title: Male_cortex_6w_WT_nuclear_RNAseq_rep2

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

description: nuclear total RNA

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq, the FASTQ files of each samples were mapped to the mouse mm10 genome by STAR (version 2.3.0) using the parameters of "--outFilterMultimapNmax 1 --outFilterMismatchNmax 3". The number of reads mapped to the whole gene body of each gene were counted using Perl scripts generated in-house. All comparisons were performed by the edgeR and DEseq2 R packages, and FDR < 0.05 was the criteria used to identify differentially expressed genes. For each comparison, the results from edgeR and DESeq2 were merged to avoid method-based biases. The mean fold changes and the mean FDRs generated from both methods were used for generating plots and heatmaps.
For GRO-seq, the FASTQ files of each samples were mapped to the mouse mm10 genome by STAR (version 2.3.0) using the parameters of "--outFilterMultimapNmax 1 --outFilterMismatchNmax 3". The number of reads mapped to the whole gene body of each gene were counted using Perl scripts generated in-house. All comparisons were performed by the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count for each gene

source_name: Cortex

growth_protocol: Experiments were conducted in accordance with the ethical guidelines of the US National Institutes of Health and with the approval of the Institutional Animal Care and Use Committee of the University of Pennsylvania. All of the experiments described were performed using mice on a congenic sv129:C57BL/6 background with the knock-in/transgenic alleles backcrossed to C57BL/6 mice (Charles River) for at least five generations, unless otherwise stated. Mice were housed in a standard 12h light/12h dark cycle with access to ample amounts of food and water.

extract_protocol:
Total RNA was prepared from FACS-isolated cortical nuclei of male mice at 6 weeks (TAVI, T158M, R106W, 2-3 mice pooled per biological replicate, 4 replicates each), male mice at 12 weeks (TAVI, T158M, 2 mice pooled per biological replicate, 3 replicates each), and female mice at 18 weeks (TAVI, T158M, R106W, single mouse per biological replicate, 2 replicates each). Nuclei were isolated from fresh cortical tissue for FACS as previously described under ice-cold and nuclease-free conditions. Mouse cortices were rapidly resected on ice and subjected to dounce homogenization in homogenization buffer (0.32M sucrose, 5mM CaCl2, 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton, 0.1mM EDTA, Roche Complete Protease Inhibitor without EDTA). Homogenates were layered onto a sucrose cushion (1.8M sucrose, 10mM Tris-HCl pH 8.0, 3mM MgAc2 Roche Complete Protease Inhibitor without EDTA) and centrifuged at 25,000 rpm at 4°C for 2.5 hours using a Beckman SW25.1 swinging bucket rotor. Nuclei were resuspended & washed once in blocking buffer (1x PBS, 0.5% BSA (Sigma A4503), RNasin Plus RNase Inhibitor (Promega)) and pelleted using a tabletop centrifuge at 5000 RCF at 4°C for 10 minutes. Nuclei were resuspended in blocking buffer to a concentration of ~6x106 nuclei/ml, blocked for 20 minutes at 4°C with rotation, then incubated with Streptavidin Dylight 650 (1:1000, Fisher 84547) and Alexa 488-conjugated anti-NeuN antibody (1:1000, Millipore MAB377X) for 30 minutes at 4°C with rotation. After a 5-minute incubation with 1:1000 DAPI to enable singlet detection during FACS, labeled nuclei were washed for an additional 30 minutes at 4°C with blocking buffer, pelleted and resuspended in blocking buffer with 1% BSA. A BD Biosciences Influx cell sorter at the University of Pennsylvania Flow Cytometry and Cell Sorting Facility was used to identify cell type-specific populations of nuclei, and 1.2 – 2.5 x105 singlet nuclei from specified populations were directly sorted into Qiagen Buffer RLT Plus for immediate lysis and stabilization of RNA transcripts. Total nuclear RNA was processed using the Qiagen AllPrep DNA/RNA mini kit according to manufacturer instructions, with exception to the on-column DNaseI treatment. RNA was eluted from RNeasy mini spin columns and treated with DNaseI (Qiagen 79254) for 25 minutes at room temperature, then precipitated with glycogen/NaOAc and stored in ethonal at -80°C. Ethanol precipitation of nuclear RNA was carried out to completion prior to initiating RT-PCR or RNA-seq library construction.
For RNA-seq, the total amount of RNA isolated from a single aliquot of sorted nuclei wasused as input for library construction; hence differential gene expression comparisons betweenFACS-isolated Mecp2 control and mutant neurons is performed using RNA from equivalentnumbers of neuronal nuclei. Total RNA was depleted of ribosomal RNAs, subjected to 5minutes of heat fragmentation, and converted to strand-specific cDNA libraries using the TruSeqTotal RNA library prep kit with RiboZero depletion (Illumina). Multiplexed libraries weresequenced at the University of Pennsylvania Next Generation Sequencing Core facility using anIllumina HiSeq 2000/2500 that typically yielded 30-40M total reads per library.

tag: gender

value: male

tag: age

value: 6 week

tag: genotype

value: WT (TAVI)

value: Cortical cells


title: neural stem cells H12

status: Public on Jun 05 2019

type: SRA

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

country: USA

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Trimmomatic – 0.35 – Paired reads were trimmed using the following parameters: SLIDINGWINDOW:4:20 MINLEN:36 LEADING:20 TRAILING:20
Reads were aligned using Star 2.5.0b - runMode = alignReads, quantMode = GeneCount, outSAMstrandField = intronMotif
Htseq-count – parameters: -r  = pos,  -i = gene_id, -a = 10,  --stranded=no,  -f = bam
Genome_build: GRCh38
Supplementary_files_format_and_content: glio_chrom_instability_normalized_expression_matrix.tsv

molecule: polyA RNA

organism: Homo sapiens

source_name: neural stem cells

growth_protocol: Cells were grown in serum-free culture conditions as described in Pollard et al, Cell Stem Cell, 568-580, 2009.

extract_protocol:
Single cells were caputured, lysed, and cDNA prepared using the C1 Single Cell Auto Prep system from Fluidigm.
Single Cell RNA seq libraries were prepared for sequencing using Illumina Nextera XT DNA sample prep kit as per the C1-RNA seq protocol.

treatment_protocol: The cells were dissociated, filter strain with 40µm, resuspended in the serum free culture medium.

tag: cell type

value: normal neural stem cells

tag: type

value: diploid

tag: cell line


title: AQF_3

type: RNA

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

country: France

institute: IHU-CRCM

description: SAMPLE 3

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis, Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours,

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner  G2505C, Image analysis and correction of intra-array signals were performed with the Feature Extraction Software10,7,3,1 (Agilent Technologies),

data_processing: Microarray data analysis was performed using the GeneSpring software, Raw data were filtered and normalized, unsupervised and supervised analyses were done using hierarchical clustering, principal composant analysis (PCA) and the signicantly modulated genes using GeneSpring Software (Agilent Technologies), Genes were considered to be differentially expressed when fold change (FC) was  FC ≥ 2 with p-value (p) was p < 0,001 in at least one of the 3 pair combination. Gene Ontology (GO) annotations attributed to biological processes and corrected p ≤ 0,001 (Bonferroni correction) allow us to identify the biological functions that were modulated,

molecule: total RNA

source_name: Acute Q Fever patient

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies

growth_protocol: RNAs were extracted from whole blood (PAXgene tubes, Qiagen, Courtaboeuf, France) with PAXgene kit with a DNase I treatment to eliminate DNA contaminants and according to the recommendations of the manufacturer (Qiagen, Courtaboeuf, France)

extract_protocol: RNA was extracted using an PAXgene kit (Qiagen, Courtaboeuf, France), The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France), The RNA was eluted in 30 µl of water and stored at -80°C,

treatment_protocol: Whole blood prelevment was realized on PAXgene tubes where RNAs extraction were performed

tag: subject status

value: Acute Q fever

tag: tissue

value: Whole blood

tag: sample group id


title: neural stem cells H11


title: neural stem cells H05


title: neural stem cells H04


title: AQF_7

description: SAMPLE 7


title: gun1-101 lincomycin treatment, biological rep3

city: Potsdam

first: Guo-Zhang

last: Wu

state: Brandenburg

address: Am Muehlenberg 1

country: Germany

institute: Max-Planck Institute of Molecular Plant Physiology

description: Gene expression data from gun1-101 mutant seedlings grew 5 days in the dark followed by 2 days in continuous light with 0.5 mM lincomycin.

hyb_protocol: Hybridization and washing were performed according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using Genechip scanner.

data_processing: The raw data were analysed and normalized at the gene level with the RMA algorithm of the Expression Console v1.3 (Affymetrix).

label: biotin

organism: Arabidopsis thaliana

source_name: gun1-101 mutant seedlings grew in the presence of lincomycin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Seeds were sow on 1/2 MS plates with or without 0.5 mM lincomycin and stratified for 2 days in the dark at 4 oC prior to germination. The seeds were first incubated for 8 h in the light to promote germination and then grown in the dark for 5 days followed by 2 days in continuous light.

extract_protocol: Total RNA was extracted with NucleoSpin® RNA Plant kit (Macherey-Nagel) performed according to the manufacturer's instructions.

treatment_protocol: The seeds were directly sow on the plates without (control) or with 0.5 mM lincomycin.

value: seedlings

value: 7 days


title: AQF_2

description: SAMPLE 2


title: gun1-101 lincomycin treatment, biological rep1


title: gun1-101 lincomycin treatment, biological rep2


title: AQF_1

description: SAMPLE 1


title: neural stem cells H02


title: gun1-101 control, biological rep2

description: Gene expression data from gun1-101 mutant seedlings grew 5 days in the dark followed by 2 days in continuous light without lincomycin

source_name: gun1-101 mutant seedlings grew in the absence of lincomycin


title: hASC transduced with LV#19 (silencing of GARP), replica 2

city: Granada

first: Per

last: Anderson

state: Granada

address: Avenida de las Fuerzas Armadas, Nº 2

department: Servicio de Análisis Clínicos e Inmunología

country: Spain

institute: Hospital Universitario Virgen de las Nieves

hyb_protocol: Standard Illumina Human-HT12 Version 4

scan_protocol: Standard Illumina Genome Studio

data_processing: The data were background corrected and normalized using the Limma package

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Passage 3 hASCs from three unrelated healthy donors were obtained from the Biobanco del Sistema Sanitario Público de Andalucía (Parque Tecnológico Ciencias de la Salud, Centro de investigación Biomédica, Granada, Spain). Cells were were plated at 10,000 cells/cm2 in complete advanced DMEM (supplemented with 10% FCS (Invitrogen, Carlsbad, CA), Glutamax and 100U/ml penicillin/streptomycin (both from GIBCO, Life Technologies, CA), and cultured at 21% O2/5% CO2 at 37°C. Cells were passaged every 3-4 days.

extract_protocol: RNA was extracted high pure RNA isolation kit from Roche, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: LVs encoding two human GARP-specific shRNAs (MISSION® shRNA plasmid DNAs, RefSeq: SHCLND-NM_005512; Sigma-Aldrich) were used, referred to in the manuscript as LV#18 (TRCN0000005218) and LV#19 (TRCN0000005219). A MISSION® pLKO.1-puro non-mammalian shRNA control plasmid (Sigma-Aldrich, MO, USA) was used as control. LVs were produced by co-transfecting 293T cells with: 1) vector LV-shRNA/LV-GARP/LV-CEWP plasmid, 2) packaging plasmid pCMVΔR8.91 and 3) envelope plasmid pMD.G. The viruses were subsequently concentrated (x25) using centrifugal filter devices (Amicon Ultra-15, 100 kD, Merck). For transduction of MSCs, 0.7 x 106 cells (passage 4-6) were gently mixed with the concentrated LVs in a 15 ml tube, left at room temperature for 10 minutes and subsequently seeded in 6-well plates and maintained at 21% O2/5% CO2 at 37°C for 5 hours. Cells were then washed to remove the LVs, seeded in T75 flasks and incubated at 21 O2/5% CO2 at 37°C. NT, LV-CTRL, LV#18, LV#19 ASCs were harvested 6 days after transduction and mixed with RNAlater®. The purification and quality control of RNA and the microarray experiments was performed by the Unidad de Genómica y Genotipado (www.genyo.es) at GENYO, PTS, Granada.

value: adipose-tissue derived multipotent mesenchymal stromal cells

tag: treatment


title: gun1-101 control, biological rep3


title: hASC transduced with LV#19 (silencing of GARP), replica 3


title: hASC transduced with LV#18 (silencing of GARP), replica 2


title: mRNA_Psng-1_rde-4_SC_Neurons_R4

city: Tel Aviv

first: Itai

middle: Antoine

last: Toker

address: Haim levanon St.

department: Neurobiology

country: Israel

institute: Tel Aviv University

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - Butter
Filter-20-23 bp
Counting - HTseq_count
Comparisons - DESeq2
Genome_build: WS220/ce10
Supplementary_files_format_and_content: HTseq_count output files

organism: Caenorhabditis elegans

growth_protocol: 20C (or25C when noted), fed on E.coli OP-50 bacteria

extract_protocol:
TRIZOL
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® or TruSeq Small RNA Library Prep Kit, Nextera XT DNA Library Preparation Kit for mRNA

treatment_protocol: Transgenic expression

tag: strain

value: BFF 32

value: Neurons

tag: genotype/variation

tag: temperature


title: hASC transduced with LV#18 (silencing of GARP), replica 1


title: hASC non-transduced, replica 3

value: non-transduced


title: hASC transduced with LV#18 (silencing of GARP), replica 3


title: Col-0 lincomycin treatment, biological rep2

description: Gene expression data from wild type seedlings grew 5 days in the dark followed by 2 days in continuous light with 0.5 mM lincomycin.

source_name: Wild type (Col-0) seedlings grew in the presence of lincomycin


title: gun1-101 control, biological rep1


title: hASC transduced with LV-CTRL, replica2

value: transduced with LV-CTRL


title: neural stem cells H01


title: hASC non-transduced, replica 1


title: hASC transduced with LV-CTRL, replica3


title: F3_Psng-1_rde-4_SC_Whole_Worms_R3

value: BFF 12

value: Whole animal

tag: generation

value: F3 of heterozygote BFF16


title: hASC transduced with LV-CTRL, replica1


title: mRNA_Psng-1_rde-4_SC_Neurons_R3


title: hASC non-transduced, replica 2


title: hASC transduced with LV#19 (silencing of GARP), replica 1


title: mRNA_Psng-1_rde-4_SC_Neurons_R1


title: mRNA_Psng-1_rde-4_SC_Neurons_R2


title: mRNA_rde-4_Neurons_R4

value: BFF 31


title: Col-0 lincomycin treatment, biological rep3


title: mRNA_rde-4_Neurons_R3


title: neural stem cells G11


title: mRNA_rde-4_Neurons_R1


title: mRNA_rde-4_Neurons_R2


title: mRNA_WT_Neurons_R4

value: BFF 30 (outcrossed OH10690)


title: Col-0 control, biological rep3

description: Gene expression data from wild type seedlings grew 5 days in the dark followed by 2 days in continuous light without lincomycin

source_name: Wild type (Col-0) seedlings grew in the absence of lincomycin


title: neural stem cells G09


title: 24 h-treated, replicate B RNA-seq

city: Baltimore

first: Daniel

last: Goldman

state: Maryland

address: 725 N. Wolfe St.

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

data_processing:
adaptor removed with skewer
low quality reads (Phred score less than 10) removed
reads less than 10 nt long removed
reads mapped to the CDS of hg38 canonical transcripts + reporter transcript using STAR, excluding reads in the first 25 codons and last 10 codons
genes with average of at least 64 counts across both footprint and RNA-seq samples were included for downstream analysis
translation efficiency (TE) was calculated as the ratio of library size-normalized footprint counts (RPKM) in the coding sequence to RNA-seq RPKM in the coding sequence. TE fold change was then calculated as the average TE of 24 hr CHX-treated duplicates divided by the average TE of 15 min CHX-treated duplicates
Genome_build: hg38 canonical transcripts + nano luciferase reporter transcript
Supplementary_files_format_and_content: for both ribosome footprints and RNA-seq, a tab-separated file of RPKM for each sample
Supplementary_files_format_and_content: a comma-separated file of calculated TE values for each gene included in the analysis

source_name: 24 h-treated, HeLa cells

growth_protocol: HeLa cells grown in DMEM with high glucose, 10% FBS, 1% non-essential amino acids, 1% penicillin-streptomycin

extract_protocol:
At each time point, cells were placed on ice, washed with 10 mL ice-cold PBS with 100 μg/mL CHX, and lysed in plate in 400 uL of cold lysis buffer (20 mM Tris, pH.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 1% Triton X-100; 50 μg/mL emetine; 25 U/mLTurbo DNase [Thermo Fisher Scientific]). Cells were then scraped off the plate, transferred to a 1.5 mL tube, and incubated on ice for 5 min. Cell debris was pelleted at 16,000 x g for 10 min at 4°C. The resulting supernatant was then snap frozen in liquid nitrogen before storing at -80°C.
Ribosome profiling was performed as previously described (Ingolia et al. 2012) with minor modifications. Briefly, cell lysates were thawed, treated with RNase I, and then pelleted over a 1 M sucrose cushion containing 100 μg/mL emetine. RNA was then size-selected by excising between the 15 and 34 nt marker oligonucleotides, and ligated to the Universal miRNA Cloning Linker (NEB). rRNA depletion was then performed using the RiboZero rRNA Removal Kit (Human version, Illumina), followed by reverse transcription, circularization, and PCR amplification. For RNA-seq, total RNA was extracted from thawed cell lysates. Libraries were then made from 0.3 μg of total RNA using the TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions, and amplified by PCR for 10 cycles. All libraries were sequenced on a HiSeq 2500 system at the Genetic Resource Core Facility of the Johns Hopkins University School of Medicine

treatment_protocol: HeLa cells were seeded in duplicate for each time point in 10 cm plates with 10 mL media. After 24 hr, cells (~50% confluency) were transfected with 5 μg of GUG-nLuc plasmid DNA using Viafect (Promega) at a 2:1 (reagent:DNA) ratio following the manufacturer’s protocol. 24 hr later, media was replaced with fresh media containing 100 μg/mL CHX and cells were grown for 15 min or 24 hr.

value: HeLa

value: CHX

tag: time


title: neural stem cells G08

value: normal neural stem cells

value: diploid


title: mRNA_WT_Neurons_R1


title: mRNA_WT_Neurons_R3


title: mRNA_WT_Neurons_R2


title: mRNA_Psng-1_rde-4_sid-1_Gonads_R3

source_name: sid-1(qt-9) ; rde-4 (ne299); Psng-1::rde-4 (Pan-neuronal rescue)

value: BFF 33

value: Gonads


title: neural stem cells G10


title: mRNA_Psng-1_rde-4_sid-1_Gonads_R2

value: sid-1(qt-9) ; rde-4 (ne299); Psng-1::rde-4 (Pan-neuronal rescue)


title: 15 min-treated, replicate B RNA-seq

source_name: 15 min-treated, HeLa cells

value: 15 min


title: mRNA_sid-1_rde-4_Gonads_R3

value: BFF 13


title: 15 min-treated, replicate A RNA-seq


title: 24 h-treated, replicate A RNA-seq


title: neural stem cells G06


title: mRNA_Psng-1_rde-4_sid-1_Gonads_R1


title: neural stem cells G03


title: mRNA_sid-1_rde-4_Gonads_R1


title: mRNA_sid-1_rde-4_Gonads_R2


title: Vehicle-treated, replicate A RNA-seq

source_name: Vehicle-treated, HeLa cells

value: control


title: neural stem cells F11


title: F3_mRNA_Psng-1_rde-4_SC_Gonads_R2


title: neural stem cells G01


title: Vehicle-treated, replicate B RNA-seq


title: Col-0 control, biological rep2

value: seedlings

value: 7 days


title: F3_mRNA_Psng-1_rde-4_SC_Gonads_R3

value: BFF 12


title: neural stem cells F10


title: Col-0 control, biological rep1


title: F3_mRNA_Psng-1_rde-4_SC_Gonads_R1


title: 24 h-treated, replicate B footprints

data_processing:
Library strategy: Ribosome footprinting
adaptor removed with skewer
low quality reads (Phred score less than 10) removed
reads less than 10 nt long removed
reads mapped to the CDS of hg38 canonical transcripts + reporter transcript using STAR, excluding reads in the first 25 codons and last 10 codons
genes with average of at least 64 counts across both footprint and RNA-seq samples were included for downstream analysis
translation efficiency (TE) was calculated as the ratio of library size-normalized footprint counts (RPKM) in the coding sequence to RNA-seq RPKM in the coding sequence. TE fold change was then calculated as the average TE of 24 hr CHX-treated duplicates divided by the average TE of 15 min CHX-treated duplicates
Genome_build: hg38 canonical transcripts + nano luciferase reporter transcript
Supplementary_files_format_and_content: for both ribosome footprints and RNA-seq, a tab-separated file of RPKM for each sample
Supplementary_files_format_and_content: a comma-separated file of calculated TE values for each gene included in the analysis


title: neural stem cells G07


title: neural stem cells F08


title: Col-0 lincomycin treatment, biological rep1


title: mRNA_Psng-1_rde-4_SC_Gonads_R1

value: BFF 16


title: mRNA_Psng-1_rde-4_SC_Gonads_R2


title: mRNA_rde-4_Gonads_R2


title: 15 min-treated, replicate B footprints


title: mRNA_rde-4_Gonads_R1


title: neural stem cells F07


title: 15 min-treated, replicate A footprints


title: 24 h-treated, replicate A footprints


title: Vehicle-treated, replicate B footprints


title: neural stem cells F05


title: HC_Psng-1_rde-4_F3_R2

value: Whole animal

value: F3 of BFF14


title: HC_Psng-1_rde-4_F3_R1


title: HC_Psng-1_rde-4_F3_R3


title: HC_Psng-1_rde-4_F1_R3

value: F1 of BFF14


title: mRNA_Psng-1_rde-4_SC_Gonads_R3


title: HC_Psng-1_rde-4_F1_R2


title: neural stem cells F02


title: HC_Psng-1_rde-4_F1_R1


title: Vehicle-treated, replicate A footprints

value: HeLa


title: neural stem cells F03


title: HC_Psng-1_rde-4_P0_R2

value: BFF 14


title: HC_Psng-1_rde-4_P0_R1


title: neural stem cells E10

value: normal neural stem cells


title: mRNA_rde-4_Gonads_R3


title: atac_klrg1_ILCP_rep2

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

library_source: genomic

data_processing:
Reads were aligned using bowtie2 with default parameters. Paired alignments spanning more than 1000 bp were filtered from the alignments.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
MACS2 software was used to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak calling files (.txt)

molecule: genomic DNA

source_name: Peripheral blood

extract_protocol:
Lymphocyte fractions were obtained from peripheral blood samples (buffy coats) donated by anonymous healthy donors. Cells were FACS-sorted using specific antibodies and YFP as described in detail in the manuscript.
Nextera DNA library construction (as described in Buenrostro et al. Nature Methods 2013).

value: FACS-purified lymphocytes

tag: markers


title: neural stem cells E11

value: diploid


title: atac_klrg1_ILCP_rep3


title: HC_Psng-1_rde-4_P0_R3


title: rde-4_whole_worm_R5

source_name: rde-4(ne299) mutant

value: rde-4(ne299) mutant


title: atac_klrg1_ILCP_rep1


title: rde-4_whole_worm_R4


title: atac_ILC2_rep3


title: Psng-1_rde-4_sid-1_Gonads_R2

value: BFF 33

value: Gonads


title: atac_ILC2_rep2


title: Psng-1_rde-4_sid-1_Gonads_R1


title: sid-1_rde-4_Gonads_R2

value: BFF 13


title: sid-1_rde-4_Gonads_R1


title: neural stem cells E07


title: atac_ILC2_rep1


title: neural stem cells E05


title: Psng-1_rde-4_SC_Gonads_R2


title: Psng-1_rde-4_SC_Gonads_R1


title: neural stem cells E04


title: F3_Psng-1_rde-4_SC_Gonads_R1

value: F3 of heterozygote BFF16


title: MJ5

city: pullman

first: Shuwen

last: Zhang

state: WASHINGTON

address: 1815 Ferdinand’s Lane

institute: Washington State University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat genome using the aligner TMAP. The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: *txt: Tab-delimited text files include normalized counts for each Sample.

organism: Rattus norvegicus

source_name: hypothalamus

extract_protocol:
Total RNA was harvested using Trizol reagent.
WTTS libraries were constructed based on our protocols. The WTTS method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, Size selection and PCR amplification.

tag: strain/background

value: Long-Evans

value: Brain (hypothalamus)

tag: developmental stage

value: Adult

value: Vaporized CPM exposure


title: neural stem cells E02


title: MJ3


title: neural stem cells D12


title: MJ2


title: nerd-1+T rep2

city: Perpignan

first: Thierry

last: Lagrange

address: 58 Avenue Paul Alduy

institute: CNRS

data_processing:
Filtering out of reads corresponding to chloroplastic, mitochondrial and rRNA genes was performed with Bowtie 2 v2.3.4 in sensitive local mode (Langmead and Salzberg, 2012).
Remaining reads were mapped against the TAIR 10 genome using gtf annotation file and default parameters of TopHat2 v2.0.7 (Kim et al, 2013).
Assembly and transcript quantification were performed with Cufflinks v2.2.1 (Trapnell et al, 2010). Finally, the low expressed transcripts - less than 1 rpkm (reads per kilobase per million mapped reads) in one of the libraries are filtered out.
The differential analysis  was conducted by Cuffdiff software, belonging to the Trapnell suite.

source_name: Seedlings

extract_protocol:
Total RNA were extracted from 14 day-old seedlings for Col0, nerd-1 and nerd-1-T plants using the RNeasy Plant Mini Kit and treated onto the column with the RNase-Free DNase Set. Two replicates were performed per line. PolyA purification, library preparation using the Illumina TruSeq stranded mRNA kit and library quality controls were performed by Fasteris SA.
RNA libraries were prepared for sequencing by Fasteris SA using standard Illumina protocols. Sequencing was performed using Illumina procedure with  single reads, 1x 125bp and 21-52x106 reads per library

tag: ecotype

value: 14 day-old seedlings


title: nerd-1+T rep1


title: neural stem cells E08


title: rde-4_Gonads_R1

source_name: rde-4 (ne299) mutant

value: BFF 12

value: rde-4 (ne299) mutant


title: F3_Psng-1_rde-4_SC_Gonads_R2


title: rde-4_Gonads_R2


title: rde-4_Gonads_R3


title: MJ1


title: nerd-1 rep2


title: neural stem cells D11


title: neural stem cells D08


title: Psng-1_rde-4_SC_Neurons_R1

value: BFF 32

value: Neurons


title: neural stem cells D07

value: normal neural stem cells


title: Psng-1_rde-4_SC_Neurons_R2


title: neural stem cells E09


title: small RNA from Co-IP

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

description: RNA from Co-IP

data_processing:
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, sequence duplication and GC-content level of the clean data were calculated. Subsequently, the clean reads were mapped to the original Metarhizium robertsii genome sequences using the SOAP.
Supplementary_files_format_and_content: counts of small RNA sequences and counts of genes

organism: Metarhizium robertsii

source_name: WT

growth_protocol: Conidia of WT were inoculated into SDAY medium at 1×107 conidia/ml at 25°C. Fungal samples were collected after 2.5 days.

extract_protocol: RNAs were obtained from Co-IP.

value: ARSEF 24

tag: antibody

tag: age


title: Control4

value: Control


title: nerd-1 rep1


title: RNA from Co-IP

description: RNA from Co-IP

value: ARSEF 23


title: WT rep2

value: WT


title: rde-4_Neurons_R2

value: BFF 31


title: Control3


title: neural stem cells D06

tag: cell type

tag: type

value: diploid


title: rde-4_Neurons_R1


title: WT rep1


title: neural stem cells D04

tag: cell line


title: Control1

tag: tissue


title: neural stem cells D01


title: WT_Neurons_R2

value: BFF 30 (outcrossed OH10690)


title: Control

city: Annamalainagar

first: Roshni

last: Mary

address: Annamalainagar

department: Department of Genetics and Plant Breeding

country: India

institute: Annamalai University

data_processing:
The data quality was checked using FastQc and MultiQC. Adapter and low quality base trimming was performed using Fastp program.
Quality trimmed reads were mapped to Rice (O. sativa japonica) build MSU RGAP 7 using STAR 2 RNAseq aligner.
Expression values were estimated as read counts using Featurecounts.
Differential expression analysis was performed using DeSeq2
Genome_build: MSU RGAP 7
Supplementary_files_format_and_content: Read counts

organism: Oryza sativa

growth_protocol: Ten rice genotypes were screened for their ability to germinate under various EC conditions viz., 0, to 14 dSm-1. Distilled water used for control and saline concentrations were prepared using four salts namely NaCl, Na2SO42-, CaCl2 and MgSO42-. CARI Dhan 7 seeds were grown invivo for 14 days under different salt concentrations.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit. The Quality was checked using Bioanalyzer RNA 600 Nano kit and quantity was checked using Qubit HS RNA kit.
800 ng of Total RNA was used as input for NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB cat# E7490S) to enrich mRNA. Enriched mRNA was used for library preperation using  NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat no: NEB #E7770S).

treatment_protocol: The seeds germinated in salinity conditions of EC6 for a period of 14 days along with control using distilled water. The plant sample was used for further isolation and analysis. 100 mg plant material or 1 x 10^7 cells can generally be processed.

tag: cultivar

value: CARI Dhan 7

value: 14-days old seedlings

value: control


title: TreatedEC6

tag: treatment

value: salinity condition


title: WT_Neurons_R1

tag: strain


title: neural stem cells C11


title: neural stem cells C12


title: neural stem cells C09


title: neural stem cells C07


title: Control2

value: Long-Evans

value: Brain (hypothalamus)

value: Adult


title: cpsf30-3 rep2 (TL7)

data_processing:
Filtering out of reads corresponding to chloroplastic, mitochondrial and rRNA genes was performed with Bowtie 2 v2.3.4 in sensitive local mode (Langmead and Salzberg, 2012).
Remaining reads were mapped against the TAIR 10 genome using gtf annotation file and default parameters of TopHat2 v2.0.7 (Kim et al, 2013).
Assembly and transcript quantification were performed with Cufflinks v2.2.1 (Trapnell et al, 2010). Finally, the low expressed transcripts - less than 1 rpkm (reads per kilobase per million mapped reads) in one of the libraries are filtered out.
The differential analysis  was conducted by Cuffdiff software, belonging to the Trapnell suite.
Genome_build: TAIR10
Supplementary_files_format_and_content: transcripts-counts

extract_protocol:
Total RNA were extracted from 9 day-old seedlings for WT, fip37L, cpsf30-3 and cpsf30-1 mutant plants using the RNeasy Plant Mini Kit and treated onto the column with the RNase-Free DNase Set. Two replicates were performed per line. PolyA purification, library preparation using the Illumina TruSeq stranded mRNA kit and library quality controls were performed by Fasteris SA.
RNA libraries were prepared for sequencing bylocal BioEnvioenment NGS platform using standard Illumina protocols. Sequencing was performed using Illumina procedure with single-end reads ,1x 75bp and 35-50x106 reads per library

value: 9 day-old seedlings

tag: genotype/variation


title: cpsf30-1 rep1 (TL4)


title: cpsf30-1 rep2 (TL8)


title: fip37L rep2 (TL6)


title: neural stem cells C05


title: neural stem cells C06


title: Morpholino_7

city: Auckland

first: Veronika

last: Sander

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

data_processing:
Read quality was assessed using FastQC.
Reads were mapped and quantified together using Salmon ver. 0.8.2.
Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0.
Genome_build: GRCz11 (transcriptome)
Supplementary_files_format_and_content: raw_counts.csv: Comma-separated text file includes gene expression for each sample (non-normalised raw counts).

organism: Danio rerio

source_name: larval kidney

extract_protocol:
Approximately 50 3 dpf larvae were collected in 2 ml eppendorf tubes, the E3 embryo medium removed, replaced by 10 mM DTT (Sigma) in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I (Gibco) Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette, the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage, the larvae are disintegrated into chunks of tissue with intact, bright GFP-positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit (Macherey-Nagel), and instantly frozen to -80C until further processing.
RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols

tag: line


title: cpsf30-3 rep1 (TL3)


title: fip37L rep1 (TL2)


title: WT rep2 (TL5)


title: neural stem cells C04

source_name: neural stem cells


title: Morpholino_5


title: neural stem cells C03


title: MB_B3: Multispecies_Biofilm_B3

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

description: Gene expression after 96h Biofilm 3 sample 3 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described (One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies) For each hybridization, 600 ng of Cy3 probes were mixed and added to 5 µL of 10x Blocking Agent and Nuclease free water in a 25 µL reaction Then, 25 µL from 2x GExHybridization buffer was added and mixed carefully The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 h in a rotating Agilent hybridization oven After hybridization, microarrays were washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37ºC (1 min).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15K array slides

data_processing:
Images from Cy3 channel were equilibrated and captured with a high-resolution scanner (Agilent) and spots quantified using Feature Extraction software (Agilent)
Background correction and normalization of data expression were performed using LIMMA

organism: Porphyromonas gingivalis ATCC 33277

source_name: Planktonic culture of P. gingivalis ATCC 33278 grown within multispecies-biofilm

label_protocol: Fluorescently labeled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen)

growth_protocol: Planktonic cultures of P. gingivalis ATCC 33277, Streptococcus oralis CECT 907T, Actinomyces naeslundii ATCC 19039, Veillonella parvula NCTC 11810, Fusobacterium  nucleatum DMSZ 20482 and Aggregatibacter actinomycetemcomitans DSMZ 8324 were grown anaerobically at 37ºC for 24 h in a protein-rich medium containing brain-heart infusion (BHI)

extract_protocol:
After 96 h of incubation, both types of samples (multispecies biofilm and planktonic P. gingivalis) cells were harvested
Total RNA was extracted from the harvested samples listed above, using the TRIzol® Max Bacterial RNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA)
RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol:
Using pre-sterilized polystyrene 24-well tissue culture plates (Greiner Bio-one, Frikenhausen, Germany), two types of growing conditions were developed:  (1) The test group (P. gingivalis growing within a multispecies biofilm). In each well of the plate, 1.5 mL of the mix solution containing the six reference strains, were deposited together with a sterile ceramic calcium hydroxyapatite discs (HA) [7-mm diameter (standard deviation, SD = 0.2 mm) and 1.8 mm thickness (Clarkson Chromatography Products, Williamsport, PA, USA)];  (2) The control group (P. gingivalis growing planktonically). In each well, a volume of 1.5 mL of pure culture of P. gingivalis (10^8 CFUs/mL) was deposited in the absence of discs.
Plates were incubated in anaerobic conditions at 37°C for 96 h


title: PgP_A3: PlanktonicPg_A3

description: Gene expression after 96h Planktonic 3 sample 3 of 3

source_name: Planktonic culture of P. gingivalis ATCC 33277


title: Morpholino_4


title: WT rep1 (TL1)


title: PgP_A2: PlanktonicPg_A2

description: Gene expression after 96h Planktonic 2 sample 2 of 3

value: Planktonic culture of P. gingivalis ATCC 33277


title: Control_3

value: wild-type


title: PgP_A1: PlanktonicPg_A1

description: Gene expression after 96h Planktonic 1 sample 1 of 3


title: Ncviv_ENV_F2

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H.  (2012) SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217).
To generate transcriptome sequences, paired-end reads originating from roots and leaves from one individual plant of  Noccaea caerulescens subsp. fimiensis (Ncfi) and Noccaea montana (Nmon) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 30 (Ncfi), 24 (Nmon). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independent samples were mapped to the Ncfi_transcriptome_v1. using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: de novo transcriptome assembly:
Ncfi_transcriptome_v1.fasta
Nmon_transcriptome_v1.fasta

organism: Noccaea caerulescens

growth_protocol: Plant samples were collected in their natural environment (serpentine soil or zinc mining site). Leaves and roots were also collected from Noccaea caerulescens subsp. firmensis and Noccaea montana hydroponically grown (Araponics, Liège, Belgium) with modified Hoagland’s  solution, supplemented with 20 μM Fe-HBED and 37.5 μM NiCl2 during 7 weeks.

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini kit (Qiagen, Hilden, Germany) and treated with DNAseI.
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Environmental samples were stabilized in in RNAlater (Sigma). The stabilization solution was removed at the laboratory and samples were stored at -80°C before RNA extraction. Hydroponic culture samples were directly frozen in liquid nitrogen and stored  at -80°C before RNA extraction.

tag: subspecies/plant

value: Viviez

tag: phenotype

value: non-nickel-accumulator

tag: geographical location

value: Viviez, Aveyron, France

tag: gps location

tag: collection date

tag: sample type

value: Environmental sample

value: Leaf


title: neural stem cells B08

value: normal neural stem cells

value: diploid


title: MB_B2: Multispecies_Biofilm_B2

description: Gene expression after 96h Biofilm 2 sample 2 of 3

value: Planktonic culture of P. gingivalis ATCC 33278 grown within multispecies-biofilm


title: MB_B1: Multispecies_Biofilm_B1

description: Gene expression after 96h Biofilm 1 sample 1 of 3


title: Control_2


title: Control_1


title: Gpru_ENV_F3

description: environmental sample

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate transcriptome sequences, paired-end reads originating from one individual plant of Geissois pruinosa (Gpru) or Geissois racemosa  (Grac) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 30 (Gpru), 24 (Grac). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Gpru_transcriptome_v1 using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: Gpru_transcriptome_v1.fasta
Supplementary_files_format_and_content: csv with read counts

organism: Geissois pruinosa

source_name: Leaf

growth_protocol: Plant samples were collected in their natural environment (serpentine maquis, rainforest on limestone)

extract_protocol:
Total RNA were extracted from frozen leaves of one individual plant using a CTAB-PVP/LiAc method (Protocol#3, Johnson et al. 2012, PLoS ONE 7(11): e50226. doi:10.1371), and treated with DNAseI. RNA were stabilized with GenTegra-RNA for shipping
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Samples were rapidly frozen in liquid nitrogen upon collection and stored at -80°C before RNA extraction

value: nickel hyperaccumulator

value: Col de Plum, Mont-Dore, New Caledonia


title: Ckmm-Cre; Gna13 flox/flox, biological rep2

city: Seoul

first: Sang Geon

last: Kim

state: Not required for this country

address: 1 Gwanak-ro, Gwanak-gu

department: College of pharmacy

country: South Korea

institute: Seoul National University

description: Gna13MKO rep2

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). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix  Expression Console Software (EC).

organism: Mus musculus

source_name: Ckmm-Cre; Gna13 fl/fl, soleus

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

growth_protocol: Mouse soleus dissected at 18 weeks after birth

extract_protocol: Total RNA was isolated via TRIzol method. cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: Fasted overnight (14 h)

value: Ckmm-Cre; Gna13 flox/flox (Gna13 MKO)

tag: gender

value: male

value: soleus


title: Ncviv_ENV_F1


title: Ncfi_ENV_F2

value: subsp firmiensis

value: Puy de Wolf, Firmi, Aveyron, France


title: Barley-Shoot-SALT3

city: Hangzhou

first: Liangbo

last: Fu

state: Zhejiang

address: Yuhangtang Road 866

department: college of agriculture and biotechnology

institute: Zhejiang University

data_processing:
The cDNA fragments were amplified and enriched by PCR and purified with adapters ligated at both ends using Illumina TruSeqTM RNA Sample Preparation Kit (Illumina, San Diego, CA).
PCR products were loaded onto Illumina HiSeq2500 platform (Illumina, San Diego, CA) for 2×100 bp pair-ends sequencing.
Raw reads were trimmed by removing adaptor sequences, empty reads and low quality reads (Q<30 and length<50 bp) to get clean data.
Sequence annotation was performed using Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) based on the released reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html).
Transcript abundance of each gene was normalized by the fragments per kilo-base per million fragments mapped reads (FPKM) method,The ratio of [FPKM (treatment)]/[FPKM (control)] was calculated as the change fold for each gene. Differentially expressed genes (DEGs) were identified by following criterion: fold>2 and false discovery rate (FDR) <0.001. GO annotation and KEGG analysis were done using Blast2GO software version 3.2 (https://www.blast2go.com) based on the sequences of DEGs.
Genome_build: reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Hordeum vulgare

growth_protocol: Seeds of Tibetan wild barley accession XZ26 and Japonica rice cultivar Nipponbare were disinfected for 30 min with 2% H2O2, rinsed 5 times using distilled water and transferred onto moist filter paper in a germination box, then placed in a growth chamber (22/18 °C, day/night) in dark. After germination, the uniform seedlings of barley and rice were transplanted into 15 L black plastic containers filled with hydroponic solution as described by Fu et al (2018). All seedlings were grown in a controlled growth room at 26 °C of 14 h day/20 °C of 10 h night, with fluorescent lamps at 250 μmol m−2 s−1.

extract_protocol:
After 7 d of salt treatments, fresh roots and the latest completely expanded leaves of barley (XZ26) and rice (Nipponbare) were sampled from both salt treatment and control, and immediately stored in liquid nitrogen for further transcriptomic analysis. Three biological replicates were done. Total RNA was extracted from approximately 0.1 g fresh tissues using the TRIzol Reagent (Invitrogen, Carlsbad, CA), and then was purified by the RNeasy Mini Kit (Qiagen, Germantown, MD). The concentration of total RNA was determined by Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA).
The RNA library construction, sequencing and data processing were performed as described by Wang et al (2016). Briefly, mRNA enrichment was obtained from total RNA by poly-T oligo-attached magnetic beads and randomly fragmented into small pieces. Double-stranded cDNA was synthesized using mRNA fragments with random hexamer-primers. The cDNA fragments were amplified and enriched by PCR and purified with adapters ligated at both ends using Illumina TruSeqTM RNA Sample Preparation Kit (Illumina, San Diego, CA). Then, PCR products were loaded onto Illumina HiSeq2500 platform (Illumina, San Diego, CA) for 2×100 bp pair-ends sequencing. Raw reads were trimmed by removing adaptor sequences, empty reads and low quality reads (Q<30 and length<50 bp) to get clean data. Sequence annotation was performed using Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) based on the released reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html). For gene expression analysis, transcript abundance of each gene was normalized by the fragments per kilo-base per million fragments mapped reads (FPKM) method (Li et al., 2018). The ratio of [FPKM (treatment)]/[FPKM (control)] was calculated as the change fold for each gene. Differentially expressed genes (DEGs) were identified by following criterion: fold>2 and false discovery rate (FDR) <0.001. GO annotation and KEGG analysis were done using Blast2GO software version 3.2 (https://www.blast2go.com) based on the sequences of DEGs.

treatment_protocol: Salt treatment was initiated to barley and rice plants by increasing 50 mM NaCl a day to reach a final concentration at 100 mM in the hydroponics. The solution without NaCl addition was used as the control.

tag: developmental stage

value: seedling stage

tag: passages

tag: accession

value: Shoot

value: SALT (100 mM NaCl)


title: Ckmm-Cre; Gna13 flox/flox, biological rep1

description: Gna13MKO rep1

tag: age


title: neural stem cells B07

data_processing:
Trimmomatic – 0.35 – Paired reads were trimmed using the following parameters: SLIDINGWINDOW:4:20 MINLEN:36 LEADING:20 TRAILING:20
Reads were aligned using Star 2.5.0b - runMode = alignReads, quantMode = GeneCount, outSAMstrandField = intronMotif
Htseq-count – parameters: -r  = pos,  -i = gene_id, -a = 10,  --stranded=no,  -f = bam
Genome_build: GRCh38
Supplementary_files_format_and_content: glio_chrom_instability_normalized_expression_matrix.tsv

extract_protocol:
Single cells were caputured, lysed, and cDNA prepared using the C1 Single Cell Auto Prep system from Fluidigm.
Single Cell RNA seq libraries were prepared for sequencing using Illumina Nextera XT DNA sample prep kit as per the C1-RNA seq protocol.

tag: cell type

tag: type

tag: cell line


title: Gna13 flox/flox, biological rep2

description: WT rep2

source_name: Gna13 fl/fl, soleus

value: Gna13 flox/flox (WT)

tag: tissue


title: neural stem cells B06


title: Ckmm-Cre; Gna13 flox/flox, biological rep3

description: Gna13MKO rep3

tag: genotype/variation


title: Gna13 flox/flox, biological rep3

description: WT rep3


title: Ncfi_ENV_F1


title: Gpru_ENV_F2

description: environmental sample

value: Pont des Japonnais, Mont-Dore, New Caledonia


title: Gna13 flox/flox, biological rep1

description: WT rep1

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix  Expression Console Software (EC).. After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix  Expression Console Software (EC).


title: neural stem cells C02


title: neural stem cells B02


title: Gpru_ENV_F1

description: environmental sample

value: N'go, Mont-Dore, New Caledonia


title: Ncfi_Ni_R

value: Hydroponic culture

value: Root


title: Barley-Shoot-SALT2

tag: treatment


title: neural stem cells A12

value: normal neural stem cells

value: diploid


title: Barley-Shoot-SALT1


title: Ncfi_Ni_F

tag: subspecies/plant

value: nickel hyperaccumulator

value: Leaf


title: Barley-Shoot-CK3

value: CK (0 mM NaCl)


title: neural stem cells B01


title: neural stem cells A10


title: Barley-Shoot-CK2


title: neural stem cells A09


title: Barley-Shoot-CK1


title: neural stem cells A07


title: Barley-Root-SALT3


title: neural stem cells A05


title: Barley-Root-CK3


title: neural stem cells A04


title: Pgab_ENV_F3

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate transcriptome sequences, paired-end reads originating from one individual plant of Psychotria gabriellae (Pgab) or Psychotria semperflorens (Psem) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 30 (Pgab), 24 (Psem). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Pgab_transcriptome_v2 using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: Pgab_transcriptome_v2.fasta
Supplementary_files_format_and_content: csv file with read counts.

organism: Psychotria gabriellae

growth_protocol: Plant samples were collected in their natural environment (rain forest on serpentine soil)

tag: phenotype

value: Monts Koghi, Dumbea, New Caledonia


title: Psem_ENV_F1

organism: Psychotria semperflorens

value: nickel-non-accumulator

tag: geographical location

value: Monts Koghis, Dumbea, New Caledonia


title: Barley-Root-CK2


title: Pgab_ENV_F1

tag: gps location


title: Nmon_ENV_F2

organism: Thlaspi montanum

value: non-nickel-accumulator

value: Suc de Clava, Eteize, Ardeche, France

tag: collection date

value: Environmental sample


title: Nmon_Ni_R

tag: sample type


title: neural stem cells A03


title: Psem_ENV_F2

value: Riviere Blanche, Yate, New Caledonia


title: Grac_ENV_F2

description: environmental sample

organism: Geissois racemosa

value: Sarramea, New Caledonia


title: Nmon_Ni_F


title: Grac_ENV_F1

description: environmental sample

value: Mont Mou, Paita, New Caledonia


title: Barley-Root-CK1

value: seedling stage


title: Pgab_ENV_F2


title: Psem_ENV_F3


title: Grac_ENV_F3

description: environmental sample

value: Col Amieu, Sarramea, New Caledonia


title: Veins_E3

status: Public on Jun 04 2019

city: New York

first: Donghoon

last: Lee

state: NY

address: 1399 Park Ave

department: Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: mRNA/microRNA

data_processing:
Trim, QC, deduplication
Alignment (RNA-STAR v2.4.1a)
Alignment (novoalign)
Peak calling (Piranha v1.2.1)
Peak calling (CIMS)
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: HUVEC

growth_protocol: HUVEC and HUAEC cells were growth in EGM Bullet Kit mededium in culture ( 5 dishes treated with 0.2% gelatin)

extract_protocol:
Cells were lysated using PXL lysis buffer (1x PBS, 1% Igepal, 0.5% sodium deoxycholate, 0.1% SDS)
Libraries were prepared according to HITS-CLIP protocol (Chi et al. 2009)
HITS-CLIP

treatment_protocol: After 3 passage cells were washed and crossinked

tag: antibody

value: panAGO-2A8 (MABE56 Millipore)


title: Veins_E2

description: mRNA/microRNA


title: Arteries_L1

description: mRNA/microRNA

source_name: HUAEC


title: neural stem cells A01

city: Memphis

first: Doug

last: Green

address: 262 Danny Thomas Pl

value: normal neural stem cells


title: neural stem cells A06

value: diploid


title: Barley-Root-SALT2

tag: developmental stage

value: Root

value: SALT (100 mM NaCl)


title: Barley-Root-SALT1

tag: passages


title: Arteries_E3

description: mRNA/microRNA


title: Nmon_ENV_F1

value: Leaf


title: Arteries_E1

description: mRNA/microRNA


title: Veins_L2

description: mRNA/microRNA


title: antiCD4_1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: CD4 depleted

hyb_protocol: Agilent : 100.0 ng at 55 degree_C during 20 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Quantile normalization and differential analysis were performed using Limma package in R / Bioconductor.

source_name: CD4 depleted

label_protocol: Agilent - Low RNA input QuickAmp.

growth_protocol: Housing 4W in an enriched environement (EE)

extract_protocol: Total RNAs were extracted from hippocampus using miRNeasy Mini kit (Qiagen).

treatment_protocol: Treated with control or anti-CD4 antobodies

tag: strain

value: Hippocampi

tag: Sex

value: Female

value: 8 weeks


title: antiCD4_3

description: CD4 depleted

tag: age


title: CTRL_1

description: Control

source_name: Control


title: antiCD4_4

description: CD4 depleted


title: CTRL_4

description: Control


title: antiCD4_2

description: CD4 depleted


title: CTRL_2

description: Control


title: CTRL_3

description: Control


title: medullary tissue_12monthRegenDay21, rep1

city: Jupiter

first: Mathew

last: Pipkin

state: Florida

address: 130 Scripps Way

department: Immunology and Microbiology

institute: Scripps Research Institute

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 21 post castration

hyb_protocol: Fragmentation/hybridization to MOE430v2.0 arrays (Affymetrix) were performed according to Affymetrix protocols

scan_protocol: Imaging was performed on a Hewlett Packard GeneArray Scanner according to standard Affymetrix protocol

data_processing: Affymetrix moe430.2 microarray .cel files were processed with the rma algorithm from the affy package in R.

label: Biotin

source_name: 12 month old microdissected medullary thymic tissue 21 days post castration

label_protocol: Biotin-labeled cRNA probes were prepared as recommended by the manufacturer (Affymetrix), using oligo-dT primers, SuperScript, and BioArray High Yield RNA Transcript kits (Affymetrix).

extract_protocol: For microdissected tissues RNA was prepared using RNAqueous Micro kits (Ambion). For purified lymphoid cells RNA was prepared using RNeasy Mini Kits (Qiagen) according to recommended protocols

value: thymic medulla

tag: cell type

tag: cell phenotype

value: 12 month day 21 post castration

tag: genotype


title: cortical lymphocyte_12monthRegenDay23, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 23 post castration

source_name: 12 month old purified cortical thymic lymphocytes 23 days post castration

tag: tissue

value: cortical lymphocyte

value: CD3-/lo AND CD45+ AND (CD90+ OR CD117+)

value: 12 month day 23 post castration


title: cortical tissue_12monthRegenDay20, rep4

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 20 post castration

source_name: 12 month old microdissected cortical thymic tissue 20 days post castration

value: thymic cortex

value: 12 month day 20 post castration


title: cortical tissue_12monthRegenDay22, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 22 post castration

source_name: 12 month old microdissected cortical thymic tissue 22 days post castration

value: 12 month day 22 post castration


title: cortical tissue_12monthRegenDay20, rep2


title: medullary lymphocyte_12monthRegenDay23, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 23 post castration

source_name: 12 month old purified medullary thymic lymphocytes 23 days post castration

value: medullary lymphocyte

value: CD3hi AND CD45+


title: medullary tissue_12monthRegenDay20, rep4

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 20 post castration

source_name: 12 month old microdissected medullary thymic tissue 20 days post castration


title: medullary lymphocyte_12monthRegenDay21, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 21 post castration

source_name: 12 month old purified medullary thymic lymphocytes 21 days post castration


title: medullary tissue_12monthRegenDay20, rep3


title: cortical tissue_12monthRegenDay21, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 21 post castration

source_name: 12 month old microdissected cortical thymic tissue 21 days post castration


title: cortical lymphocyte_12monthRegenDay21, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 21 post castration

source_name: 12 month old purified cortical thymic lymphocytes 21 days post castration


title: medullary tissue_12monthRegenDay20, rep2


title: medullary tissue_12monthRegenDay20, rep5


title: cortical tissue_12monthRegenDay20, rep5


title: cortical tissue_12monthRegenDay20, rep3


title: cortical tissue_12monthRegenDay20, rep1


title: cortical lymphocyte_12monthRegenDay22, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 22 post castration

source_name: 12 month old purified cortical thymic lymphocytes 22 days post castration


title: medullary lymphocyte_12monthRegenDay22, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 22 post castration

source_name: 12 month old purified medullary thymic lymphocytes 22 days post castration


title: medullary tissue_12monthRegenDay22, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 22 post castration

source_name: 12 month old microdissected medullary thymic tissue 22 days post castration


title: medullary tissue_12monthRegenDay20, rep1


title: medullary tissue_12monthRegenDay23, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 23 post castration

source_name: 12 month old microdissected medullary thymic tissue 23 days post castration


title: cortical tissue_12monthRegenDay23, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 23 post castration

source_name: 12 month old microdissected cortical thymic tissue 23 days post castration


title: medullary lymphocyte_12monthRegenDay20, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 20 post castration

source_name: 12 month old purified medullary thymic lymphocytes 20 days post castration


title: medullary lymphocyte_12monthRegenDay20, rep4


title: medullary lymphocyte_12monthRegenDay20, rep2


title: medullary lymphocyte_12monthRegenDay20, rep5


title: cortical lymphocyte_12monthRegenDay20, rep5

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 20 post castration

source_name: 12 month old purified cortical thymic lymphocytes 20 days post castration


title: medullary lymphocyte_12monthRegenDay20, rep3


title: cortical tissue_12monthRegenDay19, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 19 post castration

source_name: 12 month old microdissected cortical thymic tissue 19 days post castration

value: 12 month day 19 post castration


title: cortical lymphocyte_12monthRegenDay18, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 18 post castration

source_name: 12 month old purified cortical thymic lymphocytes 18 days post castration

value: 12 month day 18 post castration


title: medullary tissue_12monthRegenDay18, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 18 post castration

source_name: 12 month old microdissected medullary thymic tissue 18 days post castration


title: medullary tissue_12monthRegenDay17, rep3

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 17 post castration

source_name: 12 month old microdissected medullary thymic tissue 17 days post castration

value: 12 month day 17 post castration


title: medullary lymphocyte_12monthRegenDay19, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 19 post castration

source_name: 12 month old purified medullary thymic lymphocytes 19 days post castration


title: medullary tissue_12monthRegenDay19, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 19 post castration

source_name: 12 month old microdissected medullary thymic tissue 19 days post castration


title: cortical lymphocyte_12monthRegenDay20, rep1


title: cortical lymphocyte_12monthRegenDay20, rep4


title: medullary tissue_12monthRegenDay17, rep2


title: cortical tissue_12monthRegenDay18, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 18 post castration

source_name: 12 month old microdissected cortical thymic tissue 18 days post castration


title: medullary tissue_12monthRegenDay17, rep1


title: cortical tissue_12monthRegenDay17, rep3

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 17 post castration

source_name: 12 month old microdissected cortical thymic tissue 17 days post castration


title: cortical lymphocyte_12monthRegenDay19, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 19 post castration

source_name: 12 month old purified cortical thymic lymphocytes 19 days post castration


title: cortical tissue_12monthRegenDay17, rep2


title: cortical tissue_12monthRegenDay17, rep1


title: cortical lymphocyte_12monthRegenDay17, rep3

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 17 post castration

source_name: 12 month old purified cortical thymic lymphocytes 17 days post castration


title: cortical lymphocyte_12monthRegenDay20, rep3


title: medullary lymphocyte_12monthRegenDay17, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 17 post castration

source_name: 12 month old purified medullary thymic lymphocytes 17 days post castration


title: medullary lymphocyte_12monthRegenDay17, rep2


title: cortical lymphocyte_12monthRegenDay20, rep2


title: cortical lymphocyte_12monthRegenDay17, rep2


title: medullary tissue_12monthRegenDay16, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 16 post castration

source_name: 12 month old microdissected medullary thymic tissue 16 days post castration

value: 12 month day 16 post castration


title: medullary lymphocyte_12monthRegenDay16, rep2

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 16 post castration

source_name: 12 month old purified medullary thymic lymphocytes 16 days post castration


title: medullary tissue_12monthRegenDay16, rep2


title: medullary lymphocyte_12monthRegenDay17, rep3


title: cortical tissue_12monthRegenDay16, rep2

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 16 post castration

source_name: 12 month old microdissected cortical thymic tissue 16 days post castration


title: cortical tissue_12monthRegenDay16, rep1


title: cortical lymphocyte_12monthRegenDay16, rep2

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 16 post castration

source_name: 12 month old purified cortical thymic lymphocytes 16 days post castration


title: cortical lymphocyte_12monthRegenDay17, rep1


title: medullary tissue_12monthRegenDay15, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 15 post castration

source_name: 12 month old microdissected medullary thymic tissue 15 days post castration

value: 12 month day 15 post castration


title: medullary lymphocyte_12monthRegenDay14, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 14 post castration

source_name: 12 month old purified medullary thymic lymphocytes 14 days post castration

value: 12 month day 14 post castration


title: cortical lymphocyte_12monthRegenDay14, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 14 post castration

source_name: 12 month old purified cortical thymic lymphocytes 14 days post castration


title: medullary tissue_12monthRegenDay14, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 14 post castration

source_name: 12 month old microdissected medullary thymic tissue 14 days post castration


title: cortical lymphocyte_12monthRegenDay16, rep1


title: medullary lymphocyte_12monthRegenDay16, rep1


title: medullary lymphocyte_12monthRegenDay13, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 13 post castration

source_name: 12 month old purified medullary thymic lymphocytes 13 days post castration

value: 12 month day 13 post castration


title: medullary lymphocyte_12monthRegenDay18, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 18 post castration

source_name: 12 month old purified medullary thymic lymphocytes 18 days post castration


title: cortical tissue_12monthRegenDay14, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 14 post castration

source_name: 12 month old microdissected cortical thymic tissue 14 days post castration


title: medullary lymphocyte_12monthRegenDay15, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 15 post castration

source_name: 12 month old purified medullary thymic lymphocytes 15 days post castration


title: cortical lymphocyte_12monthRegenDay13, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 13 post castration

source_name: 12 month old purified cortical thymic lymphocytes 13 days post castration


title: medullary lymphocyte_12monthRegenDay12, rep2

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 12 post castration

source_name: 12 month old purified medullary thymic lymphocytes 12 days post castration

value: 12 month day 12 post castration


title: medullary tissue_12monthRegenDay13, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 13 post castration

source_name: 12 month old microdissected medullary thymic tissue 13 days post castration

value: thymic medulla


title: cortical lymphocyte_12monthRegenDay12, rep3

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 12 post castration

source_name: 12 month old purified cortical thymic lymphocytes 12 days post castration

value: cortical lymphocyte


title: cortical tissue_12monthRegenDay12, rep2

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 12 post castration

source_name: 12 month old microdissected cortical thymic tissue 12 days post castration


title: cortical lymphocyte_12monthRegenDay15, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 15 post castration

source_name: 12 month old purified cortical thymic lymphocytes 15 days post castration

value: CD3-/lo AND CD45+ AND (CD90+ OR CD117+)


title: cortical tissue_12monthRegenDay12, rep3


title: medullary lymphocyte_12monthRegenDay12, rep3


title: medullary tissue_12monthRegenDay12, rep2

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 12 post castration

source_name: 12 month old microdissected medullary thymic tissue 12 days post castration


title: cortical lymphocyte_12monthRegenDay12, rep2


title: medullary tissue_12monthRegenDay12, rep3


title: cortical tissue_12monthRegenDay12, rep1


title: medullary lymphocyte_12monthRegenDay12, rep1


title: medullary tissue_12monthRegenDay12, rep1


title: cortical lymphocyte_12monthRegenDay12, rep1


title: cortical tissue_12monthRegenDay13, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 13 post castration

source_name: 12 month old microdissected cortical thymic tissue 13 days post castration


title: medullary lymphocyte_12monthRegenDay10, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 10 post castration

source_name: 12 month old purified medullary thymic lymphocytes 10 days post castration

value: 12 month day 10 post castration


title: cortical tissue_12monthRegenDay10, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 10 post castration

source_name: 12 month old microdissected cortical thymic tissue 10 days post castration

value: thymic cortex


title: cortical tissue_12monthRegenDay15, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 15 post castration

source_name: 12 month old microdissected cortical thymic tissue 15 days post castration


title: cortical tissue_12monthRegenDay11, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 11 post castration

source_name: 12 month old microdissected cortical thymic tissue 11 days post castration

value: 12 month day 11 post castration


title: medullary tissue_12monthRegenDay9, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 9 post castration

source_name: 12 month old microdissected medullary thymic tissue 9 days post castration

value: 12 month day 9 post castration


title: medullary lymphocyte_12monthRegenDay9, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 9 post castration

source_name: 12 month old purified medullary thymic lymphocytes 9 days post castration

value: medullary lymphocyte


title: medullary tissue_12monthRegenDay11, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 11 post castration

source_name: 12 month old microdissected medullary thymic tissue 11 days post castration


title: medullary lymphocyte_12monthRegenDay11, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 11 post castration

source_name: 12 month old purified medullary thymic lymphocytes 11 days post castration

value: CD3hi AND CD45+


title: cortical lymphocyte_12monthRegenDay10, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 10 post castration

source_name: 12 month old purified cortical thymic lymphocytes 10 days post castration


title: cortical lymphocyte_12monthRegenDay11, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 11 post castration

source_name: 12 month old purified cortical thymic lymphocytes 11 days post castration


title: medullary tissue_12monthRegenDay10, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 10 post castration

source_name: 12 month old microdissected medullary thymic tissue 10 days post castration


title: cortical tissue_12monthRegenDay9, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 9 post castration

source_name: 12 month old microdissected cortical thymic tissue 9 days post castration


title: medullary tissue_12monthRegenDay8, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 8 post castration

source_name: 12 month old microdissected medullary thymic tissue 8 days post castration

value: 12 month day 8 post castration


title: cortical lymphocyte_12monthRegenDay9, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 9 post castration

source_name: 12 month old purified cortical thymic lymphocytes 9 days post castration


title: cortical tissue_12monthRegenDay8, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 8 post castration

source_name: 12 month old microdissected cortical thymic tissue 8 days post castration


title: medullary lymphocyte_12monthRegenDay7, rep2

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 7 post castration

source_name: 12 month old purified medullary thymic lymphocytes 7 days post castration

value: 12 month day 7 post castration


title: medullary tissue_12monthRegenDay7, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 7 post castration

source_name: 12 month old microdissected medullary thymic tissue 7 days post castration


title: cortical tissue_12monthRegenDay7, rep2

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 7 post castration

source_name: 12 month old microdissected cortical thymic tissue 7 days post castration


title: cortical lymphocyte_12monthRegenDay8, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 8 post castration

source_name: 12 month old purified cortical thymic lymphocytes 8 days post castration


title: medullary lymphocyte_12monthRegenDay8, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 8 post castration

source_name: 12 month old purified medullary thymic lymphocytes 8 days post castration


title: medullary lymphocyte_12monthRegenDay7, rep1


title: medullary tissue_12monthRegenDay6, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old day 6 post castration

source_name: 12 month old microdissected medullary thymic tissue 6 days post castration

value: 12 month day 6 post castration


title: cortical tissue_12monthRegenDay7, rep1


title: medullary tissue_12monthRegenDay7, rep2


title: cortical lymphocyte_12monthRegenDay7, rep1

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 7 post castration

source_name: 12 month old purified cortical thymic lymphocytes 7 days post castration


title: cortical tissue_12monthRegenDay6, rep1

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old day 6 post castration

source_name: 12 month old microdissected cortical thymic tissue 6 days post castration


title: cortical tissue_12monthRegenDay6, rep2


title: medullary tissue_12monthRegenDay6, rep2


title: cortical lymphocyte_12monthRegenDay7, rep2


title: medullary tissue_12month, rep1

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 12 months old

source_name: 12 month old microdissected medullary thymic tissue

value: 12 month


title: medullary lymphocyte_12monthRegenDay6, rep3

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old day 6 post castration

source_name: 12 month old purified medullary thymic lymphocytes 6 days post castration


title: medullary tissue_12month, rep4


title: cortical lymphocyte_12monthRegenDay6, rep2

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old day 6 post castration

source_name: 12 month old purified cortical thymic lymphocytes 6 days post castration


title: medullary tissue_12month, rep3


title: medullary lymphocyte_12monthRegenDay6, rep2


title: cortical tissue_12monthRegenDay6, rep3


title: medullary lymphocyte_12monthRegenDay6, rep1


title: medullary tissue_12monthRegenDay6, rep3


title: cortical tissue_12month, rep2

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 12 months old

source_name: 12 month old microdissected cortical thymic tissue


title: cortical tissue_12month, rep3


title: cortical lymphocyte_12monthRegenDay6, rep1


title: cortical lymphocyte_12monthRegenDay6, rep3


title: cortical tissue_12month, rep4


title: medullary tissue_12month, rep2


title: medullary lymphocyte_12month, rep1

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 12 months old

source_name: 12 month old purified medullary thymic lymphocytes


title: medullary lymphocyte_12month, rep3


title: cortical tissue_12month, rep1


title: medullary lymphocyte_12month, rep2


title: medullary lymphocyte_12month, rep4


title: cortical lymphocyte_12month, rep3

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 12 months old

source_name: 12 month old purified cortical thymic lymphocytes


title: cortical lymphocyte_12month, rep4


title: cortical lymphocyte_12month, rep2


title: cortical lymphocyte_12month, rep1


title: medullary tissue_5week, rep4

description: Gene expression data from microdissected whole thymic medulla from C57bl6/J male mice 5 weeks old

source_name: 5 week old microdissected medullay thymic tissue

value: 5 week


title: medullary tissue_5week, rep1


title: Myo1A_Dam_3

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

institute: CECAD Research Center  Cologne

description: PCR product

data_processing:
Sequencing data were processed using the damidseq_pipeline (Marshall and Brand, 2015) to generate normalized gff files.
Ets21c binding peaks were identified using a peak finding program based on one described by Wolfram et al. (2012).
Transcribed genes, based on Dam-PolII occupancy, were identified using a Perl script based on the one described by Southall et al. (2013).
Scripts are available on request from Tony D. Southall.
Genome_build: dm3 (D. melanogaster)
Supplementary_files_format_and_content: Peak

organism: Drosophila melanogaster

source_name: Female adult intestine

growth_protocol: Virgins of esg-Gal4, UAS-GFP, tub-Gal80-TS and Myo1A-Gal4, UAS-GFP, tub-Gal80-TS were crossed to males of UAS-LT3-Dam, UAS-LT3-Dam-PolII and UAS-LT3-Dam-ets21c-RA. Crosses were kept at room temperature, adult offspring were collected for two days and mated for additional two days. Females were transferred to 29°C for three days to allow Dam-transgene expression.

extract_protocol:
DNA extraction from dissected midguts and sequencing of methylation-specific PCR amplicons was performed according to the Nature protocols on DamID-Seq published by Vogel et al. (2007) and Marshall et al. (2016).
Sequencing libraries were generated according to the Illumina protocol for ChIP-Seq library preparation. Samples were single-end sequenced on an Illumina HiSeq 2000 instrument at 50 bp read length.

value: Myo1A-Gal4 (EC)

tag: uas

value: Dam

tag: condition

value: Mated, 72 hours at 29°C


title: Myo1A_Dam_2

description: PCR product


title: Esg_Dam_3

description: PCR product

value: Esg-Gal4 (ISC/EB)


title: Myo1A_Dam_1

description: PCR product


title: medullary tissue_5week, rep2

value: thymic medulla


title: cortical tissue_5week, rep4

description: Gene expression data from microdissected whole thymic cortex from C57bl6/J male mice 5 weeks old

source_name: 5 week old microdissected cortical thymic tissue


title: cortical tissue_5week, rep5


title: medullary tissue_5week, rep3


title: Esg_Dam_2

description: PCR product


title: Esg_Dam_1

description: PCR product


title: Myo1A_Ets21c-Dam_3

description: PCR product


title: ES cells MAPCap; replicate 2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description: cDNA

data_processing:
read trimming using cutadapt (v1.16); parameters : -a AACCGGTT -m 15 -u 9 -q 5 –trim-n
mapped using subread (1.5.2); parameters :subjunc -D 500 -d 20
duplicates removed via icetea (v1.0) filterDuplicates (default options)
coverage calculated using deepTools bamCoverage (v3.0.2); parameters: --normalizeUsing CPM -p 20 -bs 1 --Offset 1 5 (for S2 cells) and –Offset 1 for femESCs
Genome_build: dm6; mm10
Supplementary_files_format_and_content: bw

source_name: female ES Cells

growth_protocol: S2 cells (gift from the Butros lab, Heidelberg) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80 rpm. Cells were kept at a density of 1-16 million/ml. The hybrid mouse female embryonic stem cell line F1-21.6 (129Sv-Cast/EiJ) was grown on Attachment Factor (Gibco) coated dishes in 2i medium containing DMEM (Gibco) supplemented with 15 % KnockOut Serum Replacement (Gibco), Penicillin/Streptomycin (Sigma), 1000 U/mL LIF (Millipore), sodium pyruvate (Gibco), non-essential amino acids (Gibco), Glutamax (Gibco), 100 µM β-mercaptoethanol (Gibco), 5 µg/mL insulin (Sigma), 1 µM PD0325901 (Axon) and 3 µM CHIR99021 (Axon). Cells were maintained in a humidified incubator at 37 °C and 5 % CO2.

extract_protocol:
RNA from S2 cells was extracted using the DirectZol Kit (Zymo Research). RNA was eluted in 25 ul of RNase-free water. Mouse ESC RNA was prepared from 70-80 % confluent 10 cm dishes using Trizol (Ambion) according to manufacturer's instructions. Poly(A)-RNA was isolated from 5 µg of total RNA (mixed with spike-ins added at 0.05 % of input) using Dynabeads Oligo-(dT)25 (Thermo Fisher).
MAPCap

value: ES cells

value: female


title: cortical lymphocyte_5week, rep5

description: Gene expression data from FACS sorted cortical lymphocytes from C57bl6/J male mice 5 weeks old

source_name: 5 week old purified cortical thymic lymphocytes

value: cortical lymphocyte

value: CD3-/lo AND CD45+ AND (CD90+ OR CD117+)


title: Myo1A_Ets21c-Dam_1

description: PCR product


title: cortical tissue_5week, rep1

value: thymic cortex


title: Esg_Ets21c-Dam_3

description: PCR product


title: cortical tissue_5week, rep2


title: cortical lymphocyte_5week, rep3


title: ES cells MAPCap; replicate 1

description: cDNA


title: medullary lymphocyte_5week, rep3

description: Gene expression data from FACS sorted medullary lymphocytes from C57bl6/J male mice 5 weeks old

source_name: 5 week old purified medullary thymic lymphocytes

value: medullary lymphocyte


title: cortical tissue_5week, rep3


title: Esg_Ets21c-Dam_2

description: PCR product


title: Esg_Ets21c-Dam_1

description: PCR product


title: medullary lymphocyte_5week, rep2

value: CD3hi AND CD45+


title: medullary lymphocyte_5week, rep4


title: medullary tissue_5week, rep5


title: medullary lymphocyte_5week, rep1


title: medullary lymphocyte_5week, rep5


title: cortical lymphocyte_5week, rep2


title: cortical lymphocyte_5week, rep1


title: cortical lymphocyte_5week, rep4


title: Myo1A_Ets21c-Dam_2

description: PCR product


title: Myo1A_Pol2-Dam_3

description: PCR product

value: Dam-Polymerase II


title: Myo1A_Pol2-Dam_1

description: PCR product


title: Esg_Pol2-Dam_3

description: PCR product


title: Esg_Pol2-Dam_2

description: PCR product


title: Esg_Pol2-Dam_1

description: PCR product


title: Sample_159_3

city: Wuxi

first: Xiaofeng

last: Dai

address: Lihu Ave 1800

institute: JiangnanUniversity

data_processing:
Illumina HiSeq 2500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie2
Fregments Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
RNA was harvested using Trizol reagent and DNase. mRNA was extracted using Oligo(dT) attached beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: stemness

value: cancer stem cells

tag: subtype

value: Triple Negative


title: Sample_159_1


title: Sample_159_2


title: Sample_1937_3_P2


title: Sample_1937_2_P2


title: Myo1A_Pol2-Dam_2

description: PCR product


title: Brachial-NSCs from E12.5 mouse embryo n=2

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

description: Gene expression data from E12 mouse NSCs derived from brachial tissue

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16 hours.

data_processing:
Signal values were computed using the Affymetrix® GeneChip™ Command Console software. . Obtained raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).
After importing CEL files, the data were summarized and normalized with the robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis

source_name: E12.5 mouse embryo

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: NSCs were cultured in N2 media containing supplements of 1% serum-free N2 and 2% B27 , and 1% penicillin-streptomycin in Dulbecco’s modified Eagle medium (DMEM)/F12 with daily addition of bFGF (20 ng/ml) and EGF (20 ng/ml)

extract_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit).  cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer

treatment_protocol: Not applicable

value: NSCs derived from mouse embryonic brachial tissue

value: E12.5 embryonic stage


title: Tail-NSCs from E12.5 mouse embryo n=2

description: Gene expression data from E12 mouse NSCs derived from Tail tissue

value: NSCs derived from mouse embryonic Tail tissue


title: Brachial-NSCs from E12.5 mouse embryo n=3


title: Tail-NSCs from E12.5 mouse embryo n=3


title: Liver_H2Bub1_rep2

city: New Haven

first: Martina

last: Brueckner

state: CT

address: 789 Howard Ave

department: Pediatrics

institute: Yale University

description: Liver.bw

data_processing:
aligned using BWA Mem algorithm
peaks identified using Model-based Analysis of ChIP-seq (MACS) (version 2.1.0)
differentially bound sites were obtained using the "DiffBind" package in R, with a maximum q value of 0.05 and a minimum absolute fold change of 1.5
nearest genes to the differentially bound sites were obtained using the "ChIPseeker" package in R
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using fold enrichments as scores

source_name: Liver

growth_protocol: in vivo

extract_protocol:
frozen tissue were ground, DNA was sonicated on S220 sonicator, and precipitated with H2Bub1 antibody
Illumina protocol

value: Black 6


title: Tail-NSCs from E12.5 mouse embryo n=1


title: Liver_Input_rep2

description: Liver.bw


title: Liver_H2Bub1_rep1

description: Liver.bw


title: Oviduct_Input_rep2

description: Oviduct.bw

source_name: Oviduct


title: Sample_1937_1_P2


title: Oviduct_H2Bub1_rep1

description: Oviduct.bw


title: LPS-stimulated Dendritic Cells (4h) [mm_DC_LPS4h_RS259]

city: Poznań

first: Anna

last: Piaszyk-Borychowska

address: ul. Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
Alignment with TopHat v2.0.7 using default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: N/A

source_name: bone marrow

growth_protocol: VSMC were cultured in DMEM complete medium supplemented with 10% FBS, 1:100 L-glutamine and 1:100 antibiotic/antimycotic solution. On the day before treatment, complete medium was exchanged onto 2% FBS containing starving medium. Differentiated BMDM and DC were immediately placed in serum free medium or 2% FBS containing RMPI1640 supplemented with 1:100 antibiotic/antimycotic solution and 50μM β-ME, respectively, for 24 hours.

extract_protocol:
Total RNA from primary VSMC, BMDM and DC was isolated with GeneMATRIX Universal RNA Purification Kit (EURx) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.

treatment_protocol: VSMC, BMDM and DC were left unstimulated or treated with single stimulus as follows: 1000U/ml of IFN alpha or 10ng/ml of IFN gamma for 8 hours; 10ng/ml (BMDM and DC)/1μg/ml (VSMC) of LPS for 4 hours. To further study the effect of IFNs pretreatment on LPS signaling, the cells were first treated with IFN alpha/IFN gamma for 8 hours followed by LPS stimulation for another 4 hours, as abovementioned.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Bone Marrow-Derived Dendritic Cells

tag: stimulation

value: 4h, 10ng/ml, LPS


title: Sample_1937_3_P3

value: non-cancer stem cells


title: Oviduct_Input_rep1

description: Oviduct.bw


title: Liver_Input_rep1

description: Liver.bw


title: Brachial-NSCs from E12.5 mouse embryo n=1

tag: developmental stage


title: LPS-stimulated Dendritic Cells (4h) [mm_DC_LPS4h_RS250]


title: LPS-stimulated Dendritic Cells (4h) [mm_DC_LPS4h_RS241]


title: Sample_1937_2_P3


title: LPS-stimulated Dendritic Cells (4h) [mm_DC_LPS4h_RS232]


title: Oviduct_H2Bub1_rep2

description: Oviduct.bw


title: Sample_149_3_P2


title: Sample_149_2_P2


title: IFN gamma+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNG8h_LPS4h_RS242]

value: 8h, 10ng/ml, murine IFN gamma; 4h, 10ng/ml, LPS


title: IFN gamma+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNG8h_LPS4h_RS251]


title: Sample_149_3_P3


title: Sample_149_1_P2


title: IFN gamma+LPS-stimulated Dendritic Cells (8h/4h) [mm_DC_IFNG8h_LPS4h_RS233]


title: Sample_149_2_P3


title: Sample_1937_1_P3


title: IFN gamma-stimulated Dendritic Cells (8h) [mm_DC_IFNG8h_RS256]

value: 8h, 10ng/ml, murine IFN gamma


title: FV3_2

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads from each sample were mapped to the mouse or human reference genomes (mm10 or hg38 version) by using TopHat v2.1.1
Sequencing counts at the gene level were obtained using HTSeq v 0.9.1.
R (version 3.4.0) package DESeq2 was then used to normalize gene counts and identify differential expressed genes between different conditions.
Genome_build: hg38 (human)
Supplementary_files_format_and_content: tab-delimited text files include normalized gene counts values for each sample

source_name: hESC derived progenitor cells

growth_protocol: Human ESCs were broken up into colonies and suspended in hESCM for 4 days to form EBs. EBs were then switched to the NIM to guide the cells toward the NE fate for 2 days. During the period, SB431542 (2 µM, Stemgent) and LDN193189 (200 nM, Stemgent), inhibitors to block TGF-β and BMP signaling, were added to the EBs from Days 0 to 6. At Days 6-17, cell aggregates were adherently cultured and neuroectoderm cells were formed. For ventralization, a combination of SHH (250 ng/mL, R&D Systems) and the smoothened activator purmorphamine (0.3μM, Stemgent) were added to the neuroectoderm cells from day 10 to day 17. For Caudalization,  retinoic acid 1:10000 were added to the neuroectoderm cells from day 10 to day 17

extract_protocol:
MGE cells were collected, or MGE was removed from embryo. RNA was harvested using Trizol reagent. NEBNext Ultra RNA library Prep Kit for Illumina (E7530) was used with 500 ng of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using the manufacturer’s protocol

treatment_protocol: As to virus groups, ZIKA virus were added into the NIM medium from day 17, keep 3 and 6 days

value: hESC-derived neuron progenitor cells

tag: Stage

value: Day 17 after differentiation

tag: time point

value: 3 dpi

tag: agent


title: IFN gamma-stimulated Dendritic Cells (8h) [mm_DC_IFNG8h_RS238]


title: IFN gamma-stimulated Dendritic Cells (8h) [mm_DC_IFNG8h_RS247]


title: Sample_149_1_P3