title: p53_1__FOXJ1pos_Epithelium_sample266

description: Library name: DSP-1001660012748-E-D08


title: HGC27_CAF2_1

status: Public on Aug 01 2026

type: SRA

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

country: China

institute: Sichuan University

library_source: transcriptomic

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited txt file include TPM value for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: Epithelial cell

value: humangastric cancer

tag: treatment

value: Co-colture with CAF


title: Granny Val - Rep 1 -Layer 3

status: Public on Aug 03 2026

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

country: USA

institute: UNIVERSITY OF FLORIDA

description: Library name: G-1-3

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (Martin 2011) to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
Reads were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference; v2.7.9a) and the Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474; Park et al., 2022) was used as the reference genome.
Mapped reads were processed with HTSeq (v0.11.2) (Anders et al., 2015), SAMtools, and in-house scripts developed by the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida to remove PCR duplicates and count uniquely mapped reads.
Differential expression analysis was conducted using the R package, DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a log₂ fold change threshold of  ≥ 2 or ≤ –2 and adjusted p-values ≤ 0.05. KEGG enrichment analysis was performed using ShinyGO (Version 0.82, https://bioinformatics.sdstate.edu/go/). Transcription factor analysis was performed using the Plant Transcription Factor Database (PlantTFDB v5.0, https://planttfdb.gao-lab.org/). GO enrichment for candidate gene identification was performed using Panther’s Gene Ontology Resource (http://geneontology.org/). Predicted expression localization of candidates was performed using the University of Toronto’s eFP browser (https://bar.utoronto.ca/). All tools previously mentioned used the Vitis vinifera genome as a reference.
Assembly: Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Vitis rotundifolia

source_name: peel

extract_protocol:
Mature berries of ‘Alachua’, ‘Granny Val’, and ‘Supreme’ cultivars were harvested, and tissues were separated into four layers: epidermis/cuticle, hypodermis, mesocarp, and endocarp. Tissues were frozen in liquid nitrogen and stored at –80°C until further processing. Total RNA was isolated using the NucleoSpin RNA Plant and Fungi Kit (Macherey-Nagel, Hawthorne, NJ, USA), with a modified grinding step: 100–300 mg tissue was ground in 2 mL tubes with four 5-mm zirconia beads (Inframat Advanced Materials, Manchester, CT, USA) using a Mini-Beadbeater-96 (BioSpec Products, Bartlesville, OK, USA). RNA samples were treated with DNase using the PureLink™ DNase Kit (Invitrogen™, CA, USA) to remove residual DNA.
Total RNA  quality of sample was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Inc). 250 ng of total RNA was used for library construction using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol. First, 300 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide.

treatment_protocol: To assess relative skin thickness across muscadine cultivars, mature berries were harvested from 6 muscadine cultivars, 3 purple (‘Alachua’, ‘Paulk’, ‘Supreme’) and 3 green (‘Granny Val’, ‘Hall’, ‘Triumph’) from a research plot at the University of Florida Plant Science Research and Education Unit vineyard in Citra, Florida. Thirty berries per genotype were collected and transported to the postharvest laboratory in an icebox for dissection. Berry diameter was measured using ImageJ software.

tag: tissue

value: peel

value: Endocarp


title: HGC27_CAF1_3


title: RPMI8226_Water extract of Astragalus mongholicus Bunge (Low dose)_rep1

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample 2-2-7

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: RPMI8226 cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (500 ng) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced e MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. Cells were plated at a density of 5x105 cells / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: B lymphocyte

value: Water extract of Astragalus mongholicus Bunge 125 μg/mL

tag: time


title: p53_1__P53_Epithelium_sample263

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660012748-E-D05

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Fallopian tube, dysplastic lesion or invasive cancer

extract_protocol:
Tissue processing began with sectioning FFPE samples to a 5 μm thickness following the Nanostring GeoMx user manual (MAN-10132-04). After deparaffinization and rehydration, protein target retrieval was performed using Tris-EDTA antigen retrieval buffer for 20 minutes in a pressure cooker. RNA targets were retrieved through proteinase K digestion for 15 minutes at 37 °C. Tissues were then post-fixed in 10% NBF and hybridized overnight at 37 °C with RNA probes (Human Whole Transcriptome Atlas, containing 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Following hybridization, excess probes were removed by stringent washing at 37 °C and incubated in blocking buffer W (Nanostring LOT#:2-23020032). The tissue sections were subsequently stained with conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488) and p53 (Dako primary and secondary antibodies), along with CAPS (primary and secondary antibodies) and SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomic data acquisition, slides were analyzed on the GeoMx Digital Spatial Profiler (DSP) at 20× magnification. Regions of interest (ROIs) were identified based on immunofluorescence images with a pathologist's (AB) supervision and matched to regions selected in DVP. Following ROI selection, RNA probes were photocleaved using UV illumination within each ROI, and oligonucleotide barcodes were collected into a 96-well plate, allowing precise separation of tissue compartments.
Sequencing libraries were prepared using Illumina TruSeq technology for adaptor ligation and amplification. The amplified libraries underwent two rounds of Ampure XP magnetic bead cleanup (1.2:1 beads ratio) (HighPrep PCR from MAGBIO, Cat#: AC-60500). Purified libraries were sequenced on an Illumina NovaSeq flowcell PE50 at a depth of 100× per μm².

value: Epithelium

tag: cohort


title: p53_1__P53_Epithelium_sample264

description: Library name: DSP-1001660012748-E-D06

value: Fallopian tube, dysplastic lesion or invasive cancer


title: p53_1__P53_Epithelium_sample262

description: Library name: DSP-1001660012748-E-D04


title: MDA-MB-231, 2D, sample 3

city: Grand Forks

first: Colin

last: Combs

state: North Dakota

address: 1301 N Columbia Rd

department: Biomedical Sciences

institute: University of North Dakota

description: Library name: 231_2D_3

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000, and 35 million 150 bp paired-end reads were obtained per sample. Preliminary quality control analysis of fastq files was performed with FastQC v0.11.9.
Adapters were trimmed using Trimmomatic v0.39
Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Successfully mapped clean reads were assigned to genomic features using featureCounts in Rsubread v2.18.0
Differentially expressed genes between sample groups were determined using DESeq2 v1.44.0 with a significance threshold of <0.05 Benjamini-Hochberg adjusted p-value.
Assembly: Reads were aligned to a human genome (hg38) with HISAT2 v2.2.1 software.
Supplementary files format and content: tab-delimited text files including fpkm normalized count values for each sample in the matrix.

growth_protocol: The triple negative breast cancer cell line MDA-MB-231 and human THP-1 cells were obtained from ATCC (Manassas, VA, USA). Cells were maintained in D-MEM/F-12 medium (Gibco, Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Thermo Fisher Scientific Inc., MA, USA). The cells were incubated at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were washed in PBS and lysed using RNAzol RT according to the RNAzol® RT Column Kit (Molecular Research Center, Cincinnati, OH) protocol. Briefly, the lysate was mixed with water and centrifuged at 12,000×g to remove DNA and proteins. Lysate was then diluted at a 1:1 ratio with isopropanol and added to a column before another 12,000×g centrifugation. RNA was then washed twice with 100% ethanol to remove impurities. RNA was then eluted using RNase-free deionized water and stored at -80°C. Concentrations were measured using a Qubit 4 Fluorometer, and purity was checked using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Macrophage Differentiation and Polarization: THP-1 cells were stimulated with 100 nM phorbol-12-myristate 13-acetate (PMA) (Sigma-Aldrich, Saint Louis, MO, USA) in D-MEM/F-12 medium for 24 hours. Afterward, cells were activated for 24 hours into M1-like macrophages by treatment with 50ng/mL IFN-γ (R&D Systems Inc., Minneapolis, MN, USA) or into M2-like macrophages by treatment with 50ng/mL IL-4 (R&D Systems Inc., Minneapolis, MN, USA).  3D Co-cultured Spheroids: 10,000 MDA-MB-231 cells were seeded into each well of a Nunclon Sphera-treated U-shaped-bottom microplate (Thermo Fisher Scientific Inc., MA, USA). After 24 h, 5,000 polarized M1-like or M2-like macrophages were seeded into each well for co-cultures. Monocultures and co-cultures were incubated for another 4 days at 37 °C in a humidified incubator with 5% CO2 before analysis or drug treatment.

value: triple negative breast cancer cell line


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (High dose)_rep2

description: sample 3-2-5

growth_protocol: NK-92MI cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (500 ng) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

value: natural killer cell

value: Water extract of Astragalus mongholicus Bunge 500 μg/mL


title: p53_2__normal_Stroma_sample261

description: Library name: DSP-1001660012748-E-C11

value: Stroma

value: normal


title: HGC27_CAF1_2


title: RPMI8226_Water extract of Astragalus mongholicus Bunge (High dose)_rep3

description: sample 2-2-6


title: HGC27_CAF1_1


title: p53_2__normal_Stroma_sample260

description: Library name: DSP-1001660012748-E-C10


title: NK-92MI_Water extract of Astragalus mongholicus Bunge (High dose)_rep1

description: sample 3-2-4


title: H9_hESCs_sgRNActrl_D3

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

country: Canada

institute: CHU de Québec - Université Laval

description: Library name: Sample 4

data_processing:
Raw pod5 files were basecalled using Guppy v.6.5.7 using the super accurate basecalling settings.
Samples were demultiplexed according to barcodes with the guppy_barcoder software.
The resulting FASTQ reads were aligned to the GRCh38 human reference genome with Minimap2 version 2.24-r1122. Reads with MAPQ<13 were filtered out.
Aligned reads were quality-controlled with the NanoPlot software.
Strand for spliced transcripts were detemined using Minimap2's ts tag ("transcript strand"). As this tag is empty for mono-exonic transcripts, these were oriented with the pychopper software from nanoporetech's github. Stranded BAM files are provided as raw files (..._sup.XS_tag.bam files)
Read counts were performed using the Isoquant software v3.9.0, using the ENSEMBL human transcriptome v.113
Assembly: GRCh38
Supplementary files format and content: Processed_data_SNHG26_KD_hESCs.TPM.txt : Normalized per-gene read counts (in Transcripts per million, TPM) obtained with the Isoquant software. Annotation file used for this analysis was the ENSEMBL human GTF V113.

molecule: polyA RNA

growth_protocol: Primed hESCs line H9 (RRID: CVCL_9773) were routinely maintained in a humidified incubator at 37°C under 5% CO2. Cells were propagated in mTeSR™1 medium (StemCell Technologies #85850) on Geltrex™-coated plates (hESC-qualified, growth factor-reduced, ThermoFisher Scientific #A1413302). Medium was refreshed every day and hESCs were passaged every 4-5 days. For passaging, cells were washed with DPBS (ThermoFisher Scientific #14190250) and treated with Dispase (StemCell Technologies #07923) for 5 minutes. Then, Dispase was washed away using DMEM/F-12 (ThermoFisher Scientific #11330057) and cells were passaged as small clumps using a Corning™ Cell Lifter (Fisher Scientific #07-200-364) (usually 1/10 ratio). All cell lines were negative for mycoplasma. Human ESCs were obtained commercially, and all experiments pertaining to hESCs were approved by the Stem Cell Oversight Committee as outlined by Canadian Institutes of Health Research as per the Tri-Council Policy Statement: Ethical Conduct for Research Involving Humans (TCPS 2) and the Agreement on the Administration of Agency Grants and Awards by Research Institutions.

extract_protocol:
Cell lysates were homogenized with QIAshredder columns (Qiagen #79656) and total RNA was extracted using RNeasy Kit (Qiagen #74106) according to the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 Spectrophotometer (ThermoFisher #ND-2000C) and then DNase-treated using DNase I (ThermoFisher Scientific #EN0521) according to the manufacturer’s instructions. 300ng of DNase-treated and non-treated RNA were loaded onto a 1% Agarose A (Bio Basic #D0012) gel to verify the RNA integrity and purity. RNA was also quantified using the Qubit™ RNA Broad Range Kit (ThermoFisher Scientific #Q10210) on Qubit™ 4 Fluorometer (ThermoFisher Scientific #Q33238) according to the manufacturer’s instructions. RNA quality was further verified using an RNA 6000 Nano Kit (Agilent Technologies #5067-1511) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. Samples all had RNA integrity numbers of 9.5 or more.
Samples were processed with ONT's SQK-NBD114.24 kit using 50ng of total RNA, with each sample assigned to a specific barcode. Briefly, an oligo-dT primer (VNP, sequence: 5'-5phos/ACTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTVN-3' , where V=A, C, or G, and N=A, C, G, or T) was used to reverse-transcribe poly(A) RNA into cDNA with the Maxima H Minus RT (ThermoFisher Scientific). A Strand Switching Primer (SSP 5'-TTTCTGTTGGTGCTGATATTGCTmGmGmG-3' , where mG = 2' O-Methyl RNA bases) was used for strand switching during the RT reaction. Libraries were PCR amplified for 14 cycles with the NEBNext Ultra II Q5 Master Mix (NEB #M0544L). cDNA was quantified using the Qubit™ 1X dsDNA High Sensitivity Kit (ThermoFisher Scientific #Q33230) on Qubit™ 4 Fluorometer according to the manufacturer’s instructions and cDNA smear quality was verified using a DNA 12000 Kit (Agilent Technologies #5067-1508) on a 2100 Bioanalyzer instrument (Agilent Technologies #G2939B) according to the manufacturer’s instructions. The blunt DNA ends were prepared using the NEBNext Ultra II End Repair/dA-Tailing module (NEB), adding a 3' dA tail and phosphorylating the 5' end. Barcodes were ligated to the DNA fragments with a Blunt/TA ligase (NEB), barcoded samples were pooled and motor protein adapters were finally ligated with the NEBNext Quick Ligation Module (NEB). Purification of DNA between each step was performed with KAPA Hyperpure Beads (Roche). Library was loaded on a PromethION 2 Solo (ONT) sequencer using a R10.4.1 Flow Cell (ONT #FLO-PRO114M), and sequenced using the MinKNOW (v25.05.14) software.

treatment_protocol: Primed hESC lines were seeded at a density of 2.6 x 104 cells/cm2 on Geltrex™-coated plates (hESC-qualified, growth factor-reduced, ThermoFisher Scientific, #A1413302) in mTeSR™1 medium (StemCell Technologies, #85850) supplemented with 10µM Y-27632 (Tocris Bioscience #1254). The following day, medium was replaced by fresh mTeSR™1 medium and cells were co-transfected with 500ng of hyPBase transposase, 1µg of PB-TetO-AIO-dCas9-BFP-KRAB vector and 875ng of control or four SNHG26-specific pooled sgRNAs using Lipofectamine™ Stem Transfection Reagent (ThermoFisher Scientific #STEM00015) according to the manufacturer’s instructions. Cells were then selected with 500ng/mL puromycin (Bio Basic #PJ593) for 6 days. The hESCs were seeded prior to the knock-down on Geltrex™-coated plates (hESC-qualified, growth factor-reduced, ThermoFisher Scientific, #A1413302) in mTeSR™1 medium (StemCell Technologies, #85850). The knock-down was induced by adding 1 µg/mL doxycycline hyclate and ESCs were harvested after 2 or 3 days for RNA extraction.

value: hESC

tag: genotype

value: CRISPRi TetO dCas9 + control non-targeting guides

value: 3 days of DOX


title: p53_2__FOXJ1pos_Epithelium_sample259

description: Library name: DSP-1001660012748-E-C09


title: p53_2__FOXJ1neg_Epithelium_sample258

description: Library name: DSP-1001660012748-E-C08


title: HGC27_Ctrl_3

value: Epithelial cell

value: Control


title: H9_hESCs_sgRNActrl_D2

description: Library name: Sample 3

value: 2 days of DOX


title: p53_2__FOXJ1pos_Epithelium_sample257

description: Library name: DSP-1001660012748-E-C07


title: H9_hESCs_SNHG26_KD_D3

description: Library name: Sample 2

value: CRISPRi TetO dCas9 + SNHG26 target guides


title: HGC27_Ctrl_2

value: humangastric cancer


title: p53_2__FOXJ1pos_Epithelium_sample255

description: Library name: DSP-1001660012748-E-B12


title: p53_2__FOXJ1neg_Epithelium_sample256

description: Library name: DSP-1001660012748-E-C06


title: p53_2__FOXJ1neg_Epithelium_sample254

description: Library name: DSP-1001660012748-E-B11


title: HGC27_Ctrl_1


title: H9_hESCs_SNHG26_KD_D2

description: Library name: Sample 1


title: p53_2__P53_Epithelium_sample253

description: Library name: DSP-1001660012748-E-B10


title: BGC823_HOXCAS2_3

value: HOXC-AS2 Over Expression


title: Cardiac fibroblasts co-cultured with St8sia1-KO BMMCs, replicate 3

city: shanghai

first: Lisheng

last: Fu

address: No. 650, Xin Songjiang Road, Songjiang District, Shanghai

institute: shanghaijiaotong

description: Library name: KO_CF_3

data_processing:
Raw data processing: Raw reads underwent quality control and adapter trimming using fastp (v0.18.0).
Alignment (RNA-seq): Cleaned reads were aligned to the GRCm39/mm39 reference genome using HISAT2 (v2.4).
Alignment (ATAC-seq/CUT&Tag): Clean reads were aligned to the reference genome using BWA (for ATAC-seq) or Bowtie2 (for CUT&Tag).
Quantification (RNA-seq): Gene expression quantification and normalization were performed with RSEM (v1.3.3), with Transcripts Per Million (TPM) as the expression metric.
Peak Calling (ATAC-seq/CUT&Tag): Open chromatin regions (peaks) were identified for each sample using MACS2.
Assembly: GRCm39/mm39; Rattus norvegicus: rn6 (Rnor_6.0)
Supplementary files format and content: Processed data files are provided as bigWig files for genome browser visualization and as narrowPeak files for identified peaks (ATAC-seq and CUT&Tag). For RNA-seq, raw counts and TPM expression matrices are provided as tab-delimited text files.

organism: Rattus norvegicus

source_name: neonatal rat cardiac fibroblasts

growth_protocol: Bone marrow-derived mast cells (BMMCs) were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum, 4 mM L-glutamine, 0.5 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin, 0.1 mM nonessential amino acids, recombinant mouse IL-3 (10 ng/mL), recombinant SCF (10 ng/mL), and recombinant mouse IL-4 (1 ng/mL). The medium was refreshed weekly. NRCMs and cardiac fibroblasts were isolated from 1- to 3-day-old Sprague-Dawley rats.

extract_protocol:
For RNA-seq: Total RNA was extracted from frozen mouse ventricular tissue and cultured cells using RNAiso Plus (Takara). Extracted RNA underwent purification and on-column DNase digestion using the RNeasy Mini Kit (Qiagen) to eliminate genomic DNA. For ATAC-seq: BMMCs were collected, counted, and 50,000 cells were lysed to isolate nuclei. The nuclear pellet was then incubated with a fragmentation master mix containing Tn5 transposase at 37 °C for 30 minutes to tag and fragment open chromatin.For CUT&Tag: BMMCs were collected and nuclei were extracted. The nuclei were bound to ConA Beads and incubated with a primary antibody against H2A.Z (Abmart, Cat#PHB6100S) overnight at 4 °C. After secondary antibody incubation, a pA/G-Tn5 transposase complex was added and activated to fragment DNA.
For RNA-seq: Sequencing libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina. For ATAC-seq: The library was amplified for 14 cycles. A double-SPRI bead cleanup was performed to enrich for appropriately sized fragments. For CUT&Tag: The library was amplified in a 50 μL PCR reaction for 12 cycles

treatment_protocol: NRCMs and cardiac fibroblasts were co-cultured with WT or St8sia1-KO BMMCs (8 × 10³ cells/well) for 48 hours. After co-culture, non-adherent cells were removed by washing with PBS, and total RNA was extracted from the adherent cardiac cells.

value: neonatal rat cardiac fibroblasts

value: St8sia3-KO BMMCs (8×104/well, 48h)


title: STIL_3__FOXJ1pos_Epithelium_sample252

description: Library name: DSP-1001660012748-E-B09

value: Fallopian tube, dysplastic lesion or invasive cancer

value: Epithelium


title: STIL_3__FOXJ1neg_Epithelium_sample251

description: Library name: DSP-1001660012748-E-B08


title: STIL_3__STIL_Stroma_sample250

description: Library name: DSP-1001660012748-E-B07

value: STIL


title: unirradiated T cells, mouse 3

type: RNA

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The probe-level raw expression data were processed by Illumina Genome Studio v2011.1. The probe average signal intensities were background subtracted, log2 transformed and quantile normalized to adjust for technical variation. Then the data were filtered by detection p-value ≤ 0.01 for at least 19 samples and batch effects among slides were removed by ComBat program. Processed data were imported into Partek Genomics Suite (v6.6) for statistical analysis.

label: biotin

organism: Mus musculus

source_name: unirradiated T cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Tumors were established in 8-12 week old female C57BL/6 mice by s.c. injection of 1x106 MC38 cells.

extract_protocol: Intratumoral CD8 T cells were pre-enriched from tumor cell suspensions using Easy Sep mouse CD8a positive selection kit (StemCell). CD8-enriched samples were stained with anti-CD3-PEcy7 and anti-CD8-PE antibodies and CD3+CD8+ cells were sorted in Trizol LS (Invitrogen) using a FACS Aria (BD). RNA was extracted using Trizol method according to the manufacturer’s instructions.

treatment_protocol: When tumors had reached at least 500 mm3, groups of 4 mice were treated with whole body irradiation (WBI) doses of 1 Gy or 5 Gy, or left untreated.

value: CD8+T cells

tag: strain

tag: age

value: 8-12 week

value: Intratumoral T cells


title: BGC823_HOXCAS2_2


title: Cardiac fibroblasts co-cultured with St8sia1-KO BMMCs, replicate 2

description: Library name: KO_CF_2

value: St8sia2-KO BMMCs (8×104/well, 48h)


title: STIL_3__STIL_Epithelium_sample249

description: Library name: DSP-1001660012748-E-B06


title: BGC823_HOXCAS2_1


title: STIL_3__FOXJ1pos_Epithelium_sample248

description: Library name: DSP-1001660012748-E-B05


title: Cardiac fibroblasts co-cultured with St8sia1-KO BMMCs, replicate 1

description: Library name: KO_CF_1

value: St8sia1-KO BMMCs (8×104/well, 48h)


title: STIL_3__STIL_Epithelium_sample247

description: Library name: DSP-1001660012748-E-B03


title: BGC823_Ctrl_3


title: STIL_3__STIL_Epithelium_sample246

description: Library name: DSP-1001660012748-E-B01


title: C61+4 follow-up

city: Heidelberg

first: Fabienne Dorothea

last: Lusky

address: Röntgenstr. 1

country: Germany

institute: Thoraxklinik at Heidelberg University Hospital

hyb_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website

data_processing: For statistical analysis we used R and the bioconductor package simpleaffy and affy, we transformed our data using RMA Algorithm

source_name: Whole blood

extract_protocol: We used the  PAXgene Blood RNA Kit according to the manufacturer’s instructions (PreAnalytiX, Hombrechtikon, CH)

treatment_protocol: Whole blood RNA was collected in PAXGene blood RNA tubes and incubated at room temperature for 2 hours to maximize cell lysis. Samples were stored frozen at  -80°C until processing

tag: sample type

value: follow-up

tag: group


title: Cardiac fibroblasts co-cultured with WT BMMCs, replicate 3

description: Library name: WT_CF_3

value: WT BMMCs (8×104/well, 48h)


title: STIL_3__STIL_Epithelium_sample245

description: Library name: DSP-1001660012748-E-A12


title: BGC823_Ctrl_2

value: Epithelial cell

value: Control


title: STIL_3__STIL_Epithelium_sample244

description: Library name: DSP-1001660012748-E-A10


title: Cardiac fibroblasts co-cultured with WT BMMCs, replicate 2

description: Library name: WT_CF_2


title: STIL_3__STIL_Epithelium_sample243

description: Library name: DSP-1001660012748-E-A09


title: STIL_3__STIL_Epithelium_sample242

description: Library name: DSP-1001660012748-E-A06


title: Cardiac fibroblasts co-cultured with WT BMMCs, replicate 1

description: Library name: WT_CF_1


title: BGC823_Ctrl_1


title: STIL_3__STIL_Epithelium_sample241

description: Library name: DSP-1001660012748-E-A04


title: C0496

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: comma-delimited csv file include raw counts for each sample

source_name: stomach

extract_protocol:
Total RNA was extracted from 108 paired tumor and normal tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. No. 80204, Qiagen, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

tag: Sex

value: Female

value: Tumor

tag: diagnosis

value: Advanced Gastric Cancer (AGC)


title: STIL_3__STIL_Epithelium_sample240

description: Library name: DSP-1001660012748-E-A03


title: NRCMs co-cultured with St8sia1-KO BMMCs, replicate 3

description: Library name: KO_CM_3

source_name: neonatal rat cardiomyocytes

value: neonatal rat cardiomyocytes

value: St8sia3-KO BMMCs (8×104/well, 48h)


title: C0494


title: NRCMs co-cultured with St8sia1-KO BMMCs, replicate 2

description: Library name: KO_CM_2


title: HGSTIC_FT6__STIC_Stroma_sample238

description: Library name: DSP-1001660009343-C-H12

value: Fallopian tube, dysplastic lesion or invasive cancer

value: Stroma

value: STIC


title: C0491

value: Male


title: NRCMs co-cultured with St8sia1-KO BMMCs, replicate 1

description: Library name: KO_CM_1


title: STIL_3__STIL_Epithelium_sample239

description: Library name: DSP-1001660012748-E-A02

value: Epithelium

value: STIL


title: HGSTIC_FT6__STIC_Epithelium_sample235

description: Library name: DSP-1001660009343-C-H09


title: HGSTIC_FT6__STIC_Stroma_sample236

description: Library name: DSP-1001660009343-C-H10


title: C0447


title: HGSTIC_FT6__STIC_Epithelium_sample237

description: Library name: DSP-1001660009343-C-H11


title: HGSTIC_FT6__invasive_Epithelium_sample233

description: Library name: DSP-1001660009343-C-H07

value: invasive


title: NRCMs co-cultured with WT BMMCs, replicate 3

description: Library name: WT_CM_3


title: HGSTIC_FT6__invasive_Stroma_sample234

description: Library name: DSP-1001660009343-C-H08


title: C0443


title: HGSTIC_FT6__invasive_Stroma_sample232

description: Library name: DSP-1001660009343-C-H06


title: NRCMs co-cultured with WT BMMCs, replicate 2

description: Library name: WT_CM_2


title: HGSTIC_FT6__invasive_Epithelium_sample231

description: Library name: DSP-1001660009343-C-H05


title: C0441


title: HGSTIC_FT6__invasive_Stroma_sample230

description: Library name: DSP-1001660009343-C-H04


title: HGSTIC_FT6__invasive_Epithelium_sample229

description: Library name: DSP-1001660009343-C-H03


title: HGSTIC_FT6__invasive_Epithelium_sample228

description: Library name: DSP-1001660009343-C-H01


title: NRCMs co-cultured with WT BMMCs, replicate 1

description: Library name: WT_CM_1


title: preSTC9

city: Shanghai

first: yi

last: luo

address: 1111XianXia Road

institute: department of surgery,Tongren Hospital,Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 12

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: intestine

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: intestine

value: WT

value: preoperative

tag: batch


title: C0440


title: HGSTIC_FT6__invasive_Epithelium_sample227

description: Library name: DSP-1001660009343-C-G12


title: C0437


title: HGSTIC_FT6__invasive_Stroma_sample226

description: Library name: DSP-1001660009343-C-G11


title: preSTC7

description: Library name: Sample 11


title: HGSTIC_FT6__invasive_Epithelium_sample225

description: Library name: DSP-1001660009343-C-G10


title: C0434


title: preSTC5

description: Library name: Sample 10


title: HGSTIC_FT6__STIC_Epithelium_sample223

description: Library name: DSP-1001660009343-C-G08


title: HGSTIC_FT6__STIC_Stroma_sample222

description: Library name: DSP-1001660009343-C-G07


title: HGSTIC_FT6__STIC_Epithelium_sample221

description: Library name: DSP-1001660009343-C-G06


title: preSTC1

description: Library name: Sample 9


title: C0425


title: HGSTIC_FT6__STIC_Stroma_sample224

description: Library name: DSP-1001660009343-C-G09


title: C0429


title: HGSTIC_FT6__STIC_Stroma_sample220

description: Library name: DSP-1001660009343-C-G05


title: preCTC9

description: Library name: Sample 8

value: Before sham surgery


title: HGSTIC_FT6__STIC_Epithelium_sample219

description: Library name: DSP-1001660009343-C-G04


title: HGSTIC_FT5__normal_Stroma_sample218

description: Library name: DSP-1001660009343-C-G03

value: normal


title: C0419

value: stomach


title: preCTC7

description: Library name: Sample 7


title: HGSTIC_FT5__FOXJ1neg_Epithelium_sample217

description: Library name: DSP-1001660009343-C-G02


title: C0413

value: Female

value: Tumor


title: HGSTIC_FT5__FOXJ1pos_Epithelium_sample216

description: Library name: DSP-1001660009343-C-G01


title: HGSTIC_FT5__normal_Stroma_sample215

description: Library name: DSP-1001660009343-C-F12


title: C0409

value: Advanced Gastric Cancer (AGC)


title: preCTC5

description: Library name: Sample 6


title: HGSTIC_FT5__FOXJ1neg_Epithelium_sample214

description: Library name: DSP-1001660009343-C-F11


title: preCTC1

description: Library name: Sample 5


title: HGSTIC_FT5__FOXJ1pos_Epithelium_sample213

description: Library name: DSP-1001660009343-C-F10


title: C0404


title: HGSTIC_FT5__normal_Stroma_sample212

description: Library name: DSP-1001660009343-C-F09


title: C0403


title: postSTC7

description: Library name: Sample 4

value: postoperative


title: HGSTIC_FT5__FOXJ1neg_Epithelium_sample211

description: Library name: DSP-1001660009343-C-F08

value: Fallopian tube, dysplastic lesion or invasive cancer


title: HGSTIC_FT5__FOXJ1pos_Epithelium_sample210

description: Library name: DSP-1001660009343-C-F07


title: C0400


title: postSTC5

description: Library name: Sample 3


title: HGSTIC_FT5__invasive_Epithelium_sample209

description: Library name: DSP-1001660009343-C-F06


title: HGSTIC_FT5__invasive_Epithelium_sample207

description: Library name: DSP-1001660009343-C-F04


title: HGSTIC_FT5__invasive_Epithelium_sample208

description: Library name: DSP-1001660009343-C-F05


title: postSTC2

description: Library name: Sample 2


title: HGSTIC_FT5__invasive_Epithelium_sample206

description: Library name: DSP-1001660009343-C-F03


title: HGSTIC_FT5__normal_Stroma_sample205

description: Library name: DSP-1001660009343-C-F02

value: Stroma


title: postSTC1

description: Library name: Sample 1

source_name: Intestine

value: Intestine


title: C0393


title: C0386


title: HGSTIC_FT5__FOXJ1pos_Epithelium_sample203

description: Library name: DSP-1001660009343-C-E12


title: qs9, infected with bb859

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

description: Library name: qs9_b859

data_processing:
D. discoideum reads were aligned to the D. discoideum reference genome and GTF annotation file (downloaded Jan 2023 from dictybase). The segmental duplication in this reference genome (2: 3016083-3768654) was masked using bedtools v2.28.0 (Quinlan and Hall 2010). Paraburkholderia reads were aligned to draft genome assemblies (Noh et al 2022) and Prokka GFF annotation files. Host alignments were performed with STAR v2.7.5c and symbiont alignments were performed with Bowtie2 v2.4.2. Samtools v1.3.1 was used to sort and filter alignments, Picard v2.17.10 (downloaded from broadinstitute.github.io/picard) was used to assign read groups. Read counts were extracted from primary alignments with correct strand orientation using HTSeq v0.11.2 (Anders et al. 2015).
Assembly: The D. discdoideum reference genome was downloaded Jan 2023 from http://dictybase.org. Paraburkholderia draft genome assemblies are available from NCBI and https://github.com/noh-lab/clade_infection/tree/main/genome_files
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample

organism: Dictyostelium discoideum

source_name: whole organism

extract_protocol:
For uninfected host samples, cells were removed from RNAlater® and processed following a standard RNA extraction protocol using Qiagen RNeasy Mini kits. For free-living symbiont samples, cells were disrupted with a lysozyme treatment prior to RNeasy extraction, then treated with illumina Ribozero according to its product protocol. Symbiont-associated (infected) host samples were obtained by taking the supernatant of the first RLN buffer treatment of associated amoebas in the RNeasy protocol. Host-associated (intracellular) symbiont samples were obtained by taking the spun-down pellet of this same RLN buffer treatment step that contains amoeba nuclei as well as intracellular Paraburkholderia. This pellet was treated with lysozyme, then the RNeasy protocol and illumina Ribozero protocol as with the free-living symbiont samples.
All samples were then prepared with the illumina TruSeq Stranded mRNA library preparation protocol but only D. discoideum samples were subjected to the polyA enrichment step.

value: whole organism

value: infected


title: HGSTIC_FT5__FOXJ1neg_Epithelium_sample204

description: Library name: DSP-1001660009343-C-F01

value: Epithelium


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NT (rep1)

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: WTC11_NT_WCE_rep1
Whole cell extract (input control) for CTCF ChIP-seq

library_source: genomic

data_processing:
FASTQ files were processed using the ENCODE ChIP-seq pipeline (v2; https://github.com/ENCODE-DCC/chip-seq-pipeline2). Filtered BAM files generated by the pipeline were converted to bedGraph format using bedtools genomecov67, with the signal scaled by sequencing depth (bedtools genomecov -ibam ~{bam} -bg -scale ~{scale_factor} -pc | sort -k1,1 -k2,2n > ~{sample_name}.bedGraph). The resulting bedGraph files were subsequently converted to bigWig format using the UCSC bedGraphToBigWig utility68. CTCF signal intensity at the regions of interest was quantified using the pyBigWig Python library (source code available on GitHub). CTCF motifs were annotated using the JASPAR track from the UCSC Genome Browser (hg38; https://hgdownload.soe.ucsc.edu/gbdb/hg38/jaspar/JASPAR2024.bb), specifically filtering for the CTCF motif ID MA0139 (source code available on GitHub).
Assembly: human hg38
Supplementary files format and content: bigWig files

molecule: genomic DNA

growth_protocol: We grew K562 cells harboring dCas9-KRAB  in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS (Thermo Fisher Scientific), 2 mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin. We maintained K562 cells at a density between 100K and 1M per mL. We seeded human iPS cells (WTC11) harboring dCas9-KRAB in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2 µl of Normacin per ml of media (1:500 final, Invivogen), and 0.4 µl of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain an 80-90% confluence to prevent stacked cell growth.

extract_protocol:
Cells were harvested for ChIP-seq following ENCODE protocols. All CTCF ChIP-seq protocols are available at the ENCODE portal: https://www.encodeproject.org/chip-seq/transcription_factor/.
Libraries were constructed accroding to ENCODE protocols

tag: individual

value: iPSC

value: WTC11 iPSC clone carrying non-targeting control sgRNA NT1 (OligoID WTC11_Random_Screen_Crop_15807)

tag: chip antibody

value: none (input control)


title: C0374

value: Male


title: HGSTIC_FT5__normal_Stroma_sample202

description: Library name: DSP-1001660009343-C-E11


title: qs9, infected with ba70

description: Library name: qs9_b70


title: HGSTIC_FT5__FOXJ1neg_Epithelium_sample201

description: Library name: DSP-1001660009343-C-E10


title: HGSTIC_FT5__FOXJ1pos_Epithelium_sample200

description: Library name: DSP-1001660009343-C-E09


title: qs9, uninfected, sample 2

description: Library name: qs9_b159

value: uninfected


title: C0352


title: C0351


title: HGSTIC_FT5__invasive_Epithelium_sample195

description: Library name: DSP-1001660009343-C-E03

value: invasive


title: qs9, infected with ba159

description: Library name: qs9_b11


title: C0359

value: stomach


title: qs9, uninfected, sample 1

description: Library name: qs9_a1


title: HGSTIC_FT5__invasive_Stroma_sample194

description: Library name: DSP-1001660009343-C-E02


title: HGSTIC_FT5__invasive_Epithelium_sample193

description: Library name: DSP-1001660009343-C-E01


title: HGSTIC_FT5__STIC_Epithelium_sample197

description: Library name: DSP-1001660009343-C-E05

value: STIC


title: HGSTIC_FT5__invasive_Stroma_sample196

description: Library name: DSP-1001660009343-C-E04


title: HGSTIC_FT5__STIC_Stroma_sample198

description: Library name: DSP-1001660009343-C-E06


title: C0346

value: Tumor


title: HGSTIC_FT5__STIC_Epithelium_sample199

description: Library name: DSP-1001660009343-C-E07


title: qs864, infected with bb859

description: Library name: qs864_c2


title: HGSTIC_FT5__invasive_Stroma_sample192

description: Library name: DSP-1001660009343-C-D12


title: C0339

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_FT5__invasive_Epithelium_sample191

description: Library name: DSP-1001660009343-C-D11


title: HGSTIC_FT5__STIC_Stroma_sample190

description: Library name: DSP-1001660009343-C-D10


title: C0337


title: qs864, infected with ba70

description: Library name: qs864_c1


title: HGSTIC_FT5__STIC_Epithelium_sample189

description: Library name: DSP-1001660009343-C-D09


title: HGSTIC_FT5__STIC_Stroma_sample188

description: Library name: DSP-1001660009343-C-D08


title: C0334


title: qs9, infected with bh11

description: Library name: qs9_a2


title: HGSTIC_FT5__STIC_Epithelium_sample187

description: Library name: DSP-1001660009343-C-D07


title: qs864, uninfected, sample 2

description: Library name: qs864_b859


title: HGSTIC_FT5__STIC_Stroma_sample186

description: Library name: DSP-1001660009343-C-D06


title: qs864, infected with ba159

description: Library name: qs864_b70


title: C0328


title: HGSTIC_FT5__STIC_Epithelium_sample185

description: Library name: DSP-1001660009343-C-D05


title: C0325

value: Female


title: HGSTIC_FT5__STIC_Stroma_sample184

description: Library name: DSP-1001660009343-C-D04

value: Fallopian tube, dysplastic lesion or invasive cancer


title: qs864, infected with bh11

description: Library name: qs864_b159


title: HGSTIC_FT5__STIC_Epithelium_sample183

description: Library name: DSP-1001660009343-C-D03


title: HGSTIC_FT5__STIC_Stroma_sample182

description: Library name: DSP-1001660009343-C-D02

value: Stroma


title: C0322


title: qs864, uninfected, sample 1

description: Library name: qs864_b11


title: HGSTIC_FT5__STIC_Epithelium_sample181

description: Library name: DSP-1001660009343-C-D01


title: C0321


title: HGSTIC_FT5__invasive_Epithelium_sample180

description: Library name: DSP-1001660009343-C-C12


title: qs18, infected with bb859

description: Library name: qs18_b859


title: HGSTIC_FT5__invasive_Epithelium_sample179

description: Library name: DSP-1001660009343-C-C11


title: STIC_5__normal_Stroma_sample178

description: Library name: DSP-1001660009343-C-C10

value: normal


title: STIC_5__FOXJ1neg_Epithelium_sample177

description: Library name: DSP-1001660009343-C-C09


title: C0320


title: qs18, infected with ba70

description: Library name: qs18_b70

value: whole organism


title: STIC_5__FOXJ1pos_Epithelium_sample176

description: Library name: DSP-1001660009343-C-C08


title: qs18, uninfected, sample 2

description: Library name: qs18_b2


title: STIC_5__normal_Stroma_sample175

description: Library name: DSP-1001660009343-C-C07


title: C0319


title: C0306


title: STIC_5__FOXJ1neg_Epithelium_sample174

description: Library name: DSP-1001660009343-C-C06


title: qs18, infected with ba159

description: Library name: qs18_b159

value: infected


title: C0304


title: qs18, infected with bh11

description: Library name: qs18_b11


title: C0301


title: STIC_5__FOXJ1pos_Epithelium_sample170

description: Library name: DSP-1001660009343-C-C02

value: Epithelium


title: C0298


title: qs18, uninfected, sample 1

description: Library name: qs18_b1


title: STIC_5__STIC_Stroma_sample168

description: Library name: DSP-1001660009343-C-B12


title: P. promelas larvae, UP, biological replicate UP_FIELD07, lane 2, time step = NA, analyzed on 20161129

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20161129_ UP_FIELD_07_AGTCAA_L002_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP


title: STIC_5__STIC_Stroma_sample167

description: Library name: DSP-1001660009343-C-B11

tag: cell type


title: C0295

tag: tissue

value: Male


title: P. promelas larvae, UP, biological replicate UP_B17, lane 1, time step = 3, analyzed on 20161129

description: Library name: 20161129_ UP_3_B17_TAGCTT_L001_R1_001


title: STIC_5__STIC_Epithelium_sample165

description: Library name: DSP-1001660009343-C-B09


title: C0291


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 3, analyzed on 20161129

description: Library name: 20161129_ UP_3_B07_GTTTCG_L002_R1_001


title: STIC_5__STIC_Epithelium_sample164

description: Library name: DSP-1001660009343-C-B08


title: STIC_5__STIC_Epithelium_sample163

description: Library name: DSP-1001660009343-C-B07


title: HGSTIC_FT2__normal_Stroma_sample162

description: Library name: DSP-1001660009343-C-B06


title: HGSTIC_FT2__normal_Stroma_sample161

description: Library name: DSP-1001660009343-C-B05


title: P. promelas larvae, UP, biological replicate UP_B11, lane 1, time step = 2, analyzed on 20161129

description: Library name: 20161129_ UP_2_B11_ATCACG_L001_R1_001


title: C0276


title: HGSTIC_FT2__normal_Stroma_sample160

description: Library name: DSP-1001660009343-C-B04


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 2, analyzed on 20161129

description: Library name: 20161129_ UP_2_B07_GTGAAA_L002_R1_001


title: HGSTIC_FT2__FOXJ1neg_Epithelium_sample159

description: Library name: DSP-1001660009343-C-B03


title: C0273


title: HGSTIC_FT2__FOXJ1pos_Epithelium_sample158

description: Library name: DSP-1001660009343-C-B02


title: HGSTIC_FT2__FOXJ1neg_Epithelium_sample157

description: Library name: DSP-1001660009343-C-B01


title: P. promelas larvae, UP, biological replicate UP_B02, lane 2, time step = 1, analyzed on 20161129

description: Library name: 20161129_ UP_1_B02_ATGTCA_L002_R1_001


title: C0285


title: HGSTIC_FT2__FOXJ1pos_Epithelium_sample156

description: Library name: DSP-1001660009343-C-A12


title: C0265


title: C0264


title: HGSTIC_FT2__FOXJ1pos_Epithelium_sample154

description: Library name: DSP-1001660009343-C-A10


title: HGSTIC_FT2__STIC_Stroma_sample153

description: Library name: DSP-1001660009343-C-A09


title: P. promelas larvae, EMZ, biological replicate EMZ_B16, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EMZ_B16_GAGTGG_L001_R1_001

value: EMZ


title: C0262


title: HGSTIC_FT2__STIC_Epithelium_sample152

description: Library name: DSP-1001660009343-C-A08


title: C0258


title: P. promelas larvae, EFP, biological replicate EFP_FIELD07, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EFP_FIELD_07_GCCAAT_L002_R1_001

value: EFP


title: HGSTIC_FT2__STIC_Stroma_sample150

description: Library name: DSP-1001660009343-C-A05


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 1, time step = 4, analyzed on 20161129

description: Library name: 20161129_ EFP_4_B22_GTCCGC_L001_R1_001


title: C0252

value: stomach


title: HGSTIC_FT2__STIC_Epithelium_sample149

description: Library name: DSP-1001660009343-C-A03

value: STIC


title: HGSTIC_FT2__STIC_Epithelium_sample148

description: Library name: DSP-1001660009343-C-A02


title: HGSTIC_FT3__invasive_Epithelium_sample147

description: Library name: DSP-1001660009342-B-G03

value: invasive


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 1, time step = 3, analyzed on 20161129

description: Library name: 20161129_ EFP_3_B18_GGCTAC_L001_R1_001


title: C0249

value: Tumor

value: Advanced Gastric Cancer (AGC)


title: STIC_5__FOXJ1pos_Epithelium_sample173

description: Library name: DSP-1001660009343-C-C05

value: Fallopian tube, dysplastic lesion or invasive cancer


title: zebrafish_FACS_purified_cranial_motor_neurons_6dpf_biorep_01

city: Seattle

first: Austin

last: Seroka

state: WA

address: 1100 Fairview Ave. North

department: Basic Sciences

institute: Fred Hutchinson Cancer Center

description:
Library name: 6_01
10X Genomics Chromium 3' mRNA v3

data_processing:
The demultiplexing, barcoded processing and gene counting were done using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Danio_rerio.GRCz11.dna.primary_assembly
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: FACS purified hindbrain

extract_protocol:
Tg:(isl1:kaede) embryos were raised to 24, 48, 72 or 144hpf respectively prior to anesthetization in 400mg/L MESAB. Hindbrains were dissected in Calcium-Free Ringers / EDTA / 10% MESAB, prior to dissociation to single-cell suspension by pipetting in 0.25% trypsin-EDTA for 5 minutes. Cells were briefly spun down, transferred to dPBS + BSA and passed through a 40uM filter. Prior to FACS, cell health was evaluated using 2pg/mL DAPI. Kaede+ cells were isolated on a BD FACS ARIA II flow cytometer using a 100uM nozzle and collected into dPBS + 2% BSA. Collected cells were concentrated by centrifugation at 300 x g for 5 minutes at 4°C and resuspended to an optimal concentration of 1,200 cells/uL. Cell viability was assessed using a TC20 Automated Cell Counter. Libraries were prepared using the 10X Genomics Chromium 3’ mRNA v3 kit, prior to sequencing on a Novaseq S1 Flowcell
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: FACS purified hindbrain


title: HGSTIC_FT3__invasive_Stroma_sample146

description: Library name: DSP-1001660009342-B-G02

value: Stroma


title: STIC_5__STIC_Stroma_sample169

description: Library name: DSP-1001660009343-C-C01


title: STIC_5__FOXJ1neg_Epithelium_sample171

description: Library name: DSP-1001660009343-C-C03


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 2, analyzed on 20161129

description: Library name: 20161129_ EFP_2_B12_ACTGAT_L001_R1_001


title: HGSTIC_FT3__invasive_Epithelium_sample145

description: Library name: DSP-1001660009342-B-G01


title: C0246

value: Female


title: STIC_5__normal_Stroma_sample172

description: Library name: DSP-1001660009343-C-C04

value: normal


title: HGSTIC_FT3__invasive_Epithelium_sample144

description: Library name: DSP-1001660009342-B-F11

value: Epithelium


title: HGSTIC_FT3__STIC_Stroma_sample143

description: Library name: DSP-1001660009342-B-F10


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 1, analyzed on 20161129

description: Library name: 20161129_ EFP_1_B12_ACTTGA_L001_R1_001

value: whole larvae


title: C0245


title: HGSTIC_FT3__STIC_Epithelium_sample142

description: Library name: DSP-1001660009342-B-F09


title: STIC_5__STIC_Epithelium_sample166

description: Library name: DSP-1001660009343-C-B10


title: P. promelas larvae, DSP, biological replicate DSP_B22, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ DSP_B22_GCCAAT_L001_R1_001

value: 2 dpf

value: DSP


title: HGSTIC_FT3__STIC_Epithelium_sample141

description: Library name: DSP-1001660009342-B-F07


title: C0242

value: Male


title: HGSTIC_FT4__normal_Stroma_sample140

description: Library name: DSP-1001660009342-B-F06


title: HGSTIC_FT4__STIC_Stroma_sample138

description: Library name: DSP-1001660009342-B-F04


title: P. promelas larvae, MHW, biological replicate MHW_B07, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ 15-08_B07_CTTGTA_L002_R1_001

value: MHW


title: HGSTIC_FT4__normal_Stroma_sample139

description: Library name: DSP-1001660009342-B-F05


title: C0239


title: HGSTIC_FT4__normal_Stroma_sample137

description: Library name: DSP-1001660009342-B-F03


title: C0238


title: P. promelas larvae, MHW, biological replicate MHW_B08, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ 15-07_B08_ACAGTG_L002_R1_001


title: HGSTIC_FT4__STIC_Stroma_sample136

description: Library name: DSP-1001660009342-B-F02


title: P. promelas larvae, UP, biological replicate UP_FIELD49, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ UP_FIELD_49_ATCACG_L002_R1_001

value: UP


title: HGSTIC_FT4__STIC_Stroma_sample135

description: Library name: DSP-1001660009342-B-F01


title: HGSTIC_FT4__invasive_Stroma_sample134

description: Library name: DSP-1001660009342-B-E12


title: C0233

value: stomach


title: P. promelas larvae, UP, biological replicate UP_FIELD33, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ UP_FIELD_33_AGTCAA_L002_R1_001


title: HGSTIC_FT4__invasive_Epithelium_sample133

description: Library name: DSP-1001660009342-B-E11


title: C0232


title: HGSTIC_FT4__FOXJ1neg_Epithelium_sample132

description: Library name: DSP-1001660009342-B-E10


title: P. promelas larvae, UP, biological replicate UP_FIELD30, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ UP_FIELD_30_ACTGAT_L001_R1_001


title: HGSTIC_FT4__FOXJ1pos_Epithelium_sample131

description: Library name: DSP-1001660009342-B-E09


title: C0226


title: HGSTIC_FT4__FOXJ1neg_Epithelium_sample130

description: Library name: DSP-1001660009342-B-E08


title: P. promelas larvae, UP, biological replicate UP_FIELD18, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ UP_FIELD_18_GTGAAA_L001_R1_001


title: HGSTIC_FT4__FOXJ1pos_Epithelium_sample129

description: Library name: DSP-1001660009342-B-E07


title: P. promelas larvae, TR, technical replicate TR_L10-12-TR, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ TR_L10-12_ACTTGA_L002_R1_001

value: TR


title: HGSTIC_FT2__FOXJ1neg_Epithelium_sample155

description: Library name: DSP-1001660009343-C-A11


title: HGSTIC_FT4__FOXJ1pos_Epithelium_sample128

description: Library name: DSP-1001660009342-B-E05


title: C0225


title: P. promelas larvae, UP, biological replicate UP_FIELD16, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ UP_FIELD_16_GTGGCC_L001_R1_001


title: C0223


title: HGSTIC_FT4__STIC_Epithelium_sample126

description: Library name: DSP-1001660009342-B-E03

value: STIC


title: HGSTIC_FT4__STIC_Epithelium_sample127

description: Library name: DSP-1001660009342-B-E04


title: HGSTIC_FT4__invasive_Stroma_sample125

description: Library name: DSP-1001660009342-B-D12

value: invasive


title: P. promelas larvae, UP, biological replicate UP_B16, lane 1, time step = 4, analyzed on 20161129

description: Library name: 20161129_ UP_4_B16_GCCAAT_L001_R1_001


title: C0221

value: Tumor

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_FT4__invasive_Stroma_sample123

description: Library name: DSP-1001660009342-B-D10

value: Fallopian tube, dysplastic lesion or invasive cancer


title: P. promelas larvae, UP, biological replicate UP_B22, lane 2, time step = 1, analyzed on 20161129

description: Library name: 20161129_ UP_1_B22_GAGTGG_L002_R1_001


title: HGSTIC_FT4__invasive_Epithelium_sample124

description: Library name: DSP-1001660009342-B-D11


title: C0220


title: HGSTIC_FT1__normal_Stroma_sample121

description: Library name: DSP-1001660009342-B-D08

value: Stroma


title: HGSTIC_FT2__STIC_Epithelium_sample151

description: Library name: DSP-1001660009343-C-A06


title: HGSTIC_FT4__invasive_Epithelium_sample122

description: Library name: DSP-1001660009342-B-D09


title: HGSTIC_FT1__STIC_Stroma_sample120

description: Library name: DSP-1001660009342-B-D06


title: P. promelas larvae, EMZ, biological replicate EMZ_B12, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EMZ_B12_GTGGCC_L002_R1_001

value: EMZ


title: C0218

value: Female


title: P. promelas larvae, EMZ, biological replicate EMZ_B01, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EMZ_B01_GGCTAC_L001_R1_001


title: HGSTIC_FT1__normal_Stroma_sample119

description: Library name: DSP-1001660009342-B-D03

value: normal


title: C0215


title: HGSTIC_FT1__FOXJ1pos_Epithelium_sample117

description: Library name: DSP-1001660009342-B-D01

value: Epithelium


title: C0211


title: P. promelas larvae, EFP, biological replicate EFP_FIELD33, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EFP_FIELD_33_ACTTGA_L001_R1_001

value: whole larvae

value: 2 dpf

value: EFP


title: HGSTIC_FT1__FOXJ1neg_Epithelium_sample115

description: Library name: DSP-1001660009342-B-C11


title: C0207

value: Male


title: HGSTIC_FT1__FOXJ1pos_Epithelium_sample114

description: Library name: DSP-1001660009342-B-C10


title: HGSTIC_FT1__STIC_Epithelium_sample113

description: Library name: DSP-1001660009342-B-C07


title: P. promelas larvae, EFP, biological replicate EFP_FIELD28, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EFP_FIELD_28_ATCACG_L001_R1_001


title: C0206


title: HGSTIC_FT1__STIC_Epithelium_sample111

description: Library name: DSP-1001660009342-B-C05


title: P. promelas larvae, EFP, biological replicate EFP_FIELD21, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EFP_FIELD_21_ATGTCA_L001_R1_001


title: HGSTIC_FT1__STIC_Epithelium_sample112

description: Library name: DSP-1001660009342-B-C06


title: HGSTIC_FT1__STIC_Epithelium_sample110

description: Library name: DSP-1001660009342-B-C04


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 4, analyzed on 20161129

description: Library name: 20161129_ EFP_4_B12_ACAGTG_L001_R1_001


title: HGSTIC_FT1__STIC_Epithelium_sample109

description: Library name: DSP-1001660009342-B-C03


title: C0202


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 1, time step = 3, analyzed on 20161129

description: Library name: 20161129_ EFP_3_B13_AGTTCC_L001_R1_001


title: HGSTIC_FT1__STIC_Epithelium_sample107

description: Library name: DSP-1001660009342-B-C01


title: C0201


title: C0200


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 2, analyzed on 20161129

description: Library name: 20161129_ EFP_2_B17_CTTGTA_L001_R1_001


title: STIC_1__FOXJ1neg_Epithelium_sample105

description: Library name: DSP-1001660009342-B-B10


title: STIC_1__FOXJ1pos_Epithelium_sample103

description: Library name: DSP-1001660009342-B-B08


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 1, analyzed on 20161129

description: Library name: 20161129_ EFP_1_B17_AGTCAA_L001_R1_001


title: C0199


title: STIC_1__normal_Stroma_sample102

description: Library name: DSP-1001660009342-B-B06


title: P. promelas larvae, DWIP, biological replicate DWIP_B12, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ DWIP_B12_TAGCTT_L001_R1_001

value: DWIP


title: STIC_1__FOXJ1neg_Epithelium_sample101

description: Library name: DSP-1001660009342-B-B05


title: STIC_1__FOXJ1pos_Epithelium_sample100

description: Library name: DSP-1001660009342-B-B04


title: P. promelas larvae, DSP, biological replicate DSP_B28, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ DSP_B28_GTCCGC_L001_R1_001

value: DSP


title: STIC_1__FOXJ1neg_Epithelium_sample99

description: Library name: DSP-1001660009342-B-B03


title: C0191

value: stomach


title: C0189


title: P. promelas larvae, DSP, biological replicate DSP_B17, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ DSP_B17_ACTGAT_L002_R1_001


title: STIC_1__STIC_Stroma_sample97

description: Library name: DSP-1001660009342-B-A12

value: STIC


title: STIC_1__STIC_Stroma_sample98

description: Library name: DSP-1001660009342-B-B01


title: C0187


title: STIC_1__STIC_Epithelium_sample95

description: Library name: DSP-1001660009342-B-A10


title: P. promelas larvae, DSP, biological replicate DSP_B12, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ DSP_B12_GTTTCG_L001_R1_001


title: C0185


title: P. promelas larvae, MHW, biological replicate MHW_B16, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ 15-08_B16_ACTTGA_L002_R1_001

value: MHW


title: STIC_1__STIC_Epithelium_sample93

description: Library name: DSP-1001660009342-B-A08


title: C0183

value: Tumor


title: P. promelas larvae, MHW, biological replicate MHW_B21, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ 15-07_B21_GTCCGC_L002_R1_001


title: C0177

value: Advanced Gastric Cancer (AGC)


title: STIC_1__normal_Stroma_sample90

description: Library name: DSP-1001660009342-B-A05

value: Fallopian tube, dysplastic lesion or invasive cancer


title: HGSTIC_FT1__FOXJ1neg_Epithelium_sample118

description: Library name: DSP-1001660009342-B-D02


title: P. promelas larvae, MHW, biological replicate MHW_B11, lane 1, time step = NA, analyzed on 20161129

description: Library name: 20161129_ 15-07_B11_GAGTGG_L001_R1_001


title: STIC_1__STIC_Epithelium_sample88

description: Library name: DSP-1001660009342-B-A03


title: STIC_1__STIC_Epithelium_sample87

description: Library name: DSP-1001660009342-B-A02


title: HGSTIC_MET6__met_Stroma_sample86

description: Library name: DSP-1001660008418-D-H06

source_name: Omental metastasis

value: Omental metastasis

value: Stroma

value: met


title: P. promelas larvae, UP, biological replicate UP_FIELD07, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ UP_FIELD_07_AGTCAA_L001_R1_001

value: UP


title: HGSTIC_MET6__met_Epithelium_sample85

description: Library name: DSP-1001660008418-D-H05

value: Epithelium


title: C0171


title: HGSTIC_MET6__met_Stroma_sample84

description: Library name: DSP-1001660008418-D-H03


title: HGSTIC_MET6__met_Epithelium_sample83

description: Library name: DSP-1001660008418-D-H02


title: C0165

value: Female


title: HGSTIC_MET6__met_Stroma_sample82

description: Library name: DSP-1001660008418-D-H01


title: P. promelas larvae, UP, biological replicate UP_B07, lane 1, time step = 3, analyzed on 20161109

description: Library name: 20161109_ UP_3_B07_GTTTCG_L001_R1_001

value: whole larvae

value: 2 dpf


title: HGSTIC_MET6__met_Epithelium_sample81

description: Library name: DSP-1001660008418-D-G12


title: C0164

value: Male


title: HGSTIC_MET6__met_Stroma_sample80

description: Library name: DSP-1001660008418-D-G11


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 2, analyzed on 20161109

description: Library name: 20161109_ UP_2_B07_GTGAAA_L002_R1_001


title: HGSTIC_MET6__met_Epithelium_sample79

description: Library name: DSP-1001660008418-D-G10


title: C0151


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 3, analyzed on 20161109

description: Library name: 20161109_ UP_3_B07_GTTTCG_L002_R1_001


title: NK-92MI_Water extract of Atractylodes japonica Koidzumi (Low dose)_rep3

description: sample 3-3-3

tag: cell line

value: natural killer cell

tag: treatment

value: Water extract of Atractylodes japonica Koidzumi 125 μg/mL

tag: time


title: M1MO_Vehicle(PBS)_rep3

description: sample 4-1-3

growth_protocol: THP-1 cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and maintained in the medium recommended by the ATCC with 100 IU penicillin, and 100 µg/mL streptomycin in a humidified incubator. When cells reached 80–90% confluency, the growth medium was replaced every 3~4 days. Mycoplasma contamination was checked using the MycoAlert PLUS mycoplasma detection kit (Lonza, Rockland, ME, USA) and passed all. Macrophages was differentiated using THP-1 according to the protocol. THP-1 monocyte was differentiated into M0 stage macrophages by 24 h incubation with 150 nM phorbol 12-myristate 13-acetate (PMA, Sigma, P8139). M0 Macrophages differentiated with PMA were polarized in M1 macrophages by incubation with 20 ng/ml of IFN-γ (Sigma, I17001) and 10 pg/ml of LPS (Thermo Fisher Scientific, 00-4976-93) for 48h.

treatment_protocol: To determine the maximum concentration, we performed cell cytotoxicity tests and all drugs did not influence cell viability. The highest treatment concentrations (500ug/mL) were selected considering the solubility and clinical application of the drugs. To confirm the influence of concentration, we treated the cells with two concentrations (500 and 125 ug/mL). The cells treated with PBS were used as the vehicle control. THP-1 cell was plated and differenciated to macrophage at a density of 5x105 cells / well in a 12-well microplate and treated with two concentrations of drugs. After 24 hours, cells were washed two times with ice-cold PBS, and total RNA was isolated using QIAzol RNA Isolation Reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.

value: Macrophage

value: PBS


title: 188HS

city: Pisa

first: Francesca

last: Scebba

address: Piazza martiri della libertà 33

country: Italy

institute: Scuola Superiore Sant'Anna

description: Library name: 30804-053

data_processing:
Analysis was performed using CLC Genomics Server 21.0.4 with the QIAseq miRNA Quantification workflow and standard parameters. Reads were mapped to miRBase v22 after trimming of common sequences, UMIs, and adapters, followed by filtering of reads shorter than 15 nt or longer than 55 nt. Reads were then deduplicated based on their UMIs by grouping reads with the same start position, strand, and identical UMI. Singleton UMI groups were merged into non-singleton groups when their UMI differed by a single nucleotide (SNP), with assignment to the largest matching group.
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.4 was used for differential expression analysis with default settings.
Assembly: miRBase version 22
Supplementary files format and content: excel file with total miRNa count for each miRNA and each sample

source_name: saliva

extract_protocol:
RNA was isolated from 200 μl using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 5 μl total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Agilent DNA 1000 Chip)

value: saliva

tag: gender

value: female

value: healthy


title: M1MO_Water extract of BJIKT (Low dose)_rep3

description: sample 4-1-9

value: Water extract of BJIKT 125 μg/mL


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-NC2 (rep2)

description:
Library name: NC2_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq

value: iPSC

value: WTC11 iPSC clone carrying legacy non-targeting control guide NC2 (OligoID NC1)

value: none (input control)


title: HGSTIC_MET6__met_Stroma_sample78

description: Library name: DSP-1001660008418-D-G09

value: Omental metastasis

value: Stroma

tag: cohort

value: met


title: P. promelas larvae, UP, biological replicate UP_B07, lane 1, time step = 2, analyzed on 20161109

description: Library name: 20161109_ UP_2_B07_GTGAAA_L001_R1_001

value: whole larvae

tag: age

value: UP


title: HGSTIC_MET6__met_Epithelium_sample77

description: Library name: DSP-1001660008418-D-G08

value: Epithelium


title: C0148

value: stomach

value: Female

tag: genotype

value: Tumor

value: Advanced Gastric Cancer (AGC)


title: P. promelas larvae, EFP, biological replicate EFP_FIELD50, lane 2, time step = NA, analyzed on 20161129

description: Library name: 20161129_ EFP_FIELD_50_TAGCTT_L002_R1_001

value: 2 dpf

value: EFP


title: HGSTIC_MET6__met_Epithelium_sample76

description: Library name: DSP-1001660008418-D-G07


title: HGSTIC_MET6__met_Stroma_sample75

description: Library name: DSP-1001660008418-D-G06


title: C0140

tag: Sex

value: Male


title: P. promelas larvae, UP, biological replicate UP_B02, lane 2, time step = 1, analyzed on 20161109

description: Library name: 20161109_ UP_1_B02_ATGTCA_L002_R1_001


title: HGSTIC_FT1__FOXJ1neg_Epithelium_sample116

description: Library name: DSP-1001660009342-B-C12

value: Fallopian tube, dysplastic lesion or invasive cancer


title: HGSTIC_MET6__met_Epithelium_sample74

description: Library name: DSP-1001660008418-D-G05


title: P. promelas larvae, UP, biological replicate UP_B02, lane 1, time step = 1, analyzed on 20161109

description: Library name: 20161109_ UP_1_B02_ATGTCA_L001_R1_001


title: C0205

tag: diagnosis


title: irradiated T cells, 24h after 1 Gy, mouse 3

description: replicate 3

source_name: irradiated T cells, 24h after 1 Gy

value: CD8+T cells

tag: strain

value: 8-12 week

value: Intratumoral T cells


title: CTCF ChIP-seq in WTC11-NC2 (rep2)

description:
Library name: NC2_rep2
CRISPR clonal validation ChIP-seq for CTCF binding

tag: individual

value: iPSC

value: WTC11 iPSC clone carrying legacy non-targeting control guide NC2 (OligoID NC1)

value: CTCF


title: HGSTIC_MET6__met_Epithelium_sample73

description: Library name: DSP-1001660008418-D-G04

value: Omental metastasis

value: met


title: C0136


title: HGSTIC_FT1__STIC_Epithelium_sample108

description: Library name: DSP-1001660009342-B-C02

value: Epithelium

value: STIC


title: P. promelas larvae, TR, technical replicate TR_L10-12-TR, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ TR_L10-12_ACTTGA_L002_R1_001

value: whole larvae

value: TR

tag: batch


title: C0132

value: stomach

value: Tumor

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_MET6__met_Stroma_sample72

description: Library name: DSP-1001660008418-D-G03

value: Stroma


title: HGSTIC_FT1__FOXJ1neg_Epithelium_sample106

description: Library name: DSP-1001660009342-B-B12

value: Fallopian tube, dysplastic lesion or invasive cancer


title: HGSTIC_MET6__met_Epithelium_sample71

description: Library name: DSP-1001660008418-D-G02


title: HGSTIC_MET6__met_Stroma_sample69

description: Library name: DSP-1001660008418-D-F12


title: P. promelas larvae, TR, technical replicate TR_L10-12-TR, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ TR_L10-12_ACTTGA_L001_R1_001

value: 2 dpf

tag: treatment-replicate id


title: HGSTIC_MET6__met_Epithelium_sample70

description: Library name: DSP-1001660008418-D-G01


title: C0122

value: Male


title: HGSTIC_MET6__met_Stroma_sample68

description: Library name: DSP-1001660008418-D-F11


title: P. promelas larvae, EFP, biological replicate EFP_FIELD07, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ EFP_FIELD_07_GCCAAT_L002_R1_001

tag: treatment-time

value: EFP


title: STIC_1__FOXJ1neg_Epithelium_sample104

description: Library name: DSP-1001660009342-B-B09


title: HGSTIC_MET6__met_Epithelium_sample67

description: Library name: DSP-1001660008418-D-F10


title: C0119


title: HGSTIC_MET5__met_Stroma_sample66

description: Library name: DSP-1001660008418-D-F09


title: P. promelas larvae, EFP, biological replicate EFP_FIELD07, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ EFP_FIELD_07_GCCAAT_L001_R1_001

tag: treatment-location


title: HGSTIC_MET5__met_Epithelium_sample65

description: Library name: DSP-1001660008418-D-F08

tag: cell type


title: C0110

tag: tissue


title: HGSTIC_MET5__met_Stroma_sample64

description: Library name: DSP-1001660008418-D-F07


title: P. promelas larvae, MHW, biological replicate MHW_B07, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ 15-08_B07_CTTGTA_L002_R1_001

value: MHW


title: HGSTIC_MET5__met_Epithelium_sample63

description: Library name: DSP-1001660008418-D-F06


title: C0107


title: HGSTIC_MET5__met_Stroma_sample62

description: Library name: DSP-1001660008418-D-F05


title: P. promelas larvae, MHW, biological replicate MHW_B07, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ 15-08_B07_CTTGTA_L001_R1_001


title: C0105


title: P. promelas larvae, MHW, biological replicate MHW_B08, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ 15-07_B08_ACAGTG_L002_R1_001


title: HGSTIC_MET5__met_Epithelium_sample61

description: Library name: DSP-1001660008418-D-F04


title: HGSTIC_MET5__met_Stroma_sample60

description: Library name: DSP-1001660008418-D-F03


title: HGSTIC_MET5__met_Epithelium_sample59

description: Library name: DSP-1001660008418-D-F02


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G2 (rep2)

description:
Library name: FAM111A_CTCF_G2_rep2
CRISPR clonal validation ChIP-seq for CTCF binding

tag: cell line

value: iPSC

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G2 (OligoID WTC11_Random_Screen_Crop_3864) targeting a candidate CTCF-binding element near FAM111A

tag: chip antibody


title: C0104


title: CTCF ChIP-seq in WTC11-FAM111A-CTCF-G3 (rep1)

description:
Library name: FAM111A_CTCF_G3_rep1
CRISPR clonal validation ChIP-seq for CTCF binding

tag: treatment

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G3 (OligoID WTC11_Random_Screen_Crop_3866) targeting a candidate CTCF-binding element near FAM111A

value: CTCF


title: HGSTIC_MET5__met_Stroma_sample58

description: Library name: DSP-1001660008418-D-F01

value: Omental metastasis

value: met


title: HGSTIC_MET5__met_Epithelium_sample57

description: Library name: DSP-1001660008418-D-E12

value: Epithelium


title: STIC_1__STIC_Epithelium_sample96

description: Library name: DSP-1001660009342-B-A11

value: STIC


title: C0101

value: stomach


title: HGSTIC_MET5__met_Stroma_sample56

description: Library name: DSP-1001660008418-D-E11


title: P. promelas larvae, MHW, biological replicate MHW_B08, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ 15-07_B08_ACAGTG_L001_R1_001

value: whole larvae


title: P. promelas larvae, UP, biological replicate UP_B17, lane 2, time step = 3, analyzed on 20161109

description: Library name: 20161109_ UP_3_B17_TAGCTT_L002_R1_001

value: UP


title: HGSTIC_MET5__met_Epithelium_sample55

description: Library name: DSP-1001660008418-D-E10


title: unirradiated T cells, mouse 4

description: replicate 4

value: CD8+T cells

value: 8-12 week

value: Intratumoral T cells


title: STIC_1__STIC_Stroma_sample94

description: Library name: DSP-1001660009342-B-A09

value: Fallopian tube, dysplastic lesion or invasive cancer

value: Stroma


title: C0097

value: Male

value: Tumor

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_MET5__met_Stroma_sample54

description: Library name: DSP-1001660008418-D-E09


title: HGSTIC_MET5__met_Epithelium_sample53

description: Library name: DSP-1001660008418-D-E08


title: P. promelas larvae, UP, biological replicate UP_B17, lane 1, time step = 3, analyzed on 20161109

description: Library name: 20161109_ UP_3_B17_TAGCTT_L001_R1_001

value: 2 dpf


title: C0092

value: Female


title: HGSTIC_MET5__met_Stroma_sample52

description: Library name: DSP-1001660008418-D-E07

value: Omental metastasis


title: HGSTIC_MET5__met_Epithelium_sample51

description: Library name: DSP-1001660008418-D-E06

value: met


title: P. promelas larvae, UP, biological replicate UP_B11, lane 2, time step = 2, analyzed on 20161109

description: Library name: 20161109_ UP_2_B11_ATCACG_L002_R1_001


title: HGSTIC_MET5__met_Epithelium_sample49

description: Library name: DSP-1001660008418-D-E04

value: Epithelium


title: HGSTIC_MET5__met_Stroma_sample50

description: Library name: DSP-1001660008418-D-E05


title: P. promelas larvae, UP, biological replicate UP_B11, lane 1, time step = 2, analyzed on 20161109

description: Library name: 20161109_ UP_2_B11_ATCACG_L001_R1_001


title: C0090


title: STIC_1__FOXJ1neg_Epithelium_sample92

description: Library name: DSP-1001660009342-B-A07


title: C0089


title: HGSTIC_MET5__met_Stroma_sample48

description: Library name: DSP-1001660008418-D-E03


title: HGSTIC_MET5__met_Epithelium_sample47

description: Library name: DSP-1001660008418-D-E02


title: P. promelas larvae, EMZ, biological replicate EMZ_B16, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ EMZ_B16_GAGTGG_L002_R1_001

value: EMZ


title: C0087

value: stomach


title: P. promelas larvae, EMZ, biological replicate EMZ_B16, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ EMZ_B16_GAGTGG_L001_R1_001

value: whole larvae


title: HGSTIC_MET5__met_Epithelium_sample45

description: Library name: DSP-1001660008418-D-D12


title: C0086


title: C0070


title: HGSTIC_MET2__met_Epithelium_sample43

description: Library name: DSP-1001660008418-D-D10


title: HGSTIC_MET2__met_Epithelium_sample41

description: Library name: DSP-1001660008418-D-D08


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 1, time step = 4, analyzed on 20161109

description: Library name: 20161109_ EFP_4_B22_GTCCGC_L001_R1_001

value: EFP


title: C0064


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 2, time step = 3, analyzed on 20161109

description: Library name: 20161109_ EFP_3_B18_GGCTAC_L002_R1_001


title: HGSTIC_MET2__met_Epithelium_sample39

description: Library name: DSP-1001660008418-D-D06


title: HGSTIC_MET2__met_Stroma_sample40

description: Library name: DSP-1001660008418-D-D07


title: C0053


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 1, time step = 3, analyzed on 20161109

description: Library name: 20161109_ EFP_3_B18_GGCTAC_L001_R1_001


title: HGSTIC_MET2__met_Stroma_sample38

description: Library name: DSP-1001660008418-D-D05


title: C0056


title: HGSTIC_MET2__met_Stroma_sample36

description: Library name: DSP-1001660008418-D-D03


title: NK-92MI_Water extract of Panax ginseng C. A. Meyer (Low dose)_rep3

description: sample 3-2-3

value: natural killer cell

value: Water extract of Panax ginseng C. A. Meyer 125 μg/mL

tag: time


title: HGSTIC_MET2__met_Epithelium_sample35

description: Library name: DSP-1001660008418-D-D02

tag: cohort


title: NK-92MI_Water extract of Panax ginseng C. A. Meyer (High dose)_rep2

description: sample 3-1-11

value: Water extract of Panax ginseng C. A. Meyer 500 μg/mL


title: HGSTIC_MET2__met_Stroma_sample34

description: Library name: DSP-1001660008418-D-D01


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 2, analyzed on 20161109

description: Library name: 20161109_ EFP_2_B12_ACTGAT_L001_R1_001

tag: age


title: HGSTIC_MET2__met_Epithelium_sample33

description: Library name: DSP-1001660008418-D-C12


title: HGSTIC_MET2__met_Stroma_sample32

description: Library name: DSP-1001660008418-D-C11


title: C0046

tag: genotype


title: HGSTIC_MET2__met_Epithelium_sample31

description: Library name: DSP-1001660008418-D-C10


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 2, time step = 1, analyzed on 20161109

description: Library name: 20161109_ EFP_1_B12_ACTTGA_L002_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 1, analyzed on 20161109

description: Library name: 20161109_ EFP_1_B12_ACTTGA_L001_R1_001


title: C0034

tag: Sex


title: P. promelas larvae, DSP, biological replicate DSP_B22, lane 2, time step = NA, analyzed on 20161109

description: Library name: 20161109_ DSP_B22_GCCAAT_L002_R1_001

value: DSP


title: HGSTIC_MET2__met_Epithelium_sample29

description: Library name: DSP-1001660008418-D-C08


title: C0031

tag: diagnosis


title: N0496

value: Normal


title: p53_6__FOXJ1pos_Epithelium_sample24

description: Library name: DSP-1001660008418-D-C03

value: Fallopian tube, dysplastic lesion or invasive cancer


title: p53_6__normal_Stroma_sample23

description: Library name: DSP-1001660008418-D-C02

value: Stroma

value: normal


title: N0494

value: Advanced Gastric Cancer (AGC)


title: p53_6__FOXJ1neg_Epithelium_sample22

description: Library name: DSP-1001660008418-D-C01


title: P. promelas larvae, UP, biological replicate UP_FIELD49, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ UP_FIELD_49_ATCACG_L001_R1_001

value: 2 dpf

value: UP


title: N0491

value: Male


title: p53_6__FOXJ1pos_Epithelium_sample21

description: Library name: DSP-1001660008418-D-B12

value: Epithelium


title: p53_6__normal_Stroma_sample20

description: Library name: DSP-1001660008418-D-B11


title: P. promelas larvae, UP, biological replicate UP_FIELD33, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ UP_FIELD_33_AGTCAA_L002_R1_001


title: p53_6__FOXJ1neg_Epithelium_sample19

description: Library name: DSP-1001660008418-D-B10


title: N0447


title: Whole cell extract (input control) for CTCF ChIP-seq in WTC11-CDC37-CTCF-G4 (rep2)

description:
Library name: CDC37_CTCF_G4_WCE_rep2
Whole cell extract (input control) for CTCF ChIP-seq

value: iPSC

value: WTC11 iPSC clone carrying individual CRISPR sgRNA G4 (OligoID WTC11_Random_Screen_Crop_7494) targeting a candidate CTCF-binding element near CDC37

value: none (input control)


title: P. promelas larvae, UP, biological replicate UP_FIELD33, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ UP_FIELD_33_AGTCAA_L001_R1_001

value: whole larvae


title: N0443

value: stomach


title: P. promelas larvae, UP, biological replicate UP_B22, lane 2, time step = 1, analyzed on 20161108

description: Library name: 20161108_ UP_1_B22_GAGTGG_L002_R1_001


title: N0441


title: p53_6__FOXJ1pos_Epithelium_sample13

description: Library name: DSP-1001660008418-D-B03


title: N0440

value: Female


title: p53_6__normal_Stroma_sample12

description: Library name: DSP-1001660008418-D-B02


title: P. promelas larvae, EMZ, biological replicate EMZ_B12, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EMZ_B12_GTGGCC_L002_R1_001

value: EMZ


title: p53_6__FOXJ1neg_Epithelium_sample11

description: Library name: DSP-1001660008418-D-B01


title: HGSTIC_MET2__met_Stroma_sample30

description: Library name: DSP-1001660008418-D-C09

value: Omental metastasis

value: met


title: P. promelas larvae, EMZ, biological replicate EMZ_B12, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EMZ_B12_GTGGCC_L001_R1_001


title: HGSTIC_MET2__met_Epithelium_sample27

description: Library name: DSP-1001660008418-D-C06


title: p53_6__FOXJ1neg_Epithelium_sample25

description: Library name: DSP-1001660008418-D-C04

value: Fallopian tube, dysplastic lesion or invasive cancer


title: P. promelas larvae, DSP, biological replicate DSP_B22, lane 1, time step = NA, analyzed on 20161109

description: Library name: 20161109_ DSP_B22_GCCAAT_L001_R1_001

value: DSP


title: N0434

value: Normal


title: p53_6__FOXJ1pos_Epithelium_sample8

description: Library name: DSP-1001660008418-D-A10


title: P. promelas larvae, EFP, biological replicate EFP_FIELD50, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EFP_FIELD_50_TAGCTT_L002_R1_001

value: EFP


title: p53_6__FOXJ1neg_Epithelium_sample7

description: Library name: DSP-1001660008418-D-A09


title: P. promelas larvae, EFP, biological replicate EFP_FIELD50, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EFP_FIELD_50_TAGCTT_L001_R1_001

value: 2 dpf


title: p53_6__FOXJ1pos_Epithelium_sample6

description: Library name: DSP-1001660008418-D-A08


title: p53_6__P53_Epithelium_sample5

description: Library name: DSP-1001660008418-D-A07


title: p53_6__normal_Stroma_sample4

description: Library name: DSP-1001660008418-D-A06

value: Stroma

value: normal


title: P. promelas larvae, DSP, biological replicate DSP_B17, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ DSP_B17_ACTGAT_L002_R1_001


title: p53_6__FOXJ1neg_Epithelium_sample3

description: Library name: DSP-1001660008418-D-A05

value: Epithelium


title: p53_6__FOXJ1pos_Epithelium_sample2

description: Library name: DSP-1001660008418-D-A04


title: p53_6__P53_Epithelium_sample1

description: Library name: DSP-1001660008418-D-A02


title: N0425

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_MET5__met_Stroma_sample46

description: Library name: DSP-1001660008418-D-E01


title: HGSTIC_MET2__met_Stroma_sample44

description: Library name: DSP-1001660008418-D-D11


title: HGSTIC_MET2__met_Stroma_sample42

description: Library name: DSP-1001660008418-D-D09


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 2, time step = 4, analyzed on 20161109

description: Library name: 20161109_ EFP_4_B22_GTCCGC_L002_R1_001


title: HcoFi treated with siDUSP4_2

city: Suwon

first: Soon Sang

address: Worldcup-Ro 206

institute: Ajou University School of Medicine

description: Library name: siDUSP4_2

data_processing:
fastq files are processed with Altanalyze.
Assembly: hg38
Supplementary files format and content: csv files containing raw counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted using RNA extraction kit (MN) 1ug of total RNA was used for RNA library generation.
The 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: Colon

value: HCoFi

value: Fibroblast

value: Wild type


title: N0419

value: stomach

value: Male


title: C0048

value: Female

value: Tumor


title: HGSTIC_MET2__met_Epithelium_sample37

description: Library name: DSP-1001660008418-D-D04

value: Omental metastasis

value: met


title: P. promelas larvae, MHW, biological replicate MHW_B16, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ 15-08_B16_ACTTGA_L002_R1_001

value: whole larvae

value: MHW


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 2, time step = 2, analyzed on 20161109

description: Library name: 20161109_ EFP_2_B12_ACTGAT_L002_R1_001

value: 2 dpf

value: EFP


title: N0409

value: Normal


title: HcoFi treated with siDUSP4_1

description: Library name: siDUSP4_1


title: HcoFi treated with siControl_2

description: Library name: siNC1_2

value: siControl


title: P. promelas larvae, DSP, biological replicate DSP_B17, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ DSP_B17_ACTGAT_L001_R1_001

value: DSP


title: P. promelas larvae, MHW, biological replicate MHW_B16, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ 15-08_B16_ACTTGA_L001_R1_001


title: HcoFi treated with siControl_1

description: Library name: siNC1_1

value: Colon


title: C0040

value: Advanced Gastric Cancer (AGC)


title: HGSTIC_MET2__met_Stroma_sample28

description: Library name: DSP-1001660008418-D-C07

value: Stroma


title: Colonic epithelial cells treated with conditioned medium of presenescent fibroblasts2

description: Library name: Presen_CM2

value: Primary colonic epithelial cells

value: Epithelial cell

value: Wild type

value: Presenescent CM


title: N0404

value: stomach

value: Female


title: P. promelas larvae, MHW, biological replicate MHW_B21, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ 15-07_B21_GTCCGC_L002_R1_001


title: p53_6__normal_Stroma_sample26

description: Library name: DSP-1001660008418-D-C05

value: Fallopian tube, dysplastic lesion or invasive cancer

value: normal


title: Colonic epithelial cells treated with conditioned medium of presenescent fibroblasts1

description: Library name: Presen_CM1


title: N0403

value: Male


title: Colonic epithelial cells treated with conditioned medium of young fibroblasts2

description: Library name: Young_CM2

value: Young CM


title: P. promelas larvae, MHW, biological replicate MHW_B21, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ 15-07_B21_GTCCGC_L001_R1_001

value: whole larvae

value: 2 dpf

value: MHW


title: Colonic epithelial cells treated with conditioned medium of young fibroblasts1

description: Library name: Young_CM1


title: N0400

value: Normal


title: Colonic epithelial cells treated with control media2

description: Library name: Media2

value: Colon

value: Control Medium


title: P. promelas larvae, UP, biological replicate UP_FIELD34, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ UP_FIELD_34_ACAGTG_L002_R1_001

value: UP


title: Colonic epithelial cells treated with control media1

description: Library name: Media1

value: Primary colonic epithelial cells