title: Pleural mesothelioma, tumor, sample TB_CaseID_27652

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

description:
Library name: TB_CaseID_27652
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: TB_CaseID:27652

data_processing:
Reads were processed using the Drop-seq tools pipeline aligned to the hg38 transcriptome using standard parameters.
Raw sequencing data are available through controlled access in dbGaP under accession phs004285.
Processed files provided here include per-library count matrices and corresponding cell-level metadata files.
Assembly: hg38
Supplementary files format and content: Sparse counts matrices (initial and stringently filtered cells) with associated column and row name files are formatted in tab-delmited compressed text files. Metadata for cells is formatted as a compressed tab delimited text file.

source_name: Tumor

extract_protocol:
Single-cell suspensions were generated from surgical pleural specimens after tissue dissociation. Seq-Well arrays containing RNA capture beads were loaded with approximately 10,000-20,000 cells per array. For selected specimens, technical replicates were created by splitting cell suspensions across multiple arrays processed in parallel.
Single-cell RNA sequencing libraries were generated using the Seq-Well platform. Cells were loaded onto bead-containing arrays, sealed with a membrane, lysed, and RNA was captured on beads. Reverse transcription, second-strand synthesis, whole transcriptome amplification, and Nextera XT library construction were performed prior to sequencing on Illumina NextSeq 500/550 or NovaSeq 6000 instruments.

value: Tumor

tag: diagnosis

value: Pleural Mesothelioma

tag: histology

value: E

tag: age at_surgery

tag: tumor status

value: Yes

tag: subject id


title: Pleural mesothelioma, tumor, sample TB_CaseID_27650

status: Public on Apr 07 2026

type: SRA

country: USA

description:
Library name: TB_CaseID_27650
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: TB_CaseID:27650

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: B


title: nmumg_hgr_wt_4

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Library name: nmumg_hgr_wt_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d) for yeast and deeptools bamtoBigWig for mammalian samples
Assembly: Yeast-GCA_000146045.2 (R64), Mouse-mm10, Human-hg38
Supplementary files format and content: Yeast - .out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Supplementary files format and content: Mammalian- bw files contain averaged between repeats BigWIg files using CPM and bin size of 1 bp

molecule: genomic DNA

organism: Mus musculus

source_name: NMuMG

growth_protocol: Yeast - Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose; Mammalian- cells were deluted and grown until ~1.4 M cells

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021

tag: cell line

value: NMuMG

tag: treatment

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Pleural mesothelioma, tumor, sample TB_CaseID_27448

description:
Library name: TB_CaseID_27448
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: TB_CaseID:27448


title: nmumg_hgr_wt_5

description:
Library name: nmumg_hgr_wt_5
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_35

city: Galveston

first: Marie

last: Kubota

state: TX

address: 301 University Blvd

department: Otolaryngology

institute: University of Texas Medical Branch

description: Library name: Cell_35

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: mm10 (GRCm38)
Supplementary files format and content: text file with raw read counts

source_name: organoid

growth_protocol: Greater epithelial ridge cells, enriched by flow cytometry, were cultured in DMEM/F12-based proliferation medium to induce organoid formation for 1, 3, and 7 days.

extract_protocol:
Harvested organoids were rinsed in PBS and incubated in 0.25% Trypsin-EDTA at 37°C and 5% CO2 for 10-20 min. After the addition of soybean trypsin inhibitor, the samples were mechanically dissociated. Single cells were manually collected using a glass micropipette (50-60µm inner diameter) and transferred into 96-well plates.
SmartSeq2 protocol

treatment_protocol: The growth medium consisted of DMEM/F-12 supplemented with 1x N-2 Supplement, 1x B-27 Supplement, 100 µg/mL ampicillin, growth factors (20 ng/mL EGF, 10 ng/mL FGF2, and 50 ng/mL IGF1), and small molecules (3µM CHIR99021, 500 µM valproic acid, 100 µg/mL 2-phospho-L-ascorbic acid, and 2 µM TGFß receptor inhibitor 616452).

tag: strain

tag: cell source

value: P2 mouse cochlear greater epithelial ridge cells

tag: cell type

value: organoid

tag: timepoint

tag: replicate


title: nmumg_hgr_wt_3

description:
Library name: nmumg_hgr_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_36

description: Library name: Cell_36


title: KCTR1LACT-B3

city: Urbana

first: Rishabh

last: Singh

state: Iillinois

address: 1604 Melrose VAlley Ct

department: Agronomy

institute: Kansas State University

description:
Library name: Sample 40
150bp-paired end illumina sequencing

library_source: transcriptomic

data_processing:
Trimmomatic + FastQC + STAR + DESeq2
Quality of the raw RNA-Seq data was assessed and the adaptor sequences were trimmed using Trimmomatic with default parameters (Bolger et al. 2014).
Trimmed reads were aligned to the Palmer amaranth genome (Raiyemo et al. 2025; A. palmeri Hap1; JBEFMX000000000) using STAR (Dobin et al. 2013) with the  --quantModeGeneCounts function, which simultaneously performed alignment and generated per-gene read counts for each sample
Read counts per gene were then subjected to a pairwise differential gene expression (DGE) analysis using DEseq2 (Love et al. 2014).
Assembly: Reads were aligned to Palmer amaranth genome
Supplementary files format and content: csv

organism: Amaranthus palmeri

source_name: leaf

growth_protocol: plants were raised from seeds and grown under growth chamber conditions with at 32/22 C day/night (d/n) temperatures, 60 ± 10% relative humidity, and 16/8 d/n photoperiod, provided by fluorescent bulbs delivering 500 μ mol m-2 s-1 illumination at plant canopy level.

extract_protocol:
Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit® (Thermo Fischer Scientific) following manufacturer’s instructions
stranded polyA
150bp-paired end illumina sequencing

treatment_protocol: all herbicides were applied at 10-12 cm height stage using a bench type sparayer caliberated to deliver 187L/ha.

value: leaf

tag: phenotype

value: Resistant

value: lactofen

tag: batch


title: Atypical Carcinoid, pleura, sample BULKRNA138725-1

description:
Library name: BULKRNA138725-1
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA138725-1

data_processing:
Quality-controlled reads were aligned to the human reference genome (hg38) using STAR, and gene-level counts were generated using GENCODE v28 annotation.
Raw sequencing data are available through controlled access in dbGaP under accession phs004285.
Raw counts were normalized to transcripts per million (TPM), with library size adjustment performed using trimmed mean of M-values normalization in edgeR.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw and TPM-normalized gene expression values for all bulk RNA-seq libraries.
Supplementary files format and content: Tab-delimited text file containing per-sample metadata aligned to dbGaP sample identifiers

molecule: polyA RNA

source_name: Pleura

extract_protocol:
Extracted RNA from bulk tissue specimens was shipped on dry ice for library preparation. Polyadenylated RNA was enriched using poly-T oligo-attached magnetic beads.
Stranded cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit and sequenced on an Illumina NovaSeq 6000 to a depth of approximately 100 million paired-end 100 bp reads per sample.

value: Pleura

value: Atypical Carcinoid

value: NP

value: No


title: Pleural Mesothelioma, tumor, sample BULKRNA193780-O

description:
Library name: BULKRNA193780-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA193780-O


title: KCTR4NT-B3

description:
Library name: Sample 38
150bp-paired end illumina sequencing

value: control


title: nmumg_hgr_wt_1

description:
Library name: nmumg_hgr_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_34

description: Library name: Cell_34


title: KCTR4LACT-B3

description:
Library name: Sample 41
150bp-paired end illumina sequencing


title: KSS5NT-B3

description:
Library name: Sample 44
150bp-paired end illumina sequencing

value: Susceptible


title: KCTR1NT-B3

description:
Library name: Sample 37
150bp-paired end illumina sequencing


title: KCTR8NT-B3

description:
Library name: Sample 39
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_33

description: Library name: Cell_33


title: nmumg_hgr_dlbd_dn50_4

description:
Library name: nmumg_hgr_dlbd_dn50_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KCTR8LACT-B3

description:
Library name: Sample 42
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA123895-O

description:
Library name: BULKRNA123895-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA123895-O

value: Tumor

value: Pleural Mesothelioma


title: Pleural Mesothelioma, tumor, sample BULKRNA151208-2

description:
Library name: BULKRNA151208-2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA151208-2

value: E

value: Yes


title: Day7.organoid.Rep1_Cell_32

description: Library name: Cell_32


title: KSS7NT-B2

description:
Library name: Sample 36
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_31

description: Library name: Cell_31


title: nmumg_hgr_wt_2

description:
Library name: nmumg_hgr_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG


title: nmumg_hgr_dlbd_dn50_3

description:
Library name: nmumg_hgr_dlbd_dn50_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: nmumg_hgr_dlbd_dn50_2

description:
Library name: nmumg_hgr_dlbd_dn50_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KSS6NT-B2

description:
Library name: Sample 35
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA158520-O

description:
Library name: BULKRNA158520-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA158520-O


title: nmumg_hgr_dlbd_dn50_1

description:
Library name: nmumg_hgr_dlbd_dn50_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_29

description: Library name: Cell_29

value: P2 mouse cochlear greater epithelial ridge cells


title: nmumg_hgr_DBD_3

description:
Library name: nmumg_hgr_DBD_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KSS5NT-B2

description:
Library name: Sample 34
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_30

description: Library name: Cell_30

value: organoid


title: KCTR7NT-B2

description:
Library name: Sample 32
150bp-paired end illumina sequencing

value: leaf


title: Pleural Mesothelioma, tumor, sample BULKRNA195005-3

description:
Library name: BULKRNA195005-3
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA195005-3

value: S


title: Day7.organoid.Rep1_Cell_27

description: Library name: Cell_27


title: Pleural Mesothelioma, tumor, sample BULKRNA195890-O

description:
Library name: BULKRNA195890-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA195890-O


title: Day7.organoid.Rep1_Cell_28

description: Library name: Cell_28


title: KCTR8NT-B2

description:
Library name: Sample 33
150bp-paired end illumina sequencing

value: Resistant


title: nmumg_hgr_DBD_2

description:
Library name: nmumg_hgr_DBD_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA146334-O

description:
Library name: BULKRNA146334-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA146334-O


title: Pleural Mesothelioma, tumor, sample BULKRNA131427-2

description:
Library name: BULKRNA131427-2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA131427-2

value: B


title: KCTR5NT-B2

description:
Library name: Sample 31
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA106083-2

description:
Library name: BULKRNA106083-2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA106083-2


title: KSS7CHL-B2

description:
Library name: Sample 30
150bp-paired end illumina sequencing

value: chlorsulfuron


title: nmumg_hgr_dlbd_dn300_4

description:
Library name: nmumg_hgr_dlbd_dn300_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KSS5CHL-B2

description:
Library name: Sample 28
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA104124-O

description:
Library name: BULKRNA104124-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA104124-O


title: nmumg_hgr_DBD_1

description:
Library name: nmumg_hgr_DBD_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_26

description: Library name: Cell_26


title: nmumg_hgr_dlbd_dn300_3

description:
Library name: nmumg_hgr_dlbd_dn300_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_24

description: Library name: Cell_24


title: Pleural Mesothelioma, tumor, sample BULKRNA183762-O

description:
Library name: BULKRNA183762-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA183762-O


title: KSS6CHL-B2

description:
Library name: Sample 29
150bp-paired end illumina sequencing


title: nmumg_hgr_dlbd_dn300_2

description:
Library name: nmumg_hgr_dlbd_dn300_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_25

description: Library name: Cell_25


title: Day7.organoid.Rep1_Cell_23

description: Library name: Cell_23


title: KSS7ATR-B2

description:
Library name: Sample 27
150bp-paired end illumina sequencing

value: atrazine


title: nmumg_hgr_dlbd_dn300_1

description:
Library name: nmumg_hgr_dlbd_dn300_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA193332-2

description:
Library name: BULKRNA193332-2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA193332-2


title: KSS5ATR-B2

description:
Library name: Sample 25
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA151311-H

description:
Library name: BULKRNA151311-H
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA151311-H


title: nmumg_hgr_dlbd_dn250_3

description:
Library name: nmumg_hgr_dlbd_dn250_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA115261-O

description:
Library name: BULKRNA115261-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA115261-O


title: Day7.organoid.Rep1_Cell_21

description: Library name: Cell_21


title: nmumg_hgr_dlbd_dn250_4

description:
Library name: nmumg_hgr_dlbd_dn250_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_19

description: Library name: Cell_19


title: KSS6ATR-B2

description:
Library name: Sample 26
150bp-paired end illumina sequencing


title: KSS5MESO-B1

description:
Library name: Sample 22
150bp-paired end illumina sequencing

value: mesotrione


title: nmumg_hgr_dlbd_dn250_2

description:
Library name: nmumg_hgr_dlbd_dn250_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_22

description: Library name: Cell_22


title: Pleural Mesothelioma, tumor, sample BULKRNA181196-2

description:
Library name: BULKRNA181196-2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA181196-2


title: nmumg_hgr_dlbd_dn250_1

description:
Library name: nmumg_hgr_dlbd_dn250_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_20

description: Library name: Cell_20


title: KSS7MESO-B1

description:
Library name: Sample 24
150bp-paired end illumina sequencing


title: nmumg_hgr_dlbd_dn150_3

description:
Library name: nmumg_hgr_dlbd_dn150_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA188018-O

description:
Library name: BULKRNA188018-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA188018-O


title: Pleural Mesothelioma, tumor, sample BULKRNA179872-3

description:
Library name: BULKRNA179872-3
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA179872-3

value: NM


title: KSS6MESO-B1

description:
Library name: Sample 23
150bp-paired end illumina sequencing

value: Susceptible


title: nmumg_hgr_dlbd_dn150_4

description:
Library name: nmumg_hgr_dlbd_dn150_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_17

description: Library name: Cell_17


title: Pleural Mesothelioma, tumor, sample BULKRNA112946-O

description:
Library name: BULKRNA112946-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA112946-O

value: Tumor


title: KSS624D-B1

description:
Library name: Sample 20
150bp-paired end illumina sequencing


title: KSS724D-B1

description:
Library name: Sample 21
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_18

description: Library name: Cell_18


title: Day7.organoid.Rep1_Cell_16

description: Library name: Cell_16


title: Pleural Mesothelioma, tumor, sample BULKRNA194441-O

description:
Library name: BULKRNA194441-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA194441-O

value: Pleural Mesothelioma


title: Pleural Mesothelioma, tumor, sample BULKRNA155040-O

description:
Library name: BULKRNA155040-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA155040-O

value: E


title: Pleural Mesothelioma, tumor, sample BULKRNA114626-O

description:
Library name: BULKRNA114626-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA114626-O

value: Yes


title: KSS7NT-B1

description:
Library name: Sample 18
150bp-paired end illumina sequencing

value: control


title: KSS6NT-B1

description:
Library name: Sample 17
150bp-paired end illumina sequencing


title: nmumg_hgr_dlbd_2

description:
Library name: nmumg_hgr_dlbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: nmumg_hgr_dlbd_dn150_2

description:
Library name: nmumg_hgr_dlbd_dn150_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_hgr_dlbd_dn150_1

description:
Library name: nmumg_hgr_dlbd_dn150_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_15

description: Library name: Cell_15

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid


title: Pleural Mesothelioma, tumor, sample BULKRNA130099-O

description:
Library name: BULKRNA130099-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA130099-O

value: S


title: Day7.organoid.Rep1_Cell_14

description: Library name: Cell_14


title: Day7.organoid.Rep1_Cell_12

description: Library name: Cell_12


title: KSS524D-B1

description:
Library name: Sample 19
150bp-paired end illumina sequencing

value: leaf


title: nmumg_hgr_dlbd_3

description:
Library name: nmumg_hgr_dlbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KSS5NT-B1

description:
Library name: Sample 16
150bp-paired end illumina sequencing


title: nmumg_hgr_dN350_4

description:
Library name: nmumg_hgr_dN350_4
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_11

description: Library name: Cell_11


title: nmumg_hgr_dlbd_1

description:
Library name: nmumg_hgr_dlbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA105944-O

description:
Library name: BULKRNA105944-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA105944-O


title: Day7.organoid.Rep1_Cell_13

description: Library name: Cell_13


title: Pleural Mesothelioma, tumor, sample BULKRNA103805-O

description:
Library name: BULKRNA103805-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA103805-O


title: Pleural Mesothelioma, tumor, sample BULKRNA162703-O

description:
Library name: BULKRNA162703-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA162703-O


title: Day7.organoid.Rep1_Cell_9

description: Library name: Cell_9


title: nmumg_hgr_dN350_3

description:
Library name: nmumg_hgr_dN350_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_10

description: Library name: Cell_10


title: KCTR7CHL-B2

description:
Library name: Sample 14
150bp-paired end illumina sequencing

value: Resistant


title: KCTR8CHL-B2

description:
Library name: Sample 15
150bp-paired end illumina sequencing

value: chlorsulfuron


title: nmumg_hgr_dN350_2

description:
Library name: nmumg_hgr_dN350_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KCTR5CHL-B2

description:
Library name: Sample 13
150bp-paired end illumina sequencing


title: KCTR7ATR-B2

description:
Library name: Sample 11
150bp-paired end illumina sequencing

value: atrazine


title: Pleural Mesothelioma, tumor, sample BULKRNA147026-O

description:
Library name: BULKRNA147026-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA147026-O

value: B


title: nmumg_gr_dlbd_dn100_3

description:
Library name: nmumg_gr_dlbd_dn100_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KCTR8ATR-B2

description:
Library name: Sample 12
150bp-paired end illumina sequencing


title: nmumg_hgr_dN350_1

description:
Library name: nmumg_hgr_dN350_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_7

description: Library name: Cell_7


title: Pleural Mesothelioma, tumor, sample BULKRNA107932-3

description:
Library name: BULKRNA107932-3
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA107932-3


title: Pleural Mesothelioma, tumor, sample BULKRNA167915-O

description:
Library name: BULKRNA167915-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA167915-O


title: Day7.organoid.Rep1_Cell_8

description: Library name: Cell_8


title: Day7.organoid.Rep1_Cell_6

description: Library name: Cell_6


title: Pleural Mesothelioma, tumor, sample BULKRNA197652-O

description:
Library name: BULKRNA197652-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA197652-O


title: nmumg_gr_dlbd_dn100_2

description:
Library name: nmumg_gr_dlbd_dn100_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KCTR5ATR-B2

description:
Library name: Sample 10
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_5

description: Library name: Cell_5


title: KCTR8MESO-B1

description:
Library name: Sample 9
150bp-paired end illumina sequencing

value: mesotrione


title: Day7.organoid.Rep1_Cell_4

description: Library name: Cell_4


title: Pleural Mesothelioma, tumor, sample BULKRNA145511-O

description:
Library name: BULKRNA145511-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA145511-O


title: nmumg_ar_dlbd_dn200_3

description:
Library name: nmumg_ar_dlbd_dn200_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: nmumg_gr_dlbd_dn100_1

description:
Library name: nmumg_gr_dlbd_dn100_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA191242-3

description:
Library name: BULKRNA191242-3
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA191242-3


title: KCTR7MESO-B1

description:
Library name: Sample 8
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_3

description: Library name: Cell_3


title: Pleural Mesothelioma, tumor, sample BULKRNA110926-O

description:
Library name: BULKRNA110926-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA110926-O


title: nmumg_ar_dlbd_dn200_2

description:
Library name: nmumg_ar_dlbd_dn200_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep1_Cell_2

description: Library name: Cell_2


title: nmumg_ar_dlbd_dn200_1

description:
Library name: nmumg_ar_dlbd_dn200_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA131952-O

description:
Library name: BULKRNA131952-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA131952-O


title: KCTR5MESO-B1

description:
Library name: Sample 7
150bp-paired end illumina sequencing


title: KCTR724D-B1

description:
Library name: Sample 5
150bp-paired end illumina sequencing


title: Day7.organoid.Rep1_Cell_1

description: Library name: Cell_1


title: Pleural Mesothelioma, tumor, sample BULKRNA158986-O

description:
Library name: BULKRNA158986-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA158986-O


title: MMDTR, iNKT cell_4, Day9

city: Boston

first: Xi

last: Lin

state: MA

address: 77 Avenue Louis Pasteur, Rm641

institute: Brigham and Women's Hospital

description:
Library name: MMDTR_iNKT_4
CT_MMDTR_iNKT_counts.txt

data_processing:
For scRNA-seq, raw data reads were aligned to the mouse transcriptome (mm10) using the Cell Ranger toolkit (version 6.1.1), which was also used for cell selection, filtering, and unique molecular identifier (UMI) counting. For bulk RNA-seq, FASTQ raw data were uploaded to Partek Flow (Partek, building version: 10.0.21.0201) and analyzed with the default setting. Briefly, trimmed reads were aligned to the mouse genome (GRCm38/mm10) using STAR 2.5.3a, and gene expression was quantified using the Partek E/M annotation model with a default setting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
For scRNA-seq, and sorted cell bulk RNA-seq,  the entire colon from postnatal mice was collected, opened longitudinally, washed with ice-cold PBS to remove fecal content, and cut into 2–3 cm segments. Tissue segments were placed in a 50 mL Falcon tube containing 10 mL HBSS with 2mM EDTA and shaken at 250 rpm for 45 min at 37°C. The supernatant containing epithelial cells was discarded, and the remaining LP tissue was digested in 10 mL RPMI medium containing 10% FBS, 1.5% HEPES, 1 mg/mL Collagenase VIII, and 10 µg/mL DNase I. Digestion was performed at 250 rpm for 45 min at 37°C. Enzymatic activity was stopped by adding 10 mL ice-cold FACS buffer (PBS with 2% FBS and 1mM EDTA). The cell suspension was filtered through a 70 µm cell strainer, centrifuged at 1500 rpm for 5 min, and resuspended for FACS sorting. For whole tissue bulk RNA-seq, Total RNA from whole colon tissue of CT and MMDTR mice was extracted using the RNeasy Plus Mini Kit (QIAGEN, 74134) and used as input material.
For scRNA-seq, live cells were FACS-sorted for single-cell RNA sequencing, which was performed by the Brigham and Women’s Hospital Single Cell Genomics Core. Briefly, sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit (10x Genomics) according to the manufacturer’s protocol. For whole tissue bulk RNA-seq, Library preparation and transcriptome sequencing were performed by Novogene Bioinformatics Technology Co., Ltd. For FACS sorted cell bulk RNA-seq, library preparation (Illumina Nextera XT) and sequencing were performed at the Biopolymers Facility at Harvard Medical School.

value: colon

value: iNKT cell

tag: genotype

value: MMDTR


title: KCTR8NT-B1

description:
Library name: Sample 3
150bp-paired end illumina sequencing


title: Pleural Mesothelioma, tumor, sample BULKRNA168748-O

description:
Library name: BULKRNA168748-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA168748-O

value: Tumor

value: Pleural Mesothelioma


title: KCTR524D-B1

description:
Library name: Sample 4
150bp-paired end illumina sequencing


title: nmumg_ar_dlbd_dn150_3

description:
Library name: nmumg_ar_dlbd_dn150_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: MMDTR, iNKT cell_3, Day9

description:
Library name: MMDTR_iNKT_3
CT_MMDTR_iNKT_counts.txt


title: nmumg_ar_dlbd_dn150_2

description:
Library name: nmumg_ar_dlbd_dn150_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA153707-O biologic rep 2, tech rep 3

description:
Library name: BULKRNA153707-O.2.3
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA153707-O.2.3

value: E

value: Yes


title: MMDTR, iNKT cell_2, Day9

description:
Library name: MMDTR_iNKT_2
CT_MMDTR_iNKT_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA153707-O, biologic rep 2, tech rep 2

description:
Library name: BULKRNA153707-O.2.2
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA153707-O.2.2


title: MMDTR, iNKT cell_1, Day9

description:
Library name: MMDTR_iNKT_1
CT_MMDTR_iNKT_counts.txt


title: nmumg_ar_dlbd_dn150_1

description:
Library name: nmumg_ar_dlbd_dn150_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: NMuMG

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: Pleural Mesothelioma, tumor, sample BULKRNA153707-O, biologic rep 2, tech rep 1

description:
Library name: BULKRNA153707-O.2.1
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA153707-O.2.1


title: KCTR5NT-B1

description:
Library name: Sample 1
150bp-paired end illumina sequencing

value: control


title: nmumg_ar_dlbd_dn100_2

description:
Library name: nmumg_ar_dlbd_dn100_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: KCTR7NT-B1

description:
Library name: Sample 2
150bp-paired end illumina sequencing


title: nmumg_ar_dlbd_dn100_3

description:
Library name: nmumg_ar_dlbd_dn100_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA153707-O, biologic rep 1

description:
Library name: BULKRNA153707-O.1
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA153707-O.1


title: nmumg_ar_dlbd_dn100_1

description:
Library name: nmumg_ar_dlbd_dn100_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Pleural Mesothelioma, tumor, sample BULKRNA125811-O

description:
Library name: BULKRNA125811-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA125811-O


title: WT, abT cell_3, Day9

description:
Library name: WTD9abT_3
D9_NKT_abT_counts.txt

value: abT cell

value: WT


title: WT, abT cell_2, Day9

description:
Library name: WTD9abT_2
D9_NKT_abT_counts.txt


title: CT, iNKT cell_4, Day9

description:
Library name: CT_iNKT_4
CT_MMDTR_iNKT_counts.txt

value: CT


title: WT, abT cell_4, Day9

description:
Library name: WTD9abT_4
D9_NKT_abT_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA190137-O

description:
Library name: BULKRNA190137-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA190137-O


title: KCTR824D-B1

description:
Library name: Sample 6
150bp-paired end illumina sequencing

value: leaf

value: Resistant


title: HT29, scramble shRNA (negative control), biol rep 2

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description: Library name: HT29_NC_G2

data_processing:
Reads were trimmed using Trimmomatic version 0.39.
Trimmed reads were aligned to the hg38 reference genome using STAR version 2.7.7a with default parameters.
Mapped reads were indexed and sorted by samtools version 1.7.
HTSeq version 0.12.4 was used to quantify read coverage per gene.
Batch-effect corrections were performed by ComBat-seq.
Assembly: hg38
Supplementary files format and content: Tab-separated values file containing read counts per gene for each sample.

growth_protocol: Human colon cancer cells (HT-29, CACO-2, and HCT-116) obtained from the Korean Cell Line Bank were cultured in DMEM (WelGENE Inc.) containing 10% FBS (WelGENE Inc.) and antibiotics (100 units/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL Fungizone) (Life Technologies Corp.) at 37C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using RNA-spin kit (INTRON) according to the manufacturer's instructions.
Sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (Illumina Inc., USA). After pooled libraries were denatured, sequencing of each library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit with HiSeq 2500 (Illumina Inc., USA).

treatment_protocol: Lentiviral particles were generated by transfecting HEK293T cells with lentivirus-mediated shRNA plasmids (Sigma-Aldrich) targeting MYB, HDAC2, and FOXA2, along with packaging and envelope plasmid mixture (pLP1, pLP2, pLP/VSVG, Invitrogen) using Lipofectamine 2000 (Invitrogen). Medium was harvested after 48 h, filtered through a 0.22 um cellulose acetate filter, and used to infect target cells with 8 ug/mL polybrene. Scramble shRNA was used as negative control (NC). Simultaneous knockdown of MYB, HDAC2, and FOXA2 is denoted as MHF.

value: colorectal cancer cell

value: wild type

value: scramble shRNA (negative control)


title: CT, iNKT cell_1, Day9

description:
Library name: CT_iNKT_1
CT_MMDTR_iNKT_counts.txt

value: colon

value: iNKT cell


title: CT, iNKT cell_2, Day9

description:
Library name: CT_iNKT_2
CT_MMDTR_iNKT_counts.txt


title: HT29, scramble shRNA (negative control), biol rep 1

description: Library name: HT29_NC_G1


title: WT, abT cell_1, Day9

description:
Library name: WTD9abT_1
D9_NKT_abT_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA114261-O

description:
Library name: BULKRNA114261-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA114261-O

value: Tumor

value: B


title: HT29, shMYB + shHDAC2 + shFOXA2, biol rep 2

description: Library name: HT29_MHF_G2

value: MYB, HDAC2, FOXA2 knockdown

value: shMYB + shHDAC2 + shFOXA2


title: WT, P2 stromal cell_4, Day15

description:
Library name: D15P2_4
D9D15_P1P2_counts.txt

value: stromal cell


title: CT, iNKT cell_3, Day9

description:
Library name: CT_iNKT_3
CT_MMDTR_iNKT_counts.txt


title: WT, iNKT cell_4, Day9

description:
Library name: WTD9iNKT_4
D9_NKT_abT_counts.txt


title: HCT116, scramble shRNA (negative control), biol rep 2

description: Library name: HCT116_NC_G2


title: HT29, shMYB + shHDAC2 + shFOXA2, biol rep 1

description: Library name: HT29_MHF_G1


title: Pleural Mesothelioma, tumor, sample BULKRNA179506-O

description:
Library name: BULKRNA179506-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA179506-O

value: Pleural Mesothelioma

value: Yes


title: WT, iNKT cell_2, Day9

description:
Library name: WTD9iNKT_2
D9_NKT_abT_counts.txt


title: WT, P2 stromal cell_3 Day15

description:
Library name: D15P2_3
D9D15_P1P2_counts.txt


title: HCT116, scramble shRNA (negative control), biol rep 1

description: Library name: HCT116_NC_G1


title: CACO2, scramble shRNA (negative control), biol rep 2

description: Library name: CACO2_NC_G2


title: WT, P1 stromal cell_3 Day15

description:
Library name: D15P1_3
D9D15_P1P2_counts.txt


title: HCT116, shMYB + shHDAC2 + shFOXA2, biol rep 1

description: Library name: HCT116_MHF_G1


title: Pleural Mesothelioma, tumor, sample BULKRNA193472-O

description:
Library name: BULKRNA193472-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA193472-O


title: Pleural Mesothelioma, tumor, sample BULKRNA175421-O

description:
Library name: BULKRNA175421-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA175421-O


title: WT, iNKT cell_1, Day9

description:
Library name: WTD9iNKT_1
D9_NKT_abT_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA174957-O

description:
Library name: BULKRNA174957-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA174957-O


title: WT, P1 stromal cell_4, Day15

description:
Library name: D15P1_4
D9D15_P1P2_counts.txt


title: MMDTR whole colon_2, Day9

description:
Library name: D9MMDTR_2_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt

value: whole colon cell

value: MMDTR


title: WT, P2 stromal cell_1, Day15

description:
Library name: D15P2_1
D9D15_P1P2_counts.txt

value: WT


title: HCT116, shMYB + shHDAC2 + shFOXA2, biol rep 2

description: Library name: HCT116_MHF_G2


title: MMDTR, whole colon_1, Day9

description:
Library name: D9MMDTR_1_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt


title: WT, P2 stromal cell_2, Day15

description:
Library name: D15P2_2
D9D15_P1P2_counts.txt


title: WT, P1 stromal cell_2, Day15

description:
Library name: D15P1_2
D9D15_P1P2_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA120329-O

description:
Library name: BULKRNA120329-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA120329-O


title: CACO2, scramble shRNA (negative control), biol rep 1

description: Library name: CACO2_NC_G1


title: Pleural Mesothelioma, tumor, sample BULKRNA185396-O

description:
Library name: BULKRNA185396-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA185396-O


title: Pleural Mesothelioma, tumor, sample BULKRNA180154-O

description:
Library name: BULKRNA180154-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA180154-O


title: CT, whole colon_3, Day9

description:
Library name: D9CT_3_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt

value: CT


title: WT, P1 stromal cell_1, Day15

description:
Library name: D15P1_1
D9D15_P1P2_counts.txt


title: MMDTR, whole colon_3, Day9

description:
Library name: D9MMDTR_3_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt


title: CACO2, shMYB + shHDAC2 + shFOXA2, biol rep 2

description: Library name: CACO2_MHF_G2


title: WT, P2 stromal cell_4, Day9

description:
Library name: D9P2_4
D9D15_P1P2_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA101941-O

description:
Library name: BULKRNA101941-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA101941-O


title: CT, whole colon_2, Day9

description:
Library name: D9CT_2_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt


title: WT, P2 stromal cell_3 Day9

description:
Library name: D9P2_3
D9D15_P1P2_counts.txt


title: CACO2, shMYB + shHDAC2 + shFOXA2, biol rep 1

description: Library name: CACO2_MHF_G1


title: Pleural Mesothelioma, tumor, sample BULKRNA186563-O

description:
Library name: BULKRNA186563-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA186563-O

value: E


title: Pleural Mesothelioma, tumor, sample BULKRNA155007-O

description:
Library name: BULKRNA155007-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA155007-O


title: CT, whole colon_1, Day9

description:
Library name: D9CT_1_bulkRNAseq
D9_CT_MMDTR_wholecolon_counts.txt


title: Patient20,CD14+,H3K18la(ChIP)

city: jinan

first: yuanyuan

last: Zhang

address: jinan

country: China

institute: Shandong Second Medical University

description: Library name: lac-chip

data_processing:
RNA-seq:Raw reads were subjected to quality control using FastQC.Clean reads were aligned to the human reference genome using HISAT2.Gene expression levels were quantified using featureCounts.Differential expression analysis was performed using DESeq2.
ChIP-seq:Raw reads were quality-checked using FastQC.Reads were aligned to the human genome using Bowtie2.Peak calling was performed using MACS2.Peaks were annotated using HOMER.
Assembly: hg38 and mm10
Supplementary files format and content: fastq,bdg

source_name: peripheral blood

growth_protocol: CD14⁺ monocyte-derived macrophages were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C with 5% CO₂.

extract_protocol:
RNA-seq:Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer. ChIP-seq:Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was isolated, lysed, and sonicated to generate DNA fragments of 200–500 bp.
RNA-seq:RNA-seq libraries were prepared using a poly(A) selection method with the Illumina TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions. ChIP-seq:Immunoprecipitated DNA was collected using magnetic beads and used for library construction with the NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with lactate (LAC, 10 mM) for 8 hours. Control cells were treated with PBS.

value: peripheral blood

value: primary cells


title: Patient20,CD14+,Input(ChIP)

description: Library name: con-chip


title: Pleural Mesothelioma, tumor, sample BULKRNA184053-O

description:
Library name: BULKRNA184053-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA184053-O


title: WT, P2 stromal cell_2, Day9

description:
Library name: D9P2_2
D9D15_P1P2_counts.txt


title: Pleural Mesothelioma, tumor, sample BULKRNA198382-O

description:
Library name: BULKRNA198382-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA198382-O


title: Ocy454 cells PDE8A KO 3

first: Garyfallia

last: Papaioannou

state: Massachusetts

address: 55 Fruit St

department: Medicine, Endocrine

institute: Massachusetts General Hospital

description:
Library name: sample 12
WTDMSOvsKODMSO_salmon.xlsx

data_processing:
Quality of raw sequencing data was confirmed with quality control using FastQC/0.11.5. Transcripts were quantified using Salmon 100. Salmon index for mouse was generated based on the Ensembl fasta file for GRCm38. Differential expression analysis was performed using DESeq2 101 package based on the criteria of p adjusted value (padj) < 0.05 and log2|FC | ≥ 1.
Assembly: Salmon index for mouse was generated based on the Ensembl fasta file for GRCm38
Supplementary files format and content: logfold change compared to wild type/vehicle

source_name: osteocyte cell line

extract_protocol:
Total RNA was collected from cultured cells using QIAshredder (QIAGEN) and PureLink RNA mini kit (Invitrogen) following the manufacturer’s instructions. In brief, lysis buffer with 2- mercaptoethanol was added to cold PBS-washed cells and collected into QIAshredder, then centrifuged at 15,000 g for 3 min. The flow-through was collected into a new tube, and RNA isolation was carried out with PureLink RNA mini kit following the manufacturer’s instructions.
High quality RNA samples with RIN > 7 (n = 6) were processed for RNA library construction and 887 sequencing using the Novoseq6000 platform (Novogene).

value: osteocyte cell line

value: PDE8A KO


title: WT, P1 stromal cell_4, Day9

description:
Library name: D9P1_4
D9D15_P1P2_counts.txt

value: colon


title: WT, P2 stromal cell_1, Day9

description:
Library name: D9P2_1
D9D15_P1P2_counts.txt


title: Ocy454 cells PDE8A KO 2

description:
Library name: sample 11
WTDMSOvsKODMSO_salmon.xlsx


title: Pleural Mesothelioma, tumor, sample BULKRNA198160-O

description:
Library name: BULKRNA198160-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA198160-O

value: Tumor


title: Pleural Mesothelioma, tumor, sample BULKRNA172907-O

description:
Library name: BULKRNA172907-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA172907-O


title: WT, iNKT cell_3, Day9

description:
Library name: WTD9iNKT_3
D9_NKT_abT_counts.txt

value: iNKT cell


title: XR_A2780, cPVP, biol rep 1

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

institute: Hebrew University of Jerusalem

data_processing:
Flanking adapter sequences were removed from the reads using trimmomatic version 0.36 with the command options: ILLUMINACLIP:adapter_sequence.txt:2:30:10 (Bolger et al. 2014). Using this adapter sequence: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG.
Filter 50 nt length reads.
Reads were aligned to the GRCh38 human genome using bowtie 1.0.0 (Langmead et al. 2009) with the command options: -q --nomaqround --phred33-quals -p 32 -m 4 -n 2 -e 70 -l 20 --chunkmbs 800 --best –S.
Reads mapped to chromosome Y or mitochondrial chromosome were filtered.
PCR duplicates were removed using PicardCommandLine MarkDuplicates version 2.26.10  (http://broadinstitute.github.io/picard/)
All bam files of replicates from condition were merged to create a pooled bam file.
Per base read counts were calculated using bedtools genomecov and normalized per billion mapped reads per chromosome. Read counts were calculated in 25 nt windows using awk  and converted to bigwig using the bedGraphToBigWig command to create stranded signal maps in bigwig file format
Assembly: GRCh38
Supplementary files format and content: bigwig files of the data normalized to mapped reads per chromosome counts and separated by strands.
Library strategy: XR-seq

source_name: ovarian carcinoma

growth_protocol: A2780 cells (93112519 , Sigma-Aldrich) were cultured in RPMI 1640 Medium, supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/mL penicillin and 0.1 mg/mL streptomycin. Culturse were maintained in a humidified 5% CO2 incubator at 37 °C. Cells were sub-cultured every 3–4 days to maintain logarithmic growth.

extract_protocol:
390x106 cells per library were harvested and collected by centrifugation. Cells were resuspended in lysis buffer and lysed using syringes sequentially with 25 and 27 G needles.
XR-seq was performed as previously described (Hu. et al., PNAS, 2016). Briefly, primary excision products were pulled-down by TFIIH co-immunoprecipitation using anti-p62 antibody (Santa-Cruz Biotechnology, sc-293) and anti-p89 antibody (Santa-Cruz Biotechnology, sc-292). Adapters were ligated on both ends of the excision oligomer and immunoprecipitated using cisplatin-specific antibody (abcam, 103261). Cisplatin-induced damages were reversed in-vitro by incubating the samples with 200 mM NaCN at 65°C overnight. DNA was PCR amplified and purified by native polyacrylamide gel electrophoresis (PAGE) to create the library.

treatment_protocol: Cells were grown to ~80% confluence in 150 mm dishes, culture medium was replaced with media containing either 200 µM cisplatin or 30 µM cPVP, incubated for 3h.

value: ovarian carcinoma

value: cancerous

value: cPVP, 30 uM

tag: time


title: XR_A2780, cPVP, biol rep 2


title: Ocy454 cells PDE8A KO 1

description:
Library name: sample 10
WTDMSOvsKODMSO_salmon.xlsx


title: Ocy454 cells wild type PTH 3

description:
Library name: sample 9
WTDMSOvsWTPTH_salmon.xlsx

value: PTH


title: WT, P1 stromal cell_1, Day9

description:
Library name: D9P1_1
D9D15_P1P2_counts.txt

value: stromal cell


title: WT, P1 stromal cell_2, Day9

description:
Library name: D9P1_2
D9D15_P1P2_counts.txt


title: Ocy454 cells wild type PTH 2

description:
Library name: sample 8
WTDMSOvsWTPTH_salmon.xlsx


title: WT, P1 stromal cell_3 Day9

description:
Library name: D9P1_3
D9D15_P1P2_counts.txt


title: XR_A2780, cisplatin, biol rep 2

value: cisplatin, 200 uM


title: HER10 antagomiR #5

city: Davis

first: Sergi

last: Simo

state: CA

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

description:
Library name: SS_HER_15_AntagomiR_S216_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 antagomiR #5

data_processing:
Raw reads were processed and trimmed to remove phiX and adapter sequences, and to remove the first 11 bases from each read.
Processed reads were aligned to GRCh38.12 primary genome assembly using GENCODE v30 annotation, with STAR v.2.7.0e, to generate counts per gene.
Prior to analysis, genes with low expression (defined here as a those with mean CPM less than 0.5) were filtered, leaving 15,648 genes.  Differential expression analyses were conducted using the limma-voom Bioconductor pipeline
Assembly: GRCh38.12
Supplementary files format and content: Decker_et_al_CPM_counts.xlsx: Format Excel (.xlsx) file. Containing twelve columns with the following information: ensembl_gene_id; HGNC gene_symbol; HER10 mimic #1-5 CPM; HER10 antagomiR #1-5 CPM.
Supplementary files format and content: Decker_et_al_DGE.xlsx: Format Excel (.xlsx) file. Containing five columns with the following information: ensembl_gene_id; HGNC gene_symbol; logFC: log 2 fold change; Average expression (log2 CPM); p value (raw p value); adj.P.Val (Benjamini-Hochberg false discovery rate adjusted p-value); Gene description.
Supplementary files format and content: Decker_et_al-MD5 Checksum.rtf: Format etx file (rtf). Containing two columns with MD5 checksum information and the associate file.

source_name: Ad12 HER10

extract_protocol:
RNA was extracted with Total RNA Purification Plus Kit (Norgen Biotek Corp.,48300) following manufacturer instructions
Gene expression profiling was carried out using a 3’-Tag-RNA-Seq protocol. Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen) for multiplexed sequencing according to the recommendations of the manufacturer using both the UDI-adapter and UMI Second-Strand Synthesis modules (Lexogen).

value: Ad12 HER10

value: immortalized human retinoblstoma cell line


title: XR_A2780, cisplatin, biol rep 1


title: Pleural Mesothelioma, tumor, sample BULKRNA194058-O

description:
Library name: BULKRNA194058-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA194058-O

tag: diagnosis

value: Pleural Mesothelioma

value: B

value: Yes


title: WT3

city: Beijing

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

description:
Library name: sample6
Column name in raw_counts_All_Samples.txt:WT3

data_processing:
CLC genomics workbench v11.0.1
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: intestine

extract_protocol:
RNA was harvested using  Oligo(dT) beads. RNA was diluted at 2 nM for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer’s protocols.

value: intestine

value: WT


title: Pleural Mesothelioma, tumor, sample BULKRNA164161-O

description:
Library name: BULKRNA164161-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA164161-O

tag: histology


title: Ocy454 cells wild type FAKinh 3

description:
Library name: sample 6
WTDMSOvsWTPF3_salmon.xlsx

value: osteocyte cell line


title: WT2

description:
Library name: sample5
Column name in raw_counts_All_Samples.txt:WT2


title: HER10 antagomiR #4

description:
Library name: SS_HER_14_AntagomiR_S215_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 antagomiR #4


title: Ocy454 cells wild type PTH 1

description:
Library name: sample 7
WTDMSOvsWTPTH_salmon.xlsx


title: Ocy454 cells wild type FAKinh 2

description:
Library name: sample 5
WTDMSOvsWTPF3_salmon.xlsx


title: Pleural Mesothelioma, tumor, sample BULKRNA189276-O

description:
Library name: BULKRNA189276-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA189276-O

value: E

tag: age at_surgery


title: Pleural Mesothelioma, tumor, sample BULKRNA153021-O

description:
Library name: BULKRNA153021-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA153021-O

value: Tumor

tag: tumor status


title: HER10 antagomiR #2

description:
Library name: SS_HER_12_AntagomiR_S213_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 antagomiR #2


title: HET3

description:
Library name: sample3
Column name in raw_counts_All_Samples.txt:HET3

value: HET


title: HER10 antagomiR #3

description:
Library name: SS_HER_13_AntagomiR_S214_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 antagomiR #3


title: Pleural Mesothelioma, tumor, sample BULKRNA125117-O

description:
Library name: BULKRNA125117-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA125117-O

tag: subject id


title: WT1

description:
Library name: sample4
Column name in raw_counts_All_Samples.txt:WT1

tag: tissue


title: Pleural Mesothelioma, tumor, sample BULKRNA106064-O

description:
Library name: BULKRNA106064-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA106064-O


title: Ocy454 cells wild type FAKinh 1

description:
Library name: sample 4
WTDMSOvsWTPF3_salmon.xlsx

tag: cell line


title: Pleural Mesothelioma, tumor, sample BULKRNA189918-O

description:
Library name: BULKRNA189918-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA189918-O


title: HET2

description:
Library name: sample2
Column name in raw_counts_All_Samples.txt:HET2


title: Ocy454 cells wild type vehicle 3

description: Library name: sample 3

tag: treatment

value: vehicle


title: HER10 antagomiR #1

description:
Library name: SS_HER_11_AntagomiR_S212_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 antagomiR #1


title: Ocy454 cells wild type vehicle 1

description: Library name: sample 1


title: Pleural Mesothelioma, tumor, sample BULKRNA144197-O

description:
Library name: BULKRNA144197-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA144197-O


title: HER10 mimic #4

description:
Library name: SS_HER_09_Mimic_S210_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 mimic #4


title: HET1

description:
Library name: sample1
Column name in raw_counts_All_Samples.txt:HET1


title: Ocy454 cells wild type vehicle 2

description: Library name: sample 2


title: HER10 mimic #5

description:
Library name: SS_HER_10_Mimic_S211_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 mimic #5


title: Pleural mesothelioma, tumor, sample 198382

description:
Library name: 198382
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 198382


title: Pleural mesothelioma, tumor, sample 198160

description:
Library name: 198160
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 198160


title: GEMM_control_replicate_3

city: Shenzhen

first: Zeqin

last: Yan

address: No. 1, Fuxin Road, Pinghu Street, Longgang District, Shenzhen, Guangdong Province, China

institute: Shenzhen University

description: Library name: RNA_GEMM_Ctrl3-F

data_processing:
Raw reads were quantified using Salmon with reference genome. Gene-level counts were summarized using tximport. TPM normalization was applied.
Assembly: Human: GRCh38/hg38; Mouse: GRCm38/mm10
Supplementary files format and content: Tab-delimited/CSV files contain gene/transcript expression quantification. MP_count.tsv: human transcript-level raw counts; MP_tpm.tsv: human TPM values; CUUC-G_counts.csv: mouse gene-level raw counts; CUUC-G_tmp.csv: mouse TPM values; GEMM_mus_counts.exp.tsv: GEMM gene-level raw counts; GEMM_mus_tpm.exp.tsv: GEMM TPM values.

source_name: bladder

growth_protocol: Bladder cancer cell lines (MGHU3) and GEMM models were grown under standard conditions. Tumors were harvested at appropriate time points for RNA extraction.

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer's protocol.
RNA libraries were constructed using polyA selection and Illumina TruSeq Stranded mRNA library preparation kit. Libraries were sequenced on Illumina platform.

treatment_protocol: Cells/mice were treated with vehicle control, sgIGFBP5 (IGFBP5 knockdown), or chemotherapy (cisplatin + gemcitabine).

value: bladder

value: GEMM

value: control


title: GEMM_control_replicate_2

description: Library name: RNA_GEMM_Ctrl2-F


title: HER10 mimic #3

description:
Library name: SS_HER_08_Mimic_S209_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 mimic #3


title: Pleural Mesothelioma, tumor, sample BULKRNA192918-O

description:
Library name: BULKRNA192918-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA192918-O

value: S


title: Pleural mesothelioma, tumor, sample 197652

description:
Library name: 197652
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 197652


title: Pleural Mesothelioma, tumor, sample BULKRNA118014-O

description:
Library name: BULKRNA118014-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA118014-O


title: Pleural Mesothelioma, tumor, sample BULKRNA151213-O

description:
Library name: BULKRNA151213-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA151213-O


title: HER10 mimic #2

description:
Library name: SS_HER_07_Mimic_S208_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 mimic #2


title: Pleural mesothelioma, tumor, sample 195890, tech rep 2

description:
Library name: 195890.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 195890; replicate: 2.0; replicate_type: Technical


title: HER10 mimic #1

description:
Library name: SS_HER_06_Mimic_S207_L008_R1_001.fastq.gz
Column Name in Decker_et_al_CPM_counts.xlsx: HER10 mimic #1


title: Pleural Mesothelioma, tumor, sample BULKRNA141635-O

description:
Library name: BULKRNA141635-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA141635-O


title: Pleural Mesothelioma, tumor, sample BULKRNA100620-O

description:
Library name: BULKRNA100620-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA100620-O


title: Pleural mesothelioma, tumor, sample 195890, tech rep 1

description:
Library name: 195890.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 195890; replicate: 1.0; replicate_type: Technical


title: GEMM_chemotherapy_treated_replicate_2

description: Library name: RNA_GEMM_Relapse2-F

value: chemotherapy


title: GEMM_chemotherapy_treated_replicate_3

description: Library name: RNA_GEMM_Relapse3-F


title: Pleural Mesothelioma, tumor, sample BULKRNA175512-O

description:
Library name: BULKRNA175512-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA175512-O


title: Pleural mesothelioma, tumor, sample 195005, tech rep 2

description:
Library name: 195005.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 195005; replicate: 2.0; replicate_type: Technical


title: IORT_Sample_36

city: Neuherberg

first: Benedek

last: Dankó

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

description: Library name: IORT_Quantseq_36

data_processing:
trimming of adapter sequences using BBDUK  k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 6 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
indexing BAM files using samtools: samtools index Aligned.sortedByCoord.out.bam
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts

source_name: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.

growth_protocol: Primary patient-derived immune cells from wound fluid were used without in vitro expansion.

extract_protocol:
Cryopreserved immune cell samples were thawed, washed with PBS, and processed using the NucleoSpin miRNA kit (Macherey & Nagel, Cat. No. 740971) following the manufacturer’s instructions for total RNA extraction (cell lysis in buffer ML, no DNA/protein isolation). RNA was eluted in 50 µL nuclease-free water and quantified via NanoDrop.
RNA libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s instructions. Sequencing was performed by Novogene (Cambridge, UK).

treatment_protocol: Patients either received intraoperative radiotherapy (IORT, single dose during tumor resection) or underwent surgery alone (control). Wound fluid was collected on postoperative day 2 using Redon drains.

value: tissue

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.

tag: group


title: Pleural Mesothelioma, tumor, sample BULKRNA163323-O

description:
Library name: BULKRNA163323-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA163323-O

value: Pleural Mesothelioma


title: GEMM_sgScr_control_replicate_2

description: Library name: RNA_sgScr_CUUC-G_2-F


title: Pleural Mesothelioma, tumor, sample BULKRNA104538-O

description:
Library name: BULKRNA104538-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA104538-O

value: B


title: Pleural mesothelioma, tumor, sample 195005, tech rep 1

description:
Library name: 195005.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 195005; replicate: 1.0; replicate_type: Technical

value: Yes


title: IORT_Sample_37

description: Library name: IORT_Quantseq_37

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.


title: GEMM_chemotherapy_treated_replicate_1

description: Library name: RNA_GEMM_Relapse1-F


title: GEMM_control_replicate_1

description: Library name: RNA_GEMM_Ctrl1-F


title: IORT_Sample_33

description: Library name: IORT_Quantseq_33


title: GEMM_sgScr_control_replicate_3

description: Library name: RNA_sgScr_CUUC-G_3-F


title: IORT_Sample_35

description: Library name: IORT_Quantseq_35


title: Pleural mesothelioma, tumor, sample 194441

description:
Library name: 194441
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 194441


title: IORT_Sample_34

description: Library name: IORT_Quantseq_34


title: Pleural Mesothelioma, tumor, sample BULKRNA108021-O

description:
Library name: BULKRNA108021-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA108021-O


title: Pleural mesothelioma, tumor, sample 194335

description:
Library name: 194335
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 194335


title: Pleural mesothelioma, tumor, sample 194058

description:
Library name: 194058
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 194058


title: GEMM_sgIGFBP5_knockdown_replicate_2

description: Library name: RNA_sgIgfbp5_CUUC-G_2-F


title: GEMM_sgScr_control_replicate_1

description: Library name: RNA_sgScr_CUUC-G_1-F


title: Pleural mesothelioma, tumor, sample 193332, tech rep 3

description:
Library name: 193332.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 193332; replicate: 3.0; replicate_type: Technical


title: IORT_Sample_32

description: Library name: IORT_Quantseq_32


title: IORT_Sample_29

description: Library name: IORT_Quantseq_29


title: Pleural mesothelioma, tumor, sample 193472

description:
Library name: 193472
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 193472


title: Pleural mesothelioma, tumor, sample 193780

description:
Library name: 193780
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 193780


title: IORT_Sample_30

description: Library name: IORT_Quantseq_30


title: IORT_Sample_31

description: Library name: IORT_Quantseq_31


title: Pleural Mesothelioma, tumor, sample BULKRNA107957-O

description:
Library name: BULKRNA107957-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA107957-O


title: GEMM_sgIGFBP5_knockdown_replicate_3

description: Library name: RNA_sgIgfbp5_CUUC-G_3-F


title: Pleural Mesothelioma, tumor, sample BULKRNA175227-O

description:
Library name: BULKRNA175227-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA175227-O


title: GEMM_sgIGFBP5_knockdown_replicate_1

description: Library name: RNA_sgIgfbp5_CUUC-G_1-F


title: Pleural Mesothelioma, tumor, sample BULKRNA172444-O

description:
Library name: BULKRNA172444-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA172444-O


title: Pleural Mesothelioma, tumor, sample BULKRNA108535-O

description:
Library name: BULKRNA108535-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA108535-O


title: Pleural mesothelioma, tumor, sample 193332, tech rep 2

description:
Library name: 193332.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 193332; replicate: 2.0; replicate_type: Technical


title: IORT_Sample_28

description: Library name: IORT_Quantseq_28


title: Pleural mesothelioma, tumor, sample 193332, tech rep 1

description:
Library name: 193332.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 193332; replicate: 1.0; replicate_type: Technical


title: Pleural Mesothelioma, tumor, sample BULKRNA106649-O

description:
Library name: BULKRNA106649-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA106649-O


title: Tomato+, Salmonella+/Ctrl, Batch 5, Hash Tag Oligo

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

description:
Library name: TomSal_Epi_B5_HTO
b345_HTO.csv
TomSal_Epi_B5_HTO_cellranger.csv

library_source: other

data_processing:
STARsolo v2.7.10 was used to align reads and collect cell barcode transcript quantification, using multi-mapping EM mode.
Cellranger  barcodes from 3M-february-2018.txt were used a cell barcode whitelist.
EmptyDrops (DropletUtils v1.7.1) were used to exclude likely empty cells from analysis.
Cellbender (v3) was used to remove ambient contamination from analysis.
Demultiplexing of 3 or 4 experimental based on HTO abundance extracted from cellranger v7 barcode counts was performed by Pegasus demuxEM (v1.3.1) using default settings (https://github.com/lilab-bcb/demuxEM/)
Assembly: GRCm39, genecode M32
Supplementary files format and content: STARsolo output: *_features.tsv.gz, *_barcodes.tsv.gz, *_UniqueAndMult-EM.mtx.gz
Supplementary files format and content: Pegasus demuxEM output: *demuxEM_pred.csv.gz
Supplementary files format and content: PostQC cellbender corrected raw counts: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Small intestine

extract_protocol:
Small intestine was extracted and rinsed in cold Phosphate buffered saline (PBS). The tissue was opened longitudinally and sliced into small fragments roughly 2 mm long followed by incubation with 20mM EDTA-PBS on ice for 75 min. Then, the tissue was shaken vigorously, and the supernatant was collected as fraction 1 in a new conical tube. The tissue was incubated in fresh PBS, and a new fraction was collected every 5 min. Fractions were collected until the supernatant consisted almost entirely of crypts. The fractions 3-4 (enriched for crypts) were filtered through a 70 µm filter, centrifuged at 400g for 5 min, and dissociated with TrypLE Express (Gibco) for 1 min and 30 seconds at 37°C. The single-cell suspension was then passed through a 40μm filter. Cells for each condition or mouse were stained with the Dapi-NucBlue (ThermoFisher, cat no. R37605), CD45 (Biolegend, 30-F11), Biotin anti-mouse CD326 (EpCAM) antibody (cat #118204) followed by staining using TotalSeq™ PE Streptavidin (B0951 - B0955). Isolated IEC were sorted into a cooled 15 mL tube with 0.04% BSA in PBS using a Sony SH800 cell sorter. 20,000 cells EpCAM+ CD45- (IEC), EpCAM+ CD45- GFP+ (Invaded IEC) were sorted for each mouse or condition and pooled following manufacturer’s instructions. 30,000 single-cell suspension was loaded onto Next GEM Chip G targeting 15,000 cells and then ran on a Chromium Controller instrument to generate GEM emulsion. Single-cell 3’ RNA-seq libraries and cell surface protein libraries were generated according to the manufacturer’s protocol (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index). Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D5000/D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~20,000 reads per cell for gene expression libraries and ~5,000 reads per cell for cell surface protein libraries. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an S1 100 cycles reagent kit (Illumina).
A total of 8000 cells were loaded into each well of a Chromium Next GEM Chip G and run on the Chromium Controller (10X Genomics) for Gel Bead-in-emulsion (GEM) generation. The samples were processed according to the CG000317 Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) Rev. D protocol (10X Genomics) for RNA library construction.

value: Small intestine

value: Epithelial cells

value: mixed (Tomato+, Salmonella+/Ctrl)

tag: library type

value: HTO


title: IORT_Sample_27

description: Library name: IORT_Quantseq_27

tag: cell type


title: IORT_Sample_26

description: Library name: IORT_Quantseq_26


title: Listeria  24PI/Control, Batch 4, Hash Tag Oligo

description:
Library name: List_Epi_B4_HTO
b345_HTO.csv
List_Epi_B4_HTO_cellranger.csv

value: mixed (Listeria  24PI/Control)


title: Pleural Mesothelioma, tumor, sample BULKRNA155528-O

description:
Library name: BULKRNA155528-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA155528-O

value: Tumor

value: E


title: Salmonella Uninfected Control, Batch 5, Hash Tag Oligo

description:
Library name: Sal_Epi_B5_HTO
b345_HTO.csv
Sal_Epi_B5_HTO_cellranger.csv

value: mixed (Salmonella Uninfected Control)


title: Pleural mesothelioma, tumor, sample 192918

description:
Library name: 192918
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 192918


title: Pleural Mesothelioma, tumor, sample BULKRNA178133-O

description:
Library name: BULKRNA178133-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA178133-O


title: Pleural mesothelioma, tumor, sample 191242

description:
Library name: 191242
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 191242


title: Salmonella 24h PI / 24h PI GFP+, Batch 2, Hash Tag Oligo

description:
Library name: Sal_Epi_t24_B2_HTO
b345_HTO.csv
Sal_Epi_t24_B2_HTO_cellranger.csv

value: mixed (Salmonella 24h PI / 24h PI GFP+)


title: Pleural Mesothelioma, tumor, sample BULKRNA194335-O

description:
Library name: BULKRNA194335-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA194335-O


title: IORT_Sample_25

description: Library name: IORT_Quantseq_25


title: Tomato+, Salmonella+/Ctrl, Batch 5, Gene Expression

description:
Library name: TomSal_Epi_B5_GEX
b345_HTO.csv
TomSal_Epi_B5_HTO_cellranger.csv
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
STARsolo v2.7.10 was used to align reads and collect cell barcode transcript quantification, using multi-mapping EM mode.
Cellranger  barcodes from 3M-february-2018.txt were used a cell barcode whitelist.
EmptyDrops (DropletUtils v1.7.1) were used to exclude likely empty cells from analysis.
Cellbender (v3) was used to remove ambient contamination from analysis.
Demultiplexing of 3 or 4 experimental based on HTO abundance extracted from cellranger v7 barcode counts was performed by Pegasus demuxEM (v1.3.1) using default settings (https://github.com/lilab-bcb/demuxEM/)
Assembly: GRCm39, genecode M32
Supplementary files format and content: STARsolo output: *_features.tsv.gz, *_barcodes.tsv.gz, *_UniqueAndMult-EM.mtx.gz
Supplementary files format and content: Pegasus demuxEM output: *demuxEM_pred.csv.gz
Supplementary files format and content: PostQC cellbender corrected raw counts: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz

value: mRNA


title: IORT_Sample_24

description: Library name: IORT_Quantseq_24


title: Pleural mesothelioma, tumor, sample 189918

description:
Library name: 189918
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 189918


title: Pleural Mesothelioma, tumor, sample BULKRNA120271-O

description:
Library name: BULKRNA120271-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA120271-O


title: Bronchial Carcinoid, pleura, sample 189864

description:
Library name: 189864
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 189864

value: Pleura

value: Bronchial Carcinoid

value: NP

value: No


title: Salmonella Uninfected Control, Batch 5, Gene Expression

description:
Library name: Sal_Epi_B5_GEX
b345_HTO.csv
Sal_Epi_B5_HTO_cellranger.csv
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: IORT_Sample_23

description: Library name: IORT_Quantseq_23

value: tissue

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.


title: Listeria  24PI/Control, Batch 4, Gene Expression

description:
Library name: List_Epi_B4_GEX
b345_HTO.csv
List_Epi_B4_HTO_cellranger.csv
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: IORT_Sample_22

description: Library name: IORT_Quantseq_22

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.


title: Pleural mesothelioma, tumor, sample 189276

description:
Library name: 189276
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 189276

value: Pleural Mesothelioma

value: Yes


title: IORT_Sample_21

description: Library name: IORT_Quantseq_21


title: Salmonella 24h PI / 24h PI GFP+, Batch 2, Gene Expression

description:
Library name: Sal_Epi_t24_B2_GEX
b345_HTO.csv
Sal_Epi_t24_B2_HTO_cellranger.csv
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

value: Small intestine

value: Epithelial cells


title: Pleural Mesothelioma, tumor, sample BULKRNA166590-O

description:
Library name: BULKRNA166590-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA166590-O


title: Pleural Mesothelioma, tumor, sample BULKRNA189132-O

description:
Library name: BULKRNA189132-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA189132-O

value: B


title: Pleural mesothelioma, tumor, sample 189132

description:
Library name: 189132
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 189132

value: Tumor


title: IORT_Sample_20

description: Library name: IORT_Quantseq_20


title: Pleural mesothelioma, tumor, sample 188018

description:
Library name: 188018
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 188018

value: E


title: Pleural Mesothelioma, tumor, sample BULKRNA196011-O

description:
Library name: BULKRNA196011-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA196011-O


title: Pleural mesothelioma, tumor, sample 185540, bio rep 6

description:
Library name: 185540.6
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 6.0; replicate_type: Biologic

value: S


title: IORT_Sample_19

description: Library name: IORT_Quantseq_19


title: PEPITEM_3

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

description: Library name: S7

data_processing:
Cellranger v7
Assembly: mm10
Supplementary files format and content: barcodes.tsv, matrix.mtx, genes.tsv
barcode-1_1: PBS_1
barcode-1_2: PEPITEM_1
barcode-1_3: PEPITEM_2
barcode-1_4: PBS_2
barcode-1_5: PEPITEM_3
barcode-1_6: PEPITEM_4

source_name: Synovium

extract_protocol:
mRNA was extracted from CD45+ synovial cells
cDNA libraries from FACS sorted CD45+ synovial digested cells were prepared using Chromium Next GEM Single Cell 3’ Kit v3.1 (4 rxns PN-1000269) according to manufacturer’s instructions, with the aim to capture about 10,000 cells/10µl for each biological replicate.

value: Synovium

value: CD45+ synovial

value: PEPITEM


title: PBS_2

description: Library name: S5

value: PBS


title: Pleural Mesothelioma, tumor, sample BULKRNA190229-O

description:
Library name: BULKRNA190229-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA190229-O


title: IORT_Sample_18

description: Library name: IORT_Quantseq_18


title: Pleural Mesothelioma, tumor, sample BULKRNA184761-O

description:
Library name: BULKRNA184761-O
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA184761-O


title: Pleural mesothelioma, tumor, sample 185540, bio rep 4

description:
Library name: 185540.4
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 4.0; replicate_type: Biologic

data_processing:
Reads were processed using the Drop-seq tools pipeline aligned to the hg38 transcriptome using standard parameters.
Raw sequencing data are available through controlled access in dbGaP under accession phs004285.
Processed files provided here include per-library count matrices and corresponding cell-level metadata files.
Assembly: hg38
Supplementary files format and content: Sparse counts matrices (initial and stringently filtered cells) with associated column and row name files are formatted in tab-delmited compressed text files. Metadata for cells is formatted as a compressed tab delimited text file.


title: Pleural mesothelioma, tumor, sample 185540, bio rep 3

description:
Library name: 185540.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 3.0; replicate_type: Biologic


title: PEPITEM_4

description: Library name: S8


title: IORT_Sample_17

description: Library name: IORT_Quantseq_17


title: Pleural mesothelioma, tumor, sample 185540, bio rep 2

description:
Library name: 185540.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 2.0; replicate_type: Biologic


title: PBS_1

description: Library name: S1


title: Patient20,CD14+,lac2(RNA-seq)

description: Library name: lac2

value: peripheral blood

value: primary cells


title: NSCLC-Adenocarcinoma, pleura, sample BULKRNA144255-1

description:
Library name: BULKRNA144255-1
Column name in bulkRNA_TPM_matrix.tsv.gz: BULKRNA144255-1

value: Pleura

value: NSCLC-Adenocarcinoma

value: NP

value: No


title: PEPITEM_1

description: Library name: S3


title: IORT_Sample_15

description: Library name: IORT_Quantseq_15

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.

value: tissue

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.


title: Patient20,CD14+,lac3(RNA-seq)

description: Library name: lac3


title: IORT_Sample_16

description: Library name: IORT_Quantseq_16


title: Pleural mesothelioma, tumor, sample 185540, bio rep 5

description:
Library name: 185540.5
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 5.0; replicate_type: Biologic

value: Pleural Mesothelioma

value: Yes


title: Clonally traced otic and epibranchial ganglia region and surrounding tissue, embryonic day (E) 11.5

city: Solna

first: Felix

middle: Robert Nicodemus

last: Waern

state: Uppland

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Library name: exp1_otic

data_processing:
Alignment of reads was performed using 10x Genomics Cell Ranger v.70.01 with chimeric mm39 and FP genome refrence.
TREX v.0.4dev402 was used for extraction of clonal barcodes.
Assembly: chimeric mm39
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains gene expression data from Cell Ranger. It has genes as rows, cell barcodes as columns, and UMI counts for each gene in each cell.
Supplementary files format and content: umi_count_matrix.csv is a matrix of read counts with cells as columns and cloneIDs as rows and the count of each clone is each cell.

source_name: Mouse embryo, otic and epibranchial ganglia region

extract_protocol:
Embryos were harvested at E11.5 following maternal euthanasia by CO₂ overdose and cervical dislocation and were subsequently euthanized by decapitation. Mouse embryos were dissected from the uterus, sacrificed, and transferred to ice-cold Hank’s Balanced Salt Solution (HBSS). Fluorescent reporter expression (tdTomato) was assessed using a fluorescence stereomicroscope. Embryos were dissected into different regions containing olfactory and forebrain; eye, trigeminal ganglia  and midbrain and hindbrain; otic and epibranchial ganglia region; and the entire cranial region. Dissected tissues were placed in dissociation buffer containing Collagenase P (2 mg/mL) (Roche, Sigma-Aldrich), TrypLE (1×), and DNase I (1 µL/mL) prepared in HBSS with calcium and magnesium. Samples were then incubated for 20 minutes at 37 C in a preheated shaking incubator set at 150 RPM. After tissue were dissociated to stop the enzymatic were aded ice-cold HBSS supplemented with 2% FBS. Cells were pelleted by centrifugation at 500 × g for 15 minutes at 4 °C, resuspended in HBSS containing 2% FBS, and kept on ice. Prior to downstream applications, single-cell suspensions were filtered through a 40 µm cell strainer.  Flow cytometry sorting was performed using FACSAria Fusion or FACSAria III instruments (BD) equipped with a 100 µm nozzle and a 1.5 neutral density filter, and controlled via FACSDiva software (BD).
Cells (~5,000–10,000 per reaction) were processed using the 10X Genomics Chromium V3.1 kit. cDNA was synthesized and amplified by 12 PCR cycles. Gene expression libraries were prepared and indexed using Single Index Plate T Set A. CloneID sequences were enriched via nested PCR with Q5 polymerase, purified between steps using 0.8× AMPure beads, and all libraries were quantified with BioAnalyzer and/or Qubit.

treatment_protocol: At embryonic days 7.5 and 8.5 (E7.5-E8.5), pregnant CD-1 female mice were anesthetized with isoflurane, maintained on a heated surface, and given preoperative analgesia (buprenorphine, 0.05–0.1 mg/kg, subcutaneous). After preparation and sterilization of the abdominal surgical site, the uterus was gently exteriorized into a Petri dish containing PBS. Embryos were visualized using a Vevo2100 ultrasound system, and 46 nL of lentivirus was injected through the uterine wall into the amniotic cavity. The uterus was then returned to the abdomen, muscle incisions were closed with absorbable sutures, and the skin was sealed with sutures or staples. Animals recovered on a heating pad under supervision and received postoperative analgesia.

tag: developmental stage

tag: injection time

value: CD-1 (wild-type)

value: clonally barcoded lenitvirus injection (pMR671_LV_TOM_bc)


title: PEPITEM_2

description: Library name: S4

value: Synovium


title: IORT_Sample_14

description: Library name: IORT_Quantseq_14


title: Pleural mesothelioma, tumor, sample 185540, bio rep 1

description:
Library name: 185540.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185540; replicate: 1.0; replicate_type: Biologic

extract_protocol:
Single-cell suspensions were generated from surgical pleural specimens after tissue dissociation. Seq-Well arrays containing RNA capture beads were loaded with approximately 10,000-20,000 cells per array. For selected specimens, technical replicates were created by splitting cell suspensions across multiple arrays processed in parallel.
Single-cell RNA sequencing libraries were generated using the Seq-Well platform. Cells were loaded onto bead-containing arrays, sealed with a membrane, lysed, and RNA was captured on beads. Reverse transcription, second-strand synthesis, whole transcriptome amplification, and Nextera XT library construction were performed prior to sequencing on Illumina NextSeq 500/550 or NovaSeq 6000 instruments.

value: Tumor

value: S


title: Patient20,CD14+,lac1(RNA-seq)

description: Library name: lac1


title: Patient20,CD14+,control3(RNA-seq)

description: Library name: con3


title: Clonally traced olfactory and forebrain region and surrounding tissue, embryonic day (E) 11.5

description: Library name: exp1_olfactory

source_name: Mouse embryo, olfactory and forebrain region


title: Pleural mesothelioma, tumor, sample 185396

description:
Library name: 185396
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 185396

source_name: Tumor

value: B


title: IORT_Sample_12

description: Library name: IORT_Quantseq_12


title: Pleural mesothelioma, tumor, sample 181196, tech rep 3

description:
Library name: 181196.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 181196; replicate: 3.0; replicate_type: Technical

value: E


title: IORT_Sample_11

description: Library name: IORT_Quantseq_11


title: Pleural mesothelioma, tumor, sample 183762

description:
Library name: 183762
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 183762


title: Clonally traced eye, trigeminal ganglia, midbrain and hindbrain region and surrounding tissue, embryonic day (E) 11.5

description: Library name: exp1_lens

source_name: Mouse embryo, eye, trigeminal ganglia, midbrain and hindbrain region


title: Pleural mesothelioma, tumor, sample 184053

description:
Library name: 184053
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 184053


title: Clonally traced cranial region, embryonic day (E)11.5, sample 1

description: Library name: exp1_cranial1

source_name: Mouse embryo, cranial region

value: Mouse embryo, cranial region


title: Control

city: Xiamen

first: chuanfang

middle: C

last: Chen

state: Fujian

address: No.4221, Xiang'an South Road, Xiang'an District

department: College of Life Science

institute: XIAMEN university

description:
Library name: Sample 1
10X Genomics

data_processing:
Raw sequencing reads were processed using Cell Ranger v7.2.0 (10x Genomics) and aligned to the mm10 mouse reference genome.
Assembly: Mouse mm10
Supplementary files format and content: Table-separated values file and matrix files

extract_protocol:
MC38 tumor cells were subcutaneously implanted into C57BL/6 mice. PBM treatment started at day 7 daily, while tumors were harvest at day 14. Freshly excised tumors were immediately placed on ice and processed into single-cell suspensions. Tumor tissues were digested in DMEM containing 1 mg/mL type IV collagenase, 50 U/mL DNase I, and 10% FBS at 37 °C for 20 min in a shaking incubator. The suspension was passed through a 70-µm cell strainer and centrifuged (800 g, 5 min, 4 °C). The pellet was resuspended in 3 mL red blood cell lysis buffer for 3–5 min, neutralized with 6 mL FACS buffer (PBS + 1 mM EDTA + 1% FBS), and centrifuged again (800 g, 5 min, 4 °C). The final cell pellet was resuspended in FACS buffer, and CD45+ immune cell were sorted by BD Aria III for  scRNA-seq.
For scRNA-seq, sorted cells from each condition were pooled and processed for single-cell library preparation with the Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics) following the manufacturer’s protocol. Gel bead-in-emulsion (GEM) generation, barcoding, and reverse transcription were performed on a Chromium GemCode instrument (10x Genomics). Sequencing libraries were constructed according to the kit instructions and run on an Illumina NovaSeq 6000 platform to obtain high-depth paired-end reads.

value: tumor cells

value: WT


title: IORT_Sample_13

description: Library name: IORT_Quantseq_13


title: Patient20,CD14+,control1(RNA-seq)

description: Library name: con1

value: peripheral blood

value: primary cells


title: pancreatic cancer tussue

first: xin

last: zhao

address: 8#， Gong Ti South Road

institute: Beijing Chaoyang Hospital

description:
Library name: SampleB1
Pancreatic cancer tissue, spatial transcriptomics profiling via 10x Visium

data_processing:
Raw sequencing data were processed using standard 10x Genomics and bioinformatics pipelines. Detailed steps are as follows: 1. Base-calling and Demultiplexing Software: bcl2fastq2 Version: 2.20.0.422 Parameters: --use-bases-mask Y*,I8,I8,Y* --create-fastq-for-index-reads --minimum-trimmed-read-length 8 --mask-short-adapter-reads 8 Output: Demultiplexed FASTQ files with spatial barcode, UMI, and transcriptome reads. 2. Spatial Transcriptome Alignment & Quantification Software: Space Ranger Version: 2.0.0 Parameters: spaceranger count --id=Sample1 --transcriptome=Homo_sapiens_GRCh38-2020-A --fastqs=./fastq_files --sample=Sample1 --image=Sample1_HE.tif --slide=V12345-67 --area=A1 --localcores=16 --localmem=64 Output: Raw gene-barcode matrix, spatial alignment files, filtered feature-barcode matrix. 3. Data Filtering & Quality Control Software: Seurat Version: 4.3.0 Filtering Criteria: Exclude spots with detected genes < 200 or > 5000; total UMI counts < 500 or > 20000; mitochondrial gene ratio > 15%. Discard genes expressed in < 3 spots. Output: High-quality filtered gene expression matrix. 4. Additional Processing (Normalization & Dimensionality Reduction) Software: Seurat Version: 4.3.0 Parameters: Normalization (LogNormalize, scale.factor=10000); PCA (npcs=30); UMAP (dims=1:30)
Assembly: hg38
Supplementary files format and content: matrix.mtx.gz (expression counts, Matrix Market format)
Supplementary files format and content: barcodes.tsv.gz (spot barcodes, TSV format)
Supplementary files format and content: features.tsv.gz (gene info, TSV format)
Supplementary files format and content: tissue_positions_list.csv (spatial coordinates, CSV format)
Supplementary files format and content: metrics_summary.csv (sequencing & mapping QC metrics, CSV)
Supplementary files format and content: tissue_lowres_image.png (low-res H&E histology image, PNG)
Supplementary files format and content: tissue_hires_image.png (high-res H&E image, PNG)
Library strategy: Spatial Transcriptomics

source_name: pancreatic cancer tussue

extract_protocol:
Total RNA was extracted from fresh-frozen pancreatic tissue sections using Qiagen RNeasy Mini Kit according to the manufacturer's standard protocol, followed by quality assessment via NanoDrop and Agilent Bioanalyzer to ensure RNA integrity (RIN ≥ 7.0) for 10x Visium library construction.
Library construction was performed with 10x Genomics Visium Spatial Gene Expression Reagent Kit following the manufacturer’s instructions, including spatially barcoded cDNA synthesis, amplification, adapter ligation, and quality control with Bioanalyzer and Qubit.

value: pancreatic cancer tussue


title: IORT_Sample_07

description: Library name: IORT_Quantseq_07

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.

value: tissue


title: normal pancreatic tissue

description:
Library name: SampleD1
Normal pancreatic tissue, spatial transcriptomics profiling via 10x Visium

source_name: normal pancreatic tissue

value: normal pancreatic tissue


title: IORT_Sample_10

description: Library name: IORT_Quantseq_10

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.


title: RNA Sequencing of  mouse Follicle nac-4

city: Chengdu

first: Xue

last: Zhao

state: SiChuan

address: Sichuan Agricultural University, Chendu, Sichuan province

institute: Sichuan Agricultural University

description: Library name: nac-4

data_processing:
Raw sequencing data generated form Illumina sequencer are used to the following analysis. Trimmed reads (trimmed 5ÿ , 3ÿ -adaptor bases by cutadapt [9] ) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software [6] . The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2 [7] . Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated. Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Assembly: Genomic tRNA Database or tRNAscan-SE
Supplementary files format and content: Differential expression analysis of tRF & tiRNA and miRNA
Supplementary files format and content: count and CPM for each sample

source_name: Follicle

extract_protocol:
Total RNA was extracted by the chloroform method
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer

value: Follicle

tag: strain

value: mGC

tag: Sex

value: female


title: Pleural mesothelioma, tumor, sample 181196, tech rep 1

first: David

last: Severson

address: 2301 Erwin Road

institute: Duke University Health System

description:
Library name: 181196.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 181196; replicate: 1.0; replicate_type: Technical

value: Tumor

value: Pleural Mesothelioma

value: Yes


title: Patient20,CD14+,control2(RNA-seq)

description: Library name: con2

source_name: peripheral blood


title: tumor stroma

description:
Library name: SampleC1
Pancreatic tumor stroma, spatial transcriptomics profiling via 10x Visium

source_name: tumor stroma

value: tumor stroma


title: adjacent tumor tissue

description:
Library name: SampleA1
Adjacent non-tumor pancreatic tissue, spatial transcriptomics profiling via 10x Visium

source_name: adjacent tumor tissue

value: adjacent tumor tissue


title: Pleural mesothelioma, tumor, sample 181173

description:
Library name: 181173
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 181173

value: B


title: Clonally traced cranial region, embryonic day (E)11.5, sample 2

description: Library name: exp1_cranial2

value: Mouse embryo, cranial region

tag: genotype

value: CD-1 (wild-type)

value: clonally barcoded lenitvirus injection (pMR671_LV_TOM_bc)


title: PBM

description:
Library name: Sample 2
10X Genomics

value: tumor cells

value: WT


title: IORT_Sample_09

description: Library name: IORT_Quantseq_09

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.

value: tissue


title: UCSD-MGH-U3 scATAC-seq

description:
Library name: UCSD-MGH-U3-scATAC
UCSD-treated NMI MGHU3 bladder cancer cells

library_source: genomic single cell

data_processing:
Cell Ranger ATAC (v2.1.0) was used for initial alignment and peak calling. Further analysis including fragment file generation, peak matrix construction, and TF motif analysis was performed using Signac and ArchR packages in R.
Assembly: GRCh38 (hg38)
Supplementary files format and content: scATAC_fragments.tar.gz: ATAC-seq fragment files for all samples (TSV.gz format). scATAC_peak_bc_matrices.tar.gz: Peak-by-cell count matrices in 10X H5 format. scATAC_tf_bc_matrices.tar.gz: Transcription factor motif matrices in 10X H5 format. scATAC_peaks_annotations.tar.gz: Peak coordinates (BED format) and peak annotations (TSV format). All files use SRA standard sample names (CTR-MGH-U3, MP-MGH-U3, UCSD-MGH-U3).
Illumina NovaSeq 6000
Gene expression matrices were generated using Cell Ranger (10x Genomics) with default parameters. Data was filtered to include high-quality cells.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene expression matrix in h5 format (filtered_feature_bc_matrix.h5) containing UMI-counted gene expression data. Compatible with Scanpy/Seurat for analysis.

source_name: bladder tumor

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent following manufacturer's instructions. RNA quality was assessed using Bioanalyzer.
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1 Kit according to manufacturer's protocol. Libraries were quantified using Qubit.

value: bladder tumor

value: basal carcinoma

value: NMI

value: Chemotherapy

tag: batch

value: genomic DNA


title: IORT_Sample_04

description: Library name: IORT_Quantseq_04

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.


title: Pleural mesothelioma, tumor, sample 179872, tech rep 3

description:
Library name: 179872.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 179872; replicate: 3.0; replicate_type: Technical

value: Tumor

tag: diagnosis

value: Pleural Mesothelioma

value: NM

value: Yes


title: RNA Sequencing of  mouse Follicle nac-3

description: Library name: nac-3

value: Follicle

value: mGC

value: female


title: Pleural mesothelioma, tumor, sample 179872, tech rep 2

description:
Library name: 179872.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 179872; replicate: 2.0; replicate_type: Technical

tag: histology


title: MP-MGH-U3 scATAC-seq

description:
Library name: MP-MGH-U3-scATAC
Chemotherapy-treated MI MGHU3 bladder cancer cells

value: MI


title: RNA Sequencing of  mouse Follicle EC-3

description: Library name: EC-3


title: Pleural mesothelioma, tumor, sample 178133

description:
Library name: 178133
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 178133

value: B

tag: age at_surgery