title: mWTA Slide3 121422 DSP-1001660013725-A-C04

tag: tissue

tag: roi

tag: segment

value: cap

value: Ldlr-/- 3MR+GCV

tag: panel

tag: area area_(um^2)


title: patient C2P9, before apheresis, T cells

status: Public on Jul 28 2024

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a patient with MS who underwent apheresis treatment

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.3 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background reduction, intensity normalization, probe set summarization and log2 transformation. The TAC software was also utilized for the analysis of differential alternative splicing. Exon-level processed data are available on the Series record.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: T helper cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Up to ~30 ml of peripheral blood were taken from MS patients in relapse immediately before and after therapeutic apheresis.

extract_protocol: The blood was collected in BD Vacutainer Glass Cell Preparation Tubes (Fisher Scientific). The tubes were centrifuged for the isolation of peripheral blood mononuclear cells (PBMC). B cells were positively selected from the PBMC using CD19 MicroBeads. T helper cells were obtained from the negative fraction of the B-cell separation by first removing non-T cells using the Pan T Cell Isolation Kit (Miltenyi Biotec) and then isolating CD4+ T cells using CD4 MicroBeads (Miltenyi Biotec). The RNA was isolated using the miRNeasy Mini Kit and the RNase-Free DNase Set (Qiagen).

treatment_protocol: The patients were treated according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: patient id

tag: time point

value: before

tag: cell population

value: CD4+ T cells

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: male

tag: study center

value: Greifswald

tag: current smoker

value: no

tag: body mass index

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

value: yes

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

value: monosymptomatic

tag: symptomatic phenotype

value: new

tag: relapse therapy

value: plasma exchange

tag: relapse therapy phase

tag: number of apheresis sessions

tag: clinical evaluation

value: non-responder


title: patient C4P3, before apheresis, T cells

tag: patient id

tag: time point

tag: cell population

tag: purity (%)

tag: rna integrity number

value: female

value: Rostock

value: immunoadsorption

value: escalation

value: responder


title: si-PROX1 rep3

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

country: Japan

institute: Fujita Health University

hyb_protocol: 5.2 ug fragmented and labeled cDNA was hybridized for 16 h at 45 °C on Human Clariom D Array. The GeneChip was washd using the GeneChip Fluidics Station 450.

scan_protocol: The GeneChip was scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were processed with SST-RMA using the Transcriptome Analysis Console (TAC) software.

label: biotin

label_protocol: Biotinylated cDNA was prepared according to the protocol starting from 250 ng of total RNA using the GeneChip WT PLUS Reagent Kit.

growth_protocol: NCI-H727 cells were cultured in RPMI-1640 medium containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using NucleoSpin RNA reagent according to the manufacturer's instruction.

treatment_protocol: NCI-H727 cells were transfected with si-NC (20 nmol/L) or si-PROX1 (20 nmol/L), and incubated for 72 h.

tag: tissue

value: lung carcinoid cell

tag: treatment


title: mWTA Slide3 121422 DSP-1001660013725-A-C03

type: SRA

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

country: USA

institute: NIH/NCI

library_source: transcriptomic

data_processing:
Raw basecall files were demultiplexed into individual fastqs corresponding to ROI, using bclconvert software
Fastqs were converted to Digital Count Conversion files using NanoString’s GeoMx NGS Pipeline v.2.3.0.
DCC files were processed using the GeoMX tools workflow. Probe data was filtered using a minProbeRatio value of 0.1 and a percentFailGrubbs value of 20. The background noise within the study is defined as the expression signal from negative control probes. ROIs with 2 geometric standard deviations above the background were kept along with those containing> 4% gene detection rate (51 ROIs). Genes detectedin 5% of ROIswere kept. Q3 normalization was then performed on the filtered data.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc file.
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode).

organism: Mus musculus

source_name: brachiocephalic artery

extract_protocol:
The formalin-fixed, paraffin-embedded tissue blocks were cut at 5-μm thickness onto APEX treated slides to improve attachment.  After baking at 60°C overnight, deparaffinization and antigen retrieval was performed on Leica BOND RX autostainer using HIER2 (EDTA based antigen retrieval solution for 20 min) and proteinase K (15 min at 37°C, 1 μg/ml) following Nanostring’s recommendations.  The 6 slides were processed on 2 consecutive days, 2 slides (#1 and #3 on day 1 and #2, #4, #5 and #7 on day 2). RNA probes (NanoString GeoMx Whole Transcriptome Atlas Mouse RNA probes for NGS, item# 121401103) were added for hybridization at 37°C for 16 h. The slides were then washed 2X with stringent wash (50% formamide in 2XSSC for 25 min each) followed by 2X wash with 2XSSC (2 min each).  Slides were blocked with W buffer for 30 min and then incubated with anti CD31 primary antibody (1:50 dilution in W buffer) for 45 min. The slides were washed 2 times with 1X SSC (5 min each) followed by 20 min incubation with donkey anti-goat antibody conjugated to AF532 (1:100 dilution in W buffer). After 2X wash in SSC (5 min each), the slides were incubated for 60 min at RT with the antibody cocktail containing CD45-AF594 (1:40), aSMA-AF647(1:200) and Syto 83 (10 mM, nuclear stain).  The slides were washed with SSC buffer two times and scanned on the GeoMx DSP machine for selection of regions of interest (ROIs), using FITC/525 nm filter to detect CD31 (200 msec), Cy3/568 nm channel to detect nuclei (50 msec), Texas Red/615 nm to detect CD45 (200 msec) and Cy5/666 nm to detect aSMA (200 msec).  Based on the morphology of the tissues, ROIs for media, cap, core and normal wall were selected using polygons, with no masking, for a total of 83 ROIs.  The combined surface area of ROIs was 2989910.17 mm2 containing 8446 nuclei.  Oligonucleotide barcodes from each ROI were UV-photocleaved, collected into 96-well plates.
Library preparation and sequencing as recommended by the NanoString GeoMx protocol

value: brachiocephalic artery

tag: roi

tag: segment

value: core

tag: genotype

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: si-PROX1 rep1


title: NSCLC Plasma_Exo-miRNA_2_BR

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies). The supplement of a commercial synthetic DNA poly-A oligonucleotide 3’ labeled pCp-Cy3, was added to the final hybridization mix. The 30-mer synthetic oligonucleotide (HPLC purified) was synthesized by TIB Molbiol s.r.l. (Genova, Italy). The lyophilized oligonucleotide was resuspended at a final concentration of 100 pmol/μL. Before use, an aliquot was taken and through serial dilutions brought to two final concentrations of 50 and 5 amol/μL.

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number G2505C) and data extracted using Agilent feature extraction v.12.0.0.7. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Replicated probes were then averaged.

label: Cyanine 3-pCp

source_name: BR

label_protocol: Exosomal total RNA samples were processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The Agilent miRNA microarray system was performed using 6 µl or 12 µl of purified total RNA  at unknown concentration, based on the plasma input (1 mL or 0.5 mL).

growth_protocol: No growth

extract_protocol: Exosomal total RNA  samples were purified from 0.5-1 mL of plasma using the  exoRNeasy Serum/Plasma Midi kit (Qiagen, Hilden, Germany)  according to manufacturer instructions.

treatment_protocol: No treatment

tag: age

tag: histotype

value: Adc

tag: gender

value: male

tag: smoke habit

value: Current smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

tag: # prior lines of treatment

tag: performance status

tag: basal or best response

value: Best Response


title: patient C4P4, before apheresis, T cells

tag: patient id

tag: time point

value: before

tag: cell population

value: CD4+ T cells

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: study center

tag: current smoker

value: yes

tag: body mass index

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

value: polysymptomatic

tag: symptomatic phenotype

value: new

tag: relapse therapy

value: plasma exchange

tag: relapse therapy phase

tag: number of apheresis sessions

tag: clinical evaluation


title: TAMER+/+

city: Xiamen

first: Jing

last: Bi

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

country: China

institute: Xiamen University

data_processing:
Base-calling performed using CASAVA version 1.4
Reads were aligned using HISAT2 version2.0.4
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: abundance measurements

source_name: breast cancer MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10%FBS

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell line

tag: genotype

value: TAMER+/+


title: si-PROX1 rep2

tag: tissue

value: lung carcinoid cell

tag: treatment


title: patient C2P9, before apheresis, B cells

source_name: B cells from the peripheral blood

tag: patient id

tag: time point

tag: cell population

value: CD19+ B cells

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

tag: study center

value: Greifswald

tag: current smoker

value: no

value: monosymptomatic

value: non-responder


title: MEFS, Wild-Type, biorep2, rep3

city: Durham

first: Ian

middle: C

last: Lock

state: North Carolina

address: 438 research Drive

department: Radiation Oncology

institute: Duke University

data_processing:
Sequencing  aligned to GRCm39 and GRCh38 with STAR version 2.7.10a using default settings
GTF files derived from stringtie (2.0) run using GRCm39 release 109 gtf as the reference annotation
Assembly: GRCm39 and GRCh38
Supplementary files format and content: gft

source_name: mouse embryonic fibroblasts

extract_protocol:
Trizol used to isolate total RNA and Zymo Direct-Zol used for purification of RNA with 15 minute Dnase treatment
poly-a enrichment

value: mouse embryonic fibroblasts

value: MEFS

tag: cell type

value: Biological Replicate 2

value: wild-type


title: mWTA Slide3 121422 DSP-1001660013725-A-C02

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

value: Ldlr-/- 3MR+GCV

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: patient C2P9, after apheresis, B cells

value: after

value: male

tag: body mass index

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

value: yes

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

tag: symptomatic phenotype

value: new

tag: relapse therapy

value: plasma exchange

tag: relapse therapy phase

tag: number of apheresis sessions

tag: clinical evaluation


title: si-NC rep3

tag: tissue

value: lung carcinoid cell

tag: treatment

value: si-NC


title: Non-inflamed Colonic UC smRNA sample #42

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

data_processing:
Sequencing was aligned and quantified using miRquant2.0. Sequence reads were trimmed for adaptors and low quality reads using Cutadapt.
Bowtie and SHRimp were used for alignment of the reads to hg19, allowing for perfect matches and isomiRs.
All annotation is provided by miRquant using TargetScan. The alignment was done to the human genome (hg19).
Assembly: hg19
Supplementary files format and content: tab deliminated file of raw counts for each Sample
Supplementary files format and content: tab deliminated file of normalized counts for each Sample

source_name: Colon Tissue

extract_protocol:
RNA was isolated from FFPE tissue using the Roche High Pure miRNA Isolation kit.
smRNA libraries were generated using the TruSeq Small RNA Sample Preparation Kit (Illumina).

value: Colon Tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: MEFS, Wild-Type, biorep2, rep2

value: mouse embryonic fibroblasts

tag: cell line

value: MEFS

tag: cell type

value: Biological Replicate 2

tag: genotype

value: wild-type


title: mWTA Slide3 121422 DSP-1001660013725-A-C01

value: brachiocephalic artery

tag: roi

tag: segment

value: core

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

tag: area area_(um^2)

tag: nuclei count


title: MEFS, Wild-Type, biorep2, rep1


title: MEFS, Wild-Type, bioRep1, rep3

value: Biological Replicate 1


title: si-NC rep2


title: Inflamed Colonic UC smRNA sample #41

value: Inflamed


title: Inflamed Colonic UC smRNA sample #42


title: MEFS, Wild-Type, bioRep1, rep2


title: si-NC rep1


title: mWTA Slide3 121422 DSP-1001660013725-A-B12

value: Ldlr-/- 3MR+GCV

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: MEFS, E221D, rep3

value: 129SVJae Background


title: mWTA Slide3 121422 DSP-1001660013725-A-B11

value: media


title: Non-inflamed Colonic UC smRNA sample #40

value: Colon Tissue


title: MEFS, E221D, rep2


title: Non-inflamed Colonic UC smRNA sample #41

value: Non-Inflamed


title: MEFS, E221D, rep1


title: MEFS, Wild-Type, bioRep1 ,rep1


title: Non-inflamed Colonic UC smRNA sample #39

value: UC


title: mWTA Slide3 121422 DSP-1001660013725-A-B10

value: cap


title: mWTA Slide3 121422 DSP-1001660013725-A-B09


title: Non-inflamed Colonic UC smRNA sample #38


title: Inflamed Colonic UC smRNA sample #40


title: mWTA Slide1 121422 DSP-1001660013725-A-B07

value: normal wall


title: Inflamed Colonic UC smRNA sample #39


title: NSCLC Plasma_Exo-miRNA_sample_184

description: miRNA profiling

data_processing: Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the scale method, respectively. Replicated probes were then averaged.

label: Cyanine 3

source_name: NSCLC Plasma exosomes

tag: age

tag: histotype

value: Scc

tag: gender

value: male

tag: smoke habit

value: Former smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

value: no

tag: # liver metastases

value: yes

tag: # prior lines of treatment

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_183

description: miRNA profiling

value: Adc

value: Current smoker

tag: treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: NSCLC Plasma_Exo-miRNA_sample_182

description: miRNA profiling

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_181

description: miRNA profiling


title: mWTA Slide1 121422 DSP-1001660013725-A-B04

tag: tissue

value: brachiocephalic artery

tag: roi

tag: genotype

value: Ldlr-/- 3MR+GCV

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: Inflamed Colonic UC smRNA sample #38

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_180

description: miRNA profiling

value: Other

value: male


title: NSCLC Plasma_Exo-miRNA_sample_179

description: miRNA profiling

value: female

value: Never smoker

value: Nivolumab


title: NIBD Colon Sample #16

value: NIBD


title: Non-inflamed Colonic UC smRNA sample #37

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_178

description: miRNA profiling

value: Adc

value: Current smoker

value: no


title: mWTA Slide1 121422 DSP-1001660013725-A-B02

value: brachiocephalic artery

tag: segment

value: normal wall

tag: Sex

tag: panel

tag: area area_(um^2)

tag: nuclei count


title: mWTA Slide1 121422 DSP-1001660013725-A-B03

value: core

value: Ldlr-/- 3MR+GCV

value: Female


title: Non-inflamed Colonic UC smRNA sample #36

value: Colon Tissue


title: NSCLC Plasma_Exo-miRNA_sample_177

description: miRNA profiling

tag: age

tag: histotype

tag: gender

tag: smoke habit

tag: # numer of metastatic sites

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_175

description: miRNA profiling

value: Scc

tag: # brain metastases

tag: # liver metastases

tag: # prior lines of treatment

tag: performance status

tag: status at the best response (ed


title: mWTA Slide1 121422 DSP-1001660013725-A-B01

tag: tissue

tag: roi

tag: genotype

value: Ldlr-/- +GCV

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_176

description: miRNA profiling

value: male

tag: treatment


title: NSCLC Plasma_Exo-miRNA_sample_170

description: miRNA profiling

value: Nivolumab


title: mWTA Slide3 121422 DSP-1001660013725-A-B08

tag: segment

tag: Sex

tag: panel


title: NSCLC Plasma_Exo-miRNA_sample_174

description: miRNA profiling

tag: age

value: female


title: NSCLC Plasma_Exo-miRNA_sample_171

description: miRNA profiling

tag: histotype


title: NSCLC Plasma_Exo-miRNA_sample_173

description: miRNA profiling

tag: gender

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Non-inflamed Colonic UC smRNA sample #35

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: mWTA Slide1 121422 DSP-1001660013725-A-B05

value: cap

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_169

description: miRNA profiling

value: Adc

tag: smoke habit

value: Current smoker

tag: # numer of metastatic sites

tag: # brain metastases

value: no

tag: # liver metastases

tag: # prior lines of treatment


title: Inflamed Colonic UC smRNA sample #37

tag: tissue

value: Inflamed


title: mWTA Slide1 121422 DSP-1001660013725-A-A10

value: brachiocephalic artery

tag: roi

tag: genotype

value: Ldlr-/- 3MR+GCV

value: Female


title: Inflamed Colonic UC smRNA sample #36

value: Colon Tissue


title: mWTA Slide1 121422 DSP-1001660013725-A-A09

tag: segment

value: core

tag: Sex


title: mWTA Slide1 121422 DSP-1001660013725-A-A08

value: Ldlr-/- +GCV

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_172

description: miRNA profiling

tag: age

tag: histotype

tag: treatment

value: Nivolumab

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_168

description: miRNA profiling

tag: gender

value: male


title: NSCLC Plasma_Exo-miRNA_sample_166

description: miRNA profiling

tag: smoke habit

value: yes


title: mWTA Slide1 121422 DSP-1001660013725-A-A07

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_167

description: miRNA profiling

value: female

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases


title: NSCLC Plasma_Exo-miRNA_sample_165

description: miRNA profiling

value: Never smoker

tag: # prior lines of treatment


title: NSCLC Plasma_Exo-miRNA_sample_164

description: miRNA profiling

value: Adc


title: NSCLC Plasma_Exo-miRNA_sample_163

description: miRNA profiling

value: Current smoker

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Inflamed Colonic UC smRNA sample #34

tag: tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_162

description: miRNA profiling


title: Non-inflamed Colonic UC smRNA sample #33

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_161

description: miRNA profiling

value: Scc

value: no

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NSCLC Plasma_Exo-miRNA_sample_160

description: miRNA profiling


title: mWTA Slide1 121422 DSP-1001660013725-A-A12

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

tag: genotype

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel


title: mWTA Slide1 121422 DSP-1001660013725-A-A06

value: media

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_159

description: miRNA profiling

tag: age

tag: histotype

value: Other

value: male

tag: treatment

value: Nivolumab

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide1 121422 DSP-1001660013725-A-A05

tag: area area_(um^2)

tag: nuclei count


title: Non-inflamed Colonic UC smRNA sample #32

value: Colon Tissue


title: NSCLC Plasma_Exo-miRNA_sample_158

description: miRNA profiling

value: Adc

tag: gender

value: female

tag: smoke habit

value: Never smoker

tag: # numer of metastatic sites

tag: # brain metastases

value: yes

tag: # liver metastases


title: mWTA Slide1 121422 DSP-1001660013725-A-A04

tag: tissue

tag: roi

value: cap


title: Inflamed Colonic UC smRNA sample #35

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_155

description: miRNA profiling

value: Current smoker

value: no

tag: # prior lines of treatment


title: NSCLC Plasma_Exo-miRNA_sample_154

description: miRNA profiling

tag: age

value: Scc


title: NSCLC Plasma_Exo-miRNA_sample_157

description: miRNA profiling

tag: histotype

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Non-inflamed Colonic UC smRNA sample #34

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_153

description: miRNA profiling

tag: treatment


title: Non-inflamed Colonic UC smRNA sample #31


title: mWTA Slide1 121422 DSP-1001660013725-A-A02

value: brachiocephalic artery

tag: segment

value: core

tag: genotype

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: Inflamed Colonic UC smRNA sample #32

value: Colon Tissue


title: NIBD Colon Sample #15

value: NIBD


title: mWTA Slide1 121422 DSP-1001660013725-A-A03

value: media

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_152

description: miRNA profiling

value: Adc

tag: gender

value: female

tag: smoke habit

value: Nivolumab

tag: # numer of metastatic sites

tag: performance status

tag: status at the best response (ed


title: NSCLC Plasma_Exo-miRNA_sample_151

description: miRNA profiling

value: male

tag: # brain metastases

tag: # liver metastases

value: yes

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_156

description: miRNA profiling

value: Current smoker

value: no

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:missed


title: mWTA Slide4 121522 DSP-1001660013726-B-E05

tag: tissue

value: brachiocephalic artery

tag: roi

value: Ldlr-/- 3MR+GCV


title: Inflamed Colonic UC smRNA sample #33

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_150

description: miRNA profiling

tag: age

tag: histotype

value: Never smoker

tag: treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: mWTA Slide4 121522 DSP-1001660013726-B-E04

tag: segment

tag: genotype

value: Ldlr-/- 3MR+Veh

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)


title: mWTA Slide4 121522 DSP-1001660013726-B-E03

value: cap

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_146

description: miRNA profiling

value: Adc

tag: gender

value: female

tag: smoke habit

value: Nivolumab

tag: # numer of metastatic sites

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Non-inflamed Colonic UC smRNA sample #30

tag: tissue

value: Colon Tissue

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_149

description: miRNA profiling

value: Scc

value: male

value: Former smoker

tag: # brain metastases

value: yes

tag: # liver metastases

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_148

description: miRNA profiling

tag: age

tag: histotype

value: Current smoker

value: no


title: NSCLC Plasma_Exo-miRNA_sample_147

description: miRNA profiling

tag: treatment


title: NSCLC Plasma_Exo-miRNA_sample_145

description: miRNA profiling

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: NSCLC Plasma_Exo-miRNA_sample_144

description: miRNA profiling


title: mWTA Slide4 121522 DSP-1001660013726-B-E01

value: brachiocephalic artery

tag: roi

tag: segment

value: core

tag: genotype

value: Ldlr-/- 3MR+Veh

value: Female


title: NSCLC Plasma_Exo-miRNA_sample_142

description: miRNA profiling

value: Adc


title: NIBD Colon Sample #14

tag: inflammation

value: NIBD

tag: disease status


title: NSCLC Plasma_Exo-miRNA_sample_143

description: miRNA profiling

tag: gender

value: female

value: Nivolumab


title: mWTA Slide4 121522 DSP-1001660013726-B-E02

value: media

tag: Sex

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: Inflamed Colonic UC smRNA sample #30

tag: tissue

value: Colon Tissue

value: Inflamed

value: UC


title: Inflamed Colonic UC smRNA sample #31


title: NSCLC Plasma_Exo-miRNA_sample_140

description: miRNA profiling

value: Scc

value: male

tag: smoke habit

tag: # numer of metastatic sites

tag: # brain metastases

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide4 121522 DSP-1001660013726-B-D12

value: Ldlr-/- 3MR+GCV


title: Non-inflamed Colonic UC smRNA sample #29

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_139

description: miRNA profiling

tag: age

tag: histotype

value: Former smoker

tag: treatment

value: no

tag: # liver metastases

tag: # prior lines of treatment


title: mWTA Slide4 121522 DSP-1001660013726-B-D11

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

tag: genotype

value: Female


title: NSCLC Plasma_Exo-miRNA_sample_138

description: miRNA profiling

value: Other

tag: gender

value: Current smoker


title: NSCLC Plasma_Exo-miRNA_sample_137

description: miRNA profiling

value: Nivolumab

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:missed


title: mWTA Slide4 121522 DSP-1001660013726-B-D10

value: cap

tag: Sex

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)


title: Non-inflamed Colonic UC smRNA sample #28

tag: tissue

value: Colon Tissue

tag: inflammation

tag: disease status

value: UC


title: mWTA Slide4 121522 DSP-1001660013726-B-D09

value: Ldlr-/- 3MR+Veh

tag: nuclei count


title: NIBD Colon Sample #13

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_136

description: miRNA profiling

value: Scc

value: male

tag: smoke habit

tag: # numer of metastatic sites

tag: # brain metastases

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: NSCLC Plasma_Exo-miRNA_sample_135

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: female

tag: treatment

value: no

tag: # liver metastases

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_130

description: miRNA profiling

tag: gender

value: yes


title: NSCLC Plasma_Exo-miRNA_sample_134

description: miRNA profiling

value: Former smoker


title: NSCLC Plasma_Exo-miRNA_sample_141

description: miRNA profiling

value: Current smoker

value: Nivolumab


title: NSCLC Plasma_Exo-miRNA_sample_133

description: miRNA profiling

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:missed


title: mWTA Slide4 121522 DSP-1001660013726-B-D07

value: brachiocephalic artery

tag: roi

tag: segment

value: media

tag: genotype

value: Ldlr-/- 3MR+GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_131

description: miRNA profiling

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: mWTA Slide4 121522 DSP-1001660013726-B-D08

tag: tissue

value: core

value: Ldlr-/- 3MR+Veh

tag: area area_(um^2)

tag: nuclei count


title: Inflamed Colonic UC smRNA sample #28

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NIBD Colon Sample #12

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_129

description: miRNA profiling

value: Adc

value: female

tag: smoke habit

tag: # numer of metastatic sites

tag: # brain metastases

value: no

value: yes

tag: performance status

tag: status at the best response (ed


title: NSCLC Plasma_Exo-miRNA_sample_128

description: miRNA profiling

tag: age

tag: histotype

value: Scc

value: male

value: Former smoker

tag: treatment

value: Nivolumab

tag: # liver metastases

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide4 121522 DSP-1001660013726-B-D05

value: brachiocephalic artery

tag: roi

tag: segment

value: cap

tag: genotype

value: Ldlr-/- 3MR+GCV

tag: Sex

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: mWTA Slide4 121522 DSP-1001660013726-B-D06

tag: tissue

value: core

tag: panel

tag: area area_(um^2)

tag: nuclei count


title: Inflamed Colonic UC smRNA sample #27

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_126

description: miRNA profiling

tag: gender

value: female

tag: smoke habit

tag: # numer of metastatic sites

tag: # brain metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Inflamed Colonic UC smRNA sample #26


title: NSCLC Plasma_Exo-miRNA_sample_125

description: miRNA profiling

tag: age

tag: histotype

value: Other

tag: treatment

value: no

tag: # liver metastases

value: yes

tag: status at the best response (ed


title: NIBD Colon Sample #11

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_132

description: miRNA profiling

value: Current smoker

value: Nivolumab

tag: # prior lines of treatment


title: Inflamed Colonic UC smRNA sample #29

tag: tissue


title: mWTA Slide4 121522 DSP-1001660013726-B-D04

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

tag: genotype

tag: Sex

tag: panel


title: NSCLC Plasma_Exo-miRNA_sample_123

description: miRNA profiling

value: Adc

tag: gender

value: male

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_124

description: miRNA profiling

tag: smoke habit

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: mWTA Slide2 121522 DSP-1001660013726-B-D02

value: core

value: Ldlr-/- 3MR+GCV

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_121

description: miRNA profiling

value: Scc

value: female

value: Former smoker

tag: # numer of metastatic sites

tag: # brain metastases

tag: performance status


title: Inflamed Colonic UC smRNA sample #25

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: mWTA Slide2 121522 DSP-1001660013726-B-D03

value: cap


title: NSCLC Plasma_Exo-miRNA_sample_127

description: miRNA profiling

tag: age

tag: histotype

tag: treatment

value: Nivolumab

value: no

tag: # liver metastases

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: mWTA Slide2 121522 DSP-1001660013726-B-D01

tag: tissue

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

tag: genotype


title: NIBD Colon Sample #10

value: NIBD


title: Non-inflamed Colonic UC smRNA sample #27

value: Non-Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_117

description: miRNA profiling

value: Adc

tag: gender

tag: smoke habit

value: Current smoker

tag: # prior lines of treatment


title: NSCLC Plasma_Exo-miRNA_sample_112

description: miRNA profiling

value: male

tag: # numer of metastatic sites


title: mWTA Slide2 121522 DSP-1001660013726-B-C12

value: media

value: Ldlr-/- 3MR+GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_113

description: miRNA profiling

tag: age

value: female

tag: # brain metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: NSCLC Plasma_Exo-miRNA_sample_114

description: miRNA profiling

tag: histotype

tag: treatment

tag: # liver metastases


title: NSCLC Plasma_Exo-miRNA_sample_111

description: miRNA profiling

value: Former smoker

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:missed


title: NIBD Colon Sample #9

tag: tissue

value: Colon Tissue

tag: inflammation

tag: disease status


title: NSCLC Plasma_Exo-miRNA_sample_110

description: miRNA profiling

tag: gender

tag: smoke habit

value: Nivolumab

value: no

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Inflamed Colonic UC smRNA sample #24

value: Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_119

description: miRNA profiling

value: Adc

tag: # numer of metastatic sites

tag: # prior lines of treatment


title: NSCLC Plasma_Exo-miRNA_sample_108

description: miRNA profiling

value: Current smoker


title: NSCLC Plasma_Exo-miRNA_sample_120

description: miRNA profiling

value: Other

value: male

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_115

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_109

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_105

description: miRNA profiling

value: Scc

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide2 121522 DSP-1001660013726-B-C10

value: brachiocephalic artery

tag: roi

tag: segment

value: core

tag: genotype

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_107

description: miRNA profiling

tag: age

value: Nivolumab

tag: # brain metastases

value: yes

tag: performance status


title: NSCLC Plasma_Exo-miRNA_sample_106

description: miRNA profiling

tag: histotype

value: female

value: Former smoker

tag: treatment

value: no

tag: # liver metastases


title: Inflamed Colonic UC smRNA sample #22

tag: tissue

value: Colon Tissue

tag: inflammation

value: Inflamed

value: UC


title: Inflamed Colonic UC smRNA sample #23

tag: disease status


title: mWTA Slide2 121522 DSP-1001660013726-B-C08

value: media

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_103

description: miRNA profiling

value: Adc

tag: gender

value: male

tag: smoke habit

tag: # numer of metastatic sites

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: mWTA Slide2 121522 DSP-1001660013726-B-C07

value: brachiocephalic artery

tag: roi

tag: segment

tag: genotype

tag: Sex

tag: panel


title: NIBD Colon Sample #8

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_104

description: miRNA profiling

tag: age

tag: histotype

value: Scc

tag: treatment

tag: # brain metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_99

description: miRNA profiling

value: Current smoker

tag: # liver metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Non-inflamed Colonic UC smRNA sample #26

tag: tissue

tag: inflammation

value: Non-Inflamed

tag: disease status


title: NSCLC Plasma_Exo-miRNA_sample_102

description: miRNA profiling

tag: gender

tag: smoke habit

value: Nivolumab

tag: # numer of metastatic sites

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: mWTA Slide2 121522 DSP-1001660013726-B-C06

tag: roi

value: cap

value: Ldlr-/- +GCV

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_98

description: miRNA profiling

value: no

tag: # prior lines of treatment

tag: status at the best response (ed


title: mWTA Slide2 121522 DSP-1001660013726-B-C11

tag: segment

value: normal wall

tag: genotype

tag: Sex

tag: panel


title: Inflamed Colonic UC smRNA sample #21

value: Colon Tissue

value: Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_97

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: female

value: Former smoker

tag: treatment

tag: # brain metastases

tag: performance status


title: mWTA Slide2 121522 DSP-1001660013726-B-C05

tag: tissue

value: brachiocephalic artery


title: NSCLC Plasma_Exo-miRNA_sample_96

description: miRNA profiling

value: Scc

tag: gender

value: male

tag: smoke habit

tag: # liver metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: Non-inflamed Colonic UC smRNA sample #25

tag: inflammation

value: Non-Inflamed

tag: disease status


title: NSCLC Plasma_Exo-miRNA_sample_95

description: miRNA profiling

value: Other

value: Current smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_94

description: miRNA profiling

value: no

value: yes

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: mWTA Slide2 121522 DSP-1001660013726-B-C09

tag: roi

tag: segment

value: cap

tag: genotype

value: Ldlr-/- +GCV

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_93

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: female

value: Former smoker

tag: treatment


title: mWTA Slide2 121522 DSP-1001660013726-B-C03

tag: tissue

value: brachiocephalic artery

value: media

tag: Sex

tag: panel


title: mWTA Slide7 121522 DSP-1001660013726-B-C02

value: Ldlr-/- 3MR+GCV


title: mWTA Slide2 121522 DSP-1001660013726-B-C04


title: Non-inflamed Colonic UC smRNA sample #24

value: Colon Tissue

value: Non-Inflamed

value: UC


title: mWTA Slide7 121522 DSP-1001660013726-B-C01

value: Ldlr-/- 3MR+Veh


title: mWTA Slide7 121522 DSP-1001660013726-B-B12

value: core


title: NIBD Colon Sample #7

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_92

description: miRNA profiling

value: Scc

tag: gender

tag: smoke habit

value: Current smoker

value: Nivolumab

tag: # brain metastases

value: no

tag: # liver metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Inflamed Colonic UC smRNA sample #20

tag: inflammation

value: Inflamed

tag: disease status


title: Inflamed Colonic UC smRNA sample #19


title: Inflamed Colonic UC smRNA sample #18


title: mWTA Slide7 121522 DSP-1001660013726-B-B11

tag: roi

tag: segment

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: NSCLC Plasma_Exo-miRNA_sample_90

description: miRNA profiling

value: Adc

value: male

value: Former smoker

tag: # numer of metastatic sites

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NSCLC Plasma_Exo-miRNA_sample_89

description: miRNA profiling

tag: age

tag: histotype

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_91

description: miRNA profiling

tag: treatment

value: yes


title: NIBD Colon Sample #6

tag: tissue

value: Colon Tissue


title: NSCLC Plasma_Exo-miRNA_sample_82

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_86

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_88

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_85

description: miRNA profiling


title: Non-inflamed Colonic UC smRNA sample #23

value: Non-Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_81

description: miRNA profiling


title: NSCLC Plasma_Exo-miRNA_sample_78

description: miRNA profiling


title: mWTA Slide7 121522 DSP-1001660013726-B-B10

value: brachiocephalic artery

value: core

tag: genotype

value: Ldlr-/- 3MR+GCV

tag: Sex

tag: panel

tag: area area_(um^2)

tag: nuclei count


title: mWTA Slide7 121522 DSP-1001660013726-B-B09

value: media


title: NSCLC Plasma_Exo-miRNA_sample_80

description: miRNA profiling

value: Scc

tag: gender

tag: smoke habit

value: Nivolumab

tag: # brain metastases

value: no

tag: # liver metastases

tag: performance status


title: NSCLC Plasma_Exo-miRNA_sample_77

description: miRNA profiling

tag: # numer of metastatic sites

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: Inflamed Colonic UC smRNA sample #17

tag: inflammation

value: Inflamed

tag: disease status


title: mWTA Slide7 121522 DSP-1001660013726-B-B08

tag: roi

tag: segment

value: cap

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: Non-inflamed Colonic UC smRNA sample #22


title: NSCLC Plasma_Exo-miRNA_sample_83

description: miRNA profiling

tag: age

tag: histotype

value: male

value: Former smoker

tag: treatment

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NIBD Colon Sample #5

tag: tissue

value: Colon Tissue

value: NIBD


title: mWTA Slide7 121522 DSP-1001660013726-B-B06

value: brachiocephalic artery

tag: genotype

tag: Sex

tag: panel

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_76

description: miRNA profiling

tag: gender

tag: smoke habit

tag: # brain metastases

tag: # liver metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Non-inflamed Colonic UC smRNA sample #21

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_75

description: miRNA profiling

tag: age

tag: histotype

value: Adc

tag: # numer of metastatic sites

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide7 121522 DSP-1001660013726-B-B07

tag: roi

tag: segment

value: normal wall

value: Ldlr-/- 3MR+GCV


title: NSCLC Plasma_Exo-miRNA_sample_73

description: miRNA profiling

value: Scc

tag: treatment

value: Nivolumab

value: no

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_74

description: miRNA profiling

value: male

value: Current smoker

value: yes


title: mWTA Slide7 121522 DSP-1001660013726-B-B05

tag: tissue

value: core

tag: genotype

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)


title: NSCLC Plasma_Exo-miRNA_sample_84

description: miRNA profiling

value: Other

tag: gender

tag: smoke habit

value: Former smoker

tag: # brain metastases

tag: # liver metastases


title: Non-inflamed Colonic UC smRNA sample #20

value: Colon Tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_87

description: miRNA profiling

tag: age

tag: histotype

value: Adc

tag: # numer of metastatic sites

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: mWTA Slide7 121522 DSP-1001660013726-B-B04

value: brachiocephalic artery

tag: roi

tag: segment

value: normal wall

value: Ldlr-/- 3MR+GCV

tag: nuclei count


title: Inflamed Colonic UC smRNA sample #16

tag: tissue

value: Inflamed


title: Non-inflamed Colonic UC smRNA sample #19


title: mWTA Slide5 121522 DSP-1001660013726-B-B03

value: cap

tag: genotype

value: Ldlr-/- 3MR+Veh

tag: Sex


title: NSCLC Plasma_Exo-miRNA_sample_64

description: miRNA profiling

value: Scc

value: male

tag: treatment

value: Nivolumab

value: no

tag: # prior lines of treatment

tag: status at the best response (ed


title: NSCLC Plasma_Exo-miRNA_sample_63

description: miRNA profiling

tag: gender

tag: smoke habit

tag: # brain metastases


title: NSCLC Plasma_Exo-miRNA_sample_65

description: miRNA profiling

tag: # liver metastases


title: NSCLC Plasma_Exo-miRNA_sample_68

description: miRNA profiling

tag: age


title: NSCLC Plasma_Exo-miRNA_sample_69

description: miRNA profiling

tag: histotype

value: Current smoker

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NSCLC Plasma_Exo-miRNA_sample_67

description: miRNA profiling

value: Former smoker

tag: # numer of metastatic sites

value: yes


title: Non-inflamed Colonic UC smRNA sample #18

value: Colon Tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_62

description: miRNA profiling

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_71

description: miRNA profiling

value: female

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_72

description: miRNA profiling


title: mWTA Slide5 121522 DSP-1001660013726-B-B01

value: brachiocephalic artery

tag: roi

tag: segment

value: core

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: mWTA Slide5 121522 DSP-1001660013726-B-B02

tag: tissue

value: normal wall

tag: genotype

value: Ldlr-/- 3MR+Veh

tag: Sex


title: NSCLC Plasma_Exo-miRNA_sample_61

description: miRNA profiling

value: Scc

tag: gender

value: male

tag: smoke habit

tag: treatment

value: Nivolumab

value: no

tag: # prior lines of treatment

tag: status at the best response (ed


title: Non-inflamed Colonic UC smRNA sample #17


title: mWTA Slide5 121522 DSP-1001660013726-B-A12

value: media


title: NSCLC Plasma_Exo-miRNA_sample_60

description: miRNA profiling

tag: age

tag: histotype

value: Never smoker

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Non-inflamed Colonic UC smRNA sample #16

value: Colon Tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: mWTA Slide5 121522 DSP-1001660013726-B-A11

tag: roi

tag: segment

tag: panel

tag: area area_(um^2)


title: NSCLC Plasma_Exo-miRNA_sample_59

description: miRNA profiling

value: Former smoker

value: yes

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Non-inflamed Colonic UC smRNA sample #14

tag: tissue


title: mWTA Slide5 121522 DSP-1001660013726-B-A10

value: brachiocephalic artery

value: cap

tag: genotype

tag: Sex

value: Female

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_58

description: miRNA profiling

value: Adc

tag: gender

tag: smoke habit

tag: treatment

tag: # prior lines of treatment

tag: status at the best response (ed


title: NSCLC Plasma_Exo-miRNA_sample_57

description: miRNA profiling

tag: age

tag: histotype

value: female

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_55

description: miRNA profiling

value: Current smoker

value: Nivolumab


title: mWTA Slide5 121522 DSP-1001660013726-B-A09

tag: roi

tag: segment

value: media

value: Ldlr-/- 3MR+GCV

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: mWTA Slide5 121522 DSP-1001660013726-B-A08

tag: tissue

tag: area area_(um^2)


title: Non-inflamed Colonic UC smRNA sample #13

value: Colon Tissue

tag: inflammation

tag: disease status


title: NSCLC Plasma_Exo-miRNA_sample_54

description: miRNA profiling

tag: gender

value: male

value: no

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_52

description: miRNA profiling

tag: smoke habit

value: Former smoker

tag: treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Inflamed Colonic UC smRNA sample #15

value: Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_53

description: miRNA profiling

value: yes

tag: # prior lines of treatment

tag: status at the best response (ed


title: NIBD Colon Sample #4

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_56

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: mWTA Slide5 121522 DSP-1001660013726-B-A05

value: brachiocephalic artery

value: cap

tag: genotype

tag: Sex

value: Female

tag: nuclei count


title: Non-inflamed Colonic UC smRNA sample #15

value: Non-Inflamed


title: Non-inflamed Colonic UC smRNA sample #12


title: NSCLC Plasma_Exo-miRNA_sample_50

description: miRNA profiling

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases


title: mWTA Slide5 121522 DSP-1001660013726-B-A07

tag: tissue

tag: roi

tag: segment

value: core

value: Ldlr-/- 3MR+GCV

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)


title: mWTA Slide5 121522 DSP-1001660013726-B-A06

value: normal wall

value: Ldlr-/- 3MR+Veh


title: NSCLC Plasma_Exo-miRNA_sample_44

description: miRNA profiling

tag: gender

value: male

tag: smoke habit

value: Former smoker

value: no

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_48

description: miRNA profiling

value: Current smoker

tag: treatment

value: yes

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_47

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: Inflamed Colonic UC smRNA sample #14

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_46

description: miRNA profiling

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases


title: NSCLC Plasma_Exo-miRNA_sample_43

description: miRNA profiling

value: female

tag: # liver metastases


title: mWTA Slide5 121522 DSP-1001660013726-B-A04

tag: tissue

value: brachiocephalic artery

tag: roi

value: core

tag: genotype

value: Ldlr-/- 3MR+GCV

tag: Sex

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_sample_40

description: miRNA profiling

tag: gender

value: male

tag: smoke habit

value: no


title: NSCLC Plasma_Exo-miRNA_sample_51

description: miRNA profiling

value: Current smoker

tag: treatment

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: mWTA Slide5 121522 DSP-1001660013726-B-A03

tag: segment

value: media

tag: panel

tag: area area_(um^2)


title: NSCLC Plasma_Exo-miRNA_sample_45

description: miRNA profiling

tag: age

tag: histotype

value: Adc

tag: # prior lines of treatment

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_38

description: miRNA profiling

value: Former smoker

tag: # numer of metastatic sites

tag: # brain metastases

value: yes

tag: # liver metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_39

description: miRNA profiling

value: Nivolumab

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NSCLC Plasma_Exo-miRNA_sample_37

description: miRNA profiling


title: no template control DSP-1001660013726-B-A01

source_name: no template control

tag: tissue

value: no template control

tag: genotype


title: Non-inflamed Colonic UC smRNA sample #11

value: Colon Tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: Inflamed Colonic UC smRNA sample #13

value: Inflamed


title: mWTA Slide5 121522 DSP-1001660013726-B-A02

value: brachiocephalic artery

tag: roi

value: normal wall

value: Ldlr-/- 3MR+GCV

tag: Sex

value: Female

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: nuclei count


title: Wild type progenitor exhausted CD8+ T cells, replicate 2, ATACseq

city: Boston

first: Amy

last: Huang

state: MA

address: 25 Shattuck St

department: Immunology

institute: Harvard Medical School

description:
ProgExh_WT_2
NormCountsATAC.txt

library_source: genomic

data_processing:
Raw fastq files were downloaded from Illumina BaseSpace and merged across lanes
Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:30 CROP:35.
Trimmed reads were aligned to mm10 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000.
Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed.
Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3.1) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix.
Normalization and differential expression were performed using DESeq2 (v 1.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each sample at each peak
Supplementary files format and content: TDF files for each sample
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts

molecule: genomic DNA

source_name: Spleen

extract_protocol:
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.

tag: cell type

value: CD8+ T cells

tag: cell state

value: progenitor exhausted

value: Spleen

tag: strain

value: 8-15 weeks old

tag: sequencing batch

value: batch 1 and batch 2

value: Wild type


title: NIBD Colon Sample #2

value: NIBD


title: Wild type terminally exhausted CD8+ T cells, replicate 2, ATACseq

description:
TermExh_WT_2
NormCountsATAC.txt

value: terminally exhausted

tag: age


title: NSCLC Plasma_Exo-miRNA_sample_42

description: miRNA profiling

tag: histotype

value: Adc

tag: gender

value: female

tag: smoke habit

value: Former smoker

tag: treatment

value: Nivolumab

value: no

tag: # prior lines of treatment

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_33

description: miRNA profiling

value: Never smoker

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

value: yes

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: NSCLC Plasma_Exo-miRNA_sample_34

description: miRNA profiling

value: Current smoker

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NIBD Colon Sample #3

tag: tissue

value: Colon Tissue

tag: inflammation

tag: disease status


title: Wild type progenitor exhausted CD8+ T cells, replicate 1, ATACseq

description:
ProgExh_WT_1
NormCountsATAC.txt

tag: cell type

value: CD8+ T cells

tag: cell state

value: progenitor exhausted

value: Spleen

value: 8-15 weeks old

tag: genotype


title: NSCLC Plasma_Exo-miRNA_sample_35

description: miRNA profiling

tag: age


title: NSCLC Plasma_Exo-miRNA_sample_31

description: miRNA profiling

tag: histotype

value: male


title: Non-inflamed Colonic UC smRNA sample #9

value: Non-Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_41

description: miRNA profiling

value: Adc

tag: gender


title: NIBD Colon Sample #1

value: NIBD


title: NSCLC Plasma_Exo-miRNA_sample_30

description: miRNA profiling

tag: smoke habit

value: Nivolumab

value: no


title: NSCLC Plasma_Exo-miRNA_sample_29

description: miRNA profiling

value: female

tag: treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: Non-inflamed Colonic UC smRNA sample #10


title: NSCLC Plasma_Exo-miRNA_sample_28

description: miRNA profiling

value: Former smoker

tag: # prior lines of treatment


title: Wild type terminally exhausted CD8+ T cells, replicate 1, ATACseq

description:
TermExh_WT_1
NormCountsATAC.txt

value: terminally exhausted

tag: strain

tag: sequencing batch

value: batch 1 and batch 2

value: Wild type


title: Inflamed Colonic UC smRNA sample #12

value: Colon Tissue

value: Inflamed


title: Non-inflamed Colonic UC smRNA sample #8


title: NSCLC Plasma_Exo-miRNA_sample_23

description: miRNA profiling

tag: # numer of metastatic sites

tag: # brain metastases

value: yes

tag: performance status


title: NSCLC Plasma_Exo-miRNA_sample_36

description: miRNA profiling

tag: # liver metastases

tag: status at the best response (ed


title: PD-1 KO progenitor exhausted CD8+ T cells, replicate 2, ATACseq

description:
ProgExh_KO_2
NormCountsATAC.txt

value: CD8+ T cells

value: progenitor exhausted

tag: tissue

value: Spleen

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz

value: 8-15 weeks old

value: PD-1 KO


title: HCT116_NoLoop_Auxin_CaptureMicroC_Rep1

city: PARIS

first: Christophe

last: Zimmer

address: 25-28 rue du docteur Roux

department: Computational Biology

country: France

institute: Institut Pasteur

data_processing:
Raw sequencing data from BGI was checked by FastQC82 (FastQC v0.12.1). All sequencing samples were "hard trimmed" to a 50 bp length via Trim Galore (Cutadapt version 0.6.10). Next, valid Micro-C contacts were obtained with the HiC-Pro pipeline (HiC-Pro_v3.1.0). HiC-Pro uses Bowtie2 to map the reads to the chosen genome. All valid Micro-C contact pairs obtained from HiC-Pro were filtered for the corresponding region of interest and then processed via the Cooler package.
Assembly: hg19
Supplementary files format and content: .mcool file: multi-resolution cool file containing all valid Capture Micro-C pairs.
Library strategy: Capture Micro-C

growth_protocol: HCT116 cells were cultured in McCoy’s medium supplemented with GlutaMAX, 10% Fetal Bovine Serum and Penicillin-Streptomycin. Cells were grown at 37°C in a humidified incubator with 5% CO2 and split every 2-3 days. Cells were tested monthly for the presence of Mycoplasma spp., Ureaplasma spp. and A. laidlawii by qPCR

extract_protocol:
Cells were aliquoted between 1.2 to 2 x 10⁶ cells in individual Eppendorf tubes. Aliquots were spun down and washed in PBS. The supernatant was carefully removed and discarded. Cell pellets were stored at -80°C for at least a day. Pre-freezing is required to get an optimal MNase digestion profile.
Cell pellets were thawed at room temperature and then processed as prescribed by the Micro-C protocol (Dovetail). For the end repair steps, we used the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) instead of the Dovetail kit. After adapter ligation with the NEB kit, DNA was purified via SPRI beads (Beckman A63880) as described in the Dovetail kit. Ligation capture and library amplification was performed with reagents from the Dovetail kit, except for the sequence index which was taken from the NEB kit. After verifying that libraries had a correct concentration and size distribution, we continued with the Agilent SureSelectXT HS2 Kit. Capture probe design was performed by Agilent. The coordinates of capture probes were: chr8:60,458,500-61,587,500 for L1 and No Loop loci, chr2:235,182,500-236,297,500 for L2 and chr1:36,700,000-38,175,000 for T1. . We sequenced with BGI Illumina 100-bp paired-end sequencing (PE100).

treatment_protocol: Cells were treated or not with 500 𝞵M auxin for 3 hours.

tag: cell line

tag: cell type

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; NoLoop locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;

value: 3 hours 500 𝞵M auxin


title: Inflamed Colonic UC smRNA sample #11

tag: inflammation

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_27

description: miRNA profiling

tag: age

tag: histotype

value: Adc

value: female

value: Former smoker

value: Nivolumab

value: no

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: NSCLC Plasma_Exo-miRNA_sample_26

description: miRNA profiling

tag: gender

tag: smoke habit

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: NSCLC Plasma_Exo-miRNA_sample_24

description: miRNA profiling

value: Never smoker

tag: treatment

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_25

description: miRNA profiling


title: HCT116_NoLoop_NoAuxin_CaptureMicroC_Rep1

tag: genotype


title: PD-1 KO progenitor exhausted CD8+ T cells, replicate 1, ATACseq

description:
ProgExh_KO_1
NormCountsATAC.txt

value: CD8+ T cells

tag: cell state

value: progenitor exhausted

value: Spleen

tag: strain

tag: sequencing batch

value: batch 3


title: PD-1 KO terminally exhausted CD8+ T cells, replicate 2, ATACseq

description:
TermExh_KO_2
NormCountsATAC.txt

value: terminally exhausted

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz

value: 8-15 weeks old

value: PD-1 KO


title: Inflamed Colonic UC smRNA sample #10

value: Colon Tissue

value: Inflamed

value: UC


title: HCT116_T1_Auxin_CaptureMicroC_Rep2

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; T1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;

value: 3 hours 500 𝞵M auxin


title: NSCLC Plasma_Exo-miRNA_sample_22

description: miRNA profiling

value: Other

value: male

value: Former smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

value: no

tag: # liver metastases

value: yes

tag: performance status


title: NSCLC Plasma_Exo-miRNA_sample_21

description: miRNA profiling

value: Adc

value: female

value: Never smoker

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: PD-1 KO terminally exhausted CD8+ T cells, repilcate 1, ATACseq

description:
TermExh_KO_1
NormCountsATAC.txt

tag: cell type

value: CD8+ T cells

value: terminally exhausted

tag: tissue

value: Spleen

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz

value: 8-15 weeks old

value: batch 3

value: PD-1 KO


title: Inflamed Colonic UC smRNA sample #9

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: Non-inflamed Colonic UC smRNA sample #7

value: Non-Inflamed


title: Pdcd1 EnhDel progenitor exhausted CD8+ T cells, replicate 2, ATACseq

description:
ProgExh_EnhDel_2
NormCountsATAC.txt

value: progenitor exhausted

tag: age

value: Pdcd1 enhancer deleted


title: HCT116_T1_NoAuxin_CaptureMicroC_Rep2

tag: cell line

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; T1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: NSCLC Plasma_Exo-miRNA_sample_19

description: miRNA profiling

tag: histotype

value: Adc

tag: gender

value: female

tag: smoke habit

value: Current smoker

tag: treatment

value: Nivolumab

value: no

value: yes


title: Pdcd1 EnhDel terminally exhausted CD8+ T cells, replicate 2, ATACseq

description:
TermExh_EnhDel_2
NormCountsATAC.txt

value: CD8+ T cells

tag: cell state

value: terminally exhausted

value: Spleen

tag: strain

value: 8-15 weeks old

tag: genotype


title: Non-inflamed Colonic UC smRNA sample #6

value: Colon Tissue


title: NSCLC Plasma_Exo-miRNA_sample_18

description: miRNA profiling

value: male

tag: # numer of metastatic sites

tag: # brain metastases

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: HCT116_T1_NoAuxin_CaptureMicroC_Rep1


title: Pdcd1 EnhDel progenitor exhausted CD8+ T cells, replicate 1, ATACseq

description:
ProgExh_EnhDel_1
NormCountsATAC.txt

value: progenitor exhausted

tag: sequencing batch

value: batch 1 and batch 2


title: NSCLC Plasma_Exo-miRNA_sample_17

description: miRNA profiling

value: Former smoker

tag: # liver metastases

tag: performance status

tag: status at the best response (ed

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: Non-inflamed Colonic UC smRNA sample #5

tag: tissue

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: Inflamed Colonic UC smRNA sample #8

value: Inflamed


title: Pdcd1 EnhDel terminally exhausted CD8+ T cells, replicate 1, ATACseq

description:
TermExh_EnhDel_1
NormCountsATAC.txt

tag: cell type

tag: age

value: Pdcd1 enhancer deleted


title: HCT116_L2_Auxin_CaptureMicroC_Rep1

tag: cell line

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; L2 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;

value: 3 hours 500 𝞵M auxin


title: NSCLC Plasma_Exo-miRNA_sample_16

description: miRNA profiling

tag: histotype

value: Adc

tag: gender

tag: smoke habit

value: Current smoker

tag: treatment

value: Nivolumab

value: no


title: Non-inflamed Colonic UC smRNA sample #4

value: Colon Tissue


title: HCT116_T1_Auxin_CaptureMicroC_Rep1

tag: genotype

value: AtAFB2-NLS Rad21-mAID-SNAP ; T1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: Inflamed Colonic UC smRNA sample #7


title: WT, CD8+ T cells, 2

description:
10x Genomics
NormCountscRNA.txt
W2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped tab-separated values files and matrix files
Supplementary files format and content: tab-delimited text file including log normalized counts for each cell generated using Seurat in R

extract_protocol:
After CD8+ T cells were isolated from spleen, cells were pooled into two samples (sample 1: 2 mice, sample 2: 3 mice). The following cells were then sorted: (1) live CD8b+ CD44+ GFP- CD45.1+, (2)  live CD8b+ CD44+ GFP- CD45.1+ CD45.2+, (3)  live CD8b+ CD44+ GFP- CD45.2+. Cells were counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 6,000 single cells per sample.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: CD8+ T cells

value: Spleen

tag: strain

value: 8-15 weeks old

value: WT


title: HCT116_L2_Auxin_CaptureMicroC_Rep2


title: WT, CD8+ T cells, 1

description:
10x Genomics
NormCountscRNA.txt
W1


title: NSCLC Plasma_Exo-miRNA_sample_14

description: miRNA profiling

value: male

tag: # numer of metastatic sites

tag: # brain metastases

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: HCT116_L1_Auxin_CaptureMicroC_Rep2

value: AtAFB2-NLS Rad21-mAID-SNAP ; L1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: HCT116_L2_NoAuxin_CaptureMicroC_Rep2


title: Non-inflamed Colonic UC smRNA sample #3

value: Non-Inflamed

value: UC


title: HCT116_L2_NoAuxin_CaptureMicroC_Rep1

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; L2 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: EnhDel, CD8+ T cells, 2

description:
10x Genomics
NormCountscRNA.txt
D2

value: EnhDel


title: EnhDel, CD8+ T cells, 1

description:
10x Genomics
NormCountscRNA.txt
D1


title: NSCLC Plasma_Exo-miRNA_sample_12

description: miRNA profiling

value: Adc

value: Current smoker

tag: # liver metastases

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: Inflamed Colonic UC smRNA sample #6

tag: tissue

value: Colon Tissue

value: Inflamed


title: HCT116_L1_Auxin_CaptureMicroC_Rep1

value: 3 hours 500 𝞵M auxin


title: NSCLC Plasma_Exo-miRNA_sample_11

description: miRNA profiling

value: Former smoker

value: Nivolumab

value: no

tag: status at the best response (ed


title: PD-1 KO, CD8+ T cells,  2

description:
10x Genomics
NormCountscRNA.txt
K2

value: CD8+ T cells

value: Spleen

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz

value: 8-15 weeks old

value: PD-1 KO


title: Non-inflamed Colonic UC smRNA sample #2

tag: inflammation

value: Non-Inflamed

tag: disease status

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_15

description: miRNA profiling

tag: age

value: male

value: Never smoker

value: yes

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: PD-1 KO, CD8+ T cells,  1

description:
10x Genomics
NormCountscRNA.txt
K1

tag: cell type


title: HCT116_L1_NoAuxin_CaptureMicroC_Rep1

tag: cell line

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; L1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: Non-inflamed Colonic UC smRNA sample #1

value: Colon Tissue


title: Inflamed Colonic UC smRNA sample #4

value: Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_9

description: miRNA profiling

tag: histotype

value: Adc

tag: gender

value: Former smoker

value: Nivolumab

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: NSCLC Plasma_Exo-miRNA_sample_66

description: miRNA profiling

value: Scc

tag: smoke habit

tag: treatment

value: no


title: NSCLC Plasma_Exo-miRNA_sample_13

description: miRNA profiling

value: female


title: PPIA_IgG

city: Shanghai

first: He

last: Zhang

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

data_processing:
Reads were trimmed using SOAPnuke
Raw reads were aligned to the reference genome (GRCh38) using HISAT2
Read counts were calculated using StringTie
Differentially expressed genes were analyzed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene-level read counts for each Sample
Library strategy: ChIP-seq&Triplex-seq

source_name: stomach

growth_protocol: AGS cells were cultured in DMEM (GIBCO).All media were supplemented with 10% FBS (GIBCO), 1% penicillin/streptomycin (GIBCO). All cells were incubated at 37℃ and 5% CO2.

extract_protocol:
Transfection, incubation, pull down, and purification are performed according to manufacturer's instructions.
The ends of the double-stranded DNA are flattened and phosphorylated at the 5' end, and a sticky end extending an "A" from the 3' end is attached to a bulbous joint extending a "T" from the 3' end. The linked products were amplified by PCR with specific primers, and the PCR products were thermal-denatured to single strand, and the single strand DNA was looped by bridging primers to obtain a single strand circular DNA library. The built libraries are checked for quality and sorted after passing the tests.

value: stomach

value: AGS

value: The AGS cell line was derived from fragments of a tumor resected from a patient who had received no prior therapy.

tag: genotype

value: negative control

value: IgG antibody


title: PPIA

value: PPIA antibody


title: Inflamed Colonic UC smRNA sample #3

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_8

description: miRNA profiling

value: male

value: Current smoker

tag: # numer of metastatic sites

value: yes


title: NSCLC Plasma_Exo-miRNA_sample_7

description: miRNA profiling

value: Adc

value: Never smoker

tag: # brain metastases

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: lacz

value: lacz probe


title: Inflamed Colonic UC smRNA sample #2

value: Colon Tissue

value: Inflamed


title: NSCLC Plasma_Exo-miRNA_sample_5

description: miRNA profiling

value: Former smoker

value: Nivolumab

value: no

tag: # prior lines of treatment

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: HCT116_L1_NoAuxin_CaptureMicroC_Rep2

value: Human colon cancer

value: AtAFB2-NLS Rad21-mAID-SNAP ; L1 locus TetOx96 CuOx150 ; TetR-FLAG-GFP11x16-GB1-NLS HA-GB1-A206KGFP1_10-GB1-NLS V5-CymR-NLS-2xHalo ;


title: GAU1

value: stomach

value: AGS

value: The AGS cell line was derived from fragments of a tumor resected from a patient who had received no prior therapy.

value: negative control

value: GAU1 probe


title: NSCLC Plasma_Exo-miRNA_sample_10

description: miRNA profiling

value: Adc

value: female

value: yes

tag: # liver metastases


title: NSCLC Plasma_Exo-miRNA_sample_6

description: miRNA profiling

value: male

value: Never smoker

tag: performance status

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Progression of disease


title: Inflamed Colonic UC smRNA sample #5

tag: tissue

value: Colon Tissue

value: Inflamed

value: UC


title: NSCLC Plasma_Exo-miRNA_sample_4

description: miRNA profiling

value: Current smoker

value: Nivolumab

value: no

tag: status at the best response (ed


title: Inflamed Colonic UC smRNA sample #1

tag: inflammation


title: RAW 264.7 cells, LPS plus calycosin,  bio rep 3

city: Luzhou

first: Honglian

last: Wang

state: Sichuan

address: No. 182, Chunhui Road, Longmatan District

department: Research Center for Integrative Medicine

institute: the Affiliated Traditional Medicine Hospital of Southwest Medical University

data_processing:
Raw sequencing reads were filtered by Trimmomatic 0.36 software.
The clean reads were aligned to the mouse genome by HISAT2 2.0 software.
Gene expression level represented as TPM (transcripts per million) was calculated by StringTie 1.3.3b software.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file includes raw count values for each sample
Supplementary files format and content: tab-delimited csv file includes TPM values for each sample

molecule: polyA RNA

growth_protocol: RAW 264.7 cells were cultured in DMEM (Gibco, Cat# 10569044, USA) supplemented with 10% fetal bovine serum (Gibco, Cat# 16000-044, USA) at the conditions of 37 °C, 5% CO2, and 100% humidity.

extract_protocol:
Total RNA was isolated with Trizol reagent. mRNA was enriched with poly-T oligo-attached magnetic beads
The sequencing library was prepared with the Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit (YEASEN, Cat# 12301ES96, China) following the manufacturer's instruction.

treatment_protocol: For group NC, the cells were treated with vehicle (solvent). For group LPS, the cells were stimulated with 300 ng/mL LPS for 6 hours. For group CA, the cells were pretreated with 100 ug/mL calycosin for 24 hours followed by stimulation with 300 ng/mL LPS for 6 hours.

value: macrophage

value: 100 ug/mL calycosin plus 300 ng/mL LPS-treated


title: HCT116, rep2

source_name: colon

value: colon

value: Colon cancer

value: p53 Wild-type


title: RAW 264.7 cells, LPS plus calycosin,  bio rep 2


title: HCT116, rep1


title: RAW 264.7 cells, LPS plus calycosin,  bio rep 1


title: NCI-H716, rep3

source_name: cecum

value: cecum

value: colorectal adenocarcinoma


title: NSCLC Plasma_Exo-miRNA_sample_3

description: miRNA profiling

value: Other

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Stable disease


title: mice_liver_150d_preS2 deletion_rep3

first: Shiliang

last: Cai

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression in liver of mice with preS2 deletion  was detected after 150 days

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The backgroup correction and scale normalization were performed by functions in the limma package.

label_protocol: Labeling was performed according to manufacturer's standard protocol.

extract_protocol: Total RNA was extracted from liver by Trizol (Invitrogen, Life Technologies, USA) method following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PreS fragments (WT/M1/M2/preS2 deletion) or Vector  were delivered into Fah deficient mice with Sleeping Beauty transposon system at 8-10 weeks of age . After 150 days, the mice were anesthetized with carbon dioxide and sacrificed. All the RNA from their liver or tumor are extracted for gene expression chips.

value: Liver tumor


title: RAW 264.7 cells, LPS,  bio rep 3

value: 300 ng/mL LPS-treated


title: mice_liver_150d_preS2 deletion_rep1

value: Fah deficient mice with Sleeping Beauty transposon system


title: NCI-H716, rep2


title: HCT116, rep3


title: NSCLC Plasma_Exo-miRNA_sample_2

description: miRNA profiling

value: Adc

value: male

value: yes

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Partial Response


title: RAW 264.7 cells, LPS,  bio rep 2


title: NSCLC Plasma_Exo-miRNA_sample_1

description: miRNA profiling

value: Former smoker

value: Nivolumab

value: no

value: Early Death; PD:Progression Disease; PR:Partial Response, SD:Stable Disease) Based on RECIST criteria:Early death


title: mice_liver_150d_preS2 deletion_rep2


title: NCI-H716, rep1


title: mice_liver_150d_M2_rep2

description: Gene expression in liver of mice with mutation 2  was detected after 150 days

source_name: mice,liver,150d,M2,replicate 2


title: mice_liver_150d_M2_rep3

source_name: mice,liver,150d,M2,replicate 3


title: RAW 264.7 cells, LPS,  bio rep 1

value: macrophage


title: HepG2-NTCP_HBV_siDDX5-17_N2

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

institute: INSERM U1052, UCBL1, ENS de Lyon

data_processing:
Raw reads were trimmed and filtered using fastp and quality controls were performed using fastqc.
Preprocessed reads were mapped using STAR against the Homo sapiens genome (hg19, GRCH37).
Mapping results were filtered, sorted and indexed using samtools.
Reads counts per genes were computed using htseq.
DESeq2 were used to compute differentially expressed human genes.
Assembly: GRCh37 (hg19)

source_name: HepG2-NTCP cells

growth_protocol: HepG2-NTCP cells were maintained in DMEM medium supplemented with 5 % Fetal calf serum and 1 % L-Glutamine

extract_protocol:
Total RNAs were extracted with RNAzol (MRC). 2 µg were used to prepare the library.
RNAs library were constructed using the the TruSeq Stranded Total RNA Library Prep Gold

treatment_protocol: 2 days prior to HBV infection, cells were cultured in DMEM medium supplemented with 5 % fetal calf serum, 1 % L-Glutamine and 2 % DMSO, Cells were then infected with HBV at MOI250, washed tree times the day after. 4 and 6 days post-infection, cells were transfected with 25 nM control siRNAs (siCTRL) or 25 nM siRNAs against DDX5 and DDX17 mRNAs, Cells were then harvested eight days post-infection.

value: HepG2-NTCP cells


title: RAW 264.7 cells, bio rep 3

value: vechicle-treated


title: mice_liver_150d_M2_rep1

source_name: mice,liver,150d,M2,replicate 1


title: mice_liver_150d_M1_rep3

description: Gene expression in liver of mice with mutation 1  was detected after 150 days

source_name: mice,liver,150d,M1,replicate 3


title: HepG2-NTCP_HBV_siCTRL_N1


title: RAW 264.7 cells, bio rep 2


title: HepG2-NTCP_HBV_siDDX5-17_N1


title: mice_liver_150d_M1_rep2

source_name: mice,liver,150d,M1,replicate 2


title: RAW 264.7 cells, bio rep 1


title: HepG2-NTCP_HBV_siCTRL_N2


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_G02_2

status: Public on Jul 27 2024

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: ChEC-SEQ with ARO80-MNase spike in for calibration

data_processing:
Demultiplexing with bcl2fastq.
Filtering of adapter dimers using cutadapt and picard.
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d).
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.txt files contain genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome.
Library strategy: ChEC-seq

organism: Saccharomyces cerevisiae BY4741

source_name: cultured yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose.

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

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

value: cultured yeast cells

tag: tf

tag: fusion

tag: loci

value: HO

tag: delta native tf

value: TRUE

tag: promoter

value: synthetic

tag: mnase loc

value: on TF


title: mice_liver_150d_M1_rep1

source_name: mice,liver,150d,M1,replicate 1

value: Liver tumor

value: Fah deficient mice with Sleeping Beauty transposon system


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F08_2

tag: cell type


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_G02_1


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_A08_1


title: Liver tissue 3_exposed without maternal cigarette smoke exposure_rep3.

city: Iksan

first: Daram

last: Yang

address: 79, Gobong-ro

country: South Korea

institute: Jeonbuk National University

description:
Gene expression data from offspring of mothers exposed to fresh air
Cont 3

hyb_protocol: Biotin-labeled sample were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the GeneChip® Scanner.

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
A total of 36,249 unprocessed miRNAs were detected through the miRNA 4.0 Array. Next, a pre-processing was performed to exclude Flag A, which indicates that the DABG (detection above background) of the probes for each miRNA was greater than the QC cut-off. As a result, 3,128 miRNAs were selected. Finally, 48 miRNAs that showed statistically significant differences between the CS0 and CS600 groups with FC values greater than 1.5 were selected.

source_name: Liver tissue_exposed without maternal cigarette smoke exposure

label_protocol: 1 ug total RNA using the FlashTag™ Biotin HSR RNA Labeling Kit.

extract_protocol: Total RNAs were isolated from liver tissues using a RiboEx and a Hybrid-R RNA purification kit.

tag: strain

value: liver

tag: gender

value: male

tag: age

value: 4 weeks old

tag: treatment


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_A08_2


title: Liver tissue 1_exposed with maternal cigarette smoke exposure_rep1.

description:
Gene expression data from offspring of mothers exposed to cigarette smoke (600 μg/L)
CS600 1

source_name: Liver tissue_exposed with maternal cigarette smoke exposure


title: Liver tissue 2_exposed with maternal cigarette smoke exposure_rep2.

description:
Gene expression data from offspring of mothers exposed to cigarette smoke (600 μg/L)
CS600 2


title: mice_liver_150d_WT_rep1

description: Gene expression in liver of mice with Wild type was detected after 150 days

source_name: mice,liver,150d,WT,replicate 1

value: Liver tissue

tag: genotype


title: Liver tissue 2_exposed without maternal cigarette smoke exposure_rep2.

description:
Gene expression data from offspring of mothers exposed to fresh air
Cont 2


title: Yap1DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F08_1


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_G11_1


title: mice_liver_150d_WT_rep2

source_name: mice,liver,150d,WT,replicate 2


title: mice_liver_150d_WT_rep3

source_name: mice,liver,150d,WT,replicate 3


title: Liver tissue 1_exposed without maternal cigarette smoke exposure_rep1.

description:
Gene expression data from offspring of mothers exposed to fresh air
Cont 1


title: Liver tissue 3_exposed with maternal cigarette smoke exposure_rep3.

description:
Gene expression data from offspring of mothers exposed to cigarette smoke (600 μg/L)
CS600 3


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F05_2


title: mice_liver_150d_Vector_rep2

description: Gene expression in liver of mice with vector was detected after 150 days

source_name: mice,liver,150d,Vector,replicate 2


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: mice_liver_150d_Vector_rep3

source_name: mice,liver,150d,Vector,replicate 3


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_G11_2


title: mice_liver_150d_Vector_rep1

source_name: mice,liver,150d,Vector,replicate 1


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_C08_1


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_H10_2


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_H10_1


title: Msn2DBD_Gcn4AD_TEF_aro80_3

value: FALSE


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_E01_1


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F05_1


title: Yap1DBD_Gal4AD_TEF_Mnase_HO_loc_del_native_loc_TF_C08_2


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_F05_2


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_F05_1


title: Yap1_Full_TEF_Mnase_HO_loc_del_native_loc_TF_E01_2


title: Msn2DBD_Gcn4AD_native_aro80_2

value: native


title: Msn2DBD_Gal4AD_TEF_aro80_2


title: Msn2DBD_Gal4AD_TEF_aro80_3


title: Msn2DBD_Gcn4AD_TEF_aro80_1


title: Msn2_Full_TEF_aro80_3


title: Msn2DBD_Gal4AD_TEF_aro80_1


title: Msn2DBD_Gcn4AD_TEF_aro80_2


title: Msn2DBD_Gal4AD_native_aro80_1


title: Msn2_Full_native_aro80_3


title: Msn2DBD_Gcn4AD_native_aro80_3


title: Msn2DBD_Gal4AD_native_aro80_2


title: Msn2_Full_TEF_aro80_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_H08_1


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_H08_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F12_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_B09_1


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_H11_2


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_B09_2


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Msn2DBD_Gal4AD_native_aro80_3


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_G11_1


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_G11_2


title: Msn2_Full_native_aro80_1


title: Msn2_Full_TEF_aro80_1


title: Msn2_Full_native_aro80_2


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_H11_1


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Mig3DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_H04_2


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_C02_2


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_F12_2


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_F12_1


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_F10_1


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Mig3DBD_Gcn4AD_TEF_Mnase_HO_loc_del_native_loc_TF_F12_1


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_B08_2


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_C02_1


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_B08_1


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate2_A02_2


title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate1_E02_2


title: Mig3_Full_lib_Mnase_HO_loc_del_native_loc_TF_F10_2


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_1


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title: Gcn4DBD_Gcn4AD_lib_Mnase_HO_loc_del_native_loc_TF_plate1_E02_1


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_TEF_2


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_F09_1


title: Gcn4DBD_Gal4AD_lib_Mnase_HO_loc_del_native_loc_TF_E06_2


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