title: T12,ATB,PBMC,DMSO

description:
Library name: Sample 341
TS0028_Z


title: I3,IGRA+,PBMC,DMSO

status: Public on Dec 03 2025

type: SRA

city: La Jolla

first: Leila

middle: Y

last: Chihab

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Immunology

description:
Library name: Sample 227
5080_DMSO_S327_L003

library_source: transcriptomic

data_processing:
Reads that passed illumina filters were filtered to eliminate reads aligning to tRNA, rRNA, and adapter sequences. The reads were then aligned to GRCh38 reference genome using TopHat. DUST scores were calculated with PRINSEQ Lite and low complexity reads (DUST >4) were removed from the BAM files. The alignment results were parsed via SAMtools to generate SAM files. Read counts for each genomic feature were obtained with the htseq-count program.
Assembly: GRCh38
Supplementary files format and content: abundance measurementas as a matrix table

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA was purified using an miRNeasy Micro Kit (QIAGEN).
Purified total RNA (1–5 ng) was amplified following the Smart-Seq2 protocol (16 cycles of cDNA amplification). 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina)

treatment_protocol: No specific treatment involved

tag: treatment

value: DMSO

tag: cell type

value: PBMC

tag: genotype

value: IGRA+


title: biopsy_miRNA_C1

city: Taipei City

first: MIN-HSIU

last: CHEN

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical University

description: miRNA

data_processing:
Analysis of data was performed with GENEGLOBE online software (https://geneglobe.qiagen.com/pl/analyze).
DESeq2 was also used to normalize the expression (UMI reads) of each miRNA in a sample by calculating a scaling factor (for detailed information on DESeq2, please refer to the DESeq2 manual: https://www.bioconductor.org/packages/3.3/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf).
Assembly: miRBase_v22, Homo sapiens
Supplementary files format and content: tab-delimited text files include counts for each sample

source_name: Kidney

extract_protocol:
1. Isolate uEV by SBI ExoQuick-TC kit. 2. Extract miRNA from uEV and biopsied kidney tissues by QIAGEN miRNeasy micro kit.
1 ng of each miRNA sample was used for small RNA library preparation following the standard protocol of the QIAseq miRNA Library Kit.

tag: tissue

value: Kidney


title: I2,IGRA+,PBMC,DMSO

description:
Library name: Sample 225
5079_DMSO_S323_L003


title: C8,IGRA-,PBMC,MTB300

description:
Library name: Sample 229
5081_MTB300_S333_L003

value: IGRA-


title: T10,ATB,PBMC,MTB300

description:
Library name: Sample 338
TS0023_Y

value: ATB


title: T9,ATB,PBMC,MTB300

description:
Library name: Sample 337
TS0022_Y


title: uEV_miRNA_GS2

description: miRNA

source_name: Urine

value: Urine


title: uEV_miRNA_GS3

description: miRNA


title: biopsy_miRNA_C2

description: miRNA


title: C6,IGRA-,PBMC,MTB300

description:
Library name: Sample 221
5077_MTB300_S317_L003


title: C5,IGRA-,PBMC,DMSO

description:
Library name: Sample 220
5076_DMSO_S311_L003


title: uEV_miRNA_GS4

description: miRNA


title: C7,IGRA-,PBMC,DMSO

description:
Library name: Sample 224
5078_DMSO_S319_L003


title: T10,ATB,PBMC,DMSO

description:
Library name: Sample 339
TS0023_Z


title: I2,IGRA+,PBMC,MTB300

description:
Library name: Sample 226
5079_MTB300_S325_L003


title: T13,ATB,PBMC,MTB300

description:
Library name: Sample 343
TS0030_Y


title: C4,IGRA-,PBMC,MTB300

description:
Library name: Sample 218
5075_MTB300_S309_L003


title: C4,IGRA-,PBMC,DMSO

description:
Library name: Sample 217
5075_DMSO_S307_L003


title: C7,IGRA-,PBMC,MTB300

description:
Library name: Sample 223
5078_MTB300_S321_L003


title: C6,IGRA-,PBMC,DMSO

description:
Library name: Sample 222
5077_DMSO_S315_L003


title: C8,IGRA-,PBMC,DMSO

description:
Library name: Sample 230
5081_DMSO_S331_L003


title: C3,IGRA-,PBMC,MTB300

description:
Library name: Sample 214
5073_MTB300_S301_L003


title: T9,ATB,PBMC,DMSO

description:
Library name: Sample 336
TS0022_Z


title: C5,IGRA-,PBMC,MTB300

description:
Library name: Sample 219
5076_MTB300_S313_L003


title: uEV_miRNA_C2

description: miRNA


title: uEV_miRNA_GS1

description: miRNA


title: I1,IGRA+,PBMC,MTB300

description:
Library name: Sample 216
5074_MTB300_S305_L003


title: uEV_miRNA_C4

description: miRNA


title: T8,ATB,PBMC,DMSO

description:
Library name: Sample 334
TS0020_Z


title: C3,IGRA-,PBMC,DMSO

description:
Library name: Sample 215
5073_DMSO_S299_L003


title: uEV_miRNA_C1

description: miRNA


title: C1,IGRA-,PBMC,MTB300

description:
Library name: Sample 211
5071_MTB300_S37_L001


title: uEV_miRNA_C3

description: miRNA


title: S34,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 208
4242_MTB300_S293_L003

value: Sarcoidosis


title: T7,ATB,PBMC,MTB300

description:
Library name: Sample 333
TS0019_Y


title: C2,IGRA-,PBMC,MTB300

description:
Library name: Sample 213
5072_MTB300_S297_L003


title: S33,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 206
4241_MTB300_S289_L003


title: C2,IGRA-,PBMC,DMSO

description:
Library name: Sample 212
5072_DMSO_S295_L003


title: T7,ATB,PBMC,DMSO

description:
Library name: Sample 332
TS0019_Z


title: C34,IGRA-,PBMC,DMSO

description:
Library name: Sample 330
JOLLAC03_DMSO_S72_L004


title: Cbr-ivph-3_L3_R3

city: Baltimore

first: Nikita

middle: Sudhir

last: Jhaveri

address: 3400 N Charles Street

department: Biology

institute: Johns Hopkins University

description:
Library name: Cbr-ivph-3_L3_R3
column G

data_processing:
RNA sample quality was vetted for inclusion based on Bioanalyzer RIN scores
MultiQC was used to aggregate multiple results into a single report (Ewels et al. 2016).
Reads were aligned to the genome using RNA STAR, set to paired-end sequences and default settings (Dobin et al. 2013).
To count hits per gene, featureCounts was used with default settings for paired-end reads (Liao, et al. 2014).
Assembly: C. briggsae CB4 (Ross et al. 2011), with WS279 for annotation
Supplementary files format and content: Excel file (.xlsx) containing gene read counts, obtained from Featurecounts

organism: Caenorhabditis briggsae

source_name: Whole organism (hermaphrodite)

growth_protocol: Worms were grown and maintained according to established methods (Wood 1988). Cultures were propagated on the Nematode Growth Medium (NGM) plates seeded with E. coli OP50 bacteria and maintained at 20°C. C. briggsae animals (AF16 wild type or PS9217 Cbr-ivph-3(sy5216)) were developmentally synchronized using a standard bleaching method (Porta-de-la-Riva et al. 2012), with eggs recovered in M9 buffer and placed on a rotator overnight. The synchronized L1s were plated onto OP50 seeded plates and incubated at 20°C. To get the accurate stage, worms were mounted on glass slides containing a thin agar pad (2% noble agar). The animals were placed in a drop of M9 buffer that included 5 mM Sodium Azide anesthetic (Yochem 2006) and examined under the Nikon Eclipse 80i microscope for Vulval precursor cell (VPC) division. Once a few animals showed division of the Pn.p cells to the two-celled stage, the animals were washed in M9, and frozen in Trizol. RNA was recovered following the Trizol (Invitrogen) protocol. Three independent biological replicates were prepared for each genotype.

extract_protocol:
RNA was isolated using Trizol-reagent (Sigma, USA, Catalog Number T9424), chloroform, and isopropanol (Chomczynski and Sacchi 1987).
cDNA libraries were constructed from 100–200 ng RNA using an Illumina-specific commercial kit (TruSeq RNA Sample Preparation Kit v2, Set A, Catalog number RS-122-2001).

value: Whole organism (hermaphrodite)

tag: time

value: L3 stage


title: S32,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 204
4240_MTB300_S285_L003


title: S33,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 205
4241_DMSO_S287_L003


title: Cbr-ivph-3_L3_R2

description:
Library name: Cbr-ivph-3_L3_R2
column F


title: C33,IGRA-,PBMC,MTB300

description:
Library name: Sample 329
JOLLAC02_MTB300_S133_L004


title: Cbr-ivph-3_L3_R1

description:
Library name: Cbr-ivph-3_L3_R1
column E


title: S34,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 207
4242_DMSO_S291_L003


title: S32,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 203
4240_DMSO_S283_L003


title: C33,IGRA-,PBMC,DMSO

description:
Library name: Sample 328
JOLLAC02_DMSO_S71_L004


title: S31,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 202
4239_DMSO_S279_L003


title: T8,ATB,PBMC,MTB300

description:
Library name: Sample 335
TS0020_Y


title: S30,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 199
4238_DMSO_S275_L003


title: S30,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 200
4238_MTB300_S277_L003


title: C1,IGRA-,PBMC,DMSO

description:
Library name: Sample 210
5071_DMSO_S35_L001


title: S31,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 201
4239_MTB300_S281_L003


title: AF16_L3_R3

description:
Library name: AF16_L3_R3
column D


title: I25,IGRA+,PBMC,MTB300

description:
Library name: Sample 327
JOLLAB04_MTB300_S85_L004


title: C34,IGRA-,PBMC,MTB300

description:
Library name: Sample 331
JOLLAC03_MTB300_S134_L004


title: AF16_L3_R2

description:
Library name: AF16_L3_R2
column C


title: S29,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 198
4237_DMSO_S271_L003


title: Plate3_unmatched

city: Cambridge

first: Brian

last: Rabe

state: MA

address: 250 Water St

institute: Bristol Myers Squibb

description: Library name: Plate3_unmatched

data_processing:
Standard BCL2fastq was used to demultiplex by each plate containing samples with unique TSO barcodes
Plates were further demultiplexed, cDNA sequences aligned, and counts collapsed by UMI using the zUMIs pipeline
Assembly: GRCh38-ensembl93
Supplementary files format and content: Each processed file is a plain-text, tab-delimited table named “<SampleID>.counts.txt”. Column 1: gene_id - Ensembl gene identifier (e.g. ENSG00000141510) Column 2: count - integer UMI-collapsed exon counts for that gene in the sample

molecule: polyA RNA

source_name: cell line

growth_protocol: Panc0203 cells were cultured in RPMI supplemented with 1X GlutaMax, 10 mM HEPES, 10% FBS, 1 mM sodium pyruvate, and 100 U/ml pen-strep. Panc0403 cells were cultured in RPMI supplemented with 1X GlutaMax, 10 mM HEPES, 10% FBS, 20 µg/ml insulin, and 100 U/ml pen-strep. AsPC1 cells were cultured in ATCC modified RPMI supplemented with 10% FBS and 100 U/ml pen-strep. Panc-1 cells were cultured in DMEM supplemented with 10% FBS and 100 U/ml pen-strep. PACADD-188 cells were cultured in a 1:1 mixture of DMEM and KFSM, with KSFM supplements, supplemented with 20% FBS and 100 U/ml pen-strep. All cells were cultured at 37C with humidified atmosphere and 5% CO2, either with atmospheric O2 (normoxia) or 1% O2 (hypoxia).

extract_protocol:
Cells were lysed directly in well with TriReagent and extracted using the Zymo Directzol micro kit according to manufacturer protocols
To generate RNA-seq lite libraries, NEB’s Template Switching RT Enzyme mix was used (NEB Cat# M0466L). 250 ng of total RNA from each sample was brought to a final volume of 8 ul with RT buffer (final concentration 1X), oligodT RT primer with the Illumina Read2 sequence (final concentration of 1 uM), and dNTP mix (NEB Cat# N0447L, final concentration 1 mM each). Samples were then transferred to a thermocycler at 95°C for 2.5 minutes, allowing for Mg2+-mediated RNA fragmentation, and then samples were fast cooled on ice. 0.5 ul of 4X RT buffer, 0.5 ul of 75 uM template switching oligo (TSO, which contained a sample index, UMI, variable length stagger region, and the Illumina Read1 primer sequence), and 1 ul of RT enzyme were added to each sample, and reverse transcription was performed according to manufacturer protocol. Samples with unique TSO-added sample indices were then pooled and treated with RNaseA (NEB Cat# T3018L, 1 ul per pooled sample) for 30 minutes at room temperature, and then cDNA was column purified (Zymo Cat# D4013) using 7 volumes of DNA binding buffer, and eluted in 36 ul of Buffer EB (Qiagen Cat# 19086). 3 ul of each reaction were amplified in a 1/10th scale reaction, as described below, with the addition of 1X EvaGreen (VWR Cat# 76423-472) in a QuantStudio 12k Flex (ThermoFisher Scientific), and the cycle number necessary to reach ~1/3 the maximum amplification was chosen for final pool amplification. The remaining ~30 ul of cDNA was amplified using the NEBNext Ultra™ II Q5 Master Mix (NEB Cat# M0544L) and NEBNext Multiplex Oligos for Illumina (NEB Cat# E7335S) according to manufacturer instructions and using the cycle number determined above. Final sequencing libraries were purified using SPRIselect beads (Beckman Coulter Cat# B23318), with a double-sided size selection (0.5X-0.8X). Libraries were sequenced on a NextSeq 2000 (P3 flowcell kit, 200 cycles, Illumina Cat# 20040560), with a 144 cycle Read1 which contained the sample index, UMI, and cDNA insert.   RNA-lite primers:  RNA-lite_RT-primer: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT [T-30]VN  RNA-lite_TSO: ACACTCTTTCCCTACACGACGCTCTTCCGATCT[Sample Index-8][UMI-8][Stagger-0-8 bases]rGrGrG

treatment_protocol: Cells cultured in hypoxia were maintained at 1% O2 at all times. All media and solutions were equilibrated overnight to 1% O2 before being applied to cells. Tubes containing cells were tightly sealed with parafilm before being removed from hypoxia glovebox for centrifugation following trypsinization.

value: cell line

tag: cell line

value: PDAC

value: KRAS G12D

tag: batch

tag: timepoint (day)


title: I25,IGRA+,PBMC,DMSO

description:
Library name: Sample 326
JOLLAB04_DMSO_S23_L004


title: S28,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 195
4236_MTB300_S269_L003


title: S27,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 194
4235_MTB300_S265_L003


title: T5,ATB,PBMC,DMSO

description:
Library name: Sample 324
JollaA15_DMSO_S65_L004


title: AF16_L3_R1

description:
Library name: AF16_L3_R1
column B


title: T5,ATB,PBMC,MTB300

description:
Library name: Sample 323
JollaA15_MTB300_S127_L004


title: Plate3_NTC

description: Library name: Plate3_NTC

value: NTC


title: S27,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 193
4235_DMSO_S263_L003


title: I24,IGRA+,PBMC,MTB300

description:
Library name: Sample 325
JOLLAB02_MTB300_S135_L004


title: S26,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 192
4234_DMSO_S33_L001


title: S26,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 191
4234_MTB300_S34_L001


title: Plate2_unmatched

description: Library name: Plate2_unmatched


title: S28,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 196
4236_DMSO_S267_L003


title: T6,ATB,PBMC,DMSO

description:
Library name: Sample 322
JOLLAA16_DMSO_S64_L004


title: S25,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 190
4233_DMSO_S29_L001


title: Plate2_NTC

description: Library name: Plate2_NTC


title: S25,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 189
4233_MTB300_S31_L001


title: S24,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 188
4232_DMSO_S25_L001


title: T6,ATB,PBMC,MTB300

description:
Library name: Sample 321
JOLLAA16_MTB300_S126_L004


title: S29,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 197
4237_MTB300_S273_L003


title: S24,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 187
4232_MTB300_S27_L001


title: T4,ATB,PBMC,MTB300

description:
Library name: Sample 320
JollaA13_MTB300_S118_L004


title: Plate1_NTC

description: Library name: Plate1_NTC


title: S23,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 185
4231_DMSO_S21_L001


title: S23,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 186
4231_MTB300_S23_L001


title: S22,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 184
4230_DMSO_S19_L001


title: S21,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 182
4229_DMSO_S15_L001


title: T3,ATB,PBMC,DMSO

description:
Library name: Sample 318
JOLLAA10_DMSO_S73_L004


title: T4,ATB,PBMC,DMSO

description:
Library name: Sample 319
JollaA13_DMSO_S56_L004


title: T3,ATB,PBMC,MTB300

description:
Library name: Sample 317
JOLLAA10_MTB300_S136_L004


title: S21,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 181
4229_MTB300_S17_L001


title: Normoxia_Panc1_Day9_rep2

description: Library name: Normoxia_Panc1_Day9_rep2

value: Normoxia


title: S19,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 178
4227_MTB300_S10_L001


title: T2,ATB,PBMC,MTB300

description:
Library name: Sample 316
JOLLAA04_MTB300_S91_L004


title: S20,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 179
4228_DMSO_S11_L001


title: S19,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 177
4227_DMSO_S9_L001


title: T2,ATB,PBMC,DMSO

description:
Library name: Sample 315
JOLLAA04_DMSO_S29_L004


title: Normoxia_Panc1_Day7_rep3

description: Library name: Normoxia_Panc1_Day7_rep3


title: Normoxia_Panc1_Day9_rep1

description: Library name: Normoxia_Panc1_Day9_rep1


title: S20,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 180
4228_MTB300_S13_L001


title: S18,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 176
4226_MTB300_S7_L001


title: Plate1_unmatched

description: Library name: Plate1_unmatched


title: T1,ATB,PBMC,MTB300

description:
Library name: Sample 314
JOLLAA01_MTB300_S116_L004


title: Normoxia_Panc1_Day7_rep2

description: Library name: Normoxia_Panc1_Day7_rep2


title: Normoxia_Panc1_Day7_rep1

description: Library name: Normoxia_Panc1_Day7_rep1


title: S18,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 175
4226_DMSO_S5_L001


title: S17,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 174
4225_MTB300_S4_L001


title: T1,ATB,PBMC,DMSO

description:
Library name: Sample 313
JOLLAA01_DMSO_S54_L004


title: S17,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 173
TU0070_DMSO_S172_L001


title: Normoxia_Panc1_Day3_rep3

description: Library name: Normoxia_Panc1_Day3_rep3


title: I23,IGRA+,PBMC,DMSO

description:
Library name: Sample 312
GS1758_Z


title: S16,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 171
4224_DMSO_S1_L001


title: Normoxia_Panc1_Day9_rep3

description: Library name: Normoxia_Panc1_Day9_rep3


title: Ovary tissue, EMS_none  4

city: Seoul

first: YunSoo

last: Chung

address: Yonseiro 50-1, Yonsei University College of Medicine

department: OBGY

country: South Korea

institute: Severance Hospital

description:
Library name: Sample 8
8127689

data_processing:
FastQCvv011.7 and Trimmomatic 0.38 Preprocessed data were mapped to reference genomes by hierarchical indexing for spliced alignment of transcript 2 (HISAT2) version 2.1.0 (Johns Hopkins University, Baltimore, MD, USA), to produce aligned reads.
Assembly: Transcript assembly was carried out using StringTie version 2.1.3b (National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA). The pre-filtered data were then analyzed using DESeq2 (R package, v. 1.36.0).
Supplementary files format and content: Processed data saved as excel file

source_name: Ovary tissue

extract_protocol:
RNA was purified after removal of DNA contamination using DNase and a Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA).
SureSelectXT RNA Direct Protocol

value: Ovary tissue


title: S22,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 183
4230_MTB300_S20_L001


title: Ovary tissue, EMS_visanne  4

description:
Library name: Sample 7
7139439


title: Normoxia_Panc1_Day3_rep2

description: Library name: Normoxia_Panc1_Day3_rep2


title: C32,IGRA-,PBMC,DMSO

description:
Library name: Sample 310
GS1754_Z


title: Ovary tissue, EMS_none  3

description:
Library name: Sample 6
2449152


title: Normoxia_Panc1_Day3_rep1

description: Library name: Normoxia_Panc1_Day3_rep1


title: Ovary tissue, EMS_visanne  3

description:
Library name: Sample 5
11019271


title: C32,IGRA-,PBMC,MTB300

description:
Library name: Sample 309
GS1754_Y


title: Ovary tissue, EMS_none  2

description:
Library name: Sample 3
10638608


title: Normoxia_Panc1_Day14_rep3

description: Library name: Normoxia_Panc1_Day14_rep3


title: Ovary tissue, EMS_visanne  2

description:
Library name: Sample 4
10925077


title: S16,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 172
4224_MTB300_S2_L001


title: Normoxia_Panc1_Day14_rep2

description: Library name: Normoxia_Panc1_Day14_rep2


title: Ovary tissue, EMS_none  1

description:
Library name: Sample 1
10250742


title: C30,IGRA-,PBMC,MTB300

description:
Library name: Sample 304
GS1625_Y


title: C30,IGRA-,PBMC,DMSO

description:
Library name: Sample 303
GS1625_Z


title: C29,IGRA-,PBMC,MTB300

description:
Library name: Sample 302
GS1579_Y


title: C3_D9_ROI3

description: FFPE spatial transcriptomic sequencing

library_source: other

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to the visium human probeset v2 using Space Ranger's default settings to generate gene expression
Assembly: Visium human probeset v2
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_positions_list.csv
Supplementary files format and content: scalefactors_json.json
Library strategy: Spatial Transcriptomics

molecule: other

source_name: post-neoadjuvant, resected PDAC tumor

growth_protocol: primary patient PDAC tumor resections, following neadjuvant FOLFIRINOX treatment

extract_protocol:
5 um FFPE sections cut on gene expression capture slides
libraries prepared with Visium for FFPE, using human probeset v2, using manufacturer protocol (non-cytassist protocol)

treatment_protocol: 3+ neoadjuvant FOLFIRINOX cycles

value: post-neoadjuvant, resected PDAC tumor

value: neoadjuvant FOLFIRINOX


title: C3_D9_ROI4

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc1_Day14_rep1

description: Library name: Normoxia_Panc1_Day14_rep1


title: Normoxia_Panc1_Day1_rep3

description: Library name: Normoxia_Panc1_Day1_rep3


title: C3_D9_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D9_ROI2

description: FFPE spatial transcriptomic sequencing


title: C29,IGRA-,PBMC,DMSO

description:
Library name: Sample 301
GS1579_Z

value: DMSO

value: PBMC


title: Normoxia_Panc1_Day1_rep2

description: Library name: Normoxia_Panc1_Day1_rep2


title: C28,IGRA-,PBMC,MTB300

description:
Library name: Sample 300
GS1572_Y


title: C3_D8_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc1_Day1_rep1

description: Library name: Normoxia_Panc1_Day1_rep1


title: C28,IGRA-,PBMC,DMSO

description:
Library name: Sample 299
GS1572_Z


title: C3_D8_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D8_ROI1

description: FFPE spatial transcriptomic sequencing


title: Ovary tissue, EMS_visanne  1

description:
Library name: Sample 2
10532202


title: C3_D7_ROI4

description: FFPE spatial transcriptomic sequencing


title: C3_D7_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc1_Day0_rep2

description: Library name: Normoxia_Panc1_Day0_rep2


title: C26,IGRA-,PBMC,MTB300

description:
Library name: Sample 296
GS1565_Y


title: C3_D7_ROI2

description: FFPE spatial transcriptomic sequencing


title: C27,IGRA-,PBMC,MTB300

description:
Library name: Sample 297
GS1567_Y


title: C3_D6_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D7_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D6_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc1_Day0_rep1

description: Library name: Normoxia_Panc1_Day0_rep1


title: C3_D6_ROI4

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day9_rep3

description: Library name: Normoxia_Panc0403_Day9_rep3


title: C25,IGRA-,PBMC,DMSO

description:
Library name: Sample 294
GS1558_Z


title: C26,IGRA-,PBMC,DMSO

description:
Library name: Sample 295
GS1565_Z


title: C3_D5_ROI4

description: FFPE spatial transcriptomic sequencing


title: C3_D8_ROI4

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day9_rep2

description: Library name: Normoxia_Panc0403_Day9_rep2


title: C3_D5_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D6_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D5_ROI1

description: FFPE spatial transcriptomic sequencing


title: C25,IGRA-,PBMC,MTB300

description:
Library name: Sample 293
GS1558_Y


title: Normoxia_Panc0403_Day9_rep1

description: Library name: Normoxia_Panc0403_Day9_rep1


title: C27,IGRA-,PBMC,DMSO

description:
Library name: Sample 298
GS1567_Z


title: Normoxia_Panc1_Day0_rep3

description: Library name: Normoxia_Panc1_Day0_rep3


title: Normoxia_Panc0403_Day7_rep3

description: Library name: Normoxia_Panc0403_Day7_rep3


title: C3_D4_ROI4

description: FFPE spatial transcriptomic sequencing


title: C3_D4_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day7_rep2

description: Library name: Normoxia_Panc0403_Day7_rep2


title: C3_D4_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D4_ROI1

description: FFPE spatial transcriptomic sequencing


title: C24,IGRA-,PBMC,MTB300

description:
Library name: Sample 291
GS1555_Y


title: C3_D3_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day3_rep3

description: Library name: Normoxia_Panc0403_Day3_rep3


title: C3_D3_ROI4

description: FFPE spatial transcriptomic sequencing


title: C22,IGRA-,PBMC,DMSO

description:
Library name: Sample 287
GS1532_Z


title: C3_D5_ROI3

description: FFPE spatial transcriptomic sequencing


title: C3_D3_ROI2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day7_rep1

description: Library name: Normoxia_Panc0403_Day7_rep1


title: Normoxia_Panc0403_Day3_rep2

description: Library name: Normoxia_Panc0403_Day3_rep2


title: C21,IGRA-,PBMC,DMSO

description:
Library name: Sample 286
GS0162_Z


title: C3_D2_ROI3

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day3_rep1

description: Library name: Normoxia_Panc0403_Day3_rep1


title: C21,IGRA-,PBMC,MTB300

description:
Library name: Sample 285
GS0162_Y


title: C3_D2_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D2_ROI4

description: FFPE spatial transcriptomic sequencing


title: C24,IGRA-,PBMC,DMSO

description:
Library name: Sample 292
GS1555_Z


title: Normoxia_Panc0403_Day14_rep3

description: Library name: Normoxia_Panc0403_Day14_rep3


title: I21,IGRA+,PBMC,MTB300

description:
Library name: Sample 284
GS0159_Y

value: IGRA+


title: C3_D1_ROI3

description: FFPE spatial transcriptomic sequencing


title: C3_D1_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D2_ROI1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day14_rep2

description: Library name: Normoxia_Panc0403_Day14_rep2


title: C3_D1_ROI4

description: FFPE spatial transcriptomic sequencing


title: C3_D1_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D12_ROI4_s2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day14_rep1

description: Library name: Normoxia_Panc0403_Day14_rep1


title: C22,IGRA-,PBMC,MTB300

description:
Library name: Sample 288
GS1532_Y

value: IGRA-


title: C3_D3_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D12_ROI4_s1

description: FFPE spatial transcriptomic sequencing


title: C11,IGRA-,PBMC,DMSO

description:
Library name: Sample 282
87_DMSO_S30_L004


title: C11,IGRA-,PBMC,MTB300

description:
Library name: Sample 281
87_MTB300_S92_L004


title: C3_D12_ROI3_s2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day1_rep2

description: Library name: Normoxia_Panc0403_Day1_rep2


title: C3_D12_ROI2_s2

description: FFPE spatial transcriptomic sequencing


title: C3_D12_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: S48,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 280
8200_MTB300_S120_L004


title: Normoxia_Panc0403_Day1_rep1

description: Library name: Normoxia_Panc0403_Day1_rep1


title: C3_D12_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C3_D11_ROI4

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day0_rep3

description: Library name: Normoxia_Panc0403_Day0_rep3


title: I21,IGRA+,PBMC,DMSO

description:
Library name: Sample 283
GS0159_Z


title: S47,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 278
8199_DMSO_S57_L004


title: Normoxia_Panc0403_Day0_rep1

description: Library name: Normoxia_Panc0403_Day0_rep1


title: C3_D10_ROI4

description: FFPE spatial transcriptomic sequencing


title: C3_D11_ROI2

description: FFPE spatial transcriptomic sequencing


title: C3_D11_ROI1

description: FFPE spatial transcriptomic sequencing


title: C3_D11_ROI3

description: FFPE spatial transcriptomic sequencing


title: S47,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 277
8199_MTB300_S119_L004


title: S46,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 276
8198_DMSO_S50_L004


title: Normoxia_Panc0203_Day9_rep3

description: Library name: Normoxia_Panc0203_Day9_rep3


title: C3_D10_ROI2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day1_rep3

description: Library name: Normoxia_Panc0403_Day1_rep3


title: C3_D12_ROI3_s1

description: FFPE spatial transcriptomic sequencing


title: C3_D10_ROI3

description: FFPE spatial transcriptomic sequencing


title: C3_D10_ROI1

description: FFPE spatial transcriptomic sequencing


title: C2_D9_s8

description: FFPE spatial transcriptomic sequencing


title: C2_D9_s7

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day9_rep2

description: Library name: Normoxia_Panc0203_Day9_rep2


title: S48,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 279
8200_DMSO_S58_L004


title: S45,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 274
8197_MTB300_S111_L004


title: C3_D12_ROI1_s2

description: FFPE spatial transcriptomic sequencing


title: C2_D9_s6

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day9_rep1

description: Library name: Normoxia_Panc0203_Day9_rep1


title: S44,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 273
8196_MTB300_S103_L004


title: C2_D9_s5

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0403_Day0_rep2

description: Library name: Normoxia_Panc0403_Day0_rep2


title: C2_D9_s4

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day7_rep3

description: Library name: Normoxia_Panc0203_Day7_rep3


title: Normoxia_Panc0203_Day7_rep2

description: Library name: Normoxia_Panc0203_Day7_rep2


title: S43,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 271
8195_MTB300_S99_L004


title: S44,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 272
8196_DMSO_S41_L004


title: Normoxia_Panc0203_Day7_rep1

description: Library name: Normoxia_Panc0203_Day7_rep1


title: C2_D8_ROI2_s2

description: FFPE spatial transcriptomic sequencing


title: S43,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 270
8195_DMSO_S45_L004


title: S45,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 275
8197_DMSO_S49_L004


title: C2_D8_ROI1_s2

description: FFPE spatial transcriptomic sequencing


title: C2_D7_s2

description: FFPE spatial transcriptomic sequencing


title: C2_D7_s1

description: FFPE spatial transcriptomic sequencing


title: S42,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 269
8194_DMSO_S34_L004


title: Normoxia_Panc0203_Day3_rep3

description: Library name: Normoxia_Panc0203_Day3_rep3


title: Normoxia_Panc0203_Day3_rep2

description: Library name: Normoxia_Panc0203_Day3_rep2


title: C2_D6_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day3_rep1

description: Library name: Normoxia_Panc0203_Day3_rep1


title: C2_D8_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C2_D5_ROI2_s2

description: FFPE spatial transcriptomic sequencing


title: S42,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 268
8194_MTB300_S96_L004


title: C2_D4

description: FFPE spatial transcriptomic sequencing


title: S41,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 267
8193_MTB300_S95_L004


title: C2_D9_s2

description: FFPE spatial transcriptomic sequencing


title: C2_D3

description: FFPE spatial transcriptomic sequencing


title: S41,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 266
8193_DMSO_S33_L004


title: C2_D6_s2

description: FFPE spatial transcriptomic sequencing


title: C2_D2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day14_rep2

description: Library name: Normoxia_Panc0203_Day14_rep2


title: C2_D8_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: C2_D13

description: FFPE spatial transcriptomic sequencing


title: S40,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 265
8192_MTB300_S89_L004


title: C2_D12

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day14_rep1

description: Library name: Normoxia_Panc0203_Day14_rep1


title: ntTCF1bcatSOX2,V5,hBJ,input2

city: Philadelphia

first: Kenneth

last: Zaret

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: ntTCF1bcatSOX2_V5_hBJ_input2
ntTCF1bcat_SOX2_V5_hBJ.bw

library_source: genomic

data_processing:
Basecalling and Fastq generation was automated through BaseSpace.
Reads were aligned to the human genome build hg19 using bowtie2 v2.3.4.1 with run parameters --local -X 1000.
Optical and PCR duplicate reads were marked and removed using PICARD MarkDuplicates REMOVE_DUPLICATES=TRUE ASSUME_SORT_ORDER=queryname (GATK 4.2.6.0).
BED files were generated from BAMs using the bedtools command bamToBed (bedtools v2.27.1).
Peaks were called from BED files using MACS2 callpeak against a matched input control with a FDR of 0.1% (MACS2 v2.2.7.1), with final peak sets selected by taking the union of biological replicates.
Input-subtracted bigwig files were generated with deeptools (version 3.5.0).
Assembly: hg19
Supplementary files format and content: bigWig, bed (except for input samples)

molecule: genomic DNA

source_name: BJ fibroblasts

growth_protocol: DMEM, 4.5g/L D-Glucose, L-Glutamine, 110 mg/L Sodium Pyruvate, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a COVARIS.
ChIP-seq libraries were prepared using the NEBNect Ultra II for DNA Library Prep, following manufacturers protocols, with an input of 5-10 ng of immunoprecipitated DNA. The  size distribution of amplified fragments was assessed by TapeStation, and the concentration of libraries was determined by Qubit.

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: C2_D11_ROI4_s2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day1_rep3

description: Library name: Normoxia_Panc0203_Day1_rep3


title: S39,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 263
8191_MTB300_S88_L004

value: Sarcoidosis


title: C2_D11_ROI4_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day1_rep2

description: Library name: Normoxia_Panc0203_Day1_rep2


title: ntTCF1bcatSOX2,V5,hBJ,input1

description:
Library name: ntTCF1bcatSOX2_V5_hBJ_input1
ntTCF1bcat_SOX2_V5_hBJ.bw


title: Normoxia_Panc0203_Day14_rep3

description: Library name: Normoxia_Panc0203_Day14_rep3


title: S39,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 262
8191_DMSO_S26_L004


title: C2_D5_ROI1_s6

description: FFPE spatial transcriptomic sequencing


title: C2_D11_ROI3_s2

description: FFPE spatial transcriptomic sequencing


title: ntTCF1bcatSOX2,V5,hBJ,rep2

description:
Library name: ntTCF1bcatSOX2_V5_hBJ_rep2
ntTCF1bcat_SOX2_V5_hBJ.bw


title: S38,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 261
8190_DMSO_S21_L004


title: C2_D11_ROI3_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day1_rep1

description: Library name: Normoxia_Panc0203_Day1_rep1


title: C2_D11_ROI2_s2

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day0_rep3

description: Library name: Normoxia_Panc0203_Day0_rep3


title: ntTCF1delIDRSOX2,V5,hBJ,input2

description:
Library name: ntTCF1delIDRSOX2_V5_hBJ_input2
ntTCF1delIDR_SOX2_V5_hBJ.bw


title: S38,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 260
8190_MTB300_S83_L004


title: ntTCF1delIDRSOX2,V5,hBJ,input1

description:
Library name: ntTCF1delIDRSOX2_V5_hBJ_input1
ntTCF1delIDR_SOX2_V5_hBJ.bw


title: Normoxia_Panc0203_Day0_rep2

description: Library name: Normoxia_Panc0203_Day0_rep2


title: S37,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 259
8189_MTB300_S82_L004


title: C2_D11_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_Panc0203_Day0_rep1

description: Library name: Normoxia_Panc0203_Day0_rep1


title: S40,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 264
8192_DMSO_S27_L004


title: C2_D11_ROI1_s2

description: FFPE spatial transcriptomic sequencing


title: S37,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 258
8189_DMSO_S20_L004


title: ntTCF1delIDRSOX2,V5,hBJ,rep2

description:
Library name: ntTCF1delIDRSOX2_V5_hBJ_rep2
ntTCF1delIDR_SOX2_V5_hBJ.bw


title: Normoxia_PACADD188_Day9_rep3

description: Library name: Normoxia_PACADD188_Day9_rep3


title: S36,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 257
8188_MTB300_S75_L004


title: C2_D11_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_PACADD188_Day9_rep2

description: Library name: Normoxia_PACADD188_Day9_rep2


title: ntTCF1delIDRSOX2,V5,hBJ,rep1

description:
Library name: ntTCF1delIDRSOX2_V5_hBJ_rep1
ntTCF1delIDR_SOX2_V5_hBJ.bw


title: ntTCF1delBcatSOX2,V5,hBJ,input2

description:
Library name: ntTCF1delBcatSOX2_V5_hBJ_input2
ntTCF1delBcat_SOX2_V5_hBJ.bw


title: C2_D10_s4

description: FFPE spatial transcriptomic sequencing


title: S36,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 256
8188_DMSO_S13_L004


title: Normoxia_PACADD188_Day9_rep1

description: Library name: Normoxia_PACADD188_Day9_rep1


title: S35,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 255
8187_DMSO_S12_L004


title: C2_D10_s3

description: FFPE spatial transcriptomic sequencing


title: ntTCF1bcatSOX2,V5,hBJ,rep1

description:
Library name: ntTCF1bcatSOX2_V5_hBJ_rep1
ntTCF1bcat_SOX2_V5_hBJ.bw


title: ntTCF1delBcatSOX2,V5,hBJ,rep2

description:
Library name: ntTCF1delBcatSOX2_V5_hBJ_rep2
ntTCF1delBcat_SOX2_V5_hBJ.bw


title: ntTCF1delBcatSOX2,V5,hBJ,input1

description:
Library name: ntTCF1delBcatSOX2_V5_hBJ_input1
ntTCF1delBcat_SOX2_V5_hBJ.bw


title: S35,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 254
8187_MTB300_S74_L004


title: Normoxia_PACADD188_Day7_rep2

description: Library name: Normoxia_PACADD188_Day7_rep2


title: I12,IGRA+,PBMC,DMSO

description:
Library name: Sample 253
584_DMSO_S32_L004


title: C2_D10_s1

description: FFPE spatial transcriptomic sequencing


title: ntTCF1delBcatSOX2,V5,hBJ,rep1

description:
Library name: ntTCF1delBcatSOX2_V5_hBJ_rep1
ntTCF1delBcat_SOX2_V5_hBJ.bw


title: I12,IGRA+,PBMC,MTB300

description:
Library name: Sample 252
584_MTB300_S94_L004


title: C2_D10_s2

description: FFPE spatial transcriptomic sequencing


title: ntTCF1SOX2delDBD,V5,hBJ,input2

description:
Library name: ntTCF1SOX2delDBD_V5_hBJ_input2
ntTCF1_SOX2delDBD_V5_hBJ.bw


title: Normoxia_PACADD188_Day7_rep1

description: Library name: Normoxia_PACADD188_Day7_rep1


title: Normoxia_PACADD188_Day3_rep3

description: Library name: Normoxia_PACADD188_Day3_rep3


title: I18,IGRA+,PBMC,MTB300

description:
Library name: Sample 251
570_MTB300_S117_L004


title: ntTCF1SOX2delDBD,V5,hBJ,input1

description:
Library name: ntTCF1SOX2delDBD_V5_hBJ_input1
ntTCF1_SOX2delDBD_V5_hBJ.bw


title: Normoxia_PACADD188_Day3_rep2

description: Library name: Normoxia_PACADD188_Day3_rep2


title: C1_D9_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: C1_D9_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C20,IGRA-,PBMC,MTB300

description:
Library name: Sample 249
546_MTB300_S108_L004


title: I18,IGRA+,PBMC,DMSO

description:
Library name: Sample 250
570_DMSO_S55_L004


title: Normoxia_PACADD188_Day14_rep3

description: Library name: Normoxia_PACADD188_Day14_rep3


title: Normoxia_PACADD188_Day7_rep3

description: Library name: Normoxia_PACADD188_Day7_rep3


title: ntTCF1SOX2dbd,V5,hBJ,input2

description:
Library name: ntTCF1SOX2dbd_V5_hBJ_input2
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: ntTCF1SOX2delDBD,V5,hBJ,rep2

description:
Library name: ntTCF1SOX2delDBD_V5_hBJ_rep2
ntTCF1_SOX2delDBD_V5_hBJ.bw


title: ntTCF1SOX2delDBD,V5,hBJ,rep1

description:
Library name: ntTCF1SOX2delDBD_V5_hBJ_rep1
ntTCF1_SOX2delDBD_V5_hBJ.bw


title: C1_D8_ROI3_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_PACADD188_Day3_rep1

description: Library name: Normoxia_PACADD188_Day3_rep1


title: C1_D8_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C20,IGRA-,PBMC,DMSO

description:
Library name: Sample 248
546_DMSO_S46_L004


title: I14,IGRA+,PBMC,MTB300

description:
Library name: Sample 209
499_MTB300_S101_L004


title: ntTCF1SOX2dbd,V5,hBJ,input1

description:
Library name: ntTCF1SOX2dbd_V5_hBJ_input1
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: C1_D7_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_PACADD188_Day14_rep2

description: Library name: Normoxia_PACADD188_Day14_rep2


title: Normoxia_PACADD188_Day14_rep1

description: Library name: Normoxia_PACADD188_Day14_rep1


title: C2_D1

description: FFPE spatial transcriptomic sequencing


title: ntTCF1SOX2dbd,V5,hBJ,rep2

description:
Library name: ntTCF1SOX2dbd_V5_hBJ_rep2
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: I20,IGRA+,PBMC,MTB300

description:
Library name: Sample 170
394_MTB300_S81_L004


title: Normoxia_PACADD188_Day1_rep3

description: Library name: Normoxia_PACADD188_Day1_rep3


title: C1_D5_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: I20,IGRA+,PBMC,DMSO

description:
Library name: Sample 169
394_DMSO_S19_L004


title: C1_D6_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_PACADD188_Day1_rep1

description: Library name: Normoxia_PACADD188_Day1_rep1


title: Normoxia_PACADD188_Day1_rep2

description: Library name: Normoxia_PACADD188_Day1_rep2


title: C1_D4_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: ntTCF1SOX2,V5,hBJ,input

description:
Library name: ntTCF1SOX2_V5_hBJ_input
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: I17,IGRA+,PBMC,MTB300

description:
Library name: Sample 168
382_MTB300_S115_L004


title: C1_D3_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_PACADD188_Day0_rep3

description: Library name: Normoxia_PACADD188_Day0_rep3


title: C1_D2_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: S14,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 166
062_Mtb11_32_S62_L002


title: I17,IGRA+,PBMC,DMSO

description:
Library name: Sample 167
382_DMSO_S53_L004


title: C1_D1_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: SOX2ctESRRB,V5,hBJ,input3

description:
Library name: SOX2ctESRRB_V5_hBJ_input3
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: Normoxia_PACADD188_Day0_rep2

description: Library name: Normoxia_PACADD188_Day0_rep2


title: Normoxia_PACADD188_Day0_rep1

description: Library name: Normoxia_PACADD188_Day0_rep1


title: ntTCF1SOX2,V5,hBJ,rep2

description:
Library name: ntTCF1SOX2_V5_hBJ_rep2
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: S14,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 165
063_Mtb11_33_S63_L001


title: S13,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 164
057_Mtb11_27_S57_L001


title: SOX2ctESRRB,V5,hBJ,input2

description:
Library name: SOX2ctESRRB_V5_hBJ_input2
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: C1_D14_ROI3_s1

description: FFPE spatial transcriptomic sequencing


title: ntTCF1SOX2dbd,V5,hBJ,rep1

description:
Library name: ntTCF1SOX2dbd_V5_hBJ_rep1
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: S13,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 163
058_Mtb11_28_S58_L002


title: SOX2ctESRRB,V5,hBJ,input1

description:
Library name: SOX2ctESRRB_V5_hBJ_input1
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: Normoxia_AsPC1_Day9_rep2

description: Library name: Normoxia_AsPC1_Day9_rep2


title: C1_D14_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C1_D14_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_AsPC1_Day9_rep3

description: Library name: Normoxia_AsPC1_Day9_rep3


title: Normoxia_AsPC1_Day9_rep1

description: Library name: Normoxia_AsPC1_Day9_rep1


title: SOX2ctESRRB,V5,hBJ,rep3

description:
Library name: SOX2ctESRRB_V5_hBJ_rep3
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: S12,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 161
055_Mtb11_25_S55_L002


title: SOX2ctESRRB,V5,hBJ,rep2

description:
Library name: SOX2ctESRRB_V5_hBJ_rep2
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: Normoxia_AsPC1_Day7_rep3

description: Library name: Normoxia_AsPC1_Day7_rep3


title: ntTCF1SOX2,V5,hBJ,rep1

description:
Library name: ntTCF1SOX2_V5_hBJ_rep1
ntTCF1_SOX2_V5_hBJ.bw
ntTCF1_SOX2_V5_hBJ.bed


title: C1_D13_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: C1_D13_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: S11,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 160
051_Mtb11_21_S51_L002


title: SOX2ctESRRB,V5,hBJ,rep1

description:
Library name: SOX2ctESRRB_V5_hBJ_rep1
SOX2_ctESRRB_V5_hBJ.bw
SOX2_ctESRRB_hBJ_V5.bed


title: Normoxia_AsPC1_Day7_rep2

description: Library name: Normoxia_AsPC1_Day7_rep2


title: S11,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 159
052_Mtb11_22_S52_L002


title: S10,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 158
047_Mtb11_17_S47_L001


title: C1_D12_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_AsPC1_Day7_rep1

description: Library name: Normoxia_AsPC1_Day7_rep1


title: C1_D12_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: ESRRBntSOX2,V5,hBJ,input2

description:
Library name: ESRRBntSOX2_V5_hBJ_input2
ESRRBntSOX2_V5_hFib.bw


title: S10,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 157
046_Mtb11_16_S46_L002


title: ESRRBntSOX2,V5,hBJ,input1

description:
Library name: ESRRBntSOX2_V5_hBJ_input1
ESRRBntSOX2_V5_hFib.bw


title: Normoxia_AsPC1_Day3_rep3

description: Library name: Normoxia_AsPC1_Day3_rep3


title: ESRRBntSOX2,V5,hBJ,rep2

description:
Library name: ESRRBntSOX2_V5_hBJ_rep2
ESRRBntSOX2_V5_hFib.bw


title: S9,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 156
043_Mtb11_13_S43_L001


title: C1_D11_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: S12,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 162
054_Mtb11_24_S54_L001


title: ESRRBntSOX2,V5,hBJ,rep1

description:
Library name: ESRRBntSOX2_V5_hBJ_rep1
ESRRBntSOX2_V5_hFib.bw


title: Normoxia_AsPC1_Day3_rep2

description: Library name: Normoxia_AsPC1_Day3_rep2


title: Normoxia_AsPC1_Day3_rep1

description: Library name: Normoxia_AsPC1_Day3_rep1


title: C1_D10_ROI2_s1

description: FFPE spatial transcriptomic sequencing


title: S9,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 155
044_Mtb11_14_S44_L001


title: S8,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 154
037_Mtb11_7_S37_L002


title: C1_D10_ROI1_s1

description: FFPE spatial transcriptomic sequencing


title: Normoxia_AsPC1_Day14_rep3

description: Library name: Normoxia_AsPC1_Day14_rep3


title: Normoxia_AsPC1_Day14_rep2

description: Library name: Normoxia_AsPC1_Day14_rep2


title: SOX2,V5,hBJ,input1

description:
Library name: SOX2_V5_hBJ_input1
SOX2_V5_hBJ.bw
SOX2_48h_peaks_hg19.bed


title: S8,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 153
038_Mtb11_8_S38_L001


title: SOX2,V5,hBJ,rep2

description:
Library name: SOX2_V5_hBJ_rep2
SOX2_V5_hBJ.bw
SOX2_48h_peaks_hg19.bed


title: S7,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 152
031_Mtb11_1_S31_L001


title: PBMCs, n-irAEs_8, post ICI, 5' RNA

city: Berlin

first: Ambre

middle: Manon

last: Giguelay

state: Berlin

address: Hannoversche Str. 28

department: Cell Biology/Single Cells

country: Germany

institute: Berlin Institute for Health

description: 5' RNA

library_source: transcriptomic single cell

data_processing:
Raw-sequencing data were demultiplexed using CellRanger mkfastq. Demultiplexed sequencing reads were aligned to the reference genome GRCh38 using CellRanger Multi (cellranger-6.1.2) from 10x Genomics
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz (from sample_filtered_feature_bc_matrix/)
Supplementary files format and content: CellRanger output files: clonotypes.csv; filtered_contig_annotations.csv

source_name: PBMCs

extract_protocol:
PBMCs were isolated from patient peripheral blood and cryopreserved in 90% FBS, 10% DMSO. On the day of library preparation, the cells were thawed and viability sorted by FACS. Single-cell-containing Gel Beads-in-emulsion (GEMs) were generated by loading suspended cells into a 10x Genomics Chromium Controller.
scRNA-seq and TCR-seq libraries were prepared by using 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits (v2) (CG000331 Rev D)
5' Single Cell V(D)J Phenotyping & Gene Expression

value: PBMCs

value: Nivolumab/Ipilimumab

tag: patient id

tag: library type

value: mRNA (5')

tag: Sex

value: male

tag: age

tag: group

value: n-irAEs

tag: cancer entity

value: malignant melanoma

tag: non-neurological iraes

value: exanthema 1w before sample collection, myocarditis at sample collection

tag: neurological iraes

value: myositis at sample collection,  hypophysitis 4w after sample collection

tag: pre/post ici_treatment

value: post-ICI

tag: time after_ici_treatment_start_(weeks)

value: yes


title: Normoxia_AsPC1_Day14_rep1

description: Library name: Normoxia_AsPC1_Day14_rep1

value: cell line

tag: cell type

value: PDAC

value: KRAS G12D

tag: treatment

value: Normoxia


title: C1_D11_ROI2_s1

description: FFPE spatial transcriptomic sequencing

tag: tissue

value: post-neoadjuvant, resected PDAC tumor

tag: genotype

value: neoadjuvant FOLFIRINOX


title: Normoxia_AsPC1_Day1_rep3

description: Library name: Normoxia_AsPC1_Day1_rep3

tag: cell line


title: PBMCs, n-irAEs_7, post ICI, TCR

description: VDJ (TCR)

value: Atezolizumab

value: TCR

value: hepatocellular carcinoma

value: myocarditis at sample collection

value: myositis

value: no


title: S7,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 151
032_Mtb11_2_S32_L001

value: PBMC

value: Sarcoidosis


title: PBMCs, n-irAEs_7, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

value: n-irAEs


title: SOX2,V5,hBJ,rep1

description:
Library name: SOX2_V5_hBJ_rep1
SOX2_V5_hBJ.bw
SOX2_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: TCF1,V5,hBJ,rep2

description:
Library name: TCF1_V5_hBJ_rep2
TCF1_V5_hBJ.bw
TCF1_48h_peaks_hg19.bed


title: Normoxia_AsPC1_Day1_rep2

description: Library name: Normoxia_AsPC1_Day1_rep2

value: cell line

value: PDAC

value: KRAS G12D

value: Normoxia

tag: batch


title: TCF1,V5,hBJ,input

description:
Library name: TCF1_V5_hBJ_input
TCF1_V5_hBJ.bw
TCF1_48h_peaks_hg19.bed


title: C17,IGRA-,PBMC,MTB300

description:
Library name: Sample 150
376_MTB300_S114_L004

value: IGRA-


title: PBMCs, n-irAEs_6, post ICI, TCR

description: VDJ (TCR)

value: Nivolumab

value: TCR

value: malignant melanoma

value: myocarditis, dermatitis, hepatitis at sample collection + suffered previously of thyroiditis

value: encephalitis, developed myositis after sample collection

value: post-ICI


title: C17,IGRA-,PBMC,DMSO

description:
Library name: Sample 149
376_DMSO_S52_L004

value: DMSO

value: PBMC


title: Normoxia_AsPC1_Day1_rep1

description: Library name: Normoxia_AsPC1_Day1_rep1

tag: timepoint (day)


title: SOX2,V5,hBJ,input2

description:
Library name: SOX2_V5_hBJ_input2
SOX2_V5_hBJ.bw
SOX2_48h_peaks_hg19.bed


title: Normoxia_AsPC1_Day0_rep3

description: Library name: Normoxia_AsPC1_Day0_rep3


title: TCF1,V5,hBJ,rep1

description:
Library name: TCF1_V5_hBJ_rep1
TCF1_V5_hBJ.bw
TCF1_48h_peaks_hg19.bed


title: Normoxia_AsPC1_Day0_rep2

description: Library name: Normoxia_AsPC1_Day0_rep2


title: C13,IGRA-,PBMC,DMSO

description:
Library name: Sample 148
365_DMSO_S35_L004


title: PBMCs, n-irAEs_5, post ICI, TCR

description: VDJ (TCR)

value: PBMCs

value: Pembrolizumab

tag: patient id

value: male

value: n-irAEs

value: prostate cancer

value: myocarditis at sample collection

value: myasthenic syndrome and myositis

value: yes


title: PBMCs, n-irAEs_8, post ICI, TCR

description: VDJ (TCR)

value: Nivolumab/Ipilimumab

tag: library type

value: exanthema 1w before sample collection, myocarditis at sample collection

value: myositis at sample collection,  hypophysitis 4w after sample collection


title: PDX1,V5,hBJ,input2

description:
Library name: PDX1_V5_hBJ_input2
PDX1_V5_hBJ.bw
PDX1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: PBMCs, n-irAEs_6, post ICI, 5' RNA

description: 5' RNA

value: Nivolumab

value: mRNA (5')

tag: Sex

value: malignant melanoma

value: myocarditis, dermatitis, hepatitis at sample collection + suffered previously of thyroiditis

value: encephalitis, developed myositis after sample collection

value: post-ICI

value: no


title: Normoxia_AsPC1_Day0_rep1

description: Library name: Normoxia_AsPC1_Day0_rep1

value: cell line

value: PDAC

value: KRAS G12D

value: Normoxia


title: I11,IGRA+,PBMC,DMSO

description:
Library name: Sample 146
349_DMSO_S28_L004

value: DMSO

value: PBMC

value: IGRA+


title: PBMCs, n-irAEs_5, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: Pembrolizumab

value: male

tag: age

value: n-irAEs

value: prostate cancer

value: myocarditis at sample collection

value: myasthenic syndrome and myositis

value: yes


title: PDX1,V5,hBJ,input1

description:
Library name: PDX1_V5_hBJ_input1
PDX1_V5_hBJ.bw
PDX1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: PBMCs, n-irAEs_4, post ICI, TCR

description: VDJ (TCR)

value: Atezolizumab

value: TCR

tag: group

value: small cells lung cancer

value: myositis and encephalitis

value: post-ICI


title: Hypoxia_Panc1_Day9_rep3

description: Library name: Hypoxia_Panc1_Day9_rep3

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: PDX1,V5,hBJ,rep2

description:
Library name: PDX1_V5_hBJ_rep2
PDX1_V5_hBJ.bw
PDX1_48h_peaks_hg19.bed


title: I11,IGRA+,PBMC,MTB300

description:
Library name: Sample 145
349_MTB300_S90_L004

value: PBMC

value: IGRA+


title: PBMCs, n-irAEs_4, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

value: n-irAEs

tag: cancer entity


title: PDX1,V5,hBJ,rep1

description:
Library name: PDX1_V5_hBJ_rep1
PDX1_V5_hBJ.bw
PDX1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts


title: Hypoxia_Panc1_Day9_rep2

description: Library name: Hypoxia_Panc1_Day9_rep2


title: C12,IGRA-,PBMC,MTB300

description:
Library name: Sample 144
340_MTB300_S93_L004

value: IGRA-


title: RUNX1,V5,hBJ,input2

description:
Library name: RUNX1_V5_hBJ_input2
RUNX1_V5_hBJ.bw
RUNX1_48h_peaks_hg19.bed

value: 48 hour lentiviral expresion


title: C12,IGRA-,PBMC,DMSO

description:
Library name: Sample 143
340_DMSO_S31_L004

value: DMSO


title: PBMCs, n-irAEs_3, post ICI, TCR

description: VDJ (TCR)

value: Pembrolizumab

value: TCR

value: non small cells lung cancer

tag: non-neurological iraes

value: myocarditis at sample collection

value: encephalitis

value: yes


title: Hypoxia_Panc1_Day7_rep3

description: Library name: Hypoxia_Panc1_Day7_rep3

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: RUNX1,V5,hBJ,input1

description:
Library name: RUNX1_V5_hBJ_input1
RUNX1_V5_hBJ.bw
RUNX1_48h_peaks_hg19.bed


title: PBMCs, n-irAEs_3, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

tag: neurological iraes

value: post-ICI


title: S6,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 142
3338_Y

value: PBMC

value: Sarcoidosis


title: RUNX1,V5,hBJ,rep2

description:
Library name: RUNX1_V5_hBJ_rep2
RUNX1_V5_hBJ.bw
RUNX1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: PBMCs, n-irAEs_2, post ICI, TCR

description: VDJ (TCR)

value: Avelumab

value: TCR

value: n-irAEs

value: Merkel cell carcinoma

value: myopathy and neuropathy

tag: pre/post ici_treatment

value: no


title: Hypoxia_Panc1_Day7_rep2

description: Library name: Hypoxia_Panc1_Day7_rep2

value: cell line

value: PDAC

value: KRAS G12D


title: C13,IGRA-,PBMC,MTB300

description:
Library name: Sample 147
365_MTB300_S97_L004

value: IGRA-


title: Hypoxia_Panc1_Day7_rep1

description: Library name: Hypoxia_Panc1_Day7_rep1

value: Hypoxia


title: S5,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 140
3337_Y


title: PBMCs, n-irAEs_2, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

value: post-ICI

tag: time after_ici_treatment_start_(weeks)


title: RUNX1,V5,hBJ,rep1

description:
Library name: RUNX1_V5_hBJ_rep1
RUNX1_V5_hBJ.bw
RUNX1_48h_peaks_hg19.bed

value: BJ fibroblasts

tag: cell type

value: Human foreskin fibroblasts


title: PBMCs, n-irAEs_1, post ICI, TCR

description: VDJ (TCR)

tag: treatment

value: Avelumab

value: female

value: myocarditis at sample collection

value: myositis


title: PAX3,V5,hBJ,input3

description:
Library name: PAX3_V5_hBJ_input3
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed

value: 48 hour lentiviral expresion


title: S5,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 139
3337_Z

value: DMSO

value: PBMC

value: Sarcoidosis


title: PAX3,V5,hBJ,input2

description:
Library name: PAX3_V5_hBJ_input2
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed


title: PBMCs, n-irAEs_1, post ICI, 5' RNA

description: 5' RNA

tag: tissue

value: n-irAEs

value: Merkel cell carcinoma

value: no


title: Hypoxia_Panc1_Day3_rep2

description: Library name: Hypoxia_Panc1_Day3_rep2

value: cell line

value: PDAC

tag: genotype

value: KRAS G12D

value: Hypoxia


title: PAX3,V5,hBJ,input1

description:
Library name: PAX3_V5_hBJ_input1
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed

tag: cell line

value: BJ fibroblasts


title: S4,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 138
3336_Z


title: S4,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 137
3336_Y


title: Hypoxia_Panc1_Day9_rep1

description: Library name: Hypoxia_Panc1_Day9_rep1

tag: batch


title: PBMCs, Ctrl_9, pre ICI, TCR

description: VDJ (TCR)

value: PBMCs

value: TCR

value: male

value: control

value: pre-ICI


title: PAX3,V5,hBJ,rep3

description:
Library name: PAX3_V5_hBJ_rep3
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: S3,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 136
3335_Y

value: PBMC


title: S6,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 141
3338_Z

value: DMSO

value: Sarcoidosis


title: Hypoxia_Panc1_Day14_rep2

description: Library name: Hypoxia_Panc1_Day14_rep2

tag: timepoint (day)


title: PAX3,V5,hBJ,rep1

description:
Library name: PAX3_V5_hBJ_rep1
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed


title: Hypoxia_Panc1_Day14_rep3

description: Library name: Hypoxia_Panc1_Day14_rep3


title: PBMCs, Ctrl_9, pre ICI, 5' RNA

description: 5' RNA

value: Avelumab

tag: patient id

value: mRNA (5')

value: Merkel cell carcinoma


title: PBMCs, Ctrl_9, post ICI, TCR

description: VDJ (TCR)

tag: library type

value: post-ICI

value: no


title: C14,IGRA-,PBMC,DMSO

description:
Library name: Sample 134
332_DMSO_S36_L004

value: IGRA-


title: PBMCs, Ctrl_9, post ICI, 5' RNA

description: 5' RNA

tag: Sex


title: S3,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 135
3335_Z


title: PAX3,V5,hBJ,rep2

description:
Library name: PAX3_V5_hBJ_rep2
PAX3_V5_hBJ.bw
PAX3_48h_peaks_hg19.bed

value: BJ fibroblasts


title: Hypoxia_Panc1_Day3_rep3

description: Library name: Hypoxia_Panc1_Day3_rep3

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: PBMCs, Ctrl_8, post ICI, TCR

description: VDJ (TCR)

value: PBMCs

value: Nivolumab/Ipilimumab

value: TCR

value: female

tag: age

value: control

value: malignant melanoma


title: C14,IGRA-,PBMC,MTB300

description:
Library name: Sample 133
332_MTB300_S98_L004

value: PBMC


title: Hypoxia_Panc1_Day1_rep3

description: Library name: Hypoxia_Panc1_Day1_rep3


title: PAX7,V5,hBJ,input1

description:
Library name: PAX7_V5_hBJ_input1
PAX7_V5_hBJ.bw
PAX7_48h_peaks_hg19.bed

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: Hypoxia_Panc1_Day1_rep2

description: Library name: Hypoxia_Panc1_Day1_rep2


title: PAX7,V5,hBJ,input2

description:
Library name: PAX7_V5_hBJ_input2
PAX7_V5_hBJ.bw
PAX7_48h_peaks_hg19.bed


title: C19,IGRA-,PBMC,DMSO

description:
Library name: Sample 132
320_DMSO_S59_L004

value: DMSO


title: Hypoxia_Panc1_Day1_rep1

description: Library name: Hypoxia_Panc1_Day1_rep1


title: Hypoxia_Panc1_Day3_rep1

description: Library name: Hypoxia_Panc1_Day3_rep1


title: PBMCs, Ctrl_8, post ICI, 5' RNA

description: 5' RNA

value: mRNA (5')

tag: group

value: post-ICI

value: no


title: PAX7,V5,hBJ,rep2

description:
Library name: PAX7_V5_hBJ_rep2
PAX7_V5_hBJ.bw
PAX7_48h_peaks_hg19.bed

value: BJ fibroblasts


title: PBMCs, Ctrl_7, pre ICI, TCR

description: VDJ (TCR)

value: Atezolizumab

value: male

tag: cancer entity

value: hepatocellular carcinoma

value: synovitis (after sample collection)

value: pre-ICI


title: C19,IGRA-,PBMC,MTB300

description:
Library name: Sample 131
320_MTB300_S121_L004

value: IGRA-


title: PAX7,V5,hBJ,rep1

description:
Library name: PAX7_V5_hBJ_rep1
PAX7_V5_hBJ.bw
PAX7_48h_peaks_hg19.bed


title: Hypoxia_Panc0403_Day9_rep3

description: Library name: Hypoxia_Panc0403_Day9_rep3

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: ESRRB,V5,hBJ,input

description:
Library name: ESRRB_V5_hBJ_input
ESRRB_V5_hBJ.bw
ESRRB_48h_peaks_hg19.bed

value: Human foreskin fibroblasts


title: Hypoxia_Panc1_Day14_rep1

description: Library name: Hypoxia_Panc1_Day14_rep1


title: Hypoxia_Panc0403_Day9_rep2

description: Library name: Hypoxia_Panc0403_Day9_rep2


title: PBMCs, Ctrl_7, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: control

tag: non-neurological iraes


title: Hypoxia_Panc0403_Day9_rep1

description: Library name: Hypoxia_Panc0403_Day9_rep1


title: ESRRB,V5,hBJ,rep2

description:
Library name: ESRRB_V5_hBJ_rep2
ESRRB_V5_hBJ.bw
ESRRB_48h_peaks_hg19.bed

value: 48 hour lentiviral expresion


title: S1,Sarcoidosis,PBMC,DMSO

description:
Library name: Sample 129
3107_Z

value: DMSO

value: PBMC

value: Sarcoidosis


title: PBMCs, Ctrl_6, pre ICI, TCR

description: VDJ (TCR)

value: Atezolizumab

value: TCR

value: female

value: non small cells lung cancer

value: auto-immune diabetes (after sample collection)

tag: neurological iraes

value: no


title: PBMCs, Ctrl_6, pre ICI, 5' RNA

description: 5' RNA

value: mRNA (5')

tag: pre/post ici_treatment

value: pre-ICI


title: Hypoxia_Panc0403_Day7_rep2

description: Library name: Hypoxia_Panc0403_Day7_rep2

value: cell line

value: PDAC

value: KRAS G12D


title: C18,IGRA-,PBMC,DMSO

description:
Library name: Sample 128
306_DMSO_S47_L004

value: IGRA-


title: ESRRB,V5,hBJ,rep1

description:
Library name: ESRRB_V5_hBJ_rep1
ESRRB_V5_hBJ.bw
ESRRB_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts


title: Hypoxia_Panc0403_Day7_rep3

description: Library name: Hypoxia_Panc0403_Day7_rep3

value: Hypoxia


title: I19,IGRA+,PBMC,DMSO

description:
Library name: Sample 127
293_DMSO_S18_L004

value: DMSO

value: PBMC

value: IGRA+


title: EOMES,V5,hBJ,rep2

description:
Library name: EOMES_V5_hBJ_rep2
EOMES_V5_hBJ.bw
EOMES_48h_peaks_hg19.bed

value: 48 hour lentiviral expresion


title: EOMES,V5,hBJ,input

description:
Library name: EOMES_V5_hBJ_input
EOMES_V5_hBJ.bw
EOMES_48h_peaks_hg19.bed


title: PBMCs, Ctrl_5, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: Pembrolizumab

value: male

value: control

value: post-ICI

tag: time after_ici_treatment_start_(weeks)


title: I13,IGRA+,PBMC,MTB300

description:
Library name: Sample 124
270_MTB300_S107_L004

tag: cell type


title: PBMCs, Ctrl_5, post ICI, TCR

description: VDJ (TCR)

tag: treatment

value: TCR

value: non small cells lung cancer

value: no


title: Hypoxia_Panc0403_Day7_rep1

description: Library name: Hypoxia_Panc0403_Day7_rep1

tag: tissue

value: cell line

value: PDAC

value: KRAS G12D


title: Hypoxia_Panc0403_Day3_rep3

description: Library name: Hypoxia_Panc0403_Day3_rep3

tag: genotype


title: EOMES,V5,hBJ,rep1

description:
Library name: EOMES_V5_hBJ_rep1
EOMES_V5_hBJ.bw
EOMES_48h_peaks_hg19.bed

tag: cell line

value: BJ fibroblasts

value: Human foreskin fibroblasts


title: PBMCs, Ctrl_7, pre ICI, 5' RNA

description: 5' RNA

value: Atezolizumab

value: mRNA (5')

value: hepatocellular carcinoma

value: synovitis (after sample collection)

value: pre-ICI


title: Hypoxia_Panc0403_Day3_rep2

description: Library name: Hypoxia_Panc0403_Day3_rep2

value: Hypoxia

tag: batch


title: S1,Sarcoidosis,PBMC,MTB300

description:
Library name: Sample 130
3107_Y

value: PBMC

value: Sarcoidosis


title: PBMCs, Ctrl_4, pre ICI, TCR

description: VDJ (TCR)

value: PBMCs

value: male

value: control

value: small cells lung cancer

value: pneumonitis at sample collection


title: PBMCs, Ctrl_7, post ICI, TCR

description: VDJ (TCR)

value: TCR

value: post-ICI

value: no


title: EBF1,V5,hBJ,rep2

description:
Library name: EBF1_V5_hBJ_rep2
EBF1_V5_hBJ.bw
EBF1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: PBMCs, Ctrl_4, pre ICI, 5' RNA

description: 5' RNA

value: Atezolizumab

value: mRNA (5')


title: Hypoxia_Panc0403_Day3_rep1

description: Library name: Hypoxia_Panc0403_Day3_rep1

value: cell line

value: PDAC

value: KRAS G12D

tag: timepoint (day)


title: I19,IGRA+,PBMC,MTB300

description:
Library name: Sample 126
293_MTB300_S80_L004

value: PBMC

value: IGRA+


title: C15,IGRA-,PBMC,DMSO

description:
Library name: Sample 122
200_DMSO_S51_L004

value: DMSO

value: IGRA-


title: Hypoxia_Panc0403_Day14_rep3

description: Library name: Hypoxia_Panc0403_Day14_rep3

value: Hypoxia


title: EBF1,V5,hBJ,rep1

description:
Library name: EBF1_V5_hBJ_rep1
EBF1_V5_hBJ.bw
EBF1_48h_peaks_hg19.bed


title: PBMCs, Ctrl_4, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

tag: patient id

value: male

value: control

value: small cells lung cancer

value: pneumonitis at sample collection


title: C15,IGRA-,PBMC,MTB300

description:
Library name: Sample 121
200_MTB300_S113_L004


title: I13,IGRA+,PBMC,DMSO

description:
Library name: Sample 125
270_DMSO_S37_L004


title: Hypoxia_Panc0403_Day14_rep2

description: Library name: Hypoxia_Panc0403_Day14_rep2


title: PBMCs, Ctrl_4, post ICI, TCR

description: VDJ (TCR)

tag: library type

value: TCR

value: post-ICI

value: no


title: ASCL1,V5,hBJ,rep1

description:
Library name: ASCL1_V5_hBJ_rep1
ASCL1_V5_hBJ.bw
ASCL1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: PBMCs, Ctrl_3, pre ICI, TCR

description: VDJ (TCR)

value: Pembrolizumab

tag: Sex

value: non small cells lung cancer

value: dermatitis (after sample collection)

value: pre-ICI


title: C16,IGRA-,PBMC,MTB300

description:
Library name: Sample 120
184_MTB300_S84_L004

value: PBMC

value: IGRA-


title: EBF1,V5,hBJ,input

description:
Library name: EBF1_V5_hBJ_input
EBF1_V5_hBJ.bw
EBF1_48h_peaks_hg19.bed


title: C16,IGRA-,PBMC,DMSO

description:
Library name: Sample 119
184_DMSO_S22_L004

value: DMSO


title: Hypoxia_Panc0403_Day1_rep3

description: Library name: Hypoxia_Panc0403_Day1_rep3

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: PBMCs, Ctrl_3, pre ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

tag: age

value: control


title: I16,IGRA+,PBMC,DMSO

description:
Library name: Sample 118
133_DMSO_S42_L004

value: IGRA+


title: Hypoxia_Panc0403_Day1_rep2

description: Library name: Hypoxia_Panc0403_Day1_rep2


title: Hs578T_50nM Tryptase_24h_3

city: Uppsala

first: Fabio

middle: Rabelo

last: Melo

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

description:
Library name: Sample 15
Column name in raw_is: 147_015

data_processing:
Torrent SuiteTM Software v 5.10.1 edgeR package (Robinson, McCarthy, and Smyth 2010) implemented in R (version 3.6.0)
Assembly: GRCh38
Supplementary files format and content: txt file with raw counts for each sample

growth_protocol: The Hs578T cell line was cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10 percent heat-inactivated foetal bovine serum, 50 ug/ml streptomycin sulphate, 60 ug/ml penicillin G, 2 mM L-glutamine. Cell medium was replaced when cells achieved 90 - 100 percent confluency.

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
Libraries were generated and amplified using the Ion AmpliSeqTM Transcriptome Human Gene Expression Kit.

treatment_protocol: Cell were treated with 50 nM human recombinant tryptase for 6 and 24 h.

value: Triple-negative breast cancer

value: WT

value: 50nM tryptase-24h


title: Hs578T_50nM Tryptase_24h_4

description:
Library name: Sample 16
Column name in raw_is: 147_016


title: PBMCs, Ctrl_3, post ICI, TCR

description: VDJ (TCR)

value: Pembrolizumab

value: TCR

tag: group

value: non small cells lung cancer

value: dermatitis (after sample collection)

value: post-ICI

value: no


title: I15,IGRA+,PBMC,DMSO

description:
Library name: Sample 123
216_DMSO_S48_L004

value: DMSO

value: PBMC


title: Hypoxia_Panc0403_Day1_rep1

description: Library name: Hypoxia_Panc0403_Day1_rep1

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: Hs578T_50nM Tryptase_24h_2

description:
Library name: Sample 14
Column name in raw_is: 147_014


title: I16,IGRA+,PBMC,MTB300

description:
Library name: Sample 117
133_MTB300_S104_L004


title: PBMCs, Ctrl_3, post ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

value: control

tag: cancer entity


title: S1,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 116
3107_V

value: Sarcoidosis


title: Hs578T_50nM Tryptase_24h_1

description:
Library name: Sample 13
Column name in raw_is: 147_013

value: Triple-negative breast cancer

value: WT

value: 50nM tryptase-24h


title: ASCL1,V5,hBJ,input

description:
Library name: ASCL1_V5_hBJ_input
ASCL1_V5_hBJ.bw
ASCL1_48h_peaks_hg19.bed

value: BJ fibroblasts

value: Human foreskin fibroblasts

value: 48 hour lentiviral expresion


title: Hypoxia_Panc0403_Day14_rep1

description: Library name: Hypoxia_Panc0403_Day14_rep1


title: PBMCs, Ctrl_2, post ICI, 5' RNA

description: 5' RNA

value: Nivolumab

value: female

value: malignant melanoma

tag: non-neurological iraes

value: post-ICI

value: no


title: S1,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 115
3107_X

value: DMSO


title: S3,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 114
3335_V


title: Hs578T cells_24h_Control_4

description:
Library name: Sample 12
Column name in raw_is: 147_012


title: Hypoxia_Panc0203_Day9_rep2

description: Library name: Hypoxia_Panc0203_Day9_rep2

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: Hs578T cells_24h_Control_3

description:
Library name: Sample 11
Column name in raw_is: 147_011


title: PBMCs, Ctrl_1, pre ICI, 5' RNA

description: 5' RNA

value: PBMCs

value: mRNA (5')

value: male

value: control

tag: neurological iraes

value: pre-ICI


title: Hypoxia_Panc0203_Day7_rep3

description: Library name: Hypoxia_Panc0203_Day7_rep3


title: Hypoxia_Panc0203_Day9_rep1

description: Library name: Hypoxia_Panc0203_Day9_rep1


title: PBMCs, Ctrl_1, pre ICI, TCR

description: VDJ (TCR)

value: TCR

tag: pre/post ici_treatment


title: S4,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 113
3336_V

value: Sarcoidosis


title: Hypoxia_Panc0203_Day9_rep3

description: Library name: Hypoxia_Panc0203_Day9_rep3


title: Hs578T_50nM Tryptase_6h_4

description:
Library name: Sample 8
Column name in raw_is: 147_008

value: Triple-negative breast cancer

value: WT

value: 50nM tryptase-6h


title: S5,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 111
3337_X


title: Hypoxia_Panc0203_Day7_rep2

description: Library name: Hypoxia_Panc0203_Day7_rep2


title: PBMCs, Ctrl_1, post ICI, TCR

description: VDJ (TCR)

value: Nivolumab

value: malignant melanoma

value: post-ICI

tag: time after_ici_treatment_start_(weeks)


title: S4,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 112
3336_X

value: DMSO

tag: cell type


title: S5,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 110
3337_V

tag: treatment


title: PBMCs, Ctrl_1, post ICI, 5' RNA

description: 5' RNA

tag: tissue

value: no


title: Hs578T_50nM Tryptase_6h_3

description:
Library name: Sample 7
Column name in raw_is: 147_007

tag: genotype


title: PBMCs, Ctrl_2, post ICI, TCR

description: VDJ (TCR)

value: female


title: HNE_1_WT_LMP1_3; HNE_1_WT_LMP1_3_2, Day7

city: Shanghai

first: xiao

last: xiao

state: Shanghai

address: Ganhe road

country: China

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

data_processing:
1) The original whole-genome sequencing data was subjected to quality control using FastQC software (version 0.11.8), including assessing base quality, sequencing depth, GC content, and adapter content.
2) The Cutadapt software (version 3.6) [18] was used to remove adapter sequences from both read1 and read2 of the paired-end sequencing data.
3) The Burrows-Wheeler Aligner (BWA) software (version 0.7.6a)[19] was used to build an index file for the viral reference genome. The EBV NC.007605.1 sequence with a length of 171,823 bp was selected as the viral reference sequence.
4) The Fast Length Adjustment of Short Reads (FLASH) software (version 1.2.11) [20] was used to merge the quality-controlled short sequences from Read1 and Read2, generating longer fragment sequences. For successfully merged reads, BWA was then used to align them with the EBV reference sequence to extract the aligned sequences. For those unmerged reads from Read1 and Read2, BWA was used to align Read1 and Read2 separately with the reference sequence, and SAMtools software[21] was subsequently conducted to extract the sequences that aligned at both ends. If there were duplicate regions in the sequences aligned at both ends, the duplicates were removed and the sequences were merged into one. On the contrary, Read1 and Read2 sequences were kept.
5) A custom Python script was performed to integrate the processed sequences from each sample into a sequence matrix.
6) For sequence feature calculation, the nucleotide-level mutation and Shannon entropy algorithms were selected [14-16].
7) Finally, the Mann-Whitney U test was employed to select the differential mutation and entropy features between the two groups of samples as input data for the prediction model.
Assembly: NCBI
Supplementary files format and content: counts, fpkm

growth_protocol: HNE-1 cells were cultured in 1640 containing 10% FBS and 1% penicillin/streptomycin at 37°C in the presence of 5% CO2. The control plasmids (pcDNA3.1-CMV-EF1-CopGFP-T2A-Puro), wild LMP1 (aa1-aa118) and the mutant LMP1 (H101R) expressing plasmids were constructed by Hanbio Biotechnology Co., Ltd (Shanghai). For the construction of the HNE-1WT-LMP1 and HNE-1MUT-LMP1 cell lines, transfer plasmid, envelope plasmid, and packaging plasmids were co-transfected into 293T packaging cells using Lipofectamine 3000 (cat. no. L3000015; Thermo Fisher Scientific, USA.) according to the manufacturer’s instructions. The culture medium was replenished 16 hours later, and the culture supernatant was collected at 2 and 3 days post-transfection. Virus was harvested by ultracentrifugation. A total of 2×105 HNE-1 cells were seeded in 12-well plates overnight and subsequently infected with lentivirus expressing the HNE-1MUT-LMP1 gene or a HNE-1WT-LMP1 lentivirus. The transfected cells were screened using puromycin (1μg/mL) one week later.

extract_protocol:
The total RNA from HNE-1 cells were isolated using the EZ-press RNA Purification Kit (EZBioscience, China) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacture's protocols

tag: cell line

value: human nasopharyngeal carcinoma cell


title: Hs578T_50nM Tryptase_6h_2

description:
Library name: Sample 6
Column name in raw_is: 147_006


title: Hypoxia_Panc0203_Day3_rep2

description: Library name: Hypoxia_Panc0203_Day3_rep2

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia

tag: batch


title: S6,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 109
3338_V


title: Hypoxia_Panc0203_Day3_rep3

description: Library name: Hypoxia_Panc0203_Day3_rep3

tag: timepoint (day)


title: S6,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 108
3338_X


title: Hs578T_50nM Tryptase_6h_1

description:
Library name: Sample 5
Column name in raw_is: 147_005


title: Hs578T cells_24h_Control_2

description:
Library name: Sample 10
Column name in raw_is: 147_010


title: HNE_1_WT_LMP1_2; HNE_1_WT_LMP1_2_2, Day7

treatment_protocol: The transfected cells were screened using puromycin (1μg/mL) one week later.


title: Hypoxia_Panc0203_Day3_rep1

description: Library name: Hypoxia_Panc0203_Day3_rep1


title: S7,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 107
034_Mtb11_4_S34_L002


title: Hypoxia_Panc0203_Day7_rep1

description: Library name: Hypoxia_Panc0203_Day7_rep1


title: Hs578T cells_6h_Control_2

description:
Library name: Sample 2
Column name in raw_is: 147_002


title: Hypoxia_Panc0203_Day14_rep2

description: Library name: Hypoxia_Panc0203_Day14_rep2


title: Hypoxia_Panc0203_Day14_rep3

description: Library name: Hypoxia_Panc0203_Day14_rep3


title: Hs578T cells_6h_Control_3

description:
Library name: Sample 3
Column name in raw_is: 147_003


title: Hypoxia_Panc0203_Day1_rep3

description: Library name: Hypoxia_Panc0203_Day1_rep3


title: Hs578T cells_24h_Control_1

description:
Library name: Sample 9
Column name in raw_is: 147_009


title: HNE_1_MUT_LMP1_2; HNE_1_MUT_LMP1_2_2, Day7

value: MUT-LMP1 H101R


title: S10,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 103
049_Mtb11_19_S49_L001


title: HNE_1_MUT_LMP1_1; HNE_1_MUT_LMP1_1_2, Day7


title: Hs578T cells_6h_Control_1

description:
Library name: Sample 1
Column name in raw_is: 147_001


title: S7,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 106
035_Mtb11_5_S35_L002


title: S8,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 105
041_Mtb11_11_S41_L002


title: S8,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 104
040_Mtb11_10_S40_L002


title: Hs578T cells_6h_Control_4

description:
Library name: Sample 4
Column name in raw_is: 147_004


title: Donor 30, 10x 3', Stage III, Diffuse, Tumor

city: Beijing

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description:
D30T
10x Genomics

data_processing:
The sequencing reads of scRNA-seq data were aligned against GRCh38 human reference genome by Cell Ranger (version 4.0.0, 10x Genomics Inc) to generate matrixes that record UMI counts of each gene across all cells.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: barcode sequences
Supplementary files format and content: features.tsv.gz: genes
Supplementary files format and content: matrix.mtx.gz: cell x gene count matrix

source_name: Gastric cancer tumor

extract_protocol:
Fresh collected solid tissues (tumour, adjacent normal, and lymph node) were cut into small pieces (~1 mm3) in the RPMI 1640 Medium (Thermo Fisher Scientific Inc., USA) with 10% fetal bovine serum, loaded in gentleMACS C Tubes, and digested with MACS Tumour Dissociation Kit (130095929, Miltenyi Biotec) on a gentleMACS Dissociator with Heaters (Miltenyi Biotec, Germany). Continuous rotation at 37 ℃ for 30 minutes was applied.
Library was performed according to the manufacter's instruction. Roughly 10,000 ~ 20,000 cells were prepared for the 10x 5' and 3' single-cell library construction. The guidance for the library construction is detailed in the manufacturer's protocol (CG000207 and CG000183).

value: Gastric cancer tumor

value: Donor 30

tag: Stage

value: Stage III

tag: subtype

value: Diffuse


title: WT Liver, AMLN, 3 months

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

description: core_table_gene AMLN WT VS KO.xls

data_processing:
RNAseq analysis method for Dr.TOM II delivery
The sequencing data was filtered with SOAPnuke
The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: GRCm38 (mouse) and GRCh38 (human)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
RNAprep pure Tissue/Cell Kit (TIANGEN, DP431 and DP430)
mRNA Library Preparation (DNBSEQ) BGI-NGS-JK-RNA-001 A0

value: liver

value: WT

value: AMLN diet


title: HNE_1_MUT_LMP1_3; HNE_1_MUT_LMP1_3_2, Day7


title: Hypoxia_Panc0203_Day1_rep2

description: Library name: Hypoxia_Panc0203_Day1_rep2


title: S13,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 102
061_Mtb11_31_S61_L002

value: Sarcoidosis


title: Gpnmb KO Liver, AMLN, 3 months

description: core_table_gene AMLN WT VS KO.xls

value: Gpnmb knockout


title: Donor 28, 10x 3', Stage II, Indeterminate, Normal

description:
D28N
10x Genomics

source_name: Adjacent normal

value: Adjacent normal

value: Donor 28

value: Stage II

value: Indeterminate


title: Donor 30, 10x 3', Stage III, Diffuse, Normal

description:
D30N
10x Genomics


title: WT Liver, HFHC, 4 months

description: core_table_gene HFHC VS ND.xlsx

value: high fat high cholesterol diet


title: Hypoxia_PACADD188_Day9_rep3

description: Library name: Hypoxia_PACADD188_Day9_rep3

value: cell line

value: PDAC

value: KRAS G12D


title: S13,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 101
060_Mtb11_30_S60_L002

value: DMSO


title: HNE_1_WT_LMP1_1; HNE_1_WT_LMP1_1_2, Day7

value: human nasopharyngeal carcinoma cell


title: Donor 28, 10x 3', Stage II, Indeterminate, Lymph Node

description:
D28T
10x Genomics

source_name: Lymph node

value: Lymph node


title: Hypoxia_Panc0203_Day14_rep1

description: Library name: Hypoxia_Panc0203_Day14_rep1

value: Hypoxia


title: S14,Sarcoidosis,CD4m,DMSO

description:
Library name: Sample 100
065_Mtb11_35_S65_L002


title: WT Liver, ND, 4 months

description: core_table_gene HFHC VS ND.xlsx

value: liver

value: normal chow diet


title: S14,Sarcoidosis,CD4m,MTB300

description:
Library name: Sample 99
066_Mtb11_36_S66_L001


title: Donor 27, 10x 5', Stage II, Intestinal, Normal

description:
D27N
10x Genomics

value: Donor 27

value: Intestinal


title: Hypoxia_PACADD188_Day9_rep2

description: Library name: Hypoxia_PACADD188_Day9_rep2


title: Hypoxia_PACADD188_Day9_rep1

description: Library name: Hypoxia_PACADD188_Day9_rep1


title: 16fl-organoid_1

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

description: Library name: 16fl-organoid

data_processing:
nf-core pipeline rnaseq
We used Tophat 2 and Bowtie 2 to align reads.
Reads were mapped to mouse genome (MGI assembly version 10) using Tophat program.
Expression counts were normalized by library size.
Normalized gene expression values of the transcripts were computed by HTSeq
Assembly: GRCm38
Supplementary files format and content: comma separated values of the raw reads for each samples
Supplementary files format and content: comma separated values concerning sample information

source_name: colon

growth_protocol: C57BL/6J mice were purchased from Japan Clea. Reg3afl/fl mice were generated by CRISPR/Cas9-mediated insertion of loxP sites flanking exon 2–4, and subsequently crossed with Villin-Cre mice to obtain intestinal-epithelial-specific Reg3a knockout (Reg3aΔIEC) mice. All mice were maintained under specific pathogen–free conditions at the Center for Experimental Animals, Institute of Science Tokyo.

extract_protocol:
Total RNA was extracted from colonic organoids using the RNeasy Mini Kit (Qiagen). RNA quantity and integrity were assessed using RiboGreen and TapeStation; only samples with RIN >7.0 were used.
Stranded mRNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq Stranded mRNA Sample Prep Kit, following the manufacturer’s protocol.

treatment_protocol: Colonic organoids were established from Reg3afl/fl and Reg3aΔIEC mice( male, 9 week old). For each genotype, organoids were derived from one mouse (n = 1) and plated in four independent wells (technical quadruplicates). Epithelial crypts were isolated by EDTA treatment, embedded in Matrigel, and cultured in murin colon organoid medium. Organoids were collected 3 days after passage (≤15 passages). No additional treatment was applied before RNA extraction. Each genotype included organoids from three independent mice processed in technical triplicate.

value: colon

value: organoid

value: intestinal organoid

value: WT


title: 15fl-organoid_1

description: Library name: 15fl-organoid


title: Hypoxia_PACADD188_Day7_rep3

description: Library name: Hypoxia_PACADD188_Day7_rep3


title: I21,IGRA+,CD4m,MTB300

description:
Library name: Sample 98
GS0159_V

value: IGRA+


title: Donor 25, 10x 3', Stage III, Diffuse, Normal

description:
D25N
10x Genomics

value: Adjacent normal

value: Donor 25

value: Stage III

value: Diffuse


title: Donor 26, 10x 3', Stage II, Intestinal, Tumor

description:
D26T
10x Genomics

value: Gastric cancer tumor

value: Donor 26

value: Stage II


title: 13fl-organoid_1

description: Library name: 13fl-organoid


title: I21,IGRA+,CD4m,DMSO

description:
Library name: Sample 97
GS0159_X

value: DMSO


title: Donor 27, 10x 5', Stage II, Intestinal, Tumor

description:
D27T
10x Genomics


title: Hypoxia_Panc0203_Day1_rep1

description: Library name: Hypoxia_Panc0203_Day1_rep1

value: cell line

value: PDAC

value: KRAS G12D

value: Hypoxia


title: C21,IGRA-,CD4m,DMSO

description:
Library name: Sample 96
GS0162_X

value: IGRA-


title: Hypoxia_PACADD188_Day7_rep2

description: Library name: Hypoxia_PACADD188_Day7_rep2


title: 14fl-organoid_1

description: Library name: 14fl-organoid

value: colon

value: organoid


title: Hypoxia_PACADD188_Day7_rep1

description: Library name: Hypoxia_PACADD188_Day7_rep1


title: C21,IGRA-,CD4m,MTB300

description:
Library name: Sample 95
GS0162_V


title: Donor 25, 10x 3', Stage III, Diffuse, Tumor

description:
D25T
10x Genomics


title: C22,IGRA-,CD4m,DMSO

description:
Library name: Sample 94
GS1532_X


title: Hypoxia_PACADD188_Day3_rep3

description: Library name: Hypoxia_PACADD188_Day3_rep3


title: 8KO-organoid_1

description: Library name: 8KO-organoid

value: intestinal organoid

value: KO


title: Donor 24, 10x 5', Stage II, Intestinal, Peripheral Blood

description:
D24P
10x Genomics

source_name: Peripheral blood

value: Peripheral blood

value: Donor 24

value: Intestinal


title: C22,IGRA-,CD4m,MTB300

description:
Library name: Sample 93
GS1532_V


title: 7KO-organoid_1

description: Library name: 7KO-organoid


title: Hypoxia_PACADD188_Day3_rep2

description: Library name: Hypoxia_PACADD188_Day3_rep2


title: Donor 27, 10x 5', Stage II, Intestinal, Lymph Node

description:
D27L
10x Genomics

value: Donor 27


title: 6KO-organoid_1

description: Library name: 6KO-organoid


title: Donor 24, 10x 5', Stage II, Intestinal, Lymph Node

description:
D24L
10x Genomics

value: Lymph node


title: Hypoxia_PACADD188_Day3_rep1

description: Library name: Hypoxia_PACADD188_Day3_rep1


title: 5KO-organoid_1

description: Library name: 5KO-organoid


title: Donor 24, 10x 5', Stage II, Intestinal, Tumor

description:
D24T
10x Genomics

value: Gastric cancer tumor


title: Hypoxia_PACADD188_Day14_rep2

description: Library name: Hypoxia_PACADD188_Day14_rep2


title: C24,IGRA-,CD4m,DMSO

description:
Library name: Sample 92
GS1555_X


title: Donor 24, 10x 5', Stage II, Intestinal, Normal

description:
D24N
10x Genomics

value: Adjacent normal

value: Stage II


title: C25,IGRA-,CD4m,MTB300

description:
Library name: Sample 90
GS1558_V


title: Hypoxia_PACADD188_Day14_rep3

description: Library name: Hypoxia_PACADD188_Day14_rep3

value: cell line


title: C25,IGRA-,CD4m,DMSO

description:
Library name: Sample 89
GS1558_X

value: DMSO


title: KO

city: tianjin

first: Ming

last: Wei

address: No.94 weijin road

institute: Nankai University School of Medicine

description: Library name: sample 2

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Colon

extract_protocol:
An appropriate number of cells were loaded into the flow channel of the SeekOne MM chip and allowed to settle into microwells by gravity. Unsettled cells were removed, and cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle into microwells under a magnetic field. Excess CBBs were rinsed away, and cells on the MM chip were lysed to release and capture RNA.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: Colon

value: RUNX3 ko


title: WT

description: Library name: sample 1

value: RUNX3 wt


title: Hypoxia_PACADD188_Day14_rep1

description: Library name: Hypoxia_PACADD188_Day14_rep1

value: PDAC

value: KRAS G12D

value: Hypoxia


title: B6, lung mesenchymal, P8, ATAC-seq, replicate 2

city: San Diego

first: Le

last: Xu

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

description:
Library name: P8_mesenchymal_scATACseq_rep2
scATAC-seq

library_source: genomic single cell

data_processing:
For data analysis, reads alignment (mouse genome mm10) and cell barcode demultiplex were conducted by using 10x Genomics Cell Ranger ATAC (version 2.1) with default settings. Quality control, TSS enrichment, data normalization, dimensional reduction and UMAP-based cell clustering were performed by Signac. Analysis of differentially accessible peaks was performed by FindAllMarkers. ChromVAR was used to analyze differential TF binding motif activities between groups of cells. The expression features of marker genes, as well as the projection of motif enrichment scores, was profiled and visualized by R package ggplot2 (version 3.3.2). Two biological replicates were integrated using Signac.
Assembly: mouse mm10
Supplementary files format and content: For scATACseq, h5 files from cellranger and integrated Seurat object from two replicates

growth_protocol: All mice were in B6 background. All mice were housed in facilities accredited by American Association for Accreditation of Laboratory Animal Care (AAALAC) at University of California San Diego. All animal husbandry and experiments were approved by Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
The lungs were perfused with 12 ml of cold DPBS (Life Technology) and then inflated with dissociation buffer (PRMI1640 (Thermo Scientific) with 10% FBS, 1mM HEPES (Life Technology), 1mM MgCl2(Life Technology), 1mM CaCl2 (Sigma-Aldrich), 0.525mg/ml collagenase D (Roche), 5unit/ml Dispase (Stemcell Technologies) and 0.05 mg/ml DNase I (Roche)). Minced lung was placed in dissociation buffer for 30 min at 37°C, and cell solution was filtered through 70μm and 40μm strainers. Ammonium-Chloride-Potassium (ACK) lysis was used to remove blood cells, and cell pellets were resuspended in FACS buffer. Antibodies used for flow cytometry include BV510-CD45, PE-Epcam, PE-CD31, APC-PDGFRa (all from BioLegend), and DAPI to label dead cells. 18,000 cells from each group were subjected to scATAC-seq following standard protocol by Center for Epigenomics at the University of California, San Diego.
Sample preparation and library construction were performed according published protocol doi:10.7554/eLife.62522

treatment_protocol: Noon on the day of vaginal plug detection was designated embryonic day 0.5 (E0.5). The day of birth was designated postnatal day 0 (P0). At day P8, the lungs from male and female were harvested.

value: mesenchymal cells, P8

value: wild type

value: Postnatal Day 8


title: Donor 23, 10x 3', Stage II, Intestinal, Tumor

description:
D23T
10x Genomics

value: Donor 23

value: Intestinal


title: C26,IGRA-,CD4m,DMSO

description:
Library name: Sample 88
GS1565_X

value: IGRA-


title: Donor 22, 10x 3', Stage I, Diffuse, Normal

description:
D22N
10x Genomics

value: Donor 22

value: Stage I

value: Diffuse


title: Hypoxia_PACADD188_Day1_rep2

description: Library name: Hypoxia_PACADD188_Day1_rep2

value: cell line


title: Hypoxia_PACADD188_Day1_rep3

description: Library name: Hypoxia_PACADD188_Day1_rep3


title: B6, lung mesenchymal, P8, ATAC-seq, replicate 1

description:
Library name: P8_mesenchymal_scATACseq_rep1
scATAC-seq


title: C3

city: Hangzhou

first: jiahong

last: gong

address: Qingchun East Rd. 3

department: Department of Respiratory Care, Regional Medical Center for National Institute of Respiratory Diseases

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

description:
Library name: C3
control group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: myoblast

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: myoblast

value: control


title: Donor 22, 10x 3', Stage I, Diffuse, Tumor

description:
D22T
10x Genomics

value: Gastric cancer tumor


title: C2

description:
Library name: C2
control group, replicate biosample 2


title: C27,IGRA-,CD4m,DMSO

description:
Library name: Sample 86
GS1567_X

value: DMSO