title: donor procurement biopsy [D046_P]

value: right kidney

tag: donor bmi

tag: donor hypertension

tag: donor biopsy cv


title: A673_veh_3

status: Public on Dec 22 2025

type: SRA

city: Seattle

first: Emma

last: Wrenn

state: WA

address: 1920 Terry Ave

country: USA

institute: Seattle Children's Research Institute

description: Library name: E21

library_source: transcriptomic

data_processing:
Fastq file quality scored by FASTQC 0.11.9
Reads trimmed using Trimgalore 0.6.7
Reads aligned with STAR Align 2.7.10a
Duplicates marked with Picard markduplicates 3.0.0
rlog normalized counts generated in DESeq2 (v1.44.0) from STAR raw counts matrix
Assembly: GRCh38
Supplementary files format and content: TC71_A673_CHLA10_PDX305_rld.csv contains an rlog normalized counts matrix of ENSEMBL gene IDs (rows) by library name (columns). See https://github.com/LawlorLab/ for code used to generate raw and normalized counts.

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: TC71 and A673 cell lines grown in RPMI1640 + 10% FBS + 2mM L-glutamine, CHLA10 and PDX305 cells grown in IMDM + 20% FBS + 2 mM L-glutamine + 1X ITS-X

extract_protocol:
Total RNA was collected using a Qiagen RNEasy kit
mRNA library (polyA enrichment) preparation was performed by Novogene prior to sequencing on a NovaSeq X Plus (paired end 150 bp reads, 6B data per sample)

treatment_protocol: 100,000 cells were plated in 12wp, 24 hours later they were were treated with TGFβ1 (10 ng/mL), TGFβ2 (10 ng/mL), vactosertib (1uM), or vehicle controls. 24hrs after treatment total RNA was collected using Quiagen RNEasy kit.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genotype

tag: treatment

value: vehicle

tag: batch


title: donor procurement biopsy [D048_L]

type: RNA

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: The data were analyzed using the “limma”package and R studio version 4.2.2.

label: biotin

source_name: kidney biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

extract_protocol: Trizol-chloroform extraction of total RNA was performed according to the manufacturer's instructions.

tag: patient id

value: left kidney

tag: donor age

tag: donor category

value: DBD - ECD

tag: donor biopsy ct

tag: donor biopsy ci

tag: donor biopsy ah


title: NELFC-AID-Auxin-ELOA-KO_rep1_SR

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
Library name: Sample57
isoformMetadata.csv

data_processing:
Circular consensus sequences (CCS) from the Revio system were demultiplexed using lima with --hifi-preset SYMMETRIC option. Then Reverse transcription primer sequence flanking the mRNA sequences was removed using lima with --isoseq and --peek-guess to generate full-length reads. Concatemers and polyA tails were removed using isoseq3 refine with --require-polya to generate full-length non-concatemer reads. Full-length non-concatemer reads were merged using pbmerge, grouped into read cluster by hierarchical clustering using isoseq cluster2, aligned to genome using pbmm2 align, collapsed using isoseq3 collapse, and classified using SQANTI3. Short-read data were processed using kallisto bus. Short-read and long-read data were processed through standard MPAQT pipeline.
Assembly: hg38
Supplementary files format and content: isoformMetadata.csv is a dataframe containing the definition for each isoform in the transcriptome of this study, including the associated genes, associated transcripts, and SQANTI3 defined structural categories. MPAQT.(LR_)SR.tsv files for each sample contains the corrected TPMs of these isoforms in each sample.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
Long read RNA-seq libraries were prepared using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module, Iso-Seq Express oligo kit, and SMRTbell® prep kit 3.0 per manufacturer’s instructions. Library quality was assessed on Agilent Femto Pulse before the libraries were loaded onto a Revio or Sequel II flow cell. Short read RNA-seq libaries were prepared using Takara Bio SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit (Cat.# 634485) per maufacturer's instructions. Library quality was assessed on Agilent DNA ScreenTape.

value: sgELOA

value: Auxin 6hr


title: donor procurement biopsy [D047_P]

value: DBD - SCD


title: 37d_S15_Fetal-Brain_Germ-Free_Female

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description: Library name: 37d_S15

data_processing:
The trimmed sequence reads ere mapped to GRCm39 using Hisat2
fpkm files are estimted using cufflinks
Assembly: mm39
Supplementary files format and content: gene_fpkm

organism: Mus musculus

source_name: Fetal-Brain

extract_protocol:
Total RNA was extracted by using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. 80224; Qiagen, MD, USA) in accordance with the manufacturer’s protocol.
Libraries were constructed following the manufacturer’s protocol with reagents supplied in the Illumina mRNA Stranded Library Preparation Kit and sequenced at the University of Missouri Genomics Technology Core.

value: Fetal-Brain

value: Female

value: Germ-Free


title: NELFC-AID-DMSO-ELOA-KO_rep2_SR

description:
Library name: Sample56
isoformMetadata.csv

value: DMSO 6hr


title: A673_Vacto 1uM_2

description: Library name: E20

value: 1 uM vactosertib


title: 32c_S2_Placenta_Germ-Free_Female

description: Library name: 32c_S2

source_name: Placenta

value: Placenta


title: 37c_S3_Placenta_Germ-Free_Female

description: Library name: 37c_S3


title: donor procurement biopsy [D044_P]


title: donor procurement biopsy [D048_P]


title: A673_TGFB2_2

description: Library name: E19

value: 10 ng per mL human TGFB2


title: NELFC-AID-Auxin_rep2_SR

description:
Library name: Sample54
isoformMetadata.csv

value: sgControl


title: 28c_S8_Placenta_Germ-Free_Male

description: Library name: 28c_S8

value: Male


title: A673_veh_2

description: Library name: E17

value: cell line


title: A673_TGFB1_2

description: Library name: E18

value: Ewing sarcoma cell line

value: 10 ng per mL human TGFB1


title: 28d_S19_Fetal-Brain_Germ-Free_Male

description: Library name: 28d_S19


title: donor procurement biopsy [D044_L]

value: left kidney


title: NELFC-AID-Auxin_rep1_SR

description:
Library name: Sample53
isoformMetadata.csv


title: 4d_S16_Fetal-Brain_Multi-Pathogen-Free_Female

description: Library name: 4d_S16

value: Multi-Pathogen-Free


title: donor procurement biopsy [D043_P]

value: right kidney

value: DBD - ECD


title: donor procurement biopsy [D042_L]

value: DBD - SCD


title: donor procurement biopsy [D041_P]


title: A673_Vacto 1uM_1

description: Library name: E16


title: 27d_S14_Fetal-Brain_Germ-Free_Female

description: Library name: 27d_S14

value: Fetal-Brain


title: NELFC-AID-DMSO-ELOA-KO_rep1_SR

description:
Library name: Sample55
isoformMetadata.csv

value: sgELOA


title: NELFC-AID-DMSO_rep2_SR

description:
Library name: Sample52
isoformMetadata.csv


title: donor procurement biopsy [D043_L]


title: 22c_S7_Placenta_Germ-Free_Male

description: Library name: 22c_S7

value: Germ-Free


title: 1d_S21_Fetal-Brain_Multi-Pathogen-Free_Male

description: Library name: 1d_S21


title: NELFC-AID-DMSO_rep1_SR

description:
Library name: Sample51
isoformMetadata.csv

value: DMSO 6hr


title: A673_TGFB1_1

description: Library name: E14


title: A673_TGFB2_1

description: Library name: E15


title: SPT6-AID-Auxin-rep3_SR

description:
Library name: Sample50
isoformMetadata.csv

value: Auxin 6hr


title: A673_veh_1

description: Library name: E13

value: vehicle


title: SPT6-AID-Auxin-rep2_SR

description:
Library name: Sample49
isoformMetadata.csv


title: 1c_S10_Placenta_Multi-Pathogen-Free_Male

description: Library name: 1c_S10

value: Placenta


title: donor procurement biopsy [D041_L]


title: TC71_Vacto 1uM_3

description: Library name: E12

value: 1 uM vactosertib


title: SPT6-AID-Auxin-rep1_SR

description:
Library name: Sample48
isoformMetadata.csv


title: 18d_S13_Fetal-Brain_Germ-Free_Female

description: Library name: 18d_S13

value: Female


title: TC71_TGFB2_3

description: Library name: E11

value: cell line

value: 10 ng per mL human TGFB2


title: donor procurement biopsy [D040_L]


title: donor procurement biopsy [D040_P]


title: SPT6-AID-DMSO-rep3_SR

description:
Library name: Sample47
isoformMetadata.csv


title: 18c_S1_Placenta_Germ-Free_Female

description: Library name: 18c_S1


title: TC71_TGFB1_3

description: Library name: E10

value: Ewing sarcoma cell line

value: 10 ng per mL human TGFB1


title: 20d_S18_Fetal-Brain_Germ-Free_Male

description: Library name: 20d_S18

value: Male


title: donor procurement biopsy [D039_L]

value: left kidney


title: donor procurement biopsy [D039_P]

value: right kidney


title: TC71_veh_3

description: Library name: E9


title: 16c_S12_Placenta_Multi-Pathogen-Free_Male

description: Library name: 16c_S12

value: Multi-Pathogen-Free


title: SPT6-AID-DMSO-rep2_SR

description:
Library name: Sample46
isoformMetadata.csv


title: 15d_S23_Fetal-Brain_Multi-Pathogen-Free_Male

description: Library name: 15d_S23

value: Fetal-Brain


title: SPT6-AID-DMSO-rep1_SR

description:
Library name: Sample45
isoformMetadata.csv


title: donor procurement biopsy [D038_L]

value: DBD - SCD


title: SPT5-AID-Auxin-rep3_SR

description:
Library name: Sample44
isoformMetadata.csv


title: TC71_Vacto 1uM_2

description: Library name: E8


title: donor procurement biopsy [D038_P]


title: 13d_S17_Fetal-Brain_Multi-Pathogen-Free_Female

description: Library name: 13d_S17


title: donor procurement biopsy [D037_P]

value: DBD - ECD


title: SPT5-AID-Auxin-rep2_SR

description:
Library name: Sample43
isoformMetadata.csv


title: TC71_TGFB2_2

description: Library name: E7


title: 13c_S6_Placenta_Multi-Pathogen-Free_Female

description: Library name: 13c_S6


title: SPT5-AID-Auxin-rep1_SR

description:
Library name: Sample42
isoformMetadata.csv


title: donor procurement biopsy [D037_L]


title: TC71_veh_2

description: Library name: E5


title: TC71_Vacto 1uM_1

description: Library name: E4


title: SPT5-AID-DMSO-rep3_SR

description:
Library name: Sample41
isoformMetadata.csv

value: DMSO 6hr


title: Aortic cells, sample 80, ecRestKO

city: Columbus

first: Marios

last: Arvanitis

state: OH

address: 473 W 12th Ave

institute: The Ohio State University

description: Library name: Sample 80

library_source: transcriptomic single cell

data_processing:
Single nucleus RNA-seq analysis was performed using Cellranger with a modified version of the mm10 mouse genome that includes EGFP and tdTomato sequences. Diem 2.4.1 was used to identify and remove low-quality droplets, such as empty droplets containing ambient RNA or damaged nuclei with degraded transcripts. Feature barcode matrix files from individual samples were normalized using sctransform and integrated with rPCA as implemented in Seurat v5. Clustering was performed jointly on the integrated dataset using the K-nearest neighbor algorithm. Cluster identity was defined based on expression of canonical cell type markers. We utilized Speckle v1.4.0 to analyze cell proportions across the different experimental groups
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Aorta

extract_protocol:
Cdh5-CreERT2;mT/mG;Restflox/flox mice and Cdh5-CreERT2;mT/mG mice controls were treated  to activate the Cre recombinase at 8 weeks of age and induce atherosclerosis. After 16 weeks of HFD administration, mice were euthanized and their aortas were perfused with PBS. The aortas were flash frozen in liquid nitrogen. Nuclei were isolated from the frozen tissue using a nucleus isolation protocol provided by 10X. Single nucleus RNA-sequencing libraries were prepared using the 10X 3’ v4 kit. One mouse per single nucleus capture and 2 captures per group were performed targeting 10,000 cells per capture and sequenced at a read depth of 50,000 reads per cell. All snRNAseq samples were processed and sequenced at the same time as a single batch to minimize batch effects.
Single nucleus RNA-sequencing libraries were prepared according to the manufacter's instructions using the 10X 3’ v4 kit

value: Aorta

value: Tamoxifen and AAV8-mPCSK9 overexpression and 16 weeks of high fat diet


title: donor procurement biopsy [D036_P]


title: TC71_TGFB1_2

description: Library name: E6


title: Aortic cells, sample 71, CT

description: Library name: Sample 71


title: TC71_TGFB2_1

description: Library name: E3


title: SPT5-AID-DMSO-rep1_SR

description:
Library name: Sample39
isoformMetadata.csv


title: donor procurement biopsy [D035_L]


title: TC71_TGFB1_1

description: Library name: E2


title: SPT5-AID-DMSO-rep2_SR

description:
Library name: Sample40
isoformMetadata.csv


title: Aortic cells, sample 81, ecRestKO

description: Library name: Sample 81


title: PAF1-AID-Auxin-rep3_SR

description:
Library name: Sample38
isoformMetadata.csv

value: Auxin 6hr


title: TC71_veh_1

description: Library name: E1

value: vehicle


title: PAF1-AID-Auxin-rep2_SR

description:
Library name: Sample37
isoformMetadata.csv


title: donor procurement biopsy [D036_L]


title: PAF1-AID-Auxin-rep1_SR

description:
Library name: Sample36
isoformMetadata.csv


title: NPPO_1NE, DMSO, Cut&Tag

city: New York

first: Jia

middle: Jessie

last: Li

state: NY

department: Medicine

institute: Columbia University Irving Medical Center

description: Library name: NPPO_1NE_DMSO_H3K36me2_abcam

library_source: genomic

data_processing:
CUT&Tag reads were trimmed using cutadapt (v3.6) and aligned to the mouse reference genome (mm10) and Drosophila (BDGP6) using BOWTIE2 (v2.4.2) with options: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Scaling factors for spike-in normalization were determined by the ratio between the number of reads aligned to the mouse genome and Drosophila genome.
Potential PCR duplicates were removed by the markdup function of sambamba (v1.0.1).
Peak calling was performed using SEACR (v1.3) or MACS2 (v2.2.8) with IgG input as control.
The read counts of peaks across gene loci were counted by featureCounts (v1.6.1).
Genomic enrichment of CUT&Tag signal for each histone modification was analyzed by deeptools (v3.5.5) and visualized using IGV (v2.13.0).
Assembly: mm10/Drosophila S2
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: Prostate

extract_protocol:
Organoids were dissociated into single cells using TrypLE, counted using a TC20 automated cell counter, and 200,000 cells/sample used for profiling. For experiments requiring normalization of input DNA, 10,000 Drosophila Schneider 2 (S2) cells (ThermoFisher Scientific R69007) were combined with 200,000 experimental cells at a ratio of 1:20. After centrifugation at 1000 rpm at RT, cell pellets were washed once with 1 ml wash buffer (20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM spermidine (Millipore-Sigma S2501), and cOmplete™, EDTA-free protease inhibitor cocktail (Millipore-Sigma 11873580001) in nuclease-free water). Cell pellets were resuspended with 10 µl ConA beads in 0.4 ml wash buffer and incubated for 10 minutes at RT. The tubes were then placed on a magnetic stand (New England Biolabs S1515S) to clear and remove the liquid, with pellets resuspended with 50 µl ice-cold Dig-wash buffer (wash buffer with 0.05% digitonin) and placed on ice for 10 min to lyse the cells. The samples were then transferred to an 8-strip tube (EpiCypher 10-0009). Each sample was incubated with 0.5 µg primary or IgG control antibody (Supplementary Table 6) and placed on a nutator at 4°C overnight. The next day, samples were incubated with 1 µl secondary antibody in 50 µl ice-cold Dig-wash buffer on a nutator at RT for 1 hr. After washing with Dig-Wash buffer three times, beads were resuspended with 50 µl Dig-300 buffer (20 mM HEPES (pH 7.5), 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, cOmplete™, EDTA-free Protease Inhibitor Cocktail in nuclease-free water) containing 2.5 µl pA-Tn5 adapter complex (EpiCypher 15-1017) and placed on a nutator at RT for 1 hour. After washing three times with Dig-300 buffer, the beads were resuspended in 150 µl Tagmentation buffer (Dig-300 buffer with 10 mM MgCl2) and incubated at 37°C for 1 hr. To stop tagmentation and solubilize DNA fragments, 5 µL 0.5 M EDTA (ThermoFisher Scientific AM9260G), 1.5 µl 10% SDS (Millipore-Sigma 71736), 1.25 µl 20 mg/ml Proteinase K (ThermoFisher Scientific EO0491) was added to each sample and incubated at 37°C overnight. The next day, phenol:chloroform:isoamyl alcohol (25:24:1, v/v; ThermoFisher Scientific 15593049) was used to extract nucleic acids. DNA was precipitated with 100% ethanol (Millipore-Sigma E7023) and dissolved in 25 μl RNase-free water. To remove RNA contamination prior to library preparation, DNA samples were incubated with 25 µg/ml RNase A (ThermoFisher Scientific EN0531) at 37°C for 10 min.
Library DNAs were amplified by PCR using Illumina universal i5 primers, Nextera barcoded i7 primers, and NEBNext HiFi 2x PCR Master mix (New England Biolabs M0541). The PCR conditions were: cycle 1: 72°C for 5 min; cycle 2: 98°C for 30 sec; cycle 3: 98°C for 10 sec; cycle 4: 63°C for 10 sec, repeating 14 times, followed by 72°C for 1 min and hold at 8°C. Post-PCR clean-up was performed using 1:1 volume Ampure XP beads (Beckman Coulter A63880). Samples were dissolved in 10 mM Tris-HCl (pH 8; Millipore-Sigma T2694) for sequencing. Size distribution and concentration of libraries was determined by capillary electrophoresis using the 4200 TapeStation (Agilent). Paired-end sequencing (2x150 bp) was performed on pooled-libraries, with 10-12 million reads per library, using the Illumina HiSeq system.

value: Prostate

value: NPPO-1NE organods

value: Prostate NE tumor cells

tag: cut&tag antibody

value: DMSO


title: donor procurement biopsy [D034_P]


title: PAF1-AID-DMSO-rep3_SR

description:
Library name: Sample35
isoformMetadata.csv


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Vehicle H2O for 3 days, biol rep 4

city: Brussels

first: Yue

last: Tong

state: Brussels

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: TFRC_IPSCBETA_MACS_CTL_6_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

data_processing:
Raw read quality was assessed using FastQC (v0.12.1)
Low-quality reads and adapter sequences were removed using fastp (v0.23.2)
Filtered reads (processed files) were then aligned to the GRCh38 primary assembly (GENCODE v46) using Salmon (v1.10.3)
Assembly: GRCh38
Supplementary files format and content: Salmon quantification file with .sf extention, tab separated. Headers: Name (of transcripts), Length, EffectiveLength, TPM, NumReads. Each row represents one transcript.

source_name: pancreatic differentiation

growth_protocol: The control iPSC lines 1.023 (PMID: 36060810), HEL115.6 (PMID: 30247717), ESIBIe003-A-10 (PMID: 34619644), and ULBi015.18 were cultured in Matrigel-coated plates (Corning, BDAA356231) in E8 medium as described (PMID: 30247717). The 7-stage differentiation into ß-cells was done as described (PMID: 36060810) (PMID: 30247717). Cells were seeded at 2.5 × 106 cells per 3.5 cm diameter well in E8 medium containing 5 or 10 μM ROCK inhibitor (StemCell Technologies, 72304, Y-27632). Differentiation was started 24 hours later. After reaching the pancreatic progenitor stage (stage 4), cells were plated in microwell plates at 900 cells per microwell (AggreWell400, StemCell Technologies, 34411) to allow islet-like aggregate formation until 1 week into stage 7.

extract_protocol:
Total RNA from MACS-purified iPSC-ß cells was isolated using the RNeasy Plus Micro kit (Qiagen, 74034). RNA concentration and integrity were measured using the Bioanalyzer RNA 6000 Nano assay (Agilent, 5067-1511) on the Agilent 2100 Bioanalyzer.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7760L) for samples sequenced by Illumina NovaSeq6000 and Novogene NGS Stranded RNA Library Prep Set (Novogene, PT044) for samples sequenced by Illlumina NovaSeq X Plus. Paired-end sequencing (2x151bp) was performed at 200 million reads.

treatment_protocol: iPSC aggregates at stage 7 were exposed to 100 μM DFO for 3 days in Ham’s F-10 medium (Gibco, 41550) supplemented with 0.75% fatty acid-free BSA, 0.5% GlutaMAX (Gibco, 35050038), and 1% Pen/Strep (ThermoFisher, 15070063). Medium was renewed every 2 days.

value: pancreatic differentiation

value: human induced pluripotent stem cell derived pancreatic beta-like cell aggregates

value: wildtype


title: NPPO-6-H3.3K36M, H3K27me3, Cut&Tag

description: Library name: NPPO-6-H3.3K36M_H3K27me3_CST

value: NPPO-6-H3.3K36M organoids

value: H3.3K36M transgene


title: Aortic cells, sample 70, CT

description: Library name: Sample 70


title: donor procurement biopsy [D034_L]

value: left kidney


title: Ribosome profiling of NAC_KD worms replicate 2

city: Stanford

first: Jae Ho

last: Lee

state: CA

address: 318 Campus Drive E200

department: Biology

institute: Stanford University

description: ribosome-protected fragments

data_processing:
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset from the 5' end of each fragment length was estimated using Ribowaltz to assign each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribosome profiling

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Frozen worm pellets were lysed using cryo-mill. Lysed samples were thawed and spun at 21,000g for 15 minutes to clear the lysate. RNA concentration of supernatant was measured and RNAse I was added to 0.4 units per ug of RNA. The sample was incubated for 45 minutes at room temperature and 0.02ul of SUPERaseIn RNAse Inhibitor was added per ug of RNA to stop digestion. Samples were immediately layered on 1M sucrose cushion and spun at 100,000rpm for 1 hour in TLA 100.3 rotor to isolate ribosomes. Resulting ribosome pellet was resuspended and RNA was extracted using TRIzol reagent following manufacturer’s instructions.
RNA fragments in the range of ~25-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints. Samples were then depleted of rRNA using Ribo-zero with the addition of custom-designed oligos to enhance depletion efficiency. Remaining RNA fragments were reverse transcribed into cDNA, followed by circularization. Libraries were barcoded during PCR amplification and sent for sequencing.

value: whole organism

value: RNAi NAC_KD


title: NPPO-6-H3.3K36M, H3K36me3, Cut&Tag

description: Library name: NPPO-6-H3.3K36M_H3K36me3_Active motif

value: H3K36me3 (Active motif, #61101)


title: donor procurement biopsy [D033_L]

value: DBD - ECD


title: PAF1-AID-DMSO-rep2_SR

description:
Library name: Sample34
isoformMetadata.csv

value: DMSO 6hr


title: PAF1-AID-DMSO-rep1_SR

description:
Library name: Sample33
isoformMetadata.csv


title: NPPO-6-H3.3K36M, H3K36me2, Cut&Tag

description: Library name: NPPO-6-H3.3K36M_H3K36me2_abcam


title: NPPO_1NE, KTX, Cut&Tag

description: Library name: NPPO_1NE_KTX_H3K36me2_abcam


title: Ribosome profiling of NAC_KD worms replicate 1

description: ribosome-protected fragments


title: donor procurement biopsy [D033_P]

value: right kidney


title: donor procurement biopsy [D032_L]


title: NPPO_1NE, IgG, Cut&Tag

description: Library name: NPPO_1NE_IgG_CST

value: Normal Rabbit IgG (CST, #2729)

value: No


title: Ribosome profiling of N2 wild-type worms replicate 2

description: ribosome-protected fragments

value: N2 (wildtype)


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Deferoxamine for 3 days, biol rep 4

description:
Library name: TFRC_IPSCBETA_MACS_DFO_6_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

value: Deferoxamine


title: NPPO-6-EV, H3K27me3, Cut&Tag

description: Library name: NPPO-6-EV_H3K27me3_CST

value: Prostate

value: NPPO-6-EV organoids

value: Prostate NE tumor cells

value: empty vector transgene


title: Subject1_H3K4me1_CT_D4_LPS_2

city: Los Angeles

first: Aleksandr

last: Gorin

address: 611 Charles E Young Dr E 570C Boyer Hall

institute: UCLA

description: Library name: Subject1_H3K4me1_CT_D4_LPS_2

data_processing:
Low quality reads were trimmed (cutoff q=20) and adapter sequences were removed with cutadapt. Reads were aligned to the human hg38 genome using bowtie2 with default parameters except –very-sensitive and –non-deterministic options. Aligned reads were filtered based on mapping score (MAPQ ≥30) with Samtools. Duplicated reads were removed with Picard MarkDuplicates. Genome browser tracks were generated using bamCoverage function in deepTools with the following options: --binSize 10 --smoothLength 30 --normalizeUsing RPGC --effectiveGenomeSize 2913022398. MACS3 was used to identify peaks using standard options except -f BAMPE and -q 0.01. We generated a peak file for every condition and then generated a combined peak file across all conditions for each human subject (including all unstimulated and stimulated conditions). These genomic loci were used to generated a counts table using deeptools multiBamSummary for subsequent analysis.
Peaks were filtered to select only those that were in the top 50th percentile of reads in any condition during acute stimulation (unstimulated, 8 hours IFNγ or 8 hours LPS conditions).
Assembly: hg38
Supplementary files format and content: CSV file of raw reads for each peak in each subject
Library strategy: CUT&Tag

source_name: MCSF differentiated monocyte-derived macrophages

growth_protocol: Human blood from deidentified donors was obtained from the UCLA CFAR Centralized Laboratory Support Core in accordance with UCLA IRB 11-000443. PBMC were isolated from blood by Ficoll (Cytiva 17-1440-03) density centrifugation and cryopreserved in 10%DMSO (Sigma-Aldrich, D2438) in Embryonic Stem cell FBS (Gibco, 11875-093). Monocytes were purified from PBMC using pan-monocyte isolation magnetic beads (Miltenyi 130-096-537). Monocytes were plated on 6-well tissue culture plates at a density of 1.2 x106 cells/well for 6 days in 3mL of RPMI (Gibco, 11875-093) supplemented with 10% ES fetal bovine serum (Gibco, 10439-024), penicillin-streptomycin (Corning, 30-002-CI), L-glutamine (2mM; Corning, 25-005-CI) and human M-CSF (20 ng/ml; R&D systems 216-MC-100). M-CSF was replenished to a concentration of 20ng/mL by adding 60ng M-CSF to each well (assuming that all M-CSF was depleted).

extract_protocol:
Nuclear isolation and tagmentation was performed on 100,000 cells per manufacturer protocol as previously described with the CUTANA CUT&Tag pAG-Tn5 enzyme (EpiCypher, 15-1017) with the notable exception that a cocktail of 1mM dithiothreitol, 0.5mM (Sigma-Aldrich, D0632), Phenylmethanesulfonyl fluoride (Sigma-Aldrich, 206-350-2), 4µg/mL Leupeptin (Sigma-Aldrich, L9783), 1µM Pepstatin A (Sigma-Aldrich, P5318), and 0.01TIU/mL Aprotinin (Sigma-Aldrich A1153) substituted the Roche Protease inhibitor cocktail where necessary. Anti-H3K4me1 antibody (Abcam, ab8895) was used at a dilution of 1:20 as primary antibody; guinea pig anti-rabbit antibody (Abcam, ABIN101961) was used at a dilution of 1:100 as secondary antibody.
Libraries were prepared with Nextera DNA library preparation kit

treatment_protocol: Macrophages were treated with human IFNy (100nt/mL), LPS (100ng/mL) or PBS control for 8 hours. Cells were washed and subsequently cultured in either regular media or media with 1µM ruxolitinib, or media with 8µg/mL anti-IFNy neutralizing antibody for an additional 88 hours. Cells were collected for CUT&Tag on Day 0 after the 8 hour stimulation or on day 4 during (88 hours after media replacement).


title: Subject1_H3K4me1_CT_D4_LPS_1

description: Library name: Subject1_H3K4me1_CT_D4_LPS_1

value: MCSF differentiated monocyte-derived macrophages


title: NPPO-6-EV, H3K36me3, Cut&Tag

description: Library name: NPPO-6-EV_H3K36me3_Active motif


title: donor procurement biopsy [D031_L]


title: donor procurement biopsy [D031_P]


title: Ribosome profiling of N2 wild-type worms replicate 1

description: ribosome-protected fragments


title: donor procurement biopsy [D030_L]

value: DBD - SCD


title: donor procurement biopsy [D032_P]


description: Library name: Subject1_H3K4me1_CT_D4_IFNy_antiifnyab_2


title: NPPO-6-EV, H3K36me2, Cut&Tag

description: Library name: NPPO-6-EV_H3K36me2_abcam


description: Library name: Subject1_H3K4me1_CT_D4_IFNy_antiifnyab_1


title: Subject1_H3K4me1_CT_D4_IFNy_rux_2

description: Library name: Subject1_H3K4me1_CT_D4_IFNy_rux_2


title: RNAseq of membrane NAC_KD replicate 1

data_processing:
Sequencing data was aligned using STAR to custom reference transcriptome(containing CDS with 21nt flanking up/downstream of start/stop codon) used in riboseq for direct comparison.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text files include: Column1: geneID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column4: counts for the 2nd read strand aligned with RNA

extract_protocol:
Frozen worm pellets were lysed using cryo-mill with lysis buffer without detergent. For total RNA, detergent was added to thawed lysate, spun at 21,000g for 15 minutes to clear the lysate, and RNA was extracted using TRIzol reagent following manufacturer’s instructions. Soluble fraction was separated by thawing lysate without detergent, spinning at 21,000g for 15 minutes, and RNA was extracted using TRIzol reagent. Lysis buffer with detergent was added to the remaining pellet from isolating soluble fraction, incubted for 10 min, spun at 21,000g for 15 minutes to isolate detergent-extracted membrane fraction, and RNA was extracted using TRIzol reagent.
Library was prepared using TruSeq Stranded Total RNA Prep kit (Illumina) following protocol provided by manufacturer. rRNA was depleted using Ribo-Zero rRNA removal kit (Illumina).


title: NPPO-6-EV, IgG, Cut&Tag

description: Library name: NPPO-6-EV_IgG_CST


title: RNAseq of soluble(cytosolic) NAC_KD replicate 2


title: Subject1_H3K4me1_CT_D4_IFNy_rux_1

description: Library name: Subject1_H3K4me1_CT_D4_IFNy_rux_1


title: donor procurement biopsy [D029_L]

value: left kidney


title: RNAseq of soluble(cytosolic) NAC_KD replicate 1

value: whole organism


title: RNAseq of total lysate NAC_KD replicate 2

value: RNAi NAC_KD


title: NPPO-4-H3.3K36M, H3K36me2, Cut&Tag

description: Library name: NPPO-4-H3.3K36M_H3K36me2_abcam

value: NPPO-4-H3.3K36M organoids

value: H3.3K36M transgene


title: NPPO-4-H3.3K36M, H3K36me3, Cut&Tag

description: Library name: NPPO-4-H3.3K36M_H3K36me3_Active motif

value: H3K36me3 (Active motif, #61101)


title: NPPO-4-H3.3K36M, H3K27me3, Cut&Tag

description: Library name: NPPO-4-H3.3K36M_H3K27me3_CST


title: Subject1_H3K4me1_CT_D4_IFNy_2

description: Library name: Subject1_H3K4me1_CT_D4_IFNy_2


title: NPPO-4-EV, H3K27me3, Cut&Tag

description: Library name: NPPO-4-EV_H3K27me3_CST

value: NPPO-4-EV organoids


title: RNAseq of membrane NAC_KD replicate 2


title: RNAseq of total lysate NAC_KD replicate 1


title: Subject1_H3K4me1_CT_D4_IFNy_1

description: Library name: Subject1_H3K4me1_CT_D4_IFNy_1


title: Subject1_H3K4me1_CT_D0_LPS_rux_2

description: Library name: Subject1_H3K4me1_CT_D0_LPS_rux_2


title: NPPO-4-EV, H3K36me3, Cut&Tag

description: Library name: NPPO-4-EV_H3K36me3_Active motif


title: donor procurement biopsy [D028_P]

value: right kidney


title: donor procurement biopsy [D029_P]

value: DBD - ECD


title: donor procurement biopsy [D027_L]


title: donor procurement biopsy [D025_L]


title: RNAseq of membrane N2 wild-type replicate 1

value: N2 (wildtype)


title: donor procurement biopsy [D026_L]


title: Subject1_H3K4me1_CT_D0_LPS_rux_1

description: Library name: Subject1_H3K4me1_CT_D0_LPS_rux_1


title: donor procurement biopsy [D028_L]


title: donor procurement biopsy [D024_P]


title: NPPO-4-EV, IgG, Cut&Tag

description: Library name: NPPO-4-EV_IgG_CST

value: Normal Rabbit IgG (CST, #2729)


title: donor procurement biopsy [D024_L]


title: RNAseq of soluble(cytosolic) N2 wild-type replicate 2


title: RNAseq of total lysate N2 wild-type replicate 2


title: NPPO-4-EV, H3K36me2, Cut&Tag

description: Library name: NPPO-4-EV_H3K36me2_abcam

value: Prostate


title: NPPO-2-sgNsd2, H3K36me3, Cut&Tag

description: Library name: NPPO-2-sgNsd2_H3K36me3_Active motif

value: NPPO-2-sgNsd2 organods

value: Cas9+sgNSD2 guide RNA


title: RNAseq of soluble(cytosolic) N2 wild-type replicate 1


title: Subject1_H3K4me1_CT_D0_LPS_2

description: Library name: Subject1_H3K4me1_CT_D0_LPS_2


title: NPPO-2-sgNsd2, H3K27me3, Cut&Tag

description: Library name: NPPO-2-sgNsd2_H3K27me3_CST

value: Prostate NE tumor cells


title: Subject1_H3K4me1_CT_D0_IFNy_2

description: Library name: Subject1_H3K4me1_CT_D0_IFNy_2

value: MCSF differentiated monocyte-derived macrophages


title: Subject1_H3K4me1_CT_D0_LPS_1

description: Library name: Subject1_H3K4me1_CT_D0_LPS_1


title: RNAseq of membrane N2 wild-type replicate 2


title: Subject1_H3K4me1_CT_D0_IFNy_1

description: Library name: Subject1_H3K4me1_CT_D0_IFNy_1


title: Subject1_H3K4me1_CT_D0_unstim_2

description: Library name: Subject1_H3K4me1_CT_D0_unstim_2


title: NPPO-2-sgNsd2, H3K36me2, Cut&Tag

description: Library name: NPPO-2-sgNsd2_H3K36me2_abcam


title: RNAseq of total lysate N2 wild-type replicate 1


title: Subject1_H3K4me1_CT_D0_unstim_1

description: Library name: Subject1_H3K4me1_CT_D0_unstim_1


title: NPPO-2-sgControl, H3K27me3, Cut&Tag

description: Library name: NPPO-2-sgControl_H3K27me3_CST

value: NPPO-2-sgControl organods

value: Cas9+sgControl guide RNA


title: Ptrh2-CKO Mouse LV rep3

city: Torrance

first: Michelle

middle: L

last: Matter

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

description:
Library name: post partum CKO m6
CKO-PP4_S7

data_processing:
DNBSEQ-T7 Platform (Human) and Illumina NextSeq 500 sequence platform (mouse)
For Human samples: Raw data contained reads of low quality, reads with adaptor sequence and reads with high level of N base. Those reads were filtered and cleaned by cutadapt (version 1.9) and paired end were produced. Bowtie2 was used to align clean reads to reference genes and HISAT was used to align clean reads to reference genome. For mouse: Data Files were uploaded to Partek flow, contaminants were removed using Bowtie2 (version 2.2.5) and unaligned reads were aligned to STAR (version 2.7.8a) using mouse genome as reference.
Assembly: Human:GCF_000001405.39_GRCh38.p13; Mouse: Mus_musculus.GRCm38.dna
Supplementary files format and content: csv files include FPKMs for all human data and csv files include TPMs for all mouse data

source_name: Mouse LV heart

extract_protocol:
Total RNA (human and mouse) was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
Human: RNA libraries for RNAseq were prepared with MGIEasy RNA library Prep Set (Proprietary for DNBSEQ platforms). Mouse: RNA libraries for RNAseq were prepared with  Illumina Stranded Total RNA prep with Ribo-Zero Plus according to manufacturer’s instructions.

value: Mouse LV heart

value: Knockout


title: NPPO-2-sgControl, H3K36me3, Cut&Tag

description: Library name: NPPO-2-sgControl_H3K36me3_Active motif


title: donor procurement biopsy [D022_L]

value: left kidney


title: donor procurement biopsy [D022_P]


title: Ptrh2-CKO Mouse LV rep1

description:
Library name: post partum CKO m4
CKO-PP1_S5


title: Subject2_H3K4me1_CT_D4_IFNy_rux_3

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_rux_3


title: donor procurement biopsy [D018_L]

value: DBD - SCD


title: NPPO-2-sgControl, H3K36me2, Cut&Tag

description: Library name: NPPO-2-sgControl_H3K36me2_abcam


title: Subject2_H3K4me1_CT_D4_IFNy_rux_2

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_rux_2


title: Ptrh2-NT Mouse LV rep3

description:
Library name: post partum NT m3
NT-PP4_S4

value: wildtype


title: donor procurement biopsy [D018_P]


title: donor procurement biopsy [D020_P]


title: Subject2_H3K4me1_CT_D4_IFNy_rux_1

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_rux_1


title: Subject2_H3K4me1_CT_D4_IFNy_3

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_3


title: NPPO-2-sgControl, IgG, Cut&Tag

description: Library name: NPPO-2-sgControl_IgG_CST


title: NPPO-1NE-sgNsd2, H3K27me3, Cut&Tag

description: Library name: NPPO-1NE-sgNsd2_H3K27me3_CST

value: NPPO-1NE-sgNsd2 organods


title: Ptrh2-CKO Mouse LV rep2

description:
Library name: post partum CKO m5
CKO-PP2_S6


title: NPPO-1NE-sgNsd2, H3K36me3, Cut&Tag

description: Library name: NPPO-1NE-sgNsd2_H3K36me3_Active motif

value: H3K36me3 (Active motif, #61101)


title: Subject2_H3K4me1_CT_D4_IFNy_2

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_2


title: Subject2_H3K4me1_CT_D4_IFNy_1

description: Library name: Subject2_H3K4me1_CT_D4_IFNy_1


title: NPPO-1NE-sgNsd2, H3K36me2, Cut&Tag

description: Library name: NPPO-1NE-sgNsd2_H3K36me2_abcam


title: Adipose tissue SVF eYFP+ cells, 12 weeks HFD

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Library name: HFD_eYFP

data_processing:
CellRanger v4.0.0 was used to map the FASTQ filed to the mouse genome and Seurat 4.1.0 was used for scRNAseq analysis. Cells with a minimum of 100 features (unique genes), less than 12.5% mitochondrial genes, and a range of 500 to 40000 molecules detected were used, excluding any cells not meeting these criteria (Fig 5.1 B). Following doublet exclusion, the data was integrated and visualised using UMAP (Fig 5.1 C-D).
The data was de-multiplexed and analysed using CellRanger v4.0.0 and bcl2fastq v2.17.1.14.
CellRanger count pipeline was used to perform alignment against mouse genome mm10 (using STAR), filtering and counting UMIs.
Assembly: mm10
Supplementary files format and content: tsv and matrix files

source_name: Perigonadal white adipose tissue

extract_protocol:
Adipose tissue was collected in PBS with 0.5% BSA (fatty-acid-free; Sigma A3803-100G) and kept on ice until ready to process. Tissue was minced using scalpels and digested in DMEM (Thermo Fisher, 41965039) containing 2% BSA, 12.5 mM HEPES, 0.2 mg/ml liberase TL (Sigma, 5401020001) and 1/100 DNase (Sigma, 10104159001) for 30min at 37 oC with constant agitation at 180 rpm. The digestion was stopped by adding one volume DMEM, and the sample centrifuged at 250xg for 10min to separate the stromovascular (SVF) and adipocyte fractions. Cell from the SVFs were strained through a 100 μm cell strainer, centrifuged at 300xg for 3min to pellet and red blood cells lysed by resuspending in ACK lysis buffer (0.15 M NH4Cl, 1 mM KHCO3, 0.1 mM Na2EDTA, pH 7.4) for 2min. DMEM was added to stop the lysis, cells strained through a 40 μm cell strainer and centrifuged at 300xg for 3min to pellet. Cells were washed in FACS buffer (3% FBS, 2 mM EDTA) and pelleted at 300xg for 3min.  DAPI (10 ng/ml in FACS buffer) was added just before taking the samples for FACS. 100,000 events of live (DAPI-) eYFP+ cells were sortede per sample using a 100 μm nozzl into 500μl Post-sort buffer (0.04% BSA in PBS).
Libraries were prepared using the 10x Single Cell 3' v3 kit according to manufacturer specifications.

treatment_protocol: Cyp1a1 fate reporter (Cyp1a1Cre x R26LSL-eYFP) male mice were fed a purified low-fat diet (LFD; 10% fat; D12450J) or high-fat diet (HFD; 60% fat; D12492; Research Diets Inc) for 12 weeks. These were then injected with FICZ (10 mg/kg) five days prior to perigonadal white adipose tissue (gWAT) collection to promote Cyp1a1 expression.

value: Perigonadal white adipose tissue

tag: Sex

value: male

value: eYFP+ cells

value: Cyp1a1Cre x R26LSL-eYFP

value: High Fat Diet


title: Adipose tissue SVF eYFP+ cells, 12 weeks LFD

description: Library name: LFD_eYFP

value: Low Fat Diet


title: NPPO-1NE-sgControl, H3K27me3, Cut&Tag

description: Library name: NPPO-1NE-sgControl_H3K27me3_CST

value: Prostate

value: NPPO-1NE-sgControl organods

value: Prostate NE tumor cells


title: Ptrh2-NT Mouse LV rep2

description:
Library name: post partum NT m2
NT-PP2_S2


title: Subject2_H3K4me1_CT_D0_IFNy_3

description: Library name: Subject2_H3K4me1_CT_D0_IFNy_3

value: MCSF differentiated monocyte-derived macrophages


title: Ptrh2-NT Mouse LV rep1

description:
Library name: post partum NT m1
NT-PP1_S1

value: Mouse LV heart


title: Whole Synovial Tissue, OA, Patient 22

first: Deborah

middle: R

last: Winter

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
Library name: HS22
OA-WT-Synovium-P065

data_processing:
RNA-seq data were de-multiplexed using bcl2fastq, and RNA-seq reads were aligned to the human reference genome (NCBI, hg19) using TopHat2 (version 2.17.1.14) aligners (51). Gene coverage of samples was calculated using the RseQC package (52). Normalized gene counts were calculated using HTSeq.
Assembly: hg19
Supplementary files format and content: table of raw gene expression count
Supplementary files format and content: table of normalized expression by Fragments Per Kilobase per Million reads (FPKM)

molecule: polyA RNA

source_name: Joint Synovium

extract_protocol:
RA tissue was obtained by minimally invasive ultrasound guided synovial biopsy of the wrist.  OA tissue was obtained from the discards after whole joint replacement.  RNA was extracted from whole tissue cell homegenate using a QIAGEN Plus Mini kit.
Whole synovial tissue RNA-seq libraries were prepared from 90ng of total RNA using the NEBNext Ultra Kit with polyAenrichment (NEB).

value: Joint Synovium

tag: sample group

value: OA

value: all


title: Whole Synovial Tissue, OA, Patient 21

description:
Library name: HS21
OA-WT-Synovium-P064


title: NPPO-1NE-sgControl, H3K36me3, Cut&Tag

description: Library name: NPPO-1NE-sgControl_H3K36me3_Active motif

value: Cas9+sgControl guide RNA


title: Subject2_H3K4me1_CT_D0_IFNy_2

description: Library name: Subject2_H3K4me1_CT_D0_IFNy_2


title: donor procurement biopsy [D017_L]

value: left kidney

value: DBD - ECD

tag: donor bmi

tag: donor hypertension


title: donor procurement biopsy [D016_L]

tag: tissue

tag: donor biopsy cv


title: donor procurement biopsy [D019_P]

value: right kidney


title: Whole Synovial Tissue, OA, Patient 11

description:
Library name: HS11
OA-WT-Synovium-P061

tag: cell type


title: Subject2_H3K4me1_CT_D0_IFNy_1

description: Library name: Subject2_H3K4me1_CT_D0_IFNy_1


title: Whole Synovial Tissue, OA, Patient 17

description:
Library name: HS17
OA-WT-Synovium-S1004


title: donor procurement biopsy [D016_P]


title: donor procurement biopsy [D015_L]


title: Whole Synovial Tissue, OA, Patient 16

description:
Library name: HS16
OA-WT-Synovium-S1003


title: donor procurement biopsy [D015_P]


title: Subject2_H3K4me1_CT_D0_unstim_3

description: Library name: Subject2_H3K4me1_CT_D0_unstim_3


title: NPPO-7, IgG3, Cut&Tag

description: Library name: NPPO-7_IgG3_CST

tag: cell line

value: NPPO-7 organoids

value: Prostate non-NE tumor cells

value: Normal Rabbit IgG (CST, #2729)

value: No


title: donor procurement biopsy [D013_L]


title: Whole Synovial Tissue, OA, Patient 13

description:
Library name: HS13
OA-WT-Synovium-S1000


title: Subject2_H3K4me1_CT_D0_unstim_1

description: Library name: Subject2_H3K4me1_CT_D0_unstim_1


title: Whole Synovial Tissue, OA, Patient 12

description:
Library name: HS12
OA-WT-Synovium-S999


title: NPPO-7, IgG1, Cut&Tag

description: Library name: NPPO-7_IgG1_CST

tag: treatment


title: NPPO-1NE-sgControl, H3K36me2, Cut&Tag

description: Library name: NPPO-1NE-sgControl_H3K36me2_abcam


title: Subject1_ATAC_D4_LPS_2

description: Library name: Subject1_ATAC_D4_LPS_2

data_processing:
Low quality reads were trimmed (cutoff q=20) and adapter sequences were removed with cutadapt. Reads were aligned to the human hg38 genome using bowtie2 with default parameters except –very-sensitive and –non-deterministic options. Aligned reads were filtered based on mapping score (MAPQ ≥30) with Samtools. Duplicated reads were removed with Picard MarkDuplicates. Genome browser tracks were generated using bamCoverage function in deepTools with the following options: --binSize 10 --smoothLength 30 --normalizeUsing RPGC --effectiveGenomeSize 2913022398. MACS3 was used to identify peaks using standard options except -f BAMPE and -q 0.01. We generated a peak file for every condition and then generated a combined peak file across all conditions for each human subject (including all unstimulated and stimulated conditions). These genomic loci were used to generated a counts table using deeptools multiBamSummary for subsequent analysis.
Peaks were filtered to select only those that were in the top 50th percentile of reads in any condition during acute stimulation (unstimulated, 8 hours IFNγ or 8 hours LPS conditions).
Assembly: hg38
Supplementary files format and content: CSV file of raw reads for each peak in each subject

extract_protocol:
50,000 cells were used to prepare nuclei in cold lysis buffer (10mM Tris-HCl pH 7.5, 3mM MgCl2, 10mM NaCl, and 0.1% IGEPAL CA-630). Nuclei were pelleted by centrifugation at 500g for 10 minutes and suspected in transposase reaction mixture consisting of 25µL 2x TD Buffer, 2.5µL TD enzyme (Illumina, 20034197), and 22.5µL water. The transposase reaction was performed at 37C for 30 minutes in a thermomixer shaker at 800rpm.
Libraries were prepared with Nextera DNA library preparation kit

treatment_protocol: Macrophages were treated with human IFNy (100ng/mL), LPS (100ng/mL), or PBS control for 8 hours. Cells were washed and subsequently cultured in either regular media or media with 1µM ruxolitinib for an additional 88 hours. Cells were collected for ATACseq on Day 0 after the 8 hour stimulation or on day 4 during (88 hours after media replacement).


title: NPPO-1NE-sgControl, IgG, Cut&Tag

description: Library name: NPPO-1NE-sgControl_IgG_CST


title: NPPO-9, H3K27ac, Cut&Tag

description: Library name: NPPO-9_H3K27ac_CST

value: NPPO-9 organoids


title: donor procurement biopsy [D011_L]


title: donor procurement biopsy [D012_L]

value: DBD - SCD


title: donor procurement biopsy [D017_P]


title: donor procurement biopsy [D010_L]


title: Whole Synovial Tissue, OA, Patient 02

description:
Library name: HS02
OA-WT-Synovium-P054

tag: batch


title: NPPO-8, H3K27ac, Cut&Tag

description: Library name: NPPO-8_H3K27ac_CST

value: Prostate

value: NPPO-8 organoids


title: Subject2_H3K4me1_CT_D0_unstim_2

description: Library name: Subject2_H3K4me1_CT_D0_unstim_2

value: MCSF differentiated monocyte-derived macrophages


title: NPPO-7, H3K27ac, Cut&Tag

description: Library name: NPPO-7_H3K27ac_CST


title: donor procurement biopsy [D012_P]

tag: patient id


title: Subject1_ATAC_D0_LPSrux_1

description: Library name: Subject1_ATAC_D0_LPSrux_1


title: Subject1_ATAC_D0_LPSrux_2

description: Library name: Subject1_ATAC_D0_LPSrux_2


title: NPPO-1nonNE, H3K27ac, Cut&Tag

description: Library name: NPPO-1nonNE_H3K27ac_CST

value: NPPO-1nonNE organoids


title: Whole Synovial Tissue, RA, Patient 29

description:
Library name: HS29
RA-WT-Synovium-P006

value: Joint Synovium

value: RA


title: Subject1_ATAC_D0_LPS_2

description: Library name: Subject1_ATAC_D0_LPS_2


title: donor procurement biopsy [D010_P]

tag: donor age


title: donor procurement biopsy [D009_P]

tag: donor category


title: Whole Synovial Tissue, RA, Patient 20

description:
Library name: HS20
RA-WT-Synovium-P063

value: all


title: Subject1_ATAC_D0_LPS_1

description: Library name: Subject1_ATAC_D0_LPS_1


title: Subject1_ATAC_D4_LPS_1

description: Library name: Subject1_ATAC_D4_LPS_1


title: NPPO-4, H3K27ac, Cut&Tag

description: Library name: NPPO-4_H3K27ac_CST

value: NPPO-4 organoids

value: Prostate NE tumor cells


title: Whole Synovial Tissue, RA, Patient 19

description:
Library name: HS19
RA-WT-Synovium-P062


title: donor procurement biopsy [D008_P]

value: DBD - ECD

tag: donor biopsy ct


title: donor procurement biopsy [D008_L]

value: left kidney

tag: donor biopsy ci


title: donor procurement biopsy [D007_P]

value: right kidney

tag: donor biopsy ah


title: Subject1_ATAC_D4_IFNy_rux_2

description: Library name: Subject1_ATAC_D4_IFNy_rux_2


title: NPPO-2, H3K27ac, Cut&Tag

description: Library name: NPPO-2_H3K27ac_CST

value: NPPO-2 organoids

tag: cut&tag antibody


title: Whole Synovial Tissue, RA, Patient 18

description:
Library name: HS18
RA-WT-Synovium-S1005


title: Whole Synovial Tissue, RA, Patient 14

description:
Library name: HS14
RA-WT-Synovium-S1001


title: NPPO-1NE, H3K27ac, Cut&Tag

description: Library name: NPPO-1NE_H3K27ac_CST

value: NPPO-1NE organods


title: Whole Synovial Tissue, RA, Patient 23

description:
Library name: HS23
RA-WT-Synovium-P066


title: Subject1_ATAC_D4_IFNy_2

description: Library name: Subject1_ATAC_D4_IFNy_2


title: NPPO-9, H3K27me3, Cut&Tag

description: Library name: NPPO-9_H3K27me3_CST

value: Prostate non-NE tumor cells

value: No


title: donor procurement biopsy [D007_L]


title: Whole Synovial Tissue, OA, Patient 06

description:
Library name: HS06
OA-WT-Synovium-P059

value: OA


title: NPPO-6, H3K27ac, Cut&Tag

description: Library name: NPPO-6_H3K27ac_CST

value: Prostate

value: NPPO-6 organoids


title: Subject1_ATAC_D4_IFNy_1

description: Library name: Subject1_ATAC_D4_IFNy_1

value: MCSF differentiated monocyte-derived macrophages


title: Whole Synovial Tissue, RA, Patient 10

description:
Library name: HS10
RA-WT-Synovium-S998


title: NPPO-8, H3K27me3, Cut&Tag

description: Library name: NPPO-8_H3K27me3_CST

value: NPPO-8 organoids


title: donor procurement biopsy [D006_P]

value: DBD - SCD


title: NPPO-7, H3K27me3, Cut&Tag

description: Library name: NPPO-7_H3K27me3_CST

value: NPPO-7 organoids


title: donor procurement biopsy [D005_P]


title: donor procurement biopsy [D009_L]


title: Whole Synovial Tissue, RA, Patient 09

description:
Library name: HS09
RA-WT-Synovium-S997

value: Joint Synovium

value: RA

value: all


title: donor procurement biopsy [D004_P]

value: DBD - ECD


title: Whole Synovial Tissue, RA, Patient 07

description:
Library name: HS07
RA-WT-Synovium-P058


title: Subject1_ATAC_D0_IFNy_1

description: Library name: Subject1_ATAC_D0_IFNy_1


title: Subject1_ATAC_D0_IFNy_2

description: Library name: Subject1_ATAC_D0_IFNy_2


title: HPD03 on serum, RNA-Seq, Replicate 2

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

description: Library name: HPD03_serum_Rep_2

data_processing:
Transcript quantification was performed from raw reads using Salmon (v1.6.0) on transcripts defined in Ensembl 106.
Gene expression levels were estimated with tximport R package (v1.26.1).
Assembly: Human GRCh38.p13 Ensembl release 106.
Supplementary files format and content: Expression_raw counts.txt is a txt containing EnsemblID, official gene symbols and raw counts for each condition.

source_name: human induced pluripotent stem cells

growth_protocol:
Cultured on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC), or on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days following dissociation with TrypLE (Gibco 12563029) or Accutase (Sigma-Aldrich, A6964) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.

extract_protocol:
Total RNA was isolated using Total RNA Purification Kit (Norgen Biotek 37500) following the manufacturer’s instructions for HPD06 and HPD03 lines; Total RNA was isolated with the ExtractMe kit (Blirt, EM15) following the manufacturer’s instructions for Shef6 line.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction.

value: human induced pluripotent stem cells


title: Subject1_ATAC_D0_unstim_2

description: Library name: Subject1_ATAC_D0_unstim_2


title: Subject1_ATAC_D4_IFNy_rux_1

description: Library name: Subject1_ATAC_D4_IFNy_rux_1


title: donor procurement biopsy [D004_L]

value: left kidney


title: NPPO-6, H3K27me3, Cut&Tag

description: Library name: NPPO-6_H3K27me3_CST

value: Prostate NE tumor cells


title: donor procurement biopsy [D006_L]


title: HPD03 on serum, RNA-Seq, Replicate 1

description: Library name: HPD03_serum_Rep_1


title: donor procurement biopsy [D003_P]

value: right kidney


title: HPD03 on MEFs, RNA-Seq, Replicate 2

description: Library name: HPD03_MEFs_Rep_2

growth_protocol:
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC), or on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days following dissociation with TrypLE (Gibco 12563029) or Accutase (Sigma-Aldrich, A6964) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.


title: Subject1_ATAC_D0_unstim_1

description: Library name: Subject1_ATAC_D0_unstim_1


title: NPPO-4, H3K27me3, Cut&Tag

description: Library name: NPPO-4_H3K27me3_CST

value: NPPO-4 organoids


title: NPPO-2, H3K27me3, Cut&Tag

description: Library name: NPPO-2_H3K27me3_CST

value: NPPO-2 organoids

value: No


title: HPD03 on MEFs, RNA-Seq, Replicate 1

description: Library name: HPD03_MEFs_Rep_1


title: Subject2_ATAC_D4_IFNy_rux_1

description: Library name: Subject2_ATAC_D4_IFNy_rux_1


title: Subject2_ATAC_D4_IFNy_rux_2

description: Library name: Subject2_ATAC_D4_IFNy_rux_2


title: donor procurement biopsy [D003_L]


title: NPPO-1NE, H3K27me3, Cut&Tag

description: Library name: NPPO-1NE_H3K27me3_CST

value: Prostate

value: NPPO-1NE organods


title: donor procurement biopsy [D002_P]


title: Subject2_ATAC_D4_IFNy_2

description: Library name: Subject2_ATAC_D4_IFNy_2

value: MCSF differentiated monocyte-derived macrophages


title: HPD06_on serum, RNA-Seq, Replicate 2

description: Library name: HPD06_serum_Rep_2


title: NPPO-1nonNE, H3K27me3, Cut&Tag

description: Library name: NPPO-1nonNE_H3K27me3_CST

value: NPPO-1nonNE organoids

value: Prostate non-NE tumor cells


title: donor procurement biopsy [D002_L]


title: NPPO-9, H3K36me2, Cut&Tag

description: Library name: NPPO-9_H3K36me2_abcam

value: NPPO-9 organoids


title: GG_ChIP_seq_rep2

city: Beijing

first: Falong

last: Lu

address: 1 West Beichen Road Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Clean reads were aligned to the monkey reference genome (rheMac8) by Bowtie2 with the parameters: -N 1 -L 20.
Unmapped reads, multiple mapped reads and PCR duplicates were removed by samtools and sambamba.
AG H3K27me3 peaks were called by SICER-V1.1 with the parameters: --window size 200 --gap size 200.
GG H3K27me3 peaks were called by SICER-V1.1 with the parameters: --window size 300 --gap size 1200.
rheMac8
Genome_build: bigwig files were generated using bamCoverage(v3.3.1); Scores represent RPKM.
Supplementary_files_format_and_content: peak files in bed format

organism: Macaca mulatta

source_name: GG morula

growth_protocol: AG/GG embryos were obtained and developed by Xieerxin Biology Resource and the Institute of Zoology, Chinese Academy of Sciences.

extract_protocol:
Embryos were treated with acid Tyrode’s solution to remove the zona pellucida, then washed three times with CUT&RUN wash buffer. Then embryos were incubated with a rabbit anti-H3K27me3 antibody in 50ul for 2 h at 4°C in antibody incubation buffer. After unbound antibodies were washed away, 500 ng/mL protein A-MNase was added at a 1:280 ratio and incubated for 1 h at 4°C. After washing, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, and the reaction was carried out for 30 min on ice and then stopped by adding 1/10 vol of 10× STOP buffer. The protein-DNA complexes were then released by 15-min incubation at RT followed by centrifugation at 16,000g for 5 min at 4°C. After transferring the supernatant to a new Lo-bound tube, 1/100 vol of 10% SDS and 1/80 vol of 2.5 mg/mL Proteinase K were added and incubated for at least 1 h at 55°C. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation overnight.
Sequencing libraries were prepared using a NEBNext Ultra II DNA library preparation kit for Illumina according to the manufacturer’s instructions

tag: genotype

value: GG

value: morula

tag: chip antibody


title: GG_ChIP_seq_rep1


title: AG_ChIP_seq_rep2

source_name: AG morula

value: AG


title: Subject2_ATAC_D0_IFNy_2

description: Library name: Subject2_ATAC_D0_IFNy_2


title: donor procurement biopsy [D001_L]

value: DBD - ECD

tag: donor bmi


title: AG_ChIP_seq_rep1


title: NPPO-1nonNE, H3K36me2, Cut&Tag

description: Library name: NPPO-1nonNE_H3K36me2_abcam


title: Subject2_ATAC_D0_IFNy_1

description: Library name: Subject2_ATAC_D0_IFNy_1


title: GG_WGBS_rep3

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Bismark v0.19.0 was used to align reads to rheMac8 and extract the coverage depth and methylation level of each cytosine.
Genome_build: rheMac8
Supplementary_files_format_and_content: Coverage files (using 1-based genomic genomic coordinates) that feature methylated and unmethylated counts.

extract_protocol:
Transfer the unbound chromatin to a new 1.5 ml tube. 1.2 ul 10% SDS, and 1.5 ul Proteinase K (20mg/ml) were added. Mix and incubate 60 min at 55℃. Then 20 ng carrier RNA was added. After incubation at 55°C for 1 hr, DNA was purified by extraction with phenol–chloroform and precipitated by ethanol in the presence of linear acrylamide (Life Technologies) overnight at− 20 °C. Precipitated DNA was resuspended in 24.6 μ l elution buffer and 1ul of unmethylated lambda DNA (about 0.5%) was added to a final volume 25.6ul
Sequencing libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions.


title: HPD06_on serum, RNA-Seq, Replicate 1

description: Library name: HPD06_serum_Rep_1

value: human induced pluripotent stem cells


title: HPD06 on MEFs, RNA-Seq, Replicate 1

description: Library name: HPD06_MEFs_Rep_1


title: DIPG7_IgG_rep1

city: Kensington

first: Holly

last: Holliday

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

data_processing:
Quality control analysis of CUT&RUN reads was performed using fastQC (v0.11.9).
Adapter trimming was performed using cutadapt (v4.2) with parameters: --error-rate 0.1 --times 1 --overlap 3 --action trim --minimum-length 17 --pair-filter any. Reads were aligned using bowtie2 (v2.5.0) with -k 1 against the GRCh38 human reference genome.
BAM files were sorted, and optical duplicates marked using picard (v2.27.5) with parameters: --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --VALIDATION_STRINGENCY SILENT.
Marked duplicates were filtered and removed using samtools (v1.12).
Peak calling was performed using MACS2 (v2.2.7.1) using IgG as the control. Narrow peaks parameters: --keep-dup all -p 1e-5 and broad peak using parameters: --keep-dup all -q 0.05 --broad --broad-cutoff 0.05. BigWig coverage files were generated using deeptools bamCoverage (v3.5.1) with parameters: --binSize 10 --normalizeUsing BPM --effectiveGenomeSize 2913022398. Broad peak settings were used for H3K27M and H3K27me3, and narrow peaks for SPT16, BRD4, H3K27ac, H3K4me3.
Assembly: hg38
Supplementary files format and content: narrowPeak (all except H3K27me3 and IgG), broadPeak (H3K27me3)
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

source_name: Diffuse Midline Glioma

growth_protocol: HSJD-DIPG007 cells were maintained as neurospheres in Tumour Stem Cell (TSM) media consisting of a 1:1 mixture of DMEM/F12 and Neurobasal medium (Invitrogen) supplemented with Glutamax, Pyruvate, non-essential amino acids, HEPES buffer, antibiotic/antimycotic, B-27 (Invitrogen), Heparin (0.0002%), EGF (20 ng/mL), bFGF (20 ng/mL), PDGF-AA (10 ng/mL) and PDGF-BB (10 ng/mL) (StemCell Technologies).

extract_protocol:
CUT&RUN was performed using the EpiCypher CUTANA CUT&RUN kit according to the manufacturer’s instructions. Briefly, 500,000 viable cells per reaction were washed and permeabilized with 0.01% Digitonin, which was determined to be the minimum concentration for effective permeabilization. Cells were incubated with 0.5 µg antibody, or a 1:50 dilution for SPT16, on a nutator overnight at 4°C. Following washing, pAG-MNase was added to the reactions and CaCl2 was used to activate antibody-bound MNase for targeted chromatin digestion and release of DNA fragments
The entire volume of purified DNA (ranging from 1-10 ng) was used as input for NGS library preparation, according to the EpiCypher CUTANA Library Prep Kit instructions.

treatment_protocol: for H3K27me3 CUT&RUN, HSJD-DIPG007 cells were treated with 1uM of CBL0137 for 4 hours prior to harvesting cells.

value: Diffuse Midline Glioma

tag: antibody

value: EpiCypher 13-0042


title: Subject2_ATAC_D0_unstim_2

description: Library name: Subject2_ATAC_D0_unstim_2


title: NPPO-6, H3K36me2, Cut&Tag

description: Library name: NPPO-6_H3K36me2_abcam

tag: tissue

value: NPPO-6 organoids

value: Prostate NE tumor cells


title: DIPG7_H3K4me3

value: EpiCypher 13-0041


title: Subject2_ATAC_D0_unstim_1

description: Library name: Subject2_ATAC_D0_unstim_1


title: GG_WGBS_rep1


title: AG_WGBS_rep2


title: NPPO-8, H3K36me2, Cut&Tag

description: Library name: NPPO-8_H3K36me2_abcam

value: NPPO-8 organoids

value: No


title: NPPO-2, H3K36me2, Cut&Tag

description: Library name: NPPO-2_H3K36me2_abcam

value: Prostate

value: NPPO-2 organoids


title: Anaphase stage, bio rep 2

city: Bangalore

first: Kaustuv

last: Sanyal

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Center for Advanced Scientific Research

description: Library name: Anaphase_Rep2

data_processing:
Hi-C reads obtained were aligned to the C. neoformans H99 reference genome and processed using the HiC-Pro (3.1.0) pipeline (Servant, Varoquaux et al. 2015). Fastq reads were mapped by Bowtie2 (Langmead and Salzberg 2012) (2.3.5.1) using default parameters. Multiple hits, duplicates, and singletons were removed. The read pairs were assigned to the ligated restriction site DpnII, and the invalid pairs were removed. Each replicate was processed independently, and the valid pairs were merged as one file and used for downstream analysis.
The valid pairs generated were used to create balanced mcool files using cooler
Assembly: H99 (ASM1180120v1)
Supplementary files format and content: multi resolution cool files of contact matrix binned at 2, 4, 8, 16 and 32 kb resolutions. Rep1 and Rep2 merged .mcool files are provided for each stage.

organism: Cryptococcus neoformans

source_name: Fungi

growth_protocol: C. neoformans cultures were grown and maintained on YPD media (1% yeast extract, 2% peptone, and 2% dextrose) and YPG (1% yeast extract, 2% peptone, and 2% galactose) at 30°C unless otherwise specified.

extract_protocol:
This protocol was adapted and modified from the previously published literature (Rao, Huntley et al. 2014, Belaghzal, Dekker et al. 2017, Golloshi, Sanders et al. 2018). For Hi-C library preparation, approximately 50 OD600 cells from three stages were suspended in 2% YPD and fixed with formaldehyde (3% final concentration) for 20 min and then quenched with 125mM glycine final concentration for another 20 min at room temperature. The fixed cells were washed and resuspended in 1x Tris buffer (50mM Tris-HCl pH 7.5, and 150mM NaCl) with protease inhibitor cocktail, and were lysed using a Bio-spec Bead Beater. The lysate was centrifuged, and the pellet was washed with 1x NEB DpnII buffer. The pellet was digested with DpnII, followed by 14 biotin-dCTP fill in (Jena Bioscience), ligation, decrosslinking and Phenol: Chloroform: Isoamyl alcohol purification, precipitation, followed by RNase treatment as mentioned in(Golloshi, Sanders et al. 2018). DNA was fragmented using a Covaris M220 focused ultrasonicator to produce a size range of 200 to 500 bp. Sheared DNA fragments were fractionated using AMpure XP beads and pulled down using MyOne Streptavidin C1 beads.
The on-bead DNA library preparation was carried out using NEBNext Ultra II DNA library preparation kit (E7645) as reported previously (Golloshi, Sanders et al. 2018).

treatment_protocol: To obtain synchronous populations of metaphase and anaphase cells, the cells were first synchronized using hypoxia, which resulted in unbudded G2 arrest. For metaphase arrest, hypoxia-synchronized cells were released by shifting to extensive aeration in YPGalactose (YPG) media to induce overexpression of Mps1. For the anaphase stage, hypoxia-synchronized cells were first arrested using thiabendazole (10 µg/mL) for 2 h, washed, and released into fresh YPD media.

value: Fungi

value: MAT_alpha_GAL7p-myc-MPS1-NEO, chr14, SAFE HAVEN 7, (pPEE36) TUB1-GFP-NAT

value: Hypoxia synchrony followed by thiabendazole arrest and release


title: NPPO-7, H3K36me2, Cut&Tag

description: Library name: NPPO-7_H3K36me2_abcam

value: NPPO-7 organoids

value: Prostate non-NE tumor cells


title: NPPO-1NE, H3K36me2, Cut&Tag

description: Library name: NPPO-1NE_H3K36me2_abcam

value: NPPO-1NE organods


title: Anaphase stage, biol rep 1

description: Library name: Anaphase_Rep1


title: DIPG7_SPT16_rep1


title: AG_WGBS_rep1

value: AG

value: morula


title: Ribosome profiling of elution(NAC-bound) after NAC(deltaN1-53)-IP replicate 2

description: ribosome-protected fragments

value: whole organism

value: RNAi NAC, expression twinStrep-RFP-alphaNAC(deltaN1-53)


title: GG_RNA_seq_rep2

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Paired reads were aligned with STAR_2.6.0c to rheMac8.
Gene expression of RNA-seq data were quantified using Salmon (version 0.12.0).
Genome_build: rheMac8
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: read counts in txt format

extract_protocol:
Two morula embryo samples were collected in 0.2ml Eppendorf PCR tube. And reverse transcription was performed.
cDNA amplification was performed with a SMARTer Ultra Low Input RNA cDNA preparation kit.

value: GG


title: HPD06 on MEFs, RNA-Seq, Replicate 2

description: Library name: HPD06_MEFs_Rep_2

value: human induced pluripotent stem cells


title: Metaphase stage, biol rep 2

description: Library name: Metaphase_Rep2

value: Hypoxia synchrony followed by Mps1 overexpression


title: SF8628 (T0, T1) - DIPG4 (T0, T1) - GBM43 (T0, T1)

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
CRISPR experiments were analyzed using the MAGeCK algorithm, using Robust Rank Aggregation (RRA) and total read count normalization, with default settings
Assembly: GCRh38
Supplementary files format and content: Text files containing count quantificated values for each guide/barcode in each sample
Library strategy: CRISPR-Cas9

source_name: Cell Line

extract_protocol:
Genomic DNA was extracted using QIAGEN DNeasy Blood and Tissue Kit (QIAGEN #69504) according to manufacturer’s instructions. Barcoded sequencing libraries were prepared, pooled and analyzed by paired-end sequencing using NextSeq (Illumina) for each of the three DMG cell lines. The TF domain-focused sgRNA library was comprised of ~6 sgRNA per gene (1,486 genes total, including 1,373 TFs, 62 core-essential positive controls and 51 non-targeting negative controls)
Transcription factor (TF) domain-focused sgRNA library (gift from Dr. Christopher R. Vakoc to to Dr. Zhiguo Zhang) was amplified using ElectroMAX Stbl4 Competent Cells (Invitrogen #11635018) according to manufacturer’s instructions with a representation > 1,000 and used to produce lentivirus as described above. Cas9-expressing cells were spin-infected with lentivirus of the sgRNA library at 1200 rpm at 25°C for 1 hour, with a MOI ≈ 0.3 and representation >1,000. The cells were cultured with a representation > 1,000 at any time point during the screenings. Samples were collected at starting time point (day 3 post infection, T0) and end time point (12 doubling times after starting time point, T1)

value: Cell Line


title: Metaphase stage, biol rep 1

description: Library name: Metaphase_Rep1


title: Ribosome profiling of elution(NAC-bound) after NAC(deltaN1-53)-IP replicate 1

description: ribosome-protected fragments


title: GBM22 (T0, T1) - DIPG17 (T0, T1) - KNS42 (T0, T1)


title: GG_RNA_seq_rep1


title: Ribosome profiling of input(total translatome) for NAC(deltaN1-53)-IP replicate 2

description: ribosome-protected fragments


title: G1 stage, biol rep 2

description: Library name: Interphase_G1_Rep2


title: GG_WGBS_rep2


title: NPPO-4, H3K36me2, Cut&Tag

description: Library name: NPPO-4_H3K36me2_abcam

value: NPPO-4 organoids

value: Prostate NE tumor cells

value: No


title: AG_RNA_seq_rep2


title: G1 stage, biol rep 1

description: Library name: Interphase_G1_Rep1

value: Fungi


title: Plate 1B-SF8628, Untreated, DMSO, Drugs, Replicate Plate 1A

description: De-multiplexed Gene Expression Values for each well and the corresponding metadata are provided in the two supplementary files

data_processing:
RNA-seq reads were mapped to the human reference genome version GRCh38 using Kallisto, and individual drug gene counts demultiplexed by the barcoded reads
Assembly: GCRh38
Supplementary files format and content: Tab-separated values files containing the metadata (Barocdes, Well-ID, Treatment Condition) and the count matrices

source_name: Huma DMG Cell Line (SF8626)

growth_protocol: Cells were seeded onto two 384-well tissue culture plates per cell line, as for DRC generation. The next morning, compounds were added using the Echo 550 system. Each drug was dispensed at the smaller of its previously determined EC20 concentration or its calculated Cmax (maximum tolerated serum concentration), but never above 10 μM in order to avoid confounding factors from activation of cell death and drug/stress response pathways22,81,82. The Cmax was used to avoid perturbing cells with non-physiologically relevant drug concentrations. For each cell line, two replicates were done with each plate including 372 distinct drug treatments, 6 DMSO vehicle controls, and 6 untreated samples. After 24 hours, plates were spun down at 295 × g for 1 minute. Media was removed and cells were re-suspended in 30 μL of Turbo Capture Lysis (TCL) buffer (Qiagen) containing 1% beta-mercaptoethanol (BME).

extract_protocol:
Multiplexed, low depth (< 5M reads) RNA- seq profiles at 24h following treatment of each cell line were generated for each drug, DMSO vehicle, and untreated control, using the PLATE-seq microfluidic automation platform46.
The screen was performed by the Columbia JP Sulzberger Genome Center High-Throughput Screening facility of the Herbert Irving Comprehensive Cancer Center (HICCC).

treatment_protocol: An established drug library, including 372 FDA-approved and late-stage experimental oncologic compounds, was used. To determine the maximum sublethal concentration of each drug—defined as its 48h EC20 concentration—SF8628 and DIPG6 cells were seeded onto 384-well tissue culture plates (Greiner 781080 Monroe, NC; columns 1-24, 50 μL volume of adequate media) at a density of 1,000 cells per well for DIPG6 and 500 cells per well for SF8628. Plates were incubated at room temperature for 30 minutes, and then overnight in an incubator (37°C, 5% CO2). The next morning (approximately 12 hours after seeding) compounds were added using the Echo 550 acoustic dispenser. After 40μL of media were removed from each well, each drug was dispensed in ten doses, with each plate run in triplicate. After 48 hours, 25μL of CellTiter-Glo (Promega Corp, Madison, WI) were added to each well. Plates were shaken for 5 minutes before enhanced luminescence readout (EnVision, Perkin Elmer, Shelton, CT). All values were normalized by internal DMSO controls contained on each plate and analyzed for EC20 determination using Pipeline Pilot, Dassault Systems.

value: Huma DMG Cell Line (SF8626)

value: Untreated (6 Wells) - DMSO (6 Wells) - Dugs (372 Wells)


title: DIPG7_H3K27M_rep1

value: Diffuse Midline Glioma


title: Ribosome profiling of input(total translatome) for NAC(deltaN1-53)-IP replicate 1

description: ribosome-protected fragments


title: DIPG7_BRD4_rep1

value: EpiCypher 13-2003


title: AG_RNA_seq_rep1


title: Plate 1A-SF8628, Untreated, DMSO, Drugs


title: Ribosome profiling of elution(NAC-bound) after NAC-IP replicate 2

description: ribosome-protected fragments

value: RNAi NAC, expression twinStrep-RFP-alphaNAC


title: GG_DNase_seq_rep2

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Clean reads were aligned to the monkey reference genome (rheMac8) by Bowtie2 with the parameters: -N 1 -L 20.
Unmapped reads, multiple mapped reads and PCR duplicates were removed by samtools and sambamba.
DHSs were called by Hotspot-4.1.1 with default parameters.
Genome_build: rheMac8
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage(v3.3.1). Scores represent RPKM.
Supplementary_files_format_and_content: peak files in bed format

extract_protocol:
DNase I was added to final concentration of 40 U/ml and incubated at 37°C for exactly 5 min. The reaction was stopped by adding 80 ul Stop Buffer containing 40 mg Proteinase K and 20 ng circular carrier RNA. After incubation at 50°C for 1 hr, DNA was purified by extraction with phenol–chloroform and precipitated by ethanol in the presence of linear acrylamide overnight at −20 °C. Precipitated DNA was resuspended in 25.6 μ l elution buffer.
Sequencing libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions, with the exception that the adaptor ligation was performed with 0.03 μM adaptor in the ligation reaction for 30 min at 20 °C and that PCR amplification was performed using Kapa Hifi HotStart ReadyMix for eight cycles.


title: Plate 1B-DIPG6, Untreated, DMSO, Drugs, Replicate Plate 1A

source_name: Huma DMG Cell Line (DIPG6)

value: Huma DMG Cell Line (DIPG6)


title: Subject2_ATAC_D4_IFNy_1

description: Library name: Subject2_ATAC_D4_IFNy_1

value: MCSF differentiated monocyte-derived macrophages


title: anti-FLAG Control

city: Durham

first: Michael-Christopher

last: Keogh

state: NC

address: 6 Davis Dr

institute: EpiCypher, Inc

description: Library name: anti-FLAG Control

data_processing:
Paired-end fastq files were aligned to the sacCer3 reference genome using Bowtie2 (v2.2.5).
Duplicate reads were removed via SAMtools (v1.6).
Multi-aligned reads were removed via Picard (v2.26.2).
bigWig creation included RPKM normalization via bamCoverage in deeptools (v3.5.1).
Assembly: sacCer3
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Refer to methods section of main text

extract_protocol:
Nuclei extracted from yeast cells (500K) were utilized in each reaction.
CUT&RUN Libraries were prepared using CUTANA CUT&RUN Library Prep Kit. 5 ng  of DNA was used as the starting materail for all samples. Libraries were amplified using 14 PCR cycles on the thermocycler. Post amplificaiton libraries were purified using SPRI beads. Libraries were checked on an Agilent TapeStation. Samples concentrations were normalized based on concentration in 200-700bp region prior to sequencing.

value: yeast cells

tag: primary detection_reagent

tag: secondary detection_reagent

value: anti-FLAG (ThermoFisher MA1-91878)


title: DOT5-FLAG

description: Library name: DOT5-FLAG

tag: cell type


title: GG_DNase_seq_rep1

value: GG

value: morula


title: Ribosome profiling of elution(NAC-bound) after NAC-IP replicate 1

description: ribosome-protected fragments

data_processing:
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset from the 5' end of each fragment length was estimated using Ribowaltz to assign each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribosome profiling

extract_protocol:
Frozen worm pellets were lysed using cryo-mill. Lysed samples were thawed and spun at 21,000g for 15 minutes to clear the lysate. RNA concentration of supernatant was measured and RNAse I was added to 0.4 units per ug of RNA. The sample was incubated for 45 minutes at room temperature and 0.02ul of SUPERaseIn RNAse Inhibitor was added per ug of RNA to stop digestion. Samples were immediately layered on 1M sucrose cushion and spun at 100,000rpm for 1 hour in TLA 100.3 rotor to isolate ribosomes. Resulting ribosome pellet was resuspended and RNA was extracted using TRIzol reagent following manufacturer’s instructions.
RNA fragments in the range of ~25-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints. Samples were then depleted of rRNA using Ribo-zero with the addition of custom-designed oligos to enhance depletion efficiency. Remaining RNA fragments were reverse transcribed into cDNA, followed by circularization. Libraries were barcoded during PCR amplification and sent for sequencing.

value: whole organism


title: anti-H3K4me3

description: Library name: anti-H3K4me3

value: H3K4me3 (EpiCypher 13-0041)


title: Ribosome profiling of input(total translatome) for NAC-IP replicate 2

description: ribosome-protected fragments


title: IgG Control

description: Library name: IgG Control

value: IgG Control (EpiCypher 13-0042)


title: AG_DNase_seq_rep2

value: AG


title: Ribosome profiling of input(total translatome) for NAC-IP replicate 1

description: ribosome-protected fragments


title: AG_DNase_seq_rep1


title: RelA_ChIP_seq_Nfkb1_KO_BMDC_Day5

status: Public on Dec 21 2025

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Demultiplexed reads were mapped to the NCBI37/mm9 genome using Hisat2.
Binding sites were identified using HOMER peak calling (fdr < 0.01).
Binding sites were annotated to the closest gene (mm9).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample represent the strength of binding at each genomic location.

source_name: BMDC

growth_protocol: Grown for 3-5 days in RPMI + 10% FBS + 2-BME + Pen/Strep and 100ng/mL of Flt3L at 1x10^6 cells/mL. Media is replenished on day 3.

extract_protocol:
Crosslinking conditions of 1mM DSG and 1.0% formaldehyde were used. Chromatin shearing was done using the Covaris M220. Immunoprecipitation was performed with the anti-RelA antibody.
Libraries were constructed using the Kapa LTP Library Preparation Kit according to manufacturer instructions.

value: BMDC

tag: treatment

value: Flt3 Differentiation:Day 5


title: RelA_ChIP_seq_WT_BMDC_Day3

value: Wild-type (C57/B16)

value: Flt3 Differentiation:Day 3


title: RelA_ChIP_seq_WT_BMDC_Day5


title: RelA_ChIP_seq_Nfkb1_KO_BMDC_Day3


title: CD107a+ NK cells, responsive

first: Josselyn

middle: K

last: Pena

address: 1201 Welch Rd

department: Surgery

description: Library name: Sample 1

data_processing:
Demultiplexing, barcode processing, gene counting, aggregation and alignment to the GRCh38 human reference genome was generated with the 10x Genomics CellRanger Single-Cell Software Suite (v.6.0.0).
Assembly: GRCh38 human
Supplementary files format and content: Comma separated values files and matrix files

source_name: primary NK cell

extract_protocol:
NK cells were isolated from fresh blood using a magnetic separation kit and rested overnight in complete RPMI supplemented with IL-2 (300 U/mL). Cells were cocultured with autologous EBV+ LCL for 4 hours at 37°C and 5% CO2. Cells were stained with Zombie Aqua, CD56-FITC (HCD56), CD3-PerCP-Cy5.5 (UCHT1) [Biolegend] and CD107a-efluor-660 (eBioH4A3) [eBioscience]. NK cells were sorted for live CD3−CD56+ and CD107a+/- on a BD FACSAria (BD Biosciences). Cells were washed in PBS and then pelleted for library preparation.
Library was prepared according to the manufacturer's instructions using the 3' Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics).

value: primary NK cell


title: CD107a- NK cells, nonresponsive

description: Library name: Sample 2


title: Treat3

city: Harbin

last: ZHAO

address: No. 2, Xiangjiang Road, Xiangfang District, Harbin City, Heilongjiang Province

institute: Department of Integrative Medicine (Clinical), The Third Affiliated Hospital of Heilongjiang University of Chinese Medicine.

description: Library name: TSK-3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10

organism: Rattus norvegicus

source_name: kidney

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

value: kidney


title: Treat2

description: Library name: TSK-2


title: DN6

description: Library name: Model-6


title: Treat1

description: Library name: TSK-1


title: Treat4

description: Library name: TSK-4


title: DN5

description: Library name: Model-5


title: Treat5

description: Library name: TSK-5


title: Treat6

description: Library name: TSK-6


title: DN4

description: Library name: Model-4


title: DN3

description: Library name: Model-3


title: Plate 1A-DIPG6, Untreated, DMSO, Drugs

tag: cell line

value: Untreated (6 Wells) - DMSO (6 Wells) - Dugs (372 Wells)


title: DN2

description: Library name: Model-2


title: DN1

description: Library name: Model-1


title: Ctrl6

description: Library name: NC-6


title: Ctrl4

description: Library name: NC-4


title: Ctrl3

description: Library name: NC-3


title: Input_ChIP_seq

value: Flt3 Differentiation


title: Ctrl5

description: Library name: NC-5


title: Ctrl2

description: Library name: NC-2


title: Ctrl1

description: Library name: NC-1


title: NK cells from aged donor3

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

description: Library name: old 3

data_processing:
The sequencing reads were first adapter trimmed and quality filtered. The quality filtered fastq reads were next aligned to human reference genome (GRCh38) using Hista2 with dta-cufflinks option. The aligned reads were then used for transcriptome assembly using cufflinks and finally differential expression of genes were measured by cuffdiff.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and statictical values

source_name: PBMC

extract_protocol:
Total RNA was extracted from young and old primary NK cells RNeasy kit according to the manufacturer´s instructions (Qiagen). For transcriptome analysis, 1 µg of total RNA from young and old NK cells was used.
1 µg of total RNA from young and old NK cells was first rRNA depleted using either Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, Cat # E7760L).

value: PBMC

value: Natural killer cells


title: NK cells from aged donor1

description: Library name: old 1


title: NK cells from young donor1

description: Library name: young 1


title: NK cells from young donor2

description: Library name: young 2


title: NK cells from aged donor2

description: Library name: old 2


title: NK cells from young donor3

description: Library name: young 3


title: ID77, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 5

city: Boston

first: Jonathan

middle: Andrew

last: Nowak

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

description:
Library name: Sample 724
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

data_processing:
GeoMx DSP data were pre-processed using the GeoMxTools package (version 3.8.0) in R. DCC files containing raw count data from NGS, the PKC file pertaining to the GeoMx Human WTA, and a custom-made annotation file derived from the FASTQ lab worksheet files were condensed into an object of the GeoMxSetObject class. The GeoMxSetObject contained a total of 716 areas of illumination (AOIs) prior to quality control. AOIs were excluded from further analysis based on read metrics, sequencing saturation, and nuclei count. Probes were excluded from further analysis based on count distribution across AOIs and an outlier test and were then condensed into a gene-level count matrix. Next, all AOIs with at least 1% of genes detected and all genes detected in at least 1% of AOIs were retained in the dataset. After these quality control steps, a total of 676 AOIs remained in the dataset. Batch correction was then performed using the ComBat-Seq algorithm as implemented in the sva R package (3.52.0). Finally, count data were normalized to the third quantile and log2-transformed for downstream analysis.
AOIs were excluded from further analysis based on read metrics, sequencing saturation, and nuclei count.
Probes were excluded from further analysis based on count distribution across AOIs and an outlier test and were then condensed into a gene-level count matrix.
Next, all AOIs with at least 1% of genes detected and all genes detected in at least 1% of AOIs were retained in the dataset.
Batch correction was then performed using the ComBat-Seq algorithm as implemented in the sva R package (3.52.0).
Finally, count data were normalized to the third quantile and log2-transformed for downstream analysis.
Assembly: hg38
Supplementary files format and content: DCC files: Contains target probe counts linked to one area of illumination per file with quality control metadata.
Supplementary files format and content: PKC file: Contains information regarding the Geomx Whole Transcriptome Atlas gene panel.
Supplementary files format and content: annotation_file.xlsx: Derived from lab worksheets produced from each individual run and contains relevant metadata required for analysis as published, including de-identified patient characteristics, anatomic site of origin, and time of biopsy in relation to treatment.
Supplementary files format and content: GeoMxSetObject_postQC.RDS: Third-quartile normalized and batch-corrected data object used in all downstream analysis.
Library strategy: Spatial Transcriptomics

source_name: metastatic pancreatic adenocarcinoma

extract_protocol:
Two tumor biopsies were performed on most patients. One biopsy was performed during screening and one was performed after 4-6 weeks of treatment from the same metastatic site to acquire cores for formalin-fixed, paraffin-embedded (FFPE) blocks, frozen OCT blocks, and fresh tissue studies. Slides from FFPE tissue were hematoxylin and eosin (H&E)-stained, followed by review by a pathologist. If no viable tumor was identified in FFPE cores, OCT cores were converted to FFPE blocks if available.
The GeoMx DSP libraries were prepared according to the manufacturer's instructions for the GeoMx Human Whole Transcriptome Atlas (WTA) assay.

treatment_protocol: Each treatment cycle consisted of 28 days. All patients whose samples are represented in this study received albumin-bound paclitaxel followed by gemcitabine (GA). Albumin-bound paclitaxel was administered as a 30-minute infusion at a dose of 125 mg/m2 (maximum infusion time not to exceed 40 minutes) followed by 1000 mg/m2 gemcitabine as a 30-minute infusion for three consecutive weeks followed by a week of rest (treatment on days 1, 8, and 15, during a 28-day cycle). Patients assigned to the GA plus oral placebo arm received an oral placebo taken once daily that could not be physically distinguished from the oral paricalcitol pill. Patients assigned to the GA plus intravenous (IV) paricalcitol arm were initially scheduled to receive 25 mcg of IV paricalcitol three times weekly. However, due to clinical care restrictions imposed during the COVID pandemic, the dose was reduced to 75 mcg of IV paricalcitol weekly. Only one patient received thrice weekly dosing prior to the dosing change. Patients assigned to the GA plus PO paricalcitol arm received 16 mcg of oral paricalcitol daily, which was thought to be analogous to a cumulative weekly dose as 75 mcg of IV paricalcitol based upon the bioavailability of PO paricalcitol.

value: metastatic pancreatic adenocarcinoma

tag: biopsy site

value: liver

tag: segment

tag: region of_interest_number

tag: patient id

value: Gemcitabine/Nab-Paclitaxel plus Placebo

tag: biopsy timepoint

value: pre-treatment

tag: Sex

value: M

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: age

tag: batch


title: ID77, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 5

description:
Library name: Sample 723
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Center