title: Sample 18_Brain cells - 14_day_Males_rep3

city: San Diego

first: Goran

last: Bozinovic

address: 3030 Bunker Hill St

institute: Boz Life Science Research and Teaching Institute

data_processing:
Single-end sequencing reads were trimmed to remove adapter sequences via Trimmomatic 0.39.
Sortmerna-2.1 was used to remove ribosomal RNA contamination.
Base sequences with a Phred score below 32 were removed and a minimum sequence length filter of 18 was applied.
Illumina sequence reads were mapped to the reference D. melanogaster genome (FlyBase 6.32) using STAR (2.7.3a) with default parameters.
The DESeq2 package (version 2.10) implemented in R (version 2.14.1) was used to normalize counts and determine differential expression between sexes and ages.
Assembly: FlyBase 6.32
Supplementary files format and content: fly_deseq2_norm.csv, lists for Samples 1 - 18 (column names), normalized and filtered counts for gene (row names)

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Oregon wild-type Drosophila melanogaster (Carolina Biological Supply Company) were reared on standard cornmeal agar medium, 12-hour light/dark cycle at 25°C. Female and male virgin flies less than 4 hours post-eclosion were separately collected under CO2. Flies were aged to 3, 7, or 14 days post-eclosion and snap frozen at -80°C. Subsequently, brains were dissected in phosphate buffered saline.

extract_protocol:
Pooled brains (100 brains/sample) were homogenized in TRIzol via a bead mill. Total RNA was isolated using the TRIzol reagent protocol (Invitrogen, Carlsbad, CA) and stored at -80°C.
RNA quantity and quality were determined with a Qubit 4 Fluorometer and BioAnalyzer 2100 (Agilent Technologies). RNA samples were prepared for RNA sequencing using the TruSeq RNA Library Prep Kit v2 and subsequently sequenced with a NextSeq2000 at the Genomics Core at The Scripps Research Institute, San Diego.

treatment_protocol: All collected virgin flies were reared on standard cornmeal agar medium for 3, 7, or 14 days post-eclosion.

value: brain

value: Oregon wild-type

tag: Sex

value: 14 days post-eclosion

value: 100 pooled brains


title: Sample 16_Brain cells - 14_day_Males_rep1

status: Public on Mar 25 2022

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: strain

value: male

tag: age


title: Sample 17_Brain cells - 14_day_Males_rep2


title: Hepatic stellate cells - S100KD_1

city: Nanjing

first: Wen-Song

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM and count valus for each Sample

organism: Mus musculus

source_name: S100a16+/- mice (C57BL/6J background)

growth_protocol: HSCs were isolated from WT or S100a16+/- mice and cultured in FBS-containing medium for 7 days for full differentiation

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: HSCs were cultured in FBS-containing medium for 7 days

tag: cell type

value: hepatic stellate cells

tag: treatment

value: cultured in FBS-containing medium for fully activation

tag: genotype


title: Sample 15_Brain cells - 7_day_Males_rep3

value: 7 days post-eclosion


title: wild type 6 months of age rep1

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from mouse eyeball

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Mouse Gene 2.1 ST ArrayStrip (20 h, 292 48 °C)

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: eyeball

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: All animals had unlimited access to water and breeding chow (Special Diet Services, Witham, UK), and housing conditions and environmental enrichment.

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: All animals were cull at specific time-points by cervical dislocation. Eye tissues were harvested and snap-frozen in liquid nitrogen. Next, they were kept at -80C till further analysis.

value: eyeball

value: wild type

value: 6 months of age


title: APCmin/+ WHSC1 KO

city: shanghai

first: jiale

middle: jia

last: ren

state: shanghai

address: yueyang road 320

department: shanghai institute of nutrition and health

institute: CAS

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
RSEM was used to computed maximum likelihood abundance estimates. FPKM method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: mm 10
Supplementary_files_format_and_content: bigwig

source_name: intestinal epithelial cell

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

value: small intestine

value: 3 months

tag: genotype/variation

value: Whsc1 -/-


title: LB-36

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome hg38 by STAR aligner (version 2.7.5a) and gene counts were quantified by --quant  Mode GeneCounts option
Genome_build: hg38
Supplementary_files_format_and_content: txt file for gene read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Liver biopsies were isolated using Total RNeasy Mini Kit (QIAGEN Inc.). RNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: NAFLD disease

tag: gender

value: M

tag: nas

value: Steatosis


title: mRNA_H_Pylori_rep59 [2S040T1AC1]

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

data_processing:
Data was processed with using Bowtie 2 and RSEM softwares.
Genome_build: hg19
Supplementary_files_format_and_content: rsem files were generated using RSEM; Scores represent Transcripts Per Million and Fragments Per Kilobase Million.

source_name: mRNA from H Pylori negative gastric tumor tissue

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
illumina True Seq RNA Access sample Preparation Kit

tag: age range

tag: tissue type

value: tumor

tag: h. pylori infection

value: negative


title: LB-37


title: Sample 14_Brain cells - 7_day_Males_rep2

value: brain

value: Oregon wild-type


title: mRNA_H_Pylori_rep58 [2S034T1AC1]

value: female


title: mRNA_H_Pylori_rep49 [1S935T1AC1]


title: mRNA_H_Pylori_rep50 [1S948T1AC1]

value: male


title: LB-35

value: NASH


title: APCmin/+  WT

value: WT


title: LB-34

value: F


title: Sample 13_Brain cells - 7_day_Males_rep1

value: 7 days post-eclosion

value: 100 pooled brains


title: Sample 12_Brain cells - 3_day_Males_rep3

value: 3 days post-eclosion


title: puchi_36h_R2_23_07_2020

city: Montpellier

first: Soazig

last: GUYOMARC'H

address: 911 avenue Agropolis

country: France

institute: University of Montpellier

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Arabidopsis thaliana genome (NCBI TAIR10.1) with a set of gene model annotations (gff file downloaded from NCBI on November 13, 2020).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene (TAIR|NCBI GeneID|Symbol) and every sample

organism: Arabidopsis thaliana

source_name: puchi-1_36h post gravistimulation_R3

growth_protocol: Col-0 and puchi-1 seeds were surface-sterilized and sown on ½ strength Murashige and Skoog (½ MS) solid medium containing 0.7% (w/v) plant agar supplemented with B5 vitamins. Plates were kept at 4°C for 2 days and then placed in continuous light conditions (24-h light/0-h dark cycle) in vertical position.

extract_protocol:
For each replicates, root bends of more than 400 seedlings were microdissected under a binocular microscope and frozen in liquid nitrogen immediately on harvesting. For reference, approximately 400 mature root segments located between the bend and the shoot were harvested in 4d-old seedlings at 9 h after an inductive gravitropic stimulation to be used as a reference of non-gravitropic- stimulated root tissues devoid of developing LRP (termed “time point 0” in the data set).Total RNA was extracted using Qiagen RNeasy plant mini kit with an on-column DNAse treatment following the manufacturer’s recommendation (RNAse-free DNAse Set, Qiagen, Crawley, UK). RNA samples were quantified using a Nanodrop ND100 spectrophotometer (Nanodrop, Wilimington, USA) and RNA purity and integrity were evaluated using High-Resolution Automated Electrophoresis 2100 Bioanalyzer system from Agilent Technologies (https://www.agilent.com/en/product/automated-electrophoresis).
cDNA Libraries were constructed using Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions and sequenced on a complete S1 flow cell (2 lanes) of an Illumina NovaSeq 6000 in paired-end 100 nucleotides mode.

treatment_protocol: Gravistimulation were performed on 4 day-old seedlings and root bends were sampled at 12 hours (h), 18h, 24h, 30h and 36h after gravistimulation. Three biological replicates (for both Col-0 and puchi-1) were used for the RNAseq experiment.

value: Mutants puchi-1

value: 36h gravistimulation

value: Lateral root and surrounding tissues at the bend

value: 4 day-old seedlings


title: mRNA_H_Pylori_rep48 [1S931T1AC1]


title: Hepatic stellate cells - S100KD_2

value: hepatic stellate cells

value: cultured in FBS-containing medium for fully activation


title: LB-03

value: NAFLD disease


title: mRNA_H_Pylori_rep46 [1S919T1AC1]

value: tumor

value: negative


title: Sample 11_Brain cells - 3_day_Males_rep2

value: brain

value: Oregon wild-type


title: LB-33

value: M

value: NASH


title: Sample 10_Brain cells - 3_day_Males_rep1

value: male


title: mRNA_H_Pylori_rep47 [1S905T1AC1]

value: female


title: Hepatic stellate cells - S100KD_3


title: puchi_36h_R1_26_06_2020

source_name: puchi-1_36h post gravistimulation_R2


title: LB-32

value: F


title: Sample 9_Brain cells - 14_day_Females_rep3

value: 14 days post-eclosion

value: 100 pooled brains


title: placenta, control group

first: Shanshan

last: Yang

address: 101 Longmian Avenue

department: Institute of Toxicology

institute: Nanjing Medical University

description:
150383A_B
The expression profile of lncRNAs in the placentas of pregnant women with NDFMS was investigated using an Agilent Human LncRNA Microarray. Differentially expressed lncRNAs were selected for validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 mL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent)

data_processing: To select the differentially expressed genes, we used thresholdvalues of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: Human placental tissues,full-term birth (≥37 weeks and <42 weeks)

label_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 mg amplified RNA was mixed with 4 mg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 mL of 4×first-strand buffer, 2 mL of 0.1M DTT, and 1.5 mL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 mL. The cDNA was mixed with 4 mg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 mL Klenow buffer, dNTP, and  Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 mM dATP, 240 mM dGTP, 240 mM dTTP, 120 mM dCTP, and 40 mM Cy-dCTP. 1.2 mL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Following the removal of the placental tissue fetal membranes, three sections of placental tissues were randomly collected. Subsequently, the placental tissues were immediately stored at -80˚C.

extract_protocol: Total RNA was extracted from the placental tissues using TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, Inc.), according to the manufacturer's protocol. Placental tissues of appropriate size were placed in TRIzol® for RNA extraction. All procedures were performed on ice, to prevent RNA degradation. The concentration and purity of the RNA were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Inc.), and electrophoresis with 1.5% denaturing agarose gels was used to assess RNA integrity. The PrimeScript RT reagent kit (Takara Bio, Inc.) was used to reverse transcribe the RNA samples into cDNA (RR036A; Takara Bio, Inc.)

treatment_protocol: Liquid nitrogen grinds into the placental tissue

tag: group

value: control

value: placenta

tag: puerpera

value: monotocous primigravida with full-term birth (≥37 weeks and <42 weeks)

tag: delivery gestational age

tag: inclusion criteria

value: free of diabetes or other complications (placental abruption, gestational hypertension, placenta previa, and other complications) during pregnancy.


title: placenta, non-diabetic fetal macrosomia (NDFMS) group

description:
150383A_A
The expression profile of lncRNAs in the placentas of pregnant women with NDFMS was investigated using an Agilent Human LncRNA Microarray. Differentially expressed lncRNAs were selected for validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

value: non-diabetic fetal macrosomia (NDFMS)

tag: tissue

value: monotocous primigravida

value: full-term birth (≥37 weeks and <42 weeks)


title: puchi_R5_30h_04_08

source_name: puchi-1_30h post gravistimulation_R3

value: Mutants puchi-1

value: 30h gravistimulation

value: Lateral root and surrounding tissues at the bend

value: 4 day-old seedlings


title: mRNA_H_Pylori_rep43 [1S895T1AC1]

value: tumor

value: negative


title: LB-38

value: NAFLD disease

value: NASH


title: puchi_36h_R1_15_07_2020

source_name: puchi-1_36h post gravistimulation_R1

value: 36h gravistimulation


title: mRNA_H_Pylori_rep51 [1S966T1AC1]

value: female


title: LB-29

value: M

value: Steatosis


title: mRNA_H_Pylori_rep52 [1S971T1AC1]

value: male


title: mRNA_H_Pylori_rep44 [1S911T1AC1]


title: Sample 8_Brain cells - 14_day_Females_rep2

value: brain

tag: strain

value: Oregon wild-type

tag: Sex

value: 14 days post-eclosion

value: 100 pooled brains


title: LB-30

value: Borderline

tag: age


title: LB-31


title: Sample 6_Brain cells - 7_day_Females_rep3

description: outlier removed from analysis

value: 7 days post-eclosion


title: Sample 5_Brain cells - 7_day_Females_rep2


title: LB-04


title: mRNA_H_Pylori_rep40 [1S866T1AC1]


title: puchi_30h_R2_25_07_2020

source_name: puchi-1_30h post gravistimulation_R2

value: Mutants puchi-1

tag: treatment

value: 30h gravistimulation

value: Lateral root and surrounding tissues at the bend


title: Sample 4_Brain cells - 7_day_Females_rep1


title: mRNA_H_Pylori_rep41 [1S885T1AC1]

value: tumor

value: negative


title: puchi_30h_R1_15_06_2020

source_name: puchi-1_30h post gravistimulation_R1

tag: genotype

value: 4 day-old seedlings


title: mRNA_H_Pylori_rep42 [1S890T1AC1]


title: LB-02

value: NAFLD disease


title: puchi_24h_R2

source_name: puchi-1_24h post gravistimulation_R3

value: 24h gravistimulation


title: puchi_24h_R1_13_03_2020

source_name: puchi-1_24h post gravistimulation_R2


title: Sample 3_Brain cells - 3_day_Females_rep3

value: female

value: 3 days post-eclosion


title: mRNA_H_Pylori_rep39 [1S845T1AC1]


title: mRNA_H_Pylori_rep45 [1S918T1AC1]


title: puchi_24h_R1

source_name: puchi-1_24h post gravistimulation_R1


title: LB-09

value: M


title: mRNA_H_Pylori_rep38 [1S809T1AC1]

value: male


title: Sample 2_Brain cells - 3_day_Females_rep2

value: brain

value: Oregon wild-type


title: puchi_18h_R2_27_07_2020

source_name: puchi-1_18h post gravistimulation_R3

value: 18h gravistimulation


title: mRNA_H_Pylori_rep37 [1S790T1AC1]


title: LB-28

value: Steatosis


title: Sample 7_Brain cells - 14_day_Females_rep1

description: outlier removed from analysis

source_name: brain

value: 14 days post-eclosion

value: 100 pooled brains


title: mRNA_H_Pylori_rep36 [1S781T1AC1]


title: puchi_18h_R1_26_06_2020

source_name: puchi-1_18h post gravistimulation_R2

value: Mutants puchi-1


title: Sample 1_Brain cells - 3_day_Females_rep1


title: LB-05

value: F

value: Borderline


title: LB-27


title: RNAseq.iWAT.g2WT.3

city: Philadelphia

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: GeneList.iWAT.txt

data_processing:
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (mm10) using Hesat2 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene from Ensembl database was estimated using StringTie v1.3.4
ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (mm10) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script;

source_name: Adipose

extract_protocol:
Total RNA was extracted by using Trizol chloroform followed by purification with Qiagen RNeasey Mini kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
RNA libraries were prepared for sequencing by Novogene (CA).
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.

tag: cell type

value: iWAT


title: puchi_18h_R1_13_03_2020

source_name: puchi-1_18h post gravistimulation_R1

value: Lateral root and surrounding tissues at the bend

value: 4 day-old seedlings


title: mRNA_H_Pylori_rep35 [1S769T1AC1]

value: tumor

value: negative


title: LB-26

source_name: liver

tag: disease

value: NAFLD disease


title: RNAseq.iWAT.g2WT.2

description: GeneList.iWAT.txt


title: mRNA_H_Pylori_rep34 [1S766T1AC1]

source_name: mRNA from H Pylori negative gastric tumor tissue

tag: gender


title: puchi_12h_R2_27_07_2020

source_name: puchi-1_12h post gravistimulation_R3

value: 12h gravistimulation


title: LB-25

tag: nas


title: RNAseq.iWAT.g2WT.1

description: GeneList.iWAT.txt


title: puchi_12h_R1_23_06_2020

source_name: puchi-1_12h post gravistimulation_R2


title: mRNA_H_Pylori_rep33 [1S759T1AC1]

value: female

tag: age range


title: RNAseq.iWAT.g2KO.3

description: GeneList.iWAT.txt


title: puchi_12h_R1_11_03_2020

source_name: puchi-1_12h post gravistimulation_R1


title: mRNA_H_Pylori_rep32 [1S739T1AC1]

value: male

tag: tissue type


title: LB-06

value: M

value: NASH


title: LB-24


title: RNAseq.iWAT.g2KO.2

description: GeneList.iWAT.txt


title: puchi_R6_Ref_04_08_bis

source_name: puchi-1_No LR_Ref_R3

value: No treatment- reference

value: Root  above to the bend


title: LB-23


title: mRNA_H_Pylori_rep31 [1S729T1AC1]

tag: h. pylori infection


title: RNAseq.iWAT.g2KO.1

description: GeneList.iWAT.txt


title: mRNA_H_Pylori_rep30 [1S727T1AC1]


title: LB-22


title: puchi_R6_Ref_04_08

source_name: puchi-1_No LR_Ref_R2


title: RNAseq.iWAT.g1WT.3

description: GeneList.iWAT.txt


title: puchi_R4_Ref

source_name: puchi-1_No LR_Ref_R1


title: mRNA_H_Pylori_rep29 [GP152UT1AC1]


title: LB-21


title: RNAseq.iWAT.g1WT.2

description: GeneList.iWAT.txt


title: Col-0_R4_36h_05_08

source_name: Col-0_36h post gravistimulation_R3

value: Wild-type Columbia-0

value: 36h gravistimulation


title: LB-20

value: F


title: RNAseq.iWAT.g1WT.1

description: GeneList.iWAT.txt


title: Col-0_36h_R3_28_07_2020

source_name: Col-0_36h post gravistimulation_R2


title: RNAseq.iWAT.g1KO.3

description: GeneList.iWAT.txt


title: mRNA_H_Pylori_rep27 [1S693T1AC1]


title: LB-19

value: Steatosis


title: mRNA_H_Pylori_rep26 [1S676T1AC1]


title: Col-0_36h_R1

source_name: Col-0_36h post gravistimulation_R1


title: RNAseq.iWAT.g1KO.2

description: GeneList.iWAT.txt

value: iWAT


title: LB-17

value: Borderline


title: Col-0_30h_R3_28_07_2020

source_name: Col-0_30h post gravistimulation_R3

value: 30h gravistimulation

value: Lateral root and surrounding tissues at the bend

value: 4 day-old seedlings


title: mRNA_H_Pylori_rep25 [1S661T1AC1]

value: tumor

value: negative


title: Col-0_30h_R2_27_07_2020

source_name: Col-0_30h post gravistimulation_R2


title: RNAseq.iWAT.g1KO.1

description: GeneList.iWAT.txt


title: RNAseq.eWAT.g1WT.5

description: GeneList.eWAT.txt

value: eWAT


title: LB-16

value: NAFLD disease


title: mRNA_H_Pylori_rep24 [1S634T1AC1]

value: female


title: Col-0_30h_R1_25_06_2020

source_name: Col-0_30h post gravistimulation_R1


title: LB-15

value: M


title: mRNA_H_Pylori_rep23 [1S630T1AC1]

value: male


title: mRNA_H_Pylori_rep22 [1S626T1AC1]


title: RNAseq.eWAT.g1WT.3

description: GeneList.eWAT.txt


title: LB-14

value: NASH


title: RNAseq.eWAT.g1KO.5

description: GeneList.eWAT.txt


title: Col-0_R5_24h_04_08

source_name: Col-0_24h post gravistimulation_R3

value: Wild-type Columbia-0

value: 24h gravistimulation


title: Col-0_24h_R3_28_07_2020

source_name: Col-0_24h post gravistimulation_R2


title: LB-13

value: F


title: mRNA_H_Pylori_rep21 [1S614T1AC1]


title: LB-12


title: RNAseq.eWAT.g1KO.3

description: GeneList.eWAT.txt

source_name: Adipose


title: Col-0_24h_R2_17_07_2020

source_name: Col-0_24h post gravistimulation_R1


title: mRNA_H_Pylori_rep19 [1S616T1AC1]

source_name: mRNA from H Pylori negative gastric tumor tissue


title: RNAseq.eWAT.g1KO.4

description: GeneList.eWAT.txt


title: RNAseq.eWAT.g2WT.3

description: GeneList.eWAT.txt


title: Col-0_18h_R2_27_07_2020

source_name: Col-0_18h post gravistimulation_R3

value: 18h gravistimulation


title: mRNA_H_Pylori_rep18 [1S613T1AC1]


title: LB-18

source_name: liver

value: Steatosis


title: mRNA_H_Pylori_rep17 [1S516T1AC1]


title: Col-0_18h_R1_24_06_2020

source_name: Col-0_18h post gravistimulation_R2


title: mRNA_H_Pylori_rep28 [GP176UT1AC1]


title: RNAseq.eWAT.g2WT.1

description: GeneList.eWAT.txt


title: RNAseq.eWAT.g2WT.2

description: GeneList.eWAT.txt


title: LB-10


title: Col-0_18h_R1_11_03_2020

source_name: Col-0_18h post gravistimulation_R1


title: LB-11


title: LB-01


title: KYSE450 Elaiophylin 2

city: Wuhan

first: Gao

last: Lijuan

address: Luojiashan

institute: Wuhan University

description: KYSE450_gene expression profiles.txt

data_processing:
Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were mapped to the mouse reference genome (mm10) using TopHat (version 2.1.1, http://ccb.jhu.edu/software/tophat/index.shtml) with default settings.
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined as ones with the false discovery rate (FDR) less than 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Esophageal tumour

extract_protocol:
RNA isolation was performed using the TRIZOL reagent (Invitrogen) according to manufacturer’s instructions. Cells were homogenized using a glass-Teflon in 1 ml or 500 µl TRIZOL reagent on ice and phase separation was achieved with 200 µl or 100 µl chloroform. After centrifugation at 12,000× g for 15 min at 4°C, RNA was precipitated by mixing aqueous phase with equal volumes of isopropyl alcohol and 0.5 µl 20 mg/ml glycogen. Precipitation were dissolved in DNase/RNase-free water (not diethylpyrocarbonate treated, Ambion).
Total RNA was extracted as described above. The concentration and quality of RNA was measured with Nanodrop 2000c (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis. Newly synthesized cDNA was purified by AMPure XP beads (1:1) and eluted in 50 μl nucleotide-free water. RNA-seq libraries were sequenced by Illumina NovaSeq 6000 platform with pair-end reads of 150 bp. The sequencing depth was 60 million reads per library.

tag: cell line

value: Elaiophylin


title: Col-0_R5_12h_04_08

source_name: Col-0_12h post gravistimulation_R3

value: 12h gravistimulation


title: mRNA_H_Pylori_rep16 [1S511T1AC1]


title: RNAseq.eWAT.g2KO.3

description: GeneList.eWAT.txt


title: KYSE450 Elaiophylin 1

description: KYSE450_gene expression profiles.txt


title: RNAseq.eWAT.g2KO.2

description: GeneList.eWAT.txt


title: mRNA_H_Pylori_rep14 [1S472T1AC1]


title: Col-0_12h_R1_12_06_2021

source_name: Col-0_12h post gravistimulation_R1

value: Lateral root and surrounding tissues at the bend


title: Col-0_12h_R2_24_07_2020

source_name: Col-0_12h post gravistimulation_R2

value: 4 day-old seedlings


title: Col-0_R6_Ref_05_08

source_name: Col-0_No LR_Ref_R3

value: No treatment- reference

value: Root  above to the bend


title: RNAseq.eWAT.g2KO.1

description: GeneList.eWAT.txt

value: eWAT


title: Col-0_R5_Ref_04_08

source_name: Col-0_No LR_Ref_R2


title: RNAseq.eWAT.g1WT.2

description: GeneList.eWAT.txt


title: mRNA_H_Pylori_rep12 [GP132UT1AC1]

value: tumor

value: negative


title: Eca109 Elaiophylin 2

description: Eca109_gene expression profiles.txt

value: DMSO


title: mRNA_H_Pylori_rep20 [1S619T1AC1]

value: male


title: mRNA_H_Pylori_rep11 [GP131UT1AC1]


title: Col-0_R1_Ref

source_name: Col-0_No LR_Ref_R1


title: RNAseq.eWAT.g1WT.1

description: GeneList.eWAT.txt


title: Eca109 DMSO rep2

description: Eca109_gene expression profiles.txt


title: mRNA_H_Pylori_rep10 [GP130UT1AC1]

value: female


title: Eca109 Elaiophylin 1

description: Eca109_gene expression profiles.txt


title: RNAseq.eWAT.g1KO.2

description: GeneList.eWAT.txt


title: RNAseq.eWAT.g1KO.1

description: GeneList.eWAT.txt


title: Eca109 DMSO rep1

description: Eca109_gene expression profiles.txt


title: mRNA_H_Pylori_rep9 [GP129UT1AC1]


title: BACH1_KO_AFB1_3

first: Shengsong

last: Xie

state: Hubei

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University

description: RNA sequencing and transcriptome analysis data.

data_processing:
Quality control and read mapping: Sequence quality was assessed using FastQC (v0.11.7) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for all samples, and quality trimming was done using FASTX-Toolkit (v 0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/) to remove bases with Phred33 score of less than 30, while retaining the resulting reads of at least 50 bases in length. The quality trimmed reads were mapped against the reference genome of Sus scrofa genome reference (v11.1) using HISAT2 (v2.1.0).
Gene expression profiling was based on the number of reads. FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels by using stringtie (v2.2.1), samtools (v1.7) and htseq-count (v0.9.1). DEGs were obtained by DESeq2 (v1.30.1) with an P-value cutoff < = 0.05 and an absolute fold-change of >= 2.
Assembly: Sus scrofa genome reference (v11.1).
Supplementary files format and content: *.txt: Tab-delimited text files include raw gene counts.

organism: Sus scrofa

source_name: PK-15-Cas9 cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and total RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.

value: porcine kidney-15 (PK-15) cells

tag: knock-in

value: Cas9 puro

value: BACH1 KO


title: RNAseq.BAT.g2WT.4

description: GeneList.BAT.txt

value: BAT


title: BACH1_KO_AFB1_2


title: BACH1_KO_AFB1_1


title: Patient65_BCR

city: Los Angeles

first: Kenneth

middle: Howard

last: Gouin III

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description:
scSeq of TNBC samples
combined_minimum_immune.h5ad

data_processing:
Demultiplexed fastq files for gene expression libraries were processed using Cellranger count (version 4.0.0, GRCh38-2020-A transcriptome reference) with the --r1-length and --r2-length set according to the sequencing formats listed. Demultiplexed fastq files for TCR/BCR-enriched libraries were first trimmed to the read lengths listed using TrimGalore (v0.6.6) --hardtrim parameter and then processed using Cellranger vdj (version 5.0.0, GRCh38-alts-ensembl-5.0.0 reference).
T-cells were deemed to have a productive TCR if both a productive TRA and TRB chain were detected for the given cell. In the case of a cell having multiple TRA or multiple TRB sequences, the sequence with the highest UMI count was retained. A TCR was annotated as “expanded” if it contained more than 1.5 times the median frequency of cells across TCRs for a given sample. B-cells were deemed to have a productive BCR if both a productive IgH chain and either a productive IgK or IgL chain were detected for the given cell. In the case of a cell having multiple sequences for a given chain, the sequence with the highest UMI count was retained.
Genome_build: GRCh38
Supplementary_files_format_and_content: combined_minimum_immune.h5ad contains processed data for all cells passing QC filtering and were further filtered to only include immune cells. These files contain raw UMI counts for every gene in every cell as well as metadata associated with each cell (e.g. sample identity, annotated cell type, etc.).  combined_filtered_tcr_table.csv and combined_filtered_bcr_table.csv contains the final TCR and BCR information for each cell after filtering.

source_name: untreated human triple negative breast cancer

extract_protocol:
Core biopsies were obtained under local anesthesia using a 12G core needle apparatus (Bard Magnum). Biopsies were placed immediately into a 50mL conical containing ice-cold DMEM and transferred on ice from the clinic to the laboratory (generally within 30 minutes of the procedure). A portion of the biopsy was immediately placed into formalin for subsequent paraffin embedding. The remainder of the biopsy was minced with a sterile scalpel into 2 mm pieces and placed in a gentleMACS C-tube (Miltenyi Biotech) containing 4.7mL of ice-cold DMEM. Enzymes from the Human Tumor Dissociation Kit (Miltenyi Biotech) were added to the sample according to the manufacturer’s protocol for dissociation of tough tumors. After the enzymes were added, the C-tube was placed onto a gentleMACS Octo Dissociator (Miltenyi Biotech), the heating element was placed over the tube, and the 37C_h_TDK_3 program was initiated.
Prior to completion of the dissociation protocol, two 70 μm cell strainers were each placed onto a 50mL conical on ice and pre-wetted with 3mL of heat-inactivated FBS. Upon completion of the dissociation protocol, the sample was poured through the first 70 μm cell strainer and the strainer was washed with 5mL of heat-inactivated FBS. The filtrate was then poured through the second 70 μm cell strainer and the strainer was washed with 5mL of heat inactivated FBS. The sample was centrifuged at 300xg for 7 minutes at 4C. The supernatant was removed, and the sample was resuspended in 2mL of DMEM and transferred to a microcentrifuge tube on ice. An aliquot of the sample was taken for cell counting via a hemocytometer and the remaining sample was centrifuged at 300xg for 10 minutes at 4C. The supernatant was removed, and the sample was resuspended in 80μL FACS buffer per 10^7 cells. Miltenyi anti-human CD45 microbeads were added to the sample (20μL per 10^7 cells), and the sample was incubated at 4C covered with foil for 15 minutes. After incubation, 1mL FACS buffer per 10^7 cells was added to the sample and pipet mixed. The sample was centrifuged at 300xg for 10 minutes at 4C. The supernatant was removed, and the sample was resuspended with 500μL FACS buffer and transferred to a 15mL conical. The sample was placed in a pre-cooled AutoMACS tube holder and the Miltenyi AutoMACS Possel_S program was initiated. At this time, 10X Genomics reagents required for running the Single Cell 5’ v1 Assay were removed from their storage conditions to equilibrate at room temperature for 30 minutes.
Upon completion of the AutoMACS program, the CD45-positive fraction was centrifuged at 300xg for 7 minutes at 4C. The sample was resuspended in 50μL of DMEM and a cell count was performed via a hemocytometer. If possible, the sample was diluted to 1000 cells/μL and the sample was processed according to the 10X Genomics protocol for the Single Cell 5’ v1 assay with a targeted 10,000 cell recovery (or maximum recovery possible with the number of cells in the sample).
Subsequent gene expression libraries and T-cell receptor (TCR)/B-cell receptor (BCR) enriched libraries were prepared according to the 10X Genomics Single Cell 5’ v1 protocol. Libraries were sequenced using paired-end 150bp reads to an average 60-70% sequencing saturation (as calculated by 10X Genomics Cellranger v4.0.0) on an Illumina Novaseq.

tag: individual

value: triple negative breast cancer (TNBC)

tag: enrichment


title: mRNA_H_Pylori_rep8 [1S415T1AC1]


title: Patient65_TCR

tag: tissue


title: BACH1_KO_3


title: RNAseq.BAT.g2WT.3

description: GeneList.BAT.txt


title: mRNA_H_Pylori_rep15 [1S503T1AC1]


title: mRNA_H_Pylori_rep7 [1S402T1AC1]


title: KYSE450 DMSO rep2

description: KYSE450_gene expression profiles.txt

value: Elaiophylin


title: Patient65_GEX


title: BACH1_KO_1


title: RNAseq.BAT.g2WT.1

description: GeneList.BAT.txt


title: Patient62_BCR


title: RNAseq.BAT.g2KO.4

description: GeneList.BAT.txt


title: KYSE450 DMSO rep1

description: KYSE450_gene expression profiles.txt


title: mRNA_H_Pylori_rep13 [GP133UT1AC1]


title: mRNA_GastricCancer_rep5 [GP128]

source_name: Gastric Cancer tissue_with H. pylori infection

value: positive


title: mRNA_GastricCancer_rep6 [MK521]

source_name: Gastric Cancer tissue_without H. pylori infection


title: mRNA_GastricCancer_rep4 [GP127]


title: WT_AFB1_3

value: WT


title: Patient62_TCR


title: RNAseq.BAT.g2KO.3

description: GeneList.BAT.txt

source_name: Adipose


title: WT_AFB1_2


title: Patient62_GEX


title: RNAseq.BAT.g2KO.2

description: GeneList.BAT.txt


title: mRNA_GastricCancer_rep3 [1S449]


title: WT_AFB1_1


title: mRNA_GastricCancer_rep2 [1S411]


title: RNAseq.BAT.g2KO.1

description: GeneList.BAT.txt


title: WT_3


title: RNAseq.BAT.g1WT.4

description: GeneList.BAT.txt


title: Patient61_TCR


title: mRNA_GastricCancer_rep1 [1S403]


title: WT_2


title: Patient51_BCR


title: WT_1


title: RNAseq.BAT.g1WT.3

description: GeneList.BAT.txt


title: RNAseq.BAT.g1WT.2

description: GeneList.BAT.txt


title: Patient51_GEX


title: RNAseq.BAT.g1WT.1

description: GeneList.BAT.txt


title: RNAseq.BAT.g2WT.2

description: GeneList.BAT.txt


title: Ahr KO Clec4a4- eosinophil

city: St. Louis

first: Wei-Le

last: Wang

state: MO

address: BJCIH, 8th Floor, Room 8107, 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University

description:
2. AhrKO Clec4a4- 28821
Gene expression data from sorted Ahr KO Clec4a4- eosinophils.

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array or Mouse Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G 3000.

data_processing:
The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression.
Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data.

source_name: siLP eosinophil

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

extract_protocol: Eosinophil subsets were sorted from the siLP of Clec4a4-KI mCherry mice for identifying Clec4a4+ and Clec4a4− eosinophil-specific genes, WT mice, and Ahr KO mice for identifying AHR-dependent and -independent genes. RNA was extracted using the RNeasy Micro Kit according to the manufacturer instructions.

value: Small intestine

value: Ahr KO Clec4a4- eosinophils


title: PigGeCKO, AFB1, Round3

description: Sequencing result of the third challenge round of AFB1 screening.

library_source: genomic

data_processing:
Mapped read counts were subsequently used as input for the MAGeCK analysis software package (version 0.5).
Supplementary files format and content: *.txt: Tab-delimited text files include normalized counts for each sgRNA.

molecule: genomic DNA

growth_protocol: Generation of PigGeCKO cells.

extract_protocol:
Illumina sequencing of sgRNAs in the PigGeCKO cells.
Briefly, the genomic DNA from PigGeCKO cells were extracted using a Blood & Cell Culture DNA Midi Kit (QIAGEN), respectively. The sgRNA-coding region was amplified by PCR using KAPA HiFi HotStart High-Fidelity DNA Polymerase (NEB). PCR products were purified.

treatment_protocol: The PigGeCKO cells were generated by a total of ~2 × 10^8 PK-15-Cas9 cells and infected with the sgRNA library lentiviruses at an MOI of 0.3 as described in the previous publication (Zhao et al., 2020).


title: BACH1_KO_2


title: PigGeCKO, H2O2

description: Sequencing result of the challenge of H2O2 screening.


title: WT Clec4a4- eosinophil

description:
3. WT Clec4a4- 28820
Gene expression data from sorted WT Clec4a4- eosinophils.

value: WT Clec4a4- eosinophils


title: Patient51_TCR


title: RNAseq.BAT.g1KO.4

description: GeneList.BAT.txt


title: PigGeCKO, AFB1, Round2

description: Sequencing result of the second challenge round of AFB1 screening.


title: WT Clec4a4+ eosinophil

description:
1. WT Clec4a4+ 28819
Gene expression data from sorted WT Clec4a4+ eosinophils.

value: WT Clec4a4+ eosinophils


title: PigGeCKO, AFB1, Round1

description: Sequencing result of the first challenge round of AFB1 screening.


title: Patient41_BCR


title: PBMC

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

description: PBMC

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0.
R1 end, at the beginning of 16bp is CellBarcode sequence, then 10bp is UMI sequence. R2 end, we can truncate 151bp to 98bp.
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix.
Normalization and additional analysis by Seurat R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tar: Tar archives include the barcodes.tsv, features.tsv, and expression matrix.mtx files of each sample.

source_name: PBMC

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide to perform single cell suspension which were prepared before. Briefly, the single-cell samples were passed through a 40μm cells strainer and counted using a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After droplet generation, samples were transferred onto a PCR tube and reverse transcription was performed using T100 Thermal Cycler (BIO-RAD). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics followed by a Silane DynaBead clean-up as outlined in the user guide. Purified cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to determine cDNA concentration.
10X Genomics Single Cell 3' v3 Reagent Kit.

tag: diagnosis

value: Testicular seminoma with lymph node metastasis

value: PBMC


title: RNAseq.BAT.g1KO.3

description: GeneList.BAT.txt


title: Patient41_TCR


title: Pelvic lymph node Homogenate

source_name: Pelvic lymph node

value: Pelvic lymph node


title: Testicular tumor Homogenate

description: Tumor

source_name: Testicular tumor

value: Testicular tumor


title: RNAseq.BAT.g1KO.2

description: GeneList.BAT.txt


title: PigGeCKO, Control

description:
Sequencing result of sgRNA library from sorted mutant cell populations.
Same control sample as described in Zhao et al., 2020.


title: Patient41_GEX


title: Patient61_BCR


title: RNAseq.BAT.g1KO.1

description: GeneList.BAT.txt


title: Patient61_GEX


title: C2C12 on 100Kpa-hard at day 3 [D3H]

status: Public on Mar 24 2022

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Count matrices were generated from the fastq files via STAR using genome index based on GENCODE vM27
Raw count matrices were processed and analysed via DESeq2 pipeline.
Assembly: mm10
Supplementary files format and content: bulk_deseq2.h5ad:  anndata file containing counts matrices, pca and DE results. bulk_deseq2.rds: R object of the DESeqDataSet.

source_name: C2C12 on 100Kpa-hard

growth_protocol: Cells are maintained in 10% fetal bovine serum (FBS) (A3160401, Thermo Fisher Scientific) and 1% Penicillin-Streptomycin (15140-122, Thermo Fisher Scientific) in Dulbeco’s Modified Eagle’s Medium-high glucose (DMEM) (D5796, Sigma).

extract_protocol:
Cells were harvested using 0.05% Trypsin/EDTA. RNA was extracted using RNeasy micro kit with a start amoung of RNA of 100ng.
RNA libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module(E7490S), with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina(E7760) and Multiplex Oligos for illumina(96 Unique Dual Index Primer Pairs) (E6440)

treatment_protocol: C2C12 cells were seeded on soft (0.5 kPa) and 933 hard (100 kPa) laminin-coated PDMS gel, and collected every day until 5 days after seeding

tag: day

value: hard (100 kPa) laminin-coated PDMS gel


title: C2C12 on 0.5Kpa-soft at day 3 [D3S]

source_name: C2C12 on 0.5Kpa-soft

value: soft (0.5 kPa) laminin-coated PDMS gel


title: C2C12 on 0.5Kpa-soft at day 0 [D0S]


title: C2C12 on 100Kpa-hard at day 0 [D0H]


title: Ago1_KO1_mESC

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

description: reverse-stranded protocol

data_processing:
fastq files were obtained, as provided by sequencing facility (functional genomics center zurich)
Files were processed using snakePipes' RNA-seq pipeline (v2.3.1)
Genome_build: ENSEMBL GRCm38 v98

source_name: Embryonic stem cells

growth_protocol: mESCs were cultured in DMEM, 15% serum 100 U/ml LIF, 0.1 mM 2-beta-mercaptoethanol, 1% Pen/Strep on gelatin coated plates.

extract_protocol:
RNA was harvested using Trizol reagent. Illumnia TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of  sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
polyA RNA-seq

tag: strain

value: 129/Ola background

value: Blastocyst

value: AGO1 knockout cells


title: Ago1_KO2_mESC

description: reverse-stranded protocol


title: Renal hilus lymph node Homogenate

source_name: Renal hilus lymph node

value: Renal hilus lymph node


title: pristine gill (G0_3-7)

city: St. John's

first: Mohamed

last: Emam

state: NL

address: 0 Marine Lab Rd, St. John's, NL

country: Canada

institute: Memorial University

description:
pristine gill (G0)
Sample name: G0_3-7

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray slide was scanned at 5 µm resolution using a SureScan D Microarray Scanner (G2600D, Agilent Technologies) using Agilent Scan Control Software (v9.1.11.7, Agilent Technologies) by applying a built-in protocol (Agilent_HD_GX_2color). The photomultiplier tube sensitivity for Cy3 and Cy5 dye channels were adjusted at 100%.

data_processing: The signal intensity data were extracted and subjected to linear and LOESS normalization using Agilent Feature Extraction Software v12.0 (Agilent). Probes of low quality (e.g., signal not above background) or with absent values in more than 25% of all 10 arrays were removed from the dataset

organism: Salmo salar

source_name: Pristine gill (G0), pen number, individual fish

label_protocol: Five individual fish from each gill score (i.e., perstine and moderately damaged) were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified gill total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

growth_protocol: [Sampling and growth protocol]  Salmon were net pen-grown as part of a commercial aquaculture industry in the west coast of Canada. Fish were fed commercial diet, based on the information provided by the company (i.e., industry aquaculture site). The average weights for all of the collected fish in November 2017 was 1348 grams. The daily maximum water temperature increased from June (~12 °C) to August (~14.5 °C) and did not start to decrease until early October. The highest maximum water temperature, 16 °C, was recorded on August 1st at 1 m depth, and the maximum water temperature on the sampling dates (i.e., November 13-14) was 11-11.6 °C. Fluctuations in minimum salinity values showed more abrupt changes from June 1 to November 26; e.g., on June 2-3, the minimum salinity decreased from 25 ppt to 16 ppt (56 % reduction). The daily minimum salinity also seemed to increase from June to August and to increase from October onwards; however, the trend was less evident than with the maximum water temperature. The daily minimum oxygen saturation showed a progressive decrease from June (85-90 %) to August (75-80 %). Minimum oxygen saturation levels that could be considered moderate hypoxia (i.e., 70 %) were recorded on November 3-4. At the sampling dates (i.e., November 13-14), the minimum oxygen saturation was 78-80 %. During the growth period, fish were subjected to several environmental events (e.g., harmful algal blooms). Most instances in which harmful algae species were identified were between June and September. Five episodes with maximum Asterionella japonica cell concentrations > 500 cell/mL (1,200 cell/mL on July 12) were recorded during this period. Chrysochromulina sp. cell concentrations were > 100 cell/mL for most days in August, with two episodes of significance: one on August 4, when cell concentration reached 1,800 cell/mL; and another on August 16-18, a period during which cell concentration stayed > 500 cell/mL. Maximum cell concentrations < 150 cell/mL were detected on different dates in October (~one month before the sampling date) for Rhizosolenia setigera, Dictyocha speculum, Chaetoceros concavicorne, Asterionella japonica, and Heterosigma akashiwo (ordered from the most frequently detected/highest maximum cell concentration to the least frequently detected/lowest maximum cell concentration). Fish mortality for the period June 1-December 4 were recorded and classified based on the most probable cause. The most significant mortality events (> 2,000 dead fish) were 2 classified as “Mouth rot” [i.e., fish showed clinical signs compatible with ulcerative stomatitis (alias mouth rot disease)] occurring on June 21 and July 8; 8 classified as “environmental” [i.e., putatively caused by environmental stressors (e.g., harmful algae)], scattered throughout late July and early September; and one event classified as “old” (i.e., the cause of death could not assessed due to the deterioration of the fish carcass) on July 21. The closest mortality events to the sampling point, with 1000-1700 dead fish, occurred on November 1, 2, and 4.

extract_protocol: Gills were homogenized in 800 µl TRIzol (Invitrogen/Life Technologies, Carlsbad, CA, USA) with stainless steel beads (5 mm; Qiagen, Mississauga, ON, Canada) using a TissueLyser (Qiagen), and subjected to RNA extraction following manufacturers’ instructions.

treatment_protocol: Field samples were collected; moderately damaged gill, due to enviromental stressors, were compared to pristine gill (collected from the same site at the same timepoint). The fish were sampled on the 13th and 14th of November 2017. The average weights for all of the collected fish was 1348 grams.The gill samples were collected from the net pen-grown Atlantic salmon located in BC. Gills with no lesions visible and with single necrotic filament or spot were scored as G0 (i.e., pristine). Gills showing affected area up to 10% of the total gill filament were scored as G1, while G2 was defined as gills having damage affecting ~10% to 25% of the total gill filament. Gills with affected area > 25% of the total fill filament surface are scored as G3.  Fish with more than 50% of the total gill filament surface area covered with necrotic tissue were routinely observed but generally in mortalities or very moribund fish and not in healthy fish (B. Milligan, personal communication). Gills with moderate gill damged were compared to those with G0 score (i.e., pristine) using 44k microarray slides.

value: Gill

tag: condition

value: Pristine gill

tag: life stage

value: Adult

source_name: pool of all individual gill RNA samples included in the microarray experiment

value: pool of Pristine gills and Moderately damaged gills

tag: tag


title: moderately damaged gill (G2_2-12)

description:
moderately damaged gill (G2)
Sample name: G2_2-12

source_name: Moderately damaged gill (G2), pen number, individual fish

value: Moderately damaged gill


title: moderately damaged gill (G2_3-24)

description:
moderately damaged gill (G2)
Sample name: G2_3-24


title: pristine gill (G0_2-4)

description:
pristine gill (G0)
Sample name: G0_2-4


title: moderately damaged gill (G2_1-2)

description:
moderately damaged gill (G2)
Sample name: G2_1-2


title: moderately damaged gill (G2_1-13)

description:
moderately damaged gill (G2)
Sample name: G2_1-13


title: pristine gill (G0_3-13)

description:
pristine gill (G0)
Sample name: G0_3-13


title: 51_INDOM-I

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

description: Mechanisms compensating for disturbances in the activity of neuronal or humoral neuroimmune communication pathways in the model of intraperitoneal inflammation.

hyb_protocol: Hybridization to the microarrays was conducted for 20 h at 48°C.

scan_protocol: GeneAtlas System for Academic Customers.

data_processing: Affymetrix Expression Console Software, RMA, quantile normalization

organism: Rattus norvegicus

source_name: INDOM-I

label_protocol: 100 ng of a given sample that passed initial quality control screen (2100 Bioanalyzer, Agilent) were labeled and amplified using GeneChip WT PLUS Reagent Kit

growth_protocol: 3-month-old male Wistar rats (300 g ± 25 g, N=75)

extract_protocol: Samples were stored in -20°C in 200 μl of RNA-later (Thermo Fisher Scientific, USA). Total RNA was extracted from dissected hypothalamuses using spin column-based Universal RNA Purification Kit (Eurx, Poland) according to the manufacturer's protocol. RNA samples were subjected to DNase treatment on-column (RNase-free DNase I, Eurx, Poland, 15 min, room temperature) as well as in-sample (TURBO DNA-free Kit, Thermo Fisher Scientific, USA, 30 min, 37°C), to remove any residual DNA contamination. The quantity, purity and quality of RNA samples were estimated using a Nanodrop spectrophotometer (Thermo Fisher Scientific, USA) and a Bioanalyzer 2100 microcapillary electrophoresis device (Agilent, USA) with RNA 6000 Nano Assay Kit (Agilent, USA). Samples were of high quality (RNA Integrity Number > 9) and purity.

treatment_protocol: Animals belonging to group CNT were not subjected to any procedures. Groups “NaCl”, “CEL”, “SC560”, “INDOM” were subcutaneously injected for 10 days with NaCl, celecoxib, SC-560 or indometacin, respectively. Groups “vagotomy” and “sham_operation” were subjected to either subdiaphragmatic vagotomy or sham operation performed in analogous way to the vagotomy, with exception of cutting the nerves. Next, animals were allowed to recover from surgery for 30 days. On the day following the end of the treatment (11th day for “NaCl”, “CEL”, “SC560”, “INDOM” and 31th day for “vagotomy” and “sham_operation”groups), the animals received a single intraperitoneal injection of either 10 µg lipopolysaccharide dissolved in 100 μl 0.9% NaCl (groups named “-I”) or the same volume of saline (groups named “-III”). Animals were decaptitated 120 minutes after injection. Immediately after decapitation, hypothalamus samples, restricted mainly to the medial part containing the paraventricular nucleus, were disected.

value: Wistar

tag: Sex

value: male

value: hypothalamus

tag: injection

value: LPS

tag: procedure


title: pristine gill (G0_2-8)

description:
pristine gill (G0)
Sample name: G0_2-8


title: moderately damaged gill (G2_1-1)

description:
moderately damaged gill (G2)
Sample name: G2_1-1


title: 52_2_INDOM-III

source_name: INDOM-III

value: NaCl


title: 56_INDOM-III


title: 54_INDOM-III


title: 46_VAGX-I

source_name: VAGX-I

value: vagotomy


title: 49_INDOM-I


title: 50_INDOM-I


title: 47_NaCl-I

source_name: NaCl-I


title: 53_INDOM-III


title: 45_SHAM-III

source_name: SHAM-III


title: 44_SHAM-III


title: 40_SC560-III


title: 43_SHAM-III


title: 39_SC560-III


title: 41_CNT

source_name: CNT


title: 42_SHAM-I

source_name: SHAM-I


title: 55_INDOM-III


title: AI_cueR4

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Reads were trimmed from their adapter with cutadapt and aligned to the Bacillus subtilis genome (subsp. subtilis str. NCIB 3610, NZ_CM000488.1) with Bowtie2 version 2.3.4.1.
We then calculated the number of uniquely mapped reads per gene using HT-seq. change ≥ 3, and adjusted p value < 0.05.
Normalization and testing for differential expression was performed with DESeq2 version 1.16. A gene was considered to be differentially expressed using the following criteria: normalized mean read count ≥ 30, fold
Importantly, fastq files of delta-cueR samples and their controls were downsampled to 4million reads prior to the analysis.
Assembly: NZ_CM000488.1
Supplementary files format and content: crude read counts, text file

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: biofilm colony

growth_protocol: Biofilms were grown on B4 biofilm-promoting solid medium (0.4% yeast extract, 0.5% glucose, and 1.5% agar) (Barabesi et al., 2007) either supplemented with calcium acetate at 0.25% v/v (B4-Ca) or not (B4), incubated at 30°C, in a sealed box with a lit candle for enriched CO2 environment

extract_protocol:
Frozen bacterial pellets were lysed using the Fastprep homogenizer (MP Biomedicals) and RNA was extracted with the FastRNA PROT blue kit (MP Biomedicals, 116025050) according to the manufacturer’s instructions.
Libraries were contracted with NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, E7420)

tag: growth medium

tag: colony age

value: 3 day-old colony

tag: calcium concetration

value: 0.25 percent

tag: genotype

value: deltacueR


title: AI_wt1B

value: wild type


title: AI_wt3B


title: 37_SC560-III


title: 34_SC560-I


title: 36_SC560-III


title: pristine gill (G0_2-24)

description:
pristine gill (G0)
Sample name: G0_2-24


title: 35_2_SC560-I


title: 48_NaCl-III

source_name: NaCl-III


title: 33_SC560-I


title: 27_CEL-III

source_name: CEL-III


title: 23_CEL-I

source_name: CEL-I


title: 26_CEL-III


title: 28_CEL-III


title: 25_CEL-I


title: 31_SC560-I


title: 29_CEL-III


title: 32_SC560-I


title: 30_CEL-III


title: 24_CEL-I


title: 19_NaCl-III


title: AI_cueR1


title: AI_wt2B


title: 38_SC560-III


title: Sample_Set3B4D3

value: 0 percent


title: 22_CEL-I


title: Sample_Set3B4D2

value: 2-day old colony


title: Mixed, 1

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

description:
Data from co-culture; replicate 1
Asp_AspKle_counts.xlsx; Kle_AspKle_counts.xlsx

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to the concatenated genome of Aspergillus fumigatus (Af293, genome version s03-m05-r06) and Klebsiella pneumoniae (NCBI_Assembly GCF_001596075.2, sequence-region NZ_CP014696.2 1 5284734 )  using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Reads mapping to rRNA loci were removed.  Read counting was done using HTseq (Anders et al., 2014) in the union mode using the above mentioned annotations.
Assembly: Pairwise comparison of differential expression analysis of single cultures with co-cultures was performed using edgeR v3.8.6 (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts):
normalized (cpm; edgeR) read counts mapped to the indicated Aspergillus gene ID
normalized (cpm; edgeR) read counts mapped to the indicated Klebsiella gene ID

organism:
Klebsiella pneumoniae
Aspergillus fumigatus

source_name: bacterial and fungal cells

growth_protocol: Cells were cultured statically for 24 hours at 37 °C in YPD medium. For mixed cultures, Aspergillus fumigatus spores were inoculated and allowed to germinate for 12 hours prior addition of Klebsiella pneumoniae.

extract_protocol:
Total RNA was purified using the Trizol reagent.
15μg of RNA was DNase-treated, cleaned up using the RNAeasy kit fron Qiagen and total RNA was subjected to rRNA depletion. Further library construction was done at the Next Generation Sequencing core facility (VBCF) at the Vienna BioCenter.

tag: strain id

tag: culture

value: co-culture


title: Mixed, 3

description:
Data from co-culture; replicate 3
Asp_AspKle_counts.xlsx; Kle_AspKle_counts.xlsx


title: Sample_Set3B4CaD6

value: 6-day old colony


title: Mixed, 2

description:
Data from co-culture; replicate 2
Asp_AspKle_counts.xlsx; Kle_AspKle_counts.xlsx


title: AI_cueR3


title: 16_NaCl-I


title: 17_NaCl-I


title: Sample_Set3B4D1

value: 1-day old colony


title: Cattle_UterineEndometrium_F2

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

organism: Bos taurus

source_name: UterineEndometrium

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

value: Female

value: UterineEndometrium


title: 21_CEL-I

value: Wistar


title: Cattle_UterineMyometrium_F1

source_name: UterineMyometrium

value: UterineMyometrium


title: Sample_Set3B4CaD3


title: Sample_Set3B4CaD2


title: 13_2_VAGX-III

source_name: VAGX-III

value: male

value: hypothalamus


title: Cattle_Trachea_M2

source_name: Trachea

value: Male

value: Trachea


title: Sample_Set2B4D6


title: Cattle_UterineEndometrium_F1


title: 12_VAGX-I

value: LPS

value: vagotomy


title: 20_2_NaCl-III

value: NaCl


title: 15_VAGX-III


title: Cattle_Trachea_F1


title: Sample_Set3B4D6

value: wild type


title: Sample_Set2B4CaD6

value: 0.25 percent


title: 10_VAGX-I


title: 9_VAGX-I


title: Cattle_Thyroid_M1

source_name: Thyroid

value: Thyroid


title: Sample_Set2B4D2

value: 2-day old colony

value: 0 percent


title: 11_VAGX-I


title: 7_SHAM-I


title: Sample_Set2B4CaD1

value: 1-day old colony


title: Cattle_Thyroid_M2


title: Sample_Set1B4D6

value: 6-day old colony


title: Sample_Set2B4CaD2


title: Cattle_Thymus_M2

source_name: Thymus

value: Thymus


title: Cattle_Testis_M2

source_name: Testis

value: Testis


title: 18_NaCl-I

value: Wistar


title: 5_SHAM-I

value: male


title: 8_SHAM-III

value: hypothalamus


title: Cattle_Thymus_M1

value: Male


title: 3_CNT


title: Sample_Set2B4D1


title: Cattle_Thymus_F2

value: Female


title: Sample_Set1B4D2


title: Sample_Set1B4D3

value: 3 day-old colony


title: Sample_Set1B4CaD3


title: Cattle_Spleen_F2

source_name: Spleen

value: Spleen


title: 6_SHAM-I

value: LPS


title: Cattle_Spleen_F1


title: Cattle_Spleen_M2


title: Sample_Set1B4D1

value: wild type


title: 14_VAGX-III

value: NaCl

value: vagotomy


title: Sample_Set1B4CaD6

value: 0.25 percent


title: Sample_Set1B4CaD2

value: 2-day old colony


title: Sample_Set2B4CaD3


title: Cattle_Skin_M2

source_name: Skin

value: Skin


title: Cattle_Rumen_M2

source_name: Rumen

value: Rumen


title: KlePneu, single, 3

description:
Data from Klebsiella pneumoniae single culture; replicate 3
Kle_AspKle_counts.xlsx

organism: Klebsiella pneumoniae

source_name: bacterial cells

value: single culture


title: Sample_Set1B4CaD1

value: 1-day old colony


title: KlePneu, single, 1

description:
Data from Klebsiella pneumoniae single culture; replicate 1
Kle_AspKle_counts.xlsx


title: 2_CNT

source_name: CNT

value: Wistar


title: KlePneu, single, 2

description:
Data from Klebsiella pneumoniae single culture; replicate 2
Kle_AspKle_counts.xlsx


title: Cattle_Trachea_F2

value: Trachea


title: Cattle_Rumen_F2


title: Cattle_Spleen_M1


title: Cattle_Skin_F1


title: Cattle_Rumen_M1


title: DU145_YAP_KD_rep2

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
feature counts were calculated using featureCounts from Subread package
Assembly: GRCh37.p13
Supplementary files format and content: tab delimited text file containing counts of genes

source_name: prostate cancer organoid

growth_protocol: DU145 cell line were maintained in human organoid media as described previously (PMID: 25201529, 26797458).

extract_protocol:
RNA extraction was performed using TRIzol according to manufacture's instuction (Thermo Fisher Scientific #15596018).
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit, with 8 cycles of PCR amplification, starting from 500 ng of total RNA, at the Integrative Genomics Operation (IGO) at MSKCC.

treatment_protocol: DU145 cell line were transfected with a pooled ON-TARGETplus siRNAs targeting YAP, TAZ, or YAP/TAZ (Dharmacon) using RNAiMAX (Thermo Fisher Scientific #13778075) for 48 hours prior to RNA extraction.

tag: primary site

value: Prostate

tag: knockdown

value: YAP

tag: replicate

tag: cell line


title: Cattle_Testis_M1

value: Male

tag: tissue

value: Testis


title: Enoxolone_3

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude:
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Clostridium difficile R20291 genome (Genome accession: FN545816) using STAR2.7.1 and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 (57) in the R statistical computing environment.
Assembly: Clostridium difficile R20291 genome (Genome accession: FN545816)
Supplementary files format and content: tab-delimited text files include differential expression values for enoxolone vs. DMSO treatment.

organism: Clostridioides difficile

source_name: Planktonic cells

growth_protocol: Overnight cultures of C. difficile R20291 were diluted 1:100 into fresh BHI broth.

extract_protocol:
After 30 min, one volume of RNAprotect bacterial reagent (Qiagen) was added followed by centrifugation (4000 x g for 10 min). Cells were resuspended in 700 µl of Qiazol lysis reagent (Qiagen) and lysed in a Fastprep cell disruptor (Qiagen) for 5 min at force 50. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions. Integrity of RNA was estimated on an Agilent Bioanalyzer 2100 with all samples possessing an RNA Integrity Number (RIN) >7. Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit (New England Biolabs).
Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) and by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: R20291 cultures (OD600 ≈ 0.3) were supplemented with either DMSO or enoxolone (16 µM) for 30 minutes.

tag: strain

tag: cell type

value: Planktonic cells

tag: treatment

value: enoxolone (16 µM) for 30 minutes

tag: molecule type

value: rRNA-depleted RNA


title: DU145_TAZ_KD_rep2

value: TAZ


title: Cattle_Rumen_F1

tag: Sex

value: Female


title: DU145_YAP_TAZ_KD_rep1

value: YAP and TAZ


title: Enoxolone_2


title: DMSO_2

value: DMSO for 30 minutes


title: 4_CNT

value: male

value: hypothalamus

tag: injection

tag: procedure


title: Enoxolone_1


title: DMSO_3


title: DU145_YAP_KD_rep1


title: Cattle_Reticulum_M2

source_name: Reticulum

value: Reticulum


title: DMSO_1


title: 1_CNT


title: DU145_TAZ_KD_rep1


title: Cattle_Reticulum_M1


title: DU145_scr_rep2

value: Scrambled


title: DU145_scr_rep1


title: Cattle_Reticulum_F2


title: Cattle_Reticulum_F1


title: Cattle_Ovary_F2

source_name: Ovary

value: Ovary


title: CuS+/SB705498 treated A549 cells R3

city: su zhou

first: Ting

last: Li

state: jiang su

address: Ren ai road 199

department: college of pharmaceutical science

institute: Soochow university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing files were filtered for short or poor quality reads, then aligned to the ferret genome using CLC Genomics Workbench Tool (v 12)
Differentially expressed genes were identified using CLC Genomics Workbench Tool. Two-tailed Wald Test was used to calculate the p value. Genes showing altered expression with p < 0.05 and more than 2 fold changes were considered differentially expressed.
The pathway and network analysis was performed using Ingenuity (IPA). IPA computes a score for each network according to the fit of the set of supplied focus genes.
Assembly: hg38
Supplementary files format and content: Read counts and differential gene expression in .xlsx format

source_name: cancer cells

growth_protocol: A549 cancer cells were cultured in  a T75 flask in the presence of 1640 medium and 10% FBS, as well as Penicillin-Streptomycin Solution.

extract_protocol:
A549 cancer cells were treated with Trizol reagent and then RNA was harvested . 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: A549 cancer cells were treated with CuS+/SB705498 for 24 h followed by laser irradiation.

value: lung-derived cancer cells

value: CuS+/SB705498 treated


title: CuS+/SB705498 treated A549 cells R2


title: CuS+/SB705498 treated A549 cells R1


title: Cattle_Ovary_F1


title: Cattle_Omasum_M2

source_name: Omasum

value: Omasum


title: PBS treated A549 cells R3

value: untreated


title: PBS treated A549 cells R2


title: Cattle_Omasum_M1

value: Male


title: DU145_YAP_TAZ_KD_rep2

value: Prostate


title: PBS treated A549 cells R1


title: Cattle_Omasum_F2


title: Cattle_Omasum_F1


title: RNA-seq: HepG2-AtRDR1 (+)Dox

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

description:
HepG2_short_time.csv
RNA_seq_HepG2_At_plus_Dox_D2

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: hg38
Supplementary files format and content: Gene expression matrix; miRNA expression matrix

source_name: HepG2-AtRDR1 stable cell line

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme). Small RNA-seq libraries preparation using the NEBNext® Small RNA Library Prep Set for Illumina kits. Single-cell RNA-seq libraries preparation using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

tag: cell type and treatment

value: HepG2-AtRDR1 with Dox induction for 2 days

value: HepG2-AtRDR1 stable cell line

tag: fraction

value: total RNA


title: LN229_Diosmin_48hr_rep1

city: Taipei

first: Yung Lung

last: Chang

address: Rm. 7309, 7F., No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

hyb_protocol: HOA v7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluorescence intensity.

data_processing: Data processing was performed and calculated by limma package (Bioconductor). The control probes were filtered out and then normalized by the median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by empirical bayes statistics and presented by log2 ratio and p-value.

label_protocol: The 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Both cells were grown in DMEM medium with 2% FBS.

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol.

treatment_protocol: Cells were seeded in 6-well plates and then incubated overnight to allow cells to attach. Cells were harvested after the treatment of 160 nM Diosmin or DMSO control for 48 hrs.

value: Diosmin 160 nM


title: RNA-seq: HepG2-AtRDR1 (-)Dox

description:
HepG2_short_time.csv
RNA_seq_HepG2_At_no_Dox

value: HepG2-AtRDR1 without Dox induction

tag: genotype


title: Cattle_Muscle_M2

source_name: Muscle

value: Muscle


title: LN229_Diosmin_48hr_rep2


title: GBM8401_Diosmin_48hr_rep2


title: LN229_CTRL_48hr_rep1

value: Vehicle control


title: LN229_CTRL_48hr_rep2


title: GBM8401_CTRL_48hr_rep1


title: GBM8401_Diosmin_48hr_rep1


title: Patient3_cell3_RNA

city: Xiamen

first: Xing

last: Xu

state: Fujian

address: 422 Road, Siming District, Xiamen, China

institute: Xiamen University

description:
patient_RNA_expr_count.txt
patient_RNA_expr_fpkm.txt
patient_sample_annotation.txt

data_processing:
DNA sequence reads were first trimmed by Cutadapt v2.10to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality bases. The trimmed reads with less than 20bp were excluded at this stage. Clean reads were then aligned to the hg19 human genome using BWA (version 0.7.17)
CNVs across bins with variable length (500kb) were called using Ginkgo
RNA sequence reads were initially trimmed by Cutadapt v2.10 to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality sequences. The trimmed reads containing fewer than 20bp were directly discarded. Filtered reads were then aligned to the hg19 human genome using STAR v2.6.0
Using the same reference and annotation, gene expression was quantified by HTSeq v0.13.5 and converted to fragments per kilobase transcript per million mapped reads (FPKM value)
Assembly: hg19
Supplementary files format and content: CNV matix and gene expression matix in text file

source_name: multiple myeloma patients

growth_protocol: Cells are all cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
The RNAs of cells were released by using 0.2% Triton for 10 min while remaining DNAs within nucleus, and then the DNAs were released by using the alkaline lysis buffer (Vazyme Biotech, N603).
DNA libraries were constructed according to MDA (Multiple Displacement Amplification) method by using random primers and φ29 DNA polymerase to amplify DNAs, and RNA libraries were constructed according to Smart-seq2.

value: multiple myeloma cells


title: Patient3_cell4_RNA


title: RNA-seq: K562-AtRDR1 (+)Dox

description:
K562_short_time.csv
RNA_seq_K562_At_plus_Dox_D3

source_name: K562-AtRDR1 stable cell line

value: K562-AtRDR1 with Dox induction for 3 days

value: K562-AtRDR1 stable cell line


title: Cattle_Muscle_M1


title: Patient3_cell2_RNA


title: Cattle_MammaryGland_F2

source_name: MammaryGland

value: Female

value: MammaryGland


title: RNA-seq: K562-AtRDR1 (-)Dox

description:
K562_short_time.csv
RNA_seq_K562_At_no_Dox

value: K562-AtRDR1 without Dox induction


title: Patient3_cell1_RNA


title: Cattle_MammaryGland_F1


title: RNA-seq: K562--WT

description:
K562_short_time.csv
RNA_seq_K562_WT

value: WT


title: Cattle_Lung_M2

source_name: Lung

value: Lung


title: RNA-seq: H1299-AtRDR1 (+)Dox

description:
H1299_short_time.csv
RNA_seq_H1299_At_plus_Dox_D3

source_name: H1299-AtRDR1 stable cell line

value: H1299-AtRDR1 with Dox induction for 3 days

value: H1299-AtRDR1 stable cell line


title: Patient2_cell3_RNA


title: Patient2_cell2_RNA


title: RNA-seq: H1299-AtRDR1 (-)Dox

description:
H1299_short_time.csv
RNA_seq_H1299_At_no_Dox

value: H1299-AtRDR1 without Dox induction


title: Cattle_Lung_M1

value: Male


title: Cattle_Lung_F2


title: RNA-seq: H1299--WT

description:
H1299_short_time.csv
RNA_seq_H1299_WT

value: total RNA


title: Patient1_cell4_RNA


title: Cattle_Lung_F1


title: RNA-seq: HeLa-AtRDR1 (+)Dox

description:
HeLa_short_time.csv
RNA_seq_HeLa_At_plus_Dox_D3

source_name: HeLa-AtRDR1 stable cell line

value: HeLa-AtRDR1 with Dox induction for 3 days

value: HeLa-AtRDR1 stable cell line

value: HeLa


title: Cattle_Liver_M2

source_name: Liver

value: Liver


title: RNA-seq: HeLa--WT

description:
HeLa_short_time.csv
RNA_seq_HeLa_WT

source_name: HeLa


title: GBM8401_CTRL_48hr_rep2

value: Vehicle control


title: Cattle_Liver_F2


title: RNA-seq: HeLa-AtRDR1 (-)Dox

description:
HeLa_short_time.csv
RNA_seq_HeLa_At_no_Dox

value: HeLa-AtRDR1 without Dox induction


title: Patient1_cell3_RNA

value: multiple myeloma cells


title: RNA-seq: A549-OsRDR1 (+)Dox

description:
A549_short_time.csv
RNA_seq_A549_Os_plus_Dox_D3

source_name: A549-OsRDR1 stable cell line

value: A549-OsRDR1 with Dox induction for 3 days

value: A549-OsRDR1 stable cell line


title: Patient1_cell2_RNA


title: Patient1_cell1_RNA


title: HCT-116_FR_3

description:
cell_line_RNA_expr_count.txt
cell_line_RNA_expr_fpkm.txt
cell_line_sample_annotation.txt

source_name: colorectal cancer cells

value: colorectal cancer cells


title: Cattle_Kidney_M2

source_name: Kidney

value: Kidney


title: Cattle_Liver_F1

value: Female


title: RNA-seq: A549-OsRDR1 (-)Dox

description:
A549_short_time.csv
RNA_seq_A549_Os_no_Dox

value: A549-OsRDR1 without Dox induction


title: Cattle_Kidney_M1


title: RNA-seq: A549--WT

description:
A549_short_time.csv
RNA_seq_A549_WT

value: WT


title: RNA-seq: A549-EGFP-AAV-2

description:
AAV_A549.csv
RNA_seq_AAV_A549_GFP_2

source_name: A549 xenografts injected with AAV-EGFP

value: A549 xenografts injected with AAV-EGFP


title: Cattle_Kidney_F1


title: HCT-116_FR_1


title: Cattle_Kidney_F2


title: RNA-seq: HeLa (R-WT)-nano

description:
NANO_Hela.csv
RNA_seq_NANO_HeLa_At

source_name: HeLa transfected with R-PE and rAtRDR1

value: HeLa transfected with R-PE and rAtRDR1


title: RNA-seq: A549-OsRDR1-AAV

description:
AAV_A549.csv
RNA_seq_AAV_A549_Os

source_name: A549 xenografts injected with AAV-OsRDR1

value: total RNA


title: HCT-116_WR_3


title: Patient2_cell1_RNA


title: HCT-116_Bulk RNA_3


title: RNA-seq: HeLa (R-PE)-nano

description:
NANO_Hela.csv
RNA_seq_NANO_HeLa_RPE

source_name: HeLa transfected with R-PE

value: HeLa transfected with R-PE


title: Cattle_Jejunum_M2

source_name: Jejunum

value: Male

value: Jejunum


title: RNA-seq: A549-EGFP-AAV-1

description:
AAV_A549.csv
RNA_seq_AAV_A549_GFP_1


title: HCT-116_WR_2


title: HCT-116_Bulk RNA_1


title: HCT-116_WR_1


title: Cattle_Jejunum_F2


title: Cattle_Jejunum_M1


title: MCF-7_FR_4

source_name: breast cancer cells

value: breast cancer cells


title: Cattle_Isthmus_F1

source_name: Isthmus

value: Isthmus


title: RNA-seq: HeLa (R-Mut)-nano

description:
NANO_Hela.csv
RNA_seq_NANO_HeLa_Mut

source_name: HeLa transfected with R-PE and rRDR1-Mut

value: HeLa


title: RNA-seq: A549 (R-PE)-nano

description:
NANO_A549.csv
RNA_seq_NANO_A549_RPE

source_name: A549 transfected with R-PE

value: A549 transfected with R-PE


title: Cattle_Jejunum_F1


title: HCT-116_Bulk RNA_2


title: Cattle_Isthmus_F2


title: MCF-7_FR_2


title: RNA-seq: NALM6-OsRDR1 (+)Dox-xenograft

description:
XENO_NALM6.csv
RNA_seq_XENO_NALM6_Os

source_name: NALM6-OsRDR1 xenograft

value: NALM6-OsRDR1 with Dox induction

value: NALM6-OsRDR1 stable cell line


title: MCF-7_FR_1


title: MCF-7_FR_3


title: Cattle_Ileum_F2

source_name: Ileum

value: Ileum


title: Cattle_Heart_M2

source_name: Heart

value: Heart


title: HCT-116_FR_2

value: colorectal cancer cells


title: RNA-seq: A549 (R-WT)-nano

description:
NANO_A549.csv
RNA_seq_NANO_A549_At

source_name: A549 transfected with R-PE and rRDR1

value: A549 transfected with R-PE and rRDR1


title: RNA-seq: Jurkat-AtRDR1 (+)Dox-xenograft

description:
XENO_Jurkat.csv
RNA_seq_XENO_Jurkat_At

source_name: Jurkat-AtRDR1 xenograft

value: Jurkat-AtRDR1 with Dox induction

value: Jurkat-AtRDR1 stable cell line

value: Jurkat


title: MCF-7_WR_2


title: MCF-7_WR_3


title: RNA-seq: Jurkat-Vector (+)Dox-xenograft

description:
XENO_Jurkat.csv
RNA_seq_XENO_Jurkat_Vec

source_name: Jurkat-Vector xenograft

value: Jurkat-Vector with Dox induction

value: Jurkat-Vector stable cell line

value: total RNA


title: Cattle_Hypothalamus_M1

source_name: Hypothalamus

value: Male

value: Hypothalamus


title: Cattle_Ileum_F1

value: Female


title: MCF-7_Bulk RNA_3

value: breast cancer cells


title: Cattle_Esophagus_M1

source_name: Esophagus

value: Esophagus


title: RNA-seq: PC-3-OsRDR1 (+)Dox-xenograft-1

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_Os_1

source_name: PC-3-OsRDR1 xenografts

value: PC-3-OsRDR1 with Dox induction

value: PC-3-OsRDR1 stable cell line

value: PC


title: HCT-116_WR_4

source_name: colorectal cancer cells


title: RNA-seq: NALM6-RDR1-Mut (+)Dox-xenograft

description:
XENO_NALM6.csv
RNA_seq_XENO_NALM6_Mut

source_name: NALM6-RDR1-Mut xenograft

value: NALM6-RDR1-Mut with Dox induction

value: NALM6-RDR1-Mut stable cell line


title: RNA-seq: A549 (R-Mut)-nano

description:
NANO_A549.csv
RNA_seq_NANO_A549_Mut

source_name: A549 transfected with R-PE and rRDR1-Mut

value: WT


title: Cattle_Esophagus_F2


title: Cattle_Heart_M1

value: Heart


title: MCF-7_Bulk RNA_1


title: Sk-BR-3_FR_6


title: RNA-seq: PC-3-RDR1-Mut (+)Dox-xenograft-1

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_Mut_1

source_name: PC-3-RDR1-Mut xenografts

value: PC-3-RDR1-Mut with Dox induction

value: PC-3-RDR1-Mut stable cell line


title: RNA-seq: NALM6-Vector (+)Dox-xenograft

description:
XENO_NALM6.csv
RNA_seq_XENO_NALM6_Vec

source_name: NALM6-Vector xenograft

value: NALM6-Vector with Dox induction

value: NALM6-Vector stable cell line


title: MCF-7_WR_4

source_name: breast cancer cells


title: RNA-seq: PC-3-OsRDR1 (+)Dox-xenograft-2

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_Os_2

value: total RNA


title: Cattle_Heart_F1


title: Cattle_Colon_M2

source_name: Colon

value: Male

value: Colon


title: Cattle_Heart_F2

value: Female


title: Sk-BR-3_FR_4

value: breast cancer cells


title: RNA-seq: H1299-OsRDR1 (+)Dox-xenograft-2

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_Os_2

source_name: H1299-OsRDR1 xenografts

value: H1299-OsRDR1 with Dox induction

value: H1299-OsRDR1 stable cell line


title: RNA-seq: Jurkat-RDR1-Mut (+)Dox-xenograft

description:
XENO_Jurkat.csv
RNA_seq_XENO_Jurkat_Mut

source_name: Jurkat-RDR1-Mut xenograft

value: Jurkat-RDR1-Mut with Dox induction

value: Jurkat-RDR1-Mut stable cell line

value: Jurkat


title: MCF-7_WR_1


title: Sk-BR-3_FR_3


title: RNA-seq: H1299-OsRDR1 (+)Dox-xenograft-1

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_Os_1


title: Cattle_Cerebellum_M2

source_name: Cerebellum

value: Cerebellum


title: Sk-BR-3_FR_1


title: MCF-7_Bulk RNA_2


title: Cattle_Cerebellum_M1


title: Sk-BR-3_WR_4


title: Cattle_Cerebellum_F2


title: RNA-seq: PC-3-RDR1-Mut (+)Dox-xenograft-2

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_Mut_2

value: PC


title: Cattle_Cerebellum_F1


title: RNA-seq: PC-3-WT (+)Dox-xenograft-2

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_WT_2

source_name: PC-3 xenografts

value: WT with Dox induction

value: WT


title: Cattle_Esophagus_F1

value: Esophagus


title: Sk-BR-3_FR_5


title: RNA-seq: A549-OsRDR1 (+)Dox-xenograft

description:
XENO_A549.csv
RNA_seq_XENO_A549_Os

source_name: A549-OsRDR1 xenografts

value: A549-OsRDR1 with Dox induction

value: A549-OsRDR1 stable cell line


title: Cattle_Cecum_M1

source_name: Cecum

value: Cecum


title: Cattle_Colon_M1

value: Male


title: Sk-BR-3_FR_2


title: RNA-seq: PC-3-WT (+)Dox-xenograft-1

description:
XENO_PC3.csv
RNA_seq_XENO_PC3_WT_1

value: total RNA


title: RNA-seq: H1299-RDR1-Mut (+)Dox-xenograft-2

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_Mut_2

source_name: H1299-RDR1-Mut xenografts

value: H1299-RDR1-Mut with Dox induction

value: H1299-RDR1-Mut stable cell line


title: Cattle_Duodenum_M1

source_name: Duodenum

value: Duodenum


title: Sk-BR-3_Bulk RNA_2

value: breast cancer cells


title: Cattle_Cecum_F1

value: Female


title: Cattle_Esophagus_M2

source_name: Esophagus


title: Cattle_Colon_F1

value: Colon


title: RNA-seq: A549-WT (+)Dox-xenograft

description:
XENO_A549.csv
RNA_seq_XENO_A549_WT

source_name: A549 xenografts


title: Sk-BR-3_Bulk RNA_1