title: LNCaP-shTP53-1

city: Chicago

first: Young

last: Yoo

address: 303 E. Superior

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Reads were aligned to the human genome using BWA version 0.7.12-r1039
Peaks were called using HOMER version v4.11.1
Differential peak analysis was performed using HOMER v4.11.1
Assembly: hg19
Supplementary files format and content: peak files

source_name: LNCaP

extract_protocol:
Nuclei were isolated with nuclear lysis buffer (10 mM tris, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL-630) and centrifuged at low speeds. The nuclei were resuspended in 50uL of transposase reaction mixture (22.5uL nuclease-free water, 25uL of TD buffer and 2.5uL of TDE1 enzyme, Illumina #20034197). Transposition was carried out at 37°C for 30 min, followed by DNA purification with DNA Clean and Concentrator-5 kit (Zymo Research) according to the manufacturer’s recommendation
An input of 50,000 cells was first collected by low speed centrifugation (500xg), followed by washing with 1x PBS. To lyse the cells, 50 ul lysis buffer was used to suspend the cells. The cells were then incubated on ice for 5 min after brief vortexing, followed by centrifugation at 500xg at 4°C. Immediately after removal of the lysis buffer supernatant, the obtained nuclei pellet was re-suspended in the transposition reaction mix containing the Tn5 transposase, and incubated for 30 min at 37°C. After the incubation step, the reaction mix was immediately purified with the Zymo DNA Clean & Concentrator kit to stop and remove any residual Tn5 activity. A subsequent PCR amplification step with limited number of cycles was used to amplify the DNA and finish off library construction

value: LNCaP

value: Human prostate cancer

value: TP53 KD


title: LNCaP-shTP53-3

status: Public on Feb 29 2024

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype


title: Primary nasal epithelial cells, SARS-CoV-2 WA/01 infected, 96hpi, rep 3

city: Philadelphia

first: David

middle: Michael

last: Renner

state: Pennsylvania

address: 3610 Hamilton Walk

department: Microbiology

institute: University of Pennsylvania

description: Library preparation and sequencing by GeneWiz / Azenta

library_source: transcriptomic

data_processing:
Reads were trimmed for adaptor content and low quality sequences using BBDuk v38.73 (ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=20 qin=33)
Trimmed sequence reads were aligned to hg38v98 using Salmon (-p 8 --validateMappings --numBootstraps 30 --rangeFactorizationBins 4 --seqBias --gcBias)
Read count extraction and normalization were performed using DESeq2 v1.22.1
Assembly: hg38 v98
Supplementary files format and content: comma-delimited text file includes normalized counts from DESeq2 for each sample

molecule: polyA RNA

source_name: Primary nasal

growth_protocol: Sinonasal cells from four separate donors obtained from patient donors with informed consent, per protocol approved by the University of Pennsylvania Institutional Review Board (protocol #800614), were pooled together and grown to 80% confluence in in PneumaCult™-ALI Medium (STEMCELL Technologies 05001) supplemented with heparin (STEMCELLl Technologies 07980) and hydrocortisone. Once cells reach confluency in 0.4 µM pore transwell inserts, the apical growth media is removed and the basal differentiation media is replaced every 3-4 days for a minimum of 4 weeks.

extract_protocol:
Total RNA was harvested using Rneasy Mini Plus Kit (Qiagen). 2ug of RNA was sent to Azenta Life Sciences for sequencing library preparation
poly(A) selected libraries were prepared by Azenta Life Sciences

treatment_protocol:
Mucus was washed off of apical surface of cells using PBS
Cells were infected apically with each indicated virus at MOI = 0.1 for 1 hour at 37oC
Unabsorbed virus was washed off with PBS 3 times before cells were returned to 37oC and incubated for 96 hours

value: Primary nasal

value: Nasal epithelium

value: WT

tag: treatment

value: SARS-CoV-2 WA/01 Infected

tag: time


title: Library 21 mRNA

city: Leuven

first: Bart

last: De Strooper

address: Herestraat 49 box 602

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description:
10x Genomics
Mancuso2022_RNAcounts.mtx.gz
Mancuso2022_RNAcounts_genes.txt
Mancuso2022_RNAcounts_cellbarcodes.txt
Mancuso2022_NormExpr.mtx.gz
Mancuso2022_NormExpr_genes.txt
Mancuso2022_NormExpr_cellbarcodes.txt

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Genome build: Human reference, hg19 (Ensembl 87), downloaded from 10x Genomics pre-built Cell Ranger reference packages (3.0.0).
Supplementary files format and content: *.mtx.gz: Raw or SCT normalised gene expression counts per cell in a gzipped tab-separated values file.
Supplementary files format and content: *genes.txt: row names (genes) for raw or SCT normalised gene expression matrices, in txt files.

molecule: total RNA

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F, Apphu/hu or AppNL-G-FApoE-/-  mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
In this manuscript, we generated a total of 20 libraries containing 95 biological replicates for single cell RNA sequencing. In brief, we sorted 15000-20000 alive human microglia (CD11b+, hCD45+) per mouse and adjusted the final concentration to 1000 cells/µl. Out of each mouse, 2000 sorted cells were loaded into the Chromium Next GEM Chip G (PN #2000177). Since all the individual replicates were hashed using TotalSeqTM-A cell hashing antibodies, we pooled different samples into the same library. Libraries were prepared using manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). For hashtag oligo libraries, we followed manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. Libraries were sequenced on a HiSeq4000 or NovaSeq6000 (Illumina) platform with the recommended read lengths by 10X Genomics workflow targeting 90% mRNA and 10% hashtag library (50,000 reads/cell).

tag: tissue

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

tag: human cells gender

value: male

tag: mouse host gender

value: female and male

tag: timepoint

value: 3 months

tag: injection

value: Scrambled peptide, soluble amyloid-β aggregates

tag: multiplexed samples

tag: samples used for this study


title: LNCaP-shNT-3

value: control


title: Library 14 mRNA

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: female

value: 6 months


title: Library 19 mRNA

value: all


title: BMECs, POS_3, 6-h

city: Qingdao

first: Lianbin

last: Xu

address: No.700, Changcheng Road

department: College of Animal Science and Technology

country: China

institute: Qingdao Agricultural University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.20.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ensembl_bos_taurus_ars_ucd1_2_gca_002263795_2
Supplementary files format and content: FPKM.txt

organism: Bos taurus

source_name: Mammary gland

growth_protocol: Bovine mammary epithelial cells (6 passages) were grown and maintained in DMEM-F12 medium containing 1% L-glutamine with 10% (v/v) fetal bovine serum, 5 μg/mL transferrin, 5 μg/mL insulin, 5 μg/mL prolactin, 1 μg/mL hydrocortisone, 10 ng/mL epidermal growth factor, and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA was harvested according to the Trizol/Qiazol protocol (Qiagen, Cat#79306). 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.

treatment_protocol:
Cells were cultured with DMEM-F12 medium for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)

value: DMEM-F12 medium


title: BMECs, POS_4, 6-h

value: WT


title: LNCaP-shTP53-2

value: LNCaP

value: Human prostate cancer

value: TP53 KD


title: BMECs, POS_5, 6-h


title: C6

city: shenzhen

first: Zhonghao

last: Zhang

address: xueyuan

institute: shenzhen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: FPKM values and raw gene counts for each sample

organism: Mus musculus

source_name: brain

extract_protocol:
Isolated total RNA from adult microglia was used for RNA-seq analysis. cDNA library construction and sequencing were performed by Jingjie PTM BioLab (Hangzhou, China) using the Illumina platform. High-quality reads were aligned to the mouse reference genome using Hisat2 (v.2.0.5). Each sample was sequenced with a data depth of 10G. Expression levels for each of the genes were quantified by stringtie (v.2.2.0). Differential gene analysis was carried out using the DESeq2 package (v.1.20.0). Differentially expressed genes (DEGs) with ≥2-fold change and P<0.05 were identified. Gene functional annotation overrepresented by DEGs was performed using the GO (Gene Ontology) database. The gene set enrichment analysis (GSEA) was performed using the ranked list of genes based on the log-fold change obtained from the differential gene analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: strain

value: adult microglia

value: wild type (WT)


title: C4 5


title: LNCaP-shNT-2


title: Male_ACC_KO_Untrained 1

city: Durham

first: Kristina

last: Sakers

state: NC

address: 307 Research Dr

institute: Duke University

data_processing:
Reads were first processed through FastQC (v0.11.7) to check quality
Adapters were trimmed using Trimmomatic (v0.38)
Alignment was done to mm10 using STAR aligner (v2.5.3a)
Mapped reads were counted by gene using featureCounts from Subread (v1.6.3)
Assembly: mm10
Supplementary files format and content: CSV file of all samples and fragments per kilobase per million (FPKM) in each column

source_name: Brain, anterior cingulate cortex

growth_protocol: Mice were housed in a standard 12/12h light/dark cycle with access to food and water ad libitum until training at which time animals were food deprived. See methods in manuscript for full details

extract_protocol:
RNA was harvested using TriZol RNA extraction protocol and subsequently cleaned and concentrated on a Zymo Clean and Concentrator -5 kit.
Libraries were made using the Illumina TruSeq stranded mRNA kit

treatment_protocol: Mice underwent skinner box training as described in manuscript methods

value: Brain, anterior cingulate cortex

value: all brain cells (bulk RNA)

value: Thbs1/2 KO

tag: Sex

value: Male


title: LOVO_cRNA

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: Total cell RNA

data_processing:
Sequencing reads were mapped using STAR against the human genome reference (hg19), and gene level quantification was performed with featureCounts. Total counts mapped to protein-coding genes were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Comma-separated values (CSV) file with featureCounts for protein-coding genes

source_name: Large intestine; Colon

growth_protocol: All cell lines were maintained either in RPMI-1640 or DMEM medium with 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
RNA was isolated using the Roche KAPA Stranded RNA-Seq kit with RiboErase for cell lines and Invitrogen total exosome RNA & Protein Isolation kit for extracellular vesicles according to the manufacturer protocol
Roche KAPA Stranded RNA-Seq kit with RiboErase for cell lines and  SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

treatment_protocol: Not applicable

value: Large intestine; Colon

value: LoVo

value: Adenocarcinoma


title: C3


title: LNCaP-shNT-1

value: control


title: BMECs, POS_2, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)


title: Library 18 mRNA

value: Brain

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F ApoE-/-

value: male

value: female and male

value: 6 months


title: Pt13 - Day 28 - Arm B [S204]

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
library strategy: Cut&Run
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (GRCh38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38

source_name: PBMC

extract_protocol:
Briefly, isolated CD4T cells from 17 study participants in the ACTIVATE clinical trial were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac and H3K27me3 (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

value: PBMC

value: CD4 T cells

value: Day 28

tag: participant id

tag: histone mark

value: IgG

tag: group

value: Arm B

tag: participant treatment

value: panobinostat + IFN-alpha2A


title: BMECs, POS_1, 6-h

tag: cell type

tag: genotype

value: WT

value: DMEM-F12 medium


title: BMECs, Val_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with valine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

tag: treatment

tag: time


title: Library 20 mRNA

tag: tissue

tag: cell line

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F

value: female

value: all


title: Pt13 - Day 28 - Arm B [S203]


title: Library 13 mRNA

value: Brain

value: Rag2- /- Il2r{gamma}-/- hCSF1KI Apphu/hu

tag: human cells gender

tag: mouse host gender

tag: timepoint


title: Library 12 mRNA

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F ApoE-/-

tag: injection

tag: multiplexed samples

tag: samples used for this study


title: RNAseq-T-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R3

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Bulk stranded cDNA libraries were processed with the following differences compared to FACS-sorted ones. TruSeq adapter sequences instead of Nextera sequences were removed using CutAdapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). At the mapping step, the option --outSAMstrandField intronMotif was removed and the library type was set to "fr-firststrand" in Cufflinks.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Embryonic Trunk

growth_protocol: For bulk RNA-seq experiments, limbs and trunks from E14.5 mouse embryos were microdissected in PBS and dissociated in a cell suspension.

extract_protocol:
Cells were centrifuged for 5′ at 400 × g at 4 °C, supernatant was discarded, and cells frozen at −80 °C. Four biological replicates of 2× 105 cells each were used to extract total RNA using RNeasy Micro Kit (Qiagen, 74004).
Stranded mRNA Prep Ligation kit (Illumina, 20040534) was used starting from 100 ng of total RNA as input. Libraries were sequenced on an Illumina NovaSeq 6000 with single-end reads of 50 bases.

tag: background

value: Embryonic Trunk

tag: embryonic stage

tag: gfp status

value: bulk, unsorted

tag: biological replicate


title: Pt13 - Day 28 - Arm B [S202]

value: PBMC

tag: cell type

tag: participant id

tag: histone mark

tag: group

tag: participant treatment


title: RNAseq-L-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R4

source_name: Embryonic Limb

tag: tissue

value: Embryonic Limb

tag: genotype


title: BMECs, Val_4, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)

tag: treatment

value: DMEM-F12 medium devoid of all EAA and supplemented with valine

tag: time


title: RNAseq-T-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R2


title: RNAseq-T-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R4


title: RNAseq-T-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R1


title: Pt13 - Day 4 - Arm B [S201]

value: CD4 T cells

value: Day 4

value: IgG

value: Arm B

value: panobinostat + IFN-alpha2A


title: Pt13 - Day 4 - Arm B [S200]


title: BMECs, Val_2, 6-h

value: WT


title: N68

description: Healthy control

source_name: Plasma extracellular vesicles

growth_protocol: Not applicable

extract_protocol:
RNA was isolated using Invitrogen total exosome RNA & Protein Isolation kit according to the manufacturer protocol
SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

value: Plasma extracellular vesicles


title: N69

description: Healthy control


title: RNAseq-L-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R2


title: BMECs, Val_1, 6-h


title: BMECs, Val_3, 6-h


title: Pt13 - Day 0 - Arm B [S198]

value: Day 0


title: N67

description: Healthy control


title: Pt13 - Day 0 - Arm B [S197]


title: N70

description: Healthy control


title: Library 17 mRNA

value: Brain

tag: cell line

value: Microglia

tag: mouse host genotype

tag: human cells gender

value: male

tag: mouse host gender

value: female and male

tag: timepoint

value: 6 months

value: all


title: RNAseq-L-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R1

tag: background

value: Embryonic Limb

tag: embryonic stage

value: bulk, unsorted


title: BMECs, Trp_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with tryptophan for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)


title: BMECs, Val_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with valine


title: RNAseq-L-E145-Col2a1GFP;Nkx3-2ΔCE1-N1-R3

tag: gfp status

tag: biological replicate


title: N65

description: Healthy control


title: Pt13 - Day 4 - Arm B [S199]

value: PBMC

tag: cell type

value: CD4 T cells

value: Day 4

tag: participant id


title: BMECs, Trp_5, 6-h

value: WT

value: DMEM-F12 medium devoid of all EAA and supplemented with tryptophan


title: RNAseq-T-E145-Col2a1GFP;HhipΔCE2-3-R4

value: Embryonic Trunk


title: BMECs, Trp_4, 6-h


title: N64

description: Healthy control

value: Plasma extracellular vesicles


title: RNAseq-T-E145-Col2a1GFP;HhipΔCE2-3-R3


title: Pt12 - Day 28 - Arm B [S194]

value: Day 28

tag: histone mark

tag: group

value: Arm B

value: panobinostat + IFN-alpha2A


title: Pt12 - Day 28 - Arm B [S193]

tag: tissue

tag: participant treatment


title: N63

description: Healthy control


title: Pt13 - Day 0 - Arm B [S196]

value: Day 0


title: Pt12 - Day 4 - Arm B [S192]

value: IgG


title: RNAseq-T-E145-Col2a1GFP;HhipΔCE2-3-R1

tag: genotype


title: RNAseq-L-E145-Col2a1GFP;HhipΔCE2-3-R4

value: Embryonic Limb


title: BMECs, Trp_3, 6-h

tag: treatment

tag: time


title: BMECs, Trp_2, 6-h


title: RNAseq-L-E145-Col2a1GFP;HhipΔCE2-3-R3

value: bulk, unsorted


title: N61

description: Healthy control


title: N62

description: Healthy control


title: N66

description: Healthy control


title: N60

description: Healthy control


title: Pt12 - Day 4 - Arm B [S190]


title: BMECs, Thr_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with threonine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland


title: RNAseq-L-E145-Col2a1GFP;HhipΔCE2-3-R2


title: Pt12 - Day 28 - Arm B [S195]


title: BMECs, Thr_5, 6-h

value: Bovine mammary epithelial cells (bMECs)

value: DMEM-F12 medium devoid of all EAA and supplemented with threonine


title: RNAseq-T-E145-Col2a1GFP;HhipΔCE2-3-R2


title: N59

description: Healthy control


title: BMECs, Thr_4, 6-h


title: N58

description: Healthy control


title: Pt12 - Day 0 - Arm B [S189]

value: PBMC


title: RNAseq-T-E145-Col2a1GFP;Fgfr3Δhs2696-R4


title: BMECs, Thr_3, 6-h


title: RNAseq-L-E145-Col2a1GFP;HhipΔCE2-3-R1


title: Pt12 - Day 0 - Arm B [S187]

value: CD4 T cells


title: BMECs, Thr_2, 6-h


title: Pt12 - Day 4 - Arm B [S191]

value: Day 4


title: BMECs, Trp_1, 6-h

value: WT


title: N57

description: Healthy control


title: Pt15 - Day 28 - Arm C [S186]

value: Arm C


title: BMECs, Thr_1, 6-h


title: N56

description: Healthy control


title: Pt15 - Day 28 - Arm C [S185]


title: RNAseq-T-E145-Col2a1GFP;Fgfr3Δhs2696-R1

value: Embryonic Trunk


title: BMECs, Phe_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with phenylalanine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).


title: N55

description: Healthy control

value: Plasma extracellular vesicles


title: N54

description: Healthy control


title: Pt15 - Day 28 - Arm C [S184]

value: Day 28


title: N53

description: Healthy control


title: RNAseq-L-E145-Col2a1GFP;Fgfr3Δhs2696-R4


title: BMECs, Phe_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with phenylalanine


title: RNAseq-L-E145-Col2a1GFP;Fgfr3Δhs2696-R3


title: Pt15 - Day 4 - Arm C [S183]


title: Pt12 - Day 0 - Arm B [S188]

value: Arm B

value: panobinostat + IFN-alpha2A


title: BMECs, Phe_4, 6-h


title: RNAseq-L-E145-Col2a1GFP;Fgfr3Δhs2696-R2


title: N52

description: Healthy control


title: RNAseq-T-E145-Col2a1GFP;Fgfr3Δhs2696-R3


title: Pt15 - Day 4 - Arm C [S182]


title: N51

description: Healthy control


title: Pt15 - Day 4 - Arm C [S181]


title: N50

description: Healthy control


title: RNAseq-T-E145-Col2a1GFP;Fgfr3Δhs2696-R2


title: RNAseq-L-E145-Col2a1GFP;Fgfr3Δhs2696-R1


title: Pt15 - Day 0 - Arm C [S180]

value: Day 0

value: IgG


title: RNAseq-T-E145-Col2a1GFP;Δhs2697-2698-R4

value: bulk, unsorted


title: BMECs, Phe_3, 6-h

value: Mammary gland


title: Pt15 - Day 0 - Arm C [S179]


title: N49

description: Healthy control


title: N48

description: Healthy control


title: BMECs, Phe_2, 6-h

value: Bovine mammary epithelial cells (bMECs)


title: RNAseq-T-E145-Col2a1GFP;Δhs2697-2698-R2


title: BMECs, Met_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with methionine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).


title: BMECs, Met_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with methionine


title: Pt15 - Day 0 - Arm C [S178]

value: PBMC


title: N47

description: Healthy control


title: RNAseq-T-E145-Col2a1GFP;Δhs2697-2698-R1


title: N46

description: Healthy control


title: BMECs, Met_4, 6-h


title: Pt10 - Day 28 - Arm B [S176]

value: CD4 T cells


title: RNAseq-L-E145-Col2a1GFP;Δhs2697-2698-R4

value: Embryonic Limb


title: Pt10 - Day 28 - Arm B [S175]


title: RNAseq-L-E145-Col2a1GFP;Δhs2697-2698-R3


title: BMECs, Phe_1, 6-h

value: WT


title: N44

description: Healthy control


title: N45

description: Healthy control


title: Pt10 - Day 4 - Arm B [S174]

value: Day 4


title: BMECs, Met_3, 6-h


title: RNAseq-T-E145-Col2a1GFP;Δhs2697-2698-R3

value: Embryonic Trunk


title: N43

description: Healthy control

value: Plasma extracellular vesicles


title: RNAseq-L-E145-Col2a1GFP;Δhs2697-2698-R1


title: Pt10 - Day 4 - Arm B [S173]


title: BMECs, Lys_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with lysine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).


title: RNAseq-L-E145-Col2a1GFP;Δhs2697-2698-R2


title: N42

description: Healthy control


title: BMECs, Met_2, 6-h


title: Pt10 - Day 28 - Arm B [S177]

value: Day 28


title: BMECs, Met_1, 6-h


title: RNAseq-T-E145-Col2a1GFP-R4


title: N41

description: Healthy control


title: BMECs, Lys_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with lysine


title: RNAseq-T-E145-Col2a1GFP-R3


title: Pt10 - Day 4 - Arm B [S172]

value: Arm B


title: BMECs, Lys_4, 6-h


title: N40

description: Healthy control


title: Pt10 - Day 0 - Arm B [S170]

value: panobinostat + IFN-alpha2A


title: N39

description: Healthy control


title: RNAseq-T-E145-Col2a1GFP-R2


title: BMECs, Lys_3, 6-h


title: Pt10 - Day 0 - Arm B [S169]

value: Day 0


title: BMECs, Lys_1, 6-h


title: N37

description: Healthy control


title: BMECs, Lys_2, 6-h


title: N38

description: Healthy control


title: RNAseq-L-E145-Col2a1GFP-R4


title: Pt09 - Day 28 - Arm B [S167]


title: Pt09 - Day 4 - Arm B [S165]

value: IgG


title: N35

description: Healthy control


title: RNAseq-L-E145-Col2a1GFP-R2

value: bulk, unsorted


title: RNAseq-L-E145-Col2a1GFP-R3


title: RNAseq-T-E145-Col2a1GFP-R1


title: Pt09 - Day 28 - Arm B [S166]


title: BMECs, Leu_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with leucine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland


title: RNAseq-L-E145-Col2a1GFP-R1


title: Pt09 - Day 4 - Arm B [S164]


title: Pt10 - Day 0 - Arm B [S171]


title: N36

description: Healthy control


title: N33

description: Healthy control


title: BMECs, Leu_4, 6-h

value: Bovine mammary epithelial cells (bMECs)

value: DMEM-F12 medium devoid of all EAA and supplemented with leucine


title: Pt09 - Day 28 - Arm B [S168]

value: PBMC


title: Pt09 - Day 4 - Arm B [S163]

value: CD4 T cells


title: N34

description: Healthy control


title: N32

description: Healthy control


title: BMECs, Leu_5, 6-h


title: BMECs, Leu_2, 6-h


title: B2ARneg neg plus ISO MDSC, Replicate 1, scRNAseq

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Raw sequencing data were processed using Cellranger v6.0.0 software
Filtered gene-barcode matrices were used for further analyses with Seurat single cell data analysis R package.
Cells were annotated using SingleR package with ImmGen reference database
Assembly: mm10
Supplementary files format and content: gene expression count matrix

source_name: Myeloid cells

growth_protocol: WT and β2AR-/- MDSCs were generated in vitro in presence of rmIL-6 and rmGM-CFS (40 ng/mL each) and 10 µM isoproterenol (ISO).

extract_protocol:
On day 4 post differentiation, single cell libraries were generated using the 10X Genomics platform.  First, Feature Barcode conjugated molecules were bound to cell surface proteins.  Then live-CD11b+ cells were isolated using the SONY MA900 cell sorter (Sony Biotechnology).  Single-cell suspensions were pooled together and assessed with AOPI stain using a Cellometer K2 automated cell counter (Nexcelom), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells were loaded into the Chromium Controller (10X Genomics) where they were partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription was performed, and the resulting cDNA is amplified.
Amplified cDNA is separated into full-length and Feature Barcode fractions using SPRISelect beads (Beckman Coulter).  The full-length amplified cDNA was used to generate libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  Feature barcode derived cDNA was PCR amplified to incorporate Illumina adapter sequences and unique sample indexes.  The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies) and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina.  They were then pooled, denatured, and diluted to 300 pM with 1% PhiX control library added.  The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Cells were treated with 10 µM isoproterenol (ISO)

value: Myeloid cells

tag: cell line

value: Primary

value: MDSC Cells

value: B2AR KO

value: Isoproterenol


title: WT MDSC, Replicate 1, scRNAseq

value: WT


title: Pt09 - Day 0 - Arm B [S162]


title: B2ARneg neg MDSC, Replicate 1, scRNAseq


title: WT plus ISO MDSC, Replicate 1, scRNAseq


title: N31

description: Healthy control

value: Plasma extracellular vesicles


title: N30

description: Healthy control


title: N29

description: Healthy control


title: BMECs, Ile_4, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with isoleucine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).


title: N28

description: Healthy control


title: BMECs, Leu_1, 6-h


title: Pt09 - Day 0 - Arm B [S161]

value: Arm B


title: BMECs, Ile_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with isoleucine


title: E18.5 PME-1 SA2

city: yamaguchi

first: Shunta

last: Ikeda

state: yamaguchi

department: Joint faculty of veterinary medicine

country: Japan

institute: Yamaguchi University

data_processing:
The obtained next-generation sequencing data were subjected to reads cleaning with TrimGalore (version 0.6.6)
Trimmed sequence reads were mapped to the reference genome (hg38) with HISAT2 (version 2.2.1)
Read count extraction and normalization with the TPM method using StringTie (version 2.1.5)
Assembly: hg38
Supplementary files format and content: Comma-separated tab file including FPKM and TPM for each sample

growth_protocol: Mice were kept in cages with environmental enrichment placed in a temperature- and humidity-controlled room with automatic light/dark switching every 12 hours, and cages were changed once a week.

extract_protocol:
Brains were isolated from E18.5 mice. To reduce the variation among individuals, three brains were collected in one tube and designated as one sample. TRIzol Reagents (Life Technologies) was used to obtain total RNAs.
RNA libraries were prepared according to the manual using the MGIEasy RNA Directional Library Prep Set (MGI Tech Co Ltd)

value: brain

value: PME-1 S156A knock-in


title: Pt14 - Day 28 - Arm C [S158]

value: Day 28

value: Arm C


title: N27

description: Healthy control


title: BMECs, Ile_6, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)


title: Pt14 - Day 28 - Arm C [S157]

value: PBMC


title: BMECs, Ile_3, 6-h


title: E18.5 PME-1 WT3


title: BMECs, Ile_2, 6-h


title: E18.5 PME-1 SA3


title: BMECs, Ile_1, 6-h


title: Pt09 - Day 0 - Arm B [S160]

value: CD4 T cells

value: Day 0

value: panobinostat + IFN-alpha2A


title: N25

description: Healthy control


title: N26

description: Healthy control


title: E18.5 PME-1 WT2


title: Pt14 - Day 28 - Arm C [S159]

value: IgG


title: E18.5 PME-1 WT1


title: BMECs, His_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with histidine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).


title: N24

description: Healthy control


title: E18.5 PME-1 SA1


title: Pt14 - Day 4 - Arm C [S154]

value: Day 4


title: postnatal 14 days, male replicate 2, scRNAseq

city: Kansas City

first: C.

middle: Ron

last: Yu

state: MO

department: Yu Lab

institute: Stowers Institute For Medical Research

description: 10x Genomics

data_processing:
Gene by cell-barcode count matrices were generated from raw FASTQ files using the kallisto|bustools (v0.48.0|v0.41.0) workflow with the Mus musculus genome assembly GRCm39 (mm39) and GTF gene annotation files retrieved from ENSEMBL release 104. All downstream QC-filtering and analysis was performed in an R environment (v4.0.3). Empty droplets were estimated and filtered from the data using the barcodeRanks function of the DropletUtils package (v1.10.3). The count data was imported into R (v4.0.3) with the Seurat package (v4.3.0) and ambient RNA contamination was automatically estimated with the autoEstCont function and removed with the adjustCounts function from the SoupX package (v1.5.2). Cell barcodes representing multiplets were identified and removed with Scrublet (v0.2.3) interfacing with Python using reticulate (v1.30). Cell barcodes expressing <750 genes, >2.5 standard deviations above the mean number of genes or counts, or >5% of reads originating from mitochondrial genes were removed.
Assembly: mm39
Supplementary files format and content: tab separated text files, genes/rows, cell-barcodes/columns

source_name: Vomeronasal Organ

extract_protocol:
Mice VNOs were dissected in cold oxygenated ACSF following Ma et al, 2011. Dissected epitheliums were dissociated in papain solution (20mg/mL papain and 3mg/mL L-cysteine in HBSS) with RNase-free DNase I (10unit) at 37°C for 15-20 minutes. 0.01% BSA in PBS was added to the digestion solution before filtering with 70µm and 30µm filters (pluriSelect). Dissociated cells were washed twice in 0.01% BSA with final volume 1mL, followed by Draq5 (25µM) and DAPI (0.5µg/mL) staining 5min on ice. Draq5+/DAPI- cells (live/nucleated cells) were sorted on BD Influx cytometer (BD Bioscience) with 100µm nozzle. Dissociated sorted cells were assessed for concentration and viability via Luna-FL cell counter (Logos Biosystems). Cells deemed to be at least 90% viable were loaded on a Chromium Single Cell Controller (10x Genomics), based on live cell concentration.
Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions. Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific). With cells captured estimated at ~5,500-8,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 40,000 mean reads per cell on an Illumina NovaSeq 6000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*8*91bp.

value: Vomeronasal Organ

tag: Sex

value: male

tag: age

value: postnatal 14 days


title: BMECs, His_5, 6-h

value: WT

value: DMEM-F12 medium devoid of all EAA and supplemented with histidine


title: N23

description: Healthy control

value: Plasma extracellular vesicles


title: BMECs, His_4, 6-h


title: N22

description: Healthy control


title: Pt14 - Day 4 - Arm C [S156]


title: Pt14 - Day 0 - Arm C [S152]


title: postnatal 14 days, female replicate 2, scRNAseq

description: 10x Genomics

value: female


title: N21

description: Healthy control


title: BMECs, His_3, 6-h


title: Pt14 - Day 0 - Arm C [S153]


title: postnatal 14 days, male replicate 1, scRNAseq

description: 10x Genomics


title: BMECs, His_2, 6-h


title: N20

description: Healthy control


title: postnatal 14 days, female replicate 1, scRNAseq

description: 10x Genomics


title: postnatal 56 days, female replicate 2, scRNAseq

description: 10x Genomics

value: postnatal 56 days


title: Pt14 - Day 4 - Arm C [S155]

value: Arm C


title: Pt14 - Day 0 - Arm C [S151]


title: N19

description: Healthy control


title: Pt02 - Day 28 - Arm A [S149]

value: Day 28

value: Arm A

value: panobinostat


title: postnatal 56 days, female replicate 1, scRNAseq

description: 10x Genomics


title: Pt02 - Day 28 - Arm A [S148]

value: PBMC

value: CD4 T cells


title: BMECs, Arg_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA and supplemented with arginine for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)


title: N18

description: Healthy control


title: postnatal 56 days, male replicate 2, scRNAseq

description: 10x Genomics


title: N17

description: Healthy control


title: postnatal 56 days, male replicate 1, scRNAseq

description: 10x Genomics


title: BMECs, Arg_5, 6-h

value: DMEM-F12 medium devoid of all EAA and supplemented with arginine


title: Pt02 - Day 4 - Arm A [S147]

value: Day 4

value: IgG


title: BMECs, Arg_4, 6-h


title: N16

description: Healthy control


title: Pt02 - Day 28 - Arm A [S150]


title: Pt02 - Day 4 - Arm A [S146]


title: BMECs, Arg_2, 6-h


title: N14

description: Healthy control


title: BMECs, Arg_3, 6-h


title: Pt02 - Day 0 - Arm A [S144]

value: Day 0


title: Input

city: Changsha

first: Qin

last: Zeng

address: Renmin Middle Road

institute: The Second Xiangya Hospital of Central South University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output
The raw data was filtered using the software NGS QC Toolkit (Patel & Jain, 2012) to filter out low-quality sequences, N-containing sequences, and linker-containing sequences. The filtering criteria are as follows:1. Reads pairs with a high N content. If the N content of a read exceeds 5%, the entire pair of reads is removed; 2. Low quality rate high reads pairs. If the low-mass bases (bases with a mass value of 20 or less) in a read exceed 30%, removes the entire pair of reads. 3. Read pairs with adapter. If there is a sequence containing an adapter in the reads, the entire pair of reads is removed.
ChIP-seq reads were aligned to UCSC mm10 genome using bowtie1. Only uniquely mapping reads with at most two mismatches were retained
Peaks were called using MACS v2.1.0 with the significance cut-off p-value <= 1e-5
Peak calling is performed using MACS2 for analysis.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: inguinal white adipose tissue

growth_protocol: The SVF fraction was resuspended in DMEM/F12 plus 10% FBS, 100 IU/mL of penicillin, 100 mg/mL of streptomycin solution, and β-FGF (10 ng/mL, PeproTech, Cat#450-33,), at 5% CO2 and 37 °C in a humidified cell incubator. After seeding, the medium was changed 24 hours later to remove non-adherent cells and obtain mouse adipose-derived stem cells (ASCs). All experiments were conducted using cells at passage 3. For adipogenesis, confluent ASCs was used and treated with adipocyte differentiation induction cocktail: 0.5 mM IBMX, 1 μM dexamethasone, 10 μg/mL insulin, followed by maintenance treatment (10 μg/mL insulin) every 48 hours.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using Non-contact ultrasonicator (SCIENTZ08-IIIC)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation kit complemented with NEXTflex DNA Barcodes from Bioo Scientific.

value: inguinal white adipose tissue

value: primary ASCs that were induced to differentiate into mature adipocytes in vitro


title: BMECs, His_1, 6-h

value: WT

value: DMEM-F12 medium devoid of all EAA and supplemented with histidine


title: BMS-584929, rep2

city: Wuhan

first: cheng

last: xu

state: Hubei

address: Sanjiaohu Road

institute: Jianghan University

data_processing:
The quality of raw data was evaluated using Fastp (v0.22.0)
Sequencing reads were trimmed for adaptor/low-quality sequence using Trimmomatic (v0.36)
Clean data were aligned to reference genome via software Hisat2 (v2.0.4)
Quantification of gene expression level were estimated by fragments per kilobase of transcript per million fragments mapped
Differential expression analysis of two conditions/groups was performed using the DESeq2 (v1.30.1)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes counts from osteoclasts treated with Ctrl and 10 μM BMS-582949.

source_name: osteoclasts

growth_protocol: Mouse bone marrow cells from Wt mice were extracted and cultured for 3 days in α-MEM medium with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and L929 cell supernatant, which contained the equivalent of 20 ng/ml of murine rM-CSF and was used as a source of M-CSF.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent.
RNA libraries for sequencing were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: For osteoclast differentiation, the attached bone marrow-derived macrophages (BMMs) were scraped, and 4.5×104 cells/cm2 were seeded in α-MEM medium with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and CM for overnight, and then stimulated by 40 ng/ml RNAKL and 10 μM BMS-582949 for 4 days.

value: osteoclasts

value: Wt


title: N13

description: Healthy control

value: Plasma extracellular vesicles


title: BMS-584929, rep1


title: ChIP


title: BMECs, Arg_1, 6-h


title: N12

description: Healthy control


title: Pt02 - Day 0 - Arm A [S143]

value: Arm A


title: BMECs, NEG_6, 6-h

treatment_protocol:
Cells were cultured with DMEM-F12 medium devoid of all EAA for 6-h
Bovine mammary epithelial cells cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6).

value: DMEM-F12 medium devoid of all EAA


title: Ctrl, rep2

value: DMSO


title: BMECs, NEG_5, 6-h


title: Pt07 - Day 28 - Arm B [S141]

value: PBMC

value: CD4 T cells

value: Day 28

value: Arm B

value: panobinostat + IFN-alpha2A


title: Ctrl, rep1


title: Pt02 - Day 4 - Arm A [S145]

value: Day 4

value: panobinostat


title: N15

description: Healthy control


title: N10

description: Healthy control


title: Pt07 - Day 28 - Arm B [S140]


title: BMECs, NEG_4, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)


title: N9

description: Healthy control


title: Pt07 - Day 28 - Arm B [S139]


title: CTNB ckit+ BM, FLAG, replicate 1, CUT&RUN

city: London

first: Eric

last: So

address: School of Cancer and Pharmaceutical Sciences

country: United Kingdom

institute: KCL

data_processing:
Cut&Run analysis was conducted using the CUT&RUNTools pipeline with default parameters,including read trimming, alignment, and peak calling. Reads were aligned to the reference mouse genome GRCm38.
Peak calling was carried out utilizing MACS2 (IgG used as control), and the identified peaks were used to generate heatmaps and profile plots.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&RUN

source_name: HSPCs

extract_protocol:
CUT&RUN was performed according to Epicypher CUT&RUN Protocol V2.0. Briefly, 0.5 million ckit + HSPCs from WT BL6 mice or Ctnnb1-Biotin-3xFLAG knockin mice (JAX:029511) were rinsed with wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Complete Protease Inhibitor Cocktail) and incubated with the activated Concanavalin A (ConA) beads (Bangs Laboratories BP531) at RT for 10 min. 0.5 μl antibody (HOXA9 Atlas HPA061982, FLAG Genscript A00170, IgG Cell Signaling Technology 3900S DA1E) was added and incubated at 4 °C overnight. After permeabilization with digitonin buffer (wash buffer plus 0.01% digitonin), 20 ng pAG-MNase (kindly provided by Dr Paul Lavender, King’s College London) was added and bound to antibody-labelled chromatin. MNase was subsequently activated by addition of CaCl 2 to cleave and release antibody-bound chromatin. DNA purification was performed using Monarch PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, T1030).
DNA libraries were prepared using the NEB Ultra II DNA Library Prep Kit (NEB #E7103) and sequencing was carried out by Novogene UK.

value: HSPCs

value: FLAG antibody


title: CTNB ckit+ BM, IgG, replicate 1, CUT&RUN

value: IgG antibody


title: N8

description: Healthy control


title: BMECs, NEG_3, 6-h

value: WT


title: N7

description: Healthy control

value: Plasma extracellular vesicles


title: Pt07 - Day 4 - Arm B [S138]

value: IgG


title: Pt02 - Day 0 - Arm A [S142]

value: Day 0

value: Arm A


title: ckit+ WT ms BM, HOXA9, replicate 2, CUT&RUN

value: HOXA9 antibody


title: N11

description: Healthy control


title: ckit+ WT ms BM, IgG, replicate 2, CUT&RUN


title: N6

description: Healthy control


title: ckit+ WT ms BM, HOXA9, replicate 1, CUT&RUN


title: N5

description: Healthy control


title: Pt07 - Day 0 - Arm B [S135]

value: PBMC

value: CD4 T cells


title: ckit+WT ms BM, IgG, replicate 1, CUT&RUN


title: N4

description: Healthy control


title: RNAseq_70m_2

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
library strategy: Ribosome profiling
Base calling was performed on-instrument
3' adaptor sequence was removed using Cutadapt and custom python script to track unique molecular identifier (NNNNNN)
Reads mapping to non-coding RNAs were removed by aligning using Bowtie1 to a collection of RNA genes downloaded from Saccharomyces Genome Database. We allowed a 3-nt 3’ mismatch when mapping to tRNAs to account for non-templated CCA addition on mature tRNAs. Remaining reads were then aligned allowing two mismatches  using Tophat2
RNA-seq normalization to spike-ins was performed by dividing the raw read count at each position by the number of spike-in reads in the library (rps, reads per spike-in).
RNA-seq reads were also normalized to total nuclear or mitochondrial mRNA mappers, as were cytoribosome profiling and mitoribosome profiling reads, respectively (rpm, reads per million)
Read counts were normalized to the total number of filtered mappers (rpm, reads per million). To determine expression values for each gene, rpm values were summed across ORFs and normalized to ORF length (RPKM, normalized reads per kilobase). For ribosome profiling reads, the first and last five codons were excluded to remove effects of translation initiation and termination.
Translation efficiency (TE) was calculated by dividing ribosome profiling RPKM values by RNA-seq RPKM values.
Scripts for measurements described above were written in Python 2.7.5
Assembly: Saccharomyces cerevisiae  assembly R64 (UCSC: sacCer3)
Supplementary files format and content: "RP" files list RPKM counts for each time point for ribosome profiling data. These are NOT normalized to RNA abundance.
Supplementary files format and content: "TE" files list ribosome profiling RPKM values divided by RNA-seq RPKM values. Genes with an RPKM value of 2 or less are excluded
Supplementary files format and content: "RNA" files list RPKM counts for each time point for RNA-seq data.

organism: Saccharomyces cerevisiae

source_name: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1Δ::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1Δ ura3Δ0 his3Δ1 leu2Δ0 met15Δ0

growth_protocol: Cells were grown overnight at 25oC in YEPD to saturation and then diluted to OD600 ~0.013 in 2 L YEPD and allowed to grow for another ~16 hours until reaching OD600 ~0.1-0.3. Yeast cells were arrested in α-factor using standard protocols107. Briefly, α-factor was added at a concentration of 5 μg/mL and cells were allowed to grow at 30oC for 1.5 doublings (~2 hours). Shmoo-ing morphology was confirmed using light microscopy prior to washing. Cells were filtered onto nitrocellulose membranes and re-suspended in cold YEPD for two wash cycles before being re-suspended in RT YEPD to OD600~0.4. Cells were shaken in 3x2 L flasks at 30oC. At 10-minute intervals, 250 mL of cells were filtered onto nitrocellulose membranes and flash frozen on membranes in 15 mL falcon tubes. Concurrently, ~40 μL cells were pipetted into a single well in a 384-well Cell Carrier Ultra plate (Perkin ElmervPart No. 6057300), spun down at ~500 rpm for 30 seconds and imaged on the Opera Phenix using the same parameters outlined above. Samples were collected for 2 hours on two separate occasions, producing 2x13 sample replicates. Using manual image inspection, we quantified the fraction of cells in each of the six cell cycle stages used during our proteomics assays, and selected the five samples in each replicate that demonstrated the greatest synchrony to each of these stages (excluding G1 Pre-START)

extract_protocol:
Frozen cells on nitrocellulose membranes were placed in metal casings with frozen lysis buffer to a total of 4 g. Samples were harvested four at a time by placing two casings containing separate samples in a mixer mill and grinding for 3 minutes at 15 Hz, while two other casings were submerged in liquid nitrogen. Casings were swapped for six rounds of grinding, after which samples were scraped into 50 mL eppendorf tubes with a pre-chilled spatula. Lysates were pre-cleared by spinning at 3000xg for 5 minutes at 4oC, supernatant was transferred to a fresh eppendorf tube and then cleared by spinning at 20,000xg for 10 minutes at 4oC. Samples were distributed into 250 μL aliquots and flash frozen in liquid nitrogen
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter (5′ /5rApp/NNNNNNCTGTAGGCACCATCAAT/3ddC/3′). Superscript III was used for reverse transcription (with primer 5′ /5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTC/iSp18/CACTCA/ iSp18/CAAGCAGAAGACGGCATACGAGATATTGATGGTGCCTACAG 3′) and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

tag: culture condition

value: YEPD

tag: molecule subtype

value: rRNA-depleted RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: Pt07 - Day 0 - Arm B [S134]

value: Arm B

value: panobinostat + IFN-alpha2A


title: RNAseq_70m_1


title: E18 MPP4 biol rep 3

first: Melissa

last: Proven

institute: Columbia Unversity

data_processing:
Sequencing QC was performed using FastQC and MultiQC.
Paired-end reads were mapped to the mouse reference genome (GRCm38 ver104) using STAR and quantified with Feature Counts
Assembly: GRCm38 ver104
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

source_name: fetal liver

extract_protocol:
RNA was isolated from 5000 - 20,000 HSPCs using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA integrity number (RIN) was determined by Bioanalyzer (Agilent Technologies) and RNA samples with RIN > 9.0 were further processed. RNA samples were processed over multiple experimental “sort days” and stored at -80°C in RNA isolation buffer until library preparation. A total of 3biological replicates were sequenced for each population. RNA was quantified and QC using an Agilent Bioanalyzer. Illumina sequencing libraries were prepared and sequenced at the NYU Genome Technology Center (New York, NY).
The NuGen Ovation Trio low input RNA-seq library preparation kit was used for library preparation.
All libraries were prepared at the same time in order to minimize batch effects. Libraries were sequenced using an Illumina NovaSEQ 6000 instrument with paired end 50 base pair sequencing to a target depth of 40 million unique reads per sample.

value: fetal liver

value: pooled male and female

value: C57Bl/6 wild-type

value: steady state isolation


title: N3

description: Healthy control


title: Pt07 - Day 4 - Arm B [S136]

value: Day 4


title: BMECs, NEG_2, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)

value: WT

value: DMEM-F12 medium devoid of all EAA


title: Pt07 - Day 0 - Arm B [S133]

value: Day 0


title: E18 MPP4 biol rep 2


title: BMECs, NEG_1, 6-h


title: RNAseq_60m_2


title: RNAseq_90m_1


title: N2

description: Healthy control

value: Plasma extracellular vesicles


title: RNAseq_90m_2


title: Pt06 - Day 28 - Arm B [S131]

value: PBMC

value: CD4 T cells

value: Day 28


title: E18 MPP3 biol rep 3


title: RNAseq_60m_1

value: YEPD

value: rRNA-depleted RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: RNAseq_50m_2


title: Pt06 - Day 28 - Arm B [S130]

value: Arm B

value: panobinostat + IFN-alpha2A


title: E18 MPP4 biol rep 1

value: fetal liver

value: pooled male and female

value: C57Bl/6 wild-type


title: PC9-C2 osi t9 rep 3, L0131 barcod DNAseq

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1. and cell hashes were called using the scEasyMode package in Python.
A custom script for calling genomic barcodes mapping between single-cell genomic barcodes and bulk genomic barcodes collected from the same samples was used to assess population frequency and map onto single-cell transcriptomes.
Assembly: GRCh38/hg38
Supplementary files format and content: Comma separated values files and matrix files

source_name: Lung cancer

growth_protocol: A BFP-tagged barcode library (Addgene #85968) was delivered via lentiviral infection into isogenic EGFR-mutant PC9-C2 and H1975-B10 cells. Cells were sorted and serially titrated to allow for ~1000 unique barcode groups.

extract_protocol:
RNA was extracted from snap-frozen tissue or cell pellets. For tissue samples, tissue was minced using a liquid nitrogen-cooled mortar and pestle before RNA extraction. RNA isolation was performed using the RNeasy Mini kit (Qiagen) including an on-column DNase I digestion. RNA quality was assessed by automated electrophoresis using the RNA 6000 Pico Kit and an Agilent 2100 BioAnalyzer (Agilent Technologies, Inc.). RNA was quantified using the Qubit RNA HS Assay Kit and a Qubit 2.0 fluorometer (Thermo Fisher Scientific).
Cells were thawed, hashed with TotalSeq A anti-human hashtag antibodies (BioLegend), prepared as specified by BioLegend. Custom barcode amplification was performed by two rounds of PCR. Libraries were sequenced on the NovaSeq Illumina platform (Center for Advanced Technology, UCSF).

treatment_protocol: After expansion, cells were subjected to 0.1% DMSO or 2 µM osimertinib treatment and frozen down at the indicated timepoints.

value: Lung cancer

value: drug-tolerant persister

value: 2 uM osimertinib


title: RNAseq_40m_1


title: PC9-C2 osi t9 rep 2, L0130 barcod DNAseq


title: Pt06 - Day 4 - Arm B [S129]

value: Day 4

value: IgG


title: PC9-C2 osi t9 rep 1, L0129 barcod DNAseq


title: Pt06 - Day 4 - Arm B [S128]


title: E18 MPP2 biol rep 3

value: steady state isolation


title: RNAseq_20m_1


title: PC9-C2 osi t2 rep 2, L0127 barcod DNAseq

value: acute


title: Pt06 - Day 4 - Arm B [S127]

value: PBMC

value: CD4 T cells


title: RNAseq_20m_2

value: YEPD


title: E18 MPP3 biol rep 1


title: RNAseq_0m_1

value: rRNA-depleted RNA


title: Pt07 - Day 4 - Arm B [S137]


title: PC9-C2 osi t2 rep 1, L0126 barcod DNAseq


title: Pt06 - Day 0 - Arm B [S126]

value: Day 0


title: E18 MPP2 biol rep 2


title: E18 MPP2 biol rep 1


title: N1

description: Healthy control

value: Plasma extracellular vesicles


title: E18 MPP3 biol rep 2


title: Pt06 - Day 0 - Arm B [S125]

value: Arm B

value: panobinostat + IFN-alpha2A


title: E18 HSC biol rep 3

value: fetal liver

value: pooled male and female


title: PC9-C2 ctrl t2 rep 3, L0125 barcod DNAseq

value: Lung cancer

value: parental

value: untreated 0.1% DMSO 3d


title: BMECs, Leu_3, 6-h

value: Mammary gland

value: Bovine mammary epithelial cells (bMECs)

value: WT

value: DMEM-F12 medium devoid of all EAA and supplemented with leucine


title: Pt06 - Day 28 - Arm B [S132]

value: PBMC

value: Day 28

value: IgG


title: E18 HSC biol rep 2

value: C57Bl/6 wild-type

value: steady state isolation


title: Pt06 - Day 0 - Arm B [S124]

value: CD4 T cells

value: Day 0


title: CytoRP_90m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt

data_processing:
library strategy: Ribosome profiling
library strategy: Ribosome profiling
Base calling was performed on-instrument
3' adaptor sequence was removed using Cutadapt and custom python script to track unique molecular identifier (NNNNNN)
Reads mapping to non-coding RNAs were removed by aligning using Bowtie1 to a collection of RNA genes downloaded from Saccharomyces Genome Database. We allowed a 3-nt 3’ mismatch when mapping to tRNAs to account for non-templated CCA addition on mature tRNAs. Remaining reads were then aligned allowing two mismatches  using Tophat2
RNA-seq normalization to spike-ins was performed by dividing the raw read count at each position by the number of spike-in reads in the library (rps, reads per spike-in).
RNA-seq reads were also normalized to total nuclear or mitochondrial mRNA mappers, as were cytoribosome profiling and mitoribosome profiling reads, respectively (rpm, reads per million)
Read counts were normalized to the total number of filtered mappers (rpm, reads per million). To determine expression values for each gene, rpm values were summed across ORFs and normalized to ORF length (RPKM, normalized reads per kilobase). For ribosome profiling reads, the first and last five codons were excluded to remove effects of translation initiation and termination.
Translation efficiency (TE) was calculated by dividing ribosome profiling RPKM values by RNA-seq RPKM values.
Scripts for measurements described above were written in Python 2.7.5
Assembly: Saccharomyces cerevisiae  assembly R64 (UCSC: sacCer3)
Supplementary files format and content: "RP" files list RPKM counts for each time point for ribosome profiling data. These are NOT normalized to RNA abundance.
Supplementary files format and content: "TE" files list ribosome profiling RPKM values divided by RNA-seq RPKM values. Genes with an RPKM value of 2 or less are excluded
Supplementary files format and content: "RNA" files list RPKM counts for each time point for RNA-seq data.

value: YEPD

value: cytoribosome-associated RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: Pt01 - Day 28 - Arm A [S123]

value: Arm A

value: panobinostat


title: PC9-C2 ctrl t2 rep 2, L0124 barcod DNAseq

value: Lung cancer

value: parental

value: untreated 0.1% DMSO 3d


title: E18 HSC biol rep 1

value: fetal liver

value: pooled male and female


title: PC9-C2 osi t2 rep 3, L0128 barcod DNAseq

value: acute

value: 2 uM osimertinib


title: PC9-C2 ctrl t2 rep 1, L0123 barcod DNAseq


title: Pt01 - Day 28 - Arm A [S122]

value: PBMC

value: Day 28


title: PC9-C2 ctrl t0 rep 3, L0122 barcod DNAseq


title: RNAseq_0m_2

value: rRNA-depleted RNA


title: Adult MPP4 biol rep 2

source_name: bone marrow

value: bone marrow

value: 8-12 weeks

value: C57Bl/6 wild-type

value: steady state isolation


title: CytoRP_70m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt

value: YEPD

value: cytoribosome-associated RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: CytoRP_70m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: Pt01 - Day 4 - Arm A [S120]

value: CD4 T cells

value: Day 4

value: IgG

value: Arm A

value: panobinostat


title: CytoRP_60m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: Adult MPP4 biol rep 1

value: pooled male and female


title: PC9-C2 ctrl t0 rep 1, L0120 barcod DNAseq

value: Lung cancer

value: parental

value: untreated 0.1% DMSO 3d


title: Pt01 - Day 28 - Arm A [S121]

value: PBMC

value: Day 28


title: CytoRP_90m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: CytoRP_60m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt


title: Adult MPP3 biol rep 3

value: bone marrow

value: 8-12 weeks


title: PC9-C2 ctrl t0 rep 2, L0121 barcod DNAseq


title: Pt01 - Day 4 - Arm A [S119]


title: CytoRP_50m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: Pt01 - Day 4 - Arm A [S118]


title: PC9-C2 ctrl-trt all samples batch 7 scRNAseq

description: 10x Genomics

value: drug-tolerant persister

value: 2 uM osimertinib


title: Adult MPP3 biol rep 2

value: C57Bl/6 wild-type

value: steady state isolation


title: CytoRP_40m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt

value: YEPD

value: cytoribosome-associated RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: PC9-C2 ctrl-trt all samples batch 6 scRNAseq

description: 10x Genomics

value: acute


title: Pt01 - Day 0 - Arm A [S116]

value: CD4 T cells

value: Day 0

value: Arm A

value: panobinostat


title: Pt01 - Day 0 - Arm A [S117]

value: IgG


title: Adult MPP4 biol rep 3

value: pooled male and female


title: CytoRP_20m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt


title: Adult MPP2 biol rep 3


title: Pt01 - Day 0 - Arm A [S115]

value: PBMC


title: Pt05 - Day 28 - Arm B [S114]

value: Day 28

value: Arm B

value: panobinostat + IFN-alpha2A


title: Adult MPP2 biol rep 2

value: bone marrow

value: 8-12 weeks


title: CytoRP_0m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: PC9-C2 ctrl-trt all samples batch 4 scRNAseq

description: 10x Genomics

value: Lung cancer

value: parental

value: untreated 0.1% DMSO 3d


title: Adult MPP2 biol rep 1

value: C57Bl/6 wild-type

value: steady state isolation


title: CytoRP_0m_1

description:
RP_AF1_RPKM.txt
TE_AF1_Cutoff_2RPKM.txt

value: YEPD

value: cytoribosome-associated RNA

value: MATa DAD2-GFP::HIS3 CAN1pr::TDH3pr-E2Crimson::HPH::can1{delta}::STE2pr-LEU2 HTA2-mCherry::CaURA3 CDC11-TagRFP::natMX lyp1{delta} ura3{delta}0 his3{delta}1 leu2{delta}0 met15{delta}0


title: PC9-C2 ctrl-trt all samples batch 8 scRNAseq

description: 10x Genomics

value: drug-tolerant persister

value: 2 uM osimertinib


title: PC9-C2 ctrl-trt all samples batch 5 scRNAseq

description: 10x Genomics

value: acute


title: PC9-C2 ctrl-trt all samples batch 1 scRNAseq

description: 10x Genomics


title: PC9-C2 ctrl-trt all samples batch 2 scRNAseq

description: 10x Genomics


title: Pt05 - Day 28 - Arm B [S112]

value: PBMC

value: CD4 T cells


title: P78-3

value: Plasma extracellular vesicles

tag: disease stage

value: Metastatic colorectal cancer

tag: disease status

value: Progression


title: Ferulic Acid Rep 3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: Ferulic Acid

data_processing:
All paired-end FASTQ files were processed through the same pipeline. Reads were trimmed using Trimmomatic version 0.3  with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming, the reads were aligned to the N. aromaticivorans DSM12444 genome sequence (GenBank accession GCF_000013325.1) using bwa-mem (version 0.7.17-h5bf99c6_8)  with default settings. Alignment files were further processed with Picard-tools (version 2.26.10) (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools (version 1.2)  (sort and index commands). Paired aligned reads were mapped to gene locations using HTSeq version 0.6.0. The R package edgeR (version 3.30.3) with default settings was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold (57). Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: GCF_000013325.1
Supplementary files format and content: Metz_htseq_counts.txt contains the RAW gene counts for the experiments as determined by Htseq-count
Supplementary files format and content: Metz_FPKM_results.xlsx contains the FPKM normalized read counts for all experiments

organism: Novosphingobium aromaticivorans DSM 12444

growth_protocol: Four isolated N. aromaticivorans PDC12444 colonies were cultured and grown overnight. The next day, the overnight cultures were diluted 1:1 with SMB minimal medium supplemented with 1g/L glucose and grown for one hour. The cultures were then diluted 1:100 into separate cultures of SMB minimal medium supplemented with 1g/L glucose, 1g/L glucose plus 0.5mM DC-A, 1g/L glucose plus 0.5mM vanillin, or 1g/L glucose plus 0.5mM ferulic acid. These cultures were grown until they reached mid-exponential growth phase.

extract_protocol:
The cells were pelleted by centrifugation (4,300 x g for 10 minutes) at 4°C and stored at -80°C. Cell pellets were resuspended in 2 mL of lysis solution (2% sodium dodecyl sulfate, 16mM EDTA, RNase-free water) and heated at 65°C for 5 minutes. Nucleic acids were extracted using 2 mL of acidic phenol:chloroform heated to 65°C, mixed by inversion, incubated at 65°C for 5 minutes, and centrifuged at room temperature for 7 minutes at 20,000 x g. The aqueous phase was removed, extracted twice more, before addition of 2 mL of chloroform, mixed, and centrifuged once more at room temperature for 7 minutes at 20,000 x g. The aqueous layer was removed and mixed with 1/10 volume of 3M sodium acetate and equal volume of isopropanol, and incubated at -20°C for >1 hour to precipitate nucleic acids that were collected by centrifugation at 4°C for 30 minutes at 16,000 x g. The pellet was washed twice with 1 mL of 75% EtOH (prepared with RNase-free water). Once residual ethanol was removed by evaporation, the pellet was resuspended in 85 μL of RNase-free water. Samples were treated with RNase-free DNase (10 μL 10x DNase buffer, 2 μL DNase, 3 μL RNasin (Promega)) and purified using RNeasy kit (Qiagen).
RNA-seq library preparation and sequencing was performed by the Joint Genome Institute (JGI) using default parameters. rRNA in the samples was depleted using the QIAseq FastSelect kit (Qiagen, Germantown, MD). Libraries were constructed using the TruSeq stranded mRNA kit (Illumina) following standard JGI protocols.

treatment_protocol: Growth was stopped by the 1:8 addition of ice cold 5% acid phenol:chloroform (5:1) in ethanol

tag: strain

value: bacterial

value: Ferulic Acid


title: Ferulic Acid Rep 2

description: Ferulic Acid

tag: cell type


title: Ferulic Acid Rep 4

description: Ferulic Acid


title: CytoRP_20m_2

description:
RP_AF2_RPKM.txt
TE_AF2_Cutoff_2RPKM.txt


title: Adult HSC biol rep 2

value: bone marrow

value: 8-12 weeks

value: pooled male and female


title: 2 wk MPP4 biol rep 3

value: 2 weeks

value: C57Bl/6 wild-type

value: steady state isolation


title: Adult HSC biol rep 1


title: P78-2

value: Stable disease


title: Pt05 - Day 4 - Arm B [S109]

value: Day 4

tag: participant id

value: Arm B

value: panobinostat + IFN-alpha2A


title: Pt05 - Day 28 - Arm B [S113]

value: PBMC

value: Day 28

tag: histone mark


title: Adult HSC biol rep 3


title: Vanillin Rep 4

description: Vanillin

value: Vanillin


title: P77-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: Pt05 - Day 0 - Arm B [S108]

value: CD4 T cells

value: Day 0

value: IgG

tag: group


title: 2 wk MPP4 biol rep 1

tag: tissue

value: bone marrow


title: Vanillin Rep 2

description: Vanillin

value: bacterial


title: 2 wk MPP3 biol rep 3

value: 2 weeks

value: pooled male and female


title: Vanillin Rep 3

description: Vanillin


title: P76-3

value: Progression


title: Pt05 - Day 0 - Arm B [S106]

tag: participant treatment


title: Pt05 - Day 4 - Arm B [S110]


title: P76-2

value: Stable disease


title: 2 wk MPP3 biol rep 1

tag: genotype

value: C57Bl/6 wild-type

value: steady state isolation


title: DC-A Rep 4

description: DC-A

tag: treatment

value: DC-A


title: Vanillin Rep 1

description: Vanillin


title: 2 wk MPP3 biol rep 2


title: Ferulic Acid Rep 1

description: Ferulic Acid

value: Ferulic Acid


title: 2 wk MPP4 biol rep 2


title: Pt05 - Day 4 - Arm B [S111]

value: PBMC

tag: time

value: Day 4

value: Arm B

value: panobinostat + IFN-alpha2A


title: P77-2

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: DC-A Rep 3

description: DC-A


title: DC-A Rep 2

description: DC-A


title: Pt17 - Day 28 - Arm C [S103]

value: CD4 T cells

value: Day 28

value: Arm C


title: Pt17 - Day 4 - Arm C [S102]

value: IgG


title: PC9-C2 ctrl-trt all samples batch 3 scRNAseq

description: 10x Genomics

value: Lung cancer

tag: cell line

value: parental

value: untreated 0.1% DMSO 3d


title: Pt05 - Day 0 - Arm B [S107]

value: Day 0


title: 2 wk MPP2 biol rep 2

value: bone marrow

value: 2 weeks

tag: Sex

value: pooled male and female

value: C57Bl/6 wild-type

value: steady state isolation


title: 2 wk MPP2 biol rep 1

tag: age


title: DC-A Rep 1

description: DC-A

value: bacterial

value: DC-A


title: P75-2

value: Plasma extracellular vesicles

value: Stable disease


title: P75-1

value: Metastatic colorectal cancer

value: At the time of surgery (hepatectomy)


title: Pt17 - Day 4 - Arm C [S101]

value: PBMC

value: CD4 T cells

value: Day 4

value: Arm C


title: 2 wk HSC biol rep 3


title: Glucose Rep 4

description: Glucose

value: Glucose


title: Pt17 - Day 28 - Arm C [S105]

value: Day 28

value: IgG


title: Glucose Rep 3

description: Glucose


title: Pt17 - Day 4 - Arm C [S100]


title: P74-2


title: 2 wk HSC biol rep 2

value: bone marrow

value: 2 weeks


title: Pt17 - Day 28 - Arm C [S104]


title: Glucose Rep 2

description: Glucose


title: 2 wk MPP2 biol rep 3

value: pooled male and female

value: C57Bl/6 wild-type


title: P75-3

value: Progression


title: P74-1


title: 2 wk HSC biol rep 1

value: steady state isolation


title: Adult MPP3 biol rep 1

value: 8-12 weeks


title: Pt17 - Day 0 - Arm C [S099]

value: Day 0


title: dKO, replicate 1, ATAC-seq

data_processing:
Trimmed reads were aligned to the mouse reference genome GRCm38 using bowtie2 (version 2.4.2) with the options ‘-X 1000 --very-sensitive’ (Langmead & Salzberg. 2012).
Generated SAM files were converted into BAM files and sorted using SAMtools (version 1.14) (Li et al., 2009). Any reads mapped to non-canonical chromosomes, and mitochondria were removed, as well as the PCR duplicates, which were marked using the Picard tool (version 2.27.4) (http://broadinstitute.github.io/picard/).
Peaks in ATAC-seq data were detected using function callpeak from the MACS2 tool with ‘--format BAMPE’ option (Zhang et al., 2008).
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: LSK cells

extract_protocol:
50,000 LSK cells from WT or KO mouse models were used for each experiment. Cells were washed in PBS and then resuspended in lysis buffer containing 10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40. Immediately after lysis, samples were treated with 2.5μl of Tn5 transposase (Illumina, #20034197) and tagmentation reactions were carried out at 37°C for 30 min. Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen, #28004) and amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) with the following PCR conditions: 72°C for 5 min, 98°C for 30 s, followed by 10 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min.
PCR-amplified ATAC-seq libraries were purified and size-selected using AMPure beads (Beckman Coulter, #A63881) with ratios of 0.55x-1.7x, enriching for DNA fragments of 170-800 bp.

value: LSK cells

value: beta-catenin/Hoxa9 knockdown


title: P74-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: P76-1

value: At the time of surgery (hepatectomy)


title: Pt17 - Day 0 - Arm C [S098]

value: PBMC

value: CD4 T cells

value: Arm C


title: Glucose Rep 1

description: Glucose

value: bacterial

value: Glucose


title: WT, replicate 2, ATAC-seq

value: WT


title: stem, height 60 cm, 17-20 cm, rep3

city: chengdu

first: lin

middle: mao

last: he

state: sichuan

address: wenjiang

institute: sichuan agricultural university

data_processing:
Quality control:  At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome using Hisat2
Novel transcripts prediction using StringTie
Quantification of gene expression level. FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis using the DESeq2 R package
Assembly: GCF_001876935.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Asparagus officinalis

source_name: stem

extract_protocol:
RNA was harvested using Tiangen polysaccharide polyphenol kit (QIAGEN，Germany) following manufacture's protocols
strand-specific RNA-Seq library construction and sequencing were performed according to Illumina standard protocols.

value: stem


title: Pt17 - Day 0 - Arm C [S097]


title: P73-2

value: Stable disease


title: P73-3

value: Progression


title: Pt03 - Day 28 - Arm A [S096]

value: Day 28

value: IgG

value: Arm A

value: panobinostat


title: stem, height 60 cm, 17-20 cm, rep2


title: Pt03 - Day 28 - Arm A [S095]


title: P73-1


title: PRMT1_KO, replicate 2, ATAC-seq

value: LSK cells

value: PRMT1 knockdown


title: PRMT1_KO, replicate 1, ATAC-seq


title: P72-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: stem, height 60 cm, 17-20 cm, rep1


title: Pt03 - Day 4 - Arm A [S093]

value: PBMC

value: Day 4


title: stem, height 40 cm, 17-20 cm, rep2


title: stem, height 40 cm, 17-20 cm, rep3


title: P72-1

value: At the time of surgery (hepatectomy)


title: Pt03 - Day 4 - Arm A [S092]

value: CD4 T cells


title: stem, height 40 cm, 17-20 cm, rep1


title: HOXA9_KO, replicate 1, ATAC-seq

value: HOXA9 knockdown


title: HOXA9_KO, replicate 2, ATAC-seq


title: Bcat_KO, replicate 2, ATAC-seq

value: beta-catenin knockdown


title: Pt03 - Day 4 - Arm A [S091]


title: P71-3


title: P72-2


title: P71-2


title: Pt03 - Day 0 - Arm A [S090]

value: Day 0


title: Pt03 - Day 28 - Arm A [S094]


title: WT, replicate 1, ATAC-seq

value: WT


title: stem, height 25 cm, 17-20 cm, rep2

value: stem


title: Bcat_KO, replicate 1, ATAC-seq


title: stem, height 25 cm, 17-20 cm, rep3


title: P71-1


title: stem, height 25 cm, 17-20 cm, rep1


title: P70-4

value: Recurrence


title: Pt03 - Day 0 - Arm A [S089]


title: Pt03 - Day 0 - Arm A [S088]


title: stem, height 10 cm, 3-6 cm, rep3


title: Phf2 KO c2c12 2

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

country: France

institute: Cochin institut

data_processing:
Illumina NovaSeq 6000. PE150 (150bp×2 paired-end).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Fragment per Kilobase of transcript per Million mapped reads (FPKM) and TPM (Transcripts Per Kilobase Million) were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample ...

source_name: C2C12  myotubes

growth_protocol: DMEM, +2% horse serum, 1% PS

extract_protocol:
Media were removed, and after 1 wash by PBS, RNA was harvested using ISOGEN reagent.
NEBNext® Poly(A) mRNA Magnetic Isolation Module (for PolyA selection) NEBNext® UltraTM ll Directional RNA Library Prep Kit

value: C2C12 myotube

value: Phf2 KO


title: P70-3

data_processing:
Sequencing reads were mapped using STAR against the human genome reference (hg19), and gene level quantification was performed with featureCounts. Total counts mapped to protein-coding genes were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Comma-separated values (CSV) file with featureCounts for protein-coding genes

value: No evidence of disease (NED2)


title: stem, height 10 cm, 3-6 cm, rep2


title: Phf2 KO c2c12 1


title: P70-2

value: No evidence of disease (NED1)


title: P70-1


title: Pt11 - Day 28 - Arm B [S087]

data_processing:
library strategy: Cut&Run
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (GRCh38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38

value: Day 28

value: IgG

value: Arm B

value: panobinostat + IFN-alpha2A


title: Pt11 - Day 28 - Arm B [S086]

value: PBMC


title: Pt11 - Day 28 - Arm B [S085]


title: wild type C2C12 control 3

value: wild type


title: P69-4

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: wild type C2C12 control 1


title: wild type C2C12 control 2


title: Pt11 - Day 4 - Arm B [S084]

value: CD4 T cells

value: Day 4


title: P69-2


title: Pt11 - Day 4 - Arm B [S083]


title: P69-3


title: Pt11 - Day 4 - Arm B [S082]


title: P69-1

value: At the time of surgery (hepatectomy)


title: MOC22 control, scRNAseq

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Oral Squamous Cell Carcinoma

extract_protocol:
Resected mouse tumors from either control or Trp63-KD C57BL/6J mice were dissociated into single cells using the Miltenyi Mouse Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, North Rhine-Westphalia, Germany) as per the manufacturer’s protocol, reducing enzyme R to 20%. Enrichment of CD45+ cells was performed using CD45 MicroBeads (Miltenyi Biotec) and the autoMACS Pro Separator (Miltenyi Biotec).  Cell positive for CD45 cells were subsequently used in single cell RNA-Seq analysis.
Single-cell RNA-Seq libraries were prepared per the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Barcoded sequencing libraries were quantified by quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific, Waltham, MA). Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) as per the Single Cell 3′ v3.1 Reagent Kits User Guide, with a sequencing depth of ~40,000 reads/cell.

value: MOC22 cells

value: Oral Squamous Cell Carcinoma

value: 10 weeks

value: control


title: Pt11 - Day 0 - Arm B [S081]

source_name: PBMC

extract_protocol:
Briefly, isolated CD4T cells from 17 study participants in the ACTIVATE clinical trial were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac and H3K27me3 (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

value: Day 0


title: smallRNA_skin tissues, healthy,D3_3

city: Ya'an

first: Xinyue

last: Zhang

state: Sichuan

address: Xinkang street num 46

department: Department of Zoology,College of Life Science

institute: Sichuan Agricultural University

description:
sow
smallRNA_processed data.tar.gz

data_processing:
Data filtering: SOAPnuke (v1.5.6)
Sequence matching：For mRNAs and lncRNAs, their sequence alignment was performed using HISTA2 (v2.1.0) [79] software to align clean data to the reference genome sequence (Sus scrofa, GCF_000003025.6_Sscrofa11.1)；And circRNA uses Bowtie2 (v2.2.5) to compare clean data into CircBase
Data quantification：For mRNA and lncRNA, gene expression quantification was performed using RSEM (v1.3.1) software. For circRNAs, circRNAs were quantified using reads spanning the junction site (the first and last junctions of the circRNA sequence) with at least 10 bp coverage at both ends.
Assembly: Reference Genome Version: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: tar.gz. files include all processed data

organism: Sus scrofa

source_name: dorsal skin

extract_protocol:
The removed tissues were snap-frozen and the total RNA of the skin was extracted using the Trizol method kit.
Two RNA libraries were constructed for four types of RNA from the dorsal skin of the Chenghua pig at four time points, of which the mRNA, lncRNA and circRNA were unified to construct the DNBSEQ LncRNA-Seq library, and the miRNA was constructed separately as the DNBSEQ Small RNA library for high-throughput sequencing.

value: dorsal skin

tag: breed

value: Chenghua pig

value: female

tag: disease state

value: healthy

value: Day 3


title: Phf2 KO c2c12 3

value: C2C12 myotube

value: Phf2 KO


title: smallRNA_skin tissues, healthy,D3_2

description:
sow
smallRNA_processed data.tar.gz


title: P68-4

first: Anirban

last: Maitra

institute: New York University Grossman School of Medicine

extract_protocol:
RNA was isolated using Invitrogen total exosome RNA & Protein Isolation kit according to the manufacturer protocol
SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

value: Plasma extracellular vesicles

tag: disease stage

value: Recurrence


title: Pt11 - Day 0 - Arm B [S080]

first: Ce

last: Gao

institute: Ragon Institute of MGH, MIT and Harvard

value: PBMC

value: CD4 T cells

value: Arm B

value: panobinostat + IFN-alpha2A


title: smallRNA_skin tissues, healthy,D3_1

description:
sow
smallRNA_processed data.tar.gz


title: P68-3

value: Metastatic colorectal cancer

tag: disease status

value: No evidence of disease (NED2)


title: P68-2

value: No evidence of disease (NED1)


title: Pt16 - Day 28 - Arm C [S078]

value: Day 28

value: IgG

value: Arm C


title: stem, height 10 cm, 3-6 cm, rep1

value: stem


title: RC-138_(Clariom_S_Human)_G3

type: RNA

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

hyb_protocol: 2.3 µg of fragmented and labeled ss-cDNA was hybridized to the Clariom S Assay Human in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression using Transcriptome Analysis console software version 4.0.2 (Affymertix, USA) . QC passed CEL files were further analyzed using TAC software. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label: biotin

source_name: Whole blood

label_protocol: 100ng of total RNA was used for cRNA amplification with GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. After 16h of In vitro transcription cRNA synthesis, cRNA was purified using magnetic beads and 15µg of purified cRNA was used to prepare ss-cDNA, then 5.5 µg of ss-cDNA was fragmented with fragmentation buffer then labeled using DNA labeling reagent.

extract_protocol: Total RNA extracted from whole blood using PAXgene blood RNA kit

tag: gender

value: Male


title: smallRNA_skin tissues, healthy,E105_3

description:
sow
smallRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig

value: female

value: healthy

value: 105-day embryo


title: Pt11 - Day 0 - Arm B [S079]

value: PBMC

tag: cell type

value: Day 0


title: RC 96_(Clariom_S_Human)_G3


title: RC 127_(Clariom_S_Human)_G3


title: RC-134_(Clariom_S_Human)_G3

value: Female


title: Pt16 - Day 28 - Arm C [S077]

value: CD4 T cells

tag: participant id


title: P68-1

city: New York

source_name: Plasma extracellular vesicles

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: At the time of surgery (hepatectomy)


title: RC 123_(Clariom_S_Human)_G3


title: P67-4

value: Recurrence


title: Pt16 - Day 28 - Arm C [S076]

city: Cambridge

value: Day 28

tag: histone mark


title: MOC22_p63 knockout, scRNAseq

description: 10x Genomics

value: MOC22 cells

value: Oral Squamous Cell Carcinoma

tag: strain

value: 10 weeks


title: RC-100_(Clariom_S_Human)_G3

value: Male


title: smallRNA_skin tissues, healthy,E105_1

description:
sow
smallRNA_processed data.tar.gz

tag: tissue

value: dorsal skin

value: Chenghua pig


title: Pt16 - Day 4 - Arm C [S075]

value: Day 4

value: IgG

tag: group

value: Arm C

tag: participant treatment


title: smallRNA_skin tissues, healthy ,E105_2

description:
sow
smallRNA_processed data.tar.gz

value: female

value: healthy

value: 105-day embryo


title: P67-3

value: Plasma extracellular vesicles

value: No evidence of disease (NED2)


title: RC-58_(Clariom_S_Human)_G3

value: Female


title: RC-40_(Clariom_S_Human)_G3


title: smallRNA_skin tissues, healthy,E76_3

description:
sow
smallRNA_processed data.tar.gz

value: 76-day embryo


title: P67-2

value: Metastatic colorectal cancer

value: No evidence of disease (NED1)


title: PI-82_(Clariom_S_Human)_G1


title: Pt16 - Day 4 - Arm C [S074]

value: PBMC

value: CD4 T cells


title: smallRNA_skin tissues, healthy,E76_2

description:
sow
smallRNA_processed data.tar.gz


title: smallRNA_skin tissues, healthy,E76_1

description:
sow
smallRNA_processed data.tar.gz


title: P65-4

value: Recurrence


title: Pt16 - Day 0 - Arm C [S072]

value: Day 0


title: Pt16 - Day 4 - Arm C [S073]


title: PI 106_(Clariom_S_Human)_G2

value: Male


title: smallRNA_skin tissues, healthy,E56_2

description:
sow
smallRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig

value: 56-day embryo


title: P65-2


title: PI 107_(Clariom_S_Human)_G2


title: Pt16 - Day 0 - Arm C [S071]

value: Arm C


title: P65-1

value: At the time of surgery (hepatectomy)


title: smallRNA_skin tissues, healthy,E56_3

description:
sow
smallRNA_processed data.tar.gz

value: female

value: healthy


title: PI 72_(Clariom_S_Human)_G2


title: Pt16 - Day 0 - Arm C [S070]


title: P65-3

value: Plasma extracellular vesicles

value: No evidence of disease (NED2)


title: smallRNA_skin tissues, healthy,E56_1

description:
sow
smallRNA_processed data.tar.gz


title: PI 94_(Clariom_S_Human)_G1

value: Female


title: lncRNA_skin tissues, healthy,D3_3

description:
sow
IncRNA_processed data.tar.gz

value: Day 3


title: PI 51_(Clariom_S_Human)_G1


title: P64-3

value: Metastatic colorectal cancer


title: lncRNA_skin tissues, healthy,D3_2

description:
sow
IncRNA_processed data.tar.gz


title: Pt04 - Day 28 - Arm A [S068]

value: PBMC

value: Day 28

value: Arm A

value: panobinostat


title: PI 50_(Clariom_S_Human)_G1


title: P64-2

value: No evidence of disease (NED1)


title: Pt04 - Day 28 - Arm A [S067]

value: CD4 T cells


title: lncRNA_skin tissues, healthy,D3_1

description:
sow
IncRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig


title: P64-1


title: Pt04 - Day 4 - Arm A [S066]

value: Day 4

value: IgG


title: lncRNA_skin tissues, healthy,E105_3

description:
sow
IncRNA_processed data.tar.gz

value: female

value: 105-day embryo


title: PI-87_(Clariom_S_Human)_G2

value: Male


title: P63-4

value: Plasma extracellular vesicles

value: Recurrence


title: lncRNA_skin tissues, healthy ,E105_2

description:
sow
IncRNA_processed data.tar.gz

value: healthy


title: P64-4

value: Metastatic colorectal cancer


title: Pt04 - Day 4 - Arm A [S064]

value: PBMC


title: Pt04 - Day 28 - Arm A [S069]

value: Day 28


title: PI-81_(Clariom_S_Human)_G1


title: P63-1

value: At the time of surgery (hepatectomy)


title: lncRNA_skin tissues, healthy,E76_2

description:
sow
IncRNA_processed data.tar.gz

value: 76-day embryo


title: Pt04 - Day 0 - Arm A [S063]

value: Day 0

value: Arm A

value: panobinostat


title: Pt04 - Day 0 - Arm A [S062]

value: CD4 T cells


title: PI-79_(Clariom_S_Human)_G1


title: lncRNA_skin tissues, healthy,E76_3

description:
sow
IncRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig


title: P63-2

value: No evidence of disease (NED1)


title: Pt04 - Day 0 - Arm A [S061]


title: P62-4


title: PI-46_(Clariom_S_Human)_G2


title: PI 49_(Clariom_S_Human)_G1

value: Female


title: PI-69_(Clariom_S_Human)_G2


title: PI-57_(Clariom_S_Human)_G2


title: lncRNA_skin tissues, healthy,E76_1

description:
sow
IncRNA_processed data.tar.gz

value: female