title: EE501F2_093_T_T2_R2

city: East Lansing

first: Natalie

last: Kaiser

state: MI

address: 1066 Bogue Street

department: PSM

institute: Michigan State University

data_processing:
Raw reads were processed with Trimmomatic (v0.35) (MINLEN = 36, LEADING = 20, TRAILING = 20) to remove low-quality bases, adapters, and primers (Bolger et al., 2014).
Cleaned reads were aligned to the potato doubled monoploid S. tuberosum clone DM1-3 516 R44 (DM) pseudomolecules (PGSC Version 6.1) using STAR (v2.7.3a) (Dobin et al., 2013).
Alignments for each sample generated from separate Illuminia lanes were merged using the Picard tool MergeSamFiles (v2.18.27-Java-1.8) (broadinstitute.github.io/picard).
Reads aligning to annotated DM reference genes were counted using HTSeq in union mode (v0.11.2) (Anders et al., 2015).
Genome_build: Spud DB http://solanaceae.plantbiology.msu.edu/index.shtml
Supplementary_files_format_and_content: text file containing Htseq counts

organism: Solanum chacoense

source_name: leaf tissue

growth_protocol: Six in vitro plantlets of each genotype (80-1 and EE501F2_093) (N = 12 plantlets) with good roots were transplanted to 6╙ pots in SUREMIXTM media (Michigan Grower Products Inc., Galesburg, MI). Two plants of each genotype were placed in individual RESTCLOUDTM mesh insect cages (15.3╙ wide x 15.3╙ deep x 23.6╙ long) (N = 6 cages) in a growth chamber maintained under 60% relative humidity, a 16 hr photoperiod, 16íC night and 20íC day temperature and 250 mE of light intensity. After two weeks, plants received 20-20-20 Peters Professional General Purpose Fertilizer (ICL-SF USA, Summersville, SC) at a rate of 500mg/l twice weekly.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Samples were Turbo DNase (Thermo Fisher Scientific, Waltham, MA, USA) treated, and RNA quantity and quality was assessed using an Agilent 4200 TapeStation (Agilent Technologies Inc., Santa Clara, CA).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit and approximately 30,000,000 50nt single-end Illumina reads were generated for each sample on the Illumina HiSeq 4000 platform.

treatment_protocol: For each genotype, two cages received adult Colorado potato beetles (treatment) and one cage did not receive beetles (control). Adult Colorado potato beetles were collected from untreated foliage of the commercial cultivar S. tuberosum ╘Atlantic╒ at the Michigan State University Montcalm Research Center (Lakeview, MI) on July 16th, 2019. Adult beetles were starved for 6 hours prior to being put on the experimental plants. When plants were 15-weeks old, 50 beetles were applied to treatment cages and leaf tissue was harvested for RNA isolation in the following time course: T0 = immediately preceding beetle placement; T1 = 24 hours after beetle placement; T2 = 48 hours after beetle placement. At each of the three timepoints, two biological replicates were prepared by pooling equal quantities of tissue from the third fully expanded leaf each genotype and condition (treatment or control) (N = 24). Total percent defoliation was visually determined for each treatment plant at T2

tag: condition

value: Treatment

tag: time

value: T2-48 hours after beetle placement


title: AoV_CTRL3

status: Public on Mar 08 2023

type: SRA

city: Tsukuba

first: Hiromi

last: Yanagisawa

state: Ibaraki

address: 1-1-1 Tennodai

department: TARA Center

country: Japan

institute: University of Tsukuba

library_source: transcriptomic

data_processing:
Sequencing was done in MiSeq (illumina) to generate 6 gz fastq files per mouse model
Reads (FASTQ files) were analyzed by using CLC Genomics Workbench (Version 22.0, QIAGEN) and trimmed sequences were mapped on the mouse genome (GRCm39.105).
Gene expression values were presented in total read counts and TPM values
Differentially expressed genes were analyzed using the Differential Expression tool in RNA-seq and small RNA analysis on CLC Genomics Workbench. Differentially expressed genes were filtered using 2 fold change and p value < 0.05.
Assembly: GRCm39.105
Supplementary files format and content: tab-delimited text files include gene name; identifier; fold change and p value for differential expressed genes comparison between DKO vs CTRL, DKO vs ECKO and DKO vs SMKO; total read counts and TPM values in each sample.

molecule: total RNA

organism: Mus musculus

source_name: aortic valve

extract_protocol:
Hearts and aortic valves were harvested from CTRL, ECKO, SMKO, and DKO mice after perfusion with 5 ml of 1xPBS. The tissues were immediately fixed with 4% paraformaldehyde, then washed with 20% sucrose and embedded in OCT (SAKURA Finetek USA Inc., #4583) to make frozen tissue samples. Cross-sections of the aortic valves (20 μm thickness) were mounted onto PEN-Membrane slides (Leica, #11600288) and stored at -80ºC until the LMD process. The aortic valve sections on the slide were replaced at room temperature and dried up with a handy circulator. The sections were fixed briefly with 100% ethanol and stained with hematoxylin solution (Muto Pure Chemicals Co., LTD, #30141) for 3 min, then incubated in a water bath at 30ºC for 15 min. After that, the sections were cleaned with 100% ethanol and dried up completely at room temperature. Whole aortic valve leaflets were captured using LMD7 (Leica) under the 10x magnification and collected into MaxyClear (low adhesion) microtube (Corning, PCR-02-L-C) with 20 µL 99.5% ethanol and stored at -80ºC until cDNA library preparation.
cDNA library was prepared from LMD-captured aortic valves by the Nextera XT DNA library prep kit (illumina, FC-131-1024) as previously described. The amplified 0.25 ng cDNA was used for RNA-seq library preparation and sequenced on the MiSeq (illumina) with paired-end 75-base read option..

tag: strain

tag: genotype

value: CTRL

tag: tissue

value: aortic valve leaflets

tag: age

value: 2 months old


title: EE501F2_093_T_T0_R2

country: USA

value: T0-before beetle placement


title: iHEP RWV ORG + Ri_2 [I3DRi_2]

city: San francisco

first: Tammy

middle: T

last: Chang

state: CA

address: 513 parnassus Ave.

institute: UCSF

description: Processed data files_stem cells full list.xlsx

data_processing:
Raw reads in FASTQ format were processed by removing the adaptor reads or poly-N and low-quality reads.
Error rate distribution and Q20, Q30, and GC content of the cleaned data were calculated.
Quality-controlled reads were mapped to the human reference genome (hg19) with STAR alignment software
Raw reads were normalized by DESeq2 algorithm
Assembly: hg19
Supplementary files format and content: DESeq2 output

organism: Homo sapiens

source_name: liver

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit, and 1μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated by NEBNext Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocols.

value: liver

tag: cell line

value: AICS-0023 iPSC

tag: cell type

value: Induced Pluripotent Stem Cells

tag: treatment

value: iHEP RWV ORG + Ri


title: EE501F2_093_T_T2_R1


title: EE501F2_093_C_T2_R2

value: Control


title: iHEP RWV ORG + Ri_1 [I3DRi_1]


title: EE501F2_093_C_T2_R1


title: EE501F2_093_T_T1_R2

value: T1-24 hours after beetle placement


title: iHEC RWV ORG + Ri_3 [E3DRi_3]

value: iHEC RWV ORG + Ri


title: EE501F2_093_C_T1_R1


title: iHEP_3 [I0_3]

value: iHEP


title: iHEP_2 [I0_2]


title: EE501F2_093_C_T1_R2


title: iHEC MTG ORG + Ri_2 [E2DRi_2]

value: iHEC MTG ORG + Ri


title: iHEP_1 [I0_1]


title: iHEC MTG ORG + Ri_1 [E2DRi_1]


title: EE501F2_093_T_T0_R1


title: EE501F2_093_C_T0_R1


title: 80-1_T_T1_R2


title: 80-1_T_T1_R1


title: iHEC RWV ORG + Ri_1 [E3DRi_1]


title: 80-1_T_T2_R1


title: iHEC MTG ORG + Ri_3 [E2DRi_3]


title: iHEC RWV ORG_4 [E3D_4]

value: iHEC RWV ORG


title: 80-1_C_T2_R1


title: iHEC RWV ORG + Ri_2 [E3DRi_2]


title: EE501F2_093_T_T1_R1


title: iHEC RWV ORG + MTG Ri_2 [E3DRiM_2]

value: iHEC RWV ORG + MTG Ri


title: 80-1_T_T0_R3

value: Treatment


title: iHEC RWV ORG + MTG Ri_3 [E3DRiM_3]


title: iHEC RWV ORG + MTG Ri_1  [E3DRiM_1]


title: 80-1_T_T0_R2


title: iHEC RWV ORG_2 [E3D_2]


title: 80-1_C_T2_R3

value: T2-48 hours after beetle placement


title: EE501F2_093_C_T0_R2


title: iHEC MTG ORG_2 [E2D_2]

value: iHEC MTG ORG


title: iHEC RWV ORG_3 [E3D_3]


title: 80-1_C_T0_R2


title: iHEC_3 [E0_3]

value: iHEC


title: iHEC MTG ORG_1 [E2D_1]


title: 80-1_C_T1_R2


title: 80-1_C_T1_R1


title: 80-1_C_T0_R3


title: KR_C2

city: Shenzhen

first: Jin-Tang

middle: and

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd., Research Building 2B

country: China

institute: Southern University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values and gene countsfor each Sample ...

source_name: prostate cancer

extract_protocol:
Remove the supernatant and wash with PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

value: prostate cancer cells

value: untreated


title: ID87 positive

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Raw reads were trimmed by tool Trimmomatic to remove low-quality reads
Reads were aligned to human reference genome by STAR aligner, and quantified by STAR --quant  Mode GeneCounts function
Assembly: hg38
Supplementary files format and content: TXT read count

source_name: blood

extract_protocol:
Following four hours of treatment with platelet releasate, stimulated neutrophils were harvested and washed twice in PBS (500g x 5 min). RNA was isolated according to the TRIzol Reagent protocol (Invitrogen). RNA integrity (RIN) was determined, and samples were further processed if RIN > 7 and purity of > 1.9 (260nm/280nm).
Follow Illumina TruSeq kit

value: blood

value: Neutrophil

tag: gender

value: Male

tag: race

value: Asian

tag: bmi

tag: disease status

value: COVID-positive


title: iHEC_2 [E0_2]

value: liver

value: AICS-0023 iPSC

value: Induced Pluripotent Stem Cells


title: 80-1_T_T2_R2


title: ID83 positive

value: Female

value: White


title: iHEC RWV ORG + MTG_2 [E3DM_3]

value: iHEC RWV ORG + MTG


title: iHEC RWV ORG + MTG_1 [E3DM_2]


title: KR_C3


title: iHEC RWV ORG_1 [E3D_1]

value: iHEC RWV ORG


title: KQ_NTZ3

value: treated with nitazoxanide for 48 hours


title: iHEC_1 [E0_1]


title: ID90 positive


title: ID89 positive


title: iHEC MTG ORG_3 [E2D_4]

value: iHEC MTG ORG


title: S3D-Turbo_0700887171

city: Doha

first: Sara

last: Tomei

address: Gharrafa

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped to the human genome GRCh38.p13 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR_2.6.1d aligner
featureCounts v2.0.0 was used to generate the raw counts. We used DESeq2 (v1.32.0) to normalize read counts with standard settings.
Normalized data was transformed using variance-stabilizing transform (VST) and removed of the batch effect using limma::removeBatchEffect from Lima package (v3.48.2)
Heatmaps, correlation matrices and PCA plots were generated as relevant.
Assembly: hg38/GRCh38
Supplementary files format and content: VST normalized counts in excel format. File Name : VSTNormalizedCounts_batchadjustedwithlimma_60samples.xls

source_name: Blood (Tempus)

extract_protocol:
Column based and Bead based
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

tag: extraction method

value: Manual - Column Based

tag: agent

value: Dnase Treatment

tag: sample volume_(ul)

value: Blood (Tempus)


title: ID84 positive

value: blood


title: KR_C1

value: prostate cancer cells

value: untreated


title: KQ_NTZ2


title: ID134 negative

value: Neutrophil

value: Male

value: COVID-negative


title: S3C_Turbo_0700844431


title: KQ_NTZ1


title: ID143 negative

value: Asian


title: S3C_0700844371


title: S3B_Turbo_0700844421


title: KQ_C3


title: KQ_C2


title: ID98 negative


title: 6495-EC-S1_ROI_076

city: Ann Arbor

first: Marina

last: Pasca di Magliano

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

description: A total of 4 slides containing 6 tissue sections (2 healthy pancreas, 4 tumor) was submitted for spatial transcriptomics.  The Solid Tumor TME Morphology Kit was utilized according to manufacturer instructions to detect epithelial cells (pan-cytokeratin [CK]) and immune cells (CD45), together with DAPI for nuclei detection. 277 ROIs were captured for whole transcriptome profiling.

data_processing:
library strategy: NanoString GeoMx DSP
We used the GeoMxWorkflows package [https://bioconductor.org/packages/release/workflows/html/GeoMxWorkflows.html] for quality control and processing of Nanostring GeoMx data. Briefly, Quality control was performed to exclude the ROIs with less than 10% genes detection rate (less than 10% of the original WTA panel genes were detected) and exclude genes detected in less than 10% of the ROIs. Q3-normalization was performed for each ROI in the gene expression matrix followed by log normalization. For visualization purposes, we performed PCA analysis which clearly showed a batch effect. We used limma package batch correction function to regress out the batch effect which showed clustering of ROIs from the same cell type together. To define cell-type-specific markers, we used a linear mixed model to perform DGE between each cell type and the rest of the ROIs, similar to how we define markers in single cells data. The top 20 significantly upregulated marker genes were then used as a geneset for scoring using AUCell. The scores are then scaled and visualized on the UMAPs of the acinar/ductal cells subset. To score different PDAC subtypes (Classical, basal, exocrine-like, ADEX) for each ROI, we used Gene Set Variation Analysis (GSVA)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts of oligonucleotide probes for each AOI

source_name: primary PDAC tumor

growth_protocol: FFPE Blocks

extract_protocol:
Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics. During collection, each capture area was exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics. The released barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol.
The resulted libraries were sequenced by the Illumina NovaSeq 6000 platform using reversed, 2 x 27 base paired reads. The resulting GeoMx DSP data was then coupled to next generation sequencing (NGS) readout. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Slides were deparaffinized and subjected to antigen retrieval (Tris-EDTA, pH 9.0; 15 minutes; >99°C), and enzymatic exposure of RNA targets (1.0µg/ml Proteinase K; 15 minutes; 37°C). Slides were then hybridized with human whole transcriptome overnight (nanoString) at 37°C.  The next morning slides underwent stringent washes and were prepared for morphology marker staining. Slides were co-incubated with fluorescently labeled visualization antibodies to detect tumor cells (pan-cytokeratin [CK]), all immune cells (CD45), and with SYTO 13 for nuclei detection. The samples were imaged, and regions of interest (ROIs) were selected.

value: primary PDAC tumor

tag: molecule type

value: Oligonucleotide

tag: slide name

tag: roi

tag: segment

value: PANCK+(EPI)

tag: aoi

tag: area

tag: patient id

tag: diseasestatus

value: Tumor

tag: label


title: 6495-EC-S1_ROI_077

tag: tissue

tag: cell type

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6495-EC-S1_ROI_075


title: 6495-EC-S1_ROI_079

value: Acinar

value: PANCK-


title: Control.5

city: Newcaslte upon Tyne

first: James

middle: Mark

last: Allan

address: Herschel Building

country: United Kingdom

institute: Newcastle University

data_processing:
Sequencing reads were mapped to human genome build 37 (GRCh37) using STAR aligner (v2.5.3a). Two-passing mapping mode was used, with gene annotated features (Homo_sapiens.GRCh37.87.gtf) and the options of --twopassMode Basic and –sjdbOverhang 74.
Aligned reads were summarized over gene features using the featureCounts function in the R Bioconductor Rsubread package (v1.32.4).
We annotated ENSEMBL genes with the official gene symbols using R org.Hs.eg.db package (v3.7.0). ENSEMBL genes without official gene symbols were excluded. For a gene symbol with multiple ENSEMBL genes, we kept the ENSEMBLE gene having the largest number of reads across samples for that gene symbol.
Read counts of 24459 genes were then used for differential expression analysis.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes read counts in each sample

source_name: Myeloid

growth_protocol: HEL AML cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen) and quantified using a Qubit 2.0 Fluorometer with Qubit RNA BR assay kit (Thermo Fisher Scientific, MA, USA).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA with Ribo-Gold kit following the manufacturer's protocols.

value: Myeloid

tag: cell line

value: HEL AML

value: Myeloid leukaemia

tag: genotype

value: TET2 monoallelic mutation

tag: treatment


title: 6495-EC-S1_ROI_090


title: ID74 negative

value: blood

tag: gender

tag: age

tag: race

value: White

tag: bmi

tag: disease status


title: 6495-EC-S1_ROI_082

tag: molecule type

tag: slide name

tag: roi


title: 6495-EC-S1_ROI_074

tag: segment

tag: aoi

tag: area


title: KQ_C1

value: prostate cancer cells

value: untreated


title: 6495-EC-S1_ROI_081

tag: patient id

tag: diseasestatus

tag: label


title: S3A_0700886741

tag: extraction method

value: Manual - Column Based

tag: agent

tag: sample volume_(ul)

tag: cell type

value: Blood (Tempus)


title: ID70 negative

tag: tissue

value: Neutrophil

tag: gender

value: Male

tag: age

value: COVID-negative


title: 6495-EC-S1_ROI_073

value: primary PDAC tumor

value: Oligonucleotide

value: PANCK+(EPI)

value: Tumor


title: S3-50-3_0700887021

value: Automated - MAGMAX

value: Dnase Treatment


title: S3-50-2_0700887011


title: 6495-EC-S1_ROI_078

value: Acinar

value: PANCK-

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6495-EC-S1_ROI_080


title: 6495-EC-S1_ROI_070


title: Control.3

value: Myeloid

tag: cell line

value: HEL AML

value: Myeloid leukaemia

tag: genotype

value: TET2 monoallelic mutation

tag: treatment


title: Control.1


title: S3A-Turbo_0700887161

value: Manual - Column Based

value: Blood (Tempus)


title: S3-50-1_0700887001


title: S3D_0700886751


title: S3-200-3_0700887111


title: 6495-EC-S1_ROI_063

value: PanIN

tag: molecule type

tag: slide name

tag: roi


title: 6495-EC-S1_ROI_065

tag: segment

tag: aoi

tag: area


title: 6495-EC-S1_ROI_066

tag: patient id

tag: diseasestatus

tag: label


title: S3B_0700844361

tag: extraction method

tag: agent

tag: sample volume_(ul)


title: 6495-EC-S1_ROI_064

tag: tissue

tag: cell type


title: 6495-EC-S1_ROI_069


title: 6495-EC-S1_ROI_072


title: 6495-EC-S1_ROI_083


title: siRNA13D_drought_biol_rep_2

city: Montreal

first: William

last: BOUARD

state: QC

address: 141 Av. du Président-Kennedy

department: sciences biologiques

country: Canada

institute: UQAM

data_processing:
The wrapper script Trim-galore (version 0.6.3) was used to remove sequencing adapters (Illumina universal) and four additional bases at the 5’ and 3’ ends of each read, retained reads with a Phred quality score exceeding 30, and discarded reads shorter than 20 nucleotides.
Sequencing artifacts were filtered from the remaining reads using the Fastx_toolkit (version 0.0.14) and reads quality was verified with the FastQC tool (version 0.11.9).
Triticum aestivum reference transcriptome (release 52) was retrieved on Ensembl Plants and used for transcripts abundances quantification using Salmon (version 1.5.1) in quasi-mapping mode, with Kmer size set to 31.
Transcripts-levels count tables obtained with Salmon and the Triticum aestivum gff3-type annotation file (release 52 from Ensembl Plants) were used to determine differentially expressed genes in TaZFP13D OEX and TaZFP13DsiRNA samples with the DESeq2 software (version 2.11.40.7).
Assembly: triticum aestivum release 52 from Enesembl plant.
Supplementary files format and content: The processed data file is a matrix (.xlsx) containing gene-level normalized abundance measurements provided by the DESeq2 software (a mean value was calculated if different biological replicates were available).

organism: Triticum aestivum

source_name: second leaf

growth_protocol: Wheat seeds were inoculated with the 4RNAs Barley stripe mosaic virus using the previously described seed imbibition method (Cheuk and Houde 2017 Plant Methods (2017) 13:24 DOI 10.1186/s13007-017-0175-5). Wild-type plants (WT) without BSMV, were germinated in the same conditions with distilled water only. After 4 days of germination, wheat seedlings were potted in soil mix with a density of 10 plants per pot (13.5-13.5-13 cm; length-width-height).Plants were grown in a mixture of black earth, perlite, and peat moss (2:1:1, v:v:v) in E15 Conviron growth cabinets at 22 °C and 70% relative humidity, under a photon flux density of 100 µmol m-2 s-1 (fluorescent and incandescent lighting) and a 16 h / 8 h (day/night) photoperiod.

extract_protocol:
Samples are composed of complete second leaves from three different 21-days old wheat seedlings, harvested at the same time of day and flash-frozen in liquid nitrogen. Total RNA was extracted from plant tissues using the Monarch Total RNA Miniprep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control well-watered wheat plants were grown for 21 days and watered every day, while drought-treated plants were watered daily for 14 days, then, drought was initiated by withholding water for 7 days.

tag: cultivar

tag: developmental stage

value: 21 days post-germination

value: second leaf

value: Under-expressing TaZFP13D

value: well-watered 14 days and 7 days drought


title: siRNA13D_drought_biol_rep_1

tag: genotype

tag: treatment


title: 6495-EC-S1_ROI_071

value: primary PDAC tumor

tag: molecule type

value: Oligonucleotide

tag: slide name

value: PANCK+(EPI)

value: Tumor


title: S3-200-1_0700887091

value: Automated - MAGMAX

value: Dnase Treatment


title: Clone.3.3

value: Myeloid

tag: cell line

value: TET2 biallelic mutation


title: 6495-EC-S1_ROI_067

tag: roi

tag: segment

tag: aoi

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: Clone.3.4

value: HEL AML

value: Myeloid leukaemia


title: 6495-EC-S1_ROI_068

tag: area

tag: patient id

tag: diseasestatus


title: S3-200-2_0700887101

tag: extraction method

tag: agent

value: Blood (Tempus)


title: Clone.7.58

tag: tissue


title: OEX13D_drought_biol_rep_2


title: BSMV_drought

value: 4 RNAs BSMV empty vector


title: 6495-EC-S1_ROI_062

tag: cell type

value: PanIN

tag: label


title: 6495-EC-S1_ROI_058


title: OEX13D_drought_biol_rep_1

tag: cultivar

tag: developmental stage

value: 21 days post-germination

value: second leaf


title: WT_drought

tag: genotype

value: WT

tag: treatment

value: well-watered 14 days and 7 days drought


title: 6495-EC-S1_ROI_060

value: primary PDAC tumor

tag: molecule type

value: Oligonucleotide

tag: slide name


title: 6495-EC-S1_ROI_061

tag: roi

value: PANCK+(EPI)

value: Tumor


title: 6495-EC-S1_ROI_053

tag: segment


title: 6495-EC-S1_ROI_059

tag: aoi


title: siRNA13D_control_biol_rep_2

value: Under-expressing TaZFP13D

value: well-watered 21 days


title: siRNA13D_control_biol_rep_1


title: S3-150-3_0700887081

value: Automated - MAGMAX

value: Dnase Treatment

tag: sample volume_(ul)


title: S3-150-2_0700887071


title: OEX13D_control_biol_rep_2


title: S3-100-3_0700887051


title: S3-100-1_0700887031


title: S3-150-1_0700887061


title: 6495-EC-S1_ROI_056

tag: area

tag: patient id

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6495-EC-S1_ROI_049

value: Duct

tag: diseasestatus


title: 6495-EC-S1_ROI_050


title: S3-100-2_0700887041

tag: extraction method

tag: agent

value: Blood (Tempus)


title: 6495-EC-S1_ROI_048

tag: tissue

tag: cell type


title: 6495-EC-S1_ROI_057

tag: label


title: 6495-EC-S1_ROI_047

value: ADM


title: BSMV_control

tag: cultivar

tag: developmental stage

value: 4 RNAs BSMV empty vector


title: S2D_0700886731

value: Manual - Column Based


title: S2C-Turbo_0700887141


title: WT_control

value: 21 days post-germination

value: second leaf

tag: genotype

tag: treatment


title: 6495-EC-S1_ROI_046

value: Acinar

tag: molecule type

tag: slide name

value: PANCK-


title: 6495-EC-S1_ROI_039

value: primary PDAC tumor

value: Oligonucleotide

tag: roi

tag: segment


title: 6495-EC-S1_ROI_045

tag: aoi

value: Tumor


title: 6495-EC-S1_ROI_038

value: PANCK+(EPI)

tag: area


title: OEX13D_control_biol_rep_1

value: well-watered 21 days


title: 6495-EC-S1_ROI_044

tag: patient id


title: S2D-Turbo_0700887151

tag: sample volume_(ul)


title: 6495-EC-S1_ROI_042

tag: diseasestatus


title: 6495-EC-S1_ROI_043


title: 6495-EC-S1_ROI_035


title: S2C_0700886721

tag: extraction method

tag: agent


title: S2B_0700844351

tag: cell type


title: CNT_H11_P6_H11

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Alignment was performed with STAR, reads were counted with HTSeq and QC metrics were generated with RNA-SeQC.
The resulting count matrix was filtered by column for samples with more than 10^3 detected genes (counts > 0) and by row for coding genes (as defined by the MGI database) with a row sum across all samples > 500 counts (with a total number of 500 samples). The resulting normalized and filtered count matrix was then variance stabilized using the vst method from the DESeq2 R package. Surrogate variable analysis (SVA, R package) was performed on the vst count matrix to account for linear batch effects.
Assembly: mm10

source_name: Mouse INsulinoma 6

extract_protocol:
RNA was extracted from cells using TCL buffer (#1031576, Qiagen) with 1% beta-mercaptoethanol followed by an RNA clean-up with Agencourt RNA cleanup XP (#A63987, Beckman Coulter).
Bulk RNA (1 μl) was added to a 3 step cDNA synthesis reaction with 3’RT (5’- AGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’, IDT), template switching (5’-AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’, Qiagen), and ISPCR (5’-AAGCAGTGGTATCAACGCAGAGT-3’, IDT) oligos from the SMART-seq2 protocol 139. cDNA was purified using AMPure XP Agencourt (#100609, Beckman Coulter) and quantified using Qubit dsDNA High Sensitivity (#102689, Life Technologies). Samples were diluted to 0.2 ng/ul in TE and tagmented (Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina). Indexing was performed using the Nextera XT Index Kit (#FC-131-1001, Illumina). Final libraries were QCed using the Qubit dsDNA High Sensitivity kit and Bioanalyzer High Sensitivity DNA Kit (#5067-4627, Agilent).

treatment_protocol: 40,000 MIN6 cells/well were seeded in 96-well plates 24 h prior to treatment in three replicates. FFA library compound plates were transferred into assay plates which were then incubated for 24 h (n=6).

tag: cell line

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: 6495-EC-S1_ROI_037

tag: tissue

tag: label

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6495-EC-S1_ROI_036


title: 6495-EC-S1_ROI_040


title: K67375056_P6_H7

value: 24h 0.5mM Dodecanoic acid


title: 6495-EC-S1_ROI_031


title: S2B_Turbo_0700844411

value: Dnase Treatment

value: Blood (Tempus)


title: 6495-EC-S1_ROI_034

value: Duct


title: 6495-EC-S1_ROI_030


title: 6495-EC-S1_ROI_032


title: 6495-EC-S1_ROI_033


title: S2A_Turbo_0700844401

value: Manual - Column Based


title: K53322389_P6_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: S2A_0700844341


title: 6495-EC-S1_ROI_027


title: S2-50-2_0700886891

value: Automated - MAGMAX


title: CNT_H8_P6_H8


title: S2-50-3_0700886901


title: K03070961_P6_H9

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: 6495-EC-S1_ROI_041

value: Acinar

value: PANCK-


title: 6495-EC-S1_ROI_029

value: primary PDAC tumor

value: Oligonucleotide


title: 6495-EC-S1_ROI_025

value: PANCK+(EPI)

value: Tumor


title: K32311524_P6_H3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z), 8(Z)-Eicosadienoic acid


title: CNT_H5_P6_H5

value: 24h 0.5mM BSA


title: 6495-EC-S1_ROI_026

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6495-EC-S1_ROI_028


title: 6495-EC-S1_ROI_023


title: K80340869_P6_H2

value: 24h 0.5mM Tetradecanoic acid


title: S2-50-1_0700886881

value: Dnase Treatment

value: Blood (Tempus)


title: 6495-EC-S1_ROI_024


title: S2-200-2_0700886981


title: 6495-EC-S1_ROI_020


title: K46987408_P6_G11

value: 24h 0.5mM Heptadecanoic acid


title: S2-200-3_0700886991


title: 6495-EC-S1_ROI_022


title: 6495-EC-S1_ROI_017


title: 6495-EC-S1_ROI_021


title: CNT_H1_P6_H1


title: 6495-EC-S1_ROI_018


title: S2-200-1_0700886971


title: S2-150-2_0700886951


title: 6495-EC-S1_ROI_013

value: PanIN


title: K06763617_P6_H4

value: 24h 0.5mM Undecanoic acid


title: K63813237_P6_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: 6495-EC-S1_ROI_010


title: 6495-EC-S1_ROI_014


title: 6495-EC-S1_ROI_012


title: 6495-EC-S1_ROI_016


title: 6495-EC-S1_ROI_015


title: S2-150-3_0700886961

value: Automated - MAGMAX


title: K19189338_P6_G9

value: 24h 0.5mM 10-Undecenoic acid


title: 6495-EC-S1_ROI_006

value: primary PDAC tumor


title: K15536865_P6_G4


title: 6495-EC-S1_ROI_011

value: Oligonucleotide


title: S2-150-1_0700886941


title: K38686876_P6_G6

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: 6495-EC-S1_ROI_019

value: PANCK+(EPI)

value: Tumor


title: 6495-EC-S1_ROI_003


title: S2-100-3_0700886931


title: 6495-EC-S1_ROI_008


title: S2-100-2_0700886921


title: 6495-EC-S1_ROI_007


title: K75918321_P6_G3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: S2-100-1_0700886911


title: 6287-EC-S1_ROI_156

value: PANCK+(Epithelial)

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: K80325895_P6_G2

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: K91356052_P6_F11

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: 6495-EC-S1_ROI_005


title: K43021856_P6_G7

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: 6495-EC-S1_ROI_004

value: PanIN


title: S1D-Turbo_0700887131

value: Manual - Column Based

value: Dnase Treatment

value: Blood (Tempus)


title: S1B_Turbo_0700844391


title: 6495-EC-S1_ROI_009


title: CNT_F8_P6_F8

value: 24h 0.5mM BSA


title: CNT_G1_P6_G1


title: 6287-EC-S1_ROI_153

value: primary PDAC tumor

value: Acinar

value: PanCK-


title: S1B_0700844331


title: 6495-EC-S1_ROI_002

value: Oligonucleotide

value: PANCK+(EPI)


title: 6287-EC-S1_ROI_150

value: Tumor


title: S1D_0700886711


title: CNT_F12_P6_F12

value: Mouse INsulinoma 6 (MIN6)


title: 6495-EC-S1_ROI_001


title: S1C-Turbo_0700887121


title: 6287-EC-S1_ROI_157

value: Duct

value: PANCK+(Epithelial)


title: S1A_Turbo_0700844381


title: K65207153_P6_F4

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: S1-50-3_0700886781

value: Automated - MAGMAX


title: S1C_0700886701


title: 6287-EC-S1_ROI_155

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: K43930766_P6_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: 6287-EC-S1_ROI_152


title: K71795348_P6_F6

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: 6287-EC-S1_ROI_154


title: 6287-EC-S1_ROI_151


title: 6287-EC-S1_ROI_133

value: PoorlyDiffTumor


title: 6287-EC-S1_ROI_138


title: 6287-EC-S1_ROI_137


title: S1-200-3_0700886871

value: Dnase Treatment

value: Blood (Tempus)


title: CNT_F5_P6_F5

value: 24h 0.5mM BSA


title: 6287-EC-S1_ROI_130

value: primary PDAC tumor


title: S1A_0700844321

value: Manual - Column Based


title: 6287-EC-S1_ROI_136

value: Oligonucleotide


title: K95656032_P6_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: 6287-EC-S1_ROI_134

value: Tumor


title: 6287-EC-S1_ROI_132


title: 6287-EC-S1_ROI_135


title: S1-50-2_0700886771


title: K04565634_P6_E9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Octadecanoic acid


title: CNT_F1_P6_F1


title: 6287-EC-S1_ROI_124

value: Duct

value: PANCK+(Epithelial)


title: K07624241_P6_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: 6287-EC-S1_ROI_123

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6287-EC-S1_ROI_131


title: 6287-EC-S1_ROI_129


title: S1-50-1_0700886761

value: Automated - MAGMAX


title: 6287-EC-S1_ROI_149

value: Acinar

value: PanCK-


title: 6287-EC-S1_ROI_128


title: K18059238_P6_E11

value: 24h 0.5mM 6(Z), 9(Z), 12(Z)-Octadecatrienoic Acid


title: K72611551_P6_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: 6287-EC-S1_ROI_126


title: 6287-EC-S1_ROI_127


title: K81456670_P6_E2

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: S1-150-2_0700886831

value: Dnase Treatment

value: Blood (Tempus)


title: S1-200-2_0700886861


title: S1-150-3_0700886841


title: 6287-EC-S1_ROI_119

value: primary PDAC tumor

value: Oligonucleotide


title: 6287-EC-S1_ROI_125

value: Tumor


title: CNT_E1_P6_E1

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: S1-150-1_0700886821


title: 6287-EC-S1_ROI_120


title: 6287-EC-S1_ROI_122

value: Duct


title: 6287-EC-S1_ROI_121

value: PanIN

value: PANCK+(Epithelial)


title: S1-200-1_0700886851


title: 6287-EC-S1_ROI_052

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6287-EC-S1_ROI_053


title: S1-100-3_0700886811

value: Automated - MAGMAX


title: 6287-EC-S1_ROI_050


title: K00392230_P6_D11


title: K39534559_P6_D10

value: 24h 0.5mM Decanoic acid


title: 6287-EC-S1_ROI_118


title: K84290455_P6_D9

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: CNT_D8_P6_D8


title: 6287-EC-S1_ROI_046


title: 6287-EC-S1_ROI_049


title: 6287-EC-S1_ROI_044


title: 6287-EC-S1_ROI_048


title: 6287-EC-S1_ROI_047


title: 6287-EC-S1_ROI_045


title: S1-100-1_0700886791


title: 6287-EC-S1_ROI_042


title: K77749911_P6_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: CNT_D12_P6_D12


title: 6287-EC-S1_ROI_041


title: 6287-EC-S1_ROI_043


title: 6287-EC-S1_ROI_040


title: CNT_D5_P6_D5


title: K17709609_P6_D3

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: 6287-EC-S1_ROI_037


title: 6287-EC-S1_ROI_038


title: 6287-EC-S1_ROI_039


title: K29160692_P6_D2

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: S1-100-2_0700886801

value: Dnase Treatment


title: 6287-EC-S1_ROI_036


title: 6287-EC-S1_ROI_051


title: 6287-EC-S1_ROI_035

value: Acinar

value: PanCK-


title: 6287-EC-S1_ROI_034

value: primary PDAC tumor

value: Oligonucleotide


title: K80025777_P6_C11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(Z), 11(E)-octadecadienoic acid


title: K83944490_P6_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: 6287-EC-S1_ROI_032

value: Tumor


title: 6287-EC-S1_ROI_033


title: K20152659_P6_C9

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: 6287-EC-S1_ROI_031

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: K57739283_P6_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: 6287-EC-S1_ROI_029


title: 6287-EC-S1_ROI_028


title: 6287-EC-S1_ROI_030


title: 6287-EC-S1_ROI_027


title: 6287-EC-S1_ROI_026


title: K01624546_P6_C4

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: K47192521_P6_C3

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: K51131535_P6_C2

value: 24h 0.5mM 9(Z), 12(Z)-Octadecadienoic acid


title: 6287-EC-S1_ROI_020

value: PanIN

value: PANCK+(Epithelial)


title: 6287-EC-S1_ROI_024


title: 6287-EC-S1_ROI_019


title: 6287-EC-S1_ROI_025


title: 6287-EC-S1_ROI_023


title: 6287-EC-S1_ROI_022


title: 6287-EC-S1_ROI_017


title: 6287-EC-S1_ROI_016


title: K57135146_P6_B11

value: 24h 0.5mM 15(Z)-Tetracosenoic acid


title: K06914719_P6_B10

value: 24h 0.5mM 10(E)-Heptadecenoic acid


title: K57347788_P6_C7

value: 24h 0.5mM Heneicosanoic acid


title: 6287-EC-S1_ROI_015

value: primary PDAC tumor


title: 6287-EC-S1_ROI_014

value: Oligonucleotide


title: K33223064_P6_B9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Pentadecanoic acid


title: CNT_B8_P6_B8

value: 24h 0.5mM BSA


title: 6287-EC-S1_ROI_013

value: Tumor


title: 6287-EC-S1_ROI_012


title: 6287-EC-S1_ROI_011


title: 6287-EC-S1_ROI_010


title: K96144918_P6_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: 6287-EC-S1_ROI_009

value: Duct

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 6287-EC-S1_ROI_021


title: CNT_B5_P6_B5


title: 6287-EC-S1_ROI_006


title: 6287-EC-S1_ROI_005


title: 6287-EC-S1_ROI_004


title: K32862852_P6_B4

value: 24h 0.5mM 12-Methoxydodecanoic acid


title: 6287-EC-S1_ROI_003


title: 6287-EC-S1_ROI_002


title: 6287-EC-S1_ROI_001


title: 4895-EC-S7_ROI_030

source_name: donor pancreas

value: donor pancreas

value: PanCK

tag: location

value: Tail

value: Healthy


title: 4895-EC-S7_ROI_031


title: 4895-EC-S7_ROI_029

value: ADM


title: K18766551_P6_A11

tag: treatment

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: 4895-EC-S7_ROI_027

tag: molecule type


title: K14557781_P6_B7

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: 6287-EC-S1_ROI_008

value: primary PDAC tumor

value: PanIN

tag: slide name

value: PANCK+(Epithelial)


title: K25847431_P6_A9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(E), 12(E)-Octadecadienoic acid


title: 6287-EC-S1_ROI_007

value: Oligonucleotide

tag: roi

value: Tumor


title: 4895-EC-S7_ROI_026

tag: segment


title: 4895-EC-S7_ROI_023

tag: aoi


title: 4895-EC-S7_ROI_024

tag: area


title: K66986518_P6_A7

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: CNT_B12_P6_B12

value: 24h 0.5mM BSA


title: K63913457_P6_B3

value: 24h 0.5mM 11(Z), 14(Z), 17(Z)-Eicosatrienoic Acid


title: K56767655_P6_A10

value: 24h 0.5mM Eicosanoic acid


title: K04327383_P6_A6

value: 24h 0.5mM Hexadecanoic acid


title: 4895-EC-S7_ROI_022

value: donor pancreas

value: PanCK

value: Tail

tag: patient id

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 4895-EC-S7_ROI_021

value: ADM

value: Healthy


title: 4895-EC-S7_ROI_020


title: 4895-EC-S7_ROI_019

value: PanIN

value: Head


title: K16120488_P6_A4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tridecanoic acid


title: K08446574_P6_A2

value: 24h 0.5mM Nonadecanoic acid


title: 4895-EC-S7_ROI_016

value: Duct

value: Oligonucleotide


title: 4895-EC-S7_ROI_018


title: 4895-EC-S7_ROI_017


title: 4895-EC-S7_ROI_028


title: 4895-EC-S7_ROI_014


title: 4895-EC-S7_ROI_015


title: 4895-EC-S7_ROI_025


title: CNT_H12_P5_H12

value: 24h 0.5mM BSA


title: 4895-EC-S7_ROI_013


title: 4895-EC-S7_ROI_011


title: 4895-EC-S7_ROI_012


title: CNT_H11_P5_H11


title: 4895-EC-S7_ROI_010


title: 4895-EC-S7_ROI_009


title: K17040651_P5_H10

value: 24h 0.5mM 7(Z), 10(Z), 13(Z), 16(Z)-Docosatetraenoic Acid


title: 4895-EC-S7_ROI_007


title: 4895-EC-S7_ROI_008


title: K03070961_P5_H9

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: 4895-EC-S7_ROI_006


title: 4895-EC-S7_ROI_005


title: 4895-EC-S7_ROI_003


title: 4895-EC-S7_ROI_004


title: K67375056_P5_H7

value: 24h 0.5mM Dodecanoic acid


title: K53322389_P5_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: MCNT_P6_A1

value: 24h Media


title: 4895-EC-S7_ROI_001

value: donor pancreas

value: PanCK


title: K06763617_P5_H4

value: 24h 0.5mM Undecanoic acid


title: K32311524_P5_H3

value: 24h 0.5mM 5(Z), 8(Z)-Eicosadienoic acid


title: 4895-EC-S6_ROI_063

value: Acinar

value: PanCK CD45 negative

value: PanCK CD45 negative-aoi-001

value: Tail

value: Healthy

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 4895-EC-S6_ROI_062

value: Oligonucleotide


title: 4895-EC-S6_ROI_060

value: PanIN


title: 4895-EC-S6_ROI_061


title: 4895-EC-S6_ROI_059


title: K80340869_P5_H2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tetradecanoic acid


title: 4895-EC-S6_ROI_057


title: CNT_H1_P5_H1

value: 24h 0.5mM BSA


title: 4895-EC-S6_ROI_058


title: K46987408_P5_G11

value: 24h 0.5mM Heptadecanoic acid


title: CNT_H8_P5_H8


title: 4895-EC-S6_ROI_054

value: ADM


title: 4895-EC-S6_ROI_056

value: donor pancreas


title: K63813237_P5_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: 4895-EC-S6_ROI_055

value: PanCK


title: 4895-EC-S7_ROI_002

value: Head


title: 4895-EC-S6_ROI_053


title: 4895-EC-S6_ROI_052


title: 4895-EC-S6_ROI_051


title: K19189338_P5_G9

value: 24h 0.5mM 10-Undecenoic acid


title: 4895-EC-S6_ROI_050

value: Acinar

value: PanCK CD45 negative


title: 4895-EC-S6_ROI_049

value: PanCK CD45 negative-aoi-001


title: K43021856_P5_G7

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: 4895-EC-S6_ROI_048

value: Healthy

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 4895-EC-S6_ROI_064

value: Oligonucleotide

value: Tail


title: 4895-EC-S6_ROI_047


title: K38686876_P5_G6

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: 4895-EC-S6_ROI_046


title: 4895-EC-S6_ROI_045


title: 4895-EC-S6_ROI_043


title: K15536865_P5_G4


title: 4895-EC-S6_ROI_044


title: K75918321_P5_G3

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: K80325895_P5_G2

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: 4895-EC-S6_ROI_042

value: donor pancreas


title: 4895-EC-S6_ROI_040

value: Duct


title: 4895-EC-S6_ROI_041


title: CNT_G1_P5_G1

value: 24h 0.5mM BSA


title: 4895-EC-S6_ROI_037

value: PanCK

value: Head


title: 4895-EC-S6_ROI_038


title: 4895-EC-S6_ROI_035


title: 4895-EC-S6_ROI_033


title: 4895-EC-S6_ROI_036


title: CNT_F12_P5_F12


title: 4895-EC-S6_ROI_034


title: 4895-EC-S6_ROI_039


title: K57416915_P5_F10

value: 24h 0.5mM 6(E)-Octadecenoic acid


title: K91356052_P5_F11

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: K43930766_P5_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: 4895-EC-S6_ROI_031


title: 4895-EC-S6_ROI_032


title: CNT_F8_P5_F8


title: 4895-EC-S6_ROI_029

value: ADM


title: 4895-EC-S6_ROI_028

value: Healthy


title: 4895-EC-S6_ROI_030

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 4895-EC-S6_ROI_027

value: Oligonucleotide


title: K33396764_P5_F7

value: 24h 0.5mM 9(Z), 12(Z), 15(Z)-Octadecatrienoic Acid


title: K71795348_P5_F6

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: 4895-EC-S6_ROI_024


title: 4895-EC-S6_ROI_025


title: CNT_F5_P5_F5


title: K65207153_P5_F4

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: 4895-EC-S6_ROI_022


title: 4895-EC-S6_ROI_021


title: 4895-EC-S6_ROI_020

value: PanIN


title: 6287-EC-S1_ROI_018

value: primary PDAC tumor

value: PANCK+(Epithelial)

value: Tumor


title: 4895-EC-S6_ROI_018

value: donor pancreas

value: PanCK


title: K07992496_P5_F3

value: 24h 0.5mM 9(E)-Tetradecenoic acid


title: K95656032_P5_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: 4895-EC-S6_ROI_017

value: Head


title: 4895-EC-S6_ROI_015


title: 4895-EC-S6_ROI_016


title: CNT_F1_P5_F1

value: 24h 0.5mM BSA


title: 4895-EC-S6_ROI_019

value: Healthy


title: 4895-EC-S6_ROI_012

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: 4895-EC-S6_ROI_011

value: Oligonucleotide


title: K72611551_P5_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: 4895-EC-S6_ROI_026

value: ADM


title: 4895-EC-S6_ROI_013


title: K04565634_P5_E9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Octadecanoic acid


title: 4895-EC-S6_ROI_009

value: PanIN


title: 4895-EC-S6_ROI_008


title: 4895-EC-S6_ROI_007


title: 4895-EC-S6_ROI_006


title: 4895-EC-S6_ROI_023


title: 4895-EC-S6_ROI_003


title: K07624241_P5_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: 4895-EC-S6_ROI_005


title: 4895-EC-S6_ROI_002


title: 4895-EC-S6_ROI_014


title: 4895-EC-S6_ROI_001


title: 4895-EC-S7_ROI_050

value: Acinar

value: PanCK CD45 Negative

value: PanCK CD45 Negative-aoi-001


title: K18059238_P5_E11

value: 24h 0.5mM 6(Z), 9(Z), 12(Z)-Octadecatrienoic Acid


title: 4895-EC-S6_ROI_010

value: donor pancreas

value: PanCK


title: K18478158_P5_E4

value: 24h 0.5mM 6(Z), 9(Z), 12(Z), 15(Z)-Octadecatetraenoic acid


title: 4895-EC-S7_ROI_048

value: Head


title: K48097184_P5_E3

value: 24h 0.5mM 11(E)-Octadecenoic acid


title: 4895-EC-S6_ROI_004

value: Healthy

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: CNT_D12_P5_D12

value: 24h 0.5mM BSA


title: 4895-EC-S7_ROI_045

value: Oligonucleotide


title: K81456670_P5_E2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: K39965020_P5_E7


title: 4895-EC-S7_ROI_046


title: 4895-EC-S7_ROI_043

value: ADM


title: 4895-EC-S7_ROI_047


title: 4895-EC-S7_ROI_042


title: K00392230_P5_D11


title: 4895-EC-S7_ROI_041


title: K39534559_P5_D10

value: 24h 0.5mM Decanoic acid


title: 4895-EC-S7_ROI_040

value: Tail


title: 4895-EC-S7_ROI_039


title: CNT_E1_P5_E1


title: K84290455_P5_D9

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: 4895-EC-S7_ROI_038


title: CNT_D8_P5_D8


title: 4895-EC-S7_ROI_036


title: K35238727_P6_B2

value: 24h 0.5mM 12(Z) Heneicosenoic acid


title: 4895-EC-S7_ROI_037


title: K57491984_P5_D7

value: 24h 0.5mM 6(Z)-Octadecenoic acid


title: 4895-EC-S7_ROI_035

value: donor pancreas

value: Duct


title: 4895-EC-S7_ROI_034

value: PanCK


title: 4895-EC-S7_ROI_033

value: PanIN


title: K83944490_P5_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: 4895-EC-S7_ROI_032

value: Healthy


title: CNT_D5_P5_D5


title: control_WT_15

type: RNA

city: New York

first: Anna

last: Gaponova

address: 345 Park Avenue South

institute: Insilico Medicine

description: proximal tubule cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430A 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: microdissected proximal tubules of control mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Kidneys were collected for analyses at the time of sacrifice. The experimental protocols were approved by the appropriate licensing committee (Kanton Zürich Gesundheitsdirektion Veterinäramt; protocol ZH230/2019, ZH195/2020) at the University of Zurich.

extract_protocol: Total RNA extracted from microdissected proximal tubules of Ctns knockout mouse kidneys and controls.Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: CTNS WT


title: case_KO_18

description: proximal tubule cells

source_name: microdissected proximal tubules of Ctns knockout mouse

value: CTNS KO


title: control_WT_13

description: proximal tubule cells


title: control_WT_14

description: proximal tubule cells


title: K77749911_P5_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: HeLa_NS_72_2

city: Tokyo

first: Taku

last: Tanaka

address: 2-10-1 Okura, Setagaya

department: Ophthalmology

institute: National Center for Child Health and Development

hyb_protocol: 0.6 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Human Gene Expression Microarrays 8 × 60 K v3 (Agilent Technologies) for 17 hours at 65°C in a hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C with Gene Expression Wash Buffer 2 (Agilent Technologies), then air-dried immediately.

scan_protocol: Slides were scanned on an Agilent G2505C microarray scanner at 100% PMT and 3 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalized signal intensity (75th percentile shift normalized) calculated from the processed signal after Feature Extraction using the GeneSpring software version 12.1 (Agilent).

source_name: HeLa Cells

label_protocol: Total RNAs (50 ng) extracted from the macular and peripheral regions of retina were used to prepare Cy3-labelled target cRNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) followed by RNeasy column purification (QIAGEN).

growth_protocol: HeLa cells were grown in DMEM medium supplemented with 10% FBS and 1% Pen Strep.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) in accordance with the manufacturer’s instructions. The concentration and purity of the isolated RNA was evaluated using a NanoDrop LITE (Thermo Fisher Scientific, Waltham, MA, USA). The integrity of the RNA samples was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Seeded in 24-well plates 2 days before transfection, HeLa cells at a cell confluency of 50–70% were transfected with 50 µL of Opti-MEM I medium containing 5 pmol of siRNA specific for C7orf26 (C7 siRNA) and negative control siRNA with scrambled sequences (NS siRNA) using Lipofectamine™ RNAiMAX Transfection Reagent in accordance with the manufacturer’s instructions. Cells were harvested 72H after transfection for subsequent analysis.

tag: sirna

value: NS siRNA


title: Asthma patient 436

city: Seoul

first: Ji Eun

last: Lim

address: 26, Kyungheedae-ro, Dongdaemun-gu

department: Department of Biochemistry and Molecular Biology, School of Medicine

country: South Korea

institute: Kyung Hee University

data_processing:
Adapter sequences were trimmed by Trimmomatic (v0.39). Trimmed reads aligned using HISAT2 (v2.2.0) with referring hg19 genome. Aligned reads are sorted by samtools (v1.9). Raw counts of sequencing reads for the features are counted by HTSeq (v0.12.4).
The gene expressions were quantified in transcripts per million (TPM) using GENCODE v19. A gene was allowed for downstream analyses if its expression in at least 20 % of the samples was greater than 0.1 TPM and the read counts were greater than six.
Assembly: hg19
Supplementary files format and content: tab-delimited text file .txt with raw read counts for every sample
Supplementary files format and content: tab-delimited text file .txt with the Transcripts per Million (TPM) values for every sample

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted from PBMC using TRI Reagent solution (Invitrogen, USA) following manufacturer's instructions.
RNA exome sequencing libraries were prepared according to the manufacturer’s instructions (Swift RNA Library Kit and IDT Exome v2.0 kit).

value: peripheral blood mononuclear cells


title: Asthma patient 435


title: Asthma patient 434


title: K17709609_P5_D3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: HeLa_C7_72_2

value: C7 siRNA


title: HeLa_NS_72_1


title: Asthma patient 433


title: Asthma patient 431


title: HeLa_C7_72_1


title: case_KO_16

description: proximal tubule cells


title: case_KO_17

description: proximal tubule cells


title: Asthma patient 430


title: Asthma patient 432


title: K29160692_P5_D2

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: Asthma patient 428


title: CNT_D1_P5_D1

value: 24h 0.5mM BSA


title: 4895-EC-S7_ROI_049

value: Acinar

value: Oligonucleotide

value: PanCK CD45 Negative

value: PanCK CD45 Negative-aoi-001

value: Head

tag: diseasestatus

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: Asthma patient 426


title: K80025777_P5_C11

value: 24h 0.5mM 9(Z), 11(E)-octadecadienoic acid


title: K98002709_P5_C10

value: 24h 0.5mM 10(E)-Nonadecenoic acid


title: Asthma patient 425


title: Asthma patient 423


title: K20152659_P5_C9

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: Asthma patient 422


title: biopsy_EO-10_female_patient

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

country: France

institute: INRA

description: Gene expression patient

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 minutes in a volume of 55 μl containing 25× Agilent Fragmentation Buffer and 10× Agilent Blocking Agent. Subsequently, 55 μl of 2× Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array, in accordance with the recommended protocol. After hybridization, the microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37 °C using GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).

source_name: biopsy, EO-10, female, patient

label_protocol: Cyanine-3 (Cy3)-labelled cRNAs were prepared from 50 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). Specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Scientific, USA).

extract_protocol: Total RNAs were isolated using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA yield and purity were measured using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA)

treatment_protocol: Ten individuals affected by eosinophilic esophagitis (EO) and ten controls (CT) were studied. The analyses were carried out by comparing EO to CT

value: oesophagus biopsy

tag: individual

tag: Sex

value: female

tag: pathological state

value: eosinophilic esophagitis (EO) patient


title: Asthma patient 420

tag: tissue

value: peripheral blood mononuclear cells


title: K57347788_P5_C7

tag: cell line

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Heneicosanoic acid


title: Asthma patient 421


title: Asthma patient 419


title: Asthma patient 418


title: K57739283_P5_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: Asthma patient 429


title: Asthma patient 417


title: Asthma patient 416


title: K01624546_P5_C4

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: Asthma patient 427


title: Asthma patient 413


title: biopsy_EO-08_female_patient

description: Gene expression patient

source_name: biopsy, EO-08, female, patient


title: K47192521_P5_C3

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: Asthma patient 424


title: biopsy_CT-10_male_control

description: Gene expression control

source_name: biopsy, CT-10, male, control

value: male

value: control


title: Asthma patient 412


title: biopsy_EO-07_female_patient

description: Gene expression patient

source_name: biopsy, EO-07, female, patient


title: K51131535_P5_C2

value: 24h 0.5mM 9(Z), 12(Z)-Octadecadienoic acid


title: biopsy_CT-09_male_control

description: Gene expression control

source_name: biopsy, CT-09, male, control


title: biopsy_EO-09_male_patient

description: Gene expression patient

source_name: biopsy, EO-09, male, patient


title: biopsy_CT-08_male_control

description: Gene expression control

source_name: biopsy, CT-08, male, control


title: biopsy_EO-06_male_patient

description: Gene expression patient

source_name: biopsy, EO-06, male, patient


title: Asthma patient 415


title: Asthma patient 410


title: CNT_B12_P5_B12

value: 24h 0.5mM BSA


title: Asthma patient 414


title: biopsy_CT-07_male_control

description: Gene expression control

source_name: biopsy, CT-07, male, control


title: K57135146_P5_B11

value: 24h 0.5mM 15(Z)-Tetracosenoic acid


title: Asthma patient 408


title: K33223064_P5_B9

value: 24h 0.5mM Pentadecanoic acid


title: Asthma patient 407


title: Asthma patient 406


title: Asthma patient 404


title: K06914719_P5_B10

value: 24h 0.5mM 10(E)-Heptadecenoic acid


title: Asthma patient 403


title: Asthma patient 405


title: Asthma patient 409


title: Asthma patient 402


title: CNT_B8_P5_B8


title: Asthma patient 411


title: biopsy_EO-05_male_patient

description: Gene expression patient

source_name: biopsy, EO-05, male, patient


title: Asthma patient 401


title: biopsy_CT-05_male_control

description: Gene expression control

source_name: biopsy, CT-05, male, control


title: Asthma patient 399


title: Asthma patient 400


title: K14557781_P5_B7

source_name: Mouse INsulinoma 6

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: biopsy_EO-04_male_patient

description: Gene expression patient

source_name: biopsy, EO-04, male, patient

value: oesophagus biopsy


title: biopsy_CT-06_male_control

description: Gene expression control

source_name: biopsy, CT-06, male, control


title: Asthma patient 398


title: K96144918_P5_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: CNT_B5_P5_B5


title: Asthma patient 396


title: Asthma patient 397


title: biopsy_CT-03_male_control

description: Gene expression control

source_name: biopsy, CT-03, male, control


title: biopsy_EO-03_male_patient

description: Gene expression patient

source_name: biopsy, EO-03, male, patient

value: eosinophilic esophagitis (EO) patient


title: Asthma patient 394

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells


title: Asthma patient 395


title: K63913457_P5_B3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z), 14(Z), 17(Z)-Eicosatrienoic Acid


title: Asthma patient 392


title: Asthma patient 390


title: K35238727_P5_B2

value: 24h 0.5mM 12(Z) Heneicosenoic acid


title: biopsy_CT-02_male_control

description: Gene expression control

source_name: biopsy, CT-02, male, control


title: Asthma patient 388


title: K18766551_P5_A11

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: Asthma patient 389


title: biopsy_CT-01_male_control

description: Gene expression control

source_name: biopsy, CT-01, male, control


title: Asthma patient 387


title: case_S3595Nr30

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014). Quality trimming of the reads has not been performed.
RNA-Seq: Trimmed raw reads were aligned to rn5 using STAR (version 2.7.3) (Dobin et al. 2013).
Differential expression analysis between groups was performed with DESeq2 (version 1.24.0) (Love et al. 2014) in R (version 3.6.1) (R Core Team 2015). DESeq2 uses a negative binomial generalized linear model to test for differential expression based on gene counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: kidney cortex

extract_protocol:
RNA extracted from microdissected proximal tubules of Ctns knockout mouse kidneys and controls. RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
Library Preparation Kit: TruSeq Stranded mRNA (Illumina)

value: kidney cortex

tag: cell type

value: proximal tubule cells

tag: genotype

value: CTNS KO


title: K66986518_P5_A7

tag: treatment

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: Asthma patient 386


title: biopsy_EO-01_male_patient

description: Gene expression patient

source_name: biopsy, EO-01, male, patient

value: male


title: K32862852_P5_B4

value: 24h 0.5mM 12-Methoxydodecanoic acid


title: Asthma patient 393


title: Asthma patient 385


title: case_S3595Nr26


title: Asthma patient 382


title: K99906572_P5_A3

value: 24h 0.5mM 10(E)-Pentadecenoic acid


title: Asthma patient 384


title: Asthma patient 383


title: case_S3595Nr24


title: Asthma patient 380


title: Asthma patient 379


title: case_S3595Nr32


title: case_S3595Nr22


title: biopsy_CT-04_female_control

description: Gene expression control

source_name: biopsy, CT-04, female, control

value: female

value: control


title: biopsy_EO-02_male_patient

description: Gene expression patient

source_name: biopsy, EO-02, male, patient

value: oesophagus biopsy


title: case_S3595Nr20


title: Asthma patient 378


title: Asthma patient 376


title: CNT_H12_P4_H12

value: 24h 0.5mM BSA


title: Asthma patient 377


title: Asthma patient 391


title: case_S3595Nr18


title: Asthma patient 374


title: control_S3595Nr31

value: CTNS WT


title: Asthma patient 373

value: peripheral blood mononuclear cells


title: Asthma patient 375


title: K16120488_P5_A4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tridecanoic acid


title: CNT_H11_P4_H11


title: K08446574_P5_A2

value: 24h 0.5mM Nonadecanoic acid


title: Asthma patient 381


title: Asthma patient 371


title: Asthma patient 372


title: control_S3595Nr29


title: Asthma patient 369


title: K03070961_P4_H9

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: Asthma patient 370


title: control_S3595Nr27

value: kidney cortex


title: CNT_H8_P4_H8


title: Asthma patient 366


title: K67375056_P4_H7

value: 24h 0.5mM Dodecanoic acid


title: Asthma patient 368


title: control_S3595Nr25

value: proximal tubule cells


title: Asthma patient 365


title: control_S3595Nr23


title: Asthma patient 363


title: K17040651_P4_H10

value: 24h 0.5mM 7(Z), 10(Z), 13(Z), 16(Z)-Docosatetraenoic Acid


title: control_S3595Nr21


title: Asthma patient 361


title: Asthma patient 362


title: K53322389_P4_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: Asthma patient 360


title: Asthma patient 359


title: CNT_H5_P4_H5


title: control_S3595Nr17


title: Asthma patient 358


title: K80340869_P4_H2

value: 24h 0.5mM Tetradecanoic acid


title: K06763617_P4_H4

value: 24h 0.5mM Undecanoic acid


title: control_S3595Nr19


title: Asthma patient 357


title: KTZ_Low (PND22_Ktz3_m104)

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m104

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Rat reference transcriptome from the UCSC website (release rn6, downloaded in August 2020) using BWA version 0.7.4.4  was used to align the second reads
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,483 genes detected.

molecule: polyA RNA

source_name: Ovary

growth_protocol: Time-mated Sprague-Dawley rats were delivered at gestational day (GD) 3. Animals were kept under standard conditions with 12 h light/dark cycles and fed a standard soy- and alfalfa-free diet based on Altromin 1314  along with tap water in Bisphenol A-free bottles provided ad libitum. Animals were kept in pairs until GD17, thereafter individually.

extract_protocol:
RNA was isolated using Kit from Qiagen and stored at -80 ℃.
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.
3'Bulk RNA Barcoding sequencing

treatment_protocol: Rat dams were exposed to DES or KTZ from GD7. The rats were weighed and gavaged each morning with either vehicle control or test substances until three distinct postnatal stages (postnatal days 6, 14, and 22) using three different doses 3, 6 and 12 µg/kg bw/day for DES and 3, 6 and 12 mg/kg bw/day for KTZ.

value: Ovary

tag: age

value: wild type

tag: sample well

tag: barcode

value: TCGCGG

value: KTZ

tag: dose

value: 3 mg/kg bw/day


title: Asthma patient 356

value: peripheral blood mononuclear cells


title: PAOA_M_P4_G12

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Hexadecanoic acid and 9(Z)-Octadecenoic acid


title: Asthma patient 364


title: Asthma patient 355


title: KTZ_Low (PND6_Ktz3_m104)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m104

value: GGCACG


title: Asthma patient 354


title: Asthma patient 353


title: K63813237_P4_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: 4895-EC-S7_ROI_044

source_name: donor pancreas

value: donor pancreas

value: ADM

tag: molecule type

value: Oligonucleotide

tag: slide name

tag: roi

tag: segment

value: PanCK

tag: aoi

tag: area

tag: location

value: Head

value: Healthy

tag: label

value: Immunofluorescent tissue profiling was performed using PanCK (FITC) and CD45 (Cy3) to enable selection of 277 regions of interest (ROIs), segmented into panCK positive/CD45 negative areas of interest (AOIs) for spatial transcriptomics.


title: Asthma patient 352

tag: tissue


title: KTZ_Ctrl (PND6_Ctrl_m88)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m88

value: Ovary

tag: strain

value: GCTGGG

value: control

value: corn oil (vehicle control)


title: K19189338_P4_G9

tag: cell line

value: 24h 0.5mM 10-Undecenoic acid


title: Asthma patient 351

value: peripheral blood mononuclear cells


title: Asthma patient 350


title: TUN_4_P4_G8

value: Mouse INsulinoma 6 (MIN6)

value: 24h 5ng/ml Tunicamycin


title: Asthma patient 349


title: K43021856_P4_G7

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: KTZ_Ctrl (PND22_Ctrl_m88)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m88

tag: genotype

value: wild type

value: GCCTGC


title: Asthma patient 347


title: KTZ_Low (PND14_Ktz3_m104)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m104

value: GCAGGC

tag: treatment

value: KTZ

value: 3 mg/kg bw/day


title: Asthma patient 345


title: K38686876_P4_G6

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: Asthma patient 348


title: KTZ_Intermediate (PND6_Ktz6_m108)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m108

tag: age

value: CTGGGC

value: 6 mg/kg bw/day


title: THP_4_P4_G5

value: 24h 0.000001mM Thapsigargin


title: Asthma patient 343


title: Asthma patient 344


title: KTZ_Low (PND6_Ktz3_m103)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m103

value: Ovary

tag: sample well

value: CTCCGC


title: K15536865_P4_G4


title: Asthma patient 341


title: Asthma patient 342


title: Asthma patient 340


title: K75918321_P4_G3

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: KTZ_Low (PND22_Ktz3_m103)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m103

tag: barcode

value: GCGCCA


title: KTZ_Intermediate (PND22_Ktz6_m107)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m107

value: CGGCTG

tag: dose


title: Asthma patient 339

value: peripheral blood mononuclear cells


title: K80325895_P4_G2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: Asthma patient 338


title: Asthma patient 337


title: Asthma patient 346


title: KTZ_Low (PND22_Ktz3_m102)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m102

value: wild type

value: CGGAGC


title: CNT_F12_P4_F12

value: 24h 0.5mM BSA


title: Asthma patient 367


title: KTZ_Ctrl (PND22_Ctrl_m87)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m87

value: CGCGTG

value: control

value: corn oil (vehicle control)


title: KTZ_Low (PND14_Ktz3_m103)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m103

value: CGACGG

value: KTZ

value: 3 mg/kg bw/day


title: Asthma patient 336


title: Asthma patient 333


title: Asthma patient 335


title: Asthma patient 334


title: Asthma patient 332


title: K57416915_P4_F10

value: 24h 0.5mM 6(E)-Octadecenoic acid


title: Asthma patient 331


title: Asthma patient 330


title: KTZ_Ctrl (PND6_Ctrl_m87)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m87

value: Ovary

value: CGTCGC


title: KTZ_High (PND6_Ktz12_m112)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m112

value: CCGGGT

value: 12 mg/kg bw/day


title: K43930766_P4_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: Asthma patient 329

value: peripheral blood mononuclear cells


title: Asthma patient 328


title: Asthma patient 327


title: CNT_F8_P4_F8

value: Mouse INsulinoma 6 (MIN6)


title: KTZ_Intermediate (PND6_Ktz6_m107)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m107

value: wild type

value: CCGCAG

value: 6 mg/kg bw/day


title: Asthma patient 326


title: Asthma patient 325


title: K33396764_P4_F7

value: 24h 0.5mM 9(Z), 12(Z), 15(Z)-Octadecatrienoic Acid


title: KTZ_Low (PND6_Ktz3_m102)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m102

value: CCCGAG


title: K91356052_P4_F11

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: K71795348_P4_F6

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: Asthma patient 324


title: Asthma patient 323


title: KTZ_Ctrl (PND6_Ctrl_m86)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m86

value: CCCCAC

value: control

value: corn oil (vehicle control)


title: CNT_F5_P4_F5

value: 24h 0.5mM BSA


title: Asthma patient 321


title: KTZ_High (PND22_Ktz12_m112)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz12_m112

value: Ovary

value: CCACGC

value: KTZ


title: KTZ_Ctrl (PND14_Ctrl_m88)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m88

value: CCTCGG


title: KTZ_Intermediate (PND22_Ktz6_m105)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m105

value: CAGCGC


title: Asthma patient 320

value: peripheral blood mononuclear cells


title: Asthma patient 318


title: K07992496_P4_F3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(E)-Tetradecenoic acid


title: Asthma patient 317


title: Asthma patient 316


title: K95656032_P4_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: KTZ_Low (PND22_Ktz3_m101)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m101

value: wild type

value: CACCGG

value: 3 mg/kg bw/day


title: KTZ_Ctrl (PND22_Ctrl_m86)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m86

value: AGGCGG


title: Asthma patient 314


title: Asthma patient 313


title: KTZ_High (PDN14_Ktz12_m112)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz12_m112

value: AGCCGC

value: 12 mg/kg bw/day


title: BSA_M_P4_E12

value: #N/A


title: Asthma patient 312


title: Asthma patient 322


title: Asthma patient 310


title: KTZ_Intermediate (PDN14_Ktz6_m107)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz6_m107

value: ACGCGC

value: 6 mg/kg bw/day


title: Asthma patient 309


title: Asthma patient 311


title: K18059238_P4_E11

value: 24h 0.5mM 6(Z), 9(Z), 12(Z)-Octadecatrienoic Acid


title: K65207153_P4_F4

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: Asthma patient 319


title: K72611551_P4_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: Asthma patient 307


title: Asthma patient 308


title: KTZ_Low (PND14_Ktz3_m101)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m101

value: Ovary

value: ACCCGG

value: KTZ


title: Asthma patient 306

value: peripheral blood mononuclear cells


title: KTZ_Ctrl (PND14_Ctrl_m87)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m87

value: CTCTCC

value: control

value: corn oil (vehicle control)


title: K04565634_P4_E9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Octadecanoic acid


title: Asthma patient 305


title: KTZ_High (PND6_Ktz12_m111)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m111

value: wild type

value: TTGTCC


title: Asthma patient 315


title: CNT_F1_P4_F1

value: 24h 0.5mM BSA


title: TUN_3_P4_E8

value: 24h 50ng/ml Tunicamycin


title: Asthma patient 303


title: Asthma patient 301


title: KTZ_Intermediate (PND6_Ktz6_m106)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m106

value: TCCAAC

value: 6 mg/kg bw/day


title: KTZ_Low (PND6_Ktz3_m101)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m101

value: GTCAAG

value: 3 mg/kg bw/day


title: Asthma patient 300


title: K39965020_P4_E7


title: Asthma patient 302


title: K07624241_P4_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: KTZ_Ctrl (PND6_Ctrl_m85)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m85

value: Ovary

value: GGACAT


title: Asthma patient 299

value: peripheral blood mononuclear cells


title: Asthma patient 296


title: Asthma patient 295


title: Asthma patient 298


title: K48097184_P4_E3

value: 24h 0.5mM 11(E)-Octadecenoic acid


title: THP_3_P4_E5

value: 24h 0.00001mM Thapsigargin


title: K18478158_P4_E4

value: 24h 0.5mM 6(Z), 9(Z), 12(Z), 15(Z)-Octadecatetraenoic acid


title: KTZ_High (PND22_Ktz12_m111)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz12_m111

value: GAAGAC

value: KTZ

value: 12 mg/kg bw/day


title: Asthma patient 294


title: Asthma patient 297


title: Asthma patient 292


title: KTZ_Low (PND22_Ktz3_m76)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m76

value: wild type

value: CATCAG


title: KTZ_Intermediate (PND22_Ktz6_m80)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m80

value: CGACTT


title: Asthma patient 304


title: KTZ_Ctrl (PND22_Ctrl_m85)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m85

value: ATCGAG

value: control

value: corn oil (vehicle control)


title: Asthma patient 291


title: MCNT_P5_A1

value: Mouse INsulinoma 6 (MIN6)

value: 24h Media


title: case_S3595Nr28

value: kidney cortex

tag: cell type

value: proximal tubule cells

value: CTNS KO


title: KTZ_High (PDN14_Ktz12_m111)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz12_m111

value: Ovary

value: TTGGAT


title: Asthma patient 288

value: peripheral blood mononuclear cells


title: K81456670_P4_E2

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: Asthma patient 290


title: CNT_E1_P4_E1

value: 24h 0.5mM BSA


title: CNT_D12_P4_D12


title: KTZ_Intermediate (PDN14_Ktz6_m105)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz6_m105

value: TTTTAG

value: KTZ

value: 6 mg/kg bw/day


title: Asthma patient 287


title: Asthma patient 286


title: K00392230_P4_D11


title: Asthma patient 289


title: Asthma patient 293


title: KTZ_Low (PND14_Ktz3_m76)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m76

value: wild type

value: TTTATG

value: 3 mg/kg bw/day


title: K39534559_P4_D10

value: 24h 0.5mM Decanoic acid


title: Asthma patient 284


title: Asthma patient 283


title: KTZ_Ctrl (PND14_Ctrl_m86)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m86

value: TTGTTA

value: control

value: corn oil (vehicle control)


title: K84290455_P4_D9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: KTZ_High (PND6_Ktz12_m109)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m109

value: Ovary

value: TTCATA

value: 12 mg/kg bw/day


title: Asthma patient 280

value: peripheral blood mononuclear cells


title: Asthma patient 281


title: Asthma patient 285


title: CNT_D8_P4_D8

value: 24h 0.5mM BSA


title: Asthma patient 279


title: Asthma patient 278


title: Asthma patient 277


title: CNT_D5_P4_D5


title: KTZ_Low (PND6_Ktz3_m76)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m76

value: TTACTA


title: K83944490_P4_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: Asthma patient 276


title: KTZ_Intermediate (PND6_Ktz6_m105)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m105

value: TTATCA

value: KTZ

value: 6 mg/kg bw/day


title: Asthma patient 275


title: Asthma patient 273


title: Asthma patient 274


title: Asthma patient 272


title: K77749911_P4_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: KTZ_Intermediate (PND22_Ktz6_m79)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m79

value: wild type

value: TGAATA


title: K29160692_P4_D2

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: Asthma patient 270


title: Asthma patient 269


title: KTZ_Low (PND22_Ktz3_m75)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m75

value: TCTAAT

value: 3 mg/kg bw/day


title: Asthma patient 268


title: CNT_D1_P4_D1

value: Mouse INsulinoma 6 (MIN6)


title: Asthma patient 266


title: OA_M_P4_C12

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: Asthma patient 267


title: Asthma patient 264


title: KTZ_Ctrl (PND22_Ctrl_m60)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m60

value: Ovary

value: TCAAAA

value: control

value: corn oil (vehicle control)


title: KTZ_High (PDN14_Ktz12_m84)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz12_m84

value: TATTAC

value: 12 mg/kg bw/day


title: KTZ_Ctrl (PND6_Ctrl_m60)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m60

value: TTAACT


title: KTZ_High (PND22_Ktz12_m109)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz12_m109

value: TGTATT

value: KTZ


title: K80025777_P4_C11

value: 24h 0.5mM 9(Z), 11(E)-octadecadienoic acid


title: Asthma patient 271

value: peripheral blood mononuclear cells


title: Asthma patient 262


title: KTZ_Low (PND14_Ktz3_m75)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m75

value: wild type

value: TATAAG


title: KTZ_Intermediate (PDN14_Ktz6_m80)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz6_m80

value: TATCAT

value: 6 mg/kg bw/day


title: K17709609_P4_D3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: K98002709_P4_C10

value: 24h 0.5mM 10(E)-Nonadecenoic acid


title: Asthma patient 260


title: KTZ_Ctrl (PND14_Ctrl_m60)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m60

value: Ovary

value: TAGAAT


title: Asthma patient 258


title: Asthma patient 259


title: Asthma patient 257


title: TUN_2_P4_C8

value: 24h 500ng/ml Tunicamycin


title: Asthma patient 256


title: K57347788_P4_C7

value: 24h 0.5mM Heneicosanoic acid


title: Asthma patient 265


title: KTZ_High (PND6_Ktz12_m84)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m84

value: TACAAA

value: 12 mg/kg bw/day


title: Asthma patient 255


title: K57739283_P4_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: Asthma patient 254


title: Asthma patient 253


title: Asthma patient 263


title: KTZ_Intermediate (PND6_Ktz6_m80)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m80

value: TAATAG

value: KTZ


title: THP_2_P4_C5

value: 24h 0.0001mM Thapsigargin


title: KTZ_Low (PND6_Ktz3_m75)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m75

value: wild type

value: TAACAA

value: 3 mg/kg bw/day


title: Asthma patient 251

value: peripheral blood mononuclear cells


title: KTZ_Ctrl (PND6_Ctrl_m59)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m59

value: TAAAAC

value: control

value: corn oil (vehicle control)


title: K20152659_P4_C9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: K01624546_P4_C4

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: K47192521_P4_C3

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: Asthma patient 250


title: Asthma patient 249


title: Asthma patient 247


title: Asthma patient 246


title: Asthma patient 252


title: Asthma patient 248


title: K51131535_P4_C2

value: 24h 0.5mM 9(Z), 12(Z)-Octadecadienoic acid


title: KTZ_Intermediate (PND22_Ktz6_m78)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m78

value: Ovary

value: GATTAA

value: 6 mg/kg bw/day


title: Asthma patient 245


title: Asthma patient 243


title: KTZ_Low (PND22_Ktz3_m74)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m74

value: GAATAT

value: KTZ


title: CNT_B12_P4_B12

value: 24h 0.5mM BSA


title: KTZ_Ctrl (PND22_Ctrl_m59)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m59

value: wild type

value: CTTAAT


title: Asthma patient 242

value: peripheral blood mononuclear cells


title: Asthma patient 241


title: KTZ_High (PDN14_Ktz12_m83)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz12_m83

value: CTAAAA

value: 12 mg/kg bw/day


title: Asthma patient 240


title: PA_M_P4_A12

value: 24h 0.5mM Hexadecanoic acid


title: Asthma patient 239


title: KTZ_Intermediate (PDN14_Ktz6_m78)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz6_m78

value: CATAAA


title: Asthma patient 261


title: KTZ_High (PND22_Ktz12_m84)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz12_m84

value: GTTAAA


title: Asthma patient 238


title: Asthma patient 237


title: Asthma patient 236


title: K18766551_P4_A11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: KTZ_Low (PND14_Ktz3_m74)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m74

value: ATTTTG

value: 3 mg/kg bw/day


title: Asthma patient 235


title: Asthma patient 233


title: Asthma patient 234


title: K25847431_P4_A9

value: 24h 0.5mM 9(E), 12(E)-Octadecadienoic acid


title: Asthma patient 244


title: Asthma patient 282


title: KTZ_High (PND6_Ktz12_m83)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m83

value: Ovary

value: ATTATC


title: KTZ_Ctrl (PND14_Ctrl_m59)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m59

value: ATTGTT

value: control

value: corn oil (vehicle control)


title: K56767655_P4_A10

value: 24h 0.5mM Eicosanoic acid


title: TUN_1_P4_A8

value: 24h 5000ng/ml Tunicamycin


title: Asthma patient 232

value: peripheral blood mononuclear cells


title: K96144918_P4_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: Asthma patient 230


title: KTZ_Intermediate (PND6_Ktz6_m79)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m79

value: wild type

value: ATGTAA

value: KTZ

value: 6 mg/kg bw/day


title: K66986518_P4_A7

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: Asthma patient 229


title: Asthma patient 231


title: Asthma patient 228


title: K04327383_P4_A6

value: 24h 0.5mM Hexadecanoic acid


title: KTZ_Low (PND6_Ktz3_m74)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m74

value: ATCTAT

value: 3 mg/kg bw/day


title: KTZ_Ctrl (PND6_Ctrl_m58)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m58

value: Ovary

value: ATATGA


title: KTZ_High (PND22_Ktz12_m83)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz12_m83

value: ATAGAT

value: 12 mg/kg bw/day


title: Asthma patient 226


title: K99906572_P4_A3

value: 24h 0.5mM 10(E)-Pentadecenoic acid


title: KTZ_Intermediate (PND22_Ktz6_m77)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz6_m77

value: ATAAGT


title: Asthma patient 225

value: peripheral blood mononuclear cells


title: Asthma patient 224


title: Asthma patient 222


title: K08446574_P4_A2

value: 24h 0.5mM Nonadecanoic acid


title: Asthma patient 221


title: MCNT_P4_A1

value: 24h Media


title: Asthma patient 219


title: Asthma patient 220


title: Asthma patient 218


title: CNT_H12_P3_H12

value: 24h 0.5mM BSA


title: K16120488_P4_A4

value: 24h 0.5mM Tridecanoic acid


title: Asthma patient 216


title: Asthma patient 215


title: Asthma patient 214


title: K17040651_P3_H10

value: 24h 0.5mM 7(Z), 10(Z), 13(Z), 16(Z)-Docosatetraenoic Acid


title: KTZ_High (PDN14_Ktz12_m82)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz12_m82

value: wild type

value: ACTAAA

value: KTZ


title: KTZ_Intermediate (PDN14_Ktz6_m77)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PDN14_Ktz6_m77

value: AATTTC

value: 6 mg/kg bw/day


title: Asthma patient 213


title: Asthma patient 227


title: KTZ_Low (PND14_Ktz3_m73)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ktz3_m73

value: Ovary

value: AATGTA

value: 3 mg/kg bw/day


title: Asthma patient 223


title: K03070961_P3_H9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: Asthma patient 212


title: CNT_H8_P3_H8


title: KTZ_Ctrl (PND14_Ctrl_m57)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND14_Ctrl_m57

value: AATATG

value: control

value: corn oil (vehicle control)


title: Asthma patient 209

value: peripheral blood mononuclear cells


title: Asthma patient 210


title: KTZ_Ctrl (PND22_Ctrl_m57)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ctrl_m57

value: AGAATT


title: KTZ_Low (PND22_Ktz3_m73)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m73

value: AGTATA


title: KTZ_High (PND6_Ktz12_m82)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz12_m82

value: AAGTTA

value: 12 mg/kg bw/day


title: K67375056_P3_H7

value: 24h 0.5mM Dodecanoic acid


title: Asthma patient 207


title: Asthma patient 208


title: Asthma patient 217


title: K53322389_P3_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: KTZ_Intermediate (PND6_Ktz6_m77)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz6_m77

value: wild type

value: AACATA

value: KTZ


title: Asthma patient 205


title: Asthma patient 206


title: KTZ_Low (PND6_Ktz3_m73)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ktz3_m73

value: Ovary

value: AAATCA


title: Asthma patient 204


title: CNT_H11_P3_H11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: CNT_H5_P3_H5


title: K06763617_P3_H4

value: 24h 0.5mM Undecanoic acid


title: KTZ_Ctrl (PND6_Ctrl_m57)

description:
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND6_Ctrl_m57

value: AAACAT

value: control


title: DES_High (PND22_Des0,012_m100)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m100

value: TGGGCC

value: DES

value: 12 µg/kg bw/day


title: Asthma patient 202

value: peripheral blood mononuclear cells


title: Asthma patient 201


title: Asthma patient 211


title: K32311524_P3_H3

value: 24h 0.5mM 5(Z), 8(Z)-Eicosadienoic acid


title: Asthma patient 199


title: Asthma patient 198


title: Asthma patient 197


title: DES_Intermediate (PND22_Des0,003_m92)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m92

value: TCGCGG

value: 6 µg/kg bw/day


title: DES_Low (PND6_Des0,006_m96)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m96

value: wild type

value: GGCGCT

value: 3 µg/kg bw/day


title: Asthma patient 200


title: Asthma patient 196


title: Asthma patient 195


title: PAOA_M_P3_G12

value: 24h 0.5mM Hexadecanoic acid and 9(Z)-Octadecenoic acid


title: Asthma patient 194


title: DES_Ctrl (PND6_Ctrl_m88)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m88

value: Ovary

value: GCTGGG

value: corn oil (vehicle control)


title: Asthma patient 193


title: DES_High (PND22_Des0,012_m99)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m99

value: GCGTGG


title: Asthma patient 192


title: CNT_H1_P3_H1

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: K46987408_P3_G11

value: 24h 0.5mM Heptadecanoic acid


title: Asthma patient 191


title: DES_Intermediate (PND22_Des0,006_m96)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m96

value: GCGGCT

value: DES


title: Asthma patient 190

value: peripheral blood mononuclear cells


title: K63813237_P3_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: DES_Low (PND22_Des0,003_m91)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m91

value: GCGCCA


title: K19189338_P3_G9

value: 24h 0.5mM 10-Undecenoic acid


title: DES_Ctrl (PND22_Ctrl_m88)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m88

value: wild type

value: GCCTGC

value: control


title: Asthma patient 188


title: Asthma patient 186


title: Asthma patient 187


title: TUN_4_P3_G8

value: 24h 5ng/ml Tunicamycin


title: K80340869_P3_H2

value: 24h 0.5mM Tetradecanoic acid


title: Asthma patient 189


title: DES_High (PDN6_Des0,012_m100)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m100

value: Ovary

value: GACGGG

value: 12 µg/kg bw/day


title: K43021856_P3_G7

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: Asthma patient 184


title: Asthma patient 185


title: THP_4_P3_G5

value: 24h 0.000001mM Thapsigargin


title: Asthma patient 183


title: Asthma patient 182


title: Asthma patient 180


title: Asthma patient 181


title: Asthma patient 179


title: Asthma patient 178


title: K75918321_P3_G3

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: K15536865_P3_G4


title: DES_High (PND22_Des0,012_m98)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m98

value: CGGGTC

value: DES


title: Asthma patient 177

value: peripheral blood mononuclear cells


title: DES_Ctrl (PND6_Ctrl_m87)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m87

value: CGTCGC

value: corn oil (vehicle control)


title: Asthma patient 175


title: DES_Intermediate (PND22_Des0,006_m95)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m95

value: wild type

value: CGGCTG

value: 6 µg/kg bw/day


title: Asthma patient 174


title: Asthma patient 173


title: K80325895_P3_G2

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: DES_Intermediate (PND6_Des0,006_m95)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m95

value: CTGGGC


title: K38686876_P3_G6

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: CNT_G1_P3_G1

value: 24h 0.5mM BSA


title: CNT_F12_P3_F12


title: DES_Low (PND22_Des0,003_m90)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m90

value: Ovary

value: CGGAGC

value: 3 µg/kg bw/day


title: Asthma patient 170


title: Asthma patient 172


title: DES_Low (PND6_Des0,003_m91)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m91

value: CTCCGC


title: DES_Ctrl (PND22_Ctrl_m87)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m87

value: CGCGTG

value: control


title: Asthma patient 176


title: Asthma patient 168


title: Asthma patient 203


title: K57416915_P3_F10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 6(E)-Octadecenoic acid


title: DES_Ctrl (PND14_Ctrl_m88)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m88

value: CCTCGG


title: Asthma patient 169

value: peripheral blood mononuclear cells


title: Asthma patient 166


title: K91356052_P3_F11

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: Asthma patient 167


title: DES_High (PDN6_Des0,012_m99)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m99

value: wild type

value: CCGGGT

value: DES

value: 12 µg/kg bw/day


title: Asthma patient 165


title: Asthma patient 164


title: Asthma patient 158


title: Asthma patient 159


title: K71795348_P3_F6

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: CNT_F5_P3_F5

value: 24h 0.5mM BSA


title: K43930766_P3_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: Asthma patient 171


title: K33396764_P3_F7

value: 24h 0.5mM 9(Z), 12(Z), 15(Z)-Octadecatrienoic Acid


title: Asthma patient 160


title: Asthma patient 163


title: CNT_F8_P3_F8


title: Asthma patient 157


title: Asthma patient 161


title: Asthma patient 162


title: Asthma patient 156


title: DES_Intermediate (PND6_Des0,006_m94)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m94

value: Ovary

value: CCGCAG

value: 6 µg/kg bw/day


title: DES_High (PND22_Des0,012_m97)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m97

value: CCACGC


title: Asthma patient 154


title: DES_Low (PND6_Des0,003_m90)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m90

value: CCCGAG

value: 3 µg/kg bw/day


title: Asthma patient 152


title: DES_Ctrl (PND6_Ctrl_m86)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m86

value: CCCCAC

value: control

value: corn oil (vehicle control)


title: K65207153_P3_F4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: DES_Ctrl (PND22_Ctrl_m86)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m86

value: wild type

value: AGGCGG