public on Apr 27 2026

type: SRA

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

country: USA

institute: Massachusetts General Hospital / Harvard Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to reference 2020-A (Ensembl 98) transcriptome 156 and quantified using Cell Ranger v6.0.2 multipipeline.
Assembly: reference 2020-A (Ensembl 98) transcriptome
Supplementary files format and content: 10X Cell Ranger Outputs

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

tag: cell type

value: PBMC

tag: subject

tag: months after_bcg_vaccine

tag: have paired_pbmc_and_csf

tag: tissue-(cell)type

value: PBMCs

tag: stimulation treatment

value: LPS


title: Mus musculus, oocyte, Psma7 cKO, MII, biol repl 2

city: Hangzhou

first: Chen

last: Yingyan

address: No. 3 Qingchundong Road

country: China

institute: Zhejiang University

description:
Library name: Sample 14
Column name fpkm-RNAseq.xls: PM22

library_source: transcriptomic

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mm10 mouse genome using TopHat 2.1.1, with the default parameters. Expression levels of each gene were quantified as normalized fragments per kilobase of exons per million mapped fragments (FPKM) using Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: xls file includes FPKM values for all Sample

organism: Mus musculus

source_name: oocyte (MII)

extract_protocol:
Five oocytes per sample were collected from the wildtype and Psma7 cKO female mice for RNA-seq. Each sample was immediately lysed with 4 µL lysis buffer (containing 0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 0.2 µL 1:1000 ERCC mRNA spike-in dilution for mouse oocyte samples).
RNA libraries for RNA-seq were prepared using the published Smart-seq2 method.

treatment_protocol: Female mice (3–4-week-old) were injected with 5 IU pregnant mare serum gonadotropin (PMSG) and humanely euthanized 44 h later. Oocytes at the germinal vesicle (GV) stage were harvested in M2 medium. To obtain oocytes at the metaphase II (MII) stage, female mice at 3–4 weeks of age were intraperitoneally injected with 5 IU PMSG, followed by human chorionic hormone (hCG) 44 h later. Oocytes (MII) were harvested from the oviducts using M2 medium 14-16 h after hCG injection, followed by digestion using 0.3% hyaluronidase.

value: oocyte (MII)

tag: genotype

value: Zp3-Cre; Psma7 flox/flox


title: HSUR1-3

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description: Library name: 15955X5

data_processing:
A standard RNASeq alignment and differential expression analysis was performed to compare the five replicas of WT cj38637 cells and five replicase of deltaHSUR1 knockdown.  This entailed creating a STAR  (v2.7.9a) reference sequence index using a combine Callithrix jacchus (v3.2.1) and Saimiriine herpesvirus 2 (Genbank ID: X64346.1) fasta sequences. Likewise, gene annotations from Callithrix Jacchus Ensembl (v91) and X64346.1 were merged. The STAR ‘genomeGenerate’ command was used to create an index file using these reference and annotation files with ‘sjdbOverhang’ set to 149
The paired end, 150bp, NovaSeq6000 fastq datasets were processed using cutadapt (v3.4) to remove adapter sequence (R1= AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, R2= AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and aligned using STAR (--twopassMode Basic --outSAMtype BAM SortedByCoordinate --outBAMsortingBinsN 800 --quantMode TranscriptomeSAM --outWigType bedGraph --outWigStrand Unstranded --seedPerWindowNmax 30) to generate bam alignments and unique observation read depth big wig tracks for each replica.
Differential expression analysis was performed using the USeq DefinedRegionDifferentialSeq (v9.3.5, DRDS) application that maps unique alignments to transcripts (MQ>=13), wraps DESeq2((v1.14.1), estimates differential splicing events, hierarchically clusters samples, and exports a spreadsheet of differentially expressed genes and replica-gene normalized abundance estimates including the DESeq2 rLog values for principal component analysis (PCA).
Assembly: CalJac3
Supplementary files format and content: tab-delimited text file containing EnsemblID, Gene Name, Log2 Fold Change, Adjusted P-value, and DESeq2 normalized counts.
Supplementary files format and content: xxx.counts : SubBread featureCount ensembl transcript abundance estimates in the CalJac3.2 build
Supplementary files format and content: xxx.bw : Relative read depth tracks for unique paired end alignments in the CalJac3.2 build

molecule: polyA RNA

organism: Callithrix jacchus

source_name: Cell line

growth_protocol: HVS-infected Marmoset T cells were grown at at density of 500,000-1 million cells/ml in RPMI 1640 medium supplemented with 20% FBS, 100 Units of penicllin, 100 µg/ml streptomycin, 1 mM of sodium pyruvate, 2 mM glutaMAX and 0.001% b-mercaptoethanol.

extract_protocol:
For iRICC experiment, total RNA was extracted with TRIzol following the manufacturer's protocol (Invitrogen).  Poly A+ RNA was selected with oligo-dT magnetic beads following the manufacturer's protocol (New England Biolabs). Ten percent of each sample was saved as input and stored in TRIzol.  Crosslinked HSUR1-mRNA complexes were captured with HSUR1 antisense oligonucleotide and magnetic streptavidin beads (Dynabeads).  Bound RNA was released from the beads with TRIzol.  HSUR1 and control pull down samples were purified and used directly to library preparation.
Libraries for iRICC experiments were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). For RNA-seq experiments, libraries were prepared with the  NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation.

treatment_protocol: For iRICC experiments, three independent samples of 200 million HVS-infected marmoset T cells each were crosslinked with psoralen at 365 nm for one hour at 4°C.  Samples were then lysed with 6 M guanidium hydrochloride, 0.8% SDS & proteinase K and incubated at 65°C for one hour.  One milliliter of TRIzol was added to each sample and stored at -80°C.

tag: tissue

value: Cell line

tag: cell line

value: cj319 WT

value: T cell


title: 242-PBMC-14-0mo-LPS

description: 10x Genomics


title: Mus musculus, oocyte, Psma7 cKO, MII, biol repl 1

description:
Library name: Sample 13
Column name fpkm-RNAseq.xls: PM21


title: 242-PBMC-14-3mo-BCG

description: 10x Genomics

value: HKBCG


title: control 2

description: Library name: 15955X4


title: Mus musculus, oocyte, wildtype, MII, biol repl 3

description:
Library name: Sample 11
Column name fpkm-RNAseq.xls: WM23


title: 242-PBMC-14-12mo-Ctrl

description: 10x Genomics

value: Ctrl


title: ILC2 Melatonin 2

city: Los Angeles

first: Jafar

last: Cain

state: CA

address: 1450 Biggy St

department: MMI

institute: University of Southern California

description:
Library name: Sample2
21079R-09-21_S0

data_processing:
Image analysis andbase calling was carried out usingRTA 1.13.48.0. Final file formatting,demultiplexing andfastq generation were carried out usingCASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genomemm39 usingSTAR (v2.7.8) with default parameter settings
Gencode M33 annotation was used to quantify the aligned reads to genes/transcripts usingPartek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression usingPartek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Assembly: mm39
Supplementary files format and content: CSV file of normalised gene counts per sample

source_name: Lung

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: Primary

value: WT

tag: treatment

value: Melatonin


title: Mus musculus, oocyte, wildtype, MII, biol repl 2

description:
Library name: Sample 10
Column name fpkm-RNAseq.xls: WM22


title: WT-5

description: Library name: 22466X5


title: deltaH1-4

description: Library name: 22466X4


title: WT-4

description: Library name: 22466X3


title: Kidney cells, CluGFP, 30days

city: Montreal

first: Alex

last: Gregorieff

state: Quebec

country: Canada

institute: Research Institute of the McGill University Health Centre (RI-MUHC)

description:
Library name: CluGFP_30days
10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation, were made using the Cell Ranger software v7.0.1
Assembly: Mouse mm10
Supplementary files format and content: TSV and matrix files

source_name: Kidney

extract_protocol:
BAC-CluGFP mice were sacrificed at day 2, 7, or 30 after 35min IRI treatment. Kidneys were perfused with ice-cold PBS. Mice were anesthetized, sacrificed and immediately perfused with PBS  from the left ventricle, and kidneys were removed The fresh kidney tissue was finely cut in a Petri dish using a razor blade in 1 mL of cold Dulbecco’s modified Eagle’s medium (DMEM) and digested with DMEM containing Collagenase II (2 mg/mL, Gibco ), Dispase II (2mg/mL, Gibco), and DNase I (30 mg/mL, Roche) at 37°C for 20 min (pipetted every 2 min); then 5 min shaken (200 RPM, 37C). Dissociated tissue was passed through a 70 and then 40 μm cell strainer and centrifuged at 1600 rpm for 5 min at 4°C. Pellets were re-suspend in Red Blood Cell Lysing Buffer Hybri-Max (Sigma, Cat #?) for 5min at room temperature in order to remove remaining red blood cells. Cells were then sorted using FACSAria IIu Cell Sorter (Becton Dickinson). Collected gfp + cells were used for RNA seq.
Single-cell suspensions were washed and resuspended in PBS with 0.04% BSA. An aliquot of cells was used for LIVE/DEAD viability testing (Thermo Fisher Scientific). Single-cell libraries were generated using the 10x Genomics Chromium Controller instrument and Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells suspended in reverse transcription reagents, along with gel beads, were segregated into aqueous nanoliter-scale gel bead-in-emulsions (GEMs). The GEMs were then reverse transcribed in a T1000 Thermal cycler (Bio-Rad) programed at 53ºC for 45 min, 85ºC for 5 min, and hold at 4ºC. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a T1000 Thermal cycler programed at 98ºC for 3 min, 12 cycles of (98ºC for 15 s, 67ºC for 20 s, 72ºC for 1 min), 72ºC for 1 min, and hold at 4ºC. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter) with cleanup in between steps. Post-ligation product was amplified with a T1000 Thermal cycler programed at 98ºC for 45 s, 12 cycles of (98ºC for 20 s, 54ºC for 30 s, 72ºC for 20 s), 72ºC for 1 min, and hold at 4ºC. The sequencing-ready libraries were cleaned up with SPRIselect, quality controlled for size distribution and yield (LabChip GX Perkin Elmer), and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms). Libraries were loaded on MGI DNBSEQ-G400 and sequenced using the following parameters: 28 bp Read1, 8 bp Index i7, and 150 bp Read2. Raw sequencing data for each sample was converted to matrices of expression counts using the Cell Ranger software provided by 10X Genomics (version 4.0.0).

value: Kidney

value: kidney cells isolated from BAC-CluGFP transgenic mice after ischemia-reperfusion injury

value: GFP+ Clu-expressing kidney cells

value: 35 min IRI treatment

tag: time point


title: Mus musculus, oocyte, wildtype, MII, biol repl 1

description:
Library name: Sample 9
Column name fpkm-RNAseq.xls: WM21

value: wildtype


title: 242-PBMC-14-12mo-BCG

description: 10x Genomics

value: PBMC

value: PBMCs


title: deltaH1-2

description: Library name: 22466X2


title: HSUR1-2

description: Library name: 15955X3


title: control 3

description: Library name: 15955X6


title: Kidney cells, CluGFP, 7days

description:
Library name: CluGFP_7days
10X Genomics


title: WT-2

description: Library name: 22466X1


title: 242-PBMC-10-3mo-LPS

description: 10x Genomics

value: LPS


title: ILC2 Melatonin 1

description:
Library name: Sample1
21079R-09-20_S0


title: 242-PBMC-14-0mo-Ctrl

description: 10x Genomics


title: Mus musculus, oocyte, Psma7 cKO, GV, biol repl 4

description:
Library name: Sample 8
Column name fpkm-RNAseq.xls: PGV4

source_name: oocyte (GV)

value: oocyte (GV)

value: Zp3-Cre; Psma7 flox/flox


title: Kidney cells, CluGFP, 48hr

description:
Library name: CluGFP_48hr
10X Genomics


title: T-TR5

city: Hefei

first: weibin

last: wu

address: Changjiang Western Road 130

institute: Anhui Agricultural University

description: Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Ovis aries

source_name: placenta

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using  Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: placenta

value: Not available

value: Restricted feeding


title: Mus musculus, oocyte, Psma7 cKO, GV, biol repl 1

description:
Library name: Sample 5
Column name fpkm-RNAseq.xls: PGV1


title: Control Sample 3

first: Zilong

last: Li

address: The Second Affiliated Hospital of Zhejiang University Jiefangyuan District

institute: the second Affiliated Hospital of Zhejiang University

description: Library name: Control_Rep3

data_processing:
Data Processing Step Raw reads were quality-checked using FastQC. Adapters were trimmed, and low-quality bases were removed using Trimmomatic. Clean reads were aligned to the mouse reference genome (mm10) using HISAT2. Gene counts were quantified using FeatureCounts, and normalized gene expression values (FPKM/TPM) were calculated. Differential expression analysis was conducted using DESeq2, with thresholds of |log2 fold change| > 1 and FDR < 0.05.
Assembly: mm10
Supplementary files format and content: Tab-separated value files containing normalized expression data (FPKM and TPM). Matrix files for downstream analysis.

organism: Rattus norvegicus

source_name: intervertebral disc

extract_protocol:
Interverterbral disc tissues were excised from mice under aseptic conditions and processed immediately. The tissues were digested using a collagenase type I (2 mg/ml) and DNase I (40 U/ml) solution at 37°C for 30 minutes. Single-cell suspensions were prepared by passing the digested tissue through a 70 μm cell strainer. Macrophages were sorted by FACS using the markers F4/80 and CD11b, resuspended in PBS, and stored at -80°C for further RNA extraction. Total RNA was extracted using the TRIzol reagent following the manufacturer’s protocol. RNA integrity was assessed using an Agilent Bioanalyzer (RIN > 7.0).
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit. Briefly:  500 ng of total RNA was used for library preparation, including rRNA depletion and poly(A) enrichment. RNA was fragmented, reverse-transcribed into cDNA, and ligated with sequencing adapters. Libraries were amplified by PCR and purified using AMPure XP beads. Final libraries were quantified with Qubit and their quality confirmed on an Agilent Bioanalyzer. Sequencing was performed using an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads.

treatment_protocol: Rats with IVD were divided into two groups: Treated group receivedAF-PTK@LEV@SPP1 injections (dose and frequency specified in the methods section). Control group received no treatment. The treatment lasted for 14 days prior to sample collection.

value: intervertebral disc

value: Primary cells

value: intervertebral disc cells

value: Control


title: control 1

description: Library name: 15955X2

value: Cell line

value: cj319 WT

value: T cell


title: Mus musculus, oocyte, Psma7 cKO, GV, biol repl 3

description:
Library name: Sample 7
Column name fpkm-RNAseq.xls: PGV3


title: 242-PBMC-14-0mo-BCG

description: 10x Genomics

value: HKBCG


title: HSUR1-1

description: Library name: 15955X1


title: Mus musculus, oocyte, wildtype, GV, biol repl 4

description:
Library name: Sample 4
Column name fpkm-RNAseq.xls: WGV4

value: wildtype


title: Mus musculus, oocyte, Psma7 cKO, GV, biol repl 2

description:
Library name: Sample 6
Column name fpkm-RNAseq.xls: PGV2


title: T-TR3

description: Hu sheep

value: WT


title: Mus musculus, oocyte, wildtype, GV, biol repl 3

description:
Library name: Sample 3
Column name fpkm-RNAseq.xls: WGV3


title: Control Sample 1

description: Library name: Control_Rep1


title: T-TR1

description: Hu sheep


title: Kidney cells, CluGFP, Untreated

description:
Library name: CluGFP_Untreated
10X Genomics

value: Kidney

value: kidney cells isolated from BAC-CluGFP transgenic mice after ischemia-reperfusion injury

value: GFP+ Clu-expressing kidney cells

value: Untreated


title: T-TR4

description: Hu sheep

value: placenta


title: Mus musculus, oocyte, wildtype, GV, biol repl 2

description:
Library name: Sample 2
Column name fpkm-RNAseq.xls: WGV2

value: oocyte (GV)


title: 242-PBMC-10-3mo-Ctrl

description: 10x Genomics

value: PBMC

value: PBMCs

value: Ctrl


title: T-CON5

description: Hu sheep

value: Not available

value: Normal feeding


title: Treated Sample 2

description: Library name: Treated_Rep2

value: intervertebral disc

value: Primary cells

value: intervertebral disc cells


title: TPCD_2

city: New York

first: Naitao

last: Wang

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

description: Library name: Sample10

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm38) using the Cell Ranger (7.0.0) software (10X Genomics). Cells were removed if they expressed fewer than 100 unique genes, fewer than 2,000 total counts, more than 40,000 total counts, or greater than 20% mitochondrial reads. Genes detected in less than 20 cells and all mitochondrial genes were excluded from subsequent analyses. Combining samples from all cohorts yielded a count matrix of 47,777 cells by 20,618 genes, with a median of 9,037 counts and a median of 2,575 genes per cell. The count matrix was normalized by log2(10K+1) to identify the top 2,000 highly-variable genes. The count matrix was further scaled to a mean of 0 and a standard deviation of 1 for principal component analysis (PCA), UMAP dimensionality reduction, and Leiden clustering. PCA was performed on the 1,000 most variable genes and the top 50 principal components retained 41% of the variance. Cell types were determined using a combination of markers genes identified in prior literature and the web-based tool Panglao DB (https://panglaodb.se/).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix, barcode, and feature files

source_name: Stomach

growth_protocol: In this study, we used freshly dissociated stomach mucosa cells. Stomachs were collected from TY (n=2 mice), TP (n=3 mice), TCD (n=3 mice), and TPCD (n=2 mice) groups three weeks after tamoxifen administration. Stomach mucosae were stripped using tweezers and washed with cold PBS. After mincing with a scalpel, the mucosal tissues were digested for 30 minutes with TrypLE (12605010, Gibco), followed by 45 minutes with collagenase/hyaluronidase (07912, STEMCELL Technologies). Viable cells were sorted as DAPI-negative using a BD FACSymphonyTM S6 Cell Sorter.

extract_protocol:
Viable cells were directly processed for library preparation.
For each mouse, 10,000 cells were processed for encapsulation and library preparation (Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit, 10X Genomics). For each sample, 200 million reads were acquired on a NovaSeq 6000 platform.

treatment_protocol: Stomach tissues were collected three weeks after tamoxifen administration (two doses, 3mg/dose, 48h interval).

value: Stomach

value: Dissociated stomach mucosa cells

value: Kmt2c/Kmt2d/Pten knockout


title: T-CON4

description: Hu sheep

value: WT


title: 242-PBMC-10-3mo-BCG

description: 10x Genomics

value: HKBCG


title: 242-PBMC-10-12mo-LPS

description: 10x Genomics

value: LPS


title: T-TR2

description: Hu sheep

value: Restricted feeding


title: Control Sample 2

description: Library name: Control_Rep2

value: Control


title: 242-PBMC-10-12mo-Ctrl

description: 10x Genomics


title: Mus musculus, oocyte, wildtype, GV, biol repl 1

description:
Library name: Sample 1
Column name fpkm-RNAseq.xls: WGV1

value: oocyte (GV)

value: wildtype


title: T-CON2

description: Hu sheep

value: placenta


title: 242-PBMC-10-0mo-Ctrl

description: 10x Genomics

value: PBMC

value: PBMCs

value: Ctrl


title: 242-PBMC-10-12mo-BCG

description: 10x Genomics


title: TCD_2

description: Library name: Sample7

value: Kmt2c/Kmt2d knockout


title: 242-CSF-14-3mo-LPS

description: 10x Genomics

source_name: CSF

value: CSF

value: CSF Cells


title: 242-CSF-14-3mo-Ctrl

description: 10x Genomics


title: 242-CSF-14-3mo-BCG

description: 10x Genomics


title: 242-PBMC-10-0mo-LPS

description: 10x Genomics


title: XIII_ELOBKO_IgG

city: Houston

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

description: Library name: XIII_ELOBKO_C_R_IgG

library_source: genomic

data_processing:
Reads were processed with trimgalore
Reads were aligned to the genome with bowtie2
Peaks were called with MACS2
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Library strategy: CUT&Run

molecule: genomic DNA

source_name: diffuse midline glioma

growth_protocol: SU-DIPGXIII cells were maintained as gliomaspheres in DMG media (50:50 DMEM/F12 and Neurobasal A, supplements with B27 minus Vitamin A, heparin, sodium pyruvate, GlutaMAX, MEM non-essential amino acids,  HEPES, Antibiotic-Antimyotic, Heparin, hPDGF-AA, hPDGF-BB, hFGF154, and hEGF) in a humidified chamber with 5% CO2 at 37C

extract_protocol:
SU-DIPGXIII+Cas9 cells were immobilized on ConA beads, permeabilized with 0.01% Digitonin, incubated with primary antibodies, and then cut with pAG-MNase to release DNA fragments as previously described.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, E7103) following the manufacturer's instructions

treatment_protocol: Cells were not treated for this study

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: ELOBKO

value: IgG


title: Treated Sample 1

description: Library name: Treated_Rep1

value: intervertebral disc

value: Primary cells

value: intervertebral disc cells

value: WT


title: Treated Sample 3

description: Library name: Treated_Rep3


title: TPCD_1

description: Library name: Sample9

value: Stomach

value: Dissociated stomach mucosa cells

value: Kmt2c/Kmt2d/Pten knockout


title: T-CON3

description: Hu sheep

value: placenta

value: Not available

value: Normal feeding


title: 242-PBMC-10-0mo-BCG

description: 10x Genomics

value: PBMC

value: PBMCs

value: HKBCG


title: TCD_3

description: Library name: Sample8

value: Kmt2c/Kmt2d knockout


title: TCD_1

description: Library name: Sample6


title: TP_3

description: Library name: Sample5

value: Pten knockout


title: T-CON1

description: Hu sheep


title: 242-CSF-14-12mo-BCG

description: 10x Genomics

value: CSF

value: CSF Cells


title: XIII_CTL_H3K4me3

description: Library name: XIII_CTL_H3K4me3_C_R

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: CTL


title: K562 empty vector replicate 2

type: RNA

city: Santander

first: Manuel

last: Rosa-Garrido

address: Einstein 22

department: Cellular and Molecular Signaling

country: Spain

institute: The Institute of Biomedicine and Biotechnology of Cantabria

description: K562 cells stably transfected with empty pCDNA vector

hyb_protocol: Fifteen micrograms of fragmented biotin-labeled cRNA were hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array at 45°C for 16 hours in a GeneChip Hybridization Oven 640 according to the manufacturer's instructions.

scan_protocol: Arrays were washed and stained using the Affymetrix GeneChip Fluidics Station according to the standard Affymetrix protocol and scanned using the GeneChip Scanner 3000.

data_processing: Raw CEL files were processed using dChip (DNA-Chip Analyzer, version April 13, 2010). Arrays were normalized using the invariant set normalization method. Expression values were calculated using the model-based expression index (MBEI) algorithm with mismatch probe subtraction (PM-MM difference model). Differential expression between KCTCF-D11 and KpCDNA samples was determined using fold-change thresholds.

label: Biotin

source_name: K562 cells

label_protocol: Biotin-labeled cRNA was prepared from total RNA using the Affymetrix GeneChip 3′ IVT labeling protocol according to the manufacturer’s instructions. Briefly, first-strand cDNA synthesis was performed using a T7-oligo(dT) primer, followed by second-strand synthesis and in vitro transcription incorporating biotin-labeled nucleotides.

growth_protocol: The K562 cell line (obtained from American Type Culture Collection, ATCC) is derived from a human chronic myeloid leukemia. Cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum (Lonza), 150 μg/mL gentamicin, and 2 μg/mL ciprofloxacin at 37°C in a humidified atmosphere containing 5% CO₂. KCTCF-D11 and KpCDNA cells are K562 cells stably transfected with pCDNA-CTCF expression vector or the corresponding empty vector, respectively.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality and integrity were assessed prior to labeling. Biotin-labeled complementary RNA (cRNA) was synthesized from total RNA samples derived from KpCDNA and KCTCF-D11 cells and hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array at the Genomic Facility of the Centro de Investigación del Cáncer (Salamanca, Spain).

treatment_protocol: No additional treatment was applied. Samples correspond to stable transfectants (KCTCF-D11 vs empty vector control KpCDNA).


title: K562 CTCF overexpression replicate 4

description: K562 cells stably transfected with pCDNA-CTCF vector


title: K562 CTCF overexpression replicate 3


title: CD34_SP140i_H3K4me3_Rep3

city: Shanghai

first: Cui

last: Xinyu

address: Siping Road

institute: Tongji University

description: Library name: CD34_SP140i_H3K4me3_Rep3

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (hg38) using Bowtie2(v.2.3.5.1) with the parameters ` -t --local --very-sensitive-local --no-mixed --no-discordant --no-unal. The alignment files were processed using SAMtools(v.1.9). PCR duplicates were removed using Sambamba (v.0.7.0). Peaks were called using MACS2 (v.2.1.2) with the setting ‘-f BAMPE -g hs --keep-dup all --broad --broad-cutoff 0.01’. After filtering out blacklist regions, peaks detected in at least two replicates were retained, and their corresponding genomic coordinates were merged to generate a consensus peak set.
Assembly: hg38
Supplementary files format and content: bigWig,broadPeak
Library strategy: CUT&Tag

source_name: Embryoid body

extract_protocol:
Chromatin was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).
CUT&Tag libraries for sequencing were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following the manufacturer’s protocols.

value: Embryoid body

value: mesoderm


title: K562 CTCF overexpression replicate 1


title: 242-CSF-14-12mo-LPS

description: 10x Genomics

value: LPS


title: K562 CTCF overexpression replicate 2


title: XIII_CTL_IgG.3

description: Library name: XIII_CTL_C_R_IgG.3


title: CD34 IgG

description: Library name: CD34_IgG


title: 242-CSF-14-12mo-Ctrl

description: 10x Genomics

value: Ctrl


title: TP_2

description: Library name: Sample4

value: Stomach

value: Dissociated stomach mucosa cells


title: XIII_CTL_K27me3rep2

description: Library name: XIII_CTL_C_R_K27me3rep2


title: XIII_CTL_second_IgG.2

description: Library name: XIII_CTL_secondary_IgG.2


title: TY_2

description: Library name: Sample2

value: Wildtype


title: TP_1

description: Library name: Sample3


title: scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep4

city: Ithaca

first: Connor

last: Kean

address: 215 Tower Rd

institute: Cornell University

description: Library name: Adult_4_VDJ

data_processing:
The raw FASTQ data was processed using cell ranger multi (v6.0.0, 10X Genomics)
Count matrixes were filtered using Seurat v5.0.0 to remove cell barcodes with fewer than 500 genes, fewer than 1000 transcripts, and more than 7.5% mitochondrial counts
Seurat v5.0.0 was used to normalize and scale the raw counts, perform dimensionality reduction, and generate UMAP projections.
Assembly: mm10
Supplementary files format and content: Cell ranger .h5 output files: Contain Barcodes X Features sparse count matrix for each sample
Supplementary files format and content: Cell ranger filtered_contig_annotations.csv output files: Contain the TCR-sequence annotations of each cell barcode

source_name: Spleen

extract_protocol:
Murine cells were isolated from spleen two weeks post timestamp. Single cell suspensions were obtained by manual dissociation and filtration through a 40uM strainer. CD8+ T cells were isolated by positive magnetic separation using anti-CD8a microbeads. Live Va2+CD8+ cells were sorted into 0.04% BSA in PBS.
Cells were loaded in the Chromium instrument (10X Genomics) for the formation of gel bead-in-emulsions (GEMs) targeting 5-10k cells per sample. Single-cell RNA-seq and TCR libraries were prepared using the Chromium Single Cell V(D)J Reagent Kit (v1.1 Chemistry) (10X Genomics) by the BRC Genomics Facility following the manufacturer’s protocol. Libraries  were sequenced on a NovaSeq 6000  (Illumina) to an average depth of >150M reads (scRNA-seq) and >15M reads (scTCR).

value: Spleen

value: CD8+ T cell

tag: age

value: Adult (28 day timestamp)


title: CD34_SP140i_H3K4me3_Rep2

description: Library name: CD34_SP140i_H3K4me3_Rep2


title: CD34_SP140i_H3K4me3_Rep1

description: Library name: CD34_SP140i_H3K4me3_Rep1


title: XIII_ELOBKO_K27Mrep2

description: Library name: XIII_ELOBKO_C_R_K27Mrep2

value: ELOBKO


title: XIII_ELOBKO_K27me3rep1

description: Library name: XIII_ELOBKO_C_R_K27me3rep1


title: TY_1

description: Library name: Sample1


title: CD34_DMSO_H3K4me3_Rep3

description: Library name: CD34_DMSO_H3K4me3_Rep3


title: 242-CSF-14-0mo-LPS

description: 10x Genomics

value: CSF


title: XIII_ELOBKO_K27me3rep2

description: Library name: XIII_ELOBKO_C_R_K27me3rep2


title: 242-CSF-10-3mo-LPS

description: 10x Genomics

value: CSF Cells


title: 242-CSF-10-3mo-Ctrl

description: 10x Genomics


title: XIII_CTL_K27me3rep1

description: Library name: XIII_CTL_C_R_K27me3rep1

value: diffuse midline glioma


title: 242-CSF-10-3mo-BCG

description: 10x Genomics

value: HKBCG


title: 242-CSF-14-0mo-BCG

description: 10x Genomics


title: scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep2

description: Library name: Adult_2_VDJ


title: 242-CSF-14-0mo-Ctrl

description: 10x Genomics


title: 242-CSF-10-12mo-LPS

description: 10x Genomics


title: HHSEC bulk RNA-seq - PA 500uM + LY-3

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: PA_LY3
HHSEC treated with PA 500uM + LY; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

data_processing:
Libraries were sequenced at 53–90 million reads per sample following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 × 2 paired end reads on an Illumina HiSeq 4000 using the HiSeq3000/4000 Sequencing Kit and HCS version 3.3.20, collection software. Base calling was performed using Illumina RTA version 2.5.2.
Assembly: mm10
Supplementary files format and content: PA_vs_Veh_DE_statAll_normCPM.xlsx Excel file with normalized CPM counts
Supplementary files format and content: PA_vs_PA.LY_DE_statAll_normCPM.xlsx Excel file with normalized CPM counts
Supplementary files format and content: PA.800_vs_Veh_DE_statAll_normCPM.xlsx Excel file with normalized CPM counts
Supplementary files format and content: PA.800_vs_PA.LY_DE_statAll_normCPM.xlsx Excel file with normalized CPM counts

source_name: Primary human hepatic sinusoidal endothelial cells (HHSEC)

extract_protocol:
Total RNA was prepared for bulk RNA-sequencing.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA).

treatment_protocol: HHSEC treated with vehicle, 500µM PA, 800µM PA or 800 µM PA+LY, overnight.

value: PA 500uM+LY

tag: batch


title: HHSEC bulk RNA-seq - PA 500uM + LY-2

description:
Library name: PA_LY2
HHSEC treated with PA 500uM + LY; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

growth_protocol: Primary human hepatic sinusoidal endothelial cells (HHSEC)


title: scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep4

description: Library name: Adult_4_mRNA


title: K562 empty vector replicate 1


title: HHSEC bulk RNA-seq - PA 500uM + LY-1

description:
Library name: PA_LY1
HHSEC treated with PA 500uM + LY; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: Primary human hepatic sinusoidal endothelial cells (HHSEC)


title: XIII_ELOAKO_second_IgG

description: Library name: XIII_ELOAKO_secondary_IgG

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: ELOAKO

value: IgG


title: scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep1

description: Library name: Adult_1_mRNA


title: XIII_ELOBKO_second_IgG

description: Library name: XIII_ELOBKO_secondary_IgG


title: XIII_ELOBKO_K27Mrep1

description: Library name: XIII_ELOBKO_C_R_K27Mrep1


title: scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep3

description: Library name: Adult_3_VDJ


title: scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep2

description: Library name: Adult_2_mRNA


title: XIII_CTL_K27Mrep1

description: Library name: XIII_CTL_C_R_K27Mrep1

value: CTL


title: CD34_DMSO_H3K4me3_Rep1

description: Library name: CD34_DMSO_H3K4me3_Rep1

value: Embryoid body

value: mesoderm


title: scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep3

description: Library name: Adult_3_mRNA

value: Spleen


title: 242-CSF-10-0mo-Ctrl

description: 10x Genomics

value: Ctrl


title: CD34_DMSO_H3K4me3_Rep2

description: Library name: CD34_DMSO_H3K4me3_Rep2


title: XIII_CTL_K27Mrep2

description: Library name: XIII_CTL_C_R_K27Mrep2


title: HHSEC bulk RNA-seq - PA 800uM-2

description:
Library name: PA_800-2
HHSEC treated with PA 800uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: PA 800uM


title: scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep4

description: Library name: Neonate_4_VDJ

value: CD8+ T cell

value: Neonatal (1 day timestamp)


title: scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells, Rep1

description: Library name: Adult_1_VDJ

value: Adult (28 day timestamp)


title: 242-CSF-10-0mo-LPS

description: 10x Genomics

value: CSF

value: CSF Cells

value: LPS


title: HHSEC bulk RNA-seq - PA 800uM-3

description:
Library name: PA_800-3
HHSEC treated with PA 800uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: Primary human hepatic sinusoidal endothelial cells (HHSEC)


title: 242-CSF-10-12mo-Ctrl

description: 10x Genomics


title: XIII_CTL_second_IgG.1

description: Library name: XIII_CTL_secondary_IgG.1

value: diffuse midline glioma

value: SU-DIPGXIII


title: scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep4

description: Library name: Neonate_4_mRNA


title: 242-CSF-3-12mo-LPS

description: 10x Genomics


title: HHSEC bulk RNA-seq - PA 500uM-3

description:
Library name: PA-3
HHSEC treated with PA 500uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: PA 500uM


title: scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep3

description: Library name: Neonate_3_mRNA


title: 242-CSF-10-0mo-BCG

description: 10x Genomics

value: HKBCG


title: HHSEC bulk RNA-seq - PA 800uM-1

description:
Library name: PA_800-1
HHSEC treated with PA 800uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.


title: 242-CSF-10-12mo-BCG

description: 10x Genomics


title: XIII_ELOAKO_ELOBrep2

description: Library name: XIII_ELOAKO_C_R_ELOBrep2

value: patient-derived tumor cell line

value: ELOAKO

value: ELOB


title: XIII_ELOBKO_ELOBrep2

description: Library name: XIII_ELOBKO_C_R_ELOBrep2

value: ELOBKO


title: XIII_ELOAKO_ELOBrep1

description: Library name: XIII_ELOAKO_C_R_ELOBrep1


title: HHSEC bulk RNA-seq - PA 500uM-1

description:
Library name: PA-1
HHSEC treated with PA 500uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.


title: XIII_ELOBKO_ELOBrep1

description: Library name: XIII_ELOBKO_C_R_ELOBrep1


title: XIII_CTL_ELOBrep1

description: Library name: XIII_CTL_C_R_ELOBrep1

value: CTL


title: 242-CSF-3-12mo-Ctrl

description: 10x Genomics

value: Ctrl


title: 242-CSF-3-12mo-BCG

description: 10x Genomics


title: HHSEC bulk RNA-seq - PA 500uM-2

description:
Library name: PA-2
HHSEC treated with PA 500uM; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.


title: scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep2

description: Library name: Neonate_2_VDJ

value: Spleen

value: CD8+ T cell


title: 242-CSF-3-3mo-LPS

description: 10x Genomics


title: HHSEC bulk RNA-seq - Vehicle control-veh-1

description:
Library name: veh-1
HHSEC treated with Vehicle control; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: Vehicle


title: scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep3

description: Library name: Neonate_3_VDJ

value: Neonatal (1 day timestamp)


title: XIII_CTL_ELOBrep2

description: Library name: XIII_CTL_C_R_ELOBrep2


title: wildtype

city: Helsinki

first: Marika

last: Lassila

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: Sample 9
10x Genomics

data_processing:
Cell ranger (version 6.1.2, 7.0.0, or 7.0.1) was used to align the reads, quantify gene expression, generate custom references, and call the cells.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Intestinal tissue isolated from small intestine of WT mice

extract_protocol:
Small intestines of Apcfl/fl mice were cut open, washed with PBS, and incubated in 10 mM EDTA in a shaker at 37°C for 10 min. Tissues were washed twice with PBS, and the cells were scraped off with a coverslip. The cells were then centrifuged at 1500 RPM for 5 min, followed by incubation with a digestion mix composed of HBSS with Mg2+ and Ca2+ (Gibco, #14025-050) and supplemented with 1 mg/ml of collagenase type I (Gibco,#17100-017), collagenase type IV (1 mg/ml) (Gibco #17104-019), 4 mg/ml of Dispase II (Sigma Aldrich, #04942078001), and 1 µl/ml of DNase1 (Thermo Fisher Scientific, #EN0521) for 30-40 min at 37°C. After this, DMEM was added, and the cell suspension was filtered through 70 µm and twice through a 40 µm filter and centrifuged for 10 min at 150 RCF. TdTomato+ cells from the mice were sorted using BD Influx (BD Biosciences). Sorted cells were resuspended in HBSS containing 0.04% BSA and subjected to Chromium X.
Library was performed according to the manufacturer`s instructions (single cell 3' protocol, 10x Genomics)

value: Intestinal cells

value: WT


title: XIII_K27MKO_IgGrep2

description: Library name: XIII_K27MKO_C_R_IgGrep2

extract_protocol:
SU-DIPGXIII+Cas9 cells were immobilized on ConA beads, permeabilized with 0.01% Digitonin, incubated with primary antibodies, and then cut with pAG-MNase to release DNA fragments as previously described.
3-15ng of genomic DNA was used for library construction. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

tag: antibody

value: IgG


title: HHSEC bulk RNA-seq - Vehicle control-veh-3

description:
Library name: veh-3
HHSEC treated with Vehicle control; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.

value: Primary human hepatic sinusoidal endothelial cells (HHSEC)


title: scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep1

description: Library name: Neonate_1_mRNA


title: scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep2

description: Library name: Neonate_2_mRNA


title: CD31high_TOP1_IgG

description: Library name: CD31high_TOP1_IgG

value: Embryoid body

value: mesoderm


title: 242-CSF-3-3mo-BCG

description: 10x Genomics

value: CSF

value: CSF Cells

value: HKBCG


title: 242-CSF-3-3mo-Ctrl

description: 10x Genomics


title: XIII_K27MKO_IgGrep1

description: Library name: XIII_K27MKO_C_R_IgGrep1

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line


title: HHSEC bulk RNA-seq - Vehicle control-veh-2

description:
Library name: veh-2
HHSEC treated with Vehicle control; total RNA, paired-end; base calling with Illumina RTA v2.5.2; aligned and converted to CRAM; see README for details.


title: scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, Rep1

description: Library name: Neonate_1_VDJ


title: Apc flox ctrl biol rep 2

description:
Library name: Sample 8
10x Genomics

source_name: Tumor tissue isolated from small intestinal tumors of Apc flox mice

value: Tumor cells

value: Lgr5-CreERT2; Apc fl/fl


title: 242-CSF-3-0mo-BCG

description: 10x Genomics


title: CD31high_IgG

description: Library name: CD31high_IgG


title: 242-CSF-3-0mo-LPS

description: 10x Genomics

value: LPS


title: XIII_K27MKO_K27me3

description: Library name: XIII_K27MKO_C_R_K27me3


title: Apc flox;Tcf7 del biol rep 1

description:
Library name: Sample 5
10x Genomics

value: Tumor tissue isolated from small intestinal tumors of Apc flox mice

value: Lgr5-CreERT2; Apc fl/fl; Tcf7


title: CD31high_TOP1_Rep2

description: Library name: CD31high_TOP1_Rep2


title: PITX1+ Skin H3K27me3 3

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description:
CUTANA CUT&Tag Kit v1
pK27me3_rep3

data_processing:
Read quality control with FastQC
Alignment with Bowtie2
Peak calling with SEACR
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Dorsal skin, healthy

extract_protocol:
Depilated Control and PITX1+ mice dorsal skin (n=3 separate mice for each condition) was incubated in 2U/mL of dispase II for 2 hours at 25°C with gentle rotation. Skins were rinsed twice in 1X PBS before briefly drying and spreading dermis-side down on a 10mm petri dish. A #10 scalpel blade held perpendicularly to the skin was used to gently scrape the epidermis off and pool it into a gentleMACS C-Tube (Miltenyi). The Whole Skin Dissociation Kit (Miltenyi) was then used to dissociate the tissue per manufacturer's protocol. Tissues were incubated in enzymatic mixture for 1 hour at 37°C prior to cell dissociation: one cycle of 'h_skin_01' on gentleMACS Dissociator (Miltenyi), filtration of cells through 70µm and 30µm Preseparation Filters (Miltenyi), and resuspension and counting in KBM-Gold (Lonza). The vast majority (>95%) of cells were keratinocytes (intended cell type to collect) with the ~5% remaining cells consisting of melanocytes, epidermal-resident immune cells, and stray fibroblasts.
100,000 single epidermal cells were processed with the CUTANA CUT&Tag Kit v1 (Epicypher) for nuclear isolation, chromatin tagmentation, and library preparation. Cells were gently fixed in 0.1% methanol-free formaldehyde for 1 minute at room temperature and neutralized in 125mM glycine prior to nuclear extraction. 16 PCR cycles were used to amplify tagmented libraries prior to sequencing.

value: Dorsal skin, healthy

value: Epidermal (mostly keratinocytes)

tag: cut&tag antibody

value: Doxycycline


title: XIII_CTL2_IgGrep1

description: Library name: XIII_CTL2_C_R_IgGrep1

value: WT

value: IgG


title: XIII_CTL2_IgGrep2

description: Library name: XIII_CTL2_C_R_IgGrep2


title: Apc flox ctrl biol rep 1

description:
Library name: Sample 7
10x Genomics


title: Apc flox;Tcf7 del biol rep 2

description:
Library name: Sample 6
10x Genomics


title: 242-CSF-3-0mo-Ctrl2

description: 10x Genomics

value: Ctrl


title: XIII_K27MKO_K27Mrep1

description: Library name: XIII_K27MKO_C_R_K27Mrep1


title: UPN38, GEX

city: Palo Alto

first: Mark

middle: M

last: Davis

state: California

address: 240 Pasteur Drive

institute: Stanford

description:
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and umi; read 2 file contain transcript

data_processing:
CellRanger v7.1.0 multi function to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and filtered_contig_annotations.csv
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv

source_name: tonsil, blood

extract_protocol:
CD3 T cells were magnetically enriched from tonsil and spleen samples. Cells were stained were TotalSeqC antibodies, along with a tonsil- or PBMC-specific antibody barcode. Tonsil and PBMC samples  from each donor were combined and cells were captured on a 10x Genomics Chromium Controller
Individual gene expression (GEX), Antibody Dependent Tag (ADT), and T Cell Receptor (TCR) libraries were prepared according to the Chromium Next GEM Single Cell 5’ Reagents Kit v2 protocol (10x Genomics)

value: tonsil, blood

value: enriched T cells

tag: library type

value: mRNA


title: CD31high_TOP1_Rep1

description: Library name: CD31high_TOP1_Rep1

value: Embryoid body

value: mesoderm


title: UPN38, TCR

description:
polyA RNA
TCR: read1 file contains cell barcode and umi; read 2 file contains TCR reads

value: TCR


title: PITX1+ Skin H3K27me3 1

description:
CUTANA CUT&Tag Kit v1
pK27me3_rep1


title: CD31high_H3K4me3_ Rep3

description: Library name: CD31high_H3K4me3_Rep3


title: XIII_CTL2_K27Mrep2

description: Library name: XIII_CTL2_C_R_K27Mrep2

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line


title: XIII_CTL2_K27me3

description: Library name: XIII_CTL2_C_R_K27me3


title: UPN38, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and umi; read2 file contains Antibody-derived tag reads

library_source: other

molecule: protein

value: ADT

tag: adt

value: CD3_TotalSeqC, CD4_TotalSeqC, CD8_TotalSeqC, Tonsil, PBMC


title: CD31high_H3K4me3_ Rep1

description: Library name: CD31high_H3K4me3_Rep1

tag: cell type


title: 242-CSF-3-0mo-Ctrl

description: 10x Genomics

extract_protocol:
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.
Cells were mixed with 10x 5’ v2 RT Reagent Master Mix and immediately processed with the 10x Genomics Chromium Next GEM Single Cell 5’ v2 kit (10x Genomics, Pleasanton, CA), cDNA amplified, and library constructed per the manufacturer’s protocol. Library quality control (QC) was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flow cell for 26x10x10x90 cycles for estimated reads per cell. After demultiplexing,  libraries were rebalanced based on reads per cell. Normalized pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 26x10x10x90 cycles, to obtain a sequencing depth of 50K reads/cell (whole transcriptome libraries). Reads were aligned to reference 2020-A (Ensembl 98) transcriptome and quantified using Cell Ranger v6.0.2 multipipeline.

value: CSF

tag: subject

value: CSF Cells


title: PITX1+ Skin H3K27me3 2

description:
CUTANA CUT&Tag Kit v1
pK27me3_rep2

value: Dorsal skin, healthy

value: Epidermal (mostly keratinocytes)

value: Doxycycline


title: CD31high_H3K27me3_ Rep3

description: Library name: CD31high_H3K27me3_Rep3


title: CD31high_H3K4me3_ Rep2

description: Library name: CD31high_H3K4me3_Rep2


title: PITX1+ Skin H3K27ac 3

description:
CUTANA CUT&Tag Kit v1
pK27ac_rep3


title: XIII_K27MKO_K27Mrep2

description: Library name: XIII_K27MKO_C_R_K27Mrep2


title: UPN40, TCR


title: UPN40, ADT


title: XIII_CTL2_K27Mrep1

description: Library name: XIII_CTL2_C_R_K27Mrep1

value: WT


title: CD31high_H3K27me3_ Rep2

description: Library name: CD31high_H3K27me3_Rep2


title: UPN40, GEX

value: tonsil, blood


title: CD31high_H3K27me3_ Rep1

description: Library name: CD31high_H3K27me3_Rep1


title: PDAC Tumor FFPE Tissue

city: Stockholm

first: Mehran

last: Ghaderi

state: Huddinge

address: Forskningsgatan 46

department: Clintech

country: Sweden

institute: Karolinska Institutet

description: Library name: Sample 3_PDAC Tumor Tissue

data_processing:
Transcriptome data were processed and analyzed using the Chipster virtual platform provided by the IT Center for Science (CSC), Finland. Adapter sequences were trimmed, and sequencing read quality was assessed with FastQC.
Paired-end reads (40-45 million per sample) were aligned to the human reference genome (GRCh38.95) using HISAT2 aligner and assembled using Cufflinks.
RNA-seq data were processed using the Cufflinks pipeline. Transcript assembly and quantification were performed with Cufflinks, followed by differential expression analysis using Cuffdiff across three datasets. Differentially expressed genes (DEGs) were identified based on standard statistical thresholds.
Assembly: GRCh38.95
Supplementary files format and content: BAM files. Overrepresentation analysis of differentially expressed genes was performed using ConsensusPathDB, integrating pathways from over 30 publicly available databases.

source_name: Cancer

growth_protocol: No treatment was required.

extract_protocol:
Total RNA was extracted from the macrodissected FFPE samples using the Promega Maxwell® RSC RNA FFPE Kit.
RNA-seq libraries were prepared using a minimum 50 ng of purified RNA from FFPE material with a Takara PICO RNA input kit with SMART-seq2 protocol. The protocol included cDNA preparation using TSO oligos, cleanup, PCR amplification, and pooling of indexed libraries. Final libraries were then normalized to 4 nM. Library denaturation and dilution were performed following the Illumina NextSeq System Denature and Dilute Libraries Guide.

treatment_protocol: No treatment was required.

value: Cancer

value: etc

value: PDAC

value: tumor


title: CD31high_SP140_Rep3

description: Library name: CD31high_SP140_Rep3

value: Embryoid body

value: mesoderm


title: Pancreatitis FFPE

description: Library name: Sample 1_Chronic Pancreatitis

source_name: Pancreatitis

value: Pancreatitis

value: inflammation


title: PITX1+ Skin H3K27ac 1

description:
CUTANA CUT&Tag Kit v1
pK27ac_rep1


title: PITX1+ Skin H3K4me3 2

description:
CUTANA CUT&Tag Kit v1
pK4me3_rep2


title: PITX1+ Skin H3K4me3 3

description:
CUTANA CUT&Tag Kit v1
pK4me3_rep3


title: UPN22, ADT

value: enriched T cells

value: ADT


title: CD31high_SP140_Rep2

description: Library name: CD31high_SP140_Rep2


title: PDAC Normal FFPE Tissue

description: Library name: Sample 2_PDAC Normal Tissue

source_name: Normal

value: Normal

value: normal


title: PITX1+ Skin H3K4me3 1

description:
CUTANA CUT&Tag Kit v1
pK4me3_rep1

value: Dorsal skin, healthy


title: UPN22, GEX

value: mRNA


title: PITX1+ Skin H3K27ac 2

description:
CUTANA CUT&Tag Kit v1
pK27ac_rep2

value: Epidermal (mostly keratinocytes)

value: Doxycycline


title: Multiple Tissue Donor, Donor 6

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

data_processing:
scRNAseq downstream analyses were performed using the Seurat software package version 4.0 for R (http://satijalab.org/seurat/). For barcoded samples, Seurat’s 4 HTODemux() function was used as described previously (https://satijalab.org/seurat/articles/hashing_vignette). After removing unwanted cells and genes from the dataset, raw UMIs in each cell were both scaled and normalized via the SCTransform function. To improve downstream dimensionality reduction and clustering, we regressed out unwanted source of variation arising from the percentage of mitochondrial genes. Then, highly variable genes were identified and selected for PCA reduction of high-dimensional data. Cells in this reduced space were harmonized to adjust for batch effects coming from multiple donors using the Harmony tool implemented in Seurat. These low dimensional corrected Harmony embeddings were used for downstream analyses. Graph-based clustering analysis was performed on the reduced data with Seurat. The resolution in the FindClusters function from Seurat was set at values between 0.3 and 0.7, and the clustering results were shown in a computed UMAP plot (dims = 1:20). Different cell types were grouped based on top markers.
Assembly: GRCh38
Supplementary files format and content: CellRanger count output (features.tsv/matrix.mtx/barcodes.tsv), zipped

source_name: Blood, thymus

extract_protocol:
Fresh, magnetically enriched cells were washed in MACS buffer and counted to analyze cell viability. Next, cells were resuspended in a cell staining buffer and stained with antibodies for the identification of pDC. All samples were stained with the same antibodies. Specifically, samples were stained with anti-CD3 (PerCP-Cy5.5, Biolegend), anti-CD19 (PerCP-Cy5.5, Biolegend), and anti-CD14 (PerCP-Cy5.5, Biolegend) to exclude T cells, B cells and monocytes, respectively, anti-CD1c (BV510, Biolegend) to exclude mature DC2, and anti-ILT3 (PE-Cy7, Biolegend), anti-CD123 (PE, Biolegend) and anti-BDCA2 (FITC, Millteny) to select pDC. We performed purity checks and achieved a very high purity (>98%). The cells were sorted using flow cytometry on BD FACS Aria II
For library preparation, the 10X Genomics Next GEM Single Cell 3’ Reagents Kit was used. This process utilized the Chromium Next GEM Single Cell 3′ Kit v3.1 (16 rxns), Chromium Next GEM Chip G Single Cell Kit (48 rxns), and Dual Index Kit TT Set A (96 rxns). In brief, up to 23,000 cells were partitioned into nanoliter Gel-bead-in-Emulsions (GEMs) droplets, each containing retro-transcriptase reaction mix. Single-cell cDNA received a unique 12-nucleotide barcode and unique molecular identifier (UMI). Subsequently, GEM cDNA underwent 11 cycles of amplification before purification using SPRIselect beads. The generation of gene-expression (GEX) and hashtag-oligo (HTO) libraries followed the recommendations provided in the 10x Genomics Chromium Single Cell 3′ Reagent Kits User Guide (v3.1 Chemistry Dual Index), with modifications to PCR cycles based on the calculated cDNA concentration. The concentration of each library was determined using qPCR with the KAPA library Quantification Kit following the manufacturer’s protocol (KAPA Biosystems/Roche). The sequencing of normalized cDNA libraries was performed on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28×10×10×150 sequencing recipe as per the manufacturer's protocol (Illumina). A median sequencing depth of 50,000 and 5,000 reads per cell was targeted for the GEX and HTO library, respectively.

value: Blood, thymus


title: CD31high_SP140_Rep1

description: Library name: CD31high_SP140_Rep1


title: UPN19, TCR

value: tonsil, blood

value: TCR


title: UPN22, TCR


title: UPN19, ADT

value: CD3_TotalSeqC, CD4_TotalSeqC, CD8_TotalSeqC, Tonsil, PBMC


title: Multiple Tissue Donor, Donor 5

source_name: Blood, thymus, ptLN

value: Blood, thymus, ptLN


title: CD34_SP140iTOP1i_Rep3

description: Library name: CD34_SP140iTOP1i_Rep3

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (hg38) using Bowtie2 (v.2.3.5.1). Low quality mapped reads were removed using SAMtools (v.1.9) (view -q 30) and only unique reads mapping to a single genomic location and strand were kept. We removed mitochondrial sequences using ‘grep -v chrM’. Peaks were calling using MACS2 (v.2.1.2) with the setting ‘-f BAMPE -g hs’. After filtering out blacklist regions, peaks reproducibly detected in at least two replicates were retained, and their corresponding genomic coordinates were merged to generate a consensus peak set.
Assembly: hg38
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Chromatin was harvested by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme).
ATAC libraries for sequencing were prepared with Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme), following the manufacturer's protocols

value: Embryoid body

value: hemogenic endothelium


title: CD34_SP140iTOP1i_Rep2

description: Library name: CD34_SP140iTOP1i_Rep2


title: PITX1+ Skin Pitx1 3

description:
CUTANA CUT&Tag Kit v1
pPitx1_rep3


title: PITX1+ Skin Pitx1 1

description:
CUTANA CUT&Tag Kit v1
pPitx1_rep1


title: UPN19, GEX


title: Multiple Tissue Donor, Donor 4


title: Multiple Tissue Donor, Donor 2


title: PITX1+ Skin Pitx1 2

description:
CUTANA CUT&Tag Kit v1
pPitx1_rep2


title: PITX1+ Skin IgG 3

description:
CUTANA CUT&Tag Kit v1
pIgG_rep3

value: IgG


title: Multiple Tissue Donor, Donor 3


title: CD34_SP140i_Rep3

description: Library name: CD34_SP140i_Rep3


title: CD34_SP140iTOP1i_Rep1

description: Library name: CD34_SP140iTOP1i_Rep1


title: CD34_SP140i_Rep2

description: Library name: CD34_SP140i_Rep2


title: UPN41, TCR


title: Multiple Tissue Donor, Donor 1


title: PITX1+ Skin IgG 2

description:
CUTANA CUT&Tag Kit v1
pIgG_rep2


title: UPN41, ADT


title: UPN41, GEX


title: Thymus, Replicate 2, scRNAseq

source_name: Thymus

value: Thymus


title: UPN20, ADT

value: enriched T cells


title: Control Skin H3K27me3 3

description:
CUTANA CUT&Tag Kit v1
wtK27me3_rep3

value: Control

value: Vehicle


title: PITX1+ Skin IgG 1

description:
CUTANA CUT&Tag Kit v1
pIgG_rep1


title: UPN20, TCR


title: Control Skin H3K27me3 2

description:
CUTANA CUT&Tag Kit v1
wtK27me3_rep2


title: CD34_DMSO_Rep3

description: Library name: CD34_DMSO_Rep3


title: CD34_DMSO_Rep1

description: Library name: CD34_DMSO_Rep1


title: CD34_SP140i_Rep1

description: Library name: CD34_SP140i_Rep1


title: Thymus, Replicate 1, scRNAseq


title: Blood, Replicate 1, scRNAseq

source_name: Blood

value: Blood


title: ORG_SLA_2

city: Pavia

first: Matteo

last: Bordoni

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: sALS patient organoid culture

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Trimmed reads were aligned through STAR using Gencode Release h38 (GRCh38) as a reference human genome. Gene and transcript abundance were computed using FeatureCounts software, with the “stranded forward” option. Differential expression analysis was performed using R package DESeq2.
Assembly: hg38

source_name: organoids culture

extract_protocol:
RNA was extracted using TRIzol® (Invitrogen) following the manufacturer’s instructions. Nanodrop One C (ThermoFisher) was used for RNA quantification and quality checking.
Libraries were prepared starting from 500 ng of total RNA. RNA was fractioned for rRNA depletion using RiboCop V1.3 (Lexogen) and libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) following manufacturer's intructions. The quality of libraries was analyzed using 4200 Tape Station with a “DNA High sensitivity” assay (Agilent) and quantified using High Sensitivity dsDNA assay with a Qubit device (Life Technologies). Sequencing was performed using Illumina NextSeq 500.

value: organoids culture

tag: disease state

value: sALS

tag: replicate number


title: CD34_DMSO_Rep2

description: Library name: CD34_DMSO_Rep2


title: Control Skin H3K27me3 1

description:
CUTANA CUT&Tag Kit v1
wtK27me3_rep1

value: Dorsal skin, healthy

value: Epidermal (mostly keratinocytes)


title: UPN24, ADT

value: ADT


title: ORG_CTRL_3

description: Healthy control organoid culture

value: healthy control


title: Control Skin H3K27ac 3

description:
CUTANA CUT&Tag Kit v1
wtK27ac_rep3


title: UPN24, GEX

value: tonsil, blood

value: mRNA


title: CD31_SP140i_Rep2

description: Library name: CD31_SP140i_Rep2

value: mesoderm


title: UPN24, TCR

value: TCR


title: Control Skin H3K27ac 2

description:
CUTANA CUT&Tag Kit v1
wtK27ac_rep2


title: UPN20, GEX


title: ORG_CTRL_2

description: Healthy control organoid culture


title: CD31_SP140i_Rep1

description: Library name: CD31_SP140i_Rep1

value: Embryoid body


title: Control Skin H3K27ac 1

description:
CUTANA CUT&Tag Kit v1
wtK27ac_rep1


title: ORG_SLA_1

description: sALS patient organoid culture


title: UPN10, ADT

value: CD3_TotalSeqC, CD4_TotalSeqC, CD8_TotalSeqC, Tonsil, PBMC


title: UPN10, TCR


title: 2D_SLA_3

description: sALS patient 2D motor neurons culture

source_name: motor neurons culture

value: motor neurons culture


title: Control Skin H3K4me3 3

description:
CUTANA CUT&Tag Kit v1
wtK4me3_rep3


title: CD31_SP140i_Rep3

description: Library name: CD31_SP140i_Rep3


title: 2D_SLA_2

description: sALS patient 2D motor neurons culture


title: ORG_CTRL_1

description: Healthy control organoid culture


title: Control Skin H3K4me3 1

description:
CUTANA CUT&Tag Kit v1
wtK4me3_rep1


title: CD31_DMSO_Rep1

description: Library name: CD31_DMSO_Rep1


title: Control Skin H3K4me3 2

description:
CUTANA CUT&Tag Kit v1
wtK4me3_rep2


title: CD31_DMSO_Rep3

description: Library name: CD31_DMSO_Rep3


title: CD31_DMSO_Rep2

description: Library name: CD31_DMSO_Rep2


title: 2D_SLA_1

description: sALS patient 2D motor neurons culture


title: XIII_ELOBKO_ChIP_RNAPIIrepB

description: Library name: XIII_ELOBKO_ChIPseq_RNAPIIrepB

data_processing:
Reads were processed with trimgalore
Reads were aligned to the genome with bowtie2
Peaks were called with MACS2
Assembly: hg38
Supplementary files format and content: bigwig files for each sample

source_name: diffuse midline glioma

extract_protocol:
For ChIPseq, a single cell suspension of control or ELOBKO SU-DIPGXIII+Cas9 cells collected 14 days after sgRNA infection were crosslinked with 1% formadehyde for 10 minutes followed by quenching with glycine. Crosslinked chromatin was sonicated to produce DNA fragments 150 to 2000 bp in length. Soluble chromatin was pre-cleared by adding 150 ul of a 50:50 slurring of pre-washed protein G beads to each tube and incubating at 4°C for 1 hour on a rotator. Exracted chromatin from 2e6 cells was used in each IP with 5 ug of either anti-ELOB (Abcam #ab45297) or with an RNA polymerase II CTD repeat YSPTSPS antibody [8WG16] antibody (Abcam #ab817)
Libraries were constructed from 5 ng of input DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, E7103) following the manufacturer's instructions

value: diffuse midline glioma

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: ELOBKO

tag: chip antibody

value: RNAPII


title: Control Skin Pitx1 3

description:
CUTANA CUT&Tag Kit v1
wtPitx1_rep3

value: Control

value: Vehicle


title: 2D_CTRL_3

description: Healthy control 2D motor neurons culture


title: UPN10, GEX

value: enriched T cells


title: TC-71, XG knockout, rep1

city: Lund

first: Martin

middle: L

last: Olsson

address: Baravägen 18

department: Department of Laboratory Medicine

institute: Lund University

data_processing:
Sequencing was performed with NovaSeq 6000 (firmware v 1.26.10)
Demultiplexing performed using bcl2fastq2 (v 2.20.0.422-1.3) with –no-lane-splitting tag
Read mapping performed using STAR software (v 2.7.6a)
Expression counts performed using featureCounts software in Subread (v 2.0.1) package
Differential expression analysis performed using DESeq2 (v 1.38.3) in R (v 4.2.2) and RStudio (v 2022.12.0 Build 353)
Assembly: Human GRCh38 primary assembly, and annotation from gencode version 33.
Supplementary files format and content: featureCounts.txt: tab-delimited text file output from featureCounts includes counts of mapped reads for each sample
Supplementary files format and content: DESeq2_unfiltered.txt: tab-delimited text file output from DESeq2 includes fold-change data

source_name: Bone

growth_protocol: Cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% fetal bovine serum, in a humidified incubator with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using RNeasy Mini Plus kit (Qiagen) according to manufacturer's protocol. 500 ng of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep (Illumina) and IDT for Illumina TruSeq RNA UD Indexes (Illumina) following manufacturer's protocols.

value: Ewing's sarcoma

value: XG knockout


title: XIII_ELOBKO_ChIP_input

description: Library name: XIII_ELOBKO_ChIPseq_input

value: input


title: TC-71, XG knockout, rep2


title: TC-71, wildtype, rep3

value: Wildtype


title: Adult female heart Rep 4

city: Chapel Hill

first: Kayla

middle: K

last: Mason

state: NC

address: 133 N Medical Drive

institute: University of North Carolina Chapel Hill

description:
Library name: Sample 8
Deep RNA seq >80M reads
F5-3

data_processing:
Sequence quality was evaluated and reads were then trimmed. These reads were then mapped to the mm10 mouse genome. Each sample contained between 65-100 million reads. Log2FC was then determined between male and female.
Assembly: mm10
Supplementary files format and content: Differential_expression_analysis_table.csv

source_name: Heart

extract_protocol:
adult (4-6 wk.)male and female mouse hearts, n=4 for each sex, were dissected in cold PBS and immediately homogenized in Trizol solution, and were kept in -20C until use. Small RNA from individual hearts was extracted using the miRVANA miRNA isolation kit (Thermo-Fisher AM1561)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: C57Bl6/J wt


title: 2D_CTRL_1

value: healthy control


title: Control Skin Pitx1 2

description:
CUTANA CUT&Tag Kit v1
wtPitx1_rep2

value: Dorsal skin, healthy

value: Epidermal (mostly keratinocytes)


title: XIII_ELOBKO_ChIP_RNAPIIrepA

description: Library name: XIII_ELOBKO_ChIPseq_RNAPIIrepA

value: diffuse midline glioma


title: Control Skin IgG 2

description:
CUTANA CUT&Tag Kit v1
wtIgG_rep2

value: IgG


title: TC-71, XG knockout, rep3


title: Adult female heart Rep 3

description:
Library name: Sample 7
Deep RNA seq >80M reads
F3-2


title: Control Skin Pitx1 1

description:
CUTANA CUT&Tag Kit v1
wtPitx1_rep1


title: XIII_ELOBKO_ChIP_ELOBrepA

description: Library name: XIII_ELOBKO_ChIPseq_ELOBrepA

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: ELOB


title: XIII_ELOBKO_ChIP_ELOBrepB

description: Library name: XIII_ELOBKO_ChIPseq_ELOBrepB

value: ELOBKO


title: TC-71, wildtype, rep2


title: TC-71, wildtype, rep1


title: Control Skin IgG 3

description:
CUTANA CUT&Tag Kit v1
wtIgG_rep3

value: Control

value: Vehicle


title: Adult female heart Rep 2

description:
Library name: Sample 6
Deep RNA seq >80M reads
F2-1


title: Adult female heart Rep 1

description:
Library name: Sample 5
Deep RNA seq >80M reads
F1-3


title: Adult male heart Rep 5

description:
Library name: Sample 4
Deep RNA seq >80M reads
M5-2


title: Control Skin IgG 1

description:
CUTANA CUT&Tag Kit v1
wtIgG_rep1


title: control_11_1

type: genomic

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF

data_processing:
Raw idat files were processed to beta and detection p-values using the Bioconducter package minfi (v1.50.0) using single-sample normal exponential out of band (ss noob) background correction and dye bias normalization together with Bioconductor EPIC array annotations (IlluminaHumanMethylationEPICmanifest and IlluminaHumanMethylationEPICanno.ilm10b4.hg19). Probes overlapping known SNPs (MAF>1% and within 5 bp of the probe’s CpG target, based on Zhou et al PMID: 27924034), located on sex chromosomes, or with detection p-value > 0.01 were excluded.
Normalized mean Beta and detection p-value.

label: Cy3 and Cy5

source_name: blood

extract_protocol: Genomic DNA was extracted using Dneasy Blood and Tissue Kit (QIAGEN).

value: blood

value: peripheral blood leukocytes


title: control_11_2

scan_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF


title: Adult male heart Rep 4

description:
Library name: Sample 3
Deep RNA seq >80M reads
M4-3


title: XIII_CTL_ChIP_input

description: Library name: XIII_CTL_ChIPseq_input

value: CTL

value: input


title: XIII_CTL_ChIP_ELOBrepB

description: Library name: XIII_CTL_ChIPseq_ELOBrepB


title: KPC RNA

city: La Jolla

first: Kyle

last: Gaulton

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Raw fastq files from both libraries were processed with 10x Genomics Cell Ranger ARC (v2.0.0) count command. This command aligned all reads to the mm10 mouse genome reference and created bam files and raw feature barcode matrices for both snRNA and snATAC.
Fixed width ATAC-seq peaks were generated with macs2 (v2.2.7.1) callpeak tool. All peaks with FDR less than 0.05 and duplicate peaks were retained. All cell type peaks were merged into an overall peak list using and all peaks were reduced to a fixed width of 500bps around the peak summit.
Supplementary files format and content: tab separated per barcode metadata table (merged_all_bcs_metadata.txt)
Supplementary files format and content: tab separated bed file of fixed width peaks (all_fixed_width_peaks.bed)
Supplementary files format and content: fragment file and tabix index of fragment file (2merged.atac_keep_reads.tagAlign.gz)
Assembly: mm10
Supplementary files format and content: ATAC_peaks_by_bc_counts_sm.rds: sparse matrix of barcode by peaks counts data, saved as R data structure (RDS) file
Supplementary files format and content: RNA_genes_by_bc_counts_sm.rds: sparse matrix of barcode by genes counts data, saved as R data structure (RDS) file

molecule: nuclear RNA

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
PDAC tumors were harvested from two female KPC and two female AKPC mice and snap-frozen. 20-30 mg tissue samples were resuspended in 1ml of wash buffer (0.25 M sucrose, 25 mM KCI, 5 mM MgCl2, 10 mM Tris-HCI (pH 7.5), 1 mM DTT (Sigma, D9779), 1X protease inhibitor (Fischer, PIA32965), 1 U µl−1recombinant RNAsin (Promega, PAN2515), 0.1% IGEPAL (Sigma, I8896) in molecular biology water) and then homogenized using a Dounce homogenizer with 2 pestles. First, a loose pestle was used for 5-10 strokes to break the tissue into small pieces and then a tight pestle was used for 15-25 strokes to fully homogenize the sample into a uniform solution. Homogenized tissue was filtered through a 30 μm filter (CellTrics, Sysmex) and then centrifuged with a swinging-bucket centrifuge (100 rcf, 10 min, 4˚C, Eppendorf, 5920 R). Nuclei were resuspended in 1 ml of wash buffer (0.25 M sucrose, 25 mM KCI, 5 mM MgCl2, 10 mM Tris-HCI (pH 7.5), 1 mM DTT (Sigma, D9779), 1X protease inhibitor (Fischer, PIA32965), 1 U µl−1recombinant RNAsin (Promega, PAN2515) in molecular biology water) and centrifuged again (100 rcf, 10 min, 4˚C, Eppendorf, 5920 R). Next, nuclei were resuspended in 400 µl of sorting buffer (1X protease inhibitor (Fischer, PIA32965), 1 U µl−1recombinant RNAsin (Promega, PAN2515), 1% fatty acid free BSA (Proliant, 7500804), 2uM 7-AAD (Invitrogen, A1310) in PBS (Corning, 21-040-CV)) and incubated on ice for 10 minutes. 120,000 nuclei were sorted into a Lobind tube with 90 µl collection buffer (5 U µl−1recombinant RNAsin (Promega, PAN2515), 5% fatty acid free BSA (Prolian, 7500804) in PBS (Corning, 21-040-CV) using an SH800 cell sorter (Sony). The resulting nuclei suspension was centrifuged again (500 rcf, 5 min, 4˚C, Eppendorf, 5920 R) and resuspended in 100 µl of collection buffer (1% fatty acid free BSA (Proliant, 7500804), 1X protease inhibitor (Fischer, PIA32965), 10 mM Tris-HCI (pH 7.4), 0.1% Tween-20 (Sigma, P7949-100ML), 0.1% IGEPAL (Sigma, I8896), 0.01% digitonin (Promega, G9441), 1mM DTT (Sigma, D9779), 1 U µl−1recombinant RNAsin (Promega, PAN2515), 3 mM MgCl2 and 10 mM NaCl in molecular biology water). This suspension was incubated on ice for 1 minute and centrifuged again (500 rcf, 5 min, 4˚C, Eppendorf, 5920 R). The supernatant was carefully removed without disturbing the pellet and 10 µl of 1X Nuclei Buffer (10x Genomics) was used to gently resuspend the pellet. Nuclei were counted using a hemocytometer and approximately 20,000 nuclei were used as inputs for the tagmentation reaction.
Nuclei from the two KPC mice were pooled together and nuclei from the two AKPC mice were also pooled together, for a total of 2 sets of libraries. Then single cell multiome ATAC and gene expression libraries were generated according to manufacturer instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 10x Genomics, 1000283; Chromium Next GEM Chip J Single Cell Kit, 10x Genomics, 1000234; Dual Index Kit TT Set A, 10x Genomics, 1000215; Single Index Kit N Set A, 10x Genomics, 1000212). The following PCR cycles were used: 7 cycles for ATAC index PCR, 7 cycles for complementary DNA (cDNA) amplification, and 13–16 cycles for RNA index PCR. A Qubit fluorometer (Life Technologies) was used to quantify final libraries and a TapeStation (High Sensitivity D1000, Agilent) was used to check size distribution. Finally, libraries were sequenced on NovaSeq 6000 sequencers (Illumina) with the following read lengths (Read1 + Index1 + Index2 + Read2): ATAC (NovaSeq 6000), 50 + 8 + 24 + 50; ATAC (NextSeq 500 with custom recipe), 50 + 8 + 16 + 50; RNA (NextSeq 500, NovaSeq 6000), 28 + 10 + 10 + 90.
Paired snRNA-seq and snATAC-seq

value: Pancreatic ductal adenocarcinoma

value: Atm+/+; Trp53fl/fl; Kras+; p48Cre+

tag: Sex

value: Female

value: mRNA


title: control_10

label_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh ECRF

tag: genotype


title: AKPC RNA

tag: tissue

value: AKPC (Atmfl/fl; Trp53fl/fl; Kras+; p48Cre+


title: KPC ATAC

library_source: genomic single cell

value: ATAC


title: XIII_CTL_ChIP_RNAPIIrepA

description: Library name: XIII_CTL_ChIPseq_RNAPIIrepA

value: diffuse midline glioma

tag: cell line

value: RNAPII


title: Adult male heart Rep 3

description:
Library name: Sample 2
Deep RNA seq >80M reads
M3-3

value: Heart

value: C57Bl6/J wt


title: patient_10

value: DNMT3A p.S304del heterozygous


title: DIPGXIII_RNA_ELOBKO.3

description: Library name: DIPGXIII_RNAseq_ELOBKO.3

data_processing:
RNAseq reads were aligned to hg38 using STAR
Counts tables were generated using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files with transcript counts

source_name: glioma

extract_protocol:
RNA was extracted using TRIzol reagent and polyA transcripts were purified.
Libraries were generated using the NEBNext UltraDirectional RNA Library Prep Kit for Illumina (New England Biotechnology, E7420L).

treatment_protocol: These cells were not treated

value: glioma

value: SU-DIPGXIII

value: ELOBKO


title: XIII_CTL_ChIP_RNAPIIrepB

description: Library name: XIII_CTL_ChIPseq_RNAPIIrepB

value: patient-derived tumor cell line


title: S2-GrhR806A_200uM_aGrh_INPUT_R2

city: Madison

first: Melissa

last: Harrison

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
Library name: ChIPseq_12
more reads sequenced on the Illumina HiSeq 4000

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using Bowtie2 (v2.4.4). Unmapped reads, reads aligning to the mitochondrial genome or unplaced scaffolds, reads aligning more than once or low-quality reads (MAPQ<30) were removed.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized.

organism: Drosophila melanogaster

source_name: Schneider 2 cells

growth_protocol: Drosophila S2 cells were cultured in Schneider's medium with supplemented antibiotic/antimycotic and 10% FBS at 27˚C.

extract_protocol:
ChIP was performed as previously described (Gibson et al. 2024). 25x106 cells were fixed in 0.8% formaldehyde for 7 min and quenched with 125 mM gylcine. Fixed chromatin was sonicated on a Covaris S220 for five 120s rounds with 60s delay, peak power at 170, a duty factor of 10%, and 200 cycles per burst.  IPs were incubated with anti-Grh or anti-HA antibody at 4˚C overnight. Samples were purified using Dynabeads Protein A for Grh (20 uL; Thermo Fisher Scientific) or M-280 Sheep Anti-Mouse IgG for HA (60 uL; Thermo Fisher Scientific). The beads were washed, and chromatin was eluted. IPs and inputs were treated with 90ug RNaseA for 30 mins at 37˚C, and crosslinks were reversed by adding proteinase K overnight at 65˚C. DNA was isolated by phenol:chloroform extraction and concentrated overnight by ethanol precipitation.
Libraries were constructed using the NEB Next Ultra II kit.

treatment_protocol: S2 cells were treated with respective amounts of CuSO4 to induce expression for 48 hours.

value: Schneider 2 cells

tag: treatment

value: 200 uM CuSO4


title: AKPC ATAC

value: Pancreatic ductal adenocarcinoma


title: W326R_S6_dedup_assembled_clones

description: Library name: W326R_S6

data_processing:
Sequences were adaptor and quality trimmed using Trim Galore (v0.6.6)
Read were assembled with Pear v0.9.11, germline reads were removed using Bowtie2 v2.4.4 alignment to mm10, part of BabrahamLinkON v0.1 preclean step
Mispriming correction, UMI extraction was done with BabrahamLinkON v 0.1 preclean step
Deduplication and error correction was done with BabrahamLinkON v0.1 deduplicate step
Sequences were annotated as per BabrahamLinkON v0.1 assemble_clones step, with IgBlast v1.7.0 with IMGT reference and parsed with ChangO 0.3.7
Assembly: mm10
Supplementary files format and content: tsv files containing annotated V(D)J sequences from IgBlast with IMGT reference

source_name: Bone marrow

extract_protocol:
Genomic DNA was isolated as described (PMID: 31230816) with minor modifications. Equal volume 2× lysis buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 4% SDS and 200 µg/mL Proteinase K, New England Biolabs, P8107S) was added to cell suspensions, followed by 30 min incubation at 55°C with agitation (700 rpm). Next, RNase A (Thermo Fisher Scientific, EN0531) was added at 20 µg/mL, followed by 30 min incubation at 30°C with agitation. After phenol-chloroform extraction, ethanol precipitation was performed, using linear polyacrylamide (Thermo Fisher Scientific, J67830.XF) as a carrier.
Libraries were prepared as described (PMID: 29725123), modified for analysis of VH recombination only. DNA was sheared to 500bp (Covaris E220 Focused-ultrasonicator), and processed with NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs, E7546). For subsequent adapter ligation, 30 µL of Ligation Master Mix and 1 µL of Ligation Enhancer, along with 1.25µL P7 adapter F1 R1 mix (15µM) and 1.25µL P7 adapter F2 R2 mix (15 µM), were added to the previous 65µL reaction, followed by 2 h incubation at 20°C. Adapters were made with P7 adapter F1, P7 short adapter R1-block, P7 adapter F2 and P7 short adapter R2-block. Clean-up was performed with 1X volume Agencourt AMPure XP beads (Beckman Coulter, A63881), eluting the DNA in 25µL EB (10mM Tris-HCl, pH 8.5). Primer extension was then performed in 50µL reactions using Vent (exo-) DNA polymerase kit (New England Biolabs, M0257) and biotinylated J primers (Mouse_JH1_Rev_Bio, Mouse_JH2_Rev_Bio, Mouse_JH3_Rev_Bio and Mouse_JH4_Rev_Bio) as described (PMID: 29725123). Samples were purified using QIAquick PCR Purification Kit and eluted in 40µL EB; primer extension products were captured using 5µL Dynabeads MyOne streptavidin T1 beads (Invitrogen 65601) as described113, and bead-captured products resuspended in 10.5µL EB. PCR amplification then incorporated P5 adapter using P7 short adapter primer and J-P5 short primer mix (25µL reactions, Q5 High-Fidelity 2x Master Mix; New England Biolabs, M0492S; 19 cycles). After PCR, Dynabeads were removed, AMPure XP clean-up performed, and PCR products eluted in 10.5µL EB. Next, incorporation of flow-cell-binding and barcoding sequences was performed by PCR (25µL reactions, Q5 High-Fidelity, 6 cycles) with P7 flow cell and P5-I5 flow cell index primers. P5-I5_flow_cell_index_2, 5, 6, 12, 15 and 19 were used to barcode our six samples. PCR products were purified using two tandem AMPure XP beads clean-up steps, using 15µL for final elution. Barcoded sub-libraries were quantified using Agilent High Sensitivity DNA Assays on an Agilent 2100 Bioanalyzer. Equimolecular amounts of each were pooled to create a final library for paired-end sequencing (2x300bp; Illumina MiSeq).

value: Bone marrow

value: Pro B cells

value: Dnmt3a W326R/+


title: XIII_CTL_ChIP_ELOBrepA

description: Library name: XIII_CTL_ChIPseq_ELOBrepA

value: CTL

value: ELOB


title: DIPGXIII_RNA_ELOBKO.2

description: Library name: DIPGXIII_RNAseq_ELOBKO.2

value: diffuse midline glioma


title: S2-GrhC800AK807A_200uM_aGrh_INPUT_R2

description:
Library name: ChIPseq_10
more reads sequenced on the Illumina HiSeq 4000


title: control_9_1

value: blood

value: peripheral blood leukocytes

value: Control


title: patient_9

value: DNMT3A p.K335E heterozygous


title: W326R_S5_dedup_assembled_clones

description: Library name: W326R_S5


title: S2-GrhR806A_200uM_aGrh_INPUT_R1

description:
Library name: ChIPseq_11
more reads sequenced on the Illumina HiSeq 4000


title: S2-GrhC800AK807A_200uM_aGrh_INPUT_R1

description:
Library name: ChIPseq_9
more reads sequenced on the Illumina HiSeq 4000


title: patient_11

value: DNMT3A p.L300R heterozygous


title: DIPGXIII_RNA_ELOBKO.1

description: Library name: DIPGXIII_RNAseq_ELOBKO.1

value: glioma

value: SU-DIPGXIII


title: control_9_2


title: DIPGXIII_RNA_CTLsg.3

description: Library name: DIPGXIII_RNAseq_CTLsg.3

value: CTLsg


title: patient_7

value: DNMT3A p.W330S heterozygous


title: wt3_S3_dedup_assembled_clones

description: Library name: wt3_S3

value: Dnmt3a +/+


title: Adult male heart Rep 1

description:
Library name: Sample 1
Deep RNA seq >80M reads
M1-1

value: Heart

value: C57Bl6/J wt


title: patient_8

value: DNMT3A p.W306R heterozygous


title: S2-Grh_100uM_aGrh_INPUT_A_R2

description:
Library name: ChIPseq_8
more reads sequenced on the Illumina HiSeq 4000

value: Schneider 2 cells

value: 100 uM CuSO4


title: wt2_S2_dedup_assembled_clones

description: Library name: wt2_S2

value: Bone marrow

value: Pro B cells


title: S2-GrhR806A_200uM_aGrh_IP_R2

description:
Library name: ChIPseq_6
more reads sequenced on the Illumina HiSeq 4000

value: 200 uM CuSO4

value: Grh


title: DIPGXIII_RNA_CTLsg.2

description: Library name: DIPGXIII_RNAseq_CTLsg.2

value: diffuse midline glioma


title: W326R_S4_dedup_assembled_clones

description: Library name: W326R_S4

value: Dnmt3a W326R/+


title: control_7_1

value: blood

value: peripheral blood leukocytes

value: Control


title: DIPGXIII_RNA_CTLsg.1

description: Library name: DIPGXIII_RNAseq_CTLsg.1

value: glioma

value: SU-DIPGXIII

value: CTLsg


title: S2-Grh_100uM_aGrh_INPUT_A_R1

description:
Library name: ChIPseq_7
more reads sequenced on the Illumina HiSeq 4000


title: wt1_S1_dedup_assembled_clones

description: Library name: wt1_S1

value: Dnmt3a +/+


title: patient_4

value: DNMT3A p.S304del heterozygous


title: Adult DRG neurons fromwild type control - sample 1

city: Portland

first: Kevin

last: Wright

state: Oregon

address: 3181 SW Sam Jackson Rd.

department: Vollum Institute

institute: Oregon Health & Science University

description: Library name: WT-1

data_processing:
IlluminaMiSeq platform with 2× 150–base pair (bp) read length
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv file includes raw counts of each sample
Supplementary files format and content: Each text file includes FPKM values for each sample

source_name: Dorsal Root Ganglia

extract_protocol:
Whole DRGs along the entire rostro-caudal axis from 4 animals of each genotype were dissected, collected in 1.5 mL Eppendorf tubes, pelleted and snap frozen in dry ice. Frozen tissue was shipped on dry ice to Genewiz (Azenta Life Sciences) for RNA sequencing.
PolyA selection-based mRNA enrichment, mRNA fragmentation and complementary DNA (cDNA) synthesis were performed at Genewiz.

value: Dorsal Root Ganglia

value: Sensory neurons and satelite glia

value: wild type


title: control_7_2


title: Adult DRG neurons fromwild type control - sample 3

description: Library name: WT-3


title: patient_2

value: DNMT3A p.W330R heterozygous


title: Adult DRG neurons fromwild type control - sample 2

description: Library name: WT-2


title: BT245_RNA_ELOBKO.1

city: Houston

first: Jamie

last: Anastas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: BT245_RNAseq_ELOBKO.1

value: ELOBKO


title: S2-GrhC800AK807A_200uM_aGrh_IP_R2

description:
Library name: ChIPseq_4
more reads sequenced on the Illumina HiSeq 4000

value: Schneider 2 cells

value: 200 uM CuSO4


title: BT245_RNA_ELOBKO.3

description: Library name: BT245_RNAseq_ELOBKO.3

value: diffuse midline glioma


title: BT245_RNA_ELOBKO.2

description: Library name: BT245_RNAseq_ELOBKO.2


title: S2-GrhR806A_200uM_aGrh_IP_R1

description:
Library name: ChIPseq_5
more reads sequenced on the Illumina HiSeq 4000

value: Grh


title: control_4

value: blood


title: S2-GrhC800AK807A_200uM_aGrh_IP_R1

description:
Library name: ChIPseq_3
more reads sequenced on the Illumina HiSeq 4000


title: BT245_RNA_CTLsg.3

description: Library name: BT245_RNAseq_CTLsg.3


title: S2-Grh_100uM_aGrh_IP_A_R2

description:
Library name: ChIPseq_2
more reads sequenced on the Illumina HiSeq 4000

value: 100 uM CuSO4


title: BT245_RNA_CTLsg.2

description: Library name: BT245_RNAseq_CTLsg.2


title: BT245_RNA_CTLsg.1

description: Library name: BT245_RNAseq_CTLsg.1


title: Adult DRG neurons from Pten heterozygous mutant - sample 3

description: Library name: PtenHet-3

value: Pten heterozygous


title: S2-Grh_100uM_aGrh_IP_A_R1

description:
Library name: ChIPseq_1
more reads sequenced on the Illumina HiSeq 4000


title: control_3

value: peripheral blood leukocytes

value: Control


title: eDS091_TGGT1_320300_Rep2

status: Public on Apr 26 2026

city: Cambridge

first: Dominic

last: Schwarz

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

description: Library name: eDS091_119

data_processing:
Paired-end reads were trimmed using Trim Galore (v0.6.7) with a Phred quality cutoff of 20 and discarding reads shorter than 30? bp. Trimmed reads were aligned to the Toxoplasma gondii ME49 reference genome (ToxoDB v68) using Bowtie2 (v2.4.2) with the parameters: --end-to-end -D 15 -R 2 -N 1 -L 22 -i S,1,0.50 --no-mixed --no-discordant --phred33 -I 10 -X 700. Bedgraph files were generated using E. coli carryover DNA as an internal spike-in control between sample/control pairs indicated by the eDS number using genomecov (v2.29.2). eDS082_TGGT1_203950_Rep2 was used as control for eDS082_TGGT1_286920_Rep2 and eDS082_TGGT1_278440_Rep2. The matching normalized TGGT1_203950 bedgraph file is indicated by _for103_ for eDS082_TGGT1_286920_Rep2 or _for104_ for eDS082_TGGT1_278440_Rep2.
Assembly: ToxoDB v68
Supplementary files format and content: bedgraph
Library strategy: CUT&Run

organism: Toxoplasma gondii

growth_protocol: Toxoplasma gondii parasites were cultured with human foreskin fibroblasts (HFFs, ATCC SRC-1041) in Dulbecco’s Modified Eagle Medium (DMEM, GIBCO 11965118) supplemented 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts) and 3 % inactivated calf serum (ICS). Tachyzoites and HFFs were grown at 37 °C and 5 % CO2.

extract_protocol:
Intracellular parasites were harvested by mechanical disruption through a 27-gauge needle and filtration through a 5  μm membrane. A total of ~5 x 10⁷ parasites were pelleted (1500 x g, 10  min) and resuspended in wash buffer (20 mM HEPES-NaOH pH 7.5, 150  mM NaCl, 0.5  mM Spermidine, 1x EDTA-free Protease Inhibitor Cocktail) and attached to 100 μl BioMag Plus Concanavalin A beads (Polysciences) activated in bead activation buffer (20 mM HEPES-KOH pH 7.9, 10  mM KCl, 0.1  mM CaCl2, 0.1 mM MnCl2). Parasites were bound to the beads by incubation for 15 min at room temperature and rotation. Bead-bound parasites were blocked with wash buffer supplemented with 2 mM EDTA for 5 min at room temperature followed by binding of 1 µg NbALFA-MNase per sample in ice-cold wash buffer supplemented with 0.025 % Digitonin (Invitrogen) for 1 hr at 4 °C. After NbALFA-MNase binding, bead-bound parasites were washed three times with ice-cold wash buffer supplemented with 0.025 % Digitonin for 5 min at 4 °C. The cutting reaction was started by the addition of ice-cold wash buffer supplemented with 0.025 % Digitonin and 2 mM CaCl2 and incubation for 60 min on ice. The reaction was stopped by the addition of 4xSTOP buffer (400 mM NaCl, 40 mM EDTA, 8 mM EGTA, 100 µg/ml RNaseA, 80 µg/ml Glycogen and 0.025 % Digitonin) to 1x and incubation at 37 °C for 20 min. The DNA was extracted using a modified organic extraction and ethanol precipitation protocol.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s instructions with 11–12 PCR amplification cycles. Size selection and clean-up steps were performed with AMPure XP beads (Beckman Coulter).

treatment_protocol: Parasites were grown for 24 hr.

value: Toxoplasma gondii cell


title: eDS091_TGGT1_203950_Rep2

description: Library name: eDS091_118


title: Adult DRG neurons from Pten heterozygous mutant - sample 1

description: Library name: PtenHet-1


title: eDS082_TGGT1_286920_Rep2

description: Library name: eDS082_103


title: eDS076_TGGT1_286920_Rep1

description: Library name: eDS076_91


title: eDS072_TGGT1_278440_Rep1

description: Library name: eDS072_83