title: Hypo, male, ko, C2

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

description:
Library name: Adult_Hypo_male_ko_C2
BRB-seq

data_processing:
Quality control and preprocessing of data were performed by SciLicium (France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the Zebrafish reference transcriptome from the UCSC website (danRer11) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: danRer11
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 15,418 genes detected.

organism: Danio rerio

source_name: Hypo

growth_protocol: The experiments were carried out on wild-type (WT) AB strain and cyp19a1b-mutant adult zebrafish (Danio rerio) lines generated by the TALENs technology (Amagen, France) kept  in 8 L aquariums (approximately 30 zebrafish per aquarium). The zebrafish were maintained under standard conditions of housing, with a photoperiod of 14:10 light:dark and temperature controlled. Water was maintained at 27.0 °C ± 1.0 °C with an automated supply of new water resulting in a daily renewal of 20 %. Fish were fed twice a day with dry food.

extract_protocol:
RNA extraction was performed on three different parts of the brain, corresponding to the OB, the Tel and the hypothalamus. Three zebrafish of the same genotype and sex were pooled for each region. A total of 6 pools of 3 wild-type males and females were obtained, 5 pools of 3 mutant males and 4 pools of 3 mutant females. Samples were homogenized with a mixer pellet pestle (UGAP, REF: 2608725) and total RNA was extracted according to the manufacturer’s protocol (Macherey-Nagel, REF: 740406.50). RNA quantity and quality were assessed using a Nanodrop-1000 spectrophotometer (NanoDrop technology, Cambridge, UK) and a 2100 Bioanalyzer Instrument (Agilent Technologies, CA, USA) following manufacturer’s instructions. Only samples with an RNA integrity number (RIN) score>7 were included.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

value: Hypo

value: male

tag: developmental stage

value: adult

value: cyp19a1b mutant


title: MuSCs, Aged, ISR-a, 1

status: Public on Sep 03 2025

type: SRA

city: San Francisco

first: Andrew

last: Brack

state: CA

address: 35 Medical Center Way

department: Orthopaedic Surgery

country: USA

institute: UCSF

description:
Library name: Sample AGS1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were processed using the count function from CellRanger (version 5.0.1) .
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values and matrix files

molecule: total RNA

organism: Mus musculus

source_name: hindlimb and forelimb

extract_protocol:
RNA seq profiling of murine muscle stem cells of adult (4 months) and aged (22 months) were isolated by Fluorescence-activated cell sorting (FACS). And plated on extracellular coated plates (ECM) in growth media ((F10 (Gibco), 20% fetal bovine serum (FBS) (Gibco), (5 ng/ml) FGF2 (R&D Systems)) for 18 hours in DMSO or in 10 µM of the the ISR activator (ISR-a Sal003 (activated). The activated cells were dissociated using cell dissociation buffer (Gibco), stained with propidium iodide and FACS sorted to remove dead cells and debris.
Live activated cells were transferred to the 10x Chromium System for library preparation and sequencing using Illumina NovaSeq.

tag: tissue

value: hindlimb and forelimb

tag: cell type

value: Muscle Stem Cells

tag: age

value: 22 months

tag: treatment


title: Hypo, male, ko, C1

country: France

description:
Library name: Adult_Hypo_male_ko_C1
BRB-seq

library_source: transcriptomic

molecule: polyA RNA

tag: Sex

tag: genotype


title: B_7_1, TP53 MISS

city: Shanghai

first: Yiying

last: Xue

address: Siping road 1239

country: China

institute: Tongji University School of Life Sciences and Technology

description:
Library name: Sample 7
B_7_1

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: Text file includes gene TPM for each Sample

organism: Homo sapiens

source_name: peripheral blood

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

value: peripheral blood

value: TP53 MISS


title: MuSCs, Aged, DMSO, 4

description:
Library name: Sample AG4
10x Genomics

value: DMSO


title: MuSCs, Aged, ISR-a, 3

description:
Library name: Sample AGS3
10x Genomics


title: Liver - Male - WD_TN - Rep4

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 23 out of 28 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 38776 spots out of 62976 were selected.  The mean signal of the 13 first samples and 15 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33110 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All mice were housed on a 12 h light (ZT0-ZT12)/12 h dark (ZT12-ZT24) cycle.

extract_protocol: Total cellular RNA from liver was extracted with Trizol Reagent® (Molecular Research Center, Inc., Cincinnati, OH, USA).

treatment_protocol: Ctrl: Ctrl diet for 13 weeks; WD: Western diet for 13 weeks; RT = room temperature (22°C); TN= thermoneutrality (30°C).

value: Male

value: 23 weeks

tag: diet

value: WD

tag: temperature

value: TN

tag: washbatch


title: Hypo, male, ko, B2

description:
Library name: Adult_Hypo_male_ko_B2
BRB-seq


title: B_6_1, TP53 MISS

description:
Library name: Sample 6
B_6_1


title: Hypo, male, ko, B1

description:
Library name: Adult_Hypo_male_ko_B1
BRB-seq


title: MuSCs, Aged, DMSO, 3

description:
Library name: Sample AG3
10x Genomics


title: B_10_4, TP53 MISS

description:
Library name: Sample 4
B_10_4


title: MuSCs, Aged, DMSO, 2

description:
Library name: Sample AG2
10x Genomics


title: Hypo, male, ko, A1

description:
Library name: Adult_Hypo_male_ko_A1
BRB-seq


title: MuSCs, Aged, DMSO, 1

description:
Library name: Sample AG1
10x Genomics


title: Liver - Male - WD_RT - Rep2

value: RT


title: Liver - Male - WD_TN - Rep2


title: B_1_1, TP53 MISS

description:
Library name: Sample 3
B_1_1


title: A_7_8, TP53 MISS

description:
Library name: Sample 2
A_7_8


title: Hypo, male, wt, C1

description:
Library name: Adult_Hypo_male_wt_C1
BRB-seq

value: wild-type


title: MuSCs, Adult, DMSO, 3

description:
Library name: Sample AD3
10x Genomics

value: 4 months


title: Liver - Male - WD_RT - Rep7


title: Liver - Male - CTRL_RT - Rep2

value: CTRL


title: MuSCs, Adult, DMSO, 2

description:
Library name: Sample AD2
10x Genomics


title: Hypo, male, wt, B1

description:
Library name: Adult_Hypo_male_wt_B1
BRB-seq

value: Hypo

value: male


title: Vector control replicate 2 (PL45)

first: Peng

last: Chen

address: 168 Changhai Road, Shanghai, 200433,

institute: Changhai Hospital Affiliated to Navy Medical University

description: Library name: vector-2

data_processing:
Raw BCL files were demultiplexed and converted to FASTQ with bcl2fastq v2.20; read quality was assessed by FastQC v0.11.9 and summarized with MultiQC, and adapters or low-quality bases (Q < 20, read < 50 bp) were trimmed using fastp v0.23.4; clean reads were aligned to the GRCh38 reference (GENCODE v39) with HISAT2 v2.2.1 using strand-specific option “--rna-strandness RF,” and BAMs were sorted/indexed with samtools v1.15; gene-level counts were obtained with featureCounts v2.0.3 (-s 2) and FPKM values calculated in R; differential expression was analyzed with DESeq2 v1.34.0 (|log₂FC| > 1, FDR < 0.05), and significant genes were subjected to GO and KEGG enrichment using clusterProfiler v4.2.2.
Assembly: GRCh38
Supplementary files format and content: Excel file containing a matrix of raw, un-normalized integer counts. Rows correspond to genes, identified by gene symbols, and columns correspond to the samples listed above.

source_name: pancreas

growth_protocol: PL45 pancreatic ductal adenocarcinoma cells were cultured in DMEM (high glucose, Gibco) supplemented with 10 % fetal bovine serum (Gibco) and 1 % penicillin-streptomycin at 37 °C in a humidified 5 % CO₂ incubator. Cells were passaged at 70–80 % confluence and only passages < 20 were used. Mycoplasma negativity was confirmed bi-monthly by PCR

extract_protocol:
Total RNA was isolated with TRIzol reagent (Thermo Fisher, Cat #15596018) and purified using the RNeasy Mini Kit (QIAGEN) with on-column DNase I digestion. RNA integrity was assessed on an Agilent 2100 Bioanalyzer; only samples with RIN ≥ 8.0 were advanced
Strand-specific, paired-end libraries were prepared from 1 µg high-quality RNA using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, E7760) with rRNA depletion (NEBNext rRNA Depletion Kit, Human/Mouse/Rat). Fragmentation, first-/second-strand cDNA synthesis, end repair/A-tailing, adapter ligation (NEBNext Multiplex Oligos), size selection (~300 bp), and 12-cycle PCR enrichment were performed per the kit manuals. Libraries were quantified by Qubit and qPCR, pooled equimolarly, and sequenced (2 × 150 bp) on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: Cells were transfected with 4 µg pcDNA3.1-Menin or empty-vector plasmid using Lipofectamine 2000 (Thermo Fisher) according to the manufacturer’s instructions. Forty-eight hours post-transfection cells were harvested for RNA extraction.

value: pancreas

tag: cell line

value: epithelial-like (PDAC)

value: empty-vector


title: Vector control replicate 3 (PL45)

description: Library name: vector-3


title: Hypo, male, wt, A2

description:
Library name: Adult_Hypo_male_wt_A2
BRB-seq

value: adult


title: B_11_4, TP53 MISS

description:
Library name: Sample 5
B_11_4

value: peripheral blood


title: Liver - Male - CTRL_RT - Rep4


title: Vector control replicate 1 (PL45)

description: Library name: vector-1


title: MuSCs, Adult, DMSO, 1

description:
Library name: Sample AD1
10x Genomics

value: hindlimb and forelimb

value: Muscle Stem Cells


title: Tcm _P14, tumor, Rep2

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

description: Library name: Sample 6

data_processing:
All samples are paired-end sequencing files and the quality was checked by fastqc tools. Adapter trimming and low-quality sequence removal were achieved by fastp tools (PMID: 30423086) and recheck data by fastqc tools. BWA-MEM tool was used to align the data to mm10 genome. After that, aligned data were further purified by cleaning mitochondria DNA, PCR duplicates, and mm10 genome blacklist. Genrich was used to call narrowpeak and bigwig, bam and bedgraph files were prepared for visualization.
Assembly: mm10
Supplementary files format and content: Processed data files are in bigWig format, representing genome-wide chromatin accessibility signal (normalized read coverage) for each sample; two replicates processed into one bigwig file

source_name: tumor

extract_protocol:
To obtain P14 CD8 T cells in tumor, tumors were mechanically minced and digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD8, Va2, CD45.1, CD45.2, P14 cells were FACS-sorted.
ATAC-seq library was prepared using Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, TD711). Briefly, sorted cells were lysed on ice and fragment DNA in waterbath at 37℃ for 30 min. ATAC DNA Extract Beads were used for DNA extraction of fragmented products and extracted DNA fragments were amplified in a PCR instrument. Finally, ATAC DNA Clean Beads were used for two-step fragment size selection of amplified products and quality and quantity assessments are conducted using methods such as bioanalyzer or Qubit. Finally, the libraries were sequenced using paired-end sequencing, with 150 nucleotides on each end, conducted in a single lane of a NovaSeq 6000 for each sample.

value: tumor


title: Hypo, male, wt, C2

description:
Library name: Adult_Hypo_male_wt_C2
BRB-seq


title: Hypo, male, wt, A1

description:
Library name: Adult_Hypo_male_wt_A1
BRB-seq


title: A_11_4, TP53 MISS

description:
Library name: Sample 1
A_11_4

value: TP53 MISS


title: Tcm _P14, tumor, Rep1

description: Library name: Sample 5


title: Liver - Male - CTRL_TN - Rep5

value: Male

value: 23 weeks


title: Hypo, male, wt, B2

description:
Library name: Adult_Hypo_male_wt_B2
BRB-seq


title: Hypo, female, ko, C1

description:
Library name: Adult_Hypo_female_ko_C1
BRB-seq

value: female

value: cyp19a1b mutant


title: MuSCs, Adult, DMSO, 4

description:
Library name: Sample AD4
10x Genomics

value: 4 months

value: DMSO


title: Liver - Male - CTRL_RT - Rep6

value: CTRL

value: RT


title: Liver - Male - WD_TN - Rep5

value: WD

value: TN


title: Menin-OE replicate 2 (PL45)

description: Library name: Menin-2

value: pancreas

value: epithelial-like (PDAC)

value: Menin over-expressing


title: Tem _P14, tumor, Rep2

description: Library name: Sample 4


title: Liver - WD_CL316243 - Rep5

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 26 out of 32 microarrays or with a minimal weight of 6 per group from at least one experimental group. At this step, 36142 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth function from the qsmooth R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33490 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Brown adipose tissue

growth_protocol: All mice were housed on a 12 h light (ZT0-ZT12)/12 h dark (ZT12-ZT24) cycle in a ventilated cabinet at thermoneutral temperature (TN = 28-30°C) throughout the experiment.

extract_protocol: Total cellular RNA from brown adipose tissue was extracted with Trizol Reagent® (Molecular Research Center, Inc., Cincinnati, OH, USA).

treatment_protocol: Ctrl: Ctrl diet for 13 weeks; WD: Western diet for 13 weeks; CL316243 (3 mg/kg body weight; Sigma Aldrich) or vehicle (0.5% carboxymethylcellulose in sterilized water) by gavage at ZT10 and sacrificed at ZT16 (n = 8 per group).


title: DMSO treated and isolated ATMs_sample2

city: Leipzig

first: Raphaela

last: Wehr

state: Saxony

address: Liebigstraße

department: Institute of Anatomy

country: Germany

institute: Leipzig University

description:
Library name: RW_1D
DMSO control

data_processing:
Results were then analyzed using the DESeq2 package on Galaxy2. Normalized counts were calculated and are presented vs. control (DMSO)
Assembly: DESeq2 package on Galaxy
Supplementary files format and content: processed data was savged as tabular format for each group

molecule: cytoplasmic RNA

source_name: adipose tissue macrophages

growth_protocol: Adipose tissue explants were cultivated for seven days. At day 7 SVF, which contains macrophages were isolated

extract_protocol:
RNA Isolation and purification was performed using the RNAeasy micro Kit by Qiagen
RNA sequencing and analysis was performed at Leipzig University’s Core Unit ‘DNA Technologien’. RNA extraction and library preparation was performed with a sequencing depth of 10 million reads/sample.

treatment_protocol: Adipose tissue was treated with Rapamycin 0.5 µM or Apilimod 0.5 µM or Lalistat 10 µM or DMSO-control 0.5%

value: adipose tissue macrophages

value: Csf1r-eGFP reporter mice  on a C57BL/6J background


title: Liver - Male - WD_RT - Rep4


title: Tem _P14, tumor, Rep1

description: Library name: Sample 3

value: tumor


title: Hypo, female, ko, B1

description:
Library name: Adult_Hypo_female_ko_B1
BRB-seq

value: Hypo

value: adult


title: Menin-OE replicate 1 (PL45)

description: Library name: Menin-1


title: Liver - Ctrl_CL316243 - Rep1

value: Ctrl


title: Hypo, female, ko, A2

description:
Library name: Adult_Hypo_female_ko_A2
BRB-seq

value: female


title: Trm _P14, tumor, Rep2

description: Library name: Sample 2


title: THP1-IRAK4KO-CC885-3

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: 51THP-1IRAK4KOCC8853
IRAK4KO THP1 CC-885 treated cells

data_processing:
FastQC (v0.11.2) was used to test read quality.
Paired-end reads were aligned against GRCh38 genome using HISAT (v2.0.5). Stranded (RF)
Gene counts were summarized using featureCounts (v1.5.2)
Assembly: GRCh38
Supplementary files format and content: rawCounts.tsv
Supplementary files format and content: Tab-delimted raw gene counts

source_name: blood

growth_protocol: THP1 cells were cultured in RPMI with 10% FBS and 1% P/S

extract_protocol:
The cells were collected, and RNA was extracted using ZYMO RESEARCH Quick-RNA Miniprep kit (#R1055).
After the confirmation of the RNA quality using Agilent 2100 Bioanalyzer, the libraries were prepared with polyA selection using the Truseq RNA Library Prep Kit, and the libraries were sequenced at an average depth of 30M paired-end 100bp nucleotide reads. After the quality of reads was examined using FastQC (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), paired-end reads were aligned against mouse mm10 genome (iGenome,https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 (v2.0.5,http://daehwankimlab.github.io/hisat2).

treatment_protocol: Cells were electroporated using the Invitrogen Neon Transfection system with the following conditions: 1,350 V, 20 ms width, 1 pulse, using 100 µl tip and 2.0 × 106 cells per ml in R buffer (Invitrogen). Cells were transfected with 1 µg Cas9 with our without an sgRNA targeted to IRAK4. Cells were allowed to recover for 72 h in antibiotic-free RPMI-1640 medium supplemented with 10% FBS. Cells were than diluted to a density of less than one cell/well and plated into 96 well plates. Clones were allowed to expand and screened for gene editing by PCR of the targeted region. Clones of interest were sent for Sanger sequencing to confirm a functional KO of IRAK4 and WT. Cells were split and plated at a density of 500,000 cells/mL  and WT and IRAK4KO cells were treated with CC-885 or equivalent volume of DMSO for twelve hours.

value: blood

value: AML blasts

value: KO


title: Liver - Ctrl_Vehicle - Rep8

value: Vehicle


title: Menin-OE replicate 3 (PL45)

description: Library name: Menin-3


title: Liver - WD_Vehicle - Rep8


title: Hypo, female, ko, A1

description:
Library name: Adult_Hypo_female_ko_A1
BRB-seq

value: cyp19a1b mutant


title: THP1-IRAK4KO-CC885-2

description:
Library name: 51THP-1IRAK4KOCC8852
IRAK4KO THP1 CC-885 treated cells


title: mPDAC1, TIFM, gemcitabine 3

city: Chicago

first: Alex

last: Muir

email: amuir@berkeley.edu, amuir@uchicago.edu

state: Illinois

department: Ben May Department for Cancer Research

institute: University of Chicago

description: Library name: Sample_12

data_processing:
Data processing and analysis were done using the R-based Galaxy platform (https://usegalaxy.org/; Afgan et al., 2018). Quality control was performed prior and after concatenation of the raw data with the tools MultiQC and FastQC, respectively. All samples passed the quality check with most showing ~20% sequence duplication, sequence alignment greater or equal to 80%, below and below 50% GC coverage, all of which is acceptable and/or indicative of good quality for RNASeq samples
Assembly: Samples were aligned and counts were generated using the tools HISAT2 (Galaxy Version 2.2.1+galaxy0, NCBI genome build GRCm38/mm10) and featureCounts (Galaxy Version 2.0.1+galaxy1), respectively.
Supplementary files format and content: count txt file

growth_protocol: Cell culture was performed in static culture conditions. Because TIFM contains fewer nutrients than standard culture, media was changed on TIFM-cultured cell lines every 24 hours. Glucose was routinely measured using a GlucCell glucometer 109 to ensure TIFM-cultured cells never experienced more than a 30% drop in glucose availability. Lastly, passaging TIFM maintained cells using standard trypsin (0.025%)/EDTA solution to detach cells leads to loss of viability upon replating of cells. Therefore, cells were detached with a 1:1 mixture of 0.5% trypsin–EDTA (Thermo Fisher) and serum- free RPMI- 1640  media (Thermo Fisher). This allowed routine passaging and plating of cells with less loss of viability.  These modifications were followed for both TIFM and RPMI cultured cells.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004).
Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA RNA-SEQ library protocol (Illumina). Library quality and quantity were assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.

treatment_protocol: mPDAC1 RPMI and TIFM cultured cells were plated at 50,000 cells per well in 6 cm dishes overnight. The following day, cells were treated with vehicle or 125nM gemcitabine. After 24 hours, RNA was extracted from treated cells using the RNeasy Micro Kit (Qiagen, 74004), RNA quality and quantity were then assessed using the 2100 Bioanalyzer System (Agilent).

value: Pancreatic cancer epithelial cells

tag: culture medium

value: TIFM

value: Gemcitabine


title: Hypo, female, wt, C2

description:
Library name: Adult_Hypo_female_wt_C2
BRB-seq

value: wild-type


title: THP1-IRAK4KO-CC885-1

description:
Library name: 51THP-1IRAK4KOCC8851
IRAK4KO THP1 CC-885 treated cells


title: Hypo, female, wt, B2

description:
Library name: Adult_Hypo_female_wt_B2
BRB-seq


title: Hypo, female, wt, C1

description:
Library name: Adult_Hypo_female_wt_C1
BRB-seq


title: mPDAC1, TIFM, gemcitabine 1

description: Library name: Sample_10


title: THP1-IRAK4KO-DMSO-3

description:
Library name: 52THP-1IRAK4KODMSO4
IRAK4KO THP1 vehicle treated cells

value: DMSO


title: mPDAC1, TIFM, gemcitabine 2

description: Library name: Sample_11


title: THP1-IRAK4KO-DMSO-2

description:
Library name: 51THP-1IRAK4KODMSO3
IRAK4KO THP1 vehicle treated cells


title: Liver - Ctrl_CL316243 - Rep2


title: mPDAC1, TIFM, vehicle 3

description: Library name: Sample_9


title: Hypo, female, wt, B1

description:
Library name: Adult_Hypo_female_wt_B1
BRB-seq


title: Liver - Ctrl_Vehicle - Rep1


title: Liver - WD_Vehicle - Rep7

value: WD


title: Liver - Ctrl_Vehicle - Rep4


title: Liver - WD_CL316243 - Rep7


title: Trm _P14, tumor, Rep1

description: Library name: Sample 1


title: Hypo, female, wt, A2

description:
Library name: Adult_Hypo_female_wt_A2
BRB-seq


title: mPDAC1, TIFM, vehicle 2

description: Library name: Sample_8


title: THP1-IRAK4KO-DMSO-1

description:
Library name: 51THP-1IRAK4KODMSO1
IRAK4KO THP1 vehicle treated cells


title: Hypo, female, wt, A1

description:
Library name: Adult_Hypo_female_wt_A1
BRB-seq


title: THP1-WT-CC885-3

description:
Library name: 52THP-1WTCC8854
WT THP1 CC-885 treated cells

value: WT


title: mPDAC1, TIFM, vehicle 1

description: Library name: Sample_7


title: THP1-WT-CC885-2

description:
Library name: 51THP-1WTCC8852
WT THP1 CC-885 treated cells


title: Tel, male, ko, C2

description:
Library name: Adult_Tel_male_ko_C2
BRB-seq

source_name: Tel

value: Tel

value: male


title: mPDAC1, RPMI, gemcitabine 3

description: Library name: Sample_6

value: RPMI


title: THP1-WT-CC885-1

description:
Library name: 51THP-1WTCC8851
WT THP1 CC-885 treated cells


title: mPDAC1, RPMI, gemcitabine 2

description: Library name: Sample_5


title: Liver - WD_Vehicle - Rep3


title: THP1-WT-DMSO-3

description:
Library name: 52THP-1WTDMSO5
WT THP1 vehicle treated cells


title: THP1-WT-DMSO-2

description:
Library name: 52THP-1WTDMSO4
WT THP1 vehicle treated cells


title: Tel, male, ko, B2

description:
Library name: Adult_Tel_male_ko_B2
BRB-seq

value: adult


title: mPDAC1, RPMI, gemcitabine 1

description: Library name: Sample_4


title: Tel, male, ko, C1

description:
Library name: Adult_Tel_male_ko_C1
BRB-seq


title: Liver - Ctrl_CL316243 - Rep6

value: Ctrl


title: Tel, male, ko, B1

description:
Library name: Adult_Tel_male_ko_B1
BRB-seq


title: THP1-WT-DMSO-1

description:
Library name: 51THP-1WTDMSO1
WT THP1 vehicle treated cells

value: blood


title: Tel, male, ko, A1

description:
Library name: Adult_Tel_male_ko_A1
BRB-seq


title: mPDAC1, RPMI, vehicle 2

description: Library name: Sample_2


title: Tel, male, wt, C2

description:
Library name: Adult_Tel_male_wt_C2
BRB-seq


title: mPDAC1, RPMI, vehicle 1

description: Library name: Sample_1


title: Liver - Ctrl_CL316243 - Rep8


title: HK_Q_3 (IP)

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

description: Library name: HK_Q_3 (IP)

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: hg19
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: kidney

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: kidney

value: epithelial cells

value: Wild type

value: treat with colchicine


title: Liver - WD_CL316243 - Rep2


title: Liver - WD_Vehicle - Rep1

value: Vehicle


title: Liver - WD_Vehicle - Rep6


title: Liver - Ctrl_Vehicle - Rep6


title: HK_Q_2 (IP)

description: Library name: HK_Q_2 (IP)


title: Tel, male, wt, C1

description:
Library name: Adult_Tel_male_wt_C1
BRB-seq


title: HK_Q_1 (IP)

description: Library name: HK_Q_1 (IP)


title: articular cartilage from cKOAcan-DMM mice

city: NanJing

first: Chuyue

last: Pan

address: 639 Longmian Ave.

institute: China Pharmaceutical University

description:
Library name: Sample3
Gexcsope

data_processing:
Raw reads were processed to generate gene expression profiles using Cell Ranger v.3.0.2. Reads from the 10X library were mapped to GRCm38 with ensemble version 92 gene annotation. Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis. Cell type identification and clustering analysis using Seurat program.
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: articular cartilage

extract_protocol:
Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
Single-cell suspensions at a concentration of 1×105 cells ml-1 were converted to barcoded scRNA-seq libraries according to the protocols of the Chromium Single Cell 3’Library, Gel Bead & Multiplex Kit (10x Genomics). Briefly, the cells were partitioned into Gel Beads in Emulsion in the ChromiumTM Controller instrument where cell lysis and barcoded reverse transcription of RNA occurred.  All the libraries were sequenced on Illumina Novaseq 6000 with 150 bp paired end reads.

value: articular cartilage

value: cKOAcan

value: DMM


title: articular cartilage from control-DMM mice

description:
Library name: Sample2
Gexcsope


title: mPDAC1, RPMI, vehicle 3

description: Library name: Sample_3

value: Pancreatic cancer epithelial cells


title: Tel, male, wt, B1

description:
Library name: Adult_Tel_male_wt_B1
BRB-seq

value: wild-type


title: articular cartilage from control-sham mice

description:
Library name: Sample1
Gexcsope

value: WT

value: sham


title: HK_Q_2 (input)

description: Library name: HK_Q_2 (input)


title: HK_Q_3 (input)

description: Library name: HK_Q_3 (input)


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep10

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: 15

library_source: genomic

data_processing:
The quality of the data was assessed using FastQC (v0.11.8) and adapters were trimmed using TrimGalore (v0.6.2) with parameters “--illumina --stringency 5 --clip_r1 6 --three_prime_clip_r1 6”. Alignment to mm10 genome and deduplication was done using Bismark (v0.22.3) with parameters “--local --non_directional”. Allelic analysis of WGBS datasets was performed using SNPsplit.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated using export.bw function from rtracklayer Bioconductor package after merging biological replicates for each genotype. For each sample 3 BigWig files are available. Filenames with *_TOTAL.bw represent total CpG methylation levels, i.e. allelic information if ignored. Filenames with *_MAT.bw and *_PAT.bw represent CpG methylation levels on maternal (C57BL/6J) and paternal (JF1/MsJ) genomes respectively.

molecule: genomic DNA

source_name: 4-cell embryo

extract_protocol:
Genetically hybrid four-cell embryos were first treated with acidic Tyrode’s solution containing 0.01% polyvinyl alcohol (PVA) to remove the zona pellucida. The embryos were then washed in M2 medium followed by PBS containing 0.01–0.05% PVA, and subsequently lysed in RLT Plus buffer. Ten four-cell embryos were pooled into a single tube containing the lysis buffer. DNA from the lysate was subjected to bisulfite conversion using the EZ DNA Methylation-Direct Kit and purified with the PureLink Micro Kit.
Bisulfite-converted DNA underwent five rounds of strand synthesis, followed by exonuclease treatment and second-strand synthesis. The resulting DNA was then used for library preparation using NEB UDI indices and the KAPA HiFi HotStart PCR Kit. Final libraries were purified using AMPure XP beads.

value: 4-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre; JF1 WT

tag: strain

value: C57BL/6J x JF1/MsJ


title: Tel, male, wt, A2

description:
Library name: Adult_Tel_male_wt_A2
BRB-seq

value: Tel

value: male

value: adult


title: HK_Q_1 (input)

description: Library name: HK_Q_1 (input)

value: kidney

value: epithelial cells


title: Liver - Ctrl_Vehicle - Rep5

value: Ctrl


title: Liver - Ctrl_CL316243 - Rep4


title: Liver - WD_CL316243 - Rep1

value: WD


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep8

description: Library name: 13


title: HK_0_3 (IP)

description: Library name: HK_0_3 (IP)

value: Wild type

value: Control


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep9

description: Library name: 14


title: Tel, female, ko, C1

description:
Library name: Adult_Tel_female_ko_C1
BRB-seq

value: female

value: cyp19a1b mutant


title: Tel, male, wt, B2

description:
Library name: Adult_Tel_male_wt_B2
BRB-seq

value: wild-type


title: HK_0_2 (IP)

description: Library name: HK_0_2 (IP)


title: Tel, female, ko, A2

description:
Library name: Adult_Tel_female_ko_A2
BRB-seq


title: HK_0_1 (IP)

description: Library name: HK_0_1 (IP)


title: Tel, female, ko, B1

description:
Library name: Adult_Tel_female_ko_B1
BRB-seq


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep6

description: Library name: 11


title: Tel, female, ko, A1

description:
Library name: Adult_Tel_female_ko_A1
BRB-seq


title: Tel, male, wt, A1

description:
Library name: Adult_Tel_male_wt_A1
BRB-seq


title: Liver - WD_CL316243 - Rep4


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep5

description: Library name: 10


title: Liver - WD_Vehicle - Rep4

value: Vehicle


title: HK_0_2 (input)

description: Library name: HK_0_2 (input)


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep4

description: Library name: 9


title: Tel, female, wt, C2

description:
Library name: Adult_Tel_female_wt_C2
BRB-seq


title: Liver - Ctrl_CL316243 - Rep5


title: HK_0_1 (input)

description: Library name: HK_0_1 (input)


title: Liver - WD_CL316243 - Rep6


title: Liver - WD_CL316243 - Rep8


title: Tel, female, wt, C1

description:
Library name: Adult_Tel_female_wt_C1
BRB-seq


title: CLLRT6_Genotyping

city: New York

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description:
Library name: CLLRT6_Genotyping
Genotyping

data_processing:
The pooled gene expression and HTO libraries were processed with Cell Ranger (v7.0.0) using default parameters. RNA reads were aligned to the human genome GRCh38.
Analysis of the genotyping library was carried out with IronThrone-Multi, a modified version of the previously described IronThrone pipeline. Briefly, genotyping amplicon reads were screened for the presence of the LHS sequence (‘primer sequence’) and the expected RHS sequence without the mutation (‘shared sequence’). Next, IronThrone determines whether the wildtype or mutant sequence is at the expected location. This search was done once for the gene sequence and once for the probe barcode. The results were then merged as follows to determine the initial genotype for each cell. Any cell with both gene sequence and probe barcode sequence corresponding to mutant sequences was labelled as mutant. Similarly, any cell with both gene sequence and probe barcode corresponding to wildtype sequences was labelled as wildtype. These initial genotypes were then refined using a machine-learning (ML) framework to enhance accuracy and minimize false positives.  The final genotyping profiles are determined from the adjusted predictions across multiple ML models, based on the best combined performance.
Assembly: GRCh38
Supplementary files format and content: For gene expression, (1) Cellranger outputs are provided: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (2) Cell line or cell type labels are provided in a two-column table : cell barcode, cell line/type.
Supplementary files format and content: Genotyping data is provided as a table with one column for the cell barcode, and one column for their corresponding genotype for each mutation target.

source_name: primary patient sample

extract_protocol:
Cell line Mixing Experiment Extraction Protocol: Cryopreserved MCF-7 and SK-BR-3 cells were rapidly thawed at 37 °C and washed twice with of PBS (without Ca²⁺/Mg²⁺) containing 0.05% BSA. They were then pooled and fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were then hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. Genotyping of Transcriptomes for Multiple Targets and Sample Types (GoT-Multi) was performed by adapting the 10x Genomics Fixed RNA Profiling (FRP) platform.  Primary Cell Mixing Experiment Extraction Protocol: Peripheral blood cells from one IDH2-mutated AML patient and one CALR type I mutated MPN patient were rapidly thawed at 37 °C and separately incubated with hashing antibodies with sample-identifying barcodes using Hashtag Antibodies 1 or 3 (TotalSeq-B, Biolegend) following manufacturer’s instructions. Dead cells were then removed using microbeads (Miltenyi Biotec, #130-090-101) as per manufacturer’s recommendations from each sample. The live cells from the MPN patient were subsequently enriched for CD34+ cells and CD34- CD15+ cells using anti-hCD34 and anti-hCD15 microbeads (Miltenyi Biotec, #130-046-702 and #130-046-601 respectively) following manufacturer’s instructions. Next, live AML cells were pooled with live CD34+ and CD34- CD15+ cells in a 95:5 ratio and then fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were subsequently hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform.  CLL-RT Cryopreserved Cells Extraction Protocol: Single-cell suspensions from cryopreserved Chronic Lymphocytic Leukemia with Richter Transformation (CLL-RT) patient tumors were rapidly thawed at 37 °C and washed in 50 mL of RPMI-1640/20% fetal bovine serum solution. They were then stained with an antibody cocktail composed of KAPPA/LAMBDA-FITC/PE, CD20 PE-Cy7/BUV737, CD38 APC/APC-Fire750, CD45 APC-H7/V500C, CD19 BV421/PE-Cy7, CD5 BV510/BV421, CD3 BUV395 and CD4-APC-A700. Cells were subsequently sorted using a FACSAria-Fusion sorter (75-μm nozzle at 45 psi), collecting Chronic Lymphocytic Leukemia (CLL) cells, large B-cell lymphoma (LBCL) cells and T-cells from each patient tumor. T-cells were isolated based on CD3 expression. CLL cells were distinguished from LBCL cells, either through their distinct phenotyping profile reported at the clinical level or by size. Next, LBCL cells were incubated with one hashing antibody and all other cell populations with another hashing antibody following manufacturer’s instructions, such that they are distinguishable through sample-identifying barcodes (Hashtag Antibodies 1, 2, 3 or 4; TotalSeq-B, Biolegend). Cells from 1-2 samples hashed with up to four distinct hashing antibodies were then pooled together and fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were subsequently hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform. Three of the patient samples (CLL-RT 1-3) were profiled twice to increase the number of cells profiled.  CLL-RT FFPE Extraction Protocol: Three 30 µm thick FFPE tissue sections from one CLL-RT patient were first washed once with 1 mL of Xylene for 10 min at 55 °C and then twice with 1 mL of Xylene for 10 min at room temperature to remove paraffin. Subsequently, they were rehydrated via a sequence of 1 mL ethanol baths, each lasting 1 min: two rounds in 100% ethanol, then in 70%, 50%, and finally 30% ethanol. The sections were next briefly rinsed with 1 mL of RPMI-1640 (Gibco). Then, 100 μL of a digestion mix composed of 1 mg/mL Liberase TH (Roche, #5401135001), 1 mg/mL Collagenase D (Roche, #11088858001), and 1 U/μL of RNAse inhibitor (RiboLock RNAse Inhibitor, Thermo Fisher Scientific, #EO0382) in RPMI-1640 was added to the tissue sections. The tissues were physically disrupted using a pestle and then another 900 μL of digestion mix was added. Digestion was obtained by incubating tissues at 37 °C for 1 hour at 800 rpm. The tissues were next treated with 1x Nuclei Ez lysis buffer (Sigma-Aldrich, #NUC101) that included 2% BSA. Disintegration was further achieved via pipetting using a P1000 pipette. The separated nuclei were filtered through a 70 μm mesh (pluriStrainer Mini 70 μm, pluriSelect, #43-10070-50), rinsed twice with 1x PBS supplemented with 1% BSA, and once with a 0.5x PBS + 0.02% BSA blend. They were then resuspended in this blend and filtered via a 40 μm mesh (pluriStrainer Mini 40 μm, pluriSelect, #43-10040-50). The nuclei were counted using the AO/PI viability kit (Logos, #F23011) and a hemocytometer. Finally, they were loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform.
GoT-Multi Library Construction Protocol: GEM incubation and recovery were performed as per manufacturer’s instructions for 10x Genomics FRP. For the cell mixing experiments (cell lines and primary cells), the pre-amplification step and library construction steps were also performed as per manufacturer’s instructions. The transcriptomic profile was obtained from the gene expression library whereas the cell surface protein library contained both the HTO libraries and the genotyping libraries. For all other experiments, the pre-amplification step and library construction steps were first performed as per manufacturer’s instructions, to generate the gene expression and hashing (HTO) libraries. To amplify the ligated genotyping probes, 20 µL of the cleaned pre-amplified product was then re-amplified with the same protocol as the pre-amplification step but with two modifications: (1) 2 µL of an additive primer (Read2N primer, 10 µM) was added to the reaction, and (2) the PCR was run as follows: 98 °C 3 min; 8 cycles of 98 °C 15 sec, 64 °C 20 sec, 72 °C 1 min; 72 °C 1 min; 4 °C hold. The re-amplified product was then cleaned as for the pre-amplified product using SPRI beads (Beckman Coulter). The genotyping libraries were constructed with the same protocol as the HTO library but using the Dual Index Kit TN Set A plate (#1000250) instead. The genotyping and HTO libraries were spiked into the gene expression libraries to be sequenced together on a NovaSeq 6000 (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 10 cycles for i7 sample index and 10 cycles for i5 sample index.

value: primary patient sample

tag: disease type

value: Chronic Lymphocytic Leukemia with Richter's Transformation (CLL-RT)

tag: probe set

value: WTandMUTprobes


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep2

description: Library name: 7

value: 4-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre; JF1 WT

value: C57BL/6J x JF1/MsJ


title: Liver - WD_Vehicle - Rep5


title: Liver - Ctrl_Vehicle - Rep3


title: Liver - Ctrl_Vehicle - Rep7


title: Tel, female, wt, B2

description:
Library name: Adult_Tel_female_wt_B2
BRB-seq

value: Tel

value: adult


title: Tel, female, wt, B1

description:
Library name: Adult_Tel_female_wt_B1
BRB-seq


title: CLLRT_Pool4_Genotyping

description:
Library name: CLLRT_Pool4_Genotyping
Genotyping


title: Liver - Ctrl_CL316243 - Rep7


title: CLLRT_Pool5_Genotyping

description:
Library name: CLLRT_Pool5_Genotyping
Genotyping


title: 4cell_WGBS_Ctrl.Kdm2a_KO.Kdm2b_KO_rep7

description: Library name: 5

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ x JF1 WT


title: CLLRT_Pool3_Genotyping

description:
Library name: CLLRT_Pool3_Genotyping
Genotyping


title: Tel, female, wt, A2

description:
Library name: Adult_Tel_female_wt_A2
BRB-seq


title: Liver - WD_Vehicle - Rep2


title: Tel, female, wt, A1

description:
Library name: Adult_Tel_female_wt_A1
BRB-seq


title: CLLRT_Pool2_Genotyping

description:
Library name: CLLRT_Pool2_Genotyping
Genotyping


title: 4cell_WGBS_Ctrl.Kdm2a_KO.Kdm2b_KO_rep6

description: Library name: 4


title: BO, male, ko, C2

description:
Library name: Adult_BO_male_ko_C2
BRB-seq

source_name: BO

value: BO

value: male


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep3

description: Library name: 8


title: 4cell_WGBS_Ctrl.Kdm2a_KO.Kdm2b_KO_rep5

description: Library name: 3


title: 4cell_WGBS_Ctrl.Kdm2a_KO.Kdm2b_KO_rep3

description: Library name: 2


title: Liver - WD_CL316243 - Rep3

value: WD


title: HK_0_3 (input)

description: Library name: HK_0_3 (input)

value: kidney

value: epithelial cells

value: Wild type

value: Control


title: Liver - WD_CL316243 - Rep5

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 26 out of 32 microarrays or with a minimal weight of 6 per group from at least one experimental group. At this step, 35215 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth function from the qsmooth R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32566 rows each corresponding to a unique ProbeName (provided as data Matrix).


title: CLLRT6_GEX

description:
Library name: CLLRT6_GEX
10x Genomics Gene Expression and Hashing


title: Liver - Ctrl_CL316243 - Rep3

value: Ctrl


title: BO, male, ko, C1

description:
Library name: Adult_BO_male_ko_C1
BRB-seq

value: cyp19a1b mutant


title: Liver - Ctrl_Vehicle - Rep2

value: Vehicle


title: Liver - Ctrl_CL316243 - Rep1


title: 4cell_WGBS_Ctrl.Kdm2a_KO.Kdm2b_KO_rep1

description: Library name: 1


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep1

description: Library name: 6


title: BO, male, ko, B2

description:
Library name: Adult_BO_male_ko_B2
BRB-seq


title: CLLRT_Pool5_GEX

description:
Library name: CLLRT_Pool5_GEX
10x Genomics Gene Expression and Hashing

value: primary patient sample

value: Chronic Lymphocytic Leukemia with Richter's Transformation (CLL-RT)

value: WTandMUTprobes


title: Liver - WD_Vehicle - Rep8


title: BO, male, ko, A1

description:
Library name: Adult_BO_male_ko_A1
BRB-seq


title: CLLRT_Pool4_GEX+HTO

description:
Library name: CLLRT_Pool4_GEX+HTO
10x Genomics Gene Expression and Hashing


title: BO, male, ko, B1

description:
Library name: Adult_BO_male_ko_B1
BRB-seq


title: CLLRT_Pool3_GEX+HTO

description:
Library name: CLLRT_Pool3_GEX+HTO
10x Genomics Gene Expression and Hashing


title: C-1

city: shenzhen

last: Li

state: guangdong

address: A16, Life Science Valley, Jinye Avenue

department: Institute of Shenzhen Respiratory Diseases

institute: Shenzhen People's Hospital

description: Library name: wt-Mab46

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.23.0. (parameter:-l 50; -n 5; -q 20;-W 4;-M 20) ；
Assembly: Trimmed sequencereads were mapped to GRCm39 using hisat2 v2-2.1.0 (paramtrer:-p 8;-5 5;-3 5;--min-intronlen 20;--max-intronlen 500000;-k 3;--phred33)
Supplementary files format and content: Read count extraction and normaliation were performed using Htseq v2.0.1 (paramtrer:-s no;-a 10;-m union;-i gene_name;--nonunique none)

source_name: lung

extract_protocol:
RNA was extrated by Trizol
Samples were ground under liquid nitrogen in a mortar and pestle, and the resulting powder dissolved in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA), then extracted total RNA. 2） The quality and purity of RNA were examined by a NanoDrop™ One/OneC spectrophotometer (Thermo Scientific, Waltham, MA, USA) and Life Invitrogen Qubit RNA BR (Broad-Range) Assay Kit. RNA integrity was analyzed using Agilent 4200 TapeStation system (Agilent, Santa Clara, CA, USA)

treatment_protocol: Fresh lung tissues of C57BL/6J mice with M. abscessus infected and Ouabain treatment were selected for RNA sequencing.

value: lung

value: animals infected with M. abscessus and intraperitoneally injected with saline


title: BO, male, wt, C2

description:
Library name: Adult_BO_male_wt_C2
BRB-seq

value: adult

value: wild-type


title: CLLRT_Pool1_Genotyping

description:
Library name: CLLRT_Pool1_Genotyping
Genotyping


title: Liver - Ctrl_Vehicle - Rep8


title: CLLRT_Pool2_GEX+HTO

description:
Library name: CLLRT_Pool2_GEX+HTO
10x Genomics Gene Expression and Hashing


title: 4cell_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep7

description: Library name: 12

value: 4-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre; JF1 WT

value: C57BL/6J x JF1/MsJ


title: A-1

description: Library name: wt-con58

value: wt

value: non-M. abscessus infected animals and treated with saline, intraperitoneal injection with saline


title: Liver - Ctrl_Vehicle - Rep1


title: Liver - WD_Vehicle - Rep7

value: WD


title: BO, male, wt, C1

description:
Library name: Adult_BO_male_wt_C1
BRB-seq

value: BO

value: male


title: CLLRT_Pool1_GEX+HTO

description:
Library name: CLLRT_Pool1_GEX+HTO
10x Genomics Gene Expression and Hashing


title: BO, male, wt, B2

description:
Library name: Adult_BO_male_wt_B2
BRB-seq


title: AML_MPN_Genotyping

description:
Library name: AML_MPN_Genotyping
Genotyping

value: Acute myeloid leukemia (AML) and Myeloproliferative neoplasm (MPN)


title: lower, male, rep6

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

description:
Library name: 371
male

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: mg39 + Gencode-M27 Annotation
Supplementary files format and content: gene counts

source_name: whole cerebellum

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturers recommendations
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

value: whole cerebellum

value: lower


title: BO, male, wt, B1

description:
Library name: Adult_BO_male_wt_B1
BRB-seq

data_processing:
Quality control and preprocessing of data were performed by SciLicium (France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the Zebrafish reference transcriptome from the UCSC website (danRer11) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: danRer11
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 15,418 genes detected.


title: BO, male, wt, A2

description:
Library name: Adult_BO_male_wt_A2
BRB-seq


title: AML_MPN_GEX+HTO

description:
Library name: AML_MPN_GEX+HTO
10x Genomics Gene Expression and Hashing

value: primary patient sample


title: A-3

description: Library name: wt-con60


title: Liver - WD_Vehicle - Rep3

value: Vehicle


title: higher, male, rep6

description:
Library name: 361
male

value: higher


title: A-2

description: Library name: wt-con59

value: lung


title: BO, male, wt, A1

description:
Library name: Adult_BO_male_wt_A1
BRB-seq

value: adult


title: Liver - Ctrl_Vehicle - Rep4

value: Ctrl


title: MCF7_SKBR3_MUTprobesOnly_GEX

description:
Library name: MCF7_SKBR3_MUTprobesOnly_GEX
10x Genomics Gene Expression

source_name: MCF-7 and SK-BR-3

value: MCF-7 and SK-BR-3

value: breast cancer

value: MUTprobesOnly


title: Liver - Ctrl_CL316243 - Rep2


title: Liver - Ctrl_CL316243 - Rep6


title: higher, female, rep5

description:
Library name: 354
female

value: female


title: BO, female, ko, C1

description:
Library name: Adult_BO_female_ko_C1
BRB-seq

value: cyp19a1b mutant


title: Liver - WD_CL316243 - Rep2

value: WD


title: BO, female, ko, B1

description:
Library name: Adult_BO_female_ko_B1
BRB-seq

value: BO


title: BO, female, ko, A2

description:
Library name: Adult_BO_female_ko_A2
BRB-seq


title: MCF7_SKBR3_WTandMUTprobes_Genotyping

description:
Library name: MCF7_SKBR3_WTandMUTprobes_Genotyping
Genotyping

value: WTandMUTprobes


title: Liver - WD_CL316243 - Rep7


title: lower, female, rep6

description:
Library name: 374
female


title: lower, female, rep5

description:
Library name: 344
female


title: 8s

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Library name: RNA_S8112Nr99

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the H. sapiens reference genome provided by ENSEMBL, (grch38) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from Ensembl GRCh38 genome (version 109) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version 1.42).
Assembly: grch38
Supplementary files format and content: htseq-count output: tab delimited raw counts

source_name: normal bladder

extract_protocol:
Total RNA that was isolated from fresh frozen BC tumor and BM tissues using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer's instructions. Isolated RNA concentration and its purity were assessed by NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) determining the A260/280 and A260/230 ratios, respectively. RNA integrity number (RIN) and distribution value 200 (DV200) were assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA isolates were stored at -80° C. Next, 10 ng of RNA was used to prepare the RNA libraries.
During the library preparation, rRNA was depleted using KAPA RNA HyperPrep with RiboErase and KAPA Globin Depletion Hybridization Oligos (Roche, Basel, Switzerland). SMART-Seq Stranded Kit (Takara Bio, Kusatsu, Japan) was used for low input RNA quantities. The libraries were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Depths of 30 million (6Gb) paired-end 100 bp reads were generated for each sample.

value: normal bladder

value: male

tag: Stage

value: Ta + CIS

tag: grade

value: HIGH


title: Liver - WD_CL316243 - Rep4


title: MCF7_SKBR3_MUTprobesOnly_Genotyping

description:
Library name: MCF7_SKBR3_MUTprobesOnly_Genotyping
Genotyping


title: lower, male, rep5

description:
Library name: 341
male

value: whole cerebellum

value: lower


title: higher, female, rep6

description:
Library name: 364
female

value: higher


title: BO, female, wt, C2

description:
Library name: Adult_BO_female_wt_C2
BRB-seq

extract_protocol:
RNA extraction was performed on three different parts of the brain, corresponding to the OB, the Tel and the hypothalamus. Three zebrafish of the same genotype and sex were pooled for each region. A total of 6 pools of 3 wild-type males and females were obtained, 5 pools of 3 mutant males and 4 pools of 3 mutant females. Samples were homogenized with a mixer pellet pestle (UGAP, REF: 2608725) and total RNA was extracted according to the manufacturer’s protocol (Macherey-Nagel, REF: 740406.50). RNA quantity and quality were assessed using a Nanodrop-1000 spectrophotometer (NanoDrop technology, Cambridge, UK) and a 2100 Bioanalyzer Instrument (Agilent Technologies, CA, USA) following manufacturer’s instructions. Only samples with an RNA integrity number (RIN) score>7 were included.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

tag: developmental stage

value: adult

value: wild-type


title: 7s

description: Library name: RNA_S8112Nr98

tag: tissue

value: Ta

value: LOW


title: control , female, rep5

description:
Library name: 333
female

value: control


title: 4s

description: Library name: RNA_S8112Nr97


title: BO, female, ko, A1

description:
Library name: Adult_BO_female_ko_A1
BRB-seq

value: female


title: control, male, rep5

description:
Library name: 331
male


title: higher, male, rep5

description:
Library name: 351
male


title: 3S

description: Library name: RNA_S8112Nr96


title: Liver - WD_Vehicle - Rep1

value: Vehicle


title: BO, female, wt, C1

description:
Library name: Adult_BO_female_wt_C1
BRB-seq


title: MCF7_SKBR3_WTandMUTprobes_GEX

description:
Library name: MCF7_SKBR3_WTandMUTprobes_GEX
10x Genomics Gene Expression

value: MCF-7 and SK-BR-3

value: breast cancer


title: Liver - WD_Vehicle - Rep6

value: WD


title: BO, female, wt, B2

description:
Library name: Adult_BO_female_wt_B2
BRB-seq

value: BO


title: Liver - Ctrl_CL316243 - Rep8

value: Ctrl


title: control , female, rep4

description:
Library name: 314
female


title: 2S

description: Library name: RNA_S8112Nr95

value: normal bladder

value: male


title: Liver - Ctrl_Vehicle - Rep5


title: Liver - Ctrl_Vehicle - Rep6


title: BO, female, wt, B1

description:
Library name: Adult_BO_female_wt_B1
BRB-seq


title: Liver - WD_CL316243 - Rep1


title: control, male, rep4

description:
Library name: 311
male

value: whole cerebellum


title: 1S

description: Library name: RNA_S8112Nr94

value: HIGH


title: higher, female, rep4

description:
Library name: 305
female

value: higher


title: 146G

description: Library name: RNA_S8112Nr93

source_name: tumour bladder

value: tumour bladder


title: 145G

description: Library name: RNA_S8112Nr92

value: TA


title: higher, male, rep4

description:
Library name: 301
male


title: 12G

description: Library name: RNA_S8112Nr9

value: Ta(m)


title: BO, female, wt, A1

description:
Library name: Adult_BO_female_wt_A1
BRB-seq

value: adult

value: wild-type


title: kidney cells form 4 dpi zebrafish_4

city: chongqing

first: Xiaoliang

last: Liu

address: xinqiao street

institute: Xinqiao Hospital, Army Medical University (Third Military Medical University)

description: BD Rhapsody

data_processing:
The raw data was analyzed by Umi-tools (https://umi-tools.readthedocs.io/en/latest/index.html) using default parameters. Data normalization, dimensionality reduction, clustering, and differential expression analysis were performed using the Seurat package (version 4.2).
Assembly: GRCz11
Supplementary files format and content: Tab-separated walues files and matrix files
Supplementary files format and content: conbined and clustered RDS file
Supplementary files format and content: cluster_15 sub-clustered RDS file

growth_protocol: Zebrafish were maintained in standard conditions under a 14-hours-light and 10-hours-dark cycle and fed three times daily

extract_protocol:
BD Rhapsody system was used to capture the transcriptomic information of the single protoplast.
The cells of each sample were then processed with Single cell 3’ whole transcriptome amplification (WTA) protocol

treatment_protocol: We Injected gentamicin (Gent; 2.7 μg/μL, 20 μL per fish) intraperitoneally to induce AKI. After 4 days post-injury(4 dpi)

value: kidney

value: AB

value: We Injected gentamicin (Gent; 2.7 ug/uL, 20 uL per fish) intraperitoneally to induce AKI.


title: lower, female, rep4

description:
Library name: 297
female

value: lower

value: female


title: Liver - Ctrl_CL316243 - Rep4

source_name: Liver


title: lower, male, rep4

description:
Library name: 291
male


title: Liver - Ctrl_CL316243 - Rep5


title: kidney cells form 4 dpi zebrafish_3

description: BD Rhapsody


title: control , female, rep3

description:
Library name: 283
female

value: control


title: Liver - WD_CL316243 - Rep6

value: WD


title: kidney cells form 4 dpi zebrafish_2

description: BD Rhapsody


title: 144G

description: Library name: RNA_S8112Nr91


title: 143g

description: Library name: RNA_S8112Nr90

value: LOW


title: control, male, rep3

description:
Library name: 281
male

value: male


title: kidney cells form 4 dpi zebrafish_1

description: BD Rhapsody


title: Liver - Ctrl_Vehicle - Rep3

value: Ctrl

value: Vehicle


title: Liver - WD_Vehicle - Rep4


title: BO, female, wt, A2

last: Chalmel

institute: Inserm U1085-Irset

description:
Library name: Adult_BO_female_wt_A2
BRB-seq

value: BO


title: lower, female, rep3

description:
Library name: 274
female

value: whole cerebellum


title: 139g

description: Library name: RNA_S8112Nr88

value: tumour bladder

value: TA


title: 142g

description: Library name: RNA_S8112Nr89


title: Patient 82_mes114

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes114

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 5 HK genes (DHX16, ERCC3, GPATCH3, GUSB, TMUB2). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Diffuse Pleural Mesothelioma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of Diffuse Pleural Mesothelioma were reviewed by two different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 770 genes by NanoString using the nCounter PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Diagnostic biopsies or surgical pleuroctomy from Diffuse Pleural Mesothelioma patients

tag: gender

value: Male

tag: histology

value: sarcomatoid

value: WT


title: Patient 81_mes113

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes113

tag: age

value: DELETED


title: lower, male, rep3

description:
Library name: 271
male

tag: treatment

tag: Sex


title: 138G

description: Library name: RNA_S8112Nr87


title: 136G

description: Library name: RNA_S8112Nr85

value: Ta

value: HIGH


title: cochlear explants, PBS,Control3

city: Nanjing

first: Jingru

last: Ai

state: Jiangsu

address: No. 2, Sipai Lou, Xuanwu District, Nanjing 210096, China.

institute: Southeast University

data_processing:
Using Bowtie2 software (with parameters of -q -L 16 --phred64 -p 6), the clean reads were mapped with the GCF_000001635.26_GRCm38.p6 reference genome to predict miRNAs and other non-coding RNA based on the location of the sequencing data on the genome.
Furthermore, the clean reads were compared with the non-coding RNA database using AASRA software and with the Rfam database using CMSearch software to annotate non-coding RNA. In order to avoid having one small RNA compare two different annotations simultaneously and to keep a unique comment, the small RNA was traversed through the comment in order of precedence: MiRbase > Pirnabank > Rfam > other sRNA.
Assembly: The clean reads were mapped with the GCF_000001635.26_GRCm38.p6 reference genome to predict miRNAs and other non-coding RNA based on the location of the sequencing data on the genome
Supplementary files format and content: tab-delimited text file includes read count for each sample

source_name: cochlear explants-derived sEV

growth_protocol: The dissociation and culture of P3 cochlear explants was cultured with 2 ml DMEM/F12 medium (Gibco, 11330-032) supplemented with 10% (v/v) fetal bovine serum (FBS; PAN biotech, ST30-3302) and 0.05% (v/v) ampicillin at 37 ℃ with 5% CO2.

extract_protocol:
The sEV-free FBS medium was used to culture the cochlear explants with cisplatin for 48 h. The culture supernatant was collected and stored at 4℃, and sEVs were isolated from the supernatant within one week. A series of sequential centrifugation steps were employed to remove cells and cellular debris, including 600 × g for 10 min and 2000 × g for 20 min at 4°C. To remove large vesicles, the supernatant was then filtered through a 0.22 μm filter (Millipore, SLGPR33RB) and centrifugated at 16500 × g at 4°C for 20 min. After concentrating with a 100 kD molecular weight cut-off ultrafiltration device (Pall, Shanghai, China), the sEVs were precipitated by ultracentrifugation at 110,000 × g at 4°C for 2 h using a Himac CP-90NX ultracentrifuge (Himac, Japan). After removing the supernatant, the pellet was resuspended and ultracentrifuged at 110,000 × g for another 2 h to further remove any remaining contaminants. Lastly, the purified sEV pellet was resuspended in 200 μl D-PBS and then stored at –80°C for further use.
Briefly, total RNA was extracted from sEV samples for library construction. The RNA library was purified and separated from 18–30 nt RNA by PAGE electrophoresis, and then small RNA was reverse transcribed as cDNA and further amplified. After filtering by quality, the small RNA libraries were sequenced on the DNBSEQ platform.
The raw data were evaluated and further filtered to obtain clean tags, which were stored in FASTQ format and used for next analysis.

treatment_protocol: After the cochlear explants being allowed to recover overnight, the explants were washed twice using phosphate-buffered saline (PBS). 50 μM cisplatin (Sigma, P4394) or an equal volume of PBS was then treated for 48 h to induce ototoxicity ex vivo.

value: cochlear explants-derived sEV

tag: genotype

value: Control

value: PBS


title: cochlear explants, PBS, Control2


title: Patient 79_mes111

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes111


title: Patient 80_mes112

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes112


title: 135G

description: Library name: RNA_S8112Nr84

value: female

value: LOW


title: cochlear explants, PBS, Control1


title: Patient 78_mes110

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes110


title: cochlear explants, 50 μM cisplatin，Cisplatin3

value: cisplatin-induced ototoxicity

value: 50 uM cisplatin


title: Liver - WD_CL316243 - Rep8

last: Guillou

institute: INRAE

extract_protocol: Total cellular RNA from liver was extracted with Trizol Reagent® (Molecular Research Center, Inc., Cincinnati, OH, USA).

tag: diet

value: WD


title: 134G

description: Library name: RNA_S8112Nr83

value: male


title: 131G

description: Library name: RNA_S8112Nr82

value: tumour bladder


title: Liver - Ctrl_CL316243 - Rep7

value: Ctrl


title: Patient 76_mes107

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes107

value: Male


title: cochlear explants, 50 μM cisplatin，Cisplatin2


title: RK_Ars_insoluble-Rep3

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description: Library name: S24

data_processing:
Sequences were aligned to the human genome GRCh38.p13 (GRCh38_r98.all, GENCODE release 40) using STAR 2.7.2b. SAMtools (v1.2) was used to convert aligned SAM files to BAM files, and reads were counted using the feature-Counts function of the Subreads package  using a homemade gencode_v40annotation_intron.gtf annotation file. CircRNA was detected from chimeric reads by DCC 0.5.0 , the tool identifying circRNA via back-splice junctions.
Assembly: GRCh38.p13
Supplementary files format and content: Gencodecounts40INT.csv
Supplementary files format and content: Gencodecounts40INTIntron.csv
Supplementary files format and content: CircRNACount
Supplementary files format and content: LinearCount.csv

extract_protocol:
RNAs were extracted with Zymo Direct-zol RNA Microprep Kits as per manufacturer recommendations (Zymo, Tustin, CA, USA), and RNA quality was evaluated on RNA-1000 chip using Bioanalyzer (Agilent, Santa Clara, CA, USA).
RNA libraries were prepared using an established protocol with NEBNext Ultra II Directional Library Prep Kit (NEB, Lynn, MA, USA). Each library was made with one of the TruSeq barcode index sequences and had a 1:200 dilution of Spike-in SIRV_Set3 (Lexogen, Greenland, NH, USA) added.

tag: cell type

value: osteosarcoma

value: Sodium arsenite + RK-33

tag: sample group


title: Patient 75_mes106

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes106

value: sarcomatoid

value: DELETED


title: RK_Ars_insoluble-Rep2

description: Library name: S23

tag: cell line


title: Liver - WD_Vehicle - Rep5

value: Vehicle


title: Liver - WD_Vehicle - Rep2


title: 11g

description: Library name: RNA_S8112Nr8

value: Ta


title: Liver - WD_CL316243 - Rep3


title: Liver - Ctrl_Vehicle - Rep2


title: 130g

description: Library name: RNA_S8112Nr81


title: RK_Ars_insoluble-Rep1

description: Library name: S22


title: higher, female, rep3

description:
Library name: 266
female

value: whole cerebellum

tag: strain

value: higher


title: Patient 74_mes105

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes105


title: 129G

description: Library name: RNA_S8112Nr80

value: TA


title: higher, male, rep3

description:
Library name: 261
male


title: 127G

description: Library name: RNA_S8112Nr79

value: HIGH


title: RK_Ars_soluble-Rep3

description: Library name: S21


title: Patient 73_mes104

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes104

value: WT


title: Patient 77_mes109

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes109


title: RK_Ars_soluble-Rep2

description: Library name: S20


title: 126G

description: Library name: RNA_S8112Nr78


title: Liver - Ctrl_Vehicle - Rep7


title: lower, female, rep2

description:
Library name: 255
female

value: lower

value: female


title: Patient 72_mes103

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes103


title: Patient 71_mes101

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes101

value: biphasic


title: RK_Ars_soluble-Rep1

description: Library name: S19


title: lower, male, rep2

description:
Library name: 251
male

value: male


title: cochlear explants, 50 μM cisplatin，Cisplatin1

value: cochlear explants-derived sEV

value: cisplatin-induced ototoxicity

value: 50 uM cisplatin


title: Liver - Ctrl_CL316243 - Rep3

value: Ctrl


title: higher, female, rep2

description:
Library name: 245
female


title: Patient 70_mes100

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes100

value: Female

value: epithelioid


title: RK_insoluble-Rep3

description: Library name: S18

value: osteosarcoma


title: RK_insoluble-Rep2

description: Library name: S17


title: Patient 69_mes99

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes99

value: Male


title: higher, male, rep2

description:
Library name: 241
male

value: whole cerebellum


title: RK_insoluble-Rep1

description: Library name: S16


title: Patient 68_mes98

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes98

value: DELETED


title: RK_soluble-Rep3

description: Library name: S15


title: control, male, rep2

description:
Library name: 231
male

value: control


title: Patient 67_mes97

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes97


title: 123G

description: Library name: RNA_S8112Nr75

value: tumour bladder

value: TA

value: LOW


title: control , female, rep1

description:
Library name: 224
female

value: female


title: 116g

description: Library name: RNA_S8112Nr72

value: Ta


title: 125G

description: Library name: RNA_S8112Nr77


title: Patient 66_mes96

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes96

value: biphasic

value: WT


title: 115g

description: Library name: RNA_S8112Nr71


title: control, male, rep1

description:
Library name: 221
male

value: male


title: Patient 65_mes93

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes93


title: RK_soluble-Rep1

description: Library name: S13


title: Ars_insoluble-Rep3

description: Library name: S12

value: Sodium arsenite


title: 114G

description: Library name: RNA_S8112Nr70


title: 109G

description: Library name: RNA_S8112Nr68


title: Patient 64_mes88

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes88


title: 124G

description: Library name: RNA_S8112Nr76


title: lower, male, rep1

description:
Library name: 211
male

value: lower


title: lower, female, rep1

description:
Library name: 213
female


title: 106G

description: Library name: RNA_S8112Nr67


title: Patient 63_mes87

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes87

value: Female


title: Ars_insoluble-Rep2

description: Library name: S11


title: Ars_insoluble-Rep1

description: Library name: S10


title: higher, female, rep1

description:
Library name: 205
female

value: higher


title: 120g

description: Library name: RNA_S8112Nr73

value: HIGH


title: 105g

description: Library name: RNA_S8112Nr66


title: Ars_soluble-Rep3

description: Library name: S09

value: osteosarcoma


title: higher, male, rep1

description:
Library name: 201
male

value: whole cerebellum


title: 104G

description: Library name: RNA_S8112Nr65


title: RK_soluble-Rep2

description: Library name: S14


title: Patient 60_mes83

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes83

value: Male


title: Ars_soluble-Rep2

description: Library name: S08


title: DDE9-Spheroid-B16-CrisprCCRL2-day6-210120.9

city: Jette

first: Diana

last: Al Delbany

address: Laarbeeklaan 103

country: Belgium

institute: Vrije universiteit Brussel

description: Library name: Sample 9

data_processing:
The multiplexed libraries (10 pM) were loaded on flow cells, and sequences were 187 produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS from a NovaSeq 6000 188 system (Illumina) at the Brussels Interuniversity Genomics High Throughput core 189 (www.brightcore.be).
Approximately 29 to 33 million paired-end reads per sample were 190 mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR soft-191 ware to generate read alignments for each sample
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: Text file (.txt) containing raw read counts per gene (rows = genes, columns = samples). Generated using HTSeq.

source_name: Skin

growth_protocol: Spheroids were cultured in 10% FBS-370 containing medium and harvested on day 6

extract_protocol:
RNA was extracted with the RNAeasy Minikit (Qiagen) fol-183 lowing the manufacturer's instructions.RNA quality was checked using a Fragment An-184 alyzer (Agilent Technologies).
Indexed cDNA libraries were obtained using the NuGEN 185 SoLo RNA sample preparation kit (TECAN) following the manufacturer's recommenda-186 tions.

treatment_protocol: No treatement

value: Skin

value: Melanoma cells

value: CCRL2 Knockout

value: No treatment

tag: batch


title: 99G

description: Library name: RNA_S8112Nr64

value: tumour bladder

value: female

value: Ta(m)

value: LOW


title: Ars_soluble-Rep1

description: Library name: S07


title: DDE8-Spheroid-B16-CrisprCCRL2-day6-210103.8

description: Library name: Sample 8


title: Patient 59_mes81

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes81

value: biphasic

value: WT


title: Ctrl_insoluble-Rep3

description: Library name: S06

value: Control


title: 98G

description: Library name: RNA_S8112Nr63


title: Patient 58_mes80

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes80

value: DELETED


title: DDE7-Spheroid-B16-CrisprCCRL2-day6-210103.7

description: Library name: Sample 7


title: Ctrl_insoluble-Rep2

description: Library name: S05


title: 97g

description: Library name: RNA_S8112Nr62

value: Ta


title: 8g

description: Library name: RNA_S8112Nr6

value: male

value: Ta + CIS

value: HIGH


title: Patient 62_mes85

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes85

value: Male


title: Patient 57_mes79

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes79


title: Patient 56_mes78

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes78

value: sarcomatoid


title: DDE6-Spheroid-B16-CCRL2-day6-210120.6

description: Library name: Sample 6

value: Skin

value: Melanoma cells

value: CCRL2 overexpression


title: 95G

description: Library name: RNA_S8112Nr61

value: tumour bladder


title: Patient 61_mes84

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes84

value: Female


title: Ctrl_soluble-Rep3

description: Library name: S03

value: osteosarcoma


title: Patient 55_mes77

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes77

value: epithelioid


title: DDE5-Spheroid-B16-CCRL2-day6-210218.5

description: Library name: Sample 5

value: No treatment


title: Ctrl_soluble-Rep2

description: Library name: S02


title: DDE4-Spheroid-B16-CCRL2-day6-210218.4

description: Library name: Sample 4


title: 93G

description: Library name: RNA_S8112Nr60

value: female

value: Ta(m)

value: LOW


title: DDE3-Spheroid-B16-WT-day6-210218.3

description: Library name: Sample 3

value: WT


title: 92G

description: Library name: RNA_S8112Nr59


title: Ctrl_soluble-Rep1

description: Library name: S01

value: Control


title: Patient 54_mes75

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes75


title: Patient 53_mes74

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes74


title: DDE2-Spheroid-B16-WT-day6-210103.2

description: Library name: Sample 2


title: 91g

description: Library name: RNA_S8112Nr58


title: Rectal Tumor from injected AKPS SI tumor Organoid Rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description:
Library name: MGR18210204_S18
Column name in MGR18210204_Raw_counts_matrix.csv

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Rectum

growth_protocol: Organoids were grown in advanced DMEM media suplemented with L-glutamine (2mM) HEPES (10mM) Penicillin (100u/ml) Streptomycin (100ug/ml), N2 supplement (1x) B27 supplement (1x) human EGF (50ng/ml) and murine Noggin (100ng/ml). Organoids were passaged up to 3 times a week depending on growth and media was refreshed 3 times a week. Organoids were incubated at 37°C, 5% CO2, 21% O2.

extract_protocol:
For tissues, pieces of tumor or intestinal tissue were sampled from mice, placed in RNAlater and stored at -80°C before extraction. For organoids, confluent organoid samples were grown and a cell pellet was snapped frozen on dry ice. RNA was extracted from samples using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. For tissues, homogenisation was done by using Precellys ceramic bead filled tubes in a Precellys Evolution machine (Bertin Instruments). For organoid pellets, cells were dissociated using pipetting in the 1st step of the extraction protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA LT kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

value: Rectum

tag: sample type

value: Intrarectal Tumor

tag: injected organoid_id

value: RKAN15.2a SIT

value: VilCreER Apc fl/fl KrasG12D/+ p53 fl/fl Smad4 fl/fl

value: Injected SI tumor Organoids


title: control , female, rep2

description:
Library name: 234
female

value: whole cerebellum

value: control


title: Patient 52_mes73

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes73

value: Male


title: Rectal Tumor from injected AKPS SI tumor Organoid Rep 2

description:
Library name: MGR18210204_S17
Column name in MGR18210204_Raw_counts_matrix.csv


title: DDE1-Spheroid-B16-WT-day6-210103.1

description: Library name: Sample 1

value: Skin

value: Melanoma cells


title: 89g

description: Library name: RNA_S8112Nr56

value: tumour bladder

tag: Stage

value: Ta

tag: grade


title: Patient 51_mes72

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes72

value: Female

value: biphasic

value: DELETED


title: 88g

description: Library name: RNA_S8112Nr55

tag: tissue

value: female

value: LOW


title: Ctrl_insoluble-Rep1

description: Library name: S04

value: osteosarcoma

value: Control


title: Patient 50_mes71

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes71

tag: gender

value: epithelioid


title: Rectal Tumor from injected AKPS SI tumor Organoid Rep 1

description:
Library name: MGR18210204_S16
Column name in MGR18210204_Raw_counts_matrix.csv

value: Rectum

value: Intrarectal Tumor

value: RKAN15.2a SIT

value: VilCreER Apc fl/fl KrasG12D/+ p53 fl/fl Smad4 fl/fl


title: WT-IgG

first: Mike

last: Adam

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description:
Library name: WT-IgG
10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (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

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: adenocarcenoma

value: WT

value: IgG


title: 87g

description: Library name: RNA_S8112Nr54

value: tumour bladder

value: Ta(m)


title: Patient 49_mes70

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes70

value: Male

tag: histology


title: KPN Organoid from SI tumor Rep 5

description:
Library name: RJR18200309_S9
Column name in RJR18200309_Raw_counts_matrix.csv

source_name: SI

value: SI

value: Organoid from SI tumor

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: 84G

description: Library name: RNA_S8112Nr53

value: male

value: LOW


title: KPN Organoid from SI tumor Rep 4

description:
Library name: RJR18200309_S8
Column name in RJR18200309_Raw_counts_matrix.csv


title: A159V-aPD1

description:
Library name: A159V-aPD1
10x genomics


title: Patient 48_mes69

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes69

tag: age


title: 83g

description: Library name: RNA_S8112Nr52

value: HIGH


title: Patient 46_mes66

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes66

value: epithelioid


title: WT-aPD1-2, RNAseq

description: Library name: WT-aPD1-2

data_processing:
Reads were aligned to the mm10 genome to create bam files. Aligned reads were counted with the R library GenomicAlignments function summarizeOverlaps to generate a
reads per gene counts matrix for each sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values, raw counts

extract_protocol:
Qiagen; RNeasy Micro Kit
Illumina RNA-seq Library Preparation Kit

tag: treatment


title: 7g

description: Library name: RNA_S8112Nr5

tag: Sex

value: Ta


title: WT-aPD1-1, RNAseq

description: Library name: WT-aPD1-1

tag: genotype


title: A159V-IgG

description:
Library name: A159V-IgG
10x genomics


title: KPN Organoid from SI tumor Rep 2

description:
Library name: RJR18200309_S14
Column name in RJR18200309_Raw_counts_matrix.csv


title: 81MD_g

description: Library name: RNA_S8112Nr50


title: Patient 45_mes64

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes64

value: Female

value: biphasic

value: DELETED


title: KPN Organoid from SI tumor Rep 3

description:
Library name: RJR18200309_S7
Column name in RJR18200309_Raw_counts_matrix.csv


title: KPN Organoid from liver Met Rep 4

description:
Library name: RJR18200309_S15
Column name in RJR18200309_Raw_counts_matrix.csv

value: Liver

value: Organoid from Liver Metastasis


title: 78g

description: Library name: RNA_S8112Nr49


title: KPN Organoid from SI tumor Rep 1

description:
Library name: RJR18200309_S12
Column name in RJR18200309_Raw_counts_matrix.csv


title: KPN Organoid from liver Met Rep 3

description:
Library name: RJR18200309_S13
Column name in RJR18200309_Raw_counts_matrix.csv


title: WT-IgG-4, RNAseq

description: Library name: WT-IgG-4

value: adenocarcenoma

value: WT

value: IgG


title: WT-IgG-2, RNAseq

description: Library name: WT-IgG-2


title: Patient 43_mes62

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes62

value: Male


title: WT-aPD1-3, RNAseq

description: Library name: WT-aPD1-3


title: 76G

description: Library name: RNA_S8112Nr48

value: tumour bladder


title: 82g

description: Library name: RNA_S8112Nr51


title: Patient 44_mes63

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes63

value: sarcomatoid


title: Patient 42_mes61

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes61


title: WT-IgG-1, RNAseq

description: Library name: WT-IgG-1


title: KPN Organoid from liver Met Rep 2

description:
Library name: RJR18200309_S11
Column name in RJR18200309_Raw_counts_matrix.csv

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: 73G

description: Library name: RNA_S8112Nr47

value: male

value: TA


title: Colon Tumor from injected KPN SI tumor Organoid Rep 6

description:
Library name: MGR18210204_S6
Column name in MGR18210204_Raw_counts_matrix.csv

source_name: Colon

value: Colon

value: Intracolonic tumor

value: RKAC3.2f SIT

value: VilCreER KrasG12D/+ p53 fl/fl NotchTg/+

value: Injected SI tumor Organoids


title: Patient 41_mes60

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes60

value: Female

value: epithelioid

value: DELETED


title: KPN Organoid from liver Met Rep 1

description:
Library name: RJR18200309_S10
Column name in RJR18200309_Raw_counts_matrix.csv

value: Liver

value: Organoid from Liver Metastasis


title: A159V-aPD1-2, RNAseq

description: Library name: A159V-aPD1-2

value: adenocarcenoma


title: A159V-aPD1-3, RNAseq

description: Library name: A159V-aPD1-3


title: 72G

description: Library name: RNA_S8112Nr46

value: LOW


title: Patient 40_mes58

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes58

value: Male


title: 71G

description: Library name: RNA_S8112Nr45

value: tumour bladder

value: Ta