title: Treated PC3 cells

city: San Nicolás de los Garza

first: María

middle: Del Rayo

last: Camacho-Corona

state: Nuevo León

address: Av. Universidad S/N, Ciudad Universitaria

department: Facultad de Ciencias Químicas

country: Mexico

institute: Universidad Autónoma de Nuevo León

description: p-Coumaric acid treated and untreated PC3 cells

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.

source_name: Treated PC3 prostate cancer cells

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: PC3 cells were grown in RPMI 1640 medium (Invitrogen, Thermo Fisher Scientific, Inc., Waltham, MA, USA), supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 40 µg/mL gentamicin and penicillin-streptomycin (100 U/mL penicillin and 100 µg/mL streptomycin). Cultures were incubated at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: After incubation the total RNA was extracted from both cultures treated either with the compound or with the vehicle, using TRIzol Reagent (Invitrogen, Carlsbad, CA, United States) following manufacturer instructions. The RNA quality was assessed by agarose gel (1%) and total RNA was quantified in a NanoDropTM 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: PC3 cells were treated in a 6-well plate with 1 million cells per well for 24 hours with p-coumaric acid at its IC30 (150 µg/mL) and 0.6% DMSO or only with DMSO at the same concentration.

tag: cell line

tag: passage

tag: cell type

value: ATCC prostate adenocarcinoma cell line

source_name: Untreated PC3 prostate cancer cells


title: CT-10T

status: Public on Aug 04 2020

type: RNA

city: Bunkyo ku

first: Akihiko

last: Miyanaga

state: Tokyo

address: 1-1-5 Sendagi,

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

country: Japan

institute: Nippon Medical School

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip® Human Exon 1.0 ST Array using  the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console v4.0 using Thermo Fisher Scientific default analysis settings and global scaling as normalization method. The trimmed mean was used with normalized data.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: lung tissue

label_protocol: cDNA synthesis, amplification and labeling were performed with The Ambion® WT Expression Kit and Affymetrix® GeneChip® WT Terminal Labeling Kit

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit columns (Qiagen) according to the manufacturer’s protocol.

tag: tissue

value: lung carcinoid

tag: gender

value: Female

tag: age

tag: histological subtype

value: Atypical carcinoid

tag: 8th pstage

value: IIA

tag: relapse

value: Relapsed


title: P1B1: H2009 SiITGB4 and Si PXN

type: SRA

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

country: USA

institute: City of Hope

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ATCC

growth_protocol: All cell lines were cultured in RPMI 1640 medium (Corning) supplemented with fetal bovine serum (FBS) (10%), L-glutamine (2 mM), penicillin/streptomycin (50 U/ml), sodium pyruvate (1 mM), and sodium bicarbonate (0.075%) at 37°C, 5% CO2

extract_protocol: Total RNA isolation and on-column DNase digestion from cells were performed basing on the manufacturer’s protocol RNeasy Plus Mini Kit (Qiagen Cat #: 74134).

treatment_protocol: Cells were seeded in 6-well plates (200,000 cells/well) and allowed to adhere overnight. Next day, 10 nM siRNA was transfected with 4 μl jetPRIME reagent in complete growth medium for each well. Cell growth medium was changed the next day and expression was detected 72 h post-transfection by qPCR and immunoblot. The RNA extracted at 72hr of transfection was sent to the core for RNA sequencing. The experiments were repeated two times with SiRNA ITGB4 or SiRNA PXN or both SiRNA ITGB4 and PXN.

tag: disease

value: stage 4, adenocarcinoma

value: derived from metastatic site:lymph node

tag: morphology and ethinicty

value: Epithelial,  Caucasian


title: CT-18T

value: Male

value: Typical carcinoid

value: IIB

value: not relapsed


title: CT-11T


title: CT-21T


title: B2: H2009 SiITGB4


title: CT-26T


title: CT-8T


title: CT-4T


title: CT-13T

value: IIIA


title: CT-25T


title: CT-7T

value: IB


title: CT-16T


title: CT-12T


title: B1: H2009 SiITGB4


title: CT-9T


title: CT-1T


title: CT-14T


title: CT-2T


title: CT-15T


title: CT-6T

value: IIIB


title: CT-3T


title: P2: H2009 SiPXN


title: P1: H2009 SiPXN


title: C1: H2009 Control


title: C2: H2009 Control


title: CD16P_S8

city: La Jolla

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
Read count was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: read_count.txt: tab-delimited text files includes read count for each samples (Column names: Gene ID, 12 samples as described in the SAMPLES section)

source_name: MatureNeuts

extract_protocol:
Neutrophil subpopulations were FACS sorted from human fresh bone marrow
Sorted bone marrow cells in TRIzolTMLS Reagent were thawed on ice. RNA isolation was performed using the Direct-zolTMRNA MiniPrep (Zymo Research) according to manufacturer’s instructions. RNA concentration was measured on a Agilent 2200 TapeStation using the Agilent High Sensitivity RNA ScreenTape System (Agilent Technologies). Cells will be sorted directly in TriZOL LS and processed immediately into RNA using DirectZOL RNA Miniprep (Zymo Research). Library preparation and sequencing will be performed according to the Smart-Seq2 protocol in the La Jolla Institute for Immunology sequencing core.

tag: disease state

value: Healthy

value: Bone marrow

tag: cell population


title: CD71P_CD117N_S10


title: CD71P_CD117P_S11

source_name: eNeP


title: CD71P_CD117P_S7


title: CD16P_S4


title: CD16N_CD71N_S9


title: CD16N_CD71N_S5


title: CD16P_S1


title: CD16N_CD71N_S2


title: wild type MAMLD1 HA rep3

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: genomic DNA isolated using anti-HA antibody in wild type MAMLD1 (HA tagged)-expressing cells

library_source: genomic

data_processing:
library strategy: Cut & Run
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
Raw reads were aligned to the UCSC hg19 assembly using bowtie2 and peaks were called using SEACR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include called peaks for each Sample using SEACR.

molecule: genomic DNA

source_name: U5_wild type MAMLD1 HA

extract_protocol:
genomic DNA bound to targeted proteins was extracted as described here: dx.doi.org/10.17504/protocols.io.ufeetje
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line background

value: human neural stem cell line

tag: genotype/variation

value: wild type MAMLD1 overexpression

tag: antibody

value: rabbit anti-HA antibody


title: wild type MAMLD1  HA rep4

source_name: U5_wild type MAMLD1  HA

value: wild type MAMLD1  overexpression


title: wild type MAMLD1  rbIgg rep3

description: rabbit Igg control sample for wild type MAMLD1 (HA tagged)-expressing cells

source_name: U5_wild type MAMLD1  rbIgg

value: rabbit IgG antibody (Millipore, #12-370)


title: wild type MAMLD1 HA rep1


title: wild type FAM118B  HA rep4

description: genomic DNA isolated using anti-HA antibody in wild type FAM118B (HA tagged)-expressing cells

source_name: U5_wild type FAM118B  HA

value: wild type FAM118B  overexpression


title: wild type FAM118B HA rep3

source_name: U5_wild type FAM118B HA

value: wild type FAM118B overexpression


title: wild type MAMLD1  HA rep2


title: wild type FAM118B  rbIgg rep1

description: rabbit Igg control sample for wild type FAM118B (HA tagged)-expressing cells

source_name: U5_wild type FAM118B  rbIgg


title: wild type FAM118B HA rep1


title: wild type FAM118B  HA rep2


title: CD71P_CD117N_S3


title: S127-397A-YAP1 rbIgg

description: rabbit Igg control sample for S127/397A-YAP1 (HA tagged)-expressing cells

source_name: U5_S127-397A-YAP1 rbIgg

value: S127-397A-YAP1 overexpression


title: S127-397A-YAP1  TEAD4 rep1

description: genomic DNA isolated using anti-TEAD4 antibody in S127/397A-YAP1 (HA tagged)-expressing cells

value: S127-397A-YAP1  overexpression

value: mouse anti-TEAD4 antibody


title: CD71P_CD117N_S6


title: S127-397A-YAP1 HA rep2

description: genomic DNA isolated using anti-HA antibody in S127/397A-YAP1 (HA tagged)-expressing cells


title: S127-397A-YAP1  HA rep1


title: YAP1-TFE3 HA rep2

description: genomic DNA isolated using anti-HA antibody in YAP1-TFE3 (HA tagged)-expressing cells

source_name: U5_YAP1-TFE3 HA

value: YAP1-TFE3 overexpression


title: YAP1-FAM118B msIgg

description: mouse Igg control sample for YAP1-FAM118B (HA tagged)-expressing cells

source_name: U5_YAP1-FAM118B msIgg

value: YAP1-FAM118B overexpression

value: mouse IgG antibody (Millipore, #12-371)


title: YAP1-TFE3 TEAD4 rep2

description: genomic DNA isolated using anti-TEAD4 antibody in YAP1-TFE3 (HA tagged)-expressing cells

source_name: U5_YAP1-TFE3 TEAD4


title: YAP1-TFE3 TEAD4 rep1


title: YAP1-TFE3 TEAD4 msIgg

description: mouse Igg control sample for YAP1-TFE3 (HA tagged)-expressing cells

source_name: U5_YAP1-TFE3 TEAD4 msIgg


title: YAP1-FAM118B TEAD4 rep1

description: genomic DNA isolated using anti-TEAD4 antibody in YAP1-FAM118B (HA tagged)-expressing cells

source_name: U5_YAP1-FAM118B TEAD4


title: YAP1-FAM118B rbIgg

description: rabbit Igg control sample for YAP1-FAM118B (HA tagged)-expressing cells

source_name: U5_YAP1-FAM118B rbIgg


title: YAP1-TFE3  HA rep1

source_name: U5_YAP1-TFE3  HA

value: YAP1-TFE3  overexpression


title: Thiacloprid 250 ng/bee sample 5

city: Muttenz

first: Fent

last: Karl

address: Langackerstrasse 30

department: School of Life Sciences

country: Switzerland

institute: University of Applied Sciences and Arts Northwestern Switzerland

data_processing:
Trimmomatic (v. 0.39) adapter trimming and removal of low quality bases. Parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:4 TRAILIN G:4 SLIDINGWINDOW:4:10 MINLEN:30 AVGQUAL:20
Mapping to Amel_HAv3.1 with HISAT2-2.1.0 / Parameters: --dta –rna-standness R
Samtools sort and Samtools index (Samtools version 1.7)
Estimate Transcripts with StringTie v. 2.0.2: stringtie -e -B -G GCF_003254395.2_Amel_HAv3.1_genomic.gtf
Import data form StringTie via tximport 1.10.1: 1) tx2gene <- tmp[, c("t_name", "gene_name")] 2) txi <- tximport(paths, type="stringtie", tx2gene=tx2gene)
Run DESeq2 (v. 1.22.2) to compile the raw count table (provided as raw_counts.tsv)
Genome_build: Amel_HAv3.1 (GCF_003254395.2)
Supplementary_files_format_and_content: StringTie output (tab delimited t_data.ctab file) providing transcript abundance information & gene raw counts from DESeq2

molecule: polyA RNA

organism: Apis mellifera

source_name: Thiacloprid 250 ng/bee_brain tissue

growth_protocol: Bees were taken from an unpolluted control site and exposed in the laboratory

extract_protocol:
Brains of 5 bees per replicate of each treatment group (5 replicates per group) were dissected and total RNA extracted by TRI Reagent (Sigma-Aldridge)
Illumina TruSeq stranded mRNA kit. Includes a poly-A enrichment step and it is strand specific via dUTP incorporation during the second strand synthesis

treatment_protocol: Forager honey bees were exposed in PET bottles via sucrose solution for 72 h to two environmentally relevant concentrations of 25 and 250 ng/bee thiacloprid. Brains were dissected after 72 h, RNA isolated and global gene expression profile assessed by RNA-sequencing in pools of 5 bees per replicate (total 5 replicates per concentrations used).

tag: developmental stage

value: Adult worker bees

tag: treatment

value: 250ng Thiacloprid/bee

value: Brain


title: YAP1-FAM118B TEAD4 rep2

value: human neural stem cell line


title: wild type FAM118B  rbIgg rep3


title: YAP1-FAM118B HA rep2

description: genomic DNA isolated using anti-HA antibody in YAP1-FAM118B (HA tagged)-expressing cells

source_name: U5_YAP1-FAM118B HA


title: S127-397A-YAP1 msIgg

description: mouse Igg control sample for S127/397A-YAP1 (HA tagged)-expressing cells

source_name: U5_S127-397A-YAP1 msIgg


title: Thiacloprid 250 ng/bee sample 4


title: CD71P_CD117P_S82

source_name: eNeP

value: Healthy

value: Bone marrow


title: S127-397A-YAP1 TEAD4 rep2


title: Thiacloprid 250 ng/bee sample 3


title: Thiacloprid 250 ng/bee sample 2


title: wild type MAMLD1  rbIgg rep1

value: wild type MAMLD1  overexpression


title: YAP1-FAM118B HA rep1

value: rabbit anti-HA antibody


title: Thiacloprid 25 ng/bee sample 5

source_name: Thiacloprid 25 ng/bee_brain tissue

value: 25ng Thiacloprid/bee


title: Thiacloprid 25 ng/bee sample 3


title: YAP1-MAMLD1 TEAD4 rep2

description: genomic DNA isolated using anti-TEAD4 antibody in YAP1-MAMLD1 (HA tagged)-expressing cells

source_name: U5_YAP1-MAMLD1 TEAD4

value: YAP1-MAMLD1 overexpression


title: YAP1-MAMLD1 TEAD4 rep1


title: P2B2: H2009 SiITGB4 and Si PXN

source_name: ATCC

value: stage 4, adenocarcinoma

value: derived from metastatic site:lymph node

value: Epithelial,  Caucasian


title: YAP1-MAMLD1 msIgg

description: mouse Igg control sample for YAP1-MAMLD1 (HA tagged)-expressing cells

source_name: U5_YAP1-MAMLD1 msIgg


title: YAP1-TFE3 rbIgg

description: rabbit Igg control sample for YAP1-TFE3 (HA tagged)-expressing cells

source_name: U5_YAP1-TFE3 rbIgg

value: YAP1-TFE3 overexpression

value: rabbit IgG antibody (Millipore, #12-370)


title: Thiacloprid 25 ng/bee sample 1


title: Thiacloprid 25 ng/bee sample 2


title: YAP1-MAMLD1 HA rep2

description: genomic DNA isolated using anti-HA antibody in YAP1-MAMLD1 (HA tagged)-expressing cells

source_name: U5_YAP1-MAMLD1 HA


title: Thiacloprid 250 ng/bee sample 1


title: Control sample 4

source_name: Control_brain tissue

value: Solvent control


title: Control sample 3


title: YAP1-MAMLD1 HA rep1


title: Control sample 2


title: wild type YAP1 TEAD4 rep2

description: genomic DNA isolated using anti-TEAD4 antibody in wild type YAP1 (HA tagged)-expressing cells

source_name: U5_wild type YAP1 TEAD4

value: wild type YAP1 overexpression

value: mouse anti-TEAD4 antibody


title: wild type YAP1 TEAD4 rep1


title: wild type TFE3 rbIgg

description: rabbit Igg control sample for wild type TFE3 (HA tagged)-expressing cells

source_name: U5_wild type TFE3 rbIgg

value: wild type TFE3 overexpression


title: Control sample 5

value: Adult worker bees

value: Brain


title: wild type YAP1 rbIgg

description: rabbit Igg control sample for wild type YAP1 (HA tagged)-expressing cells

source_name: U5_wild type YAP1 rbIgg

value: human neural stem cell line


title: wild type TFE3 HA rep2

description: genomic DNA isolated using anti-HA antibody in wild type TFE3 (HA tagged)-expressing cells

source_name: U5_wild type TFE3 HA


title: wild type YAP1 msIgg

description: mouse Igg control sample for wild type YAP1 (HA tagged)-expressing cells

source_name: U5_wild type YAP1 msIgg

value: mouse IgG antibody (Millipore, #12-371)


title: Control sample 1


title: Thiacloprid 25 ng/bee sample 4


title: wild type TFE3 HA rep1


title: wild type YAP1 HA rep2

description: genomic DNA isolated using anti-HA antibody in wild type YAP1 (HA tagged)-expressing cells

source_name: U5_wild type YAP1 HA


title: 293_tRNA_1_DM

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

data_processing:
Processing: cutadapt ver 1.12 was used twice in succession with the following parameters first to remove two degenerate bases encoded in the RT primer (--cut 2), potential 5' adapter (-g TCCAACTGGATACTGGN -e 0.2) and then to remove the 3' CCA + adapter (-a CCAGTATCCAGTTGGAATT -e 0.2).
Mapping: bowtie2 ver 2.3.5 was used to map processed reads to a reference generated from high confidence tRNAs (unique sequences collapsed) defined in GtRNAdb (hg38) using the following parameters: (--quiet --min-score G,1,8 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5).
Downstream analyses: Mapped sam files were converted to bam files using samtools ver 1.9 (samtools view). Further analyses were carried out in Rstudio ver 1.1.463 (R ver 3.5.2 (2018-12-20) -- "Eggshell Igloo"). Read count tables over tRNA genes were generated by using featureCounts from the Rsubread package using the following parameters: strandSpecific = 1,useMetaFeatures=F,minMQS = 10.
hg38; gtRNAdb Release 18
CSV file of raw counts at the isodecoder level from 293 cells.

source_name: Embryonic kidney

growth_protocol: HEK293 T-Rex Flp-IN cells (Thermo Fisher. cat# R78007) were cultured at 37°C with 5% CO2 in complete Dulbecco’s modified essential media (Thermo Fisher) supplemented with 10% fetal bovine serum (Thermo Fisher) and 1% penicillin and streptomycin (Thermo Fisher). All passaging was performed with trypsin (Thermo Fisher) according to manufacturer’s suggested conditions. Following passaging, cells were plated at 25% confluency in 10cm tissue culture treated dishes and cultured for 48-72 hours until ~90% confluency.

extract_protocol:
At 90% confluency, media was aspirated and 1mL of ice cold Trizol (Thermo Fisher) was added to the culture and mixed on ice for 30 seconds to assure a homogeneous solution. Samples were stored in Trizol at -80C until further processing. RNA was isolated according to manufacturer’s protocol with the addition of a second ethanol precipitation step and two 75% ethanol washes following isopropanol precipitation. Samples were resuspended in distilled H2O and stored at -80°C until library preparation.
Total RNA samples were quantified using a nanodrop spectrophotometer (ThermoFisher) prior to library preparation and RNA integrity was checked on a 1.2% denaturing formaldehyde agarose gel. To remove 3’ conjugated amino acids, total RNA was deacylated in deacylation buffer (final concentration 20mM Tris-HCL pH=9.0) at a final concentration of 1ug/uL. 1 ug of deacylated total RNA from each sample was subject to demethylase treatment (rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit, ArrayStar) followed by library preparation. 10 pmol of the 3’ and 10 pmol of the 5’ single-stranded adapter mix (2.5 pmol of each adapter 5’-TGrGrA-3’, 5’-TGrGrT-3’, 5’-TGrGrG-3’, 5’-TGrGrC-3’; Table 1) were added to a 200uL thin-walled amplification tube and denatured at 95°C for 2 minutes. Then annealing buffer was added to a final concentration of 5mM Tris-HCl (pH 8.0), 0.5mM ethylenediaminetetraacetic acid (EDTA) and 10mM MgCl2 and incubated at 37°C for 15 minutes hybridizing the annealed double-stranded adapter to the total RNA. The ligation reaction was catalyzed by 5U/uL of RNA ligase 2 (NEB) with manufacturers suggested conditions at 37°C for 60 minutes then 4°C at 60 minutes. All reactions were ethanol precipitated with glycoblue (Thermo Fisher) with two 75% ethanol washes, then suspended in 10ul of dH2O. Following ligation, synthesis of cDNA began with hybridization of the reverse transcriptase primer to the ligated total RNA with a final concentration of 0.5pmol/uL. The samples were incubated at 70°C for 2 minutes and temperature was reduced to 37°C by 0.1°C/sec. Synthesis of cDNA was achieved using Superscript IV at 55°C for 60 minutes. To remove DNA-RNA dimers following cDNA synthesis, we hydrolyzed RNA with a final concentration of 0.1N NaOH in dH2O at 98°C for 20 minutes. All reactions were ethanol precipitated with glycoblue (ThermoFisher) with two 75% ethanol washes, then suspended in 12ul of dH2O. cDNA libraries were separated using 7M urea 6% denaturing polyacrylamide gels. Gels were stained with 1X SYBR gold (Thermo Fisher) in 1X TBE for 15 minutes and regions of interest (60-200 nucleotides) were excised on a UV light box. Gel slices were sheared through the bottom of a 0.5 mL tube nested in a 1.7 mL tube by centrifugation then suspended in 400uL of DNA elution buffer (300mM NaCl, 10mM Tris (pH=8.0, 1mM EDTA), incubated on dry ice for 30 minutes, and allowed to incubate at room temperature overnight on a standing rotator. Libraries were isopropanol precipitated with glycoblue followed by two 75% ethanol washes. Linear cDNA libraries were then suspended in 12ul of dH2O. Circularization of cDNA libraries was performed with CircLigase (Epicentre) with 0.5U/uL using manufacturer’s suggested conditions at 37°C for 1 hour. The reaction was terminated with incubation at 80°C for 20 minutes. All reactions were ethanol precipitated with glycoblue with two 75% ethanol washes, then suspended in 12.5ul of dH2O. cDNA libraries were amplified using the NEBnext Ultra II Q5 next-generation master mix (NEB) with manufacturer’s suggested conditions. HEK293 libraries were amplified for 7 cycles and mouse tissue libraries amplified for 7-9 cycles. Amplified libraries were gel purified from 2% agarose gels stained with 0.05mg/ml Ethidium Bromide. Regions of interest (100-250bp) were excised on a UV light box and purified using the Qiaquick (Qiagen) gel extraction kit using all optional steps. All libraries were ethanol precipitated with glycoblue (thermo) with two 75% ethanol washes, then suspended in 10ul of dH2O before sequencing.

value: Flp-In T-REx 293 Cell Line

tag: passages


title: wild type YAP1 HA rep1

tag: cell type

value: rabbit anti-HA antibody


title: TB-1

city: dongguan

first: Hou-Long

last: Luo

state: Guangdong

address: No. 1 Xincheng Road

country: China

institute: Guangdong Medical University

data_processing:
Basecalls performed using Illumina HiSeq2500 platform.
Based on the distribution of low-quality fraction of Illumina system data, we eliminated the sequence of the 3’ end and low-quality fragments data using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Sequence quality was analyzed by using the quality control software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The first step was transcriptome assembly. The clean sequence reads of each sample were mapped to UCSC human reference genome using the TopHat (version 2.0.10) software. For each sample, the alignment files were assembled using StringTie software based on the location of the known transcript, and filtered the transcripts without one read matching, and make sure the length of pairing sequences was 125bp. The index file was generated from the BWA (version 2.1.0) software used for comparing with the reference genome sequence and whole genome sequence.
In the second step, we identified circular RNAs using CIRI software (https://sourceforge.net/projects/ciri/), which provides an annotation-independent approach for circRNA detection by employing a de novo algorithm. CIRI identifies circular RNAs through the presence of paired clipping signals where two fragments of a junction read were mapped to the reference genome in a reversed order.
The differentially expressed circular RNAs between the two groups were filtrated with a log2 fold changes ≥ 1.0 and false discovery rates (FDRs) ≤ 0.05 as the criteria.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *xls: Excel files include BSRP values for each Sample; abundance measurements.

source_name: Peripheral blood mononuclear cells, APTB

extract_protocol:
Total RNA was extracted from each sample of PBMCs by Trizol reagent (Invitrogen, USA) according to the protocol of manufacturer, and treated with RNase-free DNase to remove traces of genomic DNA.
For high-throughput sequencing, we synthesized the cDNA libraries of the circRNA from each sample based on the Illumina standard protocols. Briefly, total RNA was treated with the Epicentre Ribo-Zero kit (Epicentre, USA) to remove all the ribosomal RNAs, and digested with RNase R (Epicentre, USA) to remove all the linear RNAs, thus got the pure circular RNAs. Then, the enriched circular RNAs were processed by the NEBNext® Ultra™ Directional RNA Library preparation kit (Illumina, USA) according to the Illumina protocol. The main steps involved: the fragmentation of circRNA, reverse transcription and second-strand cDNA synthesis, end repair, dA-tailing and adaptor ligation. The products of these reactions were purified and amplified by PCR to create the final circular RNA cDNA library. The libraries were paired-end sequenced on the Illumina HiSeq2500 platform (Illumina, USA).

treatment_protocol: PBMCs were freshly isolated from blood by standard Ficoll (GE Healthcare, Little Chalfont, United Kingdom) density gradient centrifugation.

tag: disease status

value: Active pulmonary tuberculosis (APTB)

value: Peripheral blood mononuclear cells (PBMCs)


title: YAP1-MAMLD1 rbIgg

description: rabbit Igg control sample for YAP1-MAMLD1 (HA tagged)-expressing cells

source_name: U5_YAP1-MAMLD1 rbIgg

value: YAP1-MAMLD1 overexpression


title: 293_tRNA_1

data_processing:
Processing: cutadapt ver 1.12 was used twice in succession with the following parameters first to remove potential 5' adapter (-g ^ACTGGATACTGG) and then to remove the 3' CCA + adapter (-a CCAGTATCCAGTTGGAATT).
Mapping: bowtie2 ver 2.3.5 was used to map processed reads to a reference generated from high confidence tRNAs (unique sequences collapsed) defined in GtRNAdb (hg38) using the following parameters: --quiet --min-score L,1,0 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5.
Downstream analyses: Mapped sam files were converted to bam files using samtools ver 1.9 (samtools view). Further analyses were carried out in Rstudio ver 1.1.463 (R ver 3.5.2 (2018-12-20) -- "Eggshell Igloo"). Read count tables over tRNA genes were generated by using featureCounts from the Rsubread package using the following parameters: strandSpecific = 1,useMetaFeatures=F,minMQS = 10.
genome build: hg38; gtRNAdb Release 18
CSV file of raw counts at the isodecoder level from 293 cells.

source_name: Embryonic kidney cell line

extract_protocol:
At 90% confluency, media was aspirated and 1mL of ice cold Trizol (Thermo Fisher) was added to the culture and mixed on ice for 30 seconds to assure a homogeneous solution. Samples were stored in Trizol at -80C until further processing. RNA was isolated according to manufacturer’s protocol with the addition of a second ethanol precipitation step and two 75% ethanol washes following isopropanol precipitation. Samples were resuspended in distilled H2O and stored at -80°C until library preparation.
Total RNA samples were quantified using a nanodrop spectrophotometer (ThermoFisher) prior to library preparation and RNA integrity was checked on a 1.2% denaturing formaldehyde agarose gel. To remove 3’ conjugated amino acids, total RNA was deacylated in deacylation buffer (final concentration 20mM Tris-HCL pH=9.0) at a final concentration of 1ug/uL. 1 ug of deacylated total RNA from each sample was subject to library preparation. 40 pmol of the 3’ and 40 pmol of the 5’ single-stranded adapter mix (10 pmol of each adapter 5’-TGrGrA-3’, 5’-TGrGrT-3’, 5’-TGrGrG-3’, 5’-TGrGrC-3’; Table 1) were added to a 200uL thin-walled amplification tube and denatured at 95°C for 2 minutes. Then annealing buffer was added to a final concentration of 5mM Tris-HCl (pH 8.0), 0.5mM ethylenediaminetetraacetic acid (EDTA) and 10mM MgCl2 and incubated at 37°C for 15 minutes hybridizing the annealed double-stranded adapter to the total RNA. The ligation reaction was catalyzed by 5U/uL of RNA ligase 2 (NEB) with manufacturers suggested conditions at 37°C for 60 minutes then 4°C at 60 minutes. All reactions were ethanol precipitated with glycoblue (Thermo Fisher) with two 75% ethanol washes, then suspended in 10ul of dH2O. Following ligation, synthesis of cDNA began with hybridization of the reverse transcriptase primer to the ligated total RNA with a final concentration of 0.5pmol/uL. The samples were incubated at 70°C for 2 minutes and temperature was reduced to 37°C by 0.1°C/sec. Synthesis of cDNA was achieved using Superscript IV at 55°C for 60 minutes. To remove DNA-RNA dimers following cDNA synthesis, we hydrolyzed RNA with a final concentration of 0.1N NaOH in dH2O at 98°C for 20 minutes. All reactions were ethanol precipitated with glycoblue (ThermoFisher) with two 75% ethanol washes, then suspended in 12ul of dH2O. cDNA libraries were separated using 7M urea 6% denaturing polyacrylamide gels. Gels were stained with 1X SYBR gold (Thermo Fisher) in 1X TBE for 15 minutes and regions of interest (60-200 nucleotides) were excised on a UV light box. Gel slices were sheared through the bottom of a 0.5 mL tube nested in a 1.7 mL tube by centrifugation then suspended in 400uL of DNA elution buffer (300mM NaCl, 10mM Tris (pH=8.0, 1mM EDTA), incubated on dry ice for 30 minutes, and allowed to incubate at room temperature overnight on a standing rotator. Libraries were isopropanol precipitated with glycoblue followed by two 75% ethanol washes. Linear cDNA libraries were then suspended in 12ul of dH2O. Circularization of cDNA libraries was performed with CircLigase (Epicentre) with 0.5U/uL using manufacturer’s suggested conditions at 37°C for 1 hour. The reaction was terminated with incubation at 80°C for 20 minutes. All reactions were ethanol precipitated with glycoblue with two 75% ethanol washes, then suspended in 12.5ul of dH2O. cDNA libraries were amplified using the NEBnext Ultra II Q5 next-generation master mix (NEB) with manufacturer’s suggested conditions. HEK293 libraries were amplified for 7 cycles and mouse tissue libraries amplified for 7-9 cycles. Amplified libraries were gel purified from 2% agarose gels stained with 0.05mg/ml Ethidium Bromide. Regions of interest (100-250bp) were excised on a UV light box and purified using the Qiaquick (Qiagen) gel extraction kit using all optional steps. All libraries were ethanol precipitated with glycoblue (thermo) with two 75% ethanol washes, then suspended in 10ul of dH2O before sequencing.

tag: tissue

value: Embryonic kidney cell line


title: TB-2


title: 293_tRNA_2


title: HC-2

source_name: Peripheral blood mononuclear cells, healthy

value: Healthy


title: siNFATC3 3d-2

city: Shang Hai

first: Hao

last: Chen

state: California

address: 320 Yueyang Road

institute: Shanghai institute of nutrition and health, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced fragments were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated .
DEGs between the two groups were identified using the R 3.1.0 software package DESeq2 1.4.5.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited excel files include stablized expression levels for each Sample ...

source_name: Human embryonic stem cells

extract_protocol:
Human ESCs were collected and  RNA was harvested using Trizol reagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell lines

value: SHhES8 hESC line

tag: culture condition

value: cultured in MEF conditioned medium

tag: sirna

tag: time point


title: 293_tRNA_2_DM


title: siPPP3CC 3d-2


title: siNT 3d-2

value: siNT


title: siNFATC3 3d-1


title: HC-1


title: siNT 3d-1


title: siPPP3CC 3d-1


title: siNFATC3 1.5d


title: siPPP3CC 1.5d


title: SUMO_HS_siz1_ChIP_rep1

city: Guangzhou

first: Danlu

last: Han

address: No. 55, West of Yat-sen Avenue

department: School of Life Science

institute: South China Normal University

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie2 for Illumina (Galaxy Version 2.3.4.2)
Mapped reads were filtered by removing PCR duplications and randomly selected certain amount of reads
Bed files were generated by using BAM to BED conversion (Galaxy Version 2.29.0)
Peaks were called by using MACS model-based analysis of ChIP-seq (Galaxy Version 1.0.1)
Supplementary_files_format_and_content: wig

organism: Arabidopsis thaliana

growth_protocol: The Arabidopsis thaliana seeds of Col-0 (wild-type) and siz1-2 (SALK_065397, obtained from Arabidopsis Stock Center, were used in the experiments. Seeds were sterilized for 2 min in 70% ethanol, then 10min in 2.5% bleach solution and 0.05 % Triton X-100, rinsed five times with sterile water, next sown on the half-concentration Murashige and Skoog (MS) medium with 1.5% sucrose and 8 % agar and stratified at 4°C in the dark for 2 days, before transferred into a 23°C greenhouse with a long day  (16 h light / 8 h dark) condition.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  10 ng of ChIP DNA immunoprecipitated by anti-SUMO1 antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2500 was used for high-throughput sequencing of the ChIP-seq library.

treatment_protocol: 10-day-old seeding grown on the medium in petri dishes (90 × 15 mm) were incubated at 37°C for 30 min in a circulating water bath. During recovery 37°C treatment, the petri dishes containing seedlings were removed from the water bath and kept at 23°C for 90 min in the greenhouse under previous growth condition(Charng et al., 2006). The seedlings were collected at the indicated time points for further experiments

value: 10 days atfer germination

tag: chip antibody

value: SUMO1(abcam, Anti-Sumo 1 antibody,ab5316)

value: seedings

tag: genotype

value: HS


title: SUMO_RT_siz1_ChIP_rep2

value: RT


title: SUMO_HS_siz1_input


title: siNT 1.5d


title: SUMO_RT_siz1_ChIP_rep1


title: SUMO_RC_WT_input

value: WT

value: RC


title: SUMO_RC_WT_ChIP_rep2


title: SUMO_RC_WT_ChIP_rep1


title: 4204

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures  in kallisto.
Statistical tests for differential expression were performed using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

organism: Mus musculus

source_name: colon

extract_protocol:
Mice were euthanized and colons dissected. Colons were placed in Trizol and homogenized. The Direct-zol kit (Zymo) was used to isolate total RNA.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on a NextSeq High Output Run.

tag: age

value: 2 wks


title: 3203


title: 4207


title: 3202


title: 4209


title: 2205


title: 2202


title: SUMO_HS_WT_ChIP_rep1


title: SUMO_HS_WT_ChIP_rep2


title: SUMO_HS_siz1_ChIP_rep2


title: 1203


title: SUMO_RT_WT_input


title: 1205


title: SUMO_RT_WT_ChIP_rep1


title: 1204


title: SUMO_RT_WT_ChIP_rep2


title: 1201


title: REG2

city: Los Angeles

first: Mengfei

last: Yu

address: 2250 Alcazar St

institute: University of Southern California

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  3_REG_3_S3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, and normalized using Upper quartile.
Lognormal with shrinkage mean value were calculated using Gene-specific analysis by Partek flow (Partek Inc., USA).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: Coronal suture

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Coronal sutures were collected for RNA isolation with an RNeasy Micro Kit (QIAGEN) at 7-month old.
The quality of RNA samples was evaluated using an Agilent 2100 Bioanalyzer and all samples used for sequencing had RNA integrity (RIN) numbers >9.0. cDNA library preparation and sequencing were performed by DNA Link, Inc. Single-end reads with 75 cycles were performed on NextSeq500 for three pairs of samples.

treatment_protocol: Suture regeneration surgeries were performed at the age of 1 month old.

tag: strain

value: 7-month old

value: Coronal suture

value: Suture regeneration surgery


title: REG1

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  2_REG_2_S2


title: REG3

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  REG2_S8


title: MUT3

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  Mut3_S6

value: No


title: SUMO_HS_WT_input


title: MUT1

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  Mut1_S4


title: WT2

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  Wt2_S2

value: Wild type


title: MUT2

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  MB4_S5


title: WT3

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  Wt3_S3


title: WT1

description:
processed data file:  Partek_mice-suture-1-6-28_GSA_GSA.txt
processed data file column:  Wt1_S1


title: 1202


title: zebrafish cells DMSO treated rep1

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts for each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: abundance measurements and Deseq2 results

organism: Danio rerio

source_name: zebrafish cells DMSO treated

growth_protocol: Dechorionated zebrafish embryos are raised and maintained with 0.3x Danieau’s Buffer at 28.5 °C and on a 14-hours light/10-hours dark cycle

extract_protocol:
Total RNAs from embryos was extracted using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 30 hpf Tg(c-mybhyper: GFP) zebrafish embryos were treated with DMSO or 60 μM Tan I  to 72hpf.

value: embryonic cells

value: DMSO


title: zebrafish cells TanI treated rep2

source_name: zebrafish cells TanI treated

value: 60 μM Tan I


title: zebrafish cells DMSO treated rep3


title: zebrafish cells TanI treated rep1


title: zebrafish cells TanI treated rep3


title: zebrafish cells DMSO treated rep2


title: miR-23b-3p_2

city: San Francisco

first: Tsukasa

last: Kadota

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

description: Total RNA extracted from bronchial epithelial cells transfected with miR-23b-3p, and 100 ng of RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent Technologies)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Immortalized human bronchial epithelial cell with miR-23b-3p

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Primary human bronchial epithelia cells  were cultured in bronchial epithelial cell growth medium (BEGM, Lonza) with 10% fetal bovine serum and 1% AA at 37 °C in 5% CO2. BEAS2B cells were cultured in RPMI-1640 (Nissui Pharmaceutical) with 10% fetal bovine serum and 1% AA at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: The bronchial epithelial cells were transfected with miR-23b-3p, miR-145-5p, miR-494-3p mimics  or negative control miRNA (Ambion, Thermo Fisher Scientific) at 30nM for 24 hours.

tag: cell line

value: primary, immortalized bronchial epithelial cell line BEAS2B

tag: transfection


title: WM-3

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
fastq files were mapped using hisat2 using a index that comes the GRCm38/mm10 genome and ENSEMBL transcriptome (“grcm38_tran” downloaded from the hisat2 website); mapping used default parameters; this resulted in sam files
sam files were converted to bam, sorted and indexed using samtools
Indexed bam files were counted using featureCounts and ENSEMBL gene definitions (“Mus_musculus.GRCm38.97.gtf” obtained from ENSEMBL website), producing ReadCounts.csv
Genome_build: GRCm38/mm110
Supplementary_files_format_and_content: ReadCounts.csv has gene ids on rows, the twelve samples on columns, and reports read counts in a comma-separated text file

source_name: RNA from whole EDL muscle

extract_protocol:
Single myofiber RNA was extracted by adding 1 ul of 10X lysis buffer and 9 ul of RNAse free water in 0.2 ml micro tubes using DNA SMART-Seq HT kit available from Takara Biosciences; whole muscle RNA was extracted using Trizol method.
Libraries were prepared using DNA SMART-Seq HT kit from Takara Biosciences following manufacturer’s recommendation.

value: whole EDL muscle


title: miR-494-3p_2

description: Total RNA extracted from bronchial epithelial cells transfected with miR-494-3p, and 100 ng of RNA for analysis

source_name: Immortalized human bronchial epithelial cell with miR-494-3p


title: miR-145-5p_2

description: Total RNA extracted from bronchial epithelial cells transfected with miR-145-5p, and 100 ng of RNA for analysis

source_name: Immortalized human bronchial epithelial cell with miR-145-5p


title: NC2

description: Total RNA extracted from bronchial epithelial cells transfected with control miRNA, and 100 ng of RNA for analysis

source_name: Immortalized human bronchial epithelial cell transfected with negative control miRNA

value: control


title: miR-494-3p_1

source_name: Primary human bronchial epithelial cell transfected with miR-494-3p

value: primary bronchial epithelial cells


title: miR-23b-3p_1

source_name: Primary human bronchial epithelial cell transfected with miR-23b-3p


title: WM-2


title: F20-3

source_name: RNA from twenty EDL myofibers

value: twenty EDL myofibers


title: NC1

source_name: Primary human bronchial epithelial cell transfected with negative control miRNA


title: WM-1


title: Tfap2b rep3

city: Goettingen

first: Yang

last: Hu

country: Germany

institute: MPIBPC

data_processing:
Following base calling, adaptor clipping was performed using cutadapt 2.4
Data was mapped against the GRCm38.p6 genome using STAR v 2.6.1d
Differentially expressed genes were analyzed using EdgeR.
Genome_build: GRCm38.p6 genome
Supplementary_files_format_and_content: tab-delimited text files include: column 1: gene ID  column 2: counts for unstranded RNA-seq  column 3: counts for the 1st read strand aligned with RNA   column 4: counts for the 2nd read strand aligned with RNA

source_name: Brain

extract_protocol:
RNA was isolated from 20-80mg of mouse brain tissue from B6N, Tfap2a+/- and Tfap2b+/- (stored in RNAlater) following the Qiagen RNeasy protocol. First, the tissue samples were homogenized with the TissueLyser (Qiagen) at 25Hz for 2 * 2 minutes in Qiazol lysis buffer. 140µl chloroform was added and after 15min centrifugation at 12,000g the aqueous phase containing the RNA was extracted. 1.5 volumes of ethanol were added and the samples were washed with Qiagen’s RWT buffer on a Qiagen RNeasy spin column. RNA was treated with 10µl of DNase I on column for 15min followed by a wash with RWT. After further washes with RPE buffer, the purified RNA was eluted with 50µl water yielding between 5 and 22µg RNA.
After quality control using Agilent’s Bioanalyzer, sequencing libraries were prepared from 500ng of total RNA per sample following Roche’s stranded “KAPA RNA HyperPrep” library preparation protocol for single indexed Illumina libraries: First the polyA-RNA fraction was enriched using oligo-dT-probed paramagnetic beads. Enriched RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing, Illumina sequencing compatible adapters were ligated. Following bead-based clean-up steps the libraries were amplified using 11 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out on an Illumina HiSeq 4000 system in PE75bp mode yielding between 27 and 37 million fragments per sample.

value: Brain

value: 3-4 months


title: F20-2


title: F20-1


title: miR-145-5p_1

source_name: Primary human bronchial epithelial cell transfected with miR-145-5p


title: D7354

city: Cambridge

first: Guangan

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the mouse genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

extract_protocol:
Qiagen RNeasy Micro Kit
KAPA mRNA HyperPrep Kit

tag: agent

value: thiostrepton by IP injection

value: TAM


title: D7365


title: D7355

value: tumor-adjacent injection


title: D7364


title: D7357


title: F5-3

source_name: RNA from five EDL myofibers

value: five EDL myofibers


title: D7361


title: D7363


title: Tfap2b rep1


title: Tfap2a rep3


title: D7359


title: F5-2


title: Tfap2a rep2


title: Tfap2b rep2


title: Tfap2a rep1


title: F5-1


title: F1-3

source_name: RNA from a single EDL myofiber

value: a single EDL myofiber


title: RNAseq_podocyte_mTmG_ADR_D14_rep1

city: Boston

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
Sequencing reads were aligned to mm9 using Bowtie v.0.12.7 with the unique option enabled (Langmead et al. 2009).
Consistency of replicates was checked by genome-wide correlation analysis and by visual inspection.
To access expression levels, Cufflinks was used with default parameters from the aligned reads. The FPKM values for the expression levels for each gene were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: txt and quantified expression levels of genes

extract_protocol:
Total RNA extracted from GFP-positive podocytes was quantified was quantified on the Qubit RNA assay (Invitrogen). RNA quality was checked using Agilent Bioanalyzer 2100 RNA Nano chip (Agilent). RNA samples exceeding an RNA integrity number (RIN) of eight were submitted to sequencing. Five micrograms of RNA was used as starting material for rRNA depletion using the Ribo-Zero Magnetic Gold Kit (human/mouse/rat (Epicentre). rRNA-depleted samples were analyzed on an Agilent Bioanalyzer to ensure that the majority of rRNA was depleted before the library was prepared.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Isolated podocytes

value: 7-8 weeks

value: D14 after ADR injection

value: wildtype


title: RNAseq_podocyte_mTmG_ADR_D9_rep3

value: D9 after ADR injection


title: B6N rep2


title: F1-2


title: RNAseq_podocyte_mTmG_ADR_D14_rep2


title: RNAseq_podocyte_mTmG_PBS_rep3

value: PBS


title: RNAseq_podocyte_mTmG_ADR_D9_rep2


title: B6N rep1


title: RNAseq_podocyte_mTmG_ADR_D9_rep1


title: RNAseq_podocyte_mTmG_ADR_D14_rep3


title: RNAseq_podocyte_mTmG_PBS_rep1


title: input_glomeruli_BALB/cJ_PBS

description:
control
WT1_glomeruli_BALBcJ_PBS_peaks.narrowPeak.bed

data_processing:
Sequencing reads were aligned to mm9 using Bowtie v.0.12.7 with the unique option enabled (Langmead et al. 2009).
Consistency of replicates was checked by genome-wide correlation analysis and by visual inspection.
Significant peaks were called by MACS2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bed and IP enrichment peaks

extract_protocol:
Chromatin from isolated glomeruli and isolated podocytes were prepared from 7-8-week old BALB/cJ, mT/mG-Nphs2cre and WT1 flox/flox/Nphs2iCRE mice. For, WT1 ChIP assays, we used per immunoprecipitation either isolated glomeruli from two kidneys or 10 million of immortalized mouse podocytes (four independent experiments were performed per condition for BALB/cJ mice and three independent experiments for mT/mG Nphs2cre mice and immortalized mouse podocytes). Samples were fixed with 1% formaldehyde in PBS for 5 min at room temperature before termination with 0.125 M glycine. Cells were then lysed in sonication buffer as previously described (4). Cross-linked chromatin was sonicated to obtain DNA fragments of 200–600 bp. Immunoprecipitations were performed as previously.
Libraries for sequencing were prepared using standard Illumina protocols.

value: BALB/cJ

value: Isolated glomeruli

tag: antibody


title: WT1_glomeruli_BALB/cJ_ADR_rep4

description:
ADR injection
WT1_glomeruli_BALBcJ_ADR_peaks.narrowPeak.bed

value: WT1 (Santa Cruz, sc-192)

value: ADR


title: input_glomeruli_BALB/cJ_ADR


title: D14 Large Wound Center scATAC-Seq

city: Calgary

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

description:
FACS strategy: No FACS Enrichment for TDTmt. Hic1CreERT2:TDTmt transgenic strain is utilized to corroberate this dataset with our previous scRNA-Seq studies (GEO Deposits: GSE108677, GSE115543).
FACS sorted cells: 10,000 cells; Recovered: 1,578 cells
single-cell ATAC-Seq

data_processing:
All raw base call (BCL) files generated by Illumina® sequencers were converted to FASTQ files using cellranger-atac mkfastq function, a wrapper around bcl2fastq from Illumina®, with additional 10x Genomics-specific features. Next, read filtering and alignment, barcode counting, and identification of transposase cut sites were detected using cellranger-atac count function using the cellranger-atac-specific mm10 reference package. The resulting filtered peak-barcode matrix was imported into Cicero, an R toolkit specifically designed for analyzing single-cell chromatin accessibility experiments.
Genome_build: refdata-cellranger-atac-mm10-1.0.0 (mm10 with pre-generated indices and other data required to run CellRanger-ATAC)
Supplementary_files_format_and_content: Filtered peak-barcode matrix output from CellRanger-ATAC (containing only detected cellular barcodes)

source_name: 14 days post injury skin wound

extract_protocol:
Large wounds from adult mice (n = 3) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in bovine serum album in HBSS before FACS purification. For FACS purification, a stringent forward and side scatter gates were used to exclude debris, and cell doublets. Following FACS, single nucleus was isolated, washed, and counted prior to use with the Chromium Single Cell ATAC protocol (as described in CG000169, Demonstrated Protocol for Nuclei Isolation ATAC Sequencing Rev B document at: https://support.10xgenomics.com/single-cell-atac/sample-prep/doc/demonstrated-protocol-nuclei-isolation-for-single-cell-atac-sequencing).
Libraries were prepared according to 10X Genomics Chromium Single Cell ATAC Library & Gel Bead Kit Chemistry. Briefly, single nuclei were first treated in bulk with Tn5 transposase to preferentially insert sequencing adaptors into accessible DNA regions. Transposed nuclei are then partitioned into GEMs in the 10x Chromium Controller. All the DNA fragments from the same nucleus share a common 10x barcode. The barcoded, accessible DNA fragments are subsequently pooled for downstream processing and library preparation. Next generation sequencing was performed using Illumina HiSeq 4000 PE with a targeted sequencing depth of >10,000 median fragments per cell. 77.4% of the fragments overlapped a targeted region and fraction of transposition events in peaks was 53.2%.

treatment_protocol: Despite our experiments being performed on Hic1CreERT2:TDTmt transgenics, cre-recombination was not initiated as no tamoxifen was applied.

tag: transgenic strain

tag: background

value: skin wound


title: WT1_glomeruli_BALB/cJ_ADR_rep2


title: WT1_glomeruli_BALB/cJ_ADR_rep1


title: B6N rep3

value: Brain

value: 3-4 months


title: WT1_glomeruli_BALB/cJ_PBS_rep4


title: Large Wound Pheripheral Hic1:tdTomato+ve 18DPI

description: # FACS sorted cells: 1,500 cells; Recovered: 573 cells

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes (1195 genes) was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (run in Seurat at: res = 0.2) was used to select only fibroblasts for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: 18 days post injury skin wound

extract_protocol:
Large and small wounds from adult mice (n = 2 per sample) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37 oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in 0.5% bovine serum album in HBSS before FACS purification. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Wildtype cells were used as negative control to determine gates for detection of tdTomato-fluorescence, then cells from Hic1CreERT2:tdTomato mice were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg/20g in sterile sunflower oil, Sigma-Aldrich) at postnatal day (P) 3 and 4.

tag: facs strategy

value: tdTomato+positive

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2


title: WT1_glomeruli_BALB/cJ_PBS_rep3

tag: tissue


title: Large Wound Center Hic1:tdTomato+ve 18DPI

description: # FACS sorted cells: 1,130 cells; Recovered: 373 cells


title: WT1_glomeruli_BALB/cJ_PBS_rep2


title: F1-1


title: RNAseq_podocyte_mTmG_PBS_rep2

tag: treatment


title: WT1_glomeruli_BALB/cJ_PBS_rep1


title: WT1_podocyte_mTmG_PBS_rep2

description:
control
WT1_podocyte_mTmG_PBS_peaks.narrowPeak.bed

value: Purified podocytes


title: WT1_podocyte_mTmG_ADR_D9_rep2

description:
D9 after ADR injection
WT1_podocyte_mTmG_ADR_D9_peaks.narrowPeak.bed


title: WT1_podocyte_mTmG_PBS_rep3


title: WT1_podocyte_mTmG_ADR_D14_rep1

description:
D14 after ADR injection
WT1_podocyte_mTmG_ADR_D14_peaks.narrowPeak.bed


title: WT1_podocyte_mTmG_PBS_rep1


title: Large Wound Pheripheral Hic1:tdTomato+ve 14DPI

description: # FACS sorted cells: 10,500 cells; Recovered: 3776 cells

value: large wound peripheral


title: Uninjuired Skin Hic1:tdTomato+ve

description: # FACS sorted cells: 10,500 cells; Recovered: 3293 cells

source_name: P. 24 Uninjured Skin

value: uninjured


title: Small Wound Hic1:tdTomato+ve 14DPI

description: # FACS sorted cells: 10,500 cells; Recovered: 4061 cells

value: small wound


title: WT1_podocyte_mTmG_ADR_D14_rep2

value: 7-8 weeks


title: Aortic sample, PWD

city: New York

first: Bhama

last: Ramkhelawon

state: NY

address: 435 East 30th - Science Building 416

department: Surgery

institute: NYU Langone Medical Center

data_processing:
FASTQ files were aligned to the MM9 Mus musculus reference genome using Tophat (version 2.0.9) with 2 mismatches allowed.
The resulting read counts were extracted using the Featurecounts program from binary alignment map (BAM) files.
Differential gene expression analysis was conducted using the DESEQ2 package from the BioconductR repository using the open source R statistical programming environment.
Genome_build: mm9
Supplementary_files_format_and_content: AAA vs PBS RNAseq, excel file with gene list, number of reads for each condition, Log 2 fold changes and p value. Contains list of signifcant genes and pathway analyses

source_name: Aortic sample

extract_protocol:
RNA was extracted from aortas using the RNEasy fibrous tissue kit as per manufacturer’s instructions (74704, Qiagen). RNA quality was verified using a Bioanalyzer (G2939BA, Agilent Technologies).
Sequencing was performed on an Illumina HiSeq 2000 as single-end reads, 50 nucleotides in length

tag: disease

value: Normal aorta

value: Apolipoprotein E deficient (ApoE-/-)

value: PBS perfusion 28 days

value: Aortic sample


title: Aortic sample, PWC


title: BMM_αKG_48h

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

description:
C57BL/6, 5-weeks old, male
αKG_Late

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: Bone marrow derived macrophage treated with dimethyl α-Ketoglutarate, MCSF, and RANKL

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Bone marrow cells isolated from tibias and femurs of male mice cultured in αMEM containing 10 % of fetal bovine serum , 1% of 200 mM L-glutamine and 100 units/ml of penicillin-streptomycin. All cells were cultured at 37℃ at humidified incubator with 5% CO2

extract_protocol: easy-BLUETM Total RNA Extraction Kit and High Capacity cDNA Reverse Transcription Kit were used to extract total RNA and to synthesis cDNA, respectively.

treatment_protocol: DW or dimetyl 1 mM dimethyl αKG were treated to cells during osteoclastogenesis

value: 5 weeks

tag: gender

value: male


title: Aortic sample, PWB


title: WT1_glomeruli_BALB/cJ_ADR_rep3

value: BALB/cJ

value: Isolated glomeruli

value: WT1 (Santa Cruz, sc-192)

value: ADR

value: wildtype


title: Aortic sample, PWA


title: BMM_αKG_12h

description:
C57BL/6, 5-weeks old, male
αKG_Intermediate


title: BMM_αKG_3h

description:
C57BL/6, 5-weeks old, male
αKG_Early


title: BMM_72h

description:
C57BL/6, 5-weeks old, male
Late

source_name: Bone marrow derived macrophage treated with DW, MCSF, and RANKL


title: BMM_αKG_24h


title: BMM_αKG_6h

description:
C57BL/6, 5-weeks old, male
αKG_Early


title: BMM_αKG_72h

description:
C57BL/6, 5-weeks old, male
αKG_Late


title: WT1_podocyte_mTmG_ADR_D9_rep1

tag: time point


title: NPC_d14_Epi_2: Neural progenitor cells d14_rep2

city: Singapore

first: Uma Sangumathi

last: Kamaraj

state: singapore

address: 8 college road

department: CVMD

country: Singapore

institute: Duke NUS

description: Neural progenitor cells (NPCs). Figure 4F. Replicate 2

data_processing:
Trimmomatic v0.39
STAR v2.7.3
featureCounts v1.6.0
Genome_build: GRCh38

source_name: Neural progenitor cells

growth_protocol: For astrocyte differentiation, cells were seeded onto flasks coated with Matrigel in neural induction medium (NIM) for 14 days (to obtain NPCs). Cells were then expanded for 7 days in NIM and replated at day 21 onto Matrigel or all factor conditions for another 21 days in astrocyte medium. Primary astrocytes were cultured in Astrocyte medium. H9 ESCs were cultured in Essential 8 medium.

extract_protocol:
following the NEB protocol using  NEBNext Ultra II directional RNA library prep kit and   NEBNext Poly(A) mRNA Magnetic: Poly A mRNA isolation, RNA fragmentation, cDNA sythesis, Adaptor ligation, PCR
Poly(A) mRNA enrichment, PCR using dual index primers

treatment_protocol: Astrocyte differentiation cultures were treated with matrigel or all predicted factors

tag: cell type

value: Neural progenitor cells derived from human embryonic stem cells


title: NPC_d14_Epi_3: Neural progenitor cells d14_rep3

description: Neural progenitor cells (NPCs). Figure 4F. Replicate 3


title: Aortic sample, AWD

value: Abdominal aortic aneurysm

tag: genotype

value: Angiotensin II perfusion 28 days


title: NPC_d14_Epi_1: Neural progenitor cells d14_rep1

description: Neural progenitor cells (NPCs). Figure 4F. Replicate 1


title: Aortic sample, AWC


title: NHA_Astro_P3_3: Normal Human Astrocytes

description: Primary astrocytes. Figure 4F. Replicate 3

source_name: Astrocyte

value: Normal primary human astrocytes


title: BMM_αKG_0.5h

description:
C57BL/6, 5-weeks old, male
αKG_Fast

tag: age


title: BMM_48h

description:
C57BL/6, 5-weeks old, male
Late

tag: strain


title: Aortic sample, AWB


title: Aortic sample, AWA


title: BMM_αKG_1h

description:
C57BL/6, 5-weeks old, male
αKG_Fast


title: NHA_Astro_P3_2: Normal Human Astrocytes

description: Primary astrocytes. Figure 4F. Replicate 2


title: BMM_24h

description:
C57BL/6, 5-weeks old, male
Intermediate


title: NHA_Astro_P3_1: Normal Human Astrocytes

description: Primary astrocytes. Figure 4F. Replicate 1


title: YAP1-TFE3 rep1

city: Seattle

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: whole tumor tissue RCAS-YAP1-TFE3

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×10^6 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse brain tumor

tag: genotype/variation


title: YAP1-TFE3 rep3


title: YAP1-FAM118B rep3

source_name: whole tumor tissue RCAS-YAP1-FAM118B


title: H9_ESC_ctrl_3: Human embryonic stem cells

description: H9 Embryonic stem cells. Figure 4F. Replicate 3

source_name: Embryonic stem cells

value: Embryonic stem cells


title: YAP1-TFE3 rep2


title: H9_ESC_ctrl_2: Human embryonic stem cells

description: H9 Embryonic stem cells. Figure 4F. Replicate 2


title: YAP1-FAM118B rep1


title: H9_ESC_ctrl_1: Human embryonic stem cells

description: H9 Embryonic stem cells. Figure 4F. Replicate 1


title: YAP1-MAMLD1-dR3R1 rep2

source_name: whole tumor tissue RCAS-YAP1-MAMLD1-dR3R1


title: BMM_12h

description:
C57BL/6, 5-weeks old, male
Intermediate


title: YAP1-MAMLD1-dR3R1 rep3


title: BMM_6h

description:
C57BL/6, 5-weeks old, male
Early


title: BMM_0h_2

description:
C57BL/6, 5-weeks old, male
Contro

source_name: Bone marrow derived macrophage treated with DW and MCSF


title: naïve (no injection) rep3

source_name: Naïve (no injection) in normal cortex

value: naive; normal


title: BMM_3h

description:
C57BL/6, 5-weeks old, male
Early


title: naïve (no injection) rep2


title: Astro_d42_Mat_3: Astrocyte differentiation with matrigel d42_rep3

description: Day 21 of differentiation on matrigel from neural progenitor cells (42 days total). Figure 4F. Replicate 3

value: Astrocytes differentiated from neural progenitor cells


title: Ex CT-26T

city: Bunkyo ku

first: Akihiko

last: Miyanaga

address: 1-1-5 Sendagi,

institute: Nippon Medical School

data_processing:
Base calling was performed using the Illumina Pipeline (CASAVA v1.8) with default parameters.
Adaptor trimming was performed using cutadapt v1.2.1 with the paramaters "-O 9 -m 32".
Read Cleaning was performed using "fastq_quality_rimmer -l 32" and "fastq_quality_filter -q 10 -p 95" command in FASTX-Toolkit v 0.0.13 followed by paired reads extraction using cmpfastq_pe.
Cleaned reads were mapped on UCSC hg19 by using "bwa aln" and "bwa sampe" command with default paramaters in BWA v0.5.9.
Duplicate Reads were marked by using Picard MarkDuplicates.
Realignment and base recalbration were performed by using RealignerTargetCreator/IndelRealigner and CountCovariates in GATK v1.6, respectively.
Somatic variant calling was performed by Strelka v1.0.14 and Virmid v1.1.1 with default parameters.
Variants were annotated by using SnpEff v3.6c
Genome_build: UCSC hg19

source_name: lung tissue

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s protocol.
All the exon genes were captured using a SureSelectXT Human All Exon kit v3 (Agilent) according to the SureSelectXT Target Enrichment for Illumina Paired-End Multiplexed Sequencing Protocol 1.1.1. Enriched libraries were sequenced using Illumina Genome Analyzer IIx.
whole-exome sequencing

value: lung carcinoid

value: Male

tag: histological subtype

value: Typical carcinoid

tag: 8th pstage

value: IIB

tag: relapse

value: not relapsed


title: naïve (no injection) rep1


title: Treated with pterostilbene 16 µM day 8 Nalm-6 screen

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

institute: University of Montreal

description: processed data file: Nalm6_sgRNA_read_counts.txt

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed.
Read counts from all control samples and time-points from each experiment were summed.
Genome_build: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library. For Jurkat screens: TKOv3 sgRNA library (Hart et al. 2017,PMID:28655737).
Supplementary_files_format_and_content: Tab-separated sgRNA read counts per sample

growth_protocol: Nalm-6 and Jurkat cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Genomic DNA was extracted and purified using the Gentra Cell Puregene kit (QIAGEN, cat. # 158388).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol:
(NALM-6) A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2018 for details). The pooled EKO library was split in different T-75 flasks and compounds were added (16 µM resveratrol, 16 µM pterostilbene, 100 µM hydroxyurea, or DMSO 0.1% v/v). Fresh media and compound was added at each cell passage.
(Jurkat) The genome-wide screen in Jurkat cells was performed by transduction of cells with the lentiviral TKOv3 library as described (Hart et al., 2017) with modifications as described. Cells were treated with 16 µM resveratrol or 0.1% DMSO v/v/ for 12 days. Fresh media and compound was added at each cell passage.

tag: cell line background

value: Nalm-6 pre-B lymphoid cell line

tag: sample type

value: pooled sgRNA library

tag: molecule subtype

value: sgRNAs PCR-amplified from genomic DNA


title: Untreated day 8 control for pterostilbene Nalm-6 screen (grown in spinner flask)


title: BMM_0h_1

description:
C57BL/6, 5-weeks old, male
Control

value: 5 weeks

value: male


title: YAP1-FAM118B rep2


title: Ex CT-22N

value: IA


title: Astro_d42_Mat_1: Astrocyte differentiation with matrigel d42_rep1

description: Day 21 of differentiation on matrigel from neural progenitor cells (42 days total). Figure 4F. Replicate 1


title: Ex CT-22T


title: Untreated day 6 control for pterostilbene Nalm-6 screen


title: YAP1-MAMLD1-dR3R1 rep1


title: Ex CT-21N

value: Atypical carcinoid

value: Relapsed


title: Untreated day 4 control for pterostilbene Nalm-6 screen


title: Astro_d42_All_3: Astrocyte differentiation with all predicted factors d42_rep3

description: Day 21 of differentiation with all factors from neural progenitor cells (42 days total). Figure 4F. Replicate 3


title: Ex CT-18N


title: Astro_d42_All_2: Astrocyte differentiation with all predicted factors d42_rep2

description: Day 21 of differentiation with all factors from neural progenitor cells (42 days total). Figure 4F. Replicate 2


title: Ex CT-20T


title: Astro_d42_All_1: Astrocyte differentiation with all predicted factors d42_rep1

description: Day 21 of differentiation with all factors from neural progenitor cells (42 days total). Figure 4F. Replicate 1


title: Untreated day 2 control for pterostilbene Nalm-6 screen


title: Astro_d42_Mat_2: Astrocyte differentiation with matrigel d42_rep2

description: Day 21 of differentiation on matrigel from neural progenitor cells (42 days total). Figure 4F. Replicate 2


title: 0.1% DMSO day 8 control for pterostilbene Nalm-6 screen


title: Day 0 control for pterostilbene Nalm-6 screen


title: Ex CT-26N


title: Ex CT-15T


title: Ex CT-15N


title: Astro_d35_Mat_3: Astrocyte differentiation with matrigel d35_rep3

description: Day 14 of differentiation on matrigel from neural progenitor cells (35 days total). Figure 4F. Replicate 3


title: Untreated day 8 control for pterostilbene Nalm-6 screen (grown in T75 flask)


title: Ex CT-18T


title: Treated with resveratrol 16 µM day 8 Nalm-6 screen


title: Astro_d35_Mat_2: Astrocyte differentiation with matrigel d35_rep2

description: Day 14 of differentiation on matrigel from neural progenitor cells (35 days total). Figure 4F. Replicate 2


title: Ex CT-14T


title: Ex CT-12N

value: Female


title: Ex CT-21T


title: Untreated day 8 control for resveratrol Nalm-6 screen


title: Astro_d35_Mat_1: Astrocyte differentiation with matrigel d35_rep1

description: Day 14 of differentiation on matrigel from neural progenitor cells (35 days total). Figure 4F. Replicate 1


title: Ex CT-12T


title: 0.1% DMSO day 8 control for resveratrol Nalm-6 screen


title: Ex CT-20N


title: Ex CT-10T

value: IIA


title: 0.1% DMSO day 6 control for resveratrol Nalm-6 screen


title: Astro_d35_All_3: Astrocyte differentiation with all predicted factors d35_rep3

description: Day 14 of differentiation with all factors from neural progenitor cells (35 days total). Figure 4F. Replicate 3


title: 0.1% DMSO day 2 control for resveratrol Nalm-6 screen


title: 0.1% DMSO day 4 control for resveratrol Nalm-6 screen


title: Ex CT-6T

value: IIIB


title: Astro_d35_All_1: Astrocyte differentiation with all predicted factors d35_rep1

description: Day 14 of differentiation with all factors from neural progenitor cells (35 days total). Figure 4F. Replicate 1

value: Astrocytes differentiated from neural progenitor cells


title: Ex CT-8T

value: lung carcinoid


title: Ex CT-5N

value: Male


title: Ex CT-5T

value: Typical carcinoid


title: Day 0 control for resveratrol Nalm-6 screen


title: Ex CT-6N


title: Ex CT-4N


title: Ex CT-10N


title: Ex CT-4T


title: Astro_d28_Mat_2: Astrocyte differentiation with matrigel d28_rep2

description: Day 7 of differentiation on matrigel from neural progenitor cells (28 days total). Figure 4F. Replicate 2


title: Ex CT-8N


title: S127-397A-YAP1 rep3

description: U5 neural stem cells transduced with two point mutations(S127/397A-YAP1)  rep 3

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: cell line

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: Astro_d35_All_2: Astrocyte differentiation with all predicted factors d35_rep2

description: Day 14 of differentiation with all factors from neural progenitor cells (35days total). Figure 4F. Replicate 2


title: Ex CT-3N

tag: tissue


title: Ex CT-3T


title: S127-397A-YAP1 rep2

description: U5 neural stem cells transduced with two point mutations(S127/397A-YAP1)  rep 2


title: CT-26T

data_processing:
Basecalls performed using CASAVA version 1.8.1.
Sequence reads marked as “passed filtering” were used for selection of fusion genes using the deFuse program.

extract_protocol:
Total RNA were prepared with RNeasy Mini Kit  (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: IIB


title: Astro_d28_All_3: Astrocyte differentiation with all predicted factors d28_rep3

description: Day 7 of differentiation with all factors from neural progenitor cells (28 days total). Figure 4F. Replicate 3


title: CT-15T

value: not relapsed


title: CT-21T


title: Astro_d28_All_2: Astrocyte differentiation with all predicted factors d28_rep2

description: Day 7 of differentiation with all factors from neural progenitor cells (28 days total). Figure 4F. Replicate 2


title: CT-20T


title: S127-397A-YAP1 rep1

description: U5 neural stem cells transduced with two point mutations(S127/397A-YAP1)  rep 1


title: GFP rep6

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 3


title: Ex CT-14N


title: GFP rep5

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 2


title: CT-10T


title: Astro_d28_All_1: Astrocyte differentiation with all predicted factors d28_rep1

description: Day 7 of differentiation with all factors from neural progenitor cells (28 days total). Figure 4F. Replicate 1


title: CT-6T


title: T5-1

city: Fuzhou

first: mi

last: zhang

address: Jiaotong Road number 88

institute: Fujian Medical University

description: Control

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: adjacent noncancerous tissues

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: subject id

tag: pairs

tag: Sex

value: M


title: T4-4

description: Control


title: Astro_d28_Mat_1: Astrocyte differentiation with matrigel d28_rep1

description: Day 7 of differentiation on matrigel from neural progenitor cells (28 days total). Figure 4F. Replicate 1


title: T6-1

description: Control


title: U5_S94A YAP1-FAM118B rep3

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-FAM118B-PGK-Puro rep 3

source_name: U5_S94A YAP1-FAM118B

value: human neural stem cell line


title: SG_oregon_wt-2

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: control sample

data_processing:
The reads obtained were mapped to BDGP R6/dm5 Drosophila transcriptome assembly using hisat2. Differential expression was calculated using DESeq software.
Genome_build: BDGP R6/dm5
Supplementary_files_format_and_content: FPKM counts for each gene in both genotypes for each of the replicas

organism: Drosophila melanogaster

source_name: salivary glands

growth_protocol: The flies were kept at 25°C

extract_protocol:
50 salivary glands were dissected for each sample.
RNA was isolated using TRIZOL reagent. 500 ng of RNA was used as a starting material for constructing RNA-seq libraries using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina  (New England Biolabs).

value: salivary glands

value: yw

tag: developmental stage


title: SG_oregon_wt-3

description: control sample


title: SG_oregon_wt-1

description: control sample


title: U5_S94A YAP1-FAM118B rep2

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-FAM118B-PGK-Puro rep 2

tag: cell type


title: T3-1

description: Control


title: Dam-SG_for_SetDB1-3

description:
control sample for SetDB1 experiment
SetDB1_SG_Females_1sd_at_FDR_0.05_probability_track.wig

data_processing:
Library strategy: DamID-seq
The reads obtained were mapped to BDGP R6/dm5 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R6/dm5
Supplementary_files_format_and_content: wig files containing scores for each GATC fragment of the genome. Score represents -Log10(P), where P is significance level assessed with exact Fisher’s test for each GATC region in the genome. Positive values were ascribed to GATC fragments enriched in Dam-X sample, while negative values to those enriched in Dam-alone sample.

growth_protocol: The flies were kept at 23°C

extract_protocol:
50 salivary glands were dissected for each sample.
DNA was isolated using phenol-chloroform method. 300ng of genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.

tag: genotype

tag: tagged protein

value: no Dam-tagged protein (Dam only control)


title: Dam-SG_for_SetDB1-2


title: SetDB1-SG-2

description: SetDB1_SG_Females_1sd_at_FDR_0.05_probability_track.wig


title: Dam-SG_for_SetDB1-1


title: SetDB1-SG-3


title: U5_S94A YAP1-FAM118B rep1

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-FAM118B-PGK-Puro rep 1


title: SetDB1-SG-1


title: Dam-SG_for_CP190-2

description:
control sample for CP190 experiment
CP190-SG_at_FDR_0.05_probability_track.wig


title: Dam-SG_for_CP190-1


title: CP190-SG-2

description: CP190-SG_at_FDR_0.05_probability_track.wig


title: T1-1

description: Control

value: F

tag: age


title: U5_S94A YAP1-MAMLD1 rep2

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-MAMLD1-PGK-Puro rep 2

source_name: U5_S94A YAP1-MAMLD1

tag: genotype/variation


title: GFP rep4

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 1


title: CP190-SG-1


title: C6-2

description: Test

source_name: tongue tumor

tag: tnm

tag: differentiation

value: Medium


title: U5_S94A YAP1-MAMLD1 rep1

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-MAMLD1-PGK-Puro rep 1


title: C4-4

description: Test


title: U5_YAP1-TFE3 rep3

description: U5 neural stem cells transduced with pLJM1-YAP1-TFE3-PGK-Puro rep 3


title: C5-3

description: Test

value: High


title: U5_YAP1-TFE3 rep2

description: U5 neural stem cells transduced with pLJM1-YAP1-TFE3-PGK-Puro rep 2


title: T03

city: Yangzhou

first: Heng

last: Jiang

state: Jiangsu

address: 88 University South Road

institute: Yangzhou University

data_processing:
Based on sequencing by synthesis (SBS) technology, Illumina HiSeq sequencing platforms were used to sequence the cDNA library.
Hisat2, designed and developed by Hopkins University in the United States, is a fast and sensitive alignment software. It is still based on BWT algorithm. Its core is based on bowtie2. Compared with tophat2, it has higher efficiency and more accurate results, and has been widely used in RNA SEQ data alignment.
Stringtie mainly uses network flow algorithm to splice more complete and accurate genes.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/335/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.fna.gz
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Tribolium castaneum

source_name: 20-day old larvae

growth_protocol: The Georgia-1 (GA-1) strain of T. castaneum was reared at 30 °C and 50% relative humidity in 5% yeasted flour under standard conditions.

extract_protocol:
Total RNA was isolated from 10 larvae of dsTcAMPKα or dsEGFP group on the sixth day after injection using TRIzol Reagent (Invitrogen, USA), and digested by RNase-free DNase I (Takara, Dalian, China) to remove genomic DNA contaminants.
1. Enrichment of eukaryotic mRNA by magnetic beads with Oligo (DT). 2. The mRNA was randomly interrupted in fragmentation buffer. 3. The first cDNA strand was synthesized by random hexamers using mRNA as template. The second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA by ampure XP beads. 4. The purified double stranded cDNA was subjected to terminal repair, A-tail was added and sequenced. The fragment size was selected by ampure XP beads. 5. Finally, the cDNA library was obtained by PCR enrichment.

treatment_protocol: The synthesized dsRNAs were diluted in diethyl pyrocarbonate (DEPC)-treated water with a concentration of 2 μg/μL, and about 200 ng of dsRNA in 200 nL IB was injected into 20-day-old larvae. A total of 10 unsexed insect larvae were collected as a sample for RNA extraction at six- days post-injection. The dsEGFP-injected larvae (CK group) were set as controls in all injection experiments. Three biologically independent replicates were carried out with at least 100 insects (≥ 200mg) in each replicate.

tag: strain

value: 20-day old larvae

tag: knockdown

value: dsEGFP-injected

tag: condition

value: CK


title: T04

value: dsTcAMPKalpha-injected

value: Treatment


title: T05


title: C3-1

description: Test


title: T06


title: T02


title: T01


title: C2-3

description: Test


title: T2-1

description: Control


title: U5_S94A YAP1-MAMLD1 rep3

description: U5 neural stem cells transduced with pLJM1-S94A-YAP1-MAMLD1-PGK-Puro rep 3


title: C1-1

description: Test


title: U5_YAP1-TFE3 rep1

description: U5 neural stem cells transduced with pLJM1-YAP1-TFE3-PGK-Puro rep 1


title: U5_YAP1-FAM118B rep2

description: U5 neural stem cells transduced with pLJM1-YAP1-FAM118B-PGK-Puro rep 2


title: Airway epithelial cells - Non smoker - p9

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
RNA-seq data analysis was performed separately for each panel (lowly and highly expressed genes), according to the following bioinformatics pipeline.
Reads were aligned to the sequences of the targeted transcript retrieved from the human reference genome (UCSC assembly hg19) using BWA (v.0.7.17).
Samtools (v.1.9) was used to generate, to sort and to index the BAM files. Read counting for each transcript was performed with the GenomicAlignments (v.1.36.0) Bioconductor package.
The geNorm algorithm implemented within the ctrlGene (v.1.0.1). R package was used to identify stably expressed genes among the set of measured housekeeping genes. The selected housekeeping genes were used within the DESeq2 (1.24.0) Bioconductor package in order to compute the size factors associated with each library.
Genome_build: human reference genome (UCSC assembly hg19)
Supplementary_files_format_and_content: normalized-expres-low-panel.csv contains the expression matrix of the low panel after normalisation based on housekeeping genes. normalized-expres-high-panel.csv contains the expression martrix of the high panel after the normalisation based on housekeeping genes.

source_name: Airway epithelial cells

growth_protocol: A large piece of cartilaginous bronchus was selected, located as far as possible from the tumour site and submitted to pronase digestion overnight at 4°C, in order to derive human broncho-epithelial cells (HBEC). HBECs were cultured in flasks in retinoic acid-supplemented Bronchial Epithelial Cell Growth Basal Medium (Lonza, Verviers, Belgium) until confluence. Cells were then detached and seeded at a density of 80,000 cells/well on 24-well polyester filter-type inserts (0.4-µm pore size; Corning, Corning, NY, USA) coated with 0.2 mg/ml collagen IV (Sigma-Aldrich, Saint-Louis, MO, USA) until a confluent monolayer. The culture was then carried out in air/liquid interface (ALI) for 14 to 20 days, according to the experiment. Once in ALI, HBECs were cultured in BEBM:DMEM (1:1) medium supplemented with penicillin (100U/ml), streptomycin (100µg/ml) (Lonza), bovine serum albumin (BSA) (1.5 µg/ml), retinoic acid (30ng/ml) (Sigma, Saint-Louis, MO), and BEGM SingleQuotsTM Supplements and Growth Factors (Lonza), including bovine pituitary extract (52µg/ml), insulin (5µg/ml), hydrocortisone (0.5g/ml), transferrin (10µg/ml), epinephrine (0.5µg/ml), epidermal growth factor (0.5ng/ml) and triiodothyronine (3.25ng/ml)

extract_protocol:
RNA was isolated from ALI-reconstituted airway epithelium cultured cells of smoker, non smoker and COPD patients. RiboPure™ RNA Purification kit from Ambion was used for the RNA extraction using bromochloropropane (BCP) instead of chloroform to avoid DNA contamination
The library preparation was performed using 50ng total RNA follwing TruSeq® Targeted RNA Expression protocol from Illumina. The libraries were single read (1x50 bp) sequenced on MiSeq (Illumina Inc)

value: ALI-reconstituted airway epithelium

tag: phenotype

value: non smoker


title: Airway epithelial cells - smoker - p10

value: smoker


title: Airway epithelial cells - smoker - p9


title: Airway epithelial cells - smoker - p8


title: Airway epithelial cells - COPD1 - p9

value: mild COPD


title: Airway epithelial cells - COPD1 - p8


title: Airway epithelial cells - Non smoker - p8


title: Airway epithelial cells - COPD2 - p10

value: moderate COPD


title: U5_YAP1-MAMLD1 rep3

description: U5 neural stem cells transduced with pLJM1-YAP1-MAMLD1-PGK-Puro rep 3

tag: cell line

value: human neural stem cell line


title: U5_YAP1-FAM118B rep3

description: U5 neural stem cells transduced with pLJM1-YAP1-FAM118B-PGK-Puro rep 3


title: Airway epithelial cells - COPD2 - p8


title: Airway epithelial cells - smoker - p7


title: Airway epithelial cells - COPD2 - p7


title: GEP-NETs Patient24_G1

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent microarray scanner (G2565BA, Agilent)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent)  using default parameters.

source_name: Tumor tissue

label_protocol: The miRNA expression levels were assessed using SurePrint G3 Human Microarray Agilent Human 8x60K miRNA Microarray (Agilent Technologies) based on Sanger miRBase release 21, according to the manufacturer’s instructions. Briefly, 100 ng of total RNA isolated from FFPE section of 18 NENs patients were firstly dephosphorylated with a calf intestine alkaline phosphatase treatment for 30 minutes at 37°C before labeling. Samples were diluted with DMSO, denatured for 10 minutes at 100°C, and labeled using pCp-Cy3 in T4 RNA ligation buffer.

growth_protocol: No growth

extract_protocol: Total RNA, including small RNA fraction, was isolated from FFPE section of 5 µm-thickness using miRNeasy FFPE kit (Qiagen) according to the manufacturer’s protocol. Total RNA was then eluted in ribonuclease-free water. The RNA concentration was determined with NanoDrop ND-2000 Spectrophotometer (Nanodrop Technologies).

treatment_protocol: No treatment

tag: disease state

value: Gastroenteropancreatic neuroendocrine tumors (GEP-NETs)

tag: sample tissue

value: FFPE tissue

tag: gender

value: Female

tag: tumor grade

tag: tumor localization

value: Stomach


title: Airway epithelial cells - smoker - p6

tag: cell type


title: Airway epithelial cells - Non smoker - p7


title: U5_YAP1-MAMLD1 rep2

description: U5 neural stem cells transduced with pLJM1-YAP1-MAMLD1-PGK-Puro rep 2


title: GEP-NETs Patient23_G1

value: Male


title: U5_wild type TFE3 rep3

description: U5 neural stem cells transduced with pLJM1-wtTFE3-PGK-Puro rep 3

source_name: U5_wild type TFE3


title: GEP-NETs Patient22_G2

value: Duodenum


title: U5_YAP1-MAMLD1 rep1

description: U5 neural stem cells transduced with pLJM1-YAP1-MAMLD1-PGK-Puro rep 1


title: Airway epithelial cells - Non smoker - p6


title: Airway epithelial cells - smoker - p4


title: GEP-NETs Patient19_G3


title: GEP-NETs Patient21_G2

value: Pancreas


title: Airway epithelial cells - smoker - p5


title: U5_wild type TFE3 rep2

description: U5 neural stem cells transduced with pLJM1-wtTFE3-PGK-Puro rep 2


title: U5_YAP1-FAM118B rep1

description: U5 neural stem cells transduced with pLJM1-YAP1-FAM118B-PGK-Puro rep 1


title: Airway epithelial cells - COPD4 - p9

value: very severe COPD


title: Airway epithelial cells - COPD2 - p6


title: Airway epithelial cells - COPD2 - p9


title: GEP-NETs Patient18_G3

value: Liver


title: GEP-NETs Patient16_G3


title: Airway epithelial cells - COPD2 - p5


title: GEP-NETs Patient15_G1


title: Airway epithelial cells - smoker - p3


title: Airway epithelial cells - COPD2 - p4


title: U5_wild type FAM118B rep1

description: U5 neural stem cells transduced with pLJM1-wtFAM118B-PGK-Puro rep 1

source_name: U5_wild type FAM118B


title: Airway epithelial cells - COPD1 - p6


title: U5_wild type FAM118B rep3

description: U5 neural stem cells transduced with pLJM1-wtFAM118B-PGK-Puro rep 3


title: U5_wild type MAMLD1 rep2

description: U5 neural stem cells transduced with pLJM1-wtMAMLD1-PGK-Puro rep 2

source_name: U5_wild type MAMLD1


title: U5_wild type FAM118B rep2

description: U5 neural stem cells transduced with pLJM1-wtFAM118B-PGK-Puro rep 2


title: Airway epithelial cells - Non smoker - p5


title: Airway epithelial cells - smoker - p2


title: GEP-NETs Patient11_G1


title: Airway epithelial cells - COPD4 - p8


title: U5_wild type TFE3 rep1

description: U5 neural stem cells transduced with pLJM1-wtTFE3-PGK-Puro rep 1


title: GEP-NETs Patient14_G3

value: Small intestine


title: Airway epithelial cells - COPD4 - p7


title: Airway epithelial cells - COPD2 - p1


title: U5_wild type MAMLD1 rep3

description: U5 neural stem cells transduced with pLJM1-wtMAMLD1-PGK-Puro rep 3


title: U5_wild type MAMLD1 rep1

description: U5 neural stem cells transduced with pLJM1-wtMAMLD1-PGK-Puro rep 1