title: VF3

value: hemolymph

value: Haemocyte

value: female

value: Vibrio parahaemolyticus

value: immune


title: plasma-chronic pancreatitis-Pancreatioc divisum-1

status: Public on Apr 10 2024

type: SRA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

library_source: transcriptomic

data_processing:
RNAseq reads were trimmed and aligned to human genome using hisat2 and counted using featurecounts
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: csv file includes counts or deseq2 data; file name includes either 'counts' for count data or 'deseq2' for deseq2 data

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatioc divisum

extract_protocol:
patient samples collected at admission (before TPIAT) and healthy donor samples collected at various time points. miRNEasy serum/plasma advanced kit was used to extract small RNA from plasma samples.
Library construction as per Illumina TruSeq Small RNA Library Prep Kit

tag: tissue

value: plasma

tag: aetiology

value: Pancreatioc divisum

tag: disease state

value: chronic pancreatitis

tag: age

tag: race

value: Caucasian


title: 18160X2 shMcam-A

city: Salt Lake City

first: Benjamin

middle: T

last: Spike

state: Utah

address: 1950 Circle of Hope Dr,

institute: Huntsman Cancer Institute, University of Utah

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A.tar mouse reference from 10X genomics using cellranger count version 5.0.1 with 6000 expected cells.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in h5 format

organism: Mus musculus

extract_protocol:
Py230 single cell suspension was isolated by trypsinization and resuspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was filtered through 40-micron cell strainer. Viability and cell count were assessed on Countess 2 (Invitrogen, Carlsbad, CA). Equilibrium to targeted cell recovery of 6,000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip G (PN-1000120) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets. Within individual GEMs, barcoded cDNA generated from captured mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumine Platforms (KK4842).
10X Genomics Next GEM Single Cell 3' Gene Expression Library prep v3.1 with UDI

tag: cell line

tag: cell type

value: Multipotent murine epithelial-like cell line

tag: genotype

value: shMcam-A


title: plasma-chronic pancreatitis-Oddi dysfunction-3

source_name: Oddi dysfunction

value: Oddi dysfunction


title: VF2

city: qingdao

first: yuxi

last: Wang

address: Laoshan District Songling Road

country: China

institute: ocean university of china

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: NCBI_ASM378908v1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Penaeus vannamei

source_name: hemolymph

growth_protocol: Use cotton balls soaked in 75% ethanol to wipe the haemocyte collection site of shrimp, aspirate an equal volume of Haemolymph using a 1ml syringe containing 400 µl pre-cooled anticoagulant

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: transfer the mixture to a 1.5mL centrifuge tube and mix well, centrifuged at 1000 g 4℃ for 5 min, he precipitate was added to 1 mL Trizol reagent, lysed on ice for 5 min, frozen in liquid nitrogen and stored at -80℃

tag: Sex

tag: agent

tag: treatment


title: plasma-chronic pancreatitis-Oddi dysfunction-2

value: White, not hispanic


title: 19877X4 Py230 B cells 2D Multiplex

description: 10X Genomics

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference from 10X genomics using cellranger multi version 7.0.0 with Gene Expression and Multiplexing Capture types.
Assembly: mm10
Supplementary files format and content: Per sample filtered feature barcode matrix in h5 format

extract_protocol:
Py230 single cell suspension was isolated by trypsinization and resuspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was filtered through 40-micron cell strainer. Viability and cell count were assessed on Countess 2 (Invitrogen, Carlsbad, CA). Equilibrium to targeted cell recovery of 6,000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip G (PN-1000120) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets. Within individual GEMs, barcoded cDNA generated from captured mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumine Platforms (KK4842).
Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000268) was used to barcode individual cells with 16nt 10x Barcode, to tag cell specific transcript molecules with 12 nt Unique Molecular Identifier (UMI) and to capture poly (A) mRNA with 30 nt ploy(dT) sequence according to the manufactures

treatment_protocol: Cells were treated with CX-4945 10μM or the equivalent DMSO vehicle control for 7 Days

value: shCon and shMcam

value: 10μM CX-4945 or equivalent amount of vehicle DMSO for 7 Days


title: 18160X1 shCon-A

description: 10X Genomics

value: shCon-A


title: sinc TERT rep1-72 hours

city: Saint Louis

first: Shayna

middle: T. J.

last: Bradford

state: MO

address: MCDONNELL MEDICAL SCIENCES BUILDING, 4565 Mckinley Ave ST 852

department: Department of Medicine, Division of Nephrology

institute: Washington University in Saint Louis

description: hTERT-RPTEC bulk RNA-seq

data_processing:
Fastq processing step: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing.  RNA-seq reads were then aligned to the GRCh38 (for human) with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts  were the output for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: The processed files are the raw read counts for each gene/sample in txt format.

source_name: hTERT-immortalized renal proximal tubule epithelial cells

growth_protocol: cell culture protocol: primary and hTERT-immortalized RPTECs were cultured in 6-well plates according to the manufacturer's protocol and then subjected to siRNA treatment for either 48- or 72- hours

extract_protocol:
Total mRNA were isolated from mouse kidney and human RPTECs using a RNA kit from Qiagen (RNEASY Mini prep kit, Cat# 74104).
Total RNA integrity was determined using Agilent 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: siRNA Experimental Design for bulk RNA-seq  Experiment 1 performed in primary-hRPTECs (12 samples total):  50nM non-targeting siRNA, 72 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 72 hours, 6 replicates    Experiment 2 performed in primary-hRPTECs (12 samples total):  50nM non-targeting siRNA , 48 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 48 hours, 6 replicates    Experiment 3 performed in hTERT-hRPTECs (12 samples total):  50nM non-targeting siRNA, 72 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 72 hours, 6 replicates     Catalog number of siRNA used in each study:   non-targeting siRNA (Horizon Discovery; D-001210-05-05)   pooled siRNA targeting human TNIK (Horizon Discovery; M-004542-03-0020)

value: ATCC (CRL-4031)

value: Male

value: non-targeting siRNA rep1

tag: treatment timepoint

value: 3 days


title: plasma-chronic pancreatitis-Oddi dysfunction-1

value: White, hispanic origin


title: BM3

value: hemolymph

value: Haemocyte

value: male

value: control

value: immune


title: siTNIK rep6-48 hours

description: primary-hRPTEC bulk RNA-seq

source_name: primary renal proximal tubule epithelial cells

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: pooled siRNA targeting human TNIK rep6

value: 2 days


title: VF1

value: female

value: Vibrio parahaemolyticus


title: CD3KO_MR1KO_chimera

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (version 6.0.0)
Assembly: mm10-2020-A for the scRNA-seq and vdj_GRCm38_alts_ensembl-3.1.0 for scTCR-seq

source_name: Thymus

extract_protocol:
Single-cell suspension of thymus was obtained as described (Salou et al. 2019). MR1:5-OP-RU tetramer staining along with an anti-TCRb-APC (clone H57-597; 1:200) was performed at room temperature for 30min in PBS 0.5% BSA 2 mM EDTA complemented with rat anti-mouse CD16/CD32 antibody and MR1:6FP to block non-specific binding following the National Institutes of Health (NIH) Tetramer Core Facility instructions. Tetramer-based magnetic enrichment was performed as described (F. P. Legoux and Moon 2012). Cells were washed and stained for surface markers with following monoclonal antibodies: anti-CD44-APC-Cy7 (IM7, Biolegend; 1:400), -CD24-PE-Cy5 (M1/69, Biolegend; 1:1600), -CD19-AF700 (ID3, Biolegend; 1:800), -B220-AF700 (RA3-6B2, eBioscience; 1:400), -CD11c-AF700 (N418, eBioscience; 1:200), -F4/80-AF700 (BM8, Biolegend; 1:200). For cell hashing in combination with 10x Chromium Single Cell 5′ Solution, TotalSeq-C anti-mouse Hashtags 2 to 7 (M1/42; 39-F11, Biolegend, 155863, 155865, 155867, 155869, 155871, 155873; 1:100 for all) were used according to manufacturer recommendations. Single-cell suspensions from 6 hematopoietic chimeras thymi were pooled and DAPI (1:1000) staining was added just before FACS sorting on an Aria III cell sorter (BD). Total TCRb+MR1:5-OP-RU+ cells were flow-sorted into PBS 0.35% BSA, centrifuged, counted, and 6,500 cells were loaded onto the Chromium 5′ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer recommendations (10× Genomics).
Three libraries were performed according to the manufacter’s instructions (single cell 5’ with feature barcode v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Total RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
5' VDJ scRNA-seq
CITE-seq

value: Thymus

value: MAIT


title: 19876X4 Py230 B cells 2D GEX

description: 10X Genomics

value: Multipotent murine epithelial-like cell line

value: shCon and shMcam

value: 10μM CX-4945 or equivalent amount of vehicle DMSO for 7 Days


title: siTNIK rep5-48 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep5


title: 19877X3 Py230 A cells 2D Multiplex

description: 10X Genomics


title: BM2

value: hemolymph


title: plasma-chronic pancreatitis-Idiopathic-5

description:
outlier
cDNA6838

source_name: Idiopathic

value: plasma

value: Idiopathic

value: chronic pancreatitis

value: White, not hispanic


title: plasma-chronic pancreatitis-Idiopathic-4

value: Caucasian


title: BF3

value: Haemocyte

value: control

value: immune


title: plasma-chronic pancreatitis-Idiopathic-3


title: 19876X3 Py230 A cells 2D GEX

description: 10X Genomics


title: BF2

value: female


title: 20603X4 shMcam 2

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108 and a reference database was created using STAR version 2.7.9a
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: Mammary Tumor

extract_protocol:
RNA was isolated via QIAzol-chloroform extraction followed by column-based purification and On-Column DNase Digestion (Qiagen #79254). The aqueous phase was brought to a final concentration of 50% ethanol, and RNA was purified using the RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions (Qiagen #74804)
Illumina TruSeq Stranded mRNA Library Prep with UDI (Illumina; poly(A) selection)

value: Mammary Tumor

value: Mcam knockdown


title: plasma-chronic pancreatitis-Idiopathic-2


title: sinc TERT rep2-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: ATCC (CRL-4031)

value: Male

value: non-targeting siRNA rep2

value: 3 days


title: 20603X3 shMcam 1

value: Multipotent murine epithelial-like cell line


title: siTNIK rep4-48 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: pooled siRNA targeting human TNIK rep4

value: 2 days


title: eIF1-2-KO_stress_RNAseq_rep3

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
sequencing adapters from read1 were removed with CutAdapt (5'adapt: AGTCCGACGATC, 3'adapt:NNNNNAGATCGGAAGAG)
in silico removal of reads mapping to toxoplasma rRNa & tRNA with bowtie2
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax 0.1,  –outFilterScoreMinOverLread=0.9, –outFilterMatchNminOverLread=0.9)
read counts from Htseq, filtered for coding genes only
differential expression with DESeq2, translational efficiency with Riborex
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: tabular files of mapped read counts

molecule: cytoplasmic RNA

organism: Toxoplasma gondii

growth_protocol: 4x10^7 parasites innoculated and grown in confluent human foreskin fibroblasts in DMEM-pH7.4+10%FBS (no antibiotic) for 2h prior to switching to fresh DMEM or to RPMI-pH8.3+3%FBS+ambient CO2 for 48h

extract_protocol:
cytoplasmic lysate was collected and an aliquot was immediately stored in Trizol for RNA-seq samples.  The rest was digested with RNaseI and monosomes were collected by ultracentrifugation on a sucrose cushion. Ribosome-protected fragments (RFP) were purified after gel electrophoresis
total RNA was fragmented by alkaline hydrolysis. Fragments were purfied by gel electrophoresis. fragments were dephosphorylated, ligated at 5' end with barcoded adapter, rRNA removal with eukaryotic Ribo-minus kit , phosphorylated, ligated at 3' end with SR-adapter, reverse transcribed & PCR with NEBnext barcoded adapters

treatment_protocol: control is DMEM pH7.4, 10% FBS, 5% CO2; treatment is RPMI pH8.3, 3% FBS, amibent CO2

value: pre-bradyzoites

value: RPMI pH8.3, ambient CO2


title: plasma-chronic pancreatitis-Hereditary-4

source_name: Hereditary

value: plasma

value: Hereditary

value: chronic pancreatitis

value: White, not hispanic


title: siTNIK rep2-48 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep2


title: 20603X1 shCon 1

value: Mammary Tumor

value: shControl


title: eIF1-2-KO_stress_RNAseq_rep2


title: plasma-chronic pancreatitis-Hereditary-3

value: Caucasian


title: eIF1-2-KO_stress_RNAseq_rep1


title: siTNIK rep1-48 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep1


title: sinc rep5-48 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep5


title: Adult (12 weeks aged) mice, DMM surgery

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

data_processing:
HISAT v2.1.0
HISAT utilized a combination of global and local indexes for efficient spliced alignment and generated alignments.
Transcript assembly and abundance estimation were performed using StringTie v1.3.4d.
Trimmed reads were aligned to Mus musculus (mm10) using STAR, and variant calling was performed using Samtools and Bcftools. Variants were filtered based on RMS mapping quality (Q ≥ 20) and read depth (d ≥ 100) using the varFilter module of VCFtools.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: injured cartilage

extract_protocol:
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).
Total RNA concentration was calculated using the Quant-IT RiboGreen kit (Invitrogen, #R11490).

value: injured cartilage

value: wild type (C57BL/6)

value: chondrocyte

value: 14 weeks


title: plasma-chronic pancreatitis-Hereditary-2

value: Hispanic


title: sinc rep4-48 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: non-targeting siRNA rep4

value: 2 days


title: siTNIK rep3-48 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep3


title: plasma-chronic pancreatitis-Hereditary-1

description:
outlier
cDNA6830

value: plasma

value: Hereditary

value: chronic pancreatitis

value: White, not hispanic


title: Adult (12 weeks aged) mice, sham surgery

source_name: sham cartilage

value: sham cartilage


title: BF1

value: hemolymph

value: Haemocyte

value: female

value: control

value: immune


title: plasma-chronic pancreatitis-Alcoholic-3

description:
outlier
cDNA6829

source_name: Alcoholic

value: Alcoholic

value: Black


title: Young (3 weeks aged) mice, DMM surgery

value: injured cartilage

value: wild type (C57BL/6)

value: chondrocyte

value: 3 weeks


title: sinc rep3-48 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: non-targeting siRNA rep3

value: 2 days


title: plasma-chronic pancreatitis-Idiopathic-1

value: plasma

value: Idiopathic

value: chronic pancreatitis

value: Caucasian


title: sinc rep2-48 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep2


title: Young (3 weeks aged) mice, sham surgery

value: sham cartilage


title: 20603X2 shCon 2

value: Mammary Tumor

value: Multipotent murine epithelial-like cell line

value: shControl


title: sinc rep6-48 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep6


title: plasma-chronic pancreatitis-Alcoholic-2

value: Alcoholic


title: eIF1-2-KO_stress_RIBOseq_rep1

data_processing:
sequencing adapters from read1 were removed with CutAdapt (5'adapt: AGTCCGACGATC, 3'adapt:NNNNNAGATCGGAAGAG)
in silico removal of reads mapping to toxoplasma rRNa & tRNA with bowtie2
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax 0.1,  –outFilterScoreMinOverLread=0.9, –outFilterMatchNminOverLread=0.9)
read counts from Htseq, filtered for coding genes only
differential expression with DESeq2, translational efficiency with Riborex
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: tabular files of mapped read counts
Library strategy: Ribo-seq

value: pre-bradyzoites

value: RPMI pH8.3, ambient CO2


title: eIF1-2-KO_tachyzoite_RNAseq_rep3

value: tachyzoites

value: DMEM pH7.4, 5%CO2


title: sinc rep1-48 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: non-targeting siRNA rep1


title: eIF1-2-KO_tachyzoite_RNAseq_rep2


title: siTNIK rep6-72 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep6

value: 3 days


title: siTNIK rep5-72 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep5


title: eIF1-2-KO_tachyzoite_RNAseq_rep1


title: OsINO80-YFP_YFP_rep2, ChIP-seq

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

description:
Oryza sativa Nipponbare
OsINO80-YFP_YFP_rep2

library_source: genomic

data_processing:
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Bowtie2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
After deduplication, SICER was used to call peaks by comparing the IP and the input.
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. To obtain the enrichment signal around the gene body, TSS and TTS, computeMatrix tool in deepTools was employed.
Assembly: MSU7
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: 14-day-old seedlings

growth_protocol: Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.

extract_protocol:
Rice seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF. Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

value: 14-day-old seedlings

tag: cultivar

value: Nipponbare

value: no treatment

tag: antibody

value: YFP


title: eIF1-2-KO_stress_RIBOseq_rep3


title: UM-UC-3 cisplatin resistant 2

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17

department: Pathology

country: Japan

institute: Sapporo Medical University

data_processing:
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags  and the sequenced CAGE tags were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after  discarding ribosomal or non-A/C/G/T base-containing RNAs.  For tag clustering, CAGE-tag 5‘ coordinates were input for CAGEr clustering (Haberle et al., Nucleic Acids  Research 2015 43:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default  parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: urothelial carcinoma cell line

growth_protocol: UM-UC-3 CR cells were cultured in DMEM 10% FBS containing 5uM CDDP.

extract_protocol: Total RNAs were isolated by an Rneasy kit (Qiagen). The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5'-cap structures of RNAs were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNAs, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: cisplatin resistant


title: siTNIK rep4-72 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep4


title: UM-UC-3 cisplatin resistant 1


title: eIF1-2-KO_tachyzoite_RIBOseq_rep3


title: UM-UC-3 wild type 2

value: wild type


title: OsINO80-YFP_input_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
OsINO80-YFP_input_rep2


title: eIF1-2-KO_stress_RIBOseq_rep2

value: pre-bradyzoites


title: siTNIK rep3-72 hours

description: primary-hRPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep3


title: UM-UC-3 wild type 1


title: eIF1-2-KO_tachyzoite_RIBOseq_rep2

value: tachyzoites


title: eIF1-2-KO_tachyzoite_RIBOseq_rep1

value: DMEM pH7.4, 5%CO2


title: siTNIK rep2--72 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: pooled siRNA targeting human TNIK rep2


title: WT_YFP_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_YFP_rep2

value: wild-type


title: siTNIK rep1-72 hours

description: primary-hRPTEC bulk RNA-seq

value: Female

value: pooled siRNA targeting human TNIK rep1


title: parental_stress_RNAseq_rep3

value: RPMI pH8.3, ambient CO2


title: plasma-chronic pancreatitis-Alcoholic-1

description:
outlier-7
cDNA6827

value: plasma

value: Alcoholic

value: chronic pancreatitis

value: Caucasian


title: WT_input_for_YFP_rep2, ChIP-seq

description:
Oryza sativa Nipponbare
WT_input_for_YFP_rep2

value: 14-day-old seedlings

value: Nipponbare

value: no treatment


title: LG03_REH_S3I_201_input

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: no antibody

data_processing:
Samples were sequenced on an Illumina NextSeq 500, using a 43bp, paired end configuration. Fastq was then demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poorquality sequences. Sequenced reads were aligned against the UCSC human reference genome (GRCh38) with Burrows-Wheeler Aligner (BWA) program with default parameters. The BAM files were subjected to removal of potential PCR and optical duplicates using Picard MarkDuplicates option. Fragment length and quality measurement for each dataset were determined using PhantomPeakQualTools based on strand cross-correlation approach. Two metrics named normalized strand cross-correlation coefficient (NSC) and relative strand cross-correlation coefficient (RSC) were used for data quality assessment. BigWig files were generated using a custom bam to bigwig script.
Assembly: GRCh38
Supplementary files format and content: ChIP-seq: bigwig files.

source_name: REH

growth_protocol: REH cells were cultured in Roswell Park Memorial Institute (RPMI), supplemented with 10% Foetal Bovine Serum (FBS), 100 U/ml Penicillin/100 μg/ml Streptomycin (Merck Life Science, Dorset, UK) and 2 mM L- glutamine (Merck life Science).

extract_protocol:
REH cells were treated for 6h with either S3I-201 (50 uM) or DMSO and then were cross-linked with 2 mM DSG for 30 minutes at room temperature. After washing the samples 3 times with PBS, cells were fixed with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched by adding glycine to final concentration 0.125 M for 5 minutes at room temperature. Fixed cells were washed twice with cold PBS, and then sequentially in lysis buffer A (0.25% TritonX100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6]) and lysis buffer B (150 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6], incubating for 10 minutes in  rotation at 4°C each time. Cells were then resuspended in incubation buffer (0.15% SDS, 1% TritonX100, 150 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES [pH 7.6]) plus protease inhibitors (Roche, Merck) and incubated for 30 minutes on ice. Lysates were then sonicated for 20 cycles (30 sec on / 30 sec off) in the Bioruptor Pico water bath sonicator (Diagenode, Liege, BE). Cleared supernatant was stored at -80°C. 250 μl of sonicated chromatin were diluted in incubation buffer supplemented with 0.1% BSA and protease inhibitors and were incubated rotating at 4°C overnight, with protein A magnetic beads (Merck Life Science) and 2 ug of anti-TP53 (C15410083  ,Diagenode) antibody. Beads were washed for 10 minutes twice in low salt buffer (0.1% SDS, 0.1% DOC, 1% Triton X-100, 0.1 mM EDTA pH 8.0, 0.5 mM EGTA, 10 mM Tris-HCl [pH 8.0], 150 mM NaCl), and once in high salt buffer (0.1% SDS, 0.1% DOC, 1% Triton X-100, 0.1 mM EDTA pH 8.0, 0.5 mM EGTA, 10 mM Tris-HCl [pH 8.0], 500 mM NaCl), LiCl Buffer (250 mM LiCl, 0.5% DOC, 0.5% NP-40, 0.1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl [pH 8.0]) and in TE buffer (10 mM Tris-HCl [pH 8.0], 0.1 mM EDTA, 0.5 mM EGTA). DNA was eluted from the ChIP samples by 20 minutes incubation in rotation at RT with elution buffer (1% SDS, 100 mM NaHCO3). Chromatin was reverse-crosslinked and subjected to RNase and proteinase K digestion and extracted by using the MinElute PCR purification kit (Qiagen).
Libraries were prepared from 1ng of ChIP DNA using the NEBNext DNA Ultra II assay (New England Biolabs, Hitchin, UK) with bead-based size selection for 200 bp fragments and 12 cycles of amplification. Samples were then sequenced on an Illumina NextSeq 500, using a 43bp, paired end configuration.

tag: tag

value: input


title: LG02_REH_DMSO_ChIP_TP53

description: TP53 C15410083,Diagenode

treatment_protocol: REH cells were treated for 6h with either S3I-201 (50 uM) or DMSO

value: DMSO

value: ChIP-seq


title: sinc rep4-72 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep4

value: 3 days


title: parental_stress_RNAseq_rep1

value: pre-bradyzoites


title: parental_stress_RIBOseq_rep3


title: LG01_REH_DMSO_input

description: no antibody


title: HL-1 cells, tachypaced rep3

city: Hangzhou

first: Wenjing

last: Chen

address: No.79 Qingchun Road

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchword (paarameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameter-mismath cost:2 insertion cost:3 deletion cost:3 length fraction: 0.8 similartiy 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 raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values

source_name: heart

growth_protocol: HL-1 cells were cultured with Claycomb Medium supplemented with 10 % FBS, 100 U/mL penicillin/streptomycin, 0.1 mM norepinephrine, and 2 mM L-glutamine.

extract_protocol:
Total RNA was obtained using Qiagen RNA extraction kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

treatment_protocol: tachypacing

value: heart

value: HL-1 cells

value: WT

value: Tachypaced


title: HL-1 cells, tachypaced rep2


title: sinc rep3-72 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: non-targeting siRNA rep3


title: LG04_REH_S3I_201_ChIP_TP53

description: TP53 C15410083,Diagenode


title: sinc rep2-72 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep2


title: parental_stress_RIBOseq_rep1

value: RPMI pH8.3, ambient CO2


title: parental_stress_RIBOseq_rep2


title: KO1rep3

city: Changchun

first: Ziqi

state: Jilin

address: No. 1363, Eco Street

department: Institute of Agricultural Biotechnology

institute: Jilin Academy of Agricultural Sciences

data_processing:
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
For processing mRNA reads, clean data were used to calculate the expression levels of genes using RSEM software (Li and Dewey, 2011). Besides indexes set by bowtie2, all parameters used in RSEM were default settings.
Gene expression levels are reported as transcripts per million. Differential Expressed genes are further identified by R package DESeq2 under the control of |Fold change| >1.5, FDR<0.05 threshold,
Assembly: B73 APGv4
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Zea mays

source_name: Leaf

growth_protocol: KO and KN5855 (WT line) plants were grown in the greenhouse of Jilin Academy of Agricultural Sciences located in Jilin province (2020&2021; China; E125°, N44°)

extract_protocol:
Total RNA was isolated using RNAiso Plus reagent (TaKaRa). The concentration and quality of RNA were evaluated by electrophoresis and Nanodrop2000c (Thermo Scientific, USA)
Solexa/Illumina sequencing was carried out by Biomarker Biotechnology Co. Ltd., China. The technology details are consistent with the described method (Kakumanu et al., 2012)

treatment_protocol: To construct RNA libraries, leaves collected from WT, and KO1 plants at V8 stage were subjected to RNA isolation with three biological replications.

value: Leaf

value: ZmGA20ox3 KO

value: normal growth


title: KO1rep2


title: parental_stress_RNAseq_rep2


title: sinc rep6-72 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep6


title: HL-1 cells, tachypaced rep1


title: AGS cells  transfected with and control vector, NC AGS 3

type: RNA

city: Fuzhou

first: Sheng

last: Yang

state: Fujian

address: Xinquan Load

institute: Fujian Medical University Union Hospital

description: Gene expression data from human gastric caner cell strain AGS without NCAPD3 knockdown

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 .

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Gstric cancer cell AGS without NCAPD3 knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human Gastric cancer cell strain AGS was cultured in RPMI-1640/DMEM containing 10% fetal bovine serum and 1% penicillin and streptomycin solution in a 37 ℃, 5% CO2 incubator.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: AGS cells were transfected with shNCAPD3 lentiviruses and control vector to construct NCAPD3-knockdown and negative control cells.

tag: strain

value: AGS

value: Human gastric cancer

value: without NCAPD3 knockdown


title: AGS cells  transfected with and  shNCAPD3 lentiviruses, NCAPD3-KD AGS 3

description: Gene expression data from human gastric caner cell strain AGS with NCAPD3 knockdown

source_name: Gstric cancer cell AGS with stable NCAPD3 knockdown

value: with stable NCAPD3 knockdown


title: parental_tachyzoite_RNAseq_rep3

value: tachyzoites

value: DMEM pH7.4, 5%CO2


title: AGS cells  transfected with and  shNCAPD3 lentiviruses, NCAPD3-KD AGS 2


title: KO1rep1


title: HL-1 cells, control rep3

value: heart

value: HL-1 cells

value: WT

value: Control


title: AGS cells  transfected with and control vector, NC AGS 1


title: sinc rep1-72 hours

description: primary-hRPTEC bulk RNA-seq

value: Lonza CC-2553; Batch0000635750;  52 Year Caucasian

value: Female

value: non-targeting siRNA rep1

value: 3 days


title: AGS cells  transfected with and  shNCAPD3 lentiviruses, NCAPD3-KD AGS 1


title: AGS cells  transfected with and control vector, NC AGS 2


title: parental_tachyzoite_RNAseq_rep2


title: sinc rep5-72 hours

description: primary-hRPTEC bulk RNA-seq

value: non-targeting siRNA rep5


title: WTrep3

value: Leaf

value: normal growth


title: skin_dna_exome

city: Tokyo

first: Makii

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Department of Molecular Endocrinology

institute: National Research

data_processing:
Sequence reads of RNA exome data were mapped by HISAT2, and those of genome DNA exome data were mapped by Burrows-Wheeler Alingner.
Variant calling and annotation were performed using GATK and ANNOVAR.
Genome_build: hg19
Supplementary_files_format_and_content: rna_exome_CS1.txt (Text file containing the variant list of the X chromosome and the depth of read harboring each variant in four RNA samples and a genome DNA sample.)

source_name: skin

growth_protocol: Skin fibroblasts were cultured in Dulbecco's modified Eagle's medium containing 17% fetal bovine serum. Single cells were picked by a single-cell picking system (ASONE) and were expanded to reach ~90% confluence in 6-well or 10-cm plates.

extract_protocol:
Total RNA was extracted with the miRNeasy mini kit (QIAGEN). Genome DNA was extracted with the Gentra Puregene kit (QIAGEN).
Libraries for RNA exome analysis were prepared using the TruSeq RNA Access Library Prep Kit (Illumina). Libraries for genome DNA exome analysis were prepared using the SureSelect V6-Post kit (Illumina).
Exome analyses for RNA and genome DNA

value: female

value: skin


title: HL-1 cells, control rep2


title: skin_fibroblast_rna_exome_clone4

source_name: skin fibroblast

value: skin fibroblast

tag: clone


title: WTrep2

tag: tissue


title: HL-1 cells, control rep1


title: parental_tachyzoite_RNAseq_rep1


title: skin_fibroblast_rna_exome_clone3


title: parental_tachyzoite_RIBOseq_rep3


title: WTrep1


title: TCR_CD3KO_MR1KO_chimera

description: 10x Genomics

library_source: other

molecule: other

value: Thymus

value: MAIT


title: skin_fibroblast_rna_exome_clone2


title: parental_tachyzoite_RIBOseq_rep2

value: tachyzoites

value: DMEM pH7.4, 5%CO2


title: KGSM_02

city: Berkeley

first: Shubham

last: Maurya

address: Rm 596, Minor Hall

institute: University of California Berkeley

data_processing:
Quality check of FASTQ files was done with FastQC v.0.11.9.
Adapters sequences were trimmed using Trim Galore! v.0.6.6.
Trimmed reads were mapped on macaque genome version Mmu10 (University of California Santa Cruz) with STAR alignment tool v.2.7.1a using RefGene annotation
The total number of read counts mapped for each gene was extracted from BAM files using FeatureCount v.1.5.3.
Count matrix was imported into Rstudio v.4.2.0. It was normalized using the Transcripts Per Million method by NormalizeTPM().
Assembly: Mmu10
Supplementary files format and content: tab-delimited text file include transcripts per million (TPM) values for each Sample …

organism: Macaca mulatta

source_name: Macaque optic nerve

extract_protocol:
RNA was isolated using the Trizol method
Sequencing libraries were prepared using SMARTer v4 Ultra Low Input RNA Kit

value: wild-type

value: untreated


title: HTO_CD3KO_MR1KO_chimera

description: 10x Genomics

source_name: Thymus


title: KGSM_01


title: skin_fibroblast_rna_exome_clone1


title: Synechococcus cells, kaiA-Ex/labA-KO, replicate 1

status: Public on Apr 09 2024

city: Nashville

first: Carl

middle: Hirschie

last: Johnson

state: Tennessee

address: 465 21st Avenue South, U-8215 BSB/MRBIII

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Tuxedo and DESeq
Sequence reads were trimmed for adaptors and low quality reads were removed using trim_galore v. 0.6.10, specifying that the sequences were paired-end
hisa2 v. 2.2.1 was used to build an index using assembly sequences available in NCBI (GenBank assembly accession: GCA_000012525.1) and to align our sequencing reads with the genome (parameters: -S, --dta, --no-spliced-alignment)
samtools v. 1.11.0 was used to convert the generated .sam files into .bam files
stringtie v. 2.1.7 was used to estimate transcript abundances, and the prepDE.py script provided with stringtie was used to generate a read counts matrix
the raw read counts were analyzed with DESeq2 v. 1.36.0 and p-values were calculated using a Wald test followed by multiple-comparisons correction using FDR. Log2FC cvalues were shrunk using adaptive shrinking to account for high levels of variation due to low counts or high dispersion values.
Assembly: GCA_000012525.1
Supplementary files format and content: comma-delimited csv file includes raw counts for the transcripts in each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cyanobacteria

growth_protocol: Cells were maintained in plates of BG-11 and grown in constant light and constant 30ºC, under ~ 40µE of illumination with fluorescent lights.

extract_protocol:
RNA was extracted from cells preserved in RNA Protect (Qiagen) and processed with the Rneasy Mini Kit (Qiagen). DNA contamination was removed with Dnase I (NEB).
Library preparation and rRNA depletion was performed using the NEBNext® rRNA Depletion Kit for Bacteria (New England BioLabs).

treatment_protocol: Prior to collection, cells were grown for 3 days in constant light in plates of BG-11 media. Then, the 3 kaiA-Ex and the 3 kaiA-Ex/labA-KO samples were given 10µM ZnCl2 and transferred to dark for 12h, while the other 6 samples (3 of wild-type and 3 of labA-KO) were not given ZnCl2 and were instead just transferred to dark for 12h. After this dark pulse, the plates were put into constant light and collected for RNAseq extraction after 12h of being in constant light.

value: cyanobacteria

tag: time

value: collected after 12h in LL (with one 12h dark pulse before)

value: kaiA over-expression and labA knock-out


title: Synechococcus cells, labA-KO, replicate 2

value: labA knock-out


title: Synechococcus cells, labA-KO, replicate 1


title: Synechococcus cells, kaiA-Ex, replicate 3

value: kaiA over-expression through Zinc induction


title: Synechococcus cells, kaiA-Ex/labA-KO, replicate 2


title: parental_tachyzoite_RIBOseq_rep1


title: Synechococcus cells, WT, replicate 3


title: Synechococcus cells, labA-KO, replicate 3


title: Synechococcus cells, WT, replicate 2


title: Synechococcus cells, WT, replicate 1


title: Synechococcus cells, kaiA-Ex, replicate 2


title: Synechococcus cells, kaiA-Ex/labA-KO, replicate 3


title: Synechococcus cells, kaiA-Ex, replicate 1


title: Patient IMF043 ROI  005

city: Madrid

first: Jon

last: Zugazagoitia

address: Avenida de Cordoba s/n

department: Medical Oncology

country: Spain

institute: Hospital Universitario 12 de Octubre

description: IMF-043 | 005 | Full ROI

data_processing:
Raw sequencing data FASTQ files were generated using Illumina NextSeq 2000 instrument.
Raw sequencing data FASTQ files were processed using GeoMx NGS Pipeline software version 3.1 to generate DCC files.
DCC files were uploaded on to the GeoMx DSP instrument to obtain gene expression raw count data.
Quality control (QC) and Q3 normalization of mRNA data were performed using the GeoMx Digital Spatial Profiler (DSP) software.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc and .pkc files.
Supplementary files format and content: IMfirst_DSP_rawcounts.xlsx: gene expression raw count data.
Supplementary files format and content: IMfirst_DSP_normalizedcounts.xlsx: gene expression normalized count data.
Supplementary files format and content: .png: image of tissue and ROIs.
Library strategy: spatial transcriptomics

source_name: Lymph Node

extract_protocol:
Formalin-fixed tissue were paraffin embedded (FFPE), 5-mm tissue sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared according to GeoMx Digital Spatial Profiler (DSP) NGS Readout User manual (MAN-10153-04).

value: Lymph Node

tag: patient id

tag: disease

value: ES-SCLC

value: Male

tag: smoking status

value: Former smoker

tag: ecog performance status at baseline

tag: cns metastases at baseline

value: No

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

value: Carbopplatin

tag: best recist response to treatment

value: Partial response

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up

value: atezolizumab + carboplatin/cisplatin + etoposide


title: Patient IMF043 ROI  006

description: IMF-043 | 006 | Full ROI

tag: tissue

tag: age

tag: Sex

tag: treatment


title: Patient IMF043 ROI  002

description: IMF-043 | 002 | Full ROI

tag: patient id

tag: disease

tag: smoking status

tag: ecog performance status at baseline


title: Patient IMF043 ROI  003

description: IMF-043 | 003 | Full ROI

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered


title: Patient IMF042 ROI  009

description: IMF-040/042 | 009 | Full ROI

source_name: Lung

value: Lung

value: Active smoker

value: Yes

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF043 ROI  001

description: IMF-043 | 001 | Full ROI

tag: tissue

tag: age

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF043 ROI  004

description: IMF-043 | 004 | Full ROI

tag: patient id

tag: disease

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: treatment


title: Patient IMF042 ROI  008

description: IMF-040/042 | 008 | Full ROI

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF042 ROI  007

description: IMF-040/042 | 007 | Full ROI

tag: tissue

tag: age

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF042 ROI  006

description: IMF-040/042 | 006 | Full ROI

tag: patient id

tag: disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF040 ROI  005

description: IMF-040/042 | 005 | Full ROI

tag: Sex

value: Female

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF040 ROI  004

description: IMF-040/042 | 004 | Full ROI

tag: tissue

tag: age

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF040 ROI  002

description: IMF-040/042 | 002 | Full ROI

tag: patient id

tag: disease

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF040 ROI  001

description: IMF-040/042 | 001 | Full ROI

tag: Sex

tag: smoking status

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF040 ROI  003

description: IMF-040/042 | 003 | Full ROI

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF039 ROI  013

description: IMF-037/039 | 013 | Full ROI

tag: patient id

tag: disease

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF039 ROI  012

description: IMF-037/039 | 012 | Full ROI

tag: Sex

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF039 ROI  009

description: IMF-037/039 | 009 | Full ROI

tag: tissue

tag: age

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF039 ROI  008

description: IMF-037/039 | 008 | Full ROI

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF039 ROI  011

description: IMF-037/039 | 011 | Full ROI

tag: Sex

tag: smoking status

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF039 ROI  010

description: IMF-037/039 | 010 | Full ROI

tag: tissue

tag: age

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF037 ROI  006

description: IMF-037/039 | 006 | Full ROI

tag: patient id

tag: disease

value: Stable disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF037 ROI  003

description: IMF-037/039 | 003 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF037 ROI  004

description: IMF-037/039 | 004 | Full ROI

tag: tissue

tag: age

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF037 ROI  001

description: IMF-037/039 | 001 | Full ROI

tag: patient id

tag: disease

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF037 ROI  002

description: IMF-037/039 | 002 | Full ROI

tag: Sex

tag: smoking status

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF037 ROI  007

description: IMF-037/039 | 007 | Full ROI

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF033 ROI  009

description: IMF-026/033 | 009 | Geometric Segment

tag: patient id

tag: disease

tag: bone metastases at baseline

tag: platinum administered

value: Cisplatin

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF037 ROI  005

description: IMF-037/039 | 005 | Full ROI

tag: Sex

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF033 ROI  007

description: IMF-026/033 | 007 | Geometric Segment

tag: tissue

tag: age

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF033 ROI  006

description: IMF-026/033 | 006 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF033 ROI  003

description: IMF-026/033 | 003 | Geometric Segment

tag: Sex

tag: smoking status

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF033 ROI  005

description: IMF-026/033 | 005 | Geometric Segment

tag: tissue

tag: age

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death


title: Patient IMF031 ROI  002

description: IMF-031/034 | 002 | Geometric Segment

tag: patient id

tag: disease

value: Progressive disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of last follow-up


title: Patient IMF033 ROI  008

description: IMF-026/033 | 008 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: treatment


title: Patient IMF030 ROI  007

description: IMF-030 | 007 | Geometric Segment

tag: tissue

tag: age

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient IMF030 ROI  006

description: IMF-030 | 006 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease


title: Patient IMF030 ROI  005

description: IMF-030 | 005 | Geometric Segment

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF030 ROI  003

description: IMF-030 | 003 | Geometric Segment

tag: Sex

tag: smoking status

tag: date of last follow-up


title: Patient IMF029 ROI  008

description: IMF-029 | 008 | Geometric Segment

source_name: Brain

value: Brain

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline


title: Patient IMF030 ROI  001

description: IMF-030 | 001 | Geometric Segment

tag: tissue

tag: age

tag: treatment


title: Patient IMF030 ROI  002

description: IMF-030 | 002 | Geometric Segment

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment


title: Patient IMF029 ROI  007

description: IMF-029 | 007 | Geometric Segment

tag: patient id

tag: disease

tag: date of first dose of treatment


title: Patient IMF030 ROI  004

description: IMF-030 | 004 | Geometric Segment

tag: disease progression or death of disease

tag: disease progression or death

tag: death


title: Patient IMF029 ROI  005

description: IMF-029 | 005 | Geometric Segment

tag: Sex

tag: smoking status

tag: death of disease


title: Patient IMF028 ROI  010

description: IMF-027/028 | 010 | Geometric Segment

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF029 ROI  003

description: IMF-029 | 003 | Geometric Segment

tag: tissue

tag: age

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: treatment


title: Patient IMF028 ROI  011

description: IMF-027/028 | 011 | Geometric Segment

tag: patient id

tag: disease

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF028 ROI  009

description: IMF-027/028 | 009 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: death

tag: death of disease


title: Patient IMF029 ROI  004

description: IMF-029 | 004 | Geometric Segment

tag: cns metastases at baseline

tag: best recist response to treatment

tag: date of last follow-up


title: Patient IMF029 ROI  001

description: IMF-029 | 001 | Geometric Segment

tag: tissue

tag: age

tag: liver metastases at baseline


title: Patient IMF028 ROI  012

description: IMF-027/028 | 012 | Geometric Segment

tag: bone metastases at baseline

tag: platinum administered

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment


title: Patient IMF029 ROI  002

description: IMF-029 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: Sex

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF029 ROI  006

description: IMF-029 | 006 | Geometric Segment

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF027 ROI  005

description: IMF-027/028 | 005 | Geometric Segment

source_name: Bone

tag: tissue

value: Bone

tag: age

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF027 ROI  008

description: IMF-027/028 | 008 | Geometric Segment

tag: patient id

tag: disease

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment


title: Patient IMF027 ROI  006

description: IMF-027/028 | 006 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF027 ROI  007

description: IMF-027/028 | 007 | Geometric Segment

tag: tissue

tag: age

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF027 ROI  004

description: IMF-027/028 | 004 | Geometric Segment

tag: patient id

tag: disease

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF031 ROI  001

description: IMF-031/034 | 001 | Geometric Segment

tag: Sex

tag: smoking status

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment


title: Patient IMF033 ROI  004

description: IMF-026/033 | 004 | Geometric Segment

tag: tissue

value: Lymph Node

tag: age

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF027 ROI  003

description: IMF-027/028 | 003 | Geometric Segment

tag: patient id

tag: disease

value: ES-SCLC

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF026 ROI  002

description: IMF-026/033 | 002 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF027 ROI  002

description: IMF-027/028 | 002 | Geometric Segment

tag: tissue

tag: age

value: Male

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment


title: Patient IMF025 ROI  013

description: IMF-024/025 | 013 | Geometric Segment

tag: patient id

tag: disease

value: Former smoker

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF025 ROI  011

description: IMF-024/025 | 011 | Geometric Segment

tag: Sex

tag: smoking status

tag: cns metastases at baseline

value: No

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF025 ROI  012

description: IMF-024/025 | 012 | Geometric Segment

tag: tissue

tag: age

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

value: Carbopplatin

tag: date of last follow-up


title: Patient IMF025 ROI  010

description: IMF-024/025 | 010 | Geometric Segment

tag: patient id

tag: disease

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment


title: Patient IMF025 ROI  008

description: IMF-024/025 | 008 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF025 ROI  009

description: IMF-024/025 | 009 | Geometric Segment

tag: tissue

tag: age

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF024 ROI  005

description: IMF-024/025 | 005 | Geometric Segment

tag: patient id

tag: disease

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

value: Partial response

tag: date of last follow-up


title: Patient IMF024 ROI  004

description: IMF-024/025 | 004 | Geometric Segment

tag: Sex

tag: smoking status

tag: date of last dose of treatment

tag: date of disease progression or death

tag: date of death

tag: treatment

value: atezolizumab + carboplatin/cisplatin + etoposide


title: Patient IMF024 ROI  003

description: IMF-024/025 | 003 | Geometric Segment

tag: tissue

value: Lung

tag: age

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF024 ROI  001

description: IMF-024/025 | 001 | Geometric Segment

tag: patient id

tag: disease

value: Active smoker

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF022 ROI  012

description: IMF-021/022 | 012 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

value: Yes

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF021 ROI  009

description: IMF-021/022 | 009 | Geometric Segment

tag: tissue

tag: age

tag: date of last dose of treatment

tag: treatment


title: Patient IMF022 ROI  011

description: IMF-021/022 | 011 | Geometric Segment

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF024 ROI  002

description: IMF-024/025 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF021 ROI  007

description: IMF-021/022 | 007 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF027 ROI  001

description: IMF-027/028 | 001 | Geometric Segment

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF021 ROI  002

description: IMF-021/022 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF021 ROI  008

description: IMF-021/022 | 008 | Geometric Segment

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF021 ROI  004

description: IMF-021/022 | 004 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF021 ROI  003

description: IMF-021/022 | 003 | Geometric Segment

tag: tissue

tag: age

tag: platinum administered

tag: date of last follow-up


title: Patient IMF021 ROI  005

description: IMF-021/022 | 005 | Geometric Segment

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF022 ROI  010

description: IMF-021/022 | 010 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF026 ROI  001

description: IMF-026/033 | 001 | Geometric Segment

tag: Sex

value: Female

tag: smoking status

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF020 ROI  013

description: IMF-019-020 | 013 | Geometric Segment

tag: tissue

tag: age

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF019 ROI  011

description: IMF-019-020 | 011 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF020 ROI  012

description: IMF-019-020 | 012 | Geometric Segment

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF021 ROI  006

description: IMF-021/022 | 006 | Geometric Segment

tag: tissue

tag: age

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF019 ROI  010

description: IMF-019-020 | 010 | Geometric Segment

tag: patient id

tag: disease

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF019 ROI  008

description: IMF-019-020 | 008 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF019 ROI  009

description: IMF-019-020 | 009 | Geometric Segment

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF021 ROI  001

description: IMF-021/022 | 001 | Geometric Segment

tag: patient id

tag: disease

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF019 ROI  007

description: IMF-019-020 | 007 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF025 ROI  007

description: IMF-024/025 | 007 | Geometric Segment

tag: tissue

tag: age

tag: ecog performance status at baseline

value: Stable disease

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF025 ROI  006

description: IMF-024/025 | 006 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF019 ROI  004

description: IMF-019-020 | 004 | Geometric Segment

tag: Sex

tag: smoking status

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF019 ROI  006

description: IMF-019-020 | 006 | Geometric Segment

tag: tissue

tag: age

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF019 ROI  002

description: IMF-019-020 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF019 ROI  001

description: IMF-019-020 | 001 | Geometric Segment

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF019 ROI  003

description: IMF-019-020 | 003 | Geometric Segment

tag: tissue

tag: age

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF018 ROI  014

description: IMF-016/018 | 014 | Geometric Segment

tag: patient id

tag: disease

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: date of last follow-up


title: Patient IMF018 ROI  012

description: IMF-016/018 | 012 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF018 ROI  013

description: IMF-016/018 | 013 | Geometric Segment

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: date of disease progression or death

tag: date of death


title: Patient IMF018 ROI  015

description: IMF-016/018 | 015 | Geometric Segment

tag: patient id

tag: disease

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF016 ROI  006

description: IMF-016/018 | 006 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

value: Cisplatin

tag: date of last follow-up


title: Patient IMF018 ROI  010

description: IMF-016/018 | 010 | Geometric Segment

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF016 ROI  005

description: IMF-016/018 | 005 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death


title: Patient IMF016 ROI  008

description: IMF-016/018 | 008 | Geometric Segment

tag: cns metastases at baseline

tag: best recist response to treatment

tag: death

tag: death of disease


title: Patient IMF016 ROI  004

description: IMF-016/018 | 004 | Geometric Segment

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF018 ROI  009

description: IMF-016/018 | 009 | Geometric Segment

tag: tissue

tag: age

tag: platinum administered

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF016 ROI  001

description: IMF-016/018 | 001 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF016 ROI  002

description: IMF-016/018 | 002 | Geometric Segment

tag: cns metastases at baseline

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF016 ROI  003

description: IMF-016/018 | 003 | Geometric Segment

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF013 ROI  009

description: IMF-013/015 | 009 | Geometric Segment

tag: patient id

tag: disease

tag: platinum administered

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF013 ROI  005

description: IMF-013/015 | 005 | Geometric Segment

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF013 ROI  004

description: IMF-013/015 | 004 | Geometric Segment

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF013 ROI  003

description: IMF-013/015 | 003 | Geometric Segment

tag: patient id

tag: disease

tag: Sex

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF013 ROI  007

description: IMF-013/015 | 007 | Geometric Segment

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: platinum administered

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF013 ROI  002

description: IMF-013/015 | 002 | Geometric Segment

tag: tissue

tag: age

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF012 ROI  007

description: IMF-011/012 | 007 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF016 ROI  007

description: IMF-016/018 | 007 | Geometric Segment

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF013 ROI  001

description: IMF-013/015 | 001 | Geometric Segment

tag: tissue

tag: age

tag: platinum administered

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF012 ROI  006

description: IMF-011/012 | 006 | Geometric Segment

tag: patient id

tag: disease

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF012 ROI  005

description: IMF-011/012 | 005 | Geometric Segment

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF012 ROI  004

description: IMF-011/012 | 004 | Geometric Segment

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF011 ROI  003

description: IMF-011/012 | 003 | Geometric Segment

tag: patient id

tag: disease

tag: platinum administered

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient IMF018 ROI  011

description: IMF-016/018 | 011 | Geometric Segment

tag: Sex

tag: smoking status

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF011 ROI  001

description: IMF-011/012 | 001 | Geometric Segment

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF011 ROI  002

description: IMF-011/012 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF010 ROI  010

description: IMF-009/010 | 010 | Geometric Segment

tag: Sex

tag: smoking status

tag: platinum administered

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF010 ROI  007

description: IMF-009/010 | 007 | Geometric Segment

tag: tissue

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: treatment


title: Patient IMF009 ROI  006

description: IMF-009/010 | 006 | Geometric Segment

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of death


title: Patient IMF009 ROI  004

description: IMF-009/010 | 004 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF009 ROI  005

description: IMF-009/010 | 005 | Geometric Segment

tag: tissue

tag: Sex

tag: smoking status

tag: platinum administered

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF009 ROI  003

description: IMF-009/010 | 003 | Geometric Segment

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: treatment


title: Patient IMF009 ROI  002

description: IMF-009/010 | 002 | Geometric Segment

tag: patient id

tag: disease progression or death

tag: death

tag: death of disease

tag: date of death


title: Patient IMF009 ROI  001

description: IMF-009/010 | 001 | Geometric Segment

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF013 ROI  006

description: IMF-013/015 | 006 | Geometric Segment

tag: tissue

tag: Sex

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death


title: Patient IMF008 ROI  003

description: IMF-007/008 | 003 | Geometric Segment

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of last follow-up

tag: treatment


title: Patient IMF007 ROI  012

description: IMF-007/008 | 012 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of death


title: Patient IMF008 ROI  001

description: IMF-007/008 | 001 | Geometric Segment

tag: tissue

tag: Sex

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF007 ROI  010

description: IMF-007/008 | 010 | Geometric Segment

tag: age

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of disease progression or death


title: Patient IMF008 ROI  002

description: IMF-007/008 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of last follow-up

tag: treatment


title: Patient IMF007 ROI  009

description: IMF-007/008 | 009 | Geometric Segment

tag: tissue

tag: Sex

tag: disease progression or death

tag: death

tag: death of disease

tag: date of death


title: Patient IMF007 ROI  008

description: IMF-007/008 | 008 | Geometric Segment

tag: age

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF007 ROI  006

description: IMF-007/008 | 006 | Geometric Segment

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of disease progression or death


title: Patient IMF007 ROI  005

description: IMF-007/008 | 005 | Geometric Segment

tag: tissue

tag: Sex

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of last follow-up

tag: treatment


title: Patient IMF007 ROI  007

description: IMF-007/008 | 007 | Geometric Segment

tag: age

tag: smoking status

tag: disease progression or death

tag: death

tag: death of disease

tag: date of death


title: Patient IMF006 ROI  007

description: IMF-005/006 | 007 | Geometric Segment

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF007 ROI  011

description: IMF-007/008 | 011 | Geometric Segment

tag: tissue

tag: Sex

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of disease progression or death


title: Patient IMF006 ROI  006

description: IMF-005/006 | 006 | Geometric Segment

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of last follow-up

tag: treatment


title: Patient IMF006 ROI  005

description: IMF-005/006 | 005 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient IMF006 ROI  004

description: IMF-005/006 | 004 | Geometric Segment

tag: tissue

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient IMF010 ROI  009

description: IMF-009/010 | 009 | Geometric Segment

tag: Sex

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of disease progression or death


title: Patient IMF006 ROI  003

description: IMF-005/006 | 003 | Geometric Segment

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of last follow-up


title: Patient IMF006 ROI  002

description: IMF-005/006 | 002 | Geometric Segment

tag: patient id

tag: disease

tag: disease progression or death

tag: death

tag: treatment


title: Patient IMF006 ROI  001

description: IMF-005/006 | 001 | Geometric Segment

tag: tissue

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: death of disease


title: Patient IMF005 ROI  012

description: IMF-005/006 | 012 | Geometric Segment

tag: Sex

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient IMF005 ROI  011

description: IMF-005/006 | 011 | Geometric Segment

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF008 ROI  004

description: IMF-007/008 | 004 | Geometric Segment

tag: tissue

tag: patient id

tag: disease

tag: disease progression or death

tag: death

tag: treatment


title: Patient IMF005 ROI  008

description: IMF-005/006 | 008 | Geometric Segment

tag: Sex

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient IMF004 ROI  004

description: IMF-003/004 | 004 | Geometric Segment

tag: age

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient IMF004 ROI  002

description: IMF-003/004 | 002 | Geometric Segment

tag: tissue

tag: patient id

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF004 ROI  001

description: IMF-003/004 | 001 | Geometric Segment

tag: disease

tag: Sex

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient IMF003 ROI  007

description: IMF-003/004 | 007 | Geometric Segment

tag: age

tag: smoking status

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient IMF002 ROI  001

description: IMF-001/002 | 001 | Geometric Segment

tag: tissue

tag: patient id

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient IMF003 ROI  006

description: IMF-003/004 | 006 | Geometric Segment

tag: disease

tag: Sex

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF003 ROI  005

description: IMF-003/004 | 005 | Geometric Segment

tag: age

tag: smoking status

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN046 ROI  009

description: CAN-044.2 CAN-046 | 009 | Full ROI

data_processing:
Raw sequencing data FASTQ files were generated using Illumina NextSeq 2000 instrument.
Raw sequencing data FASTQ files were processed using GeoMx NGS Pipeline software version 3.1 to generate DCC files.
DCC files were uploaded on to the GeoMx DSP instrument to obtain gene expression raw count data.
Quality control (QC) and Q3 normalization of mRNA data were performed using the GeoMx Digital Spatial Profiler (DSP) software.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc and .pkc files.
Supplementary files format and content: CANTABRICO_DSP_rawcounts.xlsx: gene expression raw count data.
Supplementary files format and content: CANTABRICO_DSP_normalizedcounts.xlsx: gene expression normalized count data.
Supplementary files format and content: .png: image of tissue and ROIs.
Library strategy: spatial transcriptomics

tag: tissue

tag: patient id

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

value: Carboplatin

tag: death of disease

value: durvalumab + carboplatin/cisplatin + etoposide


title: Patient CAN046 ROI  008

description: CAN-044.2 CAN-046 | 008 | Full ROI

tag: disease

tag: Sex

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN046 ROI  007

description: CAN-044.2 CAN-046 | 007 | Full ROI

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN046 ROI  010

description: CAN-044.2 CAN-046 | 010 | Full ROI

tag: tissue

tag: patient id

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN046 ROI  006

description: CAN-044.2 CAN-046 | 006 | Full ROI

tag: disease

tag: Sex

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN046 ROI  011

description: CAN-044.2 CAN-046 | 011 | Full ROI

tag: age

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN044 ROI  003

description: CAN-044.2 CAN-046 | 003 | Full ROI

tag: tissue

tag: patient id

value: Complete response

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN046 ROI  012

description: CAN-044.2 CAN-046 | 012 | Full ROI

tag: disease

tag: Sex

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN044 ROI  002

description: CAN-044.2 CAN-046 | 002 | Full ROI

tag: age

tag: smoking status

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN046 ROI  013

description: CAN-044.2 CAN-046 | 013 | Full ROI

tag: tissue

tag: patient id

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN043 ROI  006

description: CAN-042 CAN-043 | 006 | Full ROI

tag: disease

tag: Sex

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN043 ROI  007

description: CAN-042 CAN-043 | 007 | Full ROI

tag: age

tag: smoking status

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN044 ROI  005

description: CAN-044.2 CAN-046 | 005 | Full ROI

tag: tissue

tag: patient id

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN042 ROI  005

description: CAN-042 CAN-043 | 005 | Full ROI

source_name: Lymph node

value: Lymph node

tag: disease

tag: Sex

value: Current smoker

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient IMF013 ROI  008

description: IMF-013/015 | 008 | Geometric Segment

value: Lymph Node

value: ES-SCLC

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient IMF005 ROI  009

description: IMF-005/006 | 009 | Geometric Segment

tag: tissue

tag: patient id

value: Former smoker

tag: ecog performance status at baseline

value: No

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN044 ROI  004

description: CAN-044.2 CAN-046 | 004 | Full ROI

tag: disease

tag: Sex

value: Male

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient IMF005 ROI  010

description: IMF-005/006 | 010 | Geometric Segment

tag: age

tag: smoking status

tag: platinum administered

value: Carbopplatin

tag: best recist response to treatment

value: Partial response

tag: date of first dose of treatment

tag: date of death

value: atezolizumab + carboplatin/cisplatin + etoposide


title: Patient IMF004 ROI  003

description: IMF-003/004 | 003 | Geometric Segment

tag: tissue

value: Lung

tag: patient id

tag: date of last dose of treatment

tag: disease progression or death of disease

value: Yes

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN042 ROI  004

description: CAN-042 CAN-043 | 004 | Full ROI

tag: disease

tag: Sex

tag: ecog performance status at baseline

value: Stable disease

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN042 ROI  003

description: CAN-042 CAN-043 | 003 | Full ROI

tag: age

tag: smoking status

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

value: Cisplatin

tag: death of disease


title: Patient CAN042 ROI  002

description: CAN-042 CAN-043 | 002 | Full ROI

tag: tissue

tag: patient id

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN042 ROI  001

description: CAN-042 CAN-043 | 001 | Full ROI

tag: disease

tag: Sex

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN041 ROI  009

description: CAN-040 CAN-041.1 | 009 | Full ROI

tag: age

value: Female

tag: smoking status

tag: ecog performance status at baseline

value: Carboplatin

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN046 ROI  014

description: CAN-044.2 CAN-046 | 014 | Full ROI

tag: tissue

tag: patient id

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease

value: durvalumab + carboplatin/cisplatin + etoposide


title: Patient CAN041 ROI  008

description: CAN-040 CAN-041.1 | 008 | Full ROI

tag: disease

tag: Sex

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN041 ROI  007

description: CAN-040 CAN-041.1 | 007 | Full ROI

tag: age

tag: smoking status

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN040 ROI  006

description: CAN-040 CAN-041.1 | 006 | Full ROI

tag: tissue

tag: patient id

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN040 ROI  005

description: CAN-040 CAN-041.1 | 005 | Full ROI

tag: disease

tag: Sex

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN044 ROI  001

description: CAN-044.2 CAN-046 | 001 | Full ROI

tag: age

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

value: Complete response

tag: date of first dose of treatment

tag: date of death


title: Patient CAN039 ROI  004

description: CAN-037 CAN-039 | 004 | Full ROI

tag: tissue

tag: patient id

value: Current smoker

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN040 ROI  001

description: CAN-040 CAN-041.1 | 001 | Full ROI

tag: disease

tag: Sex

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN039 ROI  002

description: CAN-037 CAN-039 | 002 | Full ROI

tag: age

tag: smoking status

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN040 ROI  004

description: CAN-040 CAN-041.1 | 004 | Full ROI

tag: tissue

tag: patient id

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN037 ROI  003

description: CAN-037 CAN-039 | 003 | Full ROI

tag: disease

tag: Sex

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN029 ROI  004

description: CAN-028 CAN-029 | 004 | Full ROI

tag: age

tag: smoking status

tag: ecog performance status at baseline

value: Progressive disease

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN029 ROI  005

description: CAN-028 CAN-029 | 005 | Full ROI

tag: tissue

tag: patient id

value: ES-SCLC

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN029 ROI  006

description: CAN-028 CAN-029 | 006 | Full ROI

tag: disease

tag: Sex

value: Former smoker

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of death


title: Patient CAN022 ROI  004

description: CAN-021 CAN-022 | 004 | Full ROI

tag: age

tag: smoking status

value: No

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of last follow-up


title: Patient CAN028 ROI  001

description: CAN-028 CAN-029 | 001 | Full ROI

tag: tissue

tag: patient id

value: Male

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN024 ROI  002

description: CAN-023 CAN-024 | 002 | Full ROI

tag: disease

tag: Sex

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease


title: Patient CAN028 ROI  002

description: CAN-028 CAN-029 | 002 | Full ROI

tag: age

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment


title: Patient CAN023 ROI  001

description: CAN-023 CAN-024 | 001 | Full ROI

tag: tissue

tag: date of last dose of treatment

tag: disease progression or death of disease

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up


title: Patient CAN022 ROI  005

description: CAN-021 CAN-022 | 005 | Full ROI

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: disease progression or death

tag: death

tag: treatment


title: Patient CAN022 ROI  006

description: CAN-021 CAN-022 | 006 | Full ROI

tag: age

tag: Sex

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: death of disease