title: HTO file: CAF23 MC, DT28 SC, DT28 MC, CAF23/DT28 CC, T47DCO SC, T47DCO MC, CAF23/T47DCO CC

city: Minneapolis

first: Angela

last: Spartz

state: MN

address: 420 Delaware St SE, MMC480

department: Medicine

institute: University of Minnesota

description:
Library name: El-Ashry 002_HTO
10x Genomics

data_processing:
Barcode processing and gene counting were done using Cell Ranger Multi on Cell Ranger v 6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: refdata-cellranger-GRCh38-3.0.0
Supplementary files format and content: barcodes, features and matrix
Supplementary files format and content: tab separted value files and matrix files

source_name: CAF23, DT28, T47DCO

growth_protocol: To make in vitro clusters, equal numbers of breast cancer cells and CAF cells were either plated alone or together into ultra-low-attachment plates (Corning)  in Mammocult medium (StemCell Technologies) according to the manufacturer’s instructions and incubated at 37°C and 5% CO2 for 24 or 48 hours. The following combinations were made: MDA-MB231 mono-clusters (MC), CAF23 monoclusters, CAF23 + MDA-MB231 co-clusters (CC), DT28 mono-clusters, and CAF23 + DT28 co-clusters. 240,000 cells were used for each sample and samples with 2 types of cells were used at a 1:1 ratio. To remove any cells in the dishes that had not formed part of a cluster, the cells were filtered over a 15 µm Pluristrainer (Pluriselect 43-50015-50) and then inverted to release the clusters. Clusters were then digested with Accutase to create a single cell suspension. Cells were washed with PBS in LoBind tubes (Eppendorf) and resuspended in PBS. Single cell (SC) preparations (grown under adherent conditions) were also made for each cell line. Samples of single cells (SC), mono-clusters (MC) and co-clusters (CC) were also made with the estrogen receptor positive cell line, T47DCO and their sequences are included in the file sets. However, we did not include analysis of T47DCO in the published paper. Each sample was incubated with a separate Hashtag Oligo antibody (Supplemental Table 1); two different experiments were performed at different times and therefore HTO10 was used for two different samples.

extract_protocol:
To remove any cells in the dishes that had not formed part of a cluster, the cells were filtered over a 15 µm Pluristrainer (Pluriselect 43-50015-50) and then inverted to release the clusters. Clusters were resuspended in PBS and then digested with Accutase to create a single cell suspension. Cells were washed again with PBS in LoBind tubes (Eppendorf) and resuspended in PBS. Single cell preparations (grown under adherent conditions) were also made for each cell line and washed in PBS. Samples of single cells, mono-clusters and co-clusters were also made with the estrogen receptor positive cell line, T47DCO and their sequences are included in the file sets. However, we did not include analysis of T47DCO in the published paper. Each sample was incubated with a separate Hashtag Oligo antibody (Supplemental Table 1); two different experiments were performed at different times and therefore HTO10 was used for two different samples.
HTO stained BC and CAF cells from each sample were given to the University of Minnesota Genomics Center to be made into 10x Chromium 3’GEX cDNA libraries (10X Genomics) following the manufacturer's protocol. In the frist experiment, El-Ashry 001, 4 samples were pooled. In the second experiment, El-Ashry 002,  8 samples were pooled. Briefly, cell suspension, gel beads, and paritiioning oil were loaded into the Chromium Next GEM chip and run through the Chromium controller to produce GEMS which are then run through a reverse-transcription reaction.  After this step, beads were cleaned up and gene expressin and HTO cDNA libraries were made. during cDNA library production, enzymatic fragmentation, end repair, A-tailing, adaptor ligation, and PCR are performed. Illumina During library construction Illumina the P5 and P7 primers used for Illumina sequencing were added. cDNAs were first evaluated by a MiSeq run and then all libraries were run on a single NovaSeq S4 gel.

tag: cell line

value: CAF23, DT28, T47DCO

value: TNBC breast cancer, ER+ breast cancer, cancer associated fibroblasts


title: GEX file: CAF23 SC, MDA-MB231 SC, MDA-MB231 MC, CAF23/MDA-MB231 CC

status: Public on Jun 25 2025

type: SRA

middle: K

country: USA

description:
Library name: El-Ashry 001_GEX
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

source_name: CAF23, MDA-MB231

value: CAF23, MDA-MB231

tag: cell type

value: TNBC breast cancer, cancer associated fibroblasts


title: PyST Control R2

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Basecalls were performed using Illumina CASAVA 1.8
Raw reads containing adapters, base quality scores less than 5 and more than ten percent N’s were removed using Cutadapt v1.16.
Transcript-level counts were quantified from the processed reads using Kallisto v0.46 and the hg19 transcriptome and summarized to the gene-level. Differential expression was determined using DESeq2.
For validation, processed reads were also mapped to hg19 with STAR v2.7.3a 2-pass alignment using ENCODE parameters, first with a genome index of 100 bp overhangs and then with an index built using 75 bp overhangs and a combination of the junctions determined from the initial alignments. Unstranded gene hits were counted for both alignments using HTSeq v0.9.1 with a minimum alignment quality of 10, and differential expression determined in DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include transcript counts and abundances for each sample

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, #T2010). On-column DNase digestion was performed to remove any residual DNA. The integrity of total RNA was assessed by an Agilent Bioanalyzer 2100 at Novogene.
The cDNA library was constructed using NEBNext® Ultra™ II RNA Library Prep with Sample Purification Beads (New England Biolabs, #E7775). Briefly, a total of 400 ng RNA per sample was subjected to poly(A)-selection, followed by reverse transcription to generate cDNA. The resulting cDNA was subjected to adapter ligation and PCR amplification. Library quality control was performed using Labchip and qPCR.Sequencing was then performed on an Illumina Novaseq 6000 to generate 150 bp paired-end reads (Novogene).

value: mammary epithelial cells

tag: genotype

value: PyST

tag: treatment

value: vehicle (0.05 % DMSO v/v)

tag: time

value: 6 hours


title: PyST Control R1

description: Library name: Sample 1


title: PyST MYF0369 R2

description: Library name: Sample 4


title: HTO file: CAF23 SC, MDA-MB231 SC, MDA-MB231 MC, CAF23/MDA-MB231 CC

description:
Library name: El-Ashry 001_HTO
10x Genomics


title: PyST MYF0369 R1

description: Library name: Sample 3


title: PA#13, Tumor, scTCR-seq

city: shenzhen

first: Minmin

last: Chen

state: GuangDong

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen bay lab

description:
Library name: PA#13-Tumor-VDJ
10x Genomics V(D)J

library_source: genomic

data_processing:
Raw BCL files were processed using Cell Ranger (version 7.1.0) pipeline. Raw read sequences were aligned to the 10X reference genome based on Ensembl GRCh38. Raw data from each sample from the ‘‘filtered_contig_annotations.csv’’ output was further filtered by only including TCR alpha (TRA) or TCR beta (TRB) calls that was reported as ‘‘productive’’. TCR clonotypes were defined as the combination of Vα, Vβ, Jα, Jβ, CDR3α, and CDR3β segments, together with the CDR3α and CDR3β amino acid sequences. In total, 6,503 distinct TCR clonotypes were identified across all samples and categorized into three groups: unique (n = 1), duplicated (n = 2), and clonal (n ≥ 3).
Assembly: GRCh38
Supplementary files format and content: clonotypes.csv: Tab-delimited file containing clonotype-level summary data including clonotype IDs, frequencies, CDR3 sequences, and clonal expansion metrics from 10x Genomics V(D)J analysis.
Supplementary files format and content: filtered_contig_annotations.csv: Tab-delimited file containing cell-level TCR contig annotations including cell barcodes, V(D)J gene assignments, CDR3 sequences, chain types, and quality metrics from 10x Genomics V(D)J pipeline.
Library strategy: TCR-seq

molecule: genomic DNA

source_name: Tumor

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1 mm3 pieces and enzymatically digested with MACS Tumour Dissociation Kit (Miltenyi Biotec,130-095-929) for 40 minutes (for normal tissues) or 1 hour (for tumor tissues) on the gentleMACS™ Octo Dissociator with Heaters, following the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-μm cell-strainer (BD Bioscience, 352350) to remove debris and centrifuged at 450g for 10 min. Pelleted cells were resuspended in sorting buffer (Miltenyi Biotec, 130-091-221) and stained with FITC Mouse Anti-Human CD45 (BD Bioscience,555482) and APC anti-human CD235a (Biolegend,349114). DAPI (BD Bioscience,564907) was added to the cell suspension immediately before FACS. CD235-DAPI- live cells were FACS-sorted for single-cell RNA-sequencing.
The sorted cells were stained with Typan Blue for viability counting. Single-cell suspensions with >80% viability were processed to scRNA-seq. Libraries were generated using the Chromium Controller and the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10xGenomics, 1000244) following the manufacturer’s instructions. Briefly, cells were loaded onto the Single Cell Chip K for encapsulation into droplets, aiming to capture 10,000 cells. cDNA was amplified by 13 PCR cycles and a total of 50ng cDNA was used for library preparation. Qualitative and quantitative assessments of the final libraries were performed on a Bioanalyzer 2200 with the High Sensitivitiy DNA kit (Agilent, 5067-4626), and the Qubit 3.0 Fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854), respectively. Libraries were then normalized, pooled and sequenced on the NovaSeq 6000 (Illumina) with a 150 bp paired-end run. For TCR sequencing, we performed V(D)J amplification from the cDNA pool with the T cell mix 1&2 included in the 5’ Reagent Kits.

tag: tissue

value: Tumor


title: GEX file:CAF23 MC, DT28 SC, DT28 MC, CAF23/DT28 CC, T47DCO SC, T47DCO MC, CAF23/T47DCO CC

description:
Library name: El-Ashry 002_GEX
10x Genomics


title: PA#11, Tumor, scTCR-seq

description:
Library name: PA#11-Tumor-VDJ
10x Genomics V(D)J


title: PA#12, PBMC, scTCR-seq

description:
Library name: PA#12-PBMC-VDJ
10x Genomics V(D)J

source_name: PBMC

value: PBMC


title: B Stage I [HIV_b_a_5]

type: genomic

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: peripheral blood from HIV-1 patient

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data were processed in R using ChAMP package, normalized using BMIQ method
Normalized beta values (before cell fraction correction)

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood samples using QIAamp DNA Mini Kit (QIAGEN GmbH, Hilden, Germany)

value: Whole blood

tag: Stage

value: B Stage I

tag: age


title: PA#11, PBMC, scTCR-seq

description:
Library name: PA#11-PBMC-VDJ
10x Genomics V(D)J


title: PA#10, Tumor, scTCR-seq

description:
Library name: PA#10-Tumor-VDJ
10x Genomics V(D)J


title: PA#09, Tumor, scTCR-seq

description:
Library name: PA#09-Tumor-VDJ
10x Genomics V(D)J


title: PA#09, PBMC, scTCR-seq

description:
Library name: PA#09-PBMC-VDJ
10x Genomics V(D)J


title: PA#10, PBMC, scTCR-seq

description:
Library name: PA#10-PBMC-VDJ
10x Genomics V(D)J


title: PA#10, Normal, scTCR-seq

description:
Library name: PA#10-Normal-VDJ
10x Genomics V(D)J

source_name: Normal

value: Normal


title: HIV Positive without Hepatocellular Carcinoma, JHCC168

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

hyb_protocol: Bisulphite converted DNA was samplified, fragmented and hybridized to human infinium MethylationEPIC BeadChip (illumina) using standard illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing:
ENmix package in R environment (v4.4.0)
processed value definition: Average Beta (processed_data.txt is linked as a Supplementary file on the Series record)

label: Cy3 and Cy5

source_name: Plasma

label_protocol: Standard illumina Protocol

extract_protocol: Circulating cell-free DNA was extracted and concentrated using the QIAamp MinElute ccfDNA Kit (QIAGEN) in batches within three days of blood sample collection.

tag: participant id

tag: Sex

value: Female

tag: cancer stage

tag: group

value: Plasma

tag: bmi

tag: site

value: JUTH


title: PA#08, Tumor, scTCR-seq

description:
Library name: PA#08-Tumor-VDJ
10x Genomics V(D)J


title: PA#09, Normal, scTCR-seq

description:
Library name: PA#09-Normal-VDJ
10x Genomics V(D)J


title: PA#08, Normal, scTCR-seq

description:
Library name: PA#08-Normal-VDJ
10x Genomics V(D)J


title: PA#08, PBMC, scTCR-seq

description:
Library name: PA#08-PBMC-VDJ
10x Genomics V(D)J


title: PA#07, Tumor, scTCR-seq

description:
Library name: PA#07-Tumor-VDJ
10x Genomics V(D)J


title: PA#06, Tumor, scTCR-seq

description:
Library name: PA#06-Tumor-VDJ
10x Genomics V(D)J


title: PA#07, PBMC, scTCR-seq

description:
Library name: PA#07-PBMC-VDJ
10x Genomics V(D)J


title: PA#05, Tumor, scTCR-seq

description:
Library name: PA#05-Tumor-VDJ
10x Genomics V(D)J


title: PA#06, PBMC, scTCR-seq

description:
Library name: PA#06-PBMC-VDJ
10x Genomics V(D)J


title: PA#05, PBMC, scTCR-seq

description:
Library name: PA#05-PBMC-VDJ
10x Genomics V(D)J


title: PA#04, Tumor, scTCR-seq

description:
Library name: PA#04-Tumor-VDJ
10x Genomics V(D)J


title: PA#06, Normal, scTCR-seq

description:
Library name: PA#06-Normal-VDJ
10x Genomics V(D)J


title: PA#02, Tumor, scTCR-seq

description:
Library name: PA#02-Tumor-VDJ
10x Genomics V(D)J


title: PA#03, Tumor, scTCR-seq

description:
Library name: PA#03-Tumor-VDJ
10x Genomics V(D)J


title: PA#01, Tumor, scTCR-seq

description:
Library name: PA#01-Tumor-VDJ
10x Genomics V(D)J


title: Combi 4 Propranolol and SR59230A

city: Gothenburg

first: Bart

last: Edelbroek

address: Medicinaregatan 3B

department: Bioinformatics and Data Centre, Core Facilities

country: Sweden

institute: University of Gothenburg

description:
Library name: sample 17
Combi_6944

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file with raw counts from each sample
Supplementary files format and content: tab-delimited text file with FPKM values from each sample

source_name: LNCaP

extract_protocol:
Total RNA was extracted from the tumours of the orthotopic LNCaP xenograft model using the AllPrep DNA/ RNA/miRNA Universal Kit (# 80224, Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

tag: disease state

value: prostate cancer

value: LNCaP

value: Epithelial


title: Propranolol 6

description:
Library name: sample 13
Prop6928


title: Combi 1 Propranolol and SR59230A

description:
Library name: sample 14
Combi_6930


title: Propranolol 5

description:
Library name: sample 12
Prop6927


title: Propranolol 2

description:
Library name: sample 9
Prop6923


title: Propranolol 4

description:
Library name: sample 11
Prop6926


title: Propranolol 3

description:
Library name: sample 10
Prop6925


title: Propranolol 1

description:
Library name: sample 8
Prop6922


title: Control 7

description:
Library name: sample 7
Control_nn2


title: Control 6

description:
Library name: sample 6
Control_6937


title: Control 5

description:
Library name: sample 5
Control_6935


title: Control 4

description:
Library name: sample 4
Control_6934


title: Control 2

description:
Library name: sample 2
Control_6932


title: Control 3

description:
Library name: sample 3
Control_6933


title: Combi 6 Propranolol and SR59230A

description:
Library name: sample 19
Combi_6948


title: PA#04, Normal, scTCR-seq

description:
Library name: PA#04-Normal-VDJ
10x Genomics V(D)J


title: astrocyte_ipsc_ctrl1_tic; 71_1_plus_S48

city: London

first: Oliver

last: Ziff

address: Institute of Neurology, Queen Square

country: United Kingdom

institute: University College London

description:
Library name: 71_1_plus_S48
astrocyte_ipsc_ctrl1_tic

data_processing:
Adapter trimming with TrimGalore!
Alignment with STAR
Read quantification with Salmon
Sort and index alignments with Samtools
Quality control with RSeQC, Qualimap, dupRadar, Preseq, MultiQC
Assembly: Ensembl Homo_sapiens GRCh38 99
Supplementary files format and content: TPM read counts for each gene in each sample in TSV file

molecule: polyA RNA

source_name: ipsc

growth_protocol: iPSC-dereived neurons were differentiated in N2B27 media and grown to 100DIV. iPSC astrcoytes were generated from neuronal cultures via FGF2-mediated enrichment in N2B27 media, before being matured in N2B27 media with BMP4+LIF.

extract_protocol:
RNA was isolated using NEB Monarch Total RNA miniprep kit
KAPA mRNA Hyper Prep (Roche)

treatment_protocol: Cells were untreated, or treated with TNFa+IL1a+C1q for 24 hours priors to harvesting.

value: ipsc

value: wildtype

value: tic

tag: batch

tag: strandedness

value: forward


title: astrocyte_ipsc_ctrl5_tic; 73_2_plus_S15

description:
Library name: 73_2_plus_S15
astrocyte_ipsc_ctrl5_tic

tag: cell line


title: Combi 5 Propranolol and SR59230A

description:
Library name: sample 18
Combi_6946

tag: cell type


title: astrocyte_ipsc_ctrl5_nil; 73_2_0_S14

description:
Library name: 73_2_0_S14
astrocyte_ipsc_ctrl5_nil

tag: genotype


title: astrocyte_ipsc_ctrl1_nil; 73_1_0_S24

description:
Library name: 73_1_0_S24
astrocyte_ipsc_ctrl1_nil

tag: treatment


title: Combi 3 Propranolol and SR59230A

description:
Library name: sample 16
Combi_6943


title: astrocyte_ipsc_ctrl2_tic; 71_2_plus_S1

description:
Library name: 71_2_plus_S1
astrocyte_ipsc_ctrl2_tic


title: Control 1

description:
Library name: sample 1
Control_6931


title: Combi 2 Propranolol and SR59230A

description:
Library name: sample 15
Combi_6941


title: astrocyte_ipsc_ctrl1_tic; 73_1_plus_S13

description:
Library name: 73_1_plus_S13
astrocyte_ipsc_ctrl1_tic


title: astrocyte_ipsc_ctrl2_nil; 70_2_0_S35

description:
Library name: 70_2_0_S35
astrocyte_ipsc_ctrl2_nil


title: astrocyte_ipsc_ctrl2_nil; 71_2_0_S2

description:
Library name: 71_2_0_S2
astrocyte_ipsc_ctrl2_nil


title: astrocyte_ipsc_ctrl2_tic; 70_2_plus_S36

description:
Library name: 70_2_plus_S36
astrocyte_ipsc_ctrl2_tic


title: astrocyte_ipsc_ctrl1_nil; 71_1_0_S47

description:
Library name: 71_1_0_S47
astrocyte_ipsc_ctrl1_nil


title: astrocyte_ipsc_ctrl1_nil; 70_1_0_S33

description:
Library name: 70_1_0_S33
astrocyte_ipsc_ctrl1_nil


title: astrocyte_ipsc_ctrl1_tic; 70_1_plus_S34

description:
Library name: 70_1_plus_S34
astrocyte_ipsc_ctrl1_tic


title: astrocyte_fetal_ctrlN_tic; N2_FETAL_plus_S30

description:
Library name: N2_FETAL_plus_S30
astrocyte_fetal_ctrlN_tic

source_name: fetal

value: fetal

value: ctrlN


title: astrocyte_fetal_ctrlN_tic; N1_FETAL_plus_S26

description:
Library name: N1_FETAL_plus_S26
astrocyte_fetal_ctrlN_tic


title: astrocyte_ipsc_Y155H_tic; 73_Y_plus_S23

description:
Library name: 73_Y_plus_S23
astrocyte_ipsc_Y155H_tic


title: astrocyte_fetal_ctrlN_nil; N1_FETAL_0_S25

description:
Library name: N1_FETAL_0_S25
astrocyte_fetal_ctrlN_nil


title: astrocyte_fetal_ctrlN_nil; N2_FETAL_0_S29

description:
Library name: N2_FETAL_0_S29
astrocyte_fetal_ctrlN_nil


title: astrocyte_ipsc_Y155H_nil; 73_Y_0_S22

description:
Library name: 73_Y_0_S22
astrocyte_ipsc_Y155H_nil


title: astrocyte_ipsc_ctrlW_tic; 73_W_plus_S19

description:
Library name: 73_W_plus_S19
astrocyte_ipsc_ctrlW_tic

value: ctrlW


title: astrocyte_ipsc_ctrlW_nil; 73_W_0_S18

description:
Library name: 73_W_0_S18
astrocyte_ipsc_ctrlW_nil


title: astrocyte_ipsc_R278I_tic; 73_R_plus_S49

description:
Library name: 73_R_plus_S49
astrocyte_ipsc_R278I_tic


title: astrocyte_ipsc_R278I_nil; 73_R_0_S50

description:
Library name: 73_R_0_S50
astrocyte_ipsc_R278I_nil


title: astrocyte_ipsc_DI4_tic; 73_D_plus_S21

description:
Library name: 73_D_plus_S21
astrocyte_ipsc_DI4_tic


title: astrocyte_ipsc_ctrl3_tic; 73_3_plus_S17

description:
Library name: 73_3_plus_S17
astrocyte_ipsc_ctrl3_tic


title: astrocyte_ipsc_DI4_nil; 73_D_0_S20

description:
Library name: 73_D_0_S20
astrocyte_ipsc_DI4_nil


title: astrocyte_ipsc_ctrlW_nil; 71_W_0_S5

description:
Library name: 71_W_0_S5
astrocyte_ipsc_ctrlW_nil


title: astrocyte_ipsc_ctrl5_nil; 71_3_0_S3

description:
Library name: 71_3_0_S3
astrocyte_ipsc_ctrl5_nil


title: astrocyte_ipsc_R278I_nil; 71_R_0_S11

description:
Library name: 71_R_0_S11
astrocyte_ipsc_R278I_nil


title: astrocyte_ipsc_ctrl3_nil; 73_3_0_S16

description:
Library name: 73_3_0_S16
astrocyte_ipsc_ctrl3_nil


title: astrocyte_ipsc_ctrl5_tic; 71_3_plus_S4

description:
Library name: 71_3_plus_S4
astrocyte_ipsc_ctrl5_tic


title: astrocyte_ipsc_Y155H_nil; 70_Y_0_S43

description:
Library name: 70_Y_0_S43
astrocyte_ipsc_Y155H_nil


title: astrocyte_ipsc_R278I_tic; 71_R_plus_S12

description:
Library name: 71_R_plus_S12
astrocyte_ipsc_R278I_tic


title: astrocyte_ipsc_ctrlW_tic; 70_W_plus_S40

description:
Library name: 70_W_plus_S40
astrocyte_ipsc_ctrlW_tic


title: astrocyte_ipsc_Y155H_tic; 71_Y_plus_S10

description:
Library name: 71_Y_plus_S10
astrocyte_ipsc_Y155H_tic


title: astrocyte_ipsc_R278I_nil; 70_R_0_S45

description:
Library name: 70_R_0_S45
astrocyte_ipsc_R278I_nil


title: astrocyte_ipsc_DI4_nil; 71_D_0_S7

description:
Library name: 71_D_0_S7
astrocyte_ipsc_DI4_nil


title: astrocyte_ipsc_Y155H_tic; 70_Y_plus_S44

description:
Library name: 70_Y_plus_S44
astrocyte_ipsc_Y155H_tic


title: astrocyte_ipsc_DI4_tic; 70_D_plus_S42

description:
Library name: 70_D_plus_S42
astrocyte_ipsc_DI4_tic


title: astrocyte_ipsc_ctrlW_tic; 71_W_plus_S6

description:
Library name: 71_W_plus_S6
astrocyte_ipsc_ctrlW_tic


title: astrocyte_ipsc_R278I_tic; 70_R_plus_S46

description:
Library name: 70_R_plus_S46
astrocyte_ipsc_R278I_tic


title: astrocyte_ipsc_DI4_nil; 70_D_0_S41

description:
Library name: 70_D_0_S41
astrocyte_ipsc_DI4_nil


title: astrocyte_ipsc_ctrl3_nil; 70_3_0_S37

description:
Library name: 70_3_0_S37
astrocyte_ipsc_ctrl3_nil


title: Healthy_Skin, rep13

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: Library name: 20210406.A-10775

data_processing:
STAR v2.7.8a used for reference alignment against human genome
Rsubread v2.4.3 used for gene expression quantification
R package RUVseq v1.38 used for batch correction
R package EdgeR v4.2 used for differential gene expression analysis
Assembly: GRCh38.p13
Supplementary files format and content: Batch corrected normalized gene count matrix

source_name: Skin

extract_protocol:
Samples were thawed, and RNA extraction was carried out using Trizol along with the Qiagen RNAeasy kit (Qiagen, Germany), adhering to the manufacturer's instructions.
For RNA sequencing, total RNA (100–1,000 ng per sample) underwent ribosomal RNA depletion, was reverse-transcribed into double-stranded cDNA, and then selectively enriched by polymerase chain reaction (PCR). The enriched libraries' quality and quantity were assessed using the Fragment Analyzer (Agilent, Santa Clara, California, USA). Libraries were then normalized to a concentration of 10 nM in Tris-Cl 10 mM, pH 8.5 with 0.1 % Tween 20. Sequencing and cluster generation were performed using the HiSeq2500 (Illumina, Inc, California, USA) following the standard protocol.

value: Skin


title: astrocyte_ipsc_ctrl3_tic; 70_3_plus_S38

description:
Library name: 70_3_plus_S38
astrocyte_ipsc_ctrl3_tic


title: Healthy_Skin, rep12

description: Library name: 20210406.A-10772


title: Healthy_Skin, rep11

description: Library name: 20210406.A-10768


title: Healthy_Skin, rep10

description: Library name: 20210406.A-10765


title: Healthy_Skin, rep9

description: Library name: 20210406.A-10762


title: Healthy_Skin, rep8

description: Library name: 20210406.A-10759


title: astrocyte_ipsc_Y155H_nil; 71_Y_0_S9

description:
Library name: 71_Y_0_S9
astrocyte_ipsc_Y155H_nil


title: astrocyte_ipsc_DI4_tic; 71_D_plus_S8

description:
Library name: 71_D_plus_S8
astrocyte_ipsc_DI4_tic


title: Healthy_Skin, rep6

description: Library name: 20210406.A-10753


title: Healthy_Skin, rep7

description: Library name: 20210406.A-10756


title: Healthy_Skin, rep5

description: Library name: 20210406.A-10749


title: astrocyte_ipsc_ctrlW_nil; 70_W_0_S39

description:
Library name: 70_W_0_S39
astrocyte_ipsc_ctrlW_nil


title: Healthy_Skin, rep4

description: Library name: 20210406.A-10746


title: Healthy_Skin, rep3

description: Library name: 20210406.A-10744


title: Healthy_Skin, rep2

description: Library name: 20210406.A-10741


title: ircAE combined CTLA4/PD1 3

description: Library name: 20210406.A-BM7


title: Healthy_Skin, rep1

description: Library name: 20210406.A-1152


title: ircAE PD1-Monotherapy 4

description: Library name: 20210406.A-BM1


title: ircAE PD1-Monotherapy 5

description: Library name: 20210406.A-BM3


title: GMSM-K_RNA_Biological Replicate 3

city: Seattle

first: Robert

middle: A.

last: Cornell

state: WA

address: 1959 NE Pacific Street

department: Oral Health Sciences

institute: University of Washington

description: Library name: GMSM-K_RNA3

data_processing:
Data processing was performed by Novogene. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Reference genome (hg19) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to that gene.
Assembly: hg19
Supplementary files format and content: The processed data file "GMSM-K_FPKM_allSamples.xlsx" contains FPKM values for all the samples.
Supplementary files format and content: The processed data file "GMSM-K_gene_count_allSamples.xlsx" contains raw counts for all the samples.

source_name: GMSM-K

extract_protocol:
Total RNA was extracted from 95% confluent GMSM-K cells in three replicates using Quick-DNA/RNA Miniprep kit (Zymo Research) as per manufacturer’s instructions. Isolated RNA was treated with Turbo DNaseI (ThermoFisher) as per manufacturer’s instructions.
Library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. The library was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Further, the library was sequenced on Illumina platform.

value: GMSM-K

value: fetal oral epithelial


title: SAG + Forskolin replicate 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: Library name: 2404681_11_SF_3

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60) and mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation Human Release 31(GRCh38.p12).
Assembly: GRCh38(hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: cell line

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit
Libraries were prepared using a TruSeq Stranded Total RNA Kit (Illumina)

value: cell line

value: induced pluripotent stem cell

value: WT expressing GFP-alpha-tubulin from the endogenous TUBA1B gene

value: SAG (400 nM) + Forskolin (10 mM)

value: 24 hours after treatment


title: GMSM-K_RNA_Biological Replicate 1

description: Library name: GMSM-K_RNA1


title: SAG + Forskolin replicate 1

description: Library name: 2404679_9_SF_1


title: GMSM-K_RNA_Biological Replicate 2

description: Library name: GMSM-K_RNA2


title: SAG + Forskolin replicate 2

description: Library name: 2404680_10_SF_2


title: SAG replicate 4

description: Library name: 2404678_8_SAG_4

value: SAG (400 nM)


title: SAG replicate 3

description: Library name: 2404677_7_SAG_3


title: SAG replicate 1

description: Library name: 2404674_4_SAG_1


title: DMSO replicate 3

description: Library name: 2404673_3_DMSO_3

value: DMSO


title: DMSO replicate 2

description: Library name: 2404672_2_DMSO_2


title: DMSO replicate 4

description: Library name: 2404675_5_DMSO_4


title: DMSO replicate 1

description: Library name: 2404671_1_DMSO_1


title: hepG2_Ge_1

city: Chengdu

first: Jike

last: Li

address: Traditional Chinese Medicine Laboratory , Chengdu Public Health Clinical Center, Chengdu,610061, PR China

institute: Chengdu Public Health Clinical Center

description: Library name: sample10

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: human hepatoma cell lines

value: Geniposide treatment


title: hepG2_Ge_3

description: Library name: sample12


title: hepG2_Ctrl_3

description: Library name: sample9

value: control


title: hepG2_Ge_2

description: Library name: sample11


title: ircAE PD1-Monotherapy 6

description: Library name: 20210406.A-BM6


title: ircAE combined CTLA4/PD1 2

description: Library name: 20210406.A-BM2


title: hepG2_Ctrl_1

description: Library name: sample7


title: hepG2_Ctrl_2

description: Library name: sample8


title: SAG + Forskolin replicate 4

description: Library name: 2404682_12_SF_4


title: Huh7_Ge_3

description: Library name: sample6


title: Huh7_Ge_1

description: Library name: sample4


title: Huh7_Ctrl_2

description: Library name: sample2


title: Huh7_Ge_2

description: Library name: sample5


title: Huh7_Ctrl_3

description: Library name: sample3


title: Huh7_Ctrl_1

description: Library name: sample1


title: SAG replicate 2

description: Library name: 2404676_6_SAG_2


title: NK92_DFO_24hr_2

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

description: Library name: NK92_DFO_24hr_2

data_processing:
After trimmed by fastp version 0.21.0, reads were mapped into hg38 by HISAT2 version 2.2.1, and counted by StringTie version 2.1.6. with the RefSeq gene annotation file (GTF-formatted) available in NCBI website. The raw count matrix file was created using prepDE.
Assembly: hg38
Supplementary files format and content: CSV-formatted text data includes raw read counts for each sample.

growth_protocol: NK92 was cultured in Artemis Medium-1 with 2% human serum at 37℃ with 5% CO2 incubator.

extract_protocol:
RNA extraction was performed using Qiazol.
TruSeq Standard mRNA Library Prep was used.

treatment_protocol: DFO (500 µM) or PPMX-T003 (10 µg/mL) was added into medium for 6 or 24 hours.

value: natural killer cells

value: 500 µM DFO for 24 hours


title: NK92_T003_24hr_1

description: Library name: NK92_T003_24hr_1

value: 10 µg/mL T003 for 24 hours


title: NK92_DFO_24hr_1

description: Library name: NK92_DFO_24hr_1


title: NK92_T003_6hr_2

description: Library name: NK92_T003_6hr_2

value: 10 µg/mL T003 for 6 hours


title: NK92_T003_24hr_2

description: Library name: NK92_T003_24hr_2


title: NK92_T003_6hr_1

description: Library name: NK92_T003_6hr_1


title: TP20M204-13 Frozen Liver HFO snRNA-seq

city: Pittsburgh

first: Alexander

middle: Chih-Chieh

last: Chang

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

description: Library name: TP20M204-13_Frozen

data_processing:
CellRanger v7.1.0
Assembly: GrCh38
Supplementary files format and content: .h5 files

molecule: nuclear RNA

source_name: Liver metastases

extract_protocol:
snPathoSeq
3' V3.1 Kit for Frozen NextGEM FLEX kit for Fixed.

value: Liver metastases


title: TP19M6-14 Frozen Liver HFO snRNA-seq

description: Library name: TP19M6-14_Frozen


title: NK92_0hr_1

description: Library name: NK92_0hr_1

value: nothing


title: TP19M6-10 Frozen Liver HFO snRNA-seq

description: Library name: TP19M6-10_Frozen


title: NK92_DFO_6hr_1

description: Library name: NK92_DFO_6hr_1

value: 500 µM DFO for 6 hours


title: TDXd Xenograft F2.3

city: Nashville

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

institute: VUMC

description: Library name: 12442-AH-0009

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v4.567 and aligned to corresponding genomes (Gencode GRCh38.p13 for human) using STAR v2.7.11a68.
GTF gene annotation (Gencode v38 for human) was provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9 (www.bioinformatics.babraham.ac.uk/projects/fastqc). featureCounts v2.0.269 was used to count the number of mapped reads to each gene.
Heatmap3 v1.1.970 was used for cluster analysis and visualization.
Significantly differential expressed genes with absolute fold change ≥ 1.5 and FDR adjusted p value ≤ 0.05 were detected by DESeq2 v1.30.171.
Assembly: GRCh38.p13
Supplementary files format and content: Comma-separated value file contains normalized counts of all samples.

source_name: Xenograft

extract_protocol:
Tumor tissue was placed in a round bottom eppendorf and lysed on a TissueLyser II machine (Qiagen) for 2 min at 30 Hz with 350 uL Buffer RLT plus with 0.5% v/v Reagent Dx (Qiagen #19088) and a 5 mm stainless steel bead (Qiagen #69989) per tube. Total RNA was extracted from the homogonized lysate using the RNeasy Protect Cell Mini Kit (Qiagen) as per manufacturer’s protocol.
Illumina TruSeq mRNA sequencing libraries were prepared by sequencing core (VANTAGE, Vanderbilt Technologies for Advanced Genomics).

value: Xenograft

value: P-DXd


title: TDXd Xenograft F2.2

description: Library name: 12442-AH-0008


title: TDXd Xenograft F1.4

description: Library name: 12442-AH-0007


title: PDXd Xenograft H2.2

description: Library name: 12442-AH-0006

value: T-DXd


title: PBS Xenograft HF2.1

description: Library name: 12442-AH-0003

value: PBS


title: PDXd Xenograft H1.2

description: Library name: 12442-AH-0004


title: PBS Xenograft HF1.2

description: Library name: 12442-AH-0002


title: PDXd Xenograft H1.3

description: Library name: 12442-AH-0005


title: PBS Xenograft HF1.1

description: Library name: 12442-AH-0001


title: HEK CLDN10B-EYFP induced repl. 3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: Library name: CLDN10ind_3

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Downstream processing was performed in R2 (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi?open_page=login)
Assembly: hg38
Supplementary files format and content: csv of raw read counts

source_name: stable cell line

growth_protocol: For dynamic 3D cell culture, 1.5 million inducible HEK293 TREx cells were transferred into flasks for dynamic cell culture. After 6 hours, cells were induced with 2 mg/mL of doxycycline and analyzed by microscopy 72 h later.

extract_protocol:
RNA Isolation by Trizol
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

treatment_protocol: doxycyline for CLDN10B-EYPF and EGFP induction

value: stable cell line

value: HEK TREx

value: human embryonal kidney

value: STR confirmed

value: induced


title: HEK CLDN10B-EYFP induced repl. 2

description: Library name: CLDN10ind_2


title: HEK CLDN10B-EYFP induced repl. 1

description: Library name: CLDN10ind_1


title: HEK CLDN10B-EYFP uninduced repl. 3

description: Library name: CLDN10unind_3

value: uninduced


title: HEK CLDN10B-EYFP uninduced repl. 1

description: Library name: CLDN10unind_1


title: HEK EGFP induced repl. 3

description: Library name: EYFPind_3_S10


title: HEK CLDN10B-EYFP uninduced repl. 2

description: Library name: CLDN10unind_2


title: HEK EGFP induced repl. 2

description: Library name: EYFPind_2_S6


title: HEK EGFP induced repl. 1

description: Library name: EYFPind_1_S2


title: NK92_DFO_6hr_2

description: Library name: NK92_DFO_6hr_2

value: natural killer cells


title: HEK EGFP uninduced repl. 1

description: Library name: EYFPunind_1


title: HEK EGFP uninduced repl. 2

description: Library name: EYFPunind_2


title: NK92_0hr_2

description: Library name: NK92_0hr_2


title: HEY--siCCNL2-3

city: ji nan

first: kai

last: zhang

state: shandong

address: Jinan, Shandong, China, wenhua western road

institute: Qilu Hospital of Shandong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.23.0. (parameter:-l 50; -n 5; -q 20;-W 4;-M 20) ；  Trimmed sequencereads were mapped to GRCh38 usng hisat2 v2-2.1.0 (paramtrer:-p 8;-5 5;-3 5;--min-intronlen 20;--max-intronlen 500000;-k 3;--phred33)  ；Read count extraction and normaliation were performed using Htseq v2.0.1 (paramtrer:-s no;-a 10;-m union;-i gene_name;--nonunique none)
Assembly: GRCh38
Supplementary files format and content: Format: txt. Content: Raw counts
Supplementary files format and content: Format: txt. Content: TPM

source_name: HEY

growth_protocol: HEY cells were cultured in DMEM (Gibco, Thermo Fisher Scientific) supplemented with 10% FBS (LONSERA, Uruguay) and 1% penicillin/streptomycin.

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

treatment_protocol: Hey cells were treated with CCNL2-targeting siRNA for 48 hours

value: HEY

value: Ovarian cancer cells


title: HEK EGFP uninduced repl. 3

description: Library name: EYFPunind_3


title: HEY--siCCNL2-1


title: HEY--siCCNL2-2


title: HEY-siNC-3

value: siNC


title: Parental VCaP Biological Replicate 3

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v4.567 and aligned to corresponding genomes (Gencode GRCh38.p13 for human and Gencode GRCm38.p6 for mouse) using STAR v2.7.11a68.
GTF gene annotation (Gencode v38 for human and Gencode vM24 for mouse) was provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9 (www.bioinformatics.babraham.ac.uk/projects/fastqc). featureCounts v2.0.269 was used to count the number of mapped reads to each gene.
Heatmap3 v1.1.970 was used for cluster analysis and visualization.
Significantly differential expressed genes with absolute fold change ≥ 1.5 and FDR adjusted p value ≤ 0.05 were detected by DESeq2 v1.30.171.
Assembly: GRCh38.p13
Supplementary files format and content: Comma-separated value file contains normalized counts of all samples.

source_name: VCaP

growth_protocol: Cells were plated in triplicates in T25 flasks, cultured to a confluency of ~70%, and harvested for total RNA extraction.

extract_protocol:
Total RNA was extracted from treated cells with the RNeasy Protect Cell Mini Kit (Qiagen) as per manufacturer’s protocol.
Illumina TruSeq mRNA sequencing libraries were prepared by sequencing core (VANTAGE, Vanderbilt Technologies for Advanced Genomics).
RNA-seq performed at multiplex paired-end 150 bp on the Illumina NovaSeq 6000 (Illumina).

value: VCaP

value: Metastatic Prostate Carcinoma

tag: phenotype

value: Parental


title: Parental VCaP Biological Replicate 1


title: Enza-resistant VCaP Biological Replicate 3

value: Enza-resistant


title: Enza-resistant VCaP Biological Replicate 2


title: Parental LNCaP Biological Replicate 3

value: LNCaP


title: Parental LNCaP Biological Replicate 1


title: Enza-resistant LNCaP Biological Replicate 3


title: Enza-resistant VCaP Biological Replicate 1


title: Parental LNCaP Biological Replicate 2


title: NRG1-treated LNCaP 24hr Biological Replicate 1

growth_protocol: Cells were plated in triplicate in 6 well plates (500,000-750,000 cells/well) and allowed to adhere for 24-48 hrs.

treatment_protocol: Cells were starved in serum-free and calcium-free media (Vanderbilt Cell Culture Core) for 6-12 hours prior to treatment with buffer, 100 ng/mL rASPN (MyBioSource, Origene) or 15 ng/mL rNRG1 (R&D Systems).


title: NRG1-treated LNCaP 24hr Biological Replicate 3


title: NRG1-treated LNCaP 24hr Biological Replicate 2


title: NRG1-treated LNCaP 12hr Biological Replicate 2


title: NRG1-treated LNCaP 12hr Biological Replicate 1


title: Enza-resistant LNCaP Biological Replicate 2


title: Enza-resistant LNCaP Biological Replicate 1


title: NRG1-treated LNCaP 0hr Biological Replicate 2


title: HEY-siNC-1


title: ASPN-treated LNCaP 24hr Biological Replicate 2

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v4.567 and aligned to corresponding genomes (Gencode GRCh38.p13 for human and Gencode GRCm38.p6 for mouse) using STAR v2.7.11a68.
GTF gene annotation (Gencode v38 for human and Gencode vM24 for mouse) was provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9 (www.bioinformatics.babraham.ac.uk/projects/fastqc). featureCounts v2.0.269 was used to count the number of mapped reads to each gene.
Heatmap3 v1.1.970 was used for cluster analysis and visualization.
Significantly differential expressed genes with absolute fold change ≥ 1.5 and FDR adjusted p value ≤ 0.05 were detected by DESeq2 v1.30.171.
Assembly: GRCh38.p13
Supplementary files format and content: Comma-separated value file contains gene counts of all samples.

value: ASPN-treated


title: HEY-siNC-2


title: ASPN-treated LNCaP 24hr Biological Replicate 1


title: Parental VCaP Biological Replicate 2


title: ASPN-treated LNCaP 12hr Biological Replicate 2


title: ASPN-treated LNCaP 24hr Biological Replicate 3


title: ASPN-treated LNCaP 0hr Biological Replicate 1


title: ASPN-treated LNCaP 0hr Biological Replicate 2


title: blood, Day 28, UGA4, 272

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

institute: National Institutes of Health

data_processing:
Sequencing reads were aligned using the nf-core RNASeq pipeline, version 3.0, and standard parameters. Alignment and quanficiation were performed using STAR and Salmon.
Assembly: GRCh38
Supplementary files format and content: Length scaled gene counts. Rows = Genes, Columns = Subjects

source_name: Whole Blood

extract_protocol:
For each study day, total RNA was isolated from blood samples in randomized batches using the PAXgene Blood RNA kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations. Isolated RNA was stored at -80° C in a LoBind twin-tec 96-well PCR plate (Eppendorf). Sample concentrations were determined using the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Sample fragment size distributions were measured using an RNA Screentape on a 4200 TapeStation System.
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s protocols. In cases of sufficient RNA concentration, 1 μg of input RNA was used, but in cases of low-yield samples, the maximum possible input mass was used. AMPure XP Beads (Beckman Coulter) were used in place of the supplied NEBNext Sample Purification Beads. Libraries for each study day were prepared in separate batches across multiple 96-well plates due to high sample number. Each plate included two negative controls to monitor for reagent or sample-to-sample contamination. Libraries were barcoded with NEBNext Multiplex Oligos for Illumina (NEB), with each pool containing a unique set of barcodes. Libraries were quantified using the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent) on a 4200 TapeStation System to ensure sufficient molarity and quality for pooling and sequencing. Libraries were pooled with equimolar input to a final concentration of 3nM.

tag: tissue

value: Whole Blood

tag: time

value: Day 28

value: male

tag: vaccine response

value: Low Responder


title: blood, Day 28, UGA4, 354

value: High Responder

tag: age


title: blood, Day 28, UGA4, 365

tag: Sex

value: female


title: blood, Day 28, UGA4, 232

value: Non Responder


title: blood, Day 28, UGA4, 222


title: blood, Day 28, UGA4, 220


title: blood, Day 28, UGA4, 054


title: NRG1-treated LNCaP 12hr Biological Replicate 3


title: blood, Day 28, UGA4, 418


title: blood, Day 28, UGA4, 148


title: NRG1-treated LNCaP 0hr Biological Replicate 3


title: blood, Day 28, UGA4, 324


title: blood, Day 28, UGA4, 099


title: blood, Day 28, UGA4, 177


title: blood, Day 28, UGA4, 271


title: NRG1-treated LNCaP 0hr Biological Replicate 1


title: ASPN-treated LNCaP 12hr Biological Replicate 3


title: blood, Day 28, UGA4, 295


title: blood, Day 28, UGA4, 378


title: blood, Day 28, UGA4, 034


title: ASPN-treated LNCaP 12hr Biological Replicate 1


title: blood, Day 28, UGA4, 359


title: blood, Day 28, UGA4, 077


title: blood, Day 28, UGA4, 410


title: blood, Day 28, UGA4, 412


title: blood, Day 28, UGA4, 161


title: blood, Day 28, UGA4, 136


title: blood, Day 28, UGA4, 069


title: blood, Day 28, UGA4, 320


title: blood, Day 28, UGA4, 030


title: blood, Day 28, UGA4, 420


title: blood, Day 28, UGA4, 454


title: blood, Day 28, UGA4, 438


title: blood, Day 28, UGA4, 312


title: blood, Day 28, UGA4, 442


title: blood, Day 28, UGA4, 279


title: blood, Day 28, UGA4, 380


title: blood, Day 28, UGA4, 243


title: blood, Day 28, UGA4, 175


title: blood, Day 28, UGA4, 166


title: blood, Day 28, UGA4, 209


title: blood, Day 28, UGA4, 246


title: blood, Day 28, UGA4, 300


title: blood, Day 28, UGA4, 118


title: blood, Day 28, UGA4, 280


title: blood, Day 28, UGA4, 194


title: blood, Day 28, UGA4, 126


title: blood, Day 28, UGA4, 146


title: blood, Day 28, UGA4, 299


title: blood, Day 28, UGA4, 297


title: blood, Day 28, UGA4, 294


title: blood, Day 28, UGA4, 356


title: blood, Day 28, UGA4, 275


title: blood, Day 28, UGA4, 375


title: blood, Day 28, UGA4, 469


title: blood, Day 28, UGA4, 304


title: blood, Day 28, UGA4, 064


title: blood, Day 28, UGA4, 430


title: blood, Day 28, UGA4, 416


title: blood, Day 28, UGA4, 184


title: blood, Day 28, UGA4, 422


title: blood, Day 28, UGA4, 357


title: blood, Day 28, UGA4, 135


title: blood, Day 28, UGA4, 196


title: blood, Day 28, UGA4, 326


title: blood, Day 28, UGA4, 385


title: blood, Day 28, UGA4, 244


title: blood, Day 28, UGA4, 382


title: blood, Day 28, UGA4, 439


title: blood, Day 28, UGA4, 016


title: blood, Day 28, UGA4, 446


title: blood, Day 28, UGA4, 155


title: blood, Day 28, UGA4, 373


title: blood, Day 28, UGA4, 458


title: blood, Day 28, UGA4, 424


title: blood, Day 28, UGA4, 213


title: blood, Day 28, UGA4, 397


title: blood, Day 28, UGA4, 445


title: blood, Day 28, UGA4, 046


title: blood, Day 28, UGA4, 263


title: blood, Day 28, UGA4, 305


title: blood, Day 28, UGA4, 270


title: blood, Day 28, UGA4, 436


title: blood, Day 28, UGA4, 309


title: blood, Day 28, UGA4, 308


title: blood, Day 28, UGA4, 262


title: blood, Day 28, UGA4, 283


title: blood, Day 28, UGA4, 477


title: blood, Day 28, UGA4, 290


title: blood, Day 28, UGA4, 350


title: blood, Day 28, UGA4, 411


title: blood, Day 28, UGA4, 221


title: blood, Day 28, UGA4, 225


title: blood, Day 28, UGA4, 383


title: blood, Day 28, UGA4, 393


title: blood, Day 28, UGA4, 208


title: blood, Day 28, UGA4, 217


title: blood, Day 28, UGA4, 386


title: blood, Day 28, UGA4, 459


title: blood, Day 28, UGA4, 387


title: blood, Day 28, UGA4, 403


title: blood, Day 28, UGA4, 306


title: blood, Day 28, UGA4, 170


title: blood, Day 28, UGA4, 055


title: blood, Day 28, UGA4, 038


title: blood, Day 28, UGA4, 334


title: blood, Day 28, UGA4, 362


title: blood, Day 28, UGA4, 224


title: blood, Day 28, UGA4, 282


title: blood, Day 28, UGA4, 185


title: blood, Day 28, UGA4, 332


title: blood, Day 28, UGA4, 338


title: blood, Day 28, UGA4, 402


title: blood, Day 28, UGA4, 313


title: blood, Day 28, UGA4, 348


title: blood, Day 28, UGA4, 335


title: blood, Day 28, UGA4, 296


title: blood, Day 28, UGA4, 281


title: blood, Day 28, UGA4, 298


title: blood, Day 28, UGA4, 371


title: blood, Day 28, UGA4, 029


title: blood, Day 28, UGA4, 128


title: blood, Day 28, UGA4, 125


title: blood, Day 28, UGA4, 353


title: blood, Day 28, UGA4, 364


title: blood, Day 28, UGA4, 372


title: blood, Day 28, UGA4, 014


title: blood, Day 28, UGA4, 293


title: blood, Day 28, UGA4, 384


title: blood, Day 28, UGA4, 086


title: Hezuo pig2, liver, Day 15, -15℃±2℃

city: Lanzhou

first: Jihong

last: Yan

state: Gansu

address: Yintan Road Subdistrict, Yingmen Village, No. 1

institute: Gansu Agricultural University

description: Library name: HT2

data_processing:
The original data is further filtered through fastp to reduce the interference caused by invalid data. Delete reads containing adapters, reads with A proportion of N (base information cannot be determined) of more than 10%, reads that are all A bases, and low-quality reads (the number of bases with a quality value Q≤20 accounts for more than 50% of the entire read).
Assembly: Sus scrofa Ensembl_release95
Supplementary files format and content: Gene expression matrices are provided as xls files, It includes the calculated TPM value.

organism: Sus scrofa

source_name: liver

growth_protocol: The rearing of pigs is controlled by temperature according to different treatment methods (normal temperature 23 ± 2℃, cold stress -15 ± 2℃), maintaining ventilation, dryness, hygiene and cleanliness, and providing balanced nutrition feed.

extract_protocol:
Extract total RNA from liver tissues of all pigs in the control group and the cold treatment group for 15 days using TRIzol (Life Technologies, Carlsbad, CA, USA)
First, ribosomal RNAs (rRNAs) are removed, while mRNA and ncRNA are retained. The RNA is randomly broken into small fragments by high temperature. Then, using them as templates, the first strand of cDNA is reverse transcribed with random primers, and the second strand of cDNA is synthesized. Next, purify the cDNA fragment, perform terminal repair, add poly (A), and attach it to the Illumina sequencing adapter. Then, UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were subjected to agarose gel electrophoresis to select appropriate fragments, PCR amplification was performed, the library was establis

value: liver

value: cold stress,-15±2℃


title: blood, Day 28, UGA4, 349


title: Hezuo pig1, liver, Day 15, -15℃±2℃

description: Library name: HT1

treatment_protocol: normal temperature 23 ± 2℃, cold stress -15 ± 2℃


title: Hezuo pig3, liver, Day 15, 23℃±2℃

description: Library name: HC3

value: Room temperature, 23±2℃


title: blood, Day 28, UGA4, 267


title: blood, Day 28, UGA4, 219


title: Hezuo pig2, liver, Day 15, 23℃±2℃

description: Library name: HC2


title: blood, Day 28, UGA4, 253


title: Bama pig1, liver, Day 15, -15℃±2℃

description: Library name: BT1


title: blood, Day 28, UGA4, 431


title: Bama pig3, liver, Day 15, 23℃±2℃

description: Library name: BC3


title: Hezuo pig3, liver, Day 15, -15℃±2℃

description: Library name: HT3


title: blood, Day 28, UGA4, 083


title: Hezuo pig1, liver, Day 15, 23℃±2℃

description: Library name: HC1


title: blood, Day 28, UGA4, 207


title: blood, Day 28, UGA4, 249


title: Bama pig2, liver, Day 15, -15℃±2℃

description: Library name: BT2


title: post_Liver_5

city: Nanjing

first: Mingduo

last: Liu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
For quality control, the sequence data were verified using fastp software (https://github.com/OpenGene/fastp). StringTie (https://ccb.jhu.edu/software/stringtie) was employed to assemble the mapped reads for each sample. To estimate the expression levels of all transcripts, StringTie and Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were utilized following the generation of the final transcriptome. The expression abundance of mRNAs was determined by calculating the TPM (fragments per kilobase of transcript per million mapped reads) value using StringTie and Ballgown.
Assembly: GRCm38(mm10)
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

organism: Mus musculus

source_name: liver tissue

growth_protocol: Six-week-old female BALB/c mice of the wild-type (WT) strain were housed in a specific pathogen-free environment at Nanjing Medical University's Animal Core Facility. The mice were subjected to a 12-hour light/dark cycle with ad libitum access to food and water. For subcutaneous tumor modeling, 4T1 cells (4×10^5 in 100 μL PBS) were implanted into the right fourth mammary fat pad of BALB/c mice. Liver metastasis models were created by directly injecting 4T1 cells (2×10^5 in 20 μL PBS) into the left liver lobe's subcapsular area. Control animals received an equivalent volume of PBS via intrahepatic injection.

extract_protocol:
Tumor tissues, subcutaneously and hepatically grown for 15 days, were excised, minced, and subjected to a digestion solution containing 100 mg collagenase, 5 mg DNase, and 5 mg hyaluronidase in 50 ml DMEM, enriched with 1 ml FBS. This mixture was incubated at 37°C for 45 minutes. Post-digestion, the suspension was filtered and centrifuged at 4°C to isolate the cells. The resulting subcutaneous (SC) and intrahepatic (Liver) tumor cells were resuspended in complete DMEM and stored in liquid nitrogen.
Total RNA was isolated from frozen tumor cells using Trizol reagent (Thermo Fisher, USA) according to the manufacturer's instructions. The integrity and concentration of the extracted RNA were assessed with a Bioanalyzer 2100 (Agilent, USA), and only samples with an RNA Integrity Number (RIN) greater than 7.0 were used for further experiments. Poly(A) mRNA was purified from 1 μg of total RNA using Dyna beads Oligo (dT) (Thermo Fisher, USA) through two rounds of purification. The purified mRNA was then fragmented into smaller pieces by exposure to elevated temperatures and divalent cations. Following the protocol outlined in the mRNA-seq sample preparation kit (Illumina, USA), the fragmented RNA was reverse transcribed to construct the cDNA library. The final cDNA library had an average insert size of approximately 300 bp (±50 bp).

treatment_protocol: For the chemotherapy regimen, each mouse received a dose of 10 mg/kg of paclitaxel via intraperitoneal injection The treatment was given five times per week for a duration of two weeks. The control group was given an equivalent volume of PBS.

value: liver tissue

value: tumor

value: WT

value: paclitaxel i.p.


title: Bama pig3, liver, Day 15, -15℃±2℃

description: Library name: BT3


title: post_Liver_4


title: blood, Day 28, UGA4, 051


title: post_Liver_3


title: blood, Day 28, UGA4, 287


title: Bama pig2, liver, Day 15, 23℃±2℃

description: Library name: BC2


title: blood, Day 28, UGA4, 405


title: post_Liver_1


title: blood, Day 28, UGA4, 344


title: post_Liver_2


title: blood, Day 28, UGA4, 278


title: post_SC_3

source_name: Subcutaneous tissue

value: Subcutaneous tissue


title: blood, Day 28, UGA4, 050


title: post_SC_1


title: Bama pig1, liver, Day 15, 23℃±2℃

description: Library name: BC1


title: pre_Liver_4


title: pre_Liver_2


title: blood, Day 28, UGA4, 238


title: blood, Day 28, UGA4, 396


title: pre_Liver_1


title: blood, Day 28, UGA4, 452


title: blood, Day 28, UGA4, 450


title: blood, Day 28, UGA4, 400


title: blood, Day 28, UGA4, 407


title: pre_SC_3


title: post_SC_2


title: pre_Liver_5


title: pre_Liver_3


title: blood, Day 28, UGA4, 062


title: blood, Day 28, UGA4, 124


title: pre_SC_2


title: blood, Day 28, UGA4, 070


title: pre_SC_1


title: blood, Day 28, UGA4, 151


title: blood, Day 28, UGA4, 169


title: LPS_lot30_6h

city: Bellaterra, Catalonia

first: Jordi

last: Argilaguet

address: Campus de la Universitat Autònoma de Barcelona (UAB)

department: Sanitat animal

country: Spain

institute: IRTA-CReSA

description: Library name: ABA31865

data_processing:
Reads mapped with STAR v2.7.8a
Genes quantified with RSEM v1.3.0
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

organism: Sus scrofa domesticus

source_name: Lung

extract_protocol:
RNeasy mini Kit, QIAGEN (RNAse-free water)
RNA libraries were prepared with KAPA mRNA HyperPrep Kit, following manufacturer’s recommendations

value: Lung

value: Primary

value: Porcine alveolar macrophages

value: 6h stimulation


title: blood, Day 28, UGA4, 011

value: Whole Blood

value: Day 28


title: blood, Day 28, UGA4, 065


title: LPS_lot31_6h

description: Library name: ABA31866


title: LPS_lot29_6h

description: Library name: ABA31864


title: LPS_lot13_6h

description: Library name: ABA31863


title: blood, Day 28, UGA4, 066

value: male


title: blood, Day 28, UGA4, 129

value: female

value: High Responder


title: blood, Day 28, UGA4, 343

value: Non Responder


title: RPMI_lot31_24h

description: Library name: ABA31906

value: 24h stimulation


title: blood, Day 28, UGA4, 001


title: RPMI_lot29_24h

description: Library name: ABA31904


title: blood, Day 28, UGA4, 440


title: Hi-CReSHOG_lot31_24h

description: Library name: ABA31902


title: blood, Day 28, UGA4, 211


title: blood, Day 28, UGA4, 008


title: RPMI_lot13_24h

description: Library name: ABA31903


title: blood, Day 28, UGA4, 323


title: blood, Day 28, UGA4, 473


title: blood, Day 28, UGA4, 085


title: Hi-CReSHOG_lot29_24h

description: Library name: ABA31900


title: Hi-CReSHOG_lot13_24h

description: Library name: ABA31899


title: FracX_lot31_24h

description: Library name: ABA31897


title: FracX_lot30_24h

description: Library name: ABA31896


title: blood, Day 7, UGA4, 263

value: Day 7


title: blood, Day 7, UGA4, 293


title: FracX_lot29_24h

description: Library name: ABA31895


title: blood, Day 28, UGA4, 203

value: Low Responder


title: Pam3CKS_lot30_24h

description: Library name: ABA31892


title: Pam3CKS_lot31_24h

description: Library name: ABA31893


title: FracX_lot13_24h

description: Library name: ABA31894


title: blood, Day 7, UGA4, 362


title: blood, Day 7, UGA4, 213


title: Pam3CKS_lot29_24h

description: Library name: ABA31891


title: blood, Day 7, UGA4, 439


title: RPMI_lot30_24h

description: Library name: ABA31905


title: Hi-CReSHOG_lot30_24h

description: Library name: ABA31901


title: Pam3CKS_lot13_24h

description: Library name: ABA31890


title: LPS_lot31_24h

description: Library name: ABA31888


title: LPS_lot13_24h

description: Library name: ABA31884


title: blood, Day 7, UGA4, 065


title: blood, Day 7, UGA4, 220


title: blood, Day 7, UGA4, 332


title: blood, Day 7, UGA4, 086


title: LPS_lot30_24h

description: Library name: ABA31887


title: blood, Day 7, UGA4, 295


title: blood, Day 7, UGA4, 030


title: FracX_lot31_6h

description: Library name: ABA31874


title: blood, Day 7, UGA4, 262


title: FracX_lot30_6h

description: Library name: ABA31873


title: Pam3CKS_lot31_6h

description: Library name: ABA31870


title: blood, Day 7, UGA4, 371


title: blood, Day 7, UGA4, 320


title: blood, Day 7, UGA4, 177


title: Pam3CKS_lot30_6h

description: Library name: ABA31869


title: blood, Day 7, UGA4, 077


title: blood, Day 7, UGA4, 420


title: FracX_lot13_6h

description: Library name: ABA31871


title: Pam3CKS_lot13_6h

description: Library name: ABA31867


title: blood, Day 7, UGA4, 161


title: blood, Day 7, UGA4, 387


title: blood, Day 7, UGA4, 203


title: RPMI_lot30_6h

description: Library name: ABA31882


title: blood, Day 7, UGA4, 046


title: LPS_lot29_24h

description: Library name: ABA31886


title: RPMI_lot29_6h

description: Library name: ABA31881


title: FracX_lot29_6h

description: Library name: ABA31872


title: blood, Day 7, UGA4, 380


title: blood, Day 7, UGA4, 297


title: RPMI_lot13_6h

description: Library name: ABA31880


title: blood, Day 7, UGA4, 128


title: Hi-CReSHOG_lot31_6h

description: Library name: ABA31879


title: blood, Day 7, UGA4, 290


title: Hi-CReSHOG_lot29_6h

description: Library name: ABA31876


title: blood, Day 7, UGA4, 249


title: blood, Day 7, UGA4, 217


title: blood, Day 7, UGA4, 270


title: Hi-CReSHOG_lot30_6h

description: Library name: ABA31878


title: blood, Day 7, UGA4, 338


title: Hi-CReSHOG_lot13_6h

description: Library name: ABA31875


title: RPMI_lot31_6h

description: Library name: ABA31883


title: blood, Day 7, UGA4, 343


title: blood, Day 7, UGA4, 208


title: Pam3CKS_lot29_6h

description: Library name: ABA31868


title: blood, Day 7, UGA4, 244


title: blood, Day 7, UGA4, 312


title: blood, Day 7, UGA4, 155


title: blood, Day 7, UGA4, 126


title: blood, Day 7, UGA4, 382


title: blood, Day 7, UGA4, 324


title: blood, Day 7, UGA4, 280


title: blood, Day 7, UGA4, 283


title: blood, Day 7, UGA4, 365


title: blood, Day 7, UGA4, 458


title: blood, Day 7, UGA4, 403


title: Torin1-treated DKO, poly mRNA, experiment 2

type: RNA

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

description: Torin1-treated DKO LN18 cells

hyb_protocol: GeneChip® WT Terminal  Labeling

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing

data_processing:
The CEL files were normalized and summarized at the gene level using SST-RMA algorithm from the Transcriptome Analysis Console software (Thermo). Normalized expression and DABG (detection above background) values were retrieved from the CHP files using the affxparser package. Transcript clusters with DABG ≥ 0.05 in at least one of the samples were excluded. Data were annotated using the clariomdhumantranscriptcluster.db package in R. Only coding transcript clusters with a corresponding RefSeq ID for protein (‘NP’) were retained, and transcript clusters for the same gene were collapsed (based on max intensity) using the WGCNA package. One sample of the biological triplicates of the DMSO-treated polysome-associated RNA of WT LN18CRIPSPR cells required further processing. Since no significant changes were observed in overall translation levels of DMSO treated WT, RSK1 and RSK2 cells in comparison to DKO and Torin1-treated cells, we re-scaled the problematic sample relative to DMSO-treated WT, RSK1KO, and RSK2KO cells. First, the medians at the transcript and cell type level were obtained, and the median absolute deviation (MAD) for each transcript were calculated. Second, the transcripts from the problematic sample were separated into three sets: transcripts >= 0.75*MAD; transcripts <= 0.75*MAD; and transcripts between those limits. The three sets were re-scaled separately using the normalizeBetweenArrays (method = scale) function of the limma package. Finally, the transcripts from the different sets were combined and re-scaled using normalizeBetweenArrays (method = quantile) function.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

source_name: Torin1-treated DKO LN18 cells

label_protocol: GeneChip® WT Terminal  Labeling

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM), high glucose, GlutaMAX, pyruvate (Gibco®) containing 10% fetal calf serum.

extract_protocol: RNA was purified from the fractions of a non-linear gradient containing the polysome-associated mRNA and also from an aliquot of the original cytosolic extracts (total mRNA), using TRI-Reagent® (Sigma Aldrich) and Direct-zolTM RNA MiniPrep kit (Zymo Research).

treatment_protocol: Cells were serum-starved for 48 hours. Cells were pre-treated with 250 nM Torin1 or vehicle (DMSO) for 30 minutes, before 10% serum addition for 6 hours.

value: DKO

tag: experiment


title: Torin1-treated DKO, poly mRNA, experiment 3

description: Torin1-treated DKO LN18 cells


title: Torin1-treated DKO, total mRNA, experiment 1

description: Torin1-treated DKO LN18 cells


title: Torin1-treated DKO, total mRNA, experiment 3

description: Torin1-treated DKO LN18 cells


title: DMSO-treated DKO, poly mRNA, experiment 2

description: DMSO-treated DKO LN18 cells

source_name: DMSO-treated DKO LN18 cells

value: DMSO


title: Torin1-treated DKO, poly mRNA, experiment 1

description: Torin1-treated DKO LN18 cells


title: DMSO-treated DKO, poly mRNA, experiment 3

description: DMSO-treated DKO LN18 cells


title: DMSO-treated DKO, poly mRNA, experiment 1

description: DMSO-treated DKO LN18 cells


title: blood, Day 7, UGA4, 386


title: blood, Day 7, UGA4, 051


title: blood, Day 7, UGA4, 424


title: Torin1-treated RSK2, poly mRNA, experiment 3

description: Torin1-treated RSK2 LN18 cells

source_name: Torin1-treated RSK2 LN18 cells

value: RSK2 KO


title: Torin1-treated RSK2, poly mRNA, experiment 2

description: Torin1-treated RSK2 LN18 cells


title: Torin1-treated DKO, total mRNA, experiment 2

description: Torin1-treated DKO LN18 cells


title: blood, Day 7, UGA4, 246


title: DMSO-treated DKO, total mRNA, experiment 3

description: DMSO-treated DKO LN18 cells


title: DMSO-treated DKO, total mRNA, experiment 1

description: DMSO-treated DKO LN18 cells


title: blood, Day 7, UGA4, 402


title: Torin1-treated RSK2, total mRNA, experiment 3

description: Torin1-treated RSK2 LN18 cells


title: DMSO-treated DKO, total mRNA, experiment 2

description: DMSO-treated DKO LN18 cells


title: Torin1-treated RSK2, poly mRNA, experiment 1

description: Torin1-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 375


title: blood, Day 7, UGA4, 396


title: blood, Day 7, UGA4, 151


title: Torin1-treated RSK2, total mRNA, experiment 2

description: Torin1-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 431


title: Torin1-treated RSK2, total mRNA, experiment 1

description: Torin1-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 224


title: DMSO-treated RSK2, poly mRNA, experiment 2

description: DMSO-treated RSK2 LN18 cells

source_name: DMSO-treated RSK2 LN18 cells


title: DMSO-treated RSK2, poly mRNA, experiment 3

description: DMSO-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 364


title: DMSO-treated RSK2, total mRNA, experiment 3

description: DMSO-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 238


title: blood, Day 7, UGA4, 184


title: DMSO-treated RSK2, poly mRNA, experiment 1

description: DMSO-treated RSK2 LN18 cells


title: blood, Day 7, UGA4, 378


title: blood, Day 7, UGA4, 055


title: blood, Day 7, UGA4, 232


title: blood, Day 7, UGA4, 011


title: blood, Day 7, UGA4, 296


title: blood, Day 7, UGA4, 185


title: blood, Day 7, UGA4, 148


title: Torin1-treated RSK1, poly mRNA, experiment 3

description: Torin1-treated RSK1 LN18 cells

source_name: Torin1-treated RSK1 LN18 cells

value: RSK1 KO


title: blood, Day 7, UGA4, 357


title: DMSO-treated RSK1, poly mRNA, experiment 1

description: DMSO-treated RSK1 LN18 cells

source_name: DMSO-treated RSK1 LN18 cells


title: DMSO-treated RSK1, total mRNA, experiment 3

description: DMSO-treated RSK1 LN18 cells


title: DMSO-treated RSK1, total mRNA, experiment 2

description: DMSO-treated RSK1 LN18 cells


title: Torin1-treated RSK1, poly mRNA, experiment 1

description: Torin1-treated RSK1 LN18 cells


title: Torin1-treated RSK1, total mRNA, experiment 3

description: Torin1-treated RSK1 LN18 cells


title: blood, Day 7, UGA4, 452


title: blood, Day 7, UGA4, 384


title: blood, Day 7, UGA4, 125


title: blood, Day 7, UGA4, 211


title: Torin1-treated RSK1, total mRNA, experiment 1

description: Torin1-treated RSK1 LN18 cells


title: DMSO-treated RSK1, poly mRNA, experiment 3

description: DMSO-treated RSK1 LN18 cells


title: DMSO-treated RSK2, total mRNA, experiment 2

description: DMSO-treated RSK2 LN18 cells


title: Torin1-treated RSK1, poly mRNA, experiment 2

description: Torin1-treated RSK1 LN18 cells


title: Torin1-treated WT, poly mRNA, experiment 2

description: Torin1-treated WT LN18 cells

source_name: Torin1-treated WT LN18 cells

value: WT


title: DMSO-treated RSK1, poly mRNA, experiment 2

description: DMSO-treated RSK1 LN18 cells


title: blood, Day 7, UGA4, 085


title: blood, Day 7, UGA4, 282


title: Torin1-treated WT, poly mRNA, experiment 1

description: Torin1-treated WT LN18 cells


title: blood, Day 7, UGA4, 209


title: Torin1-treated WT, total mRNA, experiment 1

description: Torin1-treated WT LN18 cells


title: blood, Day 7, UGA4, 353


title: blood, Day 7, UGA4, 281


title: Torin1-treated WT, total mRNA, experiment 3

description: Torin1-treated WT LN18 cells


title: blood, Day 7, UGA4, 359


title: HCC-LM3, 45℃+G4_3

city: Shanghai

first: Bufu

last: Tang

address: Shanghai, China

institute: Zhongshan Hospital, Fudan University

description: Library name: Sample 6

data_processing:
Post-landing data quality control,
Matching the genome
Identification of modification sites (RNA quantification)
Identification of differential sites (differential RNA identification),
Functional enrichment analysis
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: This table contains the information of RNA modification sites identified for each sample, the corresponding RNA count numbers, and the normalized values.

source_name: Liver cancer

growth_protocol: Human HCC cell lines (HCC-LM3 was cultured in Dulbecco's Modified Eagle Medium (DMEM) complete medium supplemented with 10% fetal bovine serum (FBS) and incubated in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Lysate the cells with 1mL TRizol, transfer to a 1.5 mL RNase-free EP tube, invert 10-15 times, and place on ice for 5 minutes. Centrifuge at 12000×g, 4°C, for 5 minutes (place another set of tubes during centrifugation). After centrifugation, transfer the supernatant (1000μl) to a new tube. Add 200 μL chloroform to each tube in a TRizol:chloroform ratio of 5:1 (avoid light), invert 10-15 times, incubate on ice for 5 minutes, centrifuge at 4°C, 10,000 ×g for 15 minutes. Transfer the supernatant (400 ~ 500 μL) to a new EP tube. Add an equal volume of isopropanol, invert a few times, incubate on ice for 10 minutes, centrifuge at 4°C, 10,000 ×g for 10 minutes, visible white flocculent precipitate. Discard the supernatant, add 1 mL of 75% ethanol, resuspend the precipitate, invert evenly, centrifuge at 4°C, 10,000 ×g for 5 minutes, remove the supernatant, air-dry on a clean bench for 10 minutes, add RNA-free H2O (add 30μl for minimal precipitate, 100-300μl for abundant precipitate), gently resuspend. Use a reverse transcription kit, reverse transcribe 1ug RNA for subsequent experiments, and store the reverse transcribed product at -20°C.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol: HCC-LM3 was incubated 45°C for 10 minute, then treated G1 group or G4 group nanoparticles,after 24 hours of nanoparticle treatment, lysated the cell with 1mL TRizol.

value: Liver cancer

value: Liver cancer cells


title: blood, Day 7, UGA4, 169


title: HCC-LM3, 45℃+G1_3

description: Library name: Sample 3


title: HCC-LM3, 45℃+G1_2

description: Library name: Sample 2


title: blood, Day 7, UGA4, 275


title: blood, Day 7, UGA4, 136


title: HCC-LM3, 45℃+G1_1

description: Library name: Sample 1


title: HCC-LM3, 45℃+G4_2

description: Library name: Sample 5


title: blood, Day 7, UGA4, 279


title: blood, Day 7, UGA4, 219


title: Stroke-anti-VLA4

city: Stanford

first: Kristy

last: Zera

state: CA

address: 1201 Welch Road

department: Neurology

institute: Stanford University

description:
Library name: AHA_4_long
10x Genomics

data_processing:
Cell Ranger (v.6.0.0) analysis pipelines were utilized to align reads to the mm10-GRCh38 hybrid reference genome and count barcodes/UMIs. Reads mapping to introns were not counted. Outliers with a high ratio of mitochondrial (more than 10%, fewer than 400 features) relative to endogenous RNAs and homotypic doublets (more than 6,000 features) were removed in Seurat. Cells were also removed if they expressed fewer than 100 unique genes. Genes not detected in any cell were removed from subsequent analysis. Log-normalized (scale factor 10,000 and pseudocount of 1) expression values of genes generated by the Seurat NormalizeData command were used for clustering and differential gene expression analysis.
Mitochondrial and cell cycle gene regression was performed to ensure that clustering reflects true cell type identities. Principal component analysis was performed on the 2000 most variable genes of the dataset followed by UMAP clustering using the Seurat R Package (v. 4.3.0.1) on the first 20 principal components.
Identification of significant clusters was performed via the standard FindClusters command in Seurat with a 1.0 resolution. CD31+ and CD45+ cells were sub-clustered based on pecam1 and ptprc expression, respectively. CD31+ cells and CD45+ cells underwent principal component analysis and were re-clustered on a resolution parameter of 0.2 and 0.4, respectively. Cell counts were performed once the clusters were subset by condition. To pass QC, cells had a minimum of 300 reads, and on average had 5594 reads and 2208 expressed genes per cell. The annotation of each cluster was manually determined using published marker genes for each cell subtype (Supplementary Table 1). Next, MAST differential gene expression analysis between conditions was performed using Mast (v. 1.24.1), and Gene Ontology pathway analysis was performed with Enrichr (22–24). Finally, the normalized average expression of each gene within each cluster was generated using the Dotplot function of Seurat and plotted with GraphPad Prism 9.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: sensory cortex; infarct core

extract_protocol:
Brain tissue was dissociated with the Miltenyi neural dissociation kit following the manufacturer’s instructions, with minor adjustments to optimize the isolation of endothelial and immune cells. In brief, 4–5 mice per treatment group were anesthetized with ketamine/xylazine solution and perfused with 15mL ice cold phosphate buffered saline (PBS) following cardiac blood collection. The stroke core and peri-infarct cortex, defined as ~2mm surrounding the visible lesion, were dissected and pooled by condition, minced, and digested using the neural dissociation kit (Miltenyi, 130–092-628). Brain homogenates were further diluted in Dulbecco’s PBS (dPBS) and filtered through a 100 µm strainer. The filtered homogenate was then centrifuged (300 g for 10 minutes) and the pellets were resuspended in 0.9 M sucrose in dPBS followed by centrifugation for 20 minutes at 850 g at 4 °C to separate the myelin. Cell pellets were resuspended in FACS buffer (1% BSA in PBS with 2 mM EDTA) and blocked for 5 min on ice with Fc block (CD16/CD32, BD 553141), followed by staining for 10 minutes with anti-CD31-PE/TR594 (1:200, BD 563616) and anti-CD45-PE/Cy7 (1:200, BD 103114) antibodies. Dead cells were excluded by staining with SYTOX Blue Dead Cell Stain (1:5,000, Thermo Fisher Scientific S34857).
Reagents of the Chromium Single Cell 3’ GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer’s protocol. Cells and master mix solution were adjusted to target 10,000 cells per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols. We applied 11 PCR cycles to generate cDNA. Library construction was conducted using the Chromium Single Cell 3’ Library Construction Kit v3 (10X Genomics, 1000121). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility. Illumina sequencing of the resulting libraries was performed by Novogene (https://en.novogene.com/) on an Illumina NovaSeq S4 (Illumina). Base calling, demultiplexing, and generation of FastQ files were conducted by Novogene.

value: sensory cortex; infarct core

tag: strain

value: dMCAO stroke surgery; anti-VLA4 antibody for 10 weeks


title: Torin1-treated RSK1, total mRNA, experiment 2

description: Torin1-treated RSK1 LN18 cells


title: blood, Day 7, UGA4, 175

value: Whole Blood

tag: bmi


title: Stroke-anti-VCAM1

description:
Library name: AHA_3_long
10x Genomics

value: dMCAOstroke surgery; anti-VCAM1 antibody for 10 weeks


title: Stroke-isotype control

description:
Library name: AHA_2_long
10x Genomics

value: dMCAO stroke surgery; isotype control antibody for 10 weeks


title: HCC-LM3, 45℃+G4_1

description: Library name: Sample 4


title: blood, Day 7, UGA4, 016

value: female

value: High Responder


title: blood, Day 7, UGA4, 243


title: blood, Day 7, UGA4, 278

value: male

value: Non Responder


title: Sham-isotype control

description:
Library name: AHA_1_long
10x Genomics

value: Sham Surgery; isotype control antibody for 10 weeks


title: Torin1-treated WT, total mRNA, experiment 2

description: Torin1-treated WT LN18 cells


title: blood, Day 7, UGA4, 124

value: Day 7


title: DMSO-treated WT, poly mRNA, experiment 2

description: DMSO-treated WT LN18 cells

source_name: DMSO-treated WT LN18 cells

value: DMSO


title: DMSO-treated WT, total mRNA, experiment 3

description: DMSO-treated WT LN18 cells


title: DMSO-treated WT, total mRNA, experiment 1

description: DMSO-treated WT LN18 cells


title: blood, Day 7, UGA4, 356


title: DMSO-treated WT, poly mRNA, experiment 1

description: DMSO-treated WT LN18 cells


title: DMSO-treated RSK2, total mRNA, experiment 1

description: DMSO-treated RSK2 LN18 cells

value: RSK2 KO


title: DMSO-treated WT, poly mRNA, experiment 3

description: DMSO-treated WT LN18 cells


title: Mycn CKO, bulk RNA-seq, biol rep1

city: Minneapolis

first: Daniel

last: Garry

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

description:
Library name: P2LADMycnCKO_30DPI_LFLRHL_S5
raw_counts.txt

data_processing:
Sequencing reads were aligned to the Mus musculus (mouse) genome assembly mm10 using kallisto.
Using tximport to determine the read count for each transcript and quantified transcript abundance as transcripts per kilobase per million reads mapped
The read counts data were normalized by DESeq2, followed by differential expression analysis
Assembly: mm10
Supplementary files format and content: Tab-dlimited text file includes raw counts for each Smaple

source_name: ventricles

extract_protocol:
RNA isolated using the Qiagen Rneasy Mini kit.
Library was prerpared using the Illumina TruSeq stranded mRNA kit.

value: ventricles

value: Cells from ventricles

value: mixed

value: Mycn f/f

value: 4OHT (80 ug/g)


title: Mycn CKO, bulk RNA-seq, biol rep2

description:
Library name: P2LADMycnCKO_30DPI_RFLLFL_S6
raw_counts.txt


title: blood, Day 7, UGA4, 050


title: blood, Day 7, UGA4, 062


title: blood, Day 7, UGA4, 323


title: blood, Day 7, UGA4, 271


title: Control, bulk RNA-seq, biol rep2

description:
Library name: P2LADControl_30DPI_RFL_S2
raw_counts.txt

value: corn oil


title: F40

city: New York

first: Davit

last: Goukassian

state: NY

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

description: Library name: WG9-2F

data_processing:
FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) using the STAR aligner (version 2.7.8a) in gene count quantification mode and obtained raw gene counts. The GRCm39 release 110 GTF file was used for gene annotation.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: right ventricular tissue

extract_protocol:
Total RNA was extracted from RV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use.
A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit.

value: right ventricular tissue

tag: diet

value: Normal

tag: field

value: Gamma

tag: dose

value: 100 cGy

tag: rin


title: F38

description: Library name: WG12-3F

value: female


title: Control, bulk RNA-seq, biol rep1

state: MN

description:
Library name: P2LADControl_30DPI_LFL_S3
raw_counts.txt


title: F37

description: Library name: WG12-2F


title: blood, Day 7, UGA4, 335

source_name: Whole Blood

value: Whole Blood

value: Low Responder


title: F39

description: Library name: WG9-1F


title: blood, Day 7, UGA4, 170

value: High Responder


title: blood, Day 7, UGA4, 294

value: Day 7


title: blood, Day 7, UGA4, 196

value: male

value: Non Responder


title: F36

description: Library name: WG12-1F


title: blood, Day 7, UGA4, 326


title: F33

description: Library name: W48-1F

value: Western

value: Sham

value: 0 cGy


title: blood, Day 7, UGA4, 454


title: blood, Day 7, UGA4, 308


title: DMSO-treated RSK1, total mRNA, experiment 1

description: DMSO-treated RSK1 LN18 cells

value: RSK1 KO

value: DMSO

tag: batch


title: blood, Day 7, UGA4, 298


title: F30

description: Library name: W33-2F


title: blood, Day 7, UGA4, 350


title: F34

description: Library name: W48-2F


title: blood, Day 7, UGA4, 253


title: F32

description: Library name: W45-2F


title: DMSO-treated WT, total mRNA, experiment 2

description: DMSO-treated WT LN18 cells

value: WT


title: blood, Day 7, UGA4, 135


title: blood, Day 7, UGA4, 309


title: blood, Day 7, UGA4, 066


title: F29

description: Library name: W33-1F

value: right ventricular tissue


title: blood, Day 7, UGA4, 397


title: F31

description: Library name: W45-1F


title: blood, Day 7, UGA4, 083


title: blood, Day 7, UGA4, 349


title: F35

description: Library name: W48-3F


title: F28

description: Library name: W35-3F

value: Normal


title: F26

description: Library name: W35-1F


title: F23

description: Library name: W21-1F

value: Mix

value: 50 cGy


title: F27

description: Library name: W35-2F

value: female


title: blood, Day 7, UGA4, 008

value: Whole Blood


title: F25

description: Library name: W24-1F


title: F24

description: Library name: W21-2F


title: F22

description: Library name: W23-2F


title: F21

description: Library name: W23-1F


title: F19

description: Library name: WG7-4F

value: Gamma

value: 100 cGy


title: blood, Day 7, UGA4, 440

value: Day 7


title: blood, Day 7, UGA4, 334

value: male

value: Low Responder


title: blood, Day 7, UGA4, 348


title: blood, Day 7, UGA4, 373

value: Non Responder


title: blood, Day 7, UGA4, 222


title: F16

description: Library name: WG7-1F


title: blood, Day 7, UGA4, 146

value: High Responder


title: F17

description: Library name: WG7-2F


title: blood, Day 7, UGA4, 014


title: F14

description: Library name: W41-4F

value: Western

value: Sham

value: 0 cGy


title: blood, Day 7, UGA4, 385


title: F13

description: Library name: W41-3F


title: F15

description: Library name: W43-1F


title: F12

description: Library name: W41-2F


title: F11

description: Library name: W41-1F


title: blood, Day 7, UGA4, 372


title: blood, Day 7, UGA4, 029


title: blood, Day 7, UGA4, 305


title: blood, Day 7, UGA4, 272


title: blood, Day 7, UGA4, 194


title: F9

description: Library name: W32-1F


title: F8

description: Library name: W31-3F


title: F18

description: Library name: WG7-3F


title: Torin1-treated WT, poly mRNA, experiment 3

description: Torin1-treated WT LN18 cells

value: WT


title: F7

description: Library name: W31-2F

value: right ventricular tissue


title: blood, Day 7, UGA4, 416


title: blood, Day 7, UGA4, 034


title: F6

description: Library name: W31-1F

value: Normal


title: blood, Day 7, UGA4, 313


title: F5

description: Library name: W19A-1F

value: Mix


title: F4

description: Library name: W19-2F

value: 50 cGy


title: blood, Day 7, UGA4, 430

value: female


title: F3

description: Library name: W19-1F


title: M38

description: Library name: WG6-1


title: F2

description: Library name: W7-3F


title: blood, Day 7, UGA4, 038

value: Whole Blood


title: F1

description: Library name: W7-1F


title: blood, Day 7, UGA4, 166


title: blood, Day 7, UGA4, 129


title: blood, Day 7, UGA4, 383


title: M39

description: Library name: WG6-2

value: Gamma


title: M40

description: Library name: WG8-1

value: 100 cGy


title: blood, Day 7, UGA4, 221

value: Day 7


title: M37

description: Library name: WG4-2

value: male


title: M36

description: Library name: WG4-1


title: blood, Day 7, UGA4, 411


title: M34

description: Library name: WG55-2


title: blood, Day 7, UGA4, 064


title: blood, Day 7, UGA4, 070


title: M33

description: Library name: WG55-1


title: M32

description: Library name: WG53-2


title: blood, Day 7, UGA4, 442


title: blood, Day 7, UGA4, 446

value: Low Responder


title: blood, Day 7, UGA4, 459


title: M31

description: Library name: WG53-1


title: blood, Day 7, UGA4, 304


title: blood, Day 7, UGA4, 267


title: blood, Day 7, UGA4, 118


title: blood, Day 7, UGA4, 445


title: M27

description: Library name: W42-2


title: blood, Day 7, UGA4, 225

value: Non Responder


title: P93 BC scATAC

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

description: Library name: P93

library_source: genomic single cell

data_processing:
The initial processing of scATAC-seq data to generate barcoded and aligned read bam files was performed using the ATAC-Seq Analysis Toolkit (Bio-Rad). Sequencing data were then processed by converting BAM files into fragment files using Rsamtools (https://bioconductor.org/packages/Rsamtools).
Assembly: hg19
Supplementary files format and content: fragment file

source_name: Breast cancer

extract_protocol:
BC specimens were obtained via core needle biopsy of surgically removed tumors. The specimens were dissociated into single cells using a MACS Tumor Dissociation Kit and gentleMACS dissociation (Miltenyi Biotec), following manufacturer’s instructions. For pleural effusion samples, the drainage fluid was collected after trocar placement, centrifuged, and purified using a Red Blood Cell Lysis Solution lysis buffer (Miltenyi Biotec).
The scATAC-seq libraries were prepared according to the droplet-based combinatorial indexing method, with some modifications. The indexed-Tn5 transposase was prepared as previously described. After segmentation with the custom indexed-Tn5, the library was prepared using the SureCell ATAC-Seq Library Prep Kit (Bio-Rad) and a ddSEQ Single-Cell Isolator system (Bio-Rad). Q5 HiFi DNA Polymerase and USER II Enzyme (both from NEB) were used for a subset of samples in the Barcode Reaction mix and Enzyme Reaction mix. Then, the complete scATAC-seq libraries were loaded at 1.5 pM on a NextSeq 550 platform (Illumina) and sequencing was performed using the following read protocol: Read 1, 118 cycles; i7 index read, 8 cycles; and Read 2, 40 cycles.

value: Breast cancer


title: blood, Day 7, UGA4, 300


title: blood, Day 7, UGA4, 001

value: High Responder


title: P64 BC scATAC

description: Library name: P64


title: blood, Day 7, UGA4, 410


title: M25

description: Library name: W17-1


title: M29

description: Library name: WG45-1

value: Sham


title: M30

description: Library name: W44-1

value: 0 cGy


title: M26

description: Library name: W42-1


title: M28

description: Library name: W42-3


title: M24

description: Library name: W16-5


title: P54 BC scATAC

description: Library name: P54


title: blood, Day 7, UGA4, 354


title: M23

description: Library name: W16-4


title: P50 BC scATAC

description: Library name: P50


title: blood, Day 7, UGA4, 287


title: blood, Day 7, UGA4, 422


title: P41 BC scATAC

description: Library name: P41


title: P52 BC scATAC

description: Library name: P52


title: P51 BC scATAC

description: Library name: P51


title: blood, Day 7, UGA4, 469


title: P49 BC scATAC

description: Library name: P49


title: P39 BC scATAC

description: Library name: P39


title: P44 BC scATAC

description: Library name: P44


title: M22

description: Library name: W16-3


title: M21

description: Library name: W16-2


title: blood, Day 7, UGA4, 207


title: P35 BC scATAC

description: Library name: P35


title: blood, Day 7, UGA4, 473


title: blood, Day 7, UGA4, 054


title: M17

description: Library name: WG11-1


title: P210LR BC scATAC

description: Library name: P210LR


title: P38 BC scATAC

description: Library name: P38


title: P34 BC scATAC

description: Library name: P34


title: P33 BC scATAC

description: Library name: P33


title: P211LN BC scATAC

description: Library name: P211LN


title: M18

description: Library name: WG11-2


title: P20LN BC scATAC

description: Library name: P20LN


title: blood, Day 7, UGA4, 393


title: M16

description: Library name: WG7-1


title: P40 BC scATAC

description: Library name: P40


title: blood, Day 7, UGA4, 099


title: M19

description: Library name: WG11-3


title: blood, Day 7, UGA4, 450


title: blood, Day 7, UGA4, 436


title: M14

description: Library name: W53-4

value: Western


title: blood, Day 7, UGA4, 306


title: blood, Day 7, UGA4, 344


title: P200A BC scATAC

description: Library name: P200A


title: P190 BC scATAC

description: Library name: P190


title: P189 BC scATAC

description: Library name: P189


title: M13

description: Library name: W53-3

value: right ventricular tissue


title: P193 BC scATAC

description: Library name: P193


title: blood, Day 7, UGA4, 299


title: P181 BC scATAC

description: Library name: P181


title: M12

description: Library name: W53-2


title: M15

description: Library name: W55-1


title: blood, Day 7, UGA4, 477


title: P185 BC scATAC

description: Library name: P185


title: blood, Day 7, UGA4, 069


title: P178 BC scATAC

description: Library name: P178


title: M11

description: Library name: W53-1


title: P181LN BC scATAC

description: Library name: P181LN


title: P179 BC scATAC

description: Library name: P179


title: M35

description: Library name: WG57-1


title: M10

description: Library name: W47-2

value: Normal


title: P167 BC scATAC

description: Library name: P167


title: P180 BC scATAC

description: Library name: P180


title: P175PE BC scATAC

description: Library name: P175PE


title: blood, Day 7, UGA4, 405


title: blood, Day 7, UGA4, 412


title: P191 BC scATAC

description: Library name: P191


title: P171 BC scATAC

description: Library name: P171


title: P163PE BC scATAC

description: Library name: P163PE


title: M9

description: Library name: W47-1


title: P165 BC scATAC

description: Library name: P165


title: P166 BC scATAC

description: Library name: P166


title: M7

description: Library name: W43-3


title: blood, Day 7, UGA4, 418


title: M8

description: Library name: W45-2


title: blood, Day 7, UGA4, 438


title: blood, Day 7, UGA4, 407


title: P122 BC scATAC

description: Library name: P122


title: M4

description: Library name: W10-1

value: Mix


title: M6

description: Library name: W43-2


title: M20

description: Library name: WG12-1


title: blood, Day 7, UGA4, 400