title: AZ39_TSB3_Biofilm

description: AZ39_TSB3_Biofilm.MPS12302041-F02.3401.4

tag: genotype/variation

value: PIA- biofilm positive

tag: sample type

value: Mature biofilm in TSBg


title: Serum-5

status: Public on Jul 14 2020

type: RNA

city: Chengdu

first: Rui

last: Gao

state: Sichuan

address: No. 37 GuoXue Xiang

country: China

institute: West China Hospital, Sichuan University

description: circRNA

hyb_protocol: •The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2(8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA extracted using miRNeasy Serum/Plasma Kit (50) (Qiagen, Germany) following manufacturer's instructions

tag: age

value: over 50 years of age

tag: disease state

value: non-POCD

tag: tissue

value: serum


title: Serum-3

description: circRNA

value: Postoperative cognitive dysfunction


title: Serum-4

description: circRNA


title: AZ39_TSB2_Biofilm

type: SRA

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

country: Canada

institute: University of Ottawa

description: AZ39_TSB2_Biofilm.MPS12302041-E02.3401.4

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were subjected to trimming to remove adaptor and low quality sequences
The transcriptome of each strain has been assembled on normalized reads using the Trinity assembler (Garber et al., 2011). Transcripts were subjected to trinotate annotation and additionally BLAT against the fully sequenced reference genome, S. epidermidis genomes RP62A.
Differential exploratory analysis was applied to the gene expression levels, quantified by the counts-per-million reads by the RSEM log2(CPM) (counts-per-million reads). Differential expression analysis was done using DESeq (Anders & Huber, 2010)
Genome_build: S. epidermidis RP62A genome (GenBank accession number: CP000029.1)
Supplementary_files_format_and_content: logCPM values; normalized raw gene counts for every gene and every sample

organism: Staphylococcus epidermidis

growth_protocol: Staphylococcus epidermiis strains (AZ22, AZ39 and ST02) were routinely cultured on Trypticase Soy Agar (TSA) or in Trypticase Soy Broth (TSB) incubated aerobically overnight at 37°C. Biofilms of staphylococcal strains were grown in TSB supplemented with 0.5% glucose (TSBg) for 24 h at 37°C.

extract_protocol:
Total RNA was isolated from the mature biofilms of S. epidermidis strains grown in TSBg or PCs using FastRNA Pro Blue (MP Biomedicals, Irvine, CA, US). All RNA samples were treated with AmbionTM DNase I (Thermo Fisher Scientific) to digest genomic DNA. Samples exposed to PCs were further treated to remove contaminating eukaryotic RNA using MICROBEEnrichTM kit (Ambion).
Ribosomal RNA (rRNA) was removed using Ribo-ZeroTM Meta-Bacteria kit (Epicentre) and strand-specific sequencing libraries were constructed using TruSeq kits (Epicentre). The generation of the cluster was performed using standard Illumina protocols with sequencing performed using an Illumina HiSeq 2500 sequencer from paired-end reads with a target read length of 100 nucleotides.

treatment_protocol: S. epidermidis strains were introduced into Platelet Concentrates and incubated for 5 days at 20-24°C with agitation in a platelet incubator. Initial bacterial concentration of ~107 CFU/ml in a final volume of 50 ml was used.

tag: strain


title: Midbrain control rep2

city: Safed

first: Bodhisattwa

last: Banerjee

address: 8 Henrietta Szold Street

department: Faculty of Medicine

country: Israel

institute: Bar-Ilan University

description:
Mb_novel_lnc_raw_counts.txt
Mbc2

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads with Q≥30 were selected for the downstream analysis. The raw reads were aligned to the latest zebrafish genome (GRCz11) from Ensembl using STAR v2.7.3 and transcripts were assembled by StringTie using the reference annotation from Ensembl.
The expression level of each transcript was calculated and normalized as transcripts per million (TPM).
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Brain

extract_protocol:
A total of 18 fish (9 hypoxic and 9 normoxic) were sacrificed after anesthetizing with 0.03% tricaine (Sigma-Aldrich, Germany), and brains were separated and placed in ice-cold HBSS (1X Hank’s basal salt solution, 2.5 mM HEPES-KOH, pH 7.4, 35 mM glucose). Three sub-regions of the brain were dissected, and RNA was isolated using the NucleoSpin RNA XS kit (Macherey-Nagel, Germany) following the manufacture’s protocol. The RNA quality and concentration were measured in the QIAxcel Advanced system (Qiagen, Germany) using QIAxcel RNA QC Kit v2.0 (Qiagen) and Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA). The RNA samples with an RNA integrity score (RIS) value of more than eight were used in further processing.
Ribosomal RNA was depleted from the total RNA using the Ribo-Zero Gold rRNA removal kit (Human/Mouse/Rat) (Illumina, USA). The ribo-depleted RNA was used to create a strand-specific RNA sequencing (ssRNA-seq) library, according to the TruSeq® Stranded Total RNA sample preparation guide.

treatment_protocol: A group of zebrafish was exposed to hypoxic conditions (1.15±0.6 mg/l of dissolved oxygen)

value: midbrain

tag: developmental stage

value: adult

tag: treatment

value: control


title: muscle_35wk_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Read quality trimming was performed with Trimmomatic version 0.33 (java -jar trimmomatic-0.33.jar PE ... SLIDINGWINDOW:5:20 MINLEN:30).
Reads were mapped versus Nothobranchius furzeri genome version NotFur1 using STAR 2.4.2a (--outFilterMismatchNoverLmax 0.1).
Reads were counted per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters.
The raw gene counts were joined to a common matrix.
The matrix of gene counts was normalized with DESeq.
Genome_build: Nothobranchius furzeri NotFur1
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all homologous genes.

organism: Nothobranchius furzeri

source_name: skeletal muscle

extract_protocol:
RNA was isolated from skeletal muscle tissue from 3 fishes for each condition (young, adult and old) using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and libraries integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 30M reads per library with 2x75bp paired end setup.

value: skeletal muscle

tag: age (weeks)


title: Midbrain control rep1

description:
Mb_novel_lnc_raw_counts.txt
Mbc1


title: Male_4LFD_Adipose_biological replicate 1

city: New York City

first: Dimitris

last: Nasias

state: New York

address: 550 1st Avenue

department: Langone Medical School

country: USA

institute: New York University

hyb_protocol: as per Affymetrix instructions

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix/ThermoFisher Scientific)

data_processing: Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.2 was used first for the normalization, summarization and quality control of the microarray data. In the next step, TAC was used for the determination of the differentially expressed genes by performing p-value and fold change thresholds (Two Way Analysis of Variance (Two-Way ANOVA): p-value <0.05 and absolute fold change >1.5).

label: biotin

organism: Mus musculus

source_name: Male mouse, LFD, 4 weeks, Adipose, biological replicate 1

label_protocol: The aRNA was purified, reverse transcribed and the resulting cDNA was fragmented, labelled and hybridized overnight to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays.

growth_protocol: ApoE3Leiden and hCETP transgenic mice were obtained from TNO Leiden (Leiden, The Netherlands). All mice were bred at the animal facility of the Institute of Molecular Biology and Biotechnology of Heraklion, Greece under pathogen free conditions on a 12h light/dark cycle with free access to food and water. Heterozygous male apoE3L.CETP mice were included in the experiments.

extract_protocol: PureLink® RNA Mini Kit (ThermoFisher Scientific) was used for RNA isolation according to the manufacturer's instructions. Sample processing was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix/ThermoFisher Scientific).Starting from total RNA, first and second strand cDNA synthesis was performed. The double stranded cDNA was transcribed to aRNA (amplified RNA) during in vitro transcription (IVT).

treatment_protocol: Starting at the age of 12 weeks, heterozygous male apoE3L.CETP mice were randomized based on body weight and were fed for 4, 8 and 12 weeks with either a low fat diet (LFD) (D12450B, Research diets, New Brunswick, USA) containing 20% protein, 70% carbohydrate and 10% fat (LFD) or a high fat diet (HFD) (D14010701, Research diets, New Brunswick, USA) containing 20% protein, 20% carbohydrate, 60% fat and 0,25% cholesterol (HFD, n=6-7 mice per group). All animals were anesthetized with isoflurane and euthanized by cardiac puncture at the end of diet administration. All experimental protocols in mice were in accordance with institutional guidelines and were approved by the Greek Federal Veterinary Office (License #8595/2015).  Clinical measurements in mice have been previously described (doi: 10.1002/jcp.28649).

value: adipose

value: 16 weeks

tag: genotype

tag: diet

value: LFD, 4 weeks

tag: gender

value: male


title: muscle_35wk_2


title: Serum-2

description: circRNA


title: Serum-6

description: circRNA


title: Forebrain hypoxic rep2

description:
Fb_novel_lnc_raw_counts.txt
Fbt2

value: forebrain

value: hypoxia


title: AZ39_PC1_Biofilm

value: Mature biofilm in PC


title: AZ39_TSB1_Biofilm

description: AZ39_TSB1_Biofilm.MPS12302041-D02.3401.4

value: PIA- biofilm positive


title: Male_4LFD_Adipose_biological replicate 2

source_name: Male mouse, LFD, 4 weeks, Adipose, biological replicate 2


title: RE90 [miRNA]

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ssc10.2 whole genome using bowtie with parameters -t -a -v 1 -p 16 --sam --quiet  --phred33-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
For each miRNA expression level, reads Per Million (RPM or TPM) was calculated. For multiply aligned reads, we divided the read by its total hits and assigned the proportion to the miRNA to calculate the reads and TPM number.
DEmiRs between the test sample and control sample were analyzed by using Fisher Exact Test. Before testing, miRNA aligned reads was normalized by the lowess method. For each miRNA, the p-value was computed and the significance threshold to control FDR at a given value was calculated. The fold changes were also estimated. 0.01 p-value and 2 fold change were set as the threshold to define DEmiRs.
Genome_build: Ssc10.2
Supplementary_files_format_and_content: tab-delimited excel files include reads and TPM values for each Sample

organism: Sus scrofa

source_name: longissimus muscles

extract_protocol:
Musucle samples were harvested, flash frozen on dry ice, 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sows were fed with a normal or calorie-restricted diet after mating

value: embryo

value: longissimus muscles

tag: time

value: 90 days of gestation


title: Male_4HFD_Adipose_biological replicate 2

source_name: Male mouse, HFD, 4 weeks, Adipose, biological replicate 2

value: HFD, 4 weeks


title: muscle_35wk_1


title: Midbrain control rep3

description:
Mb_novel_lnc_raw_counts.txt
Mbc3


title: Forebrain hypoxic rep1

description:
Fb_novel_lnc_raw_counts.txt
Fbt1


title: muscle_20wk_3


title: AZ22_PC3_Biofilm


title: Male_4HFD_Adipose_biological replicate 3

source_name: Male mouse, HFD, 4 weeks, Adipose, biological replicate 3


title: Male_4HFD_Adipose_biological replicate 1

source_name: Male mouse, HFD, 4 weeks, Adipose, biological replicate 1


title: NE90 [miRNA]


title: Male_Chow_Adipose_biological replicate 2

source_name: Male mouse, chow diet, baseline, Adipose, biological replicate 2

value: 12 weeks

value: chow diet, baseline


title: AZ22_PC2_Biofilm


title: Male_Chow_Adipose_biological replicate 1

source_name: Male mouse, chow diet, baseline, Adipose, biological replicate 1


title: muscle_20wk_2


title: RE55 [miRNA]

value: 55 days of gestation


title: AZ22_PC1_Biofilm


title: Forebrain control rep2

description:
Fb_novel_lnc_raw_counts.txt
Fbc2

value: adult

value: control


title: muscle_20wk_1

value: skeletal muscle


title: Serum-1

description: circRNA

value: over 50 years of age

value: Postoperative cognitive dysfunction

value: serum


title: muscle_05wk_3


title: NE55 [miRNA]


title: AZ22_TSB3_Biofilm

description: AZ22_TSB3_Biofilm.MPS12302041-C02.3401.4

source_name: AZ22 TSB_biofilm

value: Mature biofilm in TSBg


title: RE35 [miRNA]

value: 35 days of gestation


title: Forebrain control rep1

description:
Fb_novel_lnc_raw_counts.txt
Fbc1

value: forebrain


title: AZ22_TSB2_Biofilm

description: AZ22_TSB2_Biofilm.MPS12302041-B02.3401.4

value: PIA- biofilm positive


title: muscle_05wk_1


title: muscle_05wk_2


title: NE35 [miRNA]

value: embryo


title: Forebrain control rep3

description:
Fb_novel_lnc_raw_counts.txt
Fbc3


title: AZ22_TSB1_Biofilm

description: AZ22_TSB1_Biofilm.MPS12302041-A02.3401.4


title: HJ028_Mut2: upf1 mutant rep2

status: Public on Jul 13 2020

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

data_processing:
Basecalling was performed with Illumina NextSeq Control Software/RTA2. Libraries were demultiplexed with bcl2fastq version: 2.17.1.14 .
Reads were aligned to the GRCz10 genome assembly using STAR-2.5.2b with the following settings: annotated splice junctions were based on Ensembl release 83 GTF file, maximum intron size was set to 11000. Bams obtained from reads corresponding to the same sample were merged with samtools v.1.3.1.
Detection of differential splicing events was performed using rMATS v.3.2.5 on merged bam files. Following parameters were specified: read length (75), read type (paired),  cutoff splicing difference (0.0001), analysis type (unpaired), library type (fr-firststrand). Mutant bam files were submitted as group 1 (-b1), and wild type as group 2 (-b2). Alternative splicing events supported by reads spanning splice junctions were reported.
Reads corresponding to the same samples were merged, separately for each pair mate. Transcript isoform-wise expression was quantified using salmon v.0.7.2 on merged reads and following parameters: library type ISR, maxOcc 20, maxReadOcc 20, coverage 0.8, useVBOpt, numBootstraps 30. Reference fasta file was generated by running tophat-2.0.13 gtf_to_fasta on GRCz10 genome fasta and ensemble release 83 gtf file. Fmd type salmon index was generated.
Differential transcript isoform expression analysis was performed in R 3.3.1 using R packages wasabi (v0.2) and sleuth (v. 0.28.1).
The number of reads per annotated gene (based on Ensembl 83 zebrafish gene annotation) were counted on bam files with featureCounts version v1.5.0-p1. Fragments were only counted if both ends aligned on the same chromosome (-C and -B options) with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene (library type 2). Only primary alignments were counted.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files include differential alternative splice events generated by rMATs. Tab-delimited text files include differentially expressed transcripts obtained by analysis with sleuth. Tab-delimited text files include read counts generated by featureCounts.

molecule: polyA RNA

source_name: 5 dpf larva

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma) following the  manufacturer's instructions. After treatment with Cloned DNaseI (Takara),  RNA extraction using TRI Reagent was repeated. RNA quality was determined using the 2100 Bioanalyzer instrument (Agilent) and RNA concentration was determined using Qbit 2.0 Fluorometer (Life Technologies).
RNA libraries were prepared for sequencing using the TruSeq stranded total RNA sample preparation with polyA selection (RS-122-2101).

value: homozygous for upf1  nonsense mutation

value: TLEK

value: whole body


title: HJ028_Mut3: upf1 mutant rep 3

value: homozygous for upf1 nonsense mutation


title: HJ028_Mut4: upf1 mutant rep 4


title: HJ028_WT4: control rep 4

value: wt


title: HJ028_WT2: conrol rep 2


title: HJ028_WT3: control rep 3


title: HJ028_Mut1: upf1  mutant rep1


title: HJ028_WT1: control rep 1


title: SYN

city: Shanghai

first: Hengqing

last: Cui

state: Shanghai

address: 639 Zhizaoju Road

institute: Shanghai 9th People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 version 2.1.0 with default parameters
Gene Ontology (GO) analysis was performed with R package. Top GO categories were selected according to the P values of expression changes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Polydactyly-BMSCs

extract_protocol:
Total RNAs was extracted from passage 3 of cultured MAC-BMSCs (n=2) and PD-BMSCs (n=2) by using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: polydactyly

value: male

value: bone marrow

value: PIK3CA wild type

tag: cell type

value: bone marrow mesenchymal stem cells (BMSCs)


title: ZQN


title: JJX

source_name: Macrodactyly-BMSCs

value: macrodactyly

value: female

value: PIK3CA mutation type


title: CYX


title: BCR39_Bulk_IGHV1-2

city: Cambridge

first: Maya

last: Sangesland

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT, and Harvard

data_processing:
The resulting paired end FASTQs were aligned using MiXCR (Bolotin et al., 2015).
Within this alignment step, we applied the following parameter: OvParameters.geneFeatureToAlign = {FR3Begin:Vend}, and constrained alignment to heavy chain matches only. We trimmed low sequence quality reads using the default settings within MiXCR.
Using custom scripts within immunarch (v0.5.5) tcR (Nazarov et al., 2015), we reconfigured the sequenced naïve IgM BCRs to generate frequency plots of CDRH3 length and assigned Kabat numbering for amino acid composition of 16aa length CDRH3s.
Genome_build: IMGT
Supplementary_files_format_and_content: tab delimited txt file

source_name: Splenic B cells

extract_protocol:
Mouse spleens were removed and single cell suspensions were obtained using 70 um cell strainer.
CDRH3 diversity within the transgenic mice was measured by deep sequencing the B cell receptors (BCRs) from antigen naïve IgM B cells in bulk according to our previously deployed method (Sangesland et al., 2019; Trombetta et al., 2014). Briefly, BCR libraries were enriched from B cell whole transcriptome amplification (WTA) products using the Smart-Seq2 protocol. Following WTA, antibody heavy chains were PCR amplified (FR3 to CDR3) using a forward primer specific for the FR3 region within the VH gene of interest (IGHV1-69 or IGHV1-2) and reverse primers against the heavy constant regions. These primers were attached to the Illumina P7 (FR3 region) and P5 (constant region) as described previously (Sangesland et al., 2019). We then further amplified the heavy chain sequences using step-out PCR with the Illumina sequencing adapters. The resulting PCR products (FR3 through CDRH3) were sequenced using the Illumina Miseq system (MiSeq Reagent Kit v2 500-cycle; Illumina, San Diego, US).

tag: antibody chain

value: VH

value: Splenic B cells

tag: experiment

value: Naïve Bulk

tag: molecule subtype

value: BCR Amplicon from RNA


title: BCR38_Bulk_IGHV1-69


title: Cal-L microarray sample 6

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: small intestine - whole length

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). Fortyseven of 48 Cy3-labeled samples  were used for the reference pool (Cy3 sample nr 8 was not used).

growth_protocol: C57BL/6N, 24 weeks old, male

extract_protocol: Total RNA was isolated from whole small intestine using Trizol isolation, quantified using Nanodrop (IsoGen Life Science) and qualified using Agilent RNA 6000 Nano kit (Agilent).

treatment_protocol: All mice started with a one week adaptation phase, in which they were fed a high-fat diet (except STD group). During the intervention all mice received experimental diets fo 8 weeks. Animals were fed ad libitum prior anaestetization and sacrification.   Diet details: standard chow (STD) is a low-fat (3.5 % wt/wt) chow Ssniff R/M-H (Chow; Ssniff Spezialdieten GmbH, Soest, Germany); cHF is composite corn oil-based control high-fat (cHF; fat ~35% wt/wt) supplemented with alpha-tocopherol; cHF-F (Fish oil diet)  i.e. cHF, in which 15% of lipids is replaced by EPAX1050TG concentrate (EPAX AS, Norway) containing ~60% EPA+DHA (i.e. ~31.5g EPA/DHA per kg diet); Krill-L Low-dose Krill diet i.e. cHF, supplemented with Krill oil, matching the amount (i.e. 52.5 g) of EPAX 1050TG found in the cHF-F diet and thus corresponding to approx. 1/3 of EPA/DHA content in the cHF-F diet (i.e. ~10.8g EPA/DHA per kg diet) ; Krill-H High-dose Krill diet i.e. cHF, supplemented with Krill oil, matching dietary EPA/DHA content with respect to cHF-F diet (i.e. ~31.5g EPA/DHA per kg diet); Calanus is a low-dose Calanus diet i.e. cHF, supplemented with Calanus oil, matching the amount (i.e. 52.5 g) of EPAX 1050TG found in the cHF-F diet, corresponding to approx. 1/5 of EPA/DHA content in the cHF-F diet (i.e. ~5.846 g EPA/DHA per kg diet).

tag: sample type

value: C57BL/6N, male, adult, small intestine (whole tissue)

value: adult

value: small intestine


title: Cal-L microarray sample 2

tag: age


title: Cal-L microarray sample 4


title: Cal-L microarray sample 8


title: Krill-H microarray sample 5


title: Krill-L microarray sample 2


title: Krill-L microarray sample 6


title: Barrow June 2014

type: genomic

city: Tromso

first: Brandon

middle: T

last: Hassett

address: Framstredet

department: Arctic and Marine Biology

country: Norway

institute: University of Tromso

hyb_protocol: See GeoChip protocol

scan_protocol: See GeoChip protocol

data_processing: The CORS is used to normalize the sample signal across the array and between arrays.

molecule: genomic DNA

organism: marine sediment metagenome

source_name: Under ice marine sediment

label_protocol: The biological sample was labeled with Cy3 and a common oligo nucleotide reference standard (CORS) target was labeled with Cy5.

growth_protocol: Sampled directly from environment

extract_protocol: MoBio Power Soil kit

treatment_protocol: Stored in sterile polypropylene tubes in the dark at -80C until DNA extraction

value: environmental

tag: gps

organism: synthetic construct

tag: reference


title: Krill-H microarray sample 1

tag: strain

tag: tissue


title: Krill-H microarray sample 4


title: cHF-F microarray sample 8


title: Krill-L microarray sample 8


title: Cal-L microarray sample 5


title: Cal-L microarray sample 7


title: Cal-L microarray sample 3


title: Krill-L microarray sample 1


title: Cal-L microarray sample 1


title: Krill-H microarray sample 7


title: Krill-L microarray sample 7


title: Krill-L microarray sample 3


title: Krill-L microarray sample 5


title: Krill-H microarray sample 3


title: Barrow May 2014

source_name: common oligo nucleotide reference standard


title: cHF-F microarray sample 5


title: SJ5108

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

data_processing:
Raw FASTQ files were trimmed with skewer
Trimmed reads were aligned to human transcriptome iGenomes hg38 with GSNAP
Gene counting were performed with HTSEQ-count
Individual count table were combined with R statistical software to create a raw count matrix
Raw count matrix was then normalized by size factor with DESEQ2
Genome_build: Hg38
Supplementary_files_format_and_content: Raw gene count matrix and normalized gene count matrix in tab separated value file format

source_name: Nasal brush

extract_protocol:
RNA was purified from sample lysates using the Quick-RNATM MiniPrep kit (Zymo Research). Lysates were centrifuged at 16,000xg for 2 minutes in a QIAshredder (Qiagen) to homogenize sample and remove insoluble debris before beginning standard manufacturer protocol with inclusion of optional DNase step. RNA was eluted in 30 mL of DNase/RNase free water and eluent was passed through the column one additional time to ensure maximum RNA recovery from filter.
KAPA Biosystems mRNA HyperPrep whole transcriptome libraries (Roche) were constructed with 250 ng RNA per sample and 12 cycles of library amplification. Libraries were barcoded using Illumina Dual-Index adapters (Integrated DNA Technologies) and paired-end sequenced using the  Illumina HiSeq 2000 system.

value: Nasal airway epithelium

tag: asthma status

value: healthy control


title: Krill-L microarray sample 4

value: male


title: Krill-H microarray sample 2


title: cHF-F microarray sample 1


title: Krill-H microarray sample 8


title: cHF-F microarray sample 6


title: cHF-F microarray sample 7


title: Krill-H microarray sample 6


title: cHF microarray sample 5


title: cHF microarray sample 8


title: cHF-F microarray sample 3


title: cHF-F microarray sample 4


title: STD microarray sample 8


title: cHF microarray sample 6


title: cHF microarray sample 3


title: STD microarray sample 2


title: SJ5401

value: asthmatic


title: cHF microarray sample 2


title: SJ5046


title: cHF microarray sample 7


title: cHF microarray sample 1


title: STD microarray sample 7


title: STD microarray sample 5


title: STD microarray sample 1


title: SJ1423


title: SJ1176


title: SJ1107


title: SJ1079


title: HR5709


title: HR5708


title: HR5710


title: STD microarray sample 4


title: STD microarray sample 6


title: STD microarray sample 3


title: cHF-F microarray sample 2


title: HR5725


title: HR5726


title: HR5701


title: HR5705


title: HR5703


title: HR5704


title: HR5700


title: HR5697


title: HR5698


title: HR5695


title: HR5696


title: HR5694


title: HR5706


title: HR5693


title: HR5689


title: HR5690


title: HR5692


title: HR5688


title: HR5687


title: HR5699


title: HR5686


title: HR5680


title: HR5682


title: HR5685


title: HR5683


title: HR5679


title: HR5678


title: HR5677


title: HR5676


title: HR5675


title: HR5670


title: HR5669


title: HR5672


title: HR5707


title: HR5671


title: HR5665


title: HR5666


title: HR5691


title: HR5667


title: HR5664


title: HR5684


title: HR5681


title: HR5663


title: HR5660


title: HR5674


title: HR5662


title: HR5656


title: HR5673


title: HR5658


title: HR5657


title: HR5659


title: HR5668


title: HR5655


title: HR5643


title: HR5661


title: HR5650


title: HR5644


title: HR5639


title: HR5652


title: HR5651


title: HR5649


title: HR5648


title: HR5646


title: HR5647


title: HR5638


title: HR5642


title: HR5637


title: HR5641


title: HR5654


title: HR5640


title: HR5627


title: HR5635


title: HR5653


title: HR5636


title: HR5634


title: HR5633


title: HR5632


title: HR5631


title: HR5621


title: HR5630


title: HR5629


title: HR5628


title: HR5626


title: HR5645


title: HR5625


title: HR5614


title: HR5612


title: HR5610


title: HR5611


title: HR5622


title: HR5620


title: HR5608


title: HR5604


title: HR5624


title: HR5606


title: HR5603


title: HR5605


title: HR5618


title: HR5613


title: HR5617


title: HR5615


title: HR5609


title: HR5581


title: HR5532


title: HR5523


title: HR5623


title: HR5579


title: HR5517


title: HR5616


title: HR5601


title: cHF microarray sample 4


title: HR5600


title: HR5602


title: HR5583


title: HR5582


title: HR5484


title: HR5499


title: HR5496


title: HR5495


title: HR5580


title: HR5527


title: HR5526


title: HR5510


title: HR5525


title: HR5503


title: HR5500


title: HR5501


title: HR5493


title: HR5446


title: HR5476


title: HR5478


title: HR5445


title: HR5474


title: HR5452


title: HR5443


title: HR5442


title: HR5468


title: HR5473


title: HR5434


title: HR5431


title: HR5441


title: HR5427


title: HR5429


title: HR5475


title: HR5489


title: HR5444


title: HR5438


title: HR5439


title: HR5426


title: HR5415


title: HR5424


title: HR5425


title: HR5409


title: HR5430


title: HR5399


title: HR5393


title: SJ5398


title: HR5379


title: HR5394


title: HR5384


title: HR5370


title: HR5366


title: HR5362


title: HR5392


title: HR5360


title: HR5387


title: HR5383


title: HR5372


title: HR5402


title: HR5365


title: HR5385


title: HR5390


title: HR5376


title: HR5359


title: HR5343


title: HR5349


title: HR5358


title: HR5350


title: HR5337


title: HR5357


title: HR5342


title: HR5335


title: HR5325


title: HR5333


title: HR5352


title: HR5324


title: HR5354


title: HR5348


title: HR5336


title: HR5303


title: HR5341


title: HR5317


title: HR5301


title: HR5316


title: HR5381


title: HR5363


title: HR5299


title: HR5334


title: HR5298


title: HR5295


title: HR5286


title: HR5319


title: HR5322


title: HR5285


title: HR5318


title: HR5345


title: HR5278


title: HR5314


title: HR5296


title: HR5276


title: HR5300


title: HR5274


title: HR5293


title: HR5272


title: HR5273


title: HR5263


title: HR5292


title: HR5289


title: HR5257


title: HR5287


title: HR5283


title: HR5282


title: HR5280


title: HR5275


title: HR5253


title: HR5271


title: HR5248


title: HR5279


title: HR5277


title: HR5247


title: HR5270


title: HR5267


title: HR5240


title: HR5244


title: HR5266


title: HR5238


title: HR5260


title: HR5259


title: HR5236


title: HR5246


title: HR5255


title: HR5250


title: HR5206


title: HR5172


title: HR5245


title: HR5165


title: HR5168


title: HR5241


title: HR5243


title: HR5117


title: HR5218


title: HR5212


title: HR5179


title: HR5170


title: HR5344


title: HR5148


title: HR1883


title: HR1882


title: HR1881


title: HR5147


title: HR1879


title: HR1212


title: HR5239


title: HR5111


title: HR1876


title: HR1874


title: HR5103


title: HR1873


title: HR1872


title: HR1884


title: HR1867


title: HR1868


title: HR1880


title: HR1866


title: HR1877


title: HR1860


title: HR1878


title: HR5019


title: HR1875


title: HR1856


title: HR1854


title: HR1871


title: HR1848


title: HR5109


title: HR1869


title: HR1864


title: HR1863


title: HR1865


title: HR1844


title: HR1859


title: HR1858


title: HR1857


title: HR1862


title: HR1841


title: HR1837


title: HR1836


title: HR1839


title: HR1838


title: HR1850


title: HR1835


title: HR1852


title: HR1851


title: HR1832


title: HR1846


title: HR1849


title: HR1843


title: HR1834


title: HR1855


title: HR1847


title: HR1829


title: HR1842


title: HR1840


title: HR1823


title: HR1821


title: HR1833


title: HR1828


title: HR1816


title: HR1814


title: HR1811


title: HR1827


title: HR1826


title: HR1824


title: HR1831


title: HR1825


title: HR1804


title: HR1810


title: HR1808


title: HR1820


title: HR1822


title: HR1819


title: HR1818


title: HR1799


title: HR1798


title: HR1817


title: HR1796


title: HR1812


title: HR1815


title: HR1794


title: HR1809


title: HR1807


title: HR1806


title: HR1789


title: HR1805


title: HR1802


title: HR1801


title: HR1800


title: HR1813


title: HR1777


title: HR1795


title: HR1793


title: HR1792


title: HR1791


title: HR1790


title: HR1773


title: HR1787


title: HR1788


title: HR1772


title: HR1786


title: HR1785


title: HR1770


title: HR1768


title: HR1766


title: HR1784


title: HR1783


title: HR1781


title: HR1779


title: HR1775


title: HR1780


title: HR1776


title: HR1778


title: HR1774


title: HR1765


title: HR1769


title: HR1771


title: HR1762


title: HR1763


title: HR1782


title: HR1767


title: HR1760


title: HR1759


title: HR1757


title: HR1764


title: Tumor_Neuroblast_190

city: Berlin

first: Ana

last: Veloso

state: Berlin

address: Hannoversche Strasse 28

institute: Berlin Institute for Medical Systems Biology (BIMSB-MDC)

data_processing:
Quality control, alignment and matrix generation using Pigx RNAseq pipeline (Wurmus R, Uyar B, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A. PiGx: Reproducible genomics analysis pipelines with GNU Guix. Gigascience. 2018 Oct 2.)
Genome_build: BDGP6.81 dm6 (Drosophila melanogaster)
Supplementary_files_format_and_content: NBs_gene_expression_matrix.tsv

organism: Drosophila melanogaster

growth_protocol: Third instar larvae were grown on VDRC yeasted "Normal Food" (recipe: https://www.viennabiocenter.org/fileadmin/user_upload/VBCF/VDRC/Downloads/VDRC_normal_fly_food_recipe_v4_Dec2018.pdf) at 29ºC in 60% humidity to boost UAS-Gal4-dependent over-expression

extract_protocol:
Central brains (CB) from 6-7 days old wandering third instar larvae were dissected (ventral nerve cord was manually removed during the dissection procedure) and enzymatically dissociated (see Seehorse metabolic analysis) into 200mL of PSM, filtered through. Five control (UAS-Dcr2/+; inscGal4, UAS-CD8::GFP/+; sh-mCherry/+) and three tumor CBs (UAS-Dcr2/+; inscGal4, UAS-CD8::GFP/+; sh-brat/+) were respectively dissected for this experiment. Cells were filtered through a 40mm cell strainer cap tube (Falcon) and single cells were immediately FACS-sorted into 4mL of lysis buffer [0.2% Triton-X100 complemented with 1:20 (v/v) Recombinant RNase Inhibitor (RRI, Clontech)] in 96 wells plates. Following the enzymatic dissociation (30ºC), cells were always maintained at 4ºC and immediately frozen at -80ºC once in their recipient lysis buffer.
1uL oligo dT primer (10M) and 1uL of dNTPs mix (10mM) were added to each well. Samples were incubated at 72ºC for 3min and put immediately on ice. 5.7uL of the following reverse-transcription master mix was added: 0.5uL SuperScript II (Invitrogen 18064-4-014); 0.25uL RNAse inhibitor (Clonetech 2313A); 2uL SuperScript II 1st Buffer (5x) (Invitrogen 18064-4-014); 0.5uL DTT (Invitrogen 18064-4-014); 2uL Betaine (5M) (Sigma 61962-50G); 0.06uL MgCl2 (1M) (Sigma M8266-100G); 0.2uL TSO (100uM) (IDT); 0.29uL H2O. Samples were mixed, spin down and incubated as following: 42ºC, 90min; 10x [50ºC, 2min; 42ºC, 2min]; 70ºC, 15min. 15uL of the following PCR master mix was added to each well: 12.5uL Kapa Hifi Hotstart ready mix (KK2601); 0.025uL IS Primers (IDT); 2.475uL H2O. Samples were mixed, spin down and incubated as following: 98ºC, 3min; 18x [98ºC, 20s; 67ºC, 15s; 72ºC, 6min]; 72ºC, 4min. 25uL of AMPure XP beads (Beckman Coulter) were added to each reaction. 8min incubation at room temperature (RT), 5min on the magnet. Supernatant was discarded. Beads were washed 2x with 100uL of 80-85% Ethanol. Beads were dried for 5min. 19uL of H2O was added to elute the cDNA. 3min incubation at RT, 2min on the magnet. The 17uL were transferred into a new plate.  19uL of Tn5 Tagmentation were added into each well of a new 96w plate: 14uL H2O; 4uL 5x TAPS buffer (T5130-250G); 1uL Tn5 ready to use (in house made); 1uL of cDNA was then transferred to the mastermix. Incubate 7min at 55ºC. Add 2uL of 1% SDS to each well. Incubate 10min at 70ºC.  22uL of AMPure XP beads (Beckman Coulter) were added to each reaction. 8min incubation at room temperature (RT), 5min on the magnet. Supernatant was discarded. Beads were washed 2x with 100uL of 80-85% Ethanol. Beads were dried for 5min. 12uL of H2O was added to elute the cDNA. 3min incubation at RT, 2min on the magnet. 10uL were transferred into a new plate.  Nextera primers (Sigma) (2.5uL 7xx primer; 2.5uL 5xx primer per well) and 15uL Kapa Hifi Hotstart ready mix were added to each well of the plate and incubated as followed: 98ºC, 10s; 18x [98ºC, 10s; 65ºC, 30s; 72ºC, 30s]; 72ºC, 5min. 30uL of AMPure XP beads (Beckman Coulter) were added to each reaction. 8min incubation at room temperature (RT), 5min on the magnet. Supernatant was discarded. Beads were washed 2x with 100uL of 80-85% Ethanol. Beads were dried for 5min. 19uL of H2O was added to elute the cDNA. 3min incubation at RT, 2min on the magnet. 17uL were transferred into a new plate.  Libraries were quality controlled on the Fragment Analyzer (Agilent), pooled and sequenced (50bp single-read, HiSeq 2500 Illumina Sequencing).

value: UAS-Dcr2/+; inscGal4, UAS-CD8::GFP/+; sh-brat (BL34646)/+

tag: tissue of origin

value: larval central brain

tag: developmental stage


title: Tumor_Neuroblast_191

tag: genotype

value: 6-7 days old wandering third instar larvae


title: Tumor_Neuroblast_188


title: Tumor_Neuroblast_192


title: Tumor_Neuroblast_184


title: HR1753


title: HR1755


title: HR1761


title: Tumor_Neuroblast_181


title: Tumor_Neuroblast_189


title: Tumor_Neuroblast_187


title: Tumor_Neuroblast_186


title: Tumor_Neuroblast_176


title: Tumor_Neuroblast_177


title: HR1758


title: Tumor_Neuroblast_179


title: Tumor_Neuroblast_183


title: HR1752


title: HR1751


title: HR1747


title: Tumor_Neuroblast_178


title: HR1756


title: HR1744


title: Tumor_Neuroblast_180


title: Tumor_Neuroblast_175


title: Tumor_Neuroblast_182


title: Tumor_Neuroblast_185


title: HR1743


title: HR1749


title: HR1748


title: Tumor_Neuroblast_170


title: HR1746


title: HR1742


title: Tumor_Neuroblast_171


title: HR1741


title: HR1750


title: Tumor_Neuroblast_172


title: Tumor_Neuroblast_173


title: Tumor_Neuroblast_167


title: Tumor_Neuroblast_169


title: Tumor_Neuroblast_166


title: Tumor_Neuroblast_168


title: HR1740


title: HR1738


title: HR1739


title: Tumor_Neuroblast_174


title: HR1745


title: HR1736


title: Tumor_Neuroblast_165


title: Tumor_Neuroblast_163


title: HR1735


title: Tumor_Neuroblast_162


title: HR1733


title: HR1732


title: HR1734


title: Tumor_Neuroblast_161


title: Tumor_Neuroblast_160


title: HR1731


title: Tumor_Neuroblast_159


title: Tumor_Neuroblast_158


title: Tumor_Neuroblast_157


title: HR1730


title: HR1728


title: HR1729


title: Tumor_Neuroblast_154


title: HR1737


title: HR1727


title: HR1726


title: HR1725


title: Tumor_Neuroblast_164


title: Tumor_Neuroblast_153


title: Tumor_Neuroblast_152


title: HR1723


title: Tumor_Neuroblast_150


title: Tumor_Neuroblast_149


title: HR1722


title: Tumor_Neuroblast_148


title: Tumor_Neuroblast_147


title: Tumor_Neuroblast_151


title: Tumor_Neuroblast_146


title: Tumor_Neuroblast_156


title: HR1724


title: HR1717


title: Tumor_Neuroblast_145


title: Tumor_Neuroblast_144


title: HR1718


title: HR1716


title: Tumor_Neuroblast_143


title: HR1715


title: Tumor_Neuroblast_155


title: Tumor_Neuroblast_142


title: HR1720


title: HR1714


title: Tumor_Neuroblast_141


title: Tumor_Neuroblast_140


title: Tumor_Neuroblast_139


title: HR1711


title: Tumor_Neuroblast_138


title: HR1712


title: HR1721


title: HR1709


title: HR1719


title: HR1708


title: HR1707


title: Tumor_Neuroblast_136


title: Tumor_Neuroblast_135


title: HR1706


title: Tumor_Neuroblast_134


title: HR1705


title: Tumor_Neuroblast_133


title: HR1704


title: HR1703


title: Tumor_Neuroblast_132


title: Tumor_Neuroblast_131


title: HR1701


title: Tumor_Neuroblast_130


title: Tumor_Neuroblast_129


title: HR1713


title: HR1700


title: HR1699


title: Tumor_Neuroblast_128


title: Tumor_Neuroblast_127


title: HR1698


title: Tumor_Neuroblast_126


title: Tumor_Neuroblast_137


title: Tumor_Neuroblast_125


title: HR1695


title: HR1693


title: HR1696


title: HR1692


title: HR1691


title: HR1689


title: HR1690


title: HR1688


title: HR1687


title: HR1686


title: HR1684


title: Tumor_Neuroblast_121


title: Tumor_Neuroblast_124


title: Tumor_Neuroblast_122


title: Tumor_Neuroblast_123


title: HR1683


title: HR1682


title: Tumor_Neuroblast_115


title: Tumor_Neuroblast_120


title: Tumor_Neuroblast_119


title: Tumor_Neuroblast_117


title: Tumor_Neuroblast_114


title: Tumor_Neuroblast_112


title: Tumor_Neuroblast_113


title: HR1680


title: HR1679


title: HR1678


title: Tumor_Neuroblast_118


title: Tumor_Neuroblast_109


title: Tumor_Neuroblast_110


title: Tumor_Neuroblast_116


title: HR1677


title: Tumor_Neuroblast_108


title: Tumor_Neuroblast_107


title: HR1676


title: Tumor_Neuroblast_106


title: HR1681


title: HR1675


title: Tumor_Neuroblast_105


title: Tumor_Neuroblast_103


title: HR1673


title: Tumor_Neuroblast_104


title: HR1672


title: Tumor_Neuroblast_102


title: HR1671


title: Tumor_Neuroblast_99


title: Tumor_Neuroblast_101


title: HR1669


title: Tumor_Neuroblast_111


title: HR1674


title: Tumor_Neuroblast_100


title: HR1670


title: Tumor_Neuroblast_98


title: HR1667


title: Tumor_Neuroblast_97


title: HR1668


title: HR1666


title: Tumor_Neuroblast_96


title: Tumor_Neuroblast_95


title: HR1665


title: HR1664


title: HR1663


title: Tumor_Neuroblast_93


title: Tumor_Neuroblast_94


title: HR1662


title: HR1702


title: HR1661


title: Tumor_Neuroblast_92


title: Tumor_Neuroblast_91


title: HR1660


title: HR1657


title: HR1656


title: HR1658


title: HR1659


title: Tumor_Neuroblast_87


title: Tumor_Neuroblast_90


title: Tumor_Neuroblast_89


title: HR1654


title: Tumor_Neuroblast_86


title: Tumor_Neuroblast_88


title: Tumor_Neuroblast_83


title: HR1650


title: Tumor_Neuroblast_84


title: Tumor_Neuroblast_82


title: Tumor_Neuroblast_81


title: HR1651


title: HR1652


title: HR1647


title: HR1646


title: Tumor_Neuroblast_78


title: Tumor_Neuroblast_80


title: HR1697


title: Tumor_Neuroblast_79


title: Tumor_Neuroblast_77


title: Tumor_Neuroblast_76


title: HR1644


title: HR1645


title: HR1643


title: Tumor_Neuroblast_85


title: HR1642


title: HR1653


title: HR1641


title: Tumor_Neuroblast_75


title: Tumor_Neuroblast_73


title: Tumor_Neuroblast_74


title: Tumor_Neuroblast_72


title: HR1639


title: HR1640


title: Tumor_Neuroblast_71


title: Tumor_Neuroblast_70


title: HR1636


title: HR1635


title: HR1637


title: HR1649


title: Tumor_Neuroblast_68


title: Tumor_Neuroblast_67


title: HR1633


title: Tumor_Neuroblast_65


title: HR1634


title: Tumor_Neuroblast_66


title: HR1629


title: Tumor_Neuroblast_63


title: HR1630


title: Tumor_Neuroblast_61


title: Tumor_Neuroblast_60


title: HR1628


title: HR1627


title: HR1624


title: Tumor_Neuroblast_54


title: Tumor_Neuroblast_57


title: HR1626


title: Tumor_Neuroblast_56


title: HR1619


title: HR1623


title: HR1622


title: HR1621


title: Tumor_Neuroblast_58


title: Tumor_Neuroblast_55


title: Tumor_Neuroblast_59


title: Tumor_Neuroblast_69


title: HR1620


title: Tumor_Neuroblast_53


title: Tumor_Neuroblast_50


title: HR1617


title: HR1618


title: Tumor_Neuroblast_51


title: Tumor_Neuroblast_52


title: Tumor_Neuroblast_62


title: Tumor_Neuroblast_64


title: Tumor_Neuroblast_48


title: HR1632


title: HR1631


title: Tumor_Neuroblast_49


title: HR1614


title: HR1616


title: HR1615


title: HR1625


title: HR1612


title: Tumor_Neuroblast_46


title: Tumor_Neuroblast_47


title: Tumor_Neuroblast_44


title: Tumor_Neuroblast_45


title: HR1610


title: HR1611


title: HR1613


title: HR1607


title: HR1609


title: Tumor_Neuroblast_41


title: Tumor_Neuroblast_42


title: Tumor_Neuroblast_43


title: HR1605


title: HR1604


title: Tumor_Neuroblast_40


title: Tumor_Neuroblast_38


title: Tumor_Neuroblast_37


title: HR1602


title: HR1603


title: Tumor_Neuroblast_35


title: Tumor_Neuroblast_33


title: Tumor_Neuroblast_36


title: Tumor_Neuroblast_34


title: HR1601


title: HR1554


title: HR1600


title: HR1552


title: Tumor_Neuroblast_31


title: HR1490


title: HR1606


title: HR1551


title: HR1489


title: Tumor_Neuroblast_32


title: HR1487


title: Tumor_Neuroblast_29


title: Tumor_Neuroblast_28


title: Tumor_Neuroblast_39


title: Tumor_Neuroblast_26


title: Tumor_Neuroblast_25


title: Tumor_Neuroblast_30


title: HR1474


title: HR1469


title: HR1464


title: Tumor_Neuroblast_23


title: Tumor_Neuroblast_24


title: HR1461


title: Tumor_Neuroblast_22


title: Tumor_Neuroblast_21


title: Tumor_Neuroblast_27


title: HR1460


title: HR1459


title: Tumor_Neuroblast_20


title: HR1482


title: HR1458


title: HR1485


title: HR1455


title: Tumor_Neuroblast_17


title: Tumor_Neuroblast_18


title: HR1454


title: Tumor_Neuroblast_15


title: HR1475


title: HR1451


title: HR1437


title: HR1441


title: HR1435


title: HR1428


title: HR1425


title: Tumor_Neuroblast_11


title: Tumor_Neuroblast_8


title: Tumor_Neuroblast_19


title: Tumor_Neuroblast_10


title: HR1422


title: Tumor_Neuroblast_7


title: Tumor_Neuroblast_6


title: Tumor_Neuroblast_5


title: HR1415


title: HR1416


title: Tumor_Neuroblast_16


title: HR1414


title: Tumor_Neuroblast_3


title: HR1413


title: Tumor_Neuroblast_14


title: Tumor_Neuroblast_13


title: HR1411


title: HR1408


title: Tumor_Neuroblast_2


title: Tumor_Neuroblast_12


title: HR1407


title: Control_Neuroblast_192

value: UAS-Dcr2/+; inscGal4, UAS-CD8::GFP/+; sh-mCherry (BL35785)/+


title: Tumor_Neuroblast_1


title: HR1424


title: Tumor_Neuroblast_9


title: HR1421


title: HR1405


title: HR1406


title: Control_Neuroblast_190


title: Control_Neuroblast_189


title: Control_Neuroblast_188


title: HR1401


title: Control_Neuroblast_187


title: HR1402


title: HR1400


title: HR1403


title: Control_Neuroblast_186


title: Tumor_Neuroblast_4


title: HR1398


title: Control_Neuroblast_185


title: Control_Neuroblast_184


title: HR1396


title: Control_Neuroblast_181


title: HR1395


title: Control_Neuroblast_182


title: Control_Neuroblast_183


title: HR1392


title: HR1393


title: HR1394


title: Control_Neuroblast_179


title: HR1390


title: Control_Neuroblast_191


title: HR1391


title: Control_Neuroblast_178


title: Control_Neuroblast_180


title: HR1389


title: HR1387


title: HR1386


title: Control_Neuroblast_177


title: Control_Neuroblast_176


title: Control_Neuroblast_175


title: HR1384


title: HR1383


title: Control_Neuroblast_173


title: HR1382


title: Control_Neuroblast_174


title: HR1381


title: Control_Neuroblast_172


title: HR1379


title: Control_Neuroblast_169


title: HR1377


title: HR1365


title: HR1369


title: HR1373


title: HR1363


title: HR1320


title: Control_Neuroblast_166


title: HR1319


title: Control_Neuroblast_165


title: Control_Neuroblast_167


title: HR1316


title: Control_Neuroblast_161


title: Control_Neuroblast_163


title: Control_Neuroblast_162


title: HR1308


title: Control_Neuroblast_158


title: Control_Neuroblast_171


title: Control_Neuroblast_157


title: Control_Neuroblast_160


title: HR1315


title: HR1310


title: Control_Neuroblast_156


title: Control_Neuroblast_159


title: HR1309


title: HR1302


title: HR1300


title: Control_Neuroblast_170


title: Control_Neuroblast_168


title: HR1298


title: Control_Neuroblast_154


title: HR1295


title: Control_Neuroblast_153


title: HR1289


title: HR1287


title: Control_Neuroblast_164


title: HR1292


title: Control_Neuroblast_151


title: Control_Neuroblast_152


title: Control_Neuroblast_155


title: HR1288


title: Control_Neuroblast_150


title: Control_Neuroblast_149


title: Control_Neuroblast_148


title: HR1277


title: HR1272


title: HR1273


title: HR1286


title: HR1269


title: Control_Neuroblast_144


title: Control_Neuroblast_146


title: Control_Neuroblast_142


title: Control_Neuroblast_147


title: Control_Neuroblast_145


title: Control_Neuroblast_143


title: HR1262


title: Control_Neuroblast_141


title: HR1259


title: HR1252


title: Control_Neuroblast_140


title: Control_Neuroblast_139


title: HR1248


title: HR1245


title: Control_Neuroblast_135


title: HR1283


title: Control_Neuroblast_134


title: HR1239


title: Control_Neuroblast_138


title: HR1244


title: Control_Neuroblast_132


title: Control_Neuroblast_137


title: HR1236


title: SJ1241


title: Control_Neuroblast_136


title: HR1235


title: HR1240


title: HR1234


title: Control_Neuroblast_133


title: Control_Neuroblast_128


title: HR1229


title: HR1227


title: HR1230


title: Control_Neuroblast_127


title: HR1260


title: Control_Neuroblast_129


title: HR1232


title: Control_Neuroblast_126


title: Control_Neuroblast_131


title: HR1250


title: HR1226


title: Control_Neuroblast_130


title: Control_Neuroblast_124


title: Control_Neuroblast_125


title: HR1223


title: HR1221


title: Control_Neuroblast_123


title: Control_Neuroblast_122


title: HR1218


title: HR1214


title: HR1216


title: HR1213


title: Control_Neuroblast_120


title: Control_Neuroblast_118


title: Control_Neuroblast_119


title: Control_Neuroblast_117


title: HR1210


title: Control_Neuroblast_115


title: Control_Neuroblast_114


title: Control_Neuroblast_112


title: Control_Neuroblast_113


title: HR1206


title: HR1197


title: HR1204


title: HR1207


title: HR1200


title: HR1193


title: HR1195


title: Control_Neuroblast_121


title: HR1192


title: Control_Neuroblast_109


title: Control_Neuroblast_110


title: HR1219


title: Control_Neuroblast_111


title: Control_Neuroblast_108


title: Control_Neuroblast_107


title: HR1191


title: HR1188


title: HR1186


title: HR1208


title: HR1184


title: Control_Neuroblast_105


title: Control_Neuroblast_116


title: HR1182


title: Control_Neuroblast_106


title: Control_Neuroblast_104


title: Control_Neuroblast_103


title: HR1181


title: Control_Neuroblast_102


title: HR1180


title: Control_Neuroblast_100


title: Control_Neuroblast_101


title: HR1173


title: Control_Neuroblast_99


title: HR1179


title: Control_Neuroblast_98


title: HR1169


title: Control_Neuroblast_97


title: HR1170


title: HR1171


title: Control_Neuroblast_95


title: HR1159


title: Control_Neuroblast_96


title: HR1160


title: HR1168


title: Control_Neuroblast_93


title: Control_Neuroblast_92


title: HR1156


title: HR1149


title: Control_Neuroblast_91


title: HR1124


title: Control_Neuroblast_90


title: Control_Neuroblast_89


title: HR1117


title: HR1115


title: Control_Neuroblast_86


title: Control_Neuroblast_87


title: Control_Neuroblast_84


title: Control_Neuroblast_94


title: HR1100


title: Control_Neuroblast_83


title: HR1111


title: HR1082


title: HR1065


title: HR1089


title: Control_Neuroblast_82


title: Control_Neuroblast_81


title: HR1046


title: Control_Neuroblast_80


title: HR1038


title: HR1016


title: Control_Neuroblast_79


title: Control_Neuroblast_77


title: Control_Neuroblast_88


title: HR1012


title: HR1010


title: HR1114


title: HR1009


title: Control_Neuroblast_75


title: Control_Neuroblast_78


title: Control_Neuroblast_74


title: HR1006


title: Control_Neuroblast_76


title: HR1005


title: HR1112


title: Control_Neuroblast_73


title: Control_Neuroblast_70


title: Control_Neuroblast_71


title: Control_Neuroblast_85


title: Control_Neuroblast_69


title: Control_Neuroblast_72


title: Control_Neuroblast_68


title: Control_Neuroblast_66


title: Control_Neuroblast_65


title: Control_Neuroblast_64


title: KC pancreas tuft cell 156

city: La Jolla

first: Zhibo

last: Ma

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Smartseq2: Reads were aligned to the mm10 mouse genome using STAR version 2.5.3a (73). Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads. Raw transcript Samrtseq2: counts were obtained using HTSeq version 0.9.1 (74). The union of all detected genes was compiled into a single expression table (156 cells and 27,998 genes)
Smartseq2: Cells with less than 500 unique genes and genes expressed in fewer than 3 cells were filtered using the Seurat R package.  Genes were log-normalized in Seurat.
10x Genomics: fastq files were processed using cellranger 3.1.0 and mm10 reference.The raw sequencing data from each mice was first processed separately in Cell Ranger v3.1.0 using refdata-mm10-3.0.0 and default parameters (10x Genomics). Each dataset captured similar number of cells (~4500 cells/mice) with similar sequencing depth (median ~20k reads/cell). The cellranger filtered gene-by-cell count matrices were loaded to the R package Seurat (v3.1.4) and combined into a single merged matrix. Low-quality cells were further filtered based on the percent of mitochondria gene reads, number of UMI, and number of genes detected (subset = percent.mt <7 & nCount_RNA < 25000 & nFeature_RNA >350)). After removing the low-quality cells, we applied a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurement for each cell by the total expression, mulplies this by a scaling factor of 23,000. The normalized data is further linear transformed by ScaleData() function prior to dimension reduction. Principal components analysis (PCA) was performed on the scaled data by only using the most variable 2000 genes (identified using the default “vst” method). Batch effect between mice were examine in PCA space and no obvious batch effect was observed.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts per gene per cell

source_name: KrasG12D;Ptf1aCre/+ (KC) mouse

extract_protocol:
Pancreatic tuft cells were isolated from 3, 8-10 month old KC PanIN-bearing.  The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1-1.5 mg/ml hyaluronidase (depending on tumor burden, Sigma), and 250 ml of DNAse I, shaking gently at 37°C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 mm filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA), and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS. Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Siglecf+;EpCAM+;Cd45- Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
10x Genomics scRNA-seq was conducted on immune cells and fibroblasts collected by FACS from caerulein-treated KC and KPouC pancreata.  Pancreata were digested and prepared as previously described for tuft cell isolation.  Each sample was prepared by flow sorting live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg); PI was used to exclude dead cells. Immune and non-immune stroma from each independent sample were mixed at a 7:3 ratio, respectively, prior to loading on the microfluidic chip with barcoded beads according to 10X Chromium Next GEM Single Cell 3’ (v3.1, Catalog # 1000128, 10x Genomics Inc).
SmartSeq2 libraries were constructed as previously described (Picelli et al., 2014)
10x Genomics: Cell lysis, first strand cDNA synthesis and amplification were carried out according to 10X v3.1 protocol, with cDNA amplification set for 11 cycles. Following sample indexing and bead-based library purification, cDNA fragments distribution and concentration were measured using TapeStation (Agilent Biosystems) and Qubit (ThermoFisher).The libraries were pooled in equal mole ratio and sequenced in two illumine NextSeq 550 PE-75 high-output runs.

value: Mixed

value: Pancreas

value: tuft cell

value: 8-10 month


title: KC pancreas tuft cell 148


title: KC pancreas tuft cell 153


title: KC pancreas tuft cell 151


title: KC pancreas tuft cell 152


title: KC pancreas tuft cell 154


title: KC pancreas tuft cell 150


title: KC pancreas tuft cell 155


title: KC pancreas tuft cell 149


title: Control_Neuroblast_63


title: Control_Neuroblast_62


title: Control_Neuroblast_61


title: KC pancreas tuft cell 145


title: KC pancreas tuft cell 144


title: KC pancreas tuft cell 146


title: KC pancreas tuft cell 143


title: Control_Neuroblast_58


title: Control_Neuroblast_60


title: Control_Neuroblast_57


title: Control_Neuroblast_56


title: Control_Neuroblast_59


title: KC pancreas tuft cell 142


title: KC pancreas tuft cell 140


title: KC pancreas tuft cell 141


title: Control_Neuroblast_67


title: KC pancreas tuft cell 139


title: KC pancreas tuft cell 147


title: Control_Neuroblast_55


title: KC pancreas tuft cell 138


title: KC pancreas tuft cell 134


title: Control_Neuroblast_54


title: KC pancreas tuft cell 133


title: Control_Neuroblast_50


title: Control_Neuroblast_52


title: Control_Neuroblast_51


title: KC pancreas tuft cell 137


title: KC pancreas tuft cell 135


title: KC pancreas tuft cell 132


title: Control_Neuroblast_49


title: Control_Neuroblast_53


title: KC pancreas tuft cell 130


title: Control_Neuroblast_46


title: Control_Neuroblast_45


title: KC pancreas tuft cell 129


title: KC pancreas tuft cell 127


title: KC pancreas tuft cell 128


title: Control_Neuroblast_43


title: Control_Neuroblast_44


title: Control_Neuroblast_42


title: Control_Neuroblast_41


title: Control_Neuroblast_48


title: KC pancreas tuft cell 125


title: KC pancreas tuft cell 124


title: Control_Neuroblast_39


title: Control_Neuroblast_40


title: KC pancreas tuft cell 136


title: KC pancreas tuft cell 131


title: KC pancreas tuft cell 123


title: KC pancreas tuft cell 120


title: Control_Neuroblast_47


title: Control_Neuroblast_34


title: Control_Neuroblast_36


title: KC pancreas tuft cell 118


title: KC pancreas tuft cell 126


title: KC pancreas tuft cell 119


title: KC pancreas tuft cell 117


title: Control_Neuroblast_31


title: Control_Neuroblast_33


title: Control_Neuroblast_32


title: KC pancreas tuft cell 114


title: Control_Neuroblast_30


title: KC pancreas tuft cell 115


title: KC pancreas tuft cell 113


title: Control_Neuroblast_29


title: KC pancreas tuft cell 122


title: Control_Neuroblast_38


title: KC pancreas tuft cell 112


title: KC pancreas tuft cell 121


title: Control_Neuroblast_28


title: Control_Neuroblast_37


title: KC pancreas tuft cell 111


title: KC pancreas tuft cell 110


title: Control_Neuroblast_26


title: KC pancreas tuft cell 109


title: Control_Neuroblast_35


title: Control_Neuroblast_25


title: KC pancreas tuft cell 108


title: Control_Neuroblast_24


title: KC pancreas tuft cell 116


title: KC pancreas tuft cell 107


title: KC pancreas tuft cell 106


title: Control_Neuroblast_23


title: Control_Neuroblast_22


title: Control_Neuroblast_21


title: KC pancreas tuft cell 105


title: KC pancreas tuft cell 104


title: KC pancreas tuft cell 103


title: Control_Neuroblast_20


title: KC pancreas tuft cell 102


title: Control_Neuroblast_19


title: Control_Neuroblast_18


title: KC pancreas tuft cell 101


title: Control_Neuroblast_16


title: KC pancreas tuft cell 100


title: Control_Neuroblast_27


title: KC pancreas tuft cell 99


title: KC pancreas tuft cell 97


title: Control_Neuroblast_17


title: KC pancreas tuft cell 98


title: KC pancreas tuft cell 95


title: Control_Neuroblast_15


title: KC pancreas tuft cell 96


title: Control_Neuroblast_13


title: Control_Neuroblast_14


title: KC pancreas tuft cell 94


title: Control_Neuroblast_12


title: Control_Neuroblast_10


title: KC pancreas tuft cell 90


title: KC pancreas tuft cell 93


title: KC pancreas tuft cell 92


title: Control_Neuroblast_11


title: Control_Neuroblast_4


title: Control_Neuroblast_5


title: Control_Neuroblast_6


title: Control_Neuroblast_7


title: Control_Neuroblast_8


title: KC pancreas tuft cell 89


title: KC pancreas tuft cell 91


title: Control_Neuroblast_9


title: KC pancreas tuft cell 87


title: KC pancreas tuft cell 88


title: Control_Neuroblast_3


title: Control_Neuroblast_1


title: Control_Neuroblast_2


title: KC pancreas tuft cell 86


title: KC pancreas tuft cell 84


title: KC pancreas tuft cell 85


title: KC pancreas tuft cell 83


title: poi

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

data_processing:
READemption analysis, for details see https://reademption.readthedocs.io/en/latest/example_analysis.html
Supplementary_files_format_and_content: wig files were generated using READemption; Scores represent 'coverage-tnoar_min_normalized'

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacterial culture

growth_protocol: Salmonella SL1344 cells were grown in LB media at 37 °C to an OD600 of 2.0

extract_protocol:
CoIP-Ab-beads were extracted with PCI. The aqueous layer was precipitated with ethanol and 1:30 3 M sodium acetate at pH 5.2 at -20 °C over-night. The precipitated RNA was pelleted and washed with 500 µl 75% ethanol. The pellet was dried and solubilized in 15.5 µl water. DNA was degraded by DNase I (Thermo Scientific) as described in the manual in presence of RNase inhibitor for 30 min at 37 °C. The sample was diluted with 100 µl water and the RNA was extracted by PCI. The RNA was solubilized to an OD260 of 1 and analysed in the Bioanalyzer (Agilent) for quality and quantity estimation for RNA-seq. Protein samples were recovered from the organic layer by 10 vol methanol precipitation.
RNA library preparation was conducted by the Core Unit SysMed (Kristina Döring, Würzburg). 200 ng eluted RNA from the coIP were denatured at 70 °C for 2 min, cooled down on ice, and 3´-end dephosphorylated by 10 U T4-PNK (M0201S, NEB) in the presence of 20 U RNase inhibitor (M0314L, NEB) for 60 min at 37 °C. 1.6 mM ATP and 10 U PNK were added for 5´-end phosphorylation for 60 min at 37 °C. RNA was purified by silica-based columns (Zymo RNA Clean & Concentrator kit, R1013, Zymo Research) and eluted in 15 µl nuclease-free water (436912C, VWR). RNA was denatured again and pyrophosphates were removed from the 5´-end by 10 U RppH (M0356S, NEB) in 1× NEB buffer 2 (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT) in the presence of 20 U RNase inhibitor for 60 min at 37 °C, and again column purified and eluted in 6 µl. For 3´ adaptor ligation the NEBNext Small RNA Kit (E7560S, NEB) was used: 200 ng RNA were mixed with 1 µl 1:3 diluted 3´ SR adaptors for Illumina, and denatured, 1× 3´ ligation reaction buffer was added and 3 µl ligation enzyme mix in a total volume of 20 µl for 60 min at 25 °C. 1 µl 1:3 diluted SR RT-primer for Illumina were added in a total volume of 25 µl. The annealing was conducted at 75 °C for 5 min, 37 °C at 15 min, 25 °C at 15 min, cooling at 4 °C. 1 µl 5´ SR adaptor for Illumina (freshly solubilized, denatured, and cooled on ice), 1 µl 10× 5´ ligation reaction buffer, and 2.5 µl 5´ ligation enzyme mix were added to the reaction and incubated for 60 min at 25 °C. For reverse transcription, 8 µl first strand synthesis reaction buffer, 1 µl murine RNase inhibitor, and 1 µl ProtoScript II reverse transcriptase were added and incubated for 60 min at 50 °C. PCR amplification of reverse transcripts was conducted by addition of 50 µl LongAmp Taq 2× master mix, 5 µl nuclease free water, 2.5 µl 1:3 diluted SR primer for Illumina, and 2.5 µl 1:3 diluted index primers. The reaction was cycled at 94 °C for 30 s, 14× 94 °C for 15s – 62 °C for 30 s – 70 °C for 90 s, 70 °C for 5 min, and cooled at 4 °C.   DNA was purified by MagSi-NGSPREP Plus (MDKT00010005, Steinbrenner Laborsysteme GmbH) beads with a ratio of 1.8× to reaction volume. All steps were executed in DNA-LoBind tubes (#0030108051, Eppendorf). The final supernatant was analysed by Qubit 2.0 (Thermo Scientific) with the dsDNA HS Assay Kit (Q32854, Thermo Scientific) and the Bioanalyzer 2100 (G2939BA, Agilent) with the DNA 1000 kit (5067-1504) or HS DNA 7500 kit (5067-1506).
coIP-seq

treatment_protocol: 60 OD of cells at OD 2 were resuspended in 800 µl lysis buffer (20 mM Tris/HCl pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and 800 µl 0.1 mm glass beads (BioSpecs). Cells were lysed at 30 Hz for 10 min in the Retsch MM200 at 4 °C. The lysate was cleared twice for 10 min at full-speed at 4 °C. 35 µl monoclonal anti-FLAG M2 antibody produced in mouse (Sigma-Aldrich) was added to the supernatant and incubated for 30 min at 4 °C. 75 µl pre-washed protein A sepharose (Sigma-Aldrich) was added for recovery of FLAG-antibody and incubated for 30 min. Beads were pelleted at 300 × g and washed 5 times witch lysis buffer, resuspended in 500 µl lysis buffer.


title: wt

value: wt


title: KC pancreas tuft cell 82


title: Validation cohort 26

city: Chicago

first: Joshua

middle: James

last: Meeks

state: IL

address: 676 N. St Clair St

department: Urology

institute: Northwestern University

data_processing:
Remove Illumina adapters: Trim Galore
Align reads to reference genome: STAR v2.6.0a, Ensembl GRCh38.p12 sequence
Generate read counts: Discovery cohort n=73: HTSeq v0.11.2, Ensembl v95 GTF gene annotations
Generate FPKMs: Cufflinks v2.2.1, Ensembl v95 GTF gene annotations
Trim 150-bp reads to 50-bp: Validation cohort n=26: FASTQ Toolkit v2.2.0
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Aligned read counts (discovery cohort, n=73) and Cufflinks normalized FPKMs (Discovery cohort n=73; Validation cohort n=26 for 50SE reads and 150PE reads)

source_name: T1 high-grade NMIBC

extract_protocol:
Qiagen Allprep DNA/RNA FFPE kit
Illumina TruSeq Stranded with RiboZero kit
150-bp PE reads, targeting 20M read pairs per sample

tag: treatment

value: radical cystectomy


title: Validation cohort 24


title: Validation cohort 25


title: KC pancreas tuft cell 79


title: KC pancreas tuft cell 78


title: Validation cohort 22


title: KC pancreas tuft cell 77


title: Validation cohort 21


title: KC pancreas tuft cell 76


title: KC pancreas tuft cell 75


title: KC pancreas tuft cell 74


title: KC pancreas tuft cell 73


title: Validation cohort 20


title: KC pancreas tuft cell 72


title: Validation cohort 18


title: KC pancreas tuft cell 71


title: Validation cohort 15


title: KC pancreas tuft cell 70


title: KC pancreas tuft cell 81


title: KC pancreas tuft cell 80


title: Validation cohort 14


title: Validation cohort 13


title: Validation cohort 12


title: KC pancreas tuft cell 68


title: KC pancreas tuft cell 69


title: KC pancreas tuft cell 67


title: Validation cohort 23


title: Validation cohort 11


title: Validation cohort 10


title: Validation cohort 19


title: KC pancreas tuft cell 66


title: Validation cohort 9


title: Validation cohort 16


title: KC pancreas tuft cell 64


title: Validation cohort 8


title: KC pancreas tuft cell 65


title: Validation cohort 6


title: KC pancreas tuft cell 60


title: KC pancreas tuft cell 61


title: Validation cohort 5


title: KC pancreas tuft cell 62


title: Validation cohort 4


title: KC pancreas tuft cell 59


title: KC pancreas tuft cell 58


title: Validation cohort 3


title: KC pancreas tuft cell 57


title: Validation cohort 1


title: Validation cohort 2


title: Discovery cohort 73

extract_protocol:
Roche HighPure miRNA Kit (Roche #05080576001)
Illumina TruSeq Stranded Total RNA Library Preparation Kit
50-bp single-end (SE) reads, 20-25M reads/sample

tag: recurrence

tag: progression

tag: retur

tag: processed data characteristics

value: BCG


title: KC pancreas tuft cell 56

tag: cell type


title: KC pancreas tuft cell 55


title: Discovery cohort 72


title: KC pancreas tuft cell 54


title: Validation cohort 7


title: KC pancreas tuft cell 63


title: Discovery cohort 71


title: KC pancreas tuft cell 53


title: KC pancreas tuft cell 52


title: Discovery cohort 70


title: KC pancreas tuft cell 51


title: Discovery cohort 69


title: KC pancreas tuft cell 50


title: Discovery cohort 68


title: Discovery cohort 64


title: Discovery cohort 63


title: Discovery cohort 67


title: KC pancreas tuft cell 45


title: KC pancreas tuft cell 46


title: KC pancreas tuft cell 49


title: KC pancreas tuft cell 48


title: Discovery cohort 65


title: Validation cohort 17


title: KC pancreas tuft cell 47


title: Discovery cohort 62


title: KC pancreas tuft cell 44


title: Discovery cohort 61


title: KC pancreas tuft cell 43


title: KC pancreas tuft cell 42


title: Discovery cohort 60


title: KC pancreas tuft cell 41


title: Discovery cohort 58


title: Discovery cohort 57


title: KC pancreas tuft cell 40


title: Discovery cohort 66


title: KC pancreas tuft cell 38


title: Discovery cohort 56


title: KC pancreas tuft cell 39


title: Discovery cohort 55


title: Discovery cohort 54


title: KC pancreas tuft cell 36


title: KC pancreas tuft cell 37


title: Discovery cohort 53


title: Discovery cohort 51


title: Discovery cohort 52


title: Discovery cohort 50


title: KC pancreas tuft cell 32


title: KC pancreas tuft cell 33


title: KC pancreas tuft cell 31


title: KC pancreas tuft cell 30


title: Discovery cohort 47


title: Discovery cohort 48


title: Discovery cohort 49


title: Discovery cohort 59


title: Discovery cohort 45


title: Discovery cohort 46


title: KC pancreas tuft cell 29


title: KC pancreas tuft cell 28


title: KC pancreas tuft cell 26


title: Discovery cohort 44


title: KC pancreas tuft cell 27


title: KC pancreas tuft cell 25


title: KC pancreas tuft cell 24


title: KC pancreas tuft cell 35


title: Discovery cohort 40


title: KC pancreas tuft cell 34


title: Discovery cohort 42


title: Discovery cohort 43


title: Discovery cohort 41


title: Discovery cohort 39


title: Discovery cohort 38


title: Discovery cohort 37


title: KC pancreas tuft cell 23


title: KC pancreas tuft cell 22


title: KC pancreas tuft cell 16


title: KC pancreas tuft cell 20


title: KC pancreas tuft cell 18


title: KC pancreas tuft cell 17


title: KC pancreas tuft cell 21


title: Discovery cohort 35


title: Discovery cohort 32


title: KC pancreas tuft cell 15


title: Discovery cohort 34


title: Discovery cohort 36


title: Discovery cohort 31


title: KC pancreas tuft cell 14


title: Discovery cohort 33


title: KC pancreas tuft cell 13


title: Discovery cohort 29


title: KC pancreas tuft cell 12


title: Discovery cohort 26


title: Discovery cohort 28


title: Discovery cohort 25


title: KC pancreas tuft cell 11


title: KC pancreas tuft cell 10


title: KC pancreas tuft cell 9


title: Discovery cohort 30


title: KC pancreas tuft cell 19


title: Discovery cohort 27


title: Discovery cohort 24


title: KC pancreas tuft cell 8


title: KC pancreas tuft cell 7


title: KC pancreas tuft cell 6


title: Discovery cohort 21


title: Discovery cohort 22


title: Discovery cohort 19


title: Discovery cohort 20


title: Discovery cohort 16


title: Discovery cohort 15


title: Discovery cohort 18


title: KC pancreas tuft cell 3


title: mPSC_PGD2_sample3

data_processing:
Sequencing reads were quality checked with FastQC and mapped to the mouse genome (mm9) using Hisat2. Transcript assembly and quantification were performed by Stringtie and Ballgown. Gene expression distribution between samples was checked to ensure similar transcriptome quality. Genes that have RPKM variance across samples < 1 were first removed to exclude non-expressed genes. The RPKM values were then log2 transformed and quantile normalized with the R package preprocessCore. Differential expression analysis between tuft and non-tuft epithelial cells was performed with empirical Bayes shrinkage and moderated t-test using the Limma package and p values were converted into false discovery rates (FDR) using the Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: Quantile normalized log2(RPKM+1) value for each sample

source_name: WT mouse

growth_protocol: Mouse pancreatic stellate cells (mPSCs) were isolated from the pancreata of wild-type CD1 mice as previously described.  Pancreata from 2-3 mice were pooled prior to isolation.  Briefly, pancreatic tissue was minced and digested with 0.02% Pronase (Roche), 0.05% Collagenase P (Roche), and 0.1% Dnase (Roche) in Gey’s balanced salt solution (GBSS, Sigma) at 37C for 20 min.  Digested tissue was then filtered through a 100um cell strainer (Fisher).  Washed cells were re-suspended in 9.5 ml GBSS containing 0.3% BSA (Sigma) and 8 ml of 28.7% Histodenz solution (Sigma).  The cell suspension was layered beneath GBSS containing 0.3% BSA, and centrifuged at 1400 x g for 25 min at 4C.  Cells of interest were harvested from the interface of the Histodenz solution and the aqueous solution.  Isolated mPSCs were washed with GBSS and re-suspended in DMEM (Fisher Scientific) supplemented with 20% FBS (Peak Serum), 100 mM Sodium Pyruvate (Life Technologies), 2 mM L-Glutamine (Life Technologies), 1x non-essential amino acids (Life Technologies) and antibiotics (penicillin 100 U/ml and streptomycin 100 mg/ml, Life Technologies).  mPSCs were allowed to activate in culture and were then treated for 48 hours with prostaglandins (10uM), control (methyl acetate, MeOAc), or Ppar agonists (Rosiglitazone, 100nm; GW7647, 1uM; GW501516, 100nM) in serum-free media before collection in Trizol (Thermofisher) for RT-qPCR or RNA sequencing.  A minimum of three biological replicates was analyzed per experiment.

extract_protocol:
Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
Low input bulk RNA sequencing (RNA-seq) on intestinal and pancreatic tuft cells was performed using the Smart-Seq2 protocol as previously described. In brief, three biological replicates, each with 100 tuft cells from an individual mouse, were sorted directly into 2 μl of Smart-Seq2 lysis buffer. Full-length cDNA was generated, and size distribution was checked with Agilent TapeStation 4200 to ensure RNA quality. cDNA were then amplified with 18-24 PCR cycles, tagmentated, and amplified again with 10 PCR cycles using a Nextera XT kit (Illumina FC-131-1096). The sequencing library was purified with AMPure XP beads.
For sequencing of mPSCs and BMMs, RNA quality was assessed using the Agilent TapeStation 4200 and RNA-Seq libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit v2 according to Illumina protocols. Multiplexed libraries were validated using the Agilent TapeStation 4200, normalized and pooled for sequencing
SmartSeq2 (Picelli et al., 2014) or TruSeq stranded mRNA Sample Preparation Kit v2.

value: Mouse pancreatic stellate cells

value: 12 month


title: KC pancreas tuft cell 2


title: mPSC_PGD2_sample2


title: Discovery cohort 17


title: KC pancreas tuft cell 4


title: mPSC_PGD2_sample1


title: mPSC_PGE2_sample3


title: Discovery cohort 14


title: Discovery cohort 13


title: mPSC_PGE2_sample2


title: mPSC_PGE2_sample1


title: Discovery cohort 11


title: Discovery cohort 23


title: Discovery cohort 12


title: Discovery cohort 9


title: mPSC_MeOAC_sample2


title: Discovery cohort 10


title: mPSC_MeOAC_sample3


title: BMM_LPS_PGD2_sample3

growth_protocol: Bone marrow-derived macrophages (BMM) were generated from bone marrow extracted from the femurs of male CD1 mice as previously described (Ali, W. H. et al., 2013). Briefly, femurs were extracted and cleaned.  Both ends of the bone were removed with scissors and flushed with a 22-gauge needle containing extraction media (DMEM containing FBS) into a petri dish.  Cells were washed twice with extraction media and incubated in BMM high media containing DMEM, FBS, sodium pyruvate, supernatant from L-929 cells (L-sup) and penicillin/streptomycin, which was changed day 3 post-isolation. To induce M1 polarization, macrophages were treated with 100 ng/ml LPS for 4 hours prior to control or prostaglandin treatment.  To induce M2 polarization, macrophages were treated with IL-4 and IL-13 (both 20 ng/ml) for 4 hours prior to addition of prostaglandins (10uM) or control (MeOAc).  Cells were collected 24 hours later in Trizol for RNA-sequencing.

value: Bone marrow derived macrophage


title: mPSC_MeOAC_sample1


title: KC pancreas tuft cell 5


title: Discovery cohort 8


title: KC pancreas tuft cell 1


title: Discovery cohort 7


title: Discovery cohort 6


title: BMM_LPS_PGD2_sample1


title: BMM_LPS_PGD2_sample2


title: BMM_LPS_MeOAC_sample3


title: Discovery cohort 3


title: BMM_PGD2_sample2


title: BMM_LPS_MeOAC_sample2


title: Discovery cohort 5


title: Discovery cohort 2


title: BMM_LPS_MeOAC_sample1


title: Discovery cohort 1


title: BMM_PGD2_sample1


title: BMM_MeOAC_sample2


title: MUC3874_LS34_LP_RNA_Seq

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
The STAR aligner (Github, San Francisco, USA) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the human genome assembly hg19 (GRCh37) and UCSC knownGene annotation.
To quantify the number of reads mapping to annotated genes HTseq-count in Python (Python, Leipzig, Germany) was used.
For selecting differentially expressed genes, a statistical cut-off of FDR < 0.1 and log2FC > 0.5 was applied using the package of edgeR in R (Free Software Foundation Inc., Boston, USA).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files containing unnormalized counts for all samples
Supplementary_files_format_and_content: Tab-delimited text output from EdgeR with log2FC and differential gene expression analyses

source_name: Liver

extract_protocol:
700 ng of total RNA was isolated from liver tissue using NucleoSpin® RNA Kit (Macherey-Nagel, Düren, Germany)
Libraries was prepared using the TruSeq Stranded mRNA Library Prep (Illumina, San Diego, USA). RNA libraries were assessed for quality and quantity with the 2100 BioAnalyzer (Agilent technologies, Böblingen, Germany) and the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, Waltham, USA).
RNA libraries were sequenced as 100 bp paired-end runs on a HiSeq 4000 platform (Illumina, San Diego, USA).

treatment_protocol: Morbidly obese subjects were divided into two hypocaloric (1500 kcal/day) diet groups, one receiving a low protein (LP: 10 E% protein, n=10) and another getting high protein (HP: 30 E% protein, n=9), for three weeks prior to bariatric surgery

tag: diet intervention

value: Low protein

value: Liver


title: BMM_MeOAC_sample1


title: MUC3873_LS32_LP_RNA_Seq


title: BMM_MeOAC_sample3


title: MUC3871_LS21_LP_RNA_Seq


title: MUC3870_LS19_LP_RNA_Seq


title: WT_intestine_non-tuft_sample3

growth_protocol: The proximal 5 cm of the murine small intestine was dissected, flushed, cut longitudinally, and rinsed to remove luminal contents.  Segments were incubated in a 37°C shaker for 20 min in 5 ml PBS containing 2.5 mM EDTA, 0.75 mM dithiothreitol (DTT), and 10 mg/ml DNAse I.  Tissues were shaken vigorously for 30s, large pieces of intestinal wall were removed, and cells were spun down at 4°C, 1200 rpm, for 5 min.  Supernatant was removed and cells were re-suspended in 5 ml HBSS with 1.0 U/ml Dispase and 10mg/ml DNAse I, shaking for 10 min.  Digested cells were passed through a 100 mm filter and incubated with ACK lysing buffer.

value: Intestine


title: MUC3872_LS27_LP_RNA_Seq


title: MUC3869_LS16_LP_RNA_Seq


title: MUC3868_LS15_LP_RNA_Seq


title: WT_intestine_non-tuft_sample2


title: WT_intestine_tuft_sample3


title: WT_intestine_non-tuft_sample1


title: WT_intestine_tuft_sample2


title: MUC3866_LS04_LP_RNA_Seq


title: BMM_PGD2_sample3


title: WT_intestine_tuft_sample1


title: MUC3867_LS12_LP_RNA_Seq


title: Discovery cohort 4


title: MUC3862_LS28_HP_RNA_Seq

value: High protein


title: MUC3863_LS29_HP_RNA_Seq


title: KC_pan_non-tuft_sample2

growth_protocol: The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1-1.5 mg/ml hyaluronidase (depending on tumor burden, Sigma), and 250 ul of DNAse I, shaking gently at 37C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 um filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA), and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS.


title: KC_pan_non-tuft_sample1


title: MUC3860_LS24_HP_RNA_Seq


title: KC_pan_tuft_sample2


title: MUC3857_LS13_HP_RNA_Seq


title: MUC3859_LS23_HP_RNA_Seq


title: MUC3855_LS01_HP_RNA_Seq


title: L9: CD8_Fr

city: Lausanne

first: Benoit

middle: Manuel

last: Carreres

state: Vaud

address: Bugnon 25A

department: Departement of oncology

country: Switzerland

institute: Universite de Lausanne

description:
*barcode*_9
No reads data provided due to human data policies

data_processing:
Reads mapping: Cellranger-2.2.0, function "count", parameters with suitable fastq files,  "--expect-cells" 5000 for cocultured cells, 3000 for the rest (see caracteristics "Expected cells")
Sample aggregation: Cellranger-2.2.0, function "aggr", default parameters.
Filters (all processed data files): Cells containing more than five mitochondrial genes or less than 10 ribosomal genes were filtered out. 273 cells from two small populations of cells that were identified as dendritic cells and B cells were filtered out. Genes expressed in less than 10 of our totaling 25474 cells were removed giving a final number of 16’858 genes.
Count normalization: Expression was normalized using the R package “scran”. The following parameters were used for the “quickCluster”: parameters “min.mean=0.1” and “min.size=100”. The generated clusters were subsequently used to compute the sum factors, again with the parameter “min.mean=0.1”. The sum factors were then used to correct the cell expression, and both normalized counts and normalized log counts were stored. Due to important differences in total number of reads between our samples, we further used housekeeping (HK) genes to normalize our samples. Median expressions of five HK genes in each sample were calculated and the average of these values over the five HK genes was used as normalizing factors specific for each sample. A first list of HK genes were selected from E. Eisenberg et al. (Cell, 2013), and five genes that presented a high similarity between each other were used to calculate the correction factor. The five selected HK genes are: "C1orf43", "PSMB4”, "RAB7A", "SNRPD3", and “VPS29".
genome build: GRCh38 + Transgenes (TCRβ-t2A-TCRα; TCRβ-t2A-TCRα-e2A-CD8α-p2A-CD8β.I.dNGFR)
processed data files format and content: CSV count matrices (UMI / normalized counts)

source_name: Human primary T cells, healthy donor

growth_protocol:
Fresh: PBMCs were isolated by density gradient centrifugation from a healthy donor buffy coat. Polyclonal CD4+ and CD8+ cells were positively selected with microbeads (StemCell Technologies). Cells were cryopreserved on the day of isolation (Day 0) and thawed for scRNAseq analysis on Day 21 (the day when the cocultured cells were analyzed).
Expanded: polyclonal CD4+ and CD8+ cells that were positively selected with microbeads were activated on plates coated with OKT3 and anti-CD28 antibody in the presence of IL-7 and IL-15 (10ng/ml) for three days. Cells were then transduced with retroviral supernatants for 3 days, and expanded in media with  IL-7 and IL-15. On Day 9, transgenic cells were enriched by positive selection after staining with anti-mouse TCR PE antibody and anti-PE microbeads (Miltenyi) and further expanded until Day 14. ScRNAseq on expanded cells was performed on Day 14.

extract_protocol:
10XGenomics
library strategy: 10xGenomics Chromium single cell 3' library and Gel bead kit

treatment_protocol: Cocultured: T cells were cocultured with survivin+HLA-A*02:01+ BV173 leukemia cells at an effector to target ratio of 1:1 for 4 days (from Day 17 to Day 21). T cells were reisolated from co-cultures on Day 21 where tumor cells were killed. Debris was removed with a dead cell removal kit (Miltenyi). CD4+ T cells transduced with TCR alone did not kill leukemia cells and could not be analyzed by scRNA seq due to tumor cell overgrowth. In the condition with TCR+ CD8+ T cells, residual leukemia cells were removed by depletion with CD19 microbeads (Miltenyi). Co-cultures with T8+ CD4+ T cells as well as T8+ CD8+ T cells did not contain residual BV173 cells.

tag: culture

value: Fresh:frozen on Day 0 and thawed for scRNA seq on Day 21

tag: transgenes

tag: expected cells

tag: sample process day

value: Day 21


title: KC_pan_non-tuft_sample3

tag: strain

tag: age


title: MUC3865_LS02_LP_RNA_Seq

tag: tissue


title: In7

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: King's College London

description: Incisor sc-RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads trimmed for adaptor sequences using TrimGalore. Then mapped to mm10 using Hisat2(v2) with default parameters.
Clustering analysis performed using Seurat v3
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Incisor

extract_protocol:
XLacZ4 mice were sacrificed. Molars and incisors were isolated and dissociated into single cells. Cell stained with FDG reagent. Cells possitive were isolated using FACS
Smart-Seq2. Libraries constructed using standard Illumina protocols.
Single cell RNAseq.

value: Incisor

value: pericytes


title: In6

description: Incisor sc-RNAseq


title: In3

description: Incisor sc-RNAseq


title: In5

description: Incisor sc-RNAseq


title: In4

description: Incisor sc-RNAseq


title: MUC3861_LS25_HP_RNA_Seq


title: L8: CD4_Fr

description:
*barcode*_8
No reads data provided due to human data policies


title: L6: CD4_T8_cc

description:
*barcode*_6
No reads data provided due to human data policies

value: Cocultured


title: In9

description: Incisor sc-RNAseq


title: In10

description: Incisor sc-RNAseq


title: KC_pan_tuft_sample1

value: Mixed

value: Pancreas


title: L4: CD8_T8_exp

description:
*barcode*_4
No reads data provided due to human data policies

value: Expanded

value: Day 14


title: In1

description: Incisor sc-RNAseq


title: L3: CD8_T_exp

description:
*barcode*_3
No reads data provided due to human data policies


title: MUC3856_LS03_HP_RNA_Seq


title: L5: CD8_T_cc

description:
*barcode*_5
No reads data provided due to human data policies


title: In12

description: Incisor sc-RNAseq


title: In2

description: Incisor sc-RNAseq


title: L2: CD4_T8_exp

description:
*barcode*_2
No reads data provided due to human data policies


title: In13

description: Incisor sc-RNAseq


title: HS5_R3

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

library_source: genomic

data_processing:
Raw data was filtered to remove adapter sequences and low-quality reads using NGS QC Toolkit (v2.3).
High-quality filtered reads were aligned to kabuli chickpea genome (v1) using Bismark (v0.14.3) and clonal reads were removed.
Uniquely mapped reads were used to determine methylated cytosines (mCs) using methylKit (v0.9.2).
mCs were identified showing  ≤ 0.001 significance and covered with ≥ 5 reads at a cytosine site in the chickpea genome.
Genome_build: kabuli chickpea genome (v1)
Supplementary_files_format_and_content: tab delimited text files including methylated cytosine position

organism: Cicer arietinum

source_name: Seed

growth_protocol: Plants were grown in natural field conditions and seeds undergoing late-embryogenesis (S3) and mid-maturation (S5) stages of seed development were harvested from field-grown plants.

extract_protocol:
Genomic DNA was extracted from seeds using Qiagen's DNeasy Plant mini-kit.
Genomic DNA samples were fragmented via sonication, end repired and adapters were ligated. The adapter-ligated DNA fragments were used for bisulphite conversion using EZ DNA Methylation-Gold kit. After size selection libraries were prepared using Illumina protocol.

value: Himchana 1

value: Seed

tag: development stage


title: In14

description: Incisor sc-RNAseq


title: L7: CD8_T8_cc

description:
*barcode*_7
No reads data provided due to human data policies


title: HS5_R2


title: In8

description: Incisor sc-RNAseq


title: In15

description: Incisor sc-RNAseq


title: HS5_R1


title: HS3_R2


title: In11

description: Incisor sc-RNAseq


title: In19

description: Incisor sc-RNAseq


title: In18

description: Incisor sc-RNAseq


title: In20

description: Incisor sc-RNAseq


title: In16

description: Incisor sc-RNAseq


title: JS7_R1 [BiSulfite-seq]

data_processing:
Raw data was filtered to remove adapter sequences and low-quality reads using NGS QC Toolkit (v2.3).
High-quality filtered reads were aligned to kabuli chickpea genome (v1) using Bismark (v0.14.3) and clonal reads were removed.
Uniquely mapped reads were used to calculate methylated cytosines (mCs) using methylKit (v0.9.2).
mCs were identified showing  P-value ≤ 0.001 significance and covered with ≥ 5 reads at each cytosine site in the chickpea genome.
Genome_build: kabuli chickpea genome (v1)
Supplementary_files_format_and_content: tab delimited text files including methylated cytosine position

growth_protocol: Plants were grown in natural field conditions and seeds undergoing early-embryogenesis (S1), mid-embryogenesis (S2), late-embryogenesis (S3), mid-maturation (S5) and late-maturation (S7) stages of seed development were harvested from field-grown plants.

value: JGK 3


title: In21

description: Incisor sc-RNAseq


title: In23

description: Incisor sc-RNAseq


title: JS5_R3 [BiSulfite-seq]


title: JS5_R1 [BiSulfite-seq]


title: JS3_R2 [BiSulfite-seq]


title: JS5_R2 [BiSulfite-seq]


title: JS7_R2 [BiSulfite-seq]


title: In22

description: Incisor sc-RNAseq


title: In24

description: Incisor sc-RNAseq


title: L1: CD4_T_exp

description:
*barcode*_1
No reads data provided due to human data policies


title: In25

description: Incisor sc-RNAseq


title: JS3_R1 [BiSulfite-seq]


title: JS2_R2 [BiSulfite-seq]


title: JS2_R1 [BiSulfite-seq]


title: In26

description: Incisor sc-RNAseq


title: JS1_R2 [BiSulfite-seq]


title: MUC3858_LS14_HP_RNA_Seq


title: In17

description: Incisor sc-RNAseq


title: HS3_R1


title: In28

description: Incisor sc-RNAseq


title: JS1_R1 [BiSulfite-seq]


title: JS7_R2

data_processing:
Data obtained in FASTQ files were processed to remove adapter sequences using cutadapt (v1.12) and low-quality reads using qrqc package in R.
High-quality filtered identical reads were collapsed into a unique reads to estimate abundance of small RNAs at different stages of seed development and leaf tissue.
Supplementary_files_format_and_content: FASTA files containing non-redundant reads with their read counts.

growth_protocol: Plants were grown in natural field conditions and seeds undergoing different stages of development were harvested from field-grown plants.

extract_protocol:
Total RNA was isolated followed by preparation of small RNA sequencing libraries using TruSeq Small RNA Sample Prep Kit (Illumina Technologies).
Small RNA libraries were prepared for sequencing using Illumina's standard protocols.

value: Late maturation (S7)


title: In29

description: Incisor sc-RNAseq


title: In30

description: Incisor sc-RNAseq


title: In32

description: Incisor sc-RNAseq


title: JS6_R2

value: Late maturation (S6)


title: JS7_R1


title: In31

description: Incisor sc-RNAseq


title: JS6_R1


title: JS5_R1

value: Mid maturation (S5)


title: Mo3

description: Molar sc-RNAseq

source_name: Molar

value: Molar


title: Mo1

description: Molar sc-RNAseq


title: JS4_R1

value: Early maturation (S4)


title: JS4_R2


title: Mo4

description: Molar sc-RNAseq


title: Mo5

description: Molar sc-RNAseq


title: JS3_R2

value: Late embryogenesis (S3)


title: JS3_R1


title: Mo2

description: Molar sc-RNAseq


title: Mo6

description: Molar sc-RNAseq


title: In27

description: Incisor sc-RNAseq


title: JS2_R2

value: Mid embryogenesis (S2)


title: JS2_R1


title: Mo8

description: Molar sc-RNAseq


title: JS1_R2

value: Early embryogenesis (S1)


title: Mo9

description: Molar sc-RNAseq

value: pericytes


title: Mo7

description: Molar sc-RNAseq


title: JS1_R1


title: Mo10

description: Molar sc-RNAseq


title: Mo11

description: Molar sc-RNAseq


title: Jleaf_R2

source_name: Leaf

value: Leaf