title: Sample 9_Incubation with Ag

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 9


title: WM3_ATAC

status: Public on Nov 20 2018

type: SRA

city: PORTLAND

first: Yulong

last: Su

state: OR

address: Oregon Health & Science University CLSB, 4N082, 2730 SW Moody Ave

department: MMG

country: USA

institute: Oregon Health & Science Univeristy

library_source: genomic

data_processing:
Base calling - using RTA Version 1.13.48.0.
Conversion to FASTQ using CASAVA 1.8.2.
Reads were aligned using boa men followed by duplicate removal using samtools.
Peaks were called using mac s2 with default parameters.
We then constructed a sites × samples counts matrix that served as the basis for all subsequent analyses using the union peak setWe then constructed a sites × samples counts matrix that served as the basis for all subsequent analyses using the union peak set
Genome_build: mm10
Supplementary_files_format_and_content: File in bed format with merged peak locations from all ATAC-seq samples.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: Cells were maintained and plated in DMEM with 10% FBS and pen/strep

extract_protocol: ATAC-seq was performed using the Omni-ATAC protocol (Corces et al., 2017).

treatment_protocol: Passage 2 primary wildtype or PIN1 knockout MEFs were grown to denstiy arrest. Cells were split to ~50% confluency in 0.2% FBS media and starved for 2 days. ChIPs were done 4 hrs post serum stimulation by 20% FBS media.

tag: cell type

value: mouse embryonic fibroblasts

tag: genotype/variation

value: Wild Type

tag: starved/stimulated

value: Stimulated


title: Ishikawa_siEfp

type: RNA

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from Ishikawa cells treated with siRNA targeting Efp

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Human Gene 1.0 ST Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ishikawa cells treated with siEfp

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human endometrial cancer cells, Ishikawa and HEC-1A, were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: Cells were transfected with Efp siRNA or control siRNA.

tag: cell line

value: Ishikawa


title: sh-TFEB ECs pool 1

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

hyb_protocol: 750 ng of cRNA was hybridized on HumanHT-12_v.4 for 18 h. Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

source_name: Human endothelial cells isolated from veins of umbilical cords (HUVEC)  infected with specific shRNA against TFEB (sh-TFEB ECs)

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: Human ECs were isolated from veins of umbilical cords and maintained as described (Eremina et al., 2003; Sison et al., 2010). To minimize cell variability, pools of 5 different donors were used.

extract_protocol: Total RNA was extracted from scr-shRNA ECs and sh-TFEB ECs with miRNeasy mini kit (Qiagen)

treatment_protocol: Loss-of-function experiments were carried out with shRNAs against TFEB (TRCN0000013111, NM_007162.2; Sigma) cloned in pLKO.1-puro non-Mammalian vector.   ECs were transduced with specific lentiviral particles (MOI=1) prepared according to (Eremina et al., 2008; Eremina et al., 2003) in the presence of 8 μg/ml polybrene (Sigma). After 24h the medium was replaced, and cells stably expressing the lentivirus were selected by puromycin (1 μg/ml, Sigma) for 24h.

value: HUVEC


title: NHF_p62_rep1

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

hyb_protocol: Agilent Gene Expression Hybridization Kit was using according to the manusfacturer's instructions.

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

data_processing: Data was extracted using Agilent Feature Extraction software.  Normalization was performed using the normalizeBetweenArrays function from R package limma with method=quantile.

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

growth_protocol: NHFs was cultured in DMEM supplemented with 10% FBS (Gibico). Cells were cultured in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol: Prepare the RNA sample using TRIzol® Reagent. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.

treatment_protocol: We used (normal human fibroblasts) NHFs at passage 62 as replicative senescence model and NHFs at passage 11 as control. To obtain oxidative stress-induced senescent cells, we applied a single dose of 600μM H2O2 to NHFs at passage 11 for five days.

tag: tissue

value: Foreskin

value: NHF

tag: passage

value: passage 62


title: scr-shRNA ECs pool 2

source_name: Human endothelial cells isolated from veins of umbilical cords (HUVEC)  infected with pLKO.1-puro vector (scr-shRNA ECs)


title: Sample 8_Incubation with Ag

city: Montreal

first: Orcun

last: Hacariz

state: Quebec

address: 1001 Boul Décarie, Site Glen Pavilion E / Block E. E02.2143

institute: Research Institute of the McGill University Health Centre

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 8

library_source: transcriptomic

data_processing:
Standard Illumina base calling (CASAVA; version 1.8) was performed.
Read quality was checked with FASTQC (version 0.11.3) and adapter related sequences were removed using Trim Galore (version 0.4.5) (https://www.bioinformatics.babraham.ac.uk/projects/).
The genome sequence of C. elegans and GTF file (Caenorhabditis_elegans.WBcel235.91.gtf) were downloaded from ENSEMBL (https://www.ensembl.org/).
Reads were aligned to the C. elegans genome with HISAT2 (version 2.1.0) (doi: 10.1038/nmeth.3317) and sorted alignment files were generated by SAMtools (version 1.7, doi: 10.1093/bioinformatics/btp352).
Raw read counts were extracted using HTSeq (version 0.9.1, doi: 10.1093/bioinformatics/btu638) with the intersection-strict mode. For comparison, we also applied Kallisto - a new ultra-fast RNASeq quantification method based on pseudoalignment (doi: 10.1038/nbt.3519). For this purpose, transcriptome information was obtained from the genome file using gffread (version 0.9.12) (http://ccb.jhu.edu/software/stringtie/gff.shtml) to build the required index and gene level counts were estimated using tximport (doi: 10.12688/f1000research.7563.2).
Genome_build: WBcel235
Supplementary_files_format_and_content: Raw read counts for genes were obtained using HTSeq or Kallisto/Tximport

organism: Caenorhabditis elegans

source_name: Whole tissue

growth_protocol: Around 350 to 400 L1 C. elegans N2 were grown in individual wells of a 12-well plate and supplemented with E. coli OP50, until the worms reached the adult day 1 stage (72 hours at 21˚C).

extract_protocol:
The contents of the wells were centrifuged at 1,000 rpm for 2 minutes, the supernatant was decanted and the worm pellet was washed twice with 1X M9 buffer. 200 µl of Trizol (Ambion, USA) was then added to the worm pellet. The worm pellet then was flash-frozen in liquid nitrogen, followed by a quick thaw. These two steps were repeated once.
RNA libraries were prepared with standard Illumina protocols

treatment_protocol: C. elegans (adult day 1 stage) was incubated in wells containing either 0, 10 µg/ml Ag nanoparticles or 10 µg/ml SiO2 nanoparticles

tag: strain

value: Whole worm

tag: age

value: adult day 1 stage


title: NHF_con_rep3

value: passage 11


title: sh-TFEB ECs pool 3


title: ansc_ko_rna_rep3

city: Worcester

first: Botao

last: Liu

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Cytoplamic mRNA
ansc.ribo.rna.rsem.gene.summary.counts.txt
ansc.ribo.rna.rsem.gene.summary.tpm.txt
ansc.deg.anota2seq.sva.gene.summary.txt

data_processing:
Basecallling and fastq file generation were performed by Illumina Basespace.
For ribosome profiling data, individual samples were separated from the raw fastq files based on the barcode sequences. Barcode and UMI sequences were trimmed and moved to the read names. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1).
Trimmed reads were quality filtered and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9).
PCR duplicates were marked based on the UMI sequences and only uniquely mapped reads without duplicates were retained with samtools (0.0.19) for the downstream analysis.
Cleaned bam files of ribosome footprints were converted to fastq files with bedtools (2.22.0). Cleaned fastq files without rRNA or tRNA were used for RNA-seq quantification. For both ribosome profiling and RNA-seq, gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks.
Genes were filtered with minimum 10 reads across all replicates and then the read counts were batch-corrected with the Combat function in sva (3.24.4) using a full model matrix.
Batch-corrected counts were normalized with trimmed mean of M values (TMM) method and used to identify differential expressed genes (DEGs) with anota2seq (1.0.0). Relaxed cut-offs (absolute fold changes > 1.2 and adjusted p-value < 0.2) were used to obtained sufficient DEGs for the downstream analysis. Instead of using the default setting, the priorities of translation and buffering groups were determined by the adjusted p-values and were set to be higher than the priority of mRNA only groups.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TPM values from RSEM, as well as batch-corrected counts, TPM, and anota2seq (differential translation analysis) output values for each sample

source_name: Dentate gyrus

growth_protocol: Adult-derived NSCs were isolated from the dentate gyrus (DG) of 8- to 10-week-old male Fmr1 KO mice and wild-type (WT) littermate controls based on our published method (Guo et al., 2012). Briefly, DG were dissected using forceps and 27gauge needle (BD, #305109) and placed in Hank’s balanced salt solution (HBSS, Invitrogen, # 14025-126) on ice. Tissue was spun down and digested using MACS Neural Tissue Dissociation kit (Miltenyi Biotech, #130-090-753). After dissociation with a fire-polished glass pipette, cells were filtered through a 70-μm cell strainer (BD Falcon, #252350) and washed with HBSS, the single-cell suspension from each sample was collected and cultured in proliferation medium [Neurobasal medium containing B27 serum-free supplement (Invitrogen, #17504-044), 20 ng/ml basic fibroblast growth factor (FGF-2, PeproTech, #K1606), 20 ng/ml epidermal growth factor (EGF, PeproTech, #A2306), 1% Antibiotic-Antimycotic, and 2 mM L-glutamine], in a 5% CO2 incubator at 37°C. Half of the medium was replaced every two days. Independently isolated cells serve as biological replicates.

extract_protocol:
Frozen cell pellets were thawed in ice-cold polysome lysis buffer [20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide, 25U/ml Turbo DNaseI (Ambion, #AM2238), 1% TritonX-100 in nuclease-free water] and lysed by trituration through a 25-G need for 10 times. After 10-min incubation on ice, lysates were clarified by centrifugation at 14,000g 4 °C for 10min. The supernatants were collected and the amounts of nucleic acids (A260 units) were measured with Nanodrop (Thermo Fisher Scientific). For each sample, cytoplasmic RNA for RNA-seq was purified from one fourth of the lysate with TRIzol LS reagent (Invitrogen, #10296028). The other three fourths of the lysate was digested with 100ng/A260 RNase A (Ambion, #AM2270) and 60U/A260 RNAse T1 (Thermo Fisher Scientific, #EN0542) at 25°C for 30min. The digestion was stopped by adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694) and chilling on ice. Digested lysates were loaded on 10%-50% sucrose gradients prepared in 1Xpolysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection interval through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS.
Ovation RNA‑Seq System V2 (NuGEN)
For the cytoplasmic RNA-seq, 500ng total RNA per sample was used for the library preparation with the Ovation RNA‑Seq System V2 (NuGEN, #0304) following manufacturer’s instructions. HL-dsDNase (ArcticZymes, #70800-201) method was used to eliminate DNA contamination and cDNA was fragmented with M220 Covaris Focused-ultrasonicator for a target median fragment size of 300bp (peak power: 50.0, duty factor 20.0, cycles/burst: 200, treatment time: 75sec). qPCR test was performed with EvaGreen Dye (Biotium, #31000-T) to determine the optimal PCR cycles. For the ribosome profiling samples, libraries were prepared following the published protocols (Heyer et al., 2015; Ingolia et al., 2012). Briefly, rRNA was depleted from the purified monosomal RNA samples with RiboZero (Illumina, #MRZG12324). Remaining RNA samples were separated on a 15% TBU gel (National Diagnostics, #EC-833) and the ribosome footprints were size-selected based on the 26 and 34nt markers. RNA was eluted from the crushed gel pieces in RNA elution buffer (300mM NaOAc pH5.5, 1mM EDTA, 0.25% SDS) at RT overnight, filtered with Spin-X Centrifuge Tube Filters (Corning, #8162) and precipitated with equal volume of isopropanol. Recovered RNA was dephosphorylated with T4 Polynucleotide Kinase (NEB, #M0201S) and ligated with preadenylated adaptor in miRCat®-33 Conversion Oligos Pack (IDT) using T4RNL2Tr.K227Q ligase (NEB, #M0351L). Reverse transcription was performed with RT primers with 5nt-barcode and 5nt or 8nt unique molecular identifier (UMI) and SuperScript III (Invitrogen, #18080-044) in 1X first-strand buffer without MgCl2 (50 mM Tris-HCl, pH 8.3, 75 mM KCl). RT products were separated on a 10% TBU gel and the 130-140nt region was selected. cDNA was eluted in DNA elution buffer (10mM Tris pH 8.0, 300mM NaCl, 1mM EDTA) at RT overnight, filtered, and precipitated with isopropanol. Purified cDNA was circularized with CircLigase (Epicentre, #CL4115K). cDNA derived from remaining rRNA was hybridized to biotin-labelled antisense probes (IDT) and further depleted with Dynabeads MyOne Streptavidin C1 (Inivtrogen, #65001). Optimal PCR cycle was determined empirically by test PCR reactions with titrated cycle numbers. Final PCR amplification was performed with KAPA Library Amplification Kit (Kapa Biosystems, #KK2611) and 180-190bp products were size-selected on an 8% TBE gel. DNA was eluted in DNA elution buffer and precipitated with isopropanol. The final library DNA was purified with AMPure XP beads (Beckman Coulter, #A63880)

treatment_protocol: Cycloheximide (CHX, Sigma-Aldrich, #C7698) was added into cultured aNSCs to a final concentration of 100μg/ml, and let cells incubate at 37 °C for 10 min in order to stabilize ribosomes. Then, cells were transported to cold room and spun down gently at 1000g for 3 min and the supernatant was carefully discarded. Cells were washed twice with ice-cold PBS containing 100μg/ml CHX and were spun down at 1000g for 3 minutes. The supernatant was carefully removed to collect the cell pellet. The cell pellet was immediately stored and kept in -80 °C freezer for later analysis.

value: Dentate gyrus

value: Adult neural stem cells

value: FVB/N

tag: genotype

tag: Sex

value: male

value: 8-10 weeks


title: scr-shRNA ECs pool 1


title: NHF_con_rep1


title: KV1_ATAC

value: PIN1 knockout

value: Starved


title: NHF_con_rep2


title: KM2_ATAC

value: mouse embryonic fibroblasts


title: KM1_ATAC

value: Stimulated


title: Sample 10_Incubation with Ag

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 10


title: NHF_p62_rep2


title: Sample 4_Control

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 4


title: NHF_H2O2_rep2

tag: treatment


title: NHF_H2O2_rep1


title: WT_1_RNA

data_processing:
Base calling - using RTA Version 1.13.48.0.
Conversion to FASTQ using CASAVA 1.8.2.
Reads were trimmed to 44 bases (first 5 bases were discarded, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to mm9 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to count tags that aligned to the exons of UCSC RefSeq gene models and calculate values normalized for sequencing depth.  Processed files contain the in exon tag counts and the nomalized values for each RefSeq gene model.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with tag counts and normalized values for each RefSeq gene model.

extract_protocol: Total RNA was extracted using Qiagen PCR purification kit as per manufacturer's protocol.

treatment_protocol: Passage 2 primary wildtype or PIN1 knockout MEFs were grown to denstiy arrest. Cells were split to ~50% confluency in 0.2% FBS media and starved for 2 days. RNA was harvested 4 hrs post serum stimulation by 20% FBS media.

tag: strain/background

value: Wild Type


title: Sample 5_Control

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 5


title: NHF_H2O2_rep3


title: WM2_ATAC


title: Sample 7_Incubation with Ag

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 7


title: WV1_ATAC


title: PIN1_KO_2_ChIP

data_processing:
Base calling - using RTA Version 1.13.48.0.
Conversion to FASTQ using CASAVA 1.8.2.
Reads were trimmed to 44 bases (first 5 bases were discarded, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to mm9 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to create wiggle tracks from the aligned data.  The wiggle tracks show significantly enriched peaks based on a sliding window approach.  Tag duplication was limited to 2, additional duplicates were removed.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary files  are UCSC wig format for use with the genome browser.

extract_protocol: ChIP DNA was extracted using Qiagen PCR purification kit as per manufacturer's protocol.

tag: chip antibody

value: c-Myc (N-262) (Santa Cruz, SC-764x, cat# G2916)


title: WV3_ATAC


title: WV2_ATAC


title: PIN1_KO_1_ChIP


title: mouse_mef_7day_control_RNAseq_gene_counts_2

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: RNA-seq

data_processing:
For RRBS: raw sequencing reads were aligned to the mm9 build of the mouse genome using MAQ (H. Li, Ruan, & Durbin, 2008). We used custom Python scripts to call methylation at each CpG, computed as the ratio of methylated reads to total reads at that genomic position. For RNA-seq: raw sequencing reads were aligned to the mm9 genome with Ensembl gene models (release 67) using Tophat2. For ChIP-seq: raw sequencing reads were aligned to mm9 genome using Bowtie 2. Peak calling was done using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: RRBS processed data column headers are: chromosome, start, end, (methylated reads / total reads), methylation score (0 - 1000), strand. Process RNA-seq gene count text files: Geneid, Chr, Start, End, Strand Length, counts.

molecule: polyA RNA

growth_protocol: MEFs were cultured in knockout Dulbecco's modified Eagle's medium (KD DMEM, Life Technologies) supplemented with 10% fetal bovine serum (Seradigm).

extract_protocol:
DNA was either harvested from mouse tissues, or from cultured MEFs.
Flash-frozen mouse tissues and cell pellets were lysed in 300-600µl DNA lysis buffer (10 mM Tris-HCl pD 8.0, 10mM EDTA, 10mM NaCl and 0.5% wt/vol SDS) supplemented with 50 ng/µl Dnase-free Rnase (Roche) and 1 ng/µl proteinase K (NEB) at 55°C overnight. After phenol:chloroform extraction and ethanol precipitation, DNA was resuspended in elution buffer (10 mM Tris-HCl pH 8.0, 1mM EDTA)
For RRBS: 100 ng genomic DNA was used to make libraries as previously described (Boyle et al., 2012).

treatment_protocol: "Treatment time" refers to length of time that mice were treated for - either control (no doxycycline) or with doxycycline supplied in the drinking water. This was either from birth (0 months: 0M) to 1.5M, 0-3M or 3-6M, described in the sample name. Or 1 day/7days for mouse embryonic fibroblasts.

tag: strain background

tag: tissue/cell type

value: embryonic fibroblasts

tag: dnmt3b oe

value: no

tag: treatment time

value: 7 days


title: WT_2_ChIP

tag: cell type


title: WT_1_ChIP

tag: genotype/variation


title: PIN1_KO_2_RNA


title: WT_2_RNA


title: YKL-06-102_rep3

city: Wien

first: Georg

middle: E

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

description:
RNA-seq after 6h YKL-06-102 (200 nM) treatment
YKL_3

data_processing:
conversion and demultiplexing: Illumina2bam
trimming: trimmomatic-0.36 using default settings
alignment: STAR aligner 2.5.2b against an index based on UCSC hg38 and Ensembl 87 transcript annotation
read counting: htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw read counts for each gene

source_name: MV4-11 AML cell line

growth_protocol: MV4-11 cells were grown in RPMI medium supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
RNA was isolated using QIAGEN Rneasy kit according to manufacturer's instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

treatment_protocol: Cells were treated for 6 h with 200 nM BSJ-03-123, YKL-06-102, Palbociclib or vehicle (DMSO)

value: AML

tag: barcode

value: GCCAAT


title: WM1_ATAC

tag: starved/stimulated


title: Sample 3_Control

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 3

tag: tissue

value: Whole worm

value: adult day 1 stage


title: PIN1_KO_1_RNA


title: Sample 6_Incubation with Ag

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 6


title: Sample 1_Control

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 1


title: mouse_mef_7day_dox_RNAseq_gene_counts_3

description: RNA-seq

value: yes


title: mouse_mef_7day_dox_RNAseq_gene_counts_2

description: RNA-seq


title: Sample 2_Control

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 2


title: Palbociclib_rep3

description:
RNA-seq after 6h Palbociclib (200 nM) treatment
Palbo_3

tag: cell line

value: CCGTCC


title: mouse_mef_7day_control_RNAseq_gene_counts_3

description: RNA-seq


title: Palbociclib_rep1

description:
RNA-seq after 6h Palbociclib (200 nM) treatment
Palbo_1

value: TAGCTT


title: BSJ-03-123_rep3

description:
RNA-seq after 6h BSJ-03-123 (200 nM) treatment
BSJ_3

value: GATCAG


title: mouse_intestine_3-6M_dox_RRBS_r4

description: RRBS

value: intestine

value: 3 months


title: mouse_intestine_3-6M_control_RRBS_r4

description: RRBS


title: mouse_mef_control_Input_ChIP

description: ChIP input


title: mouse_mef_7day_dox_RNAseq_gene_counts_1

description: RNA-seq


title: mouse_liver_0-3M_dox_H3K27me3_ChIP_1

description: H3K27me3 ChIP

value: liver

tag: chip-seq antibody

value: H3K27me3 (Millipore 07-449)


title: mouse_mef_7day_control_H3K4me3_ChIP

description: H3K4me3 ChIP

value: H3K4me3  (Millipore, 07-473)


title: Palbociclib_rep2

description:
RNA-seq after 6h Palbociclib (200 nM) treatment
Palbo_2

value: GGCTAC


title: mouse_mef_7day_control_RNAseq_gene_counts_1

description: RNA-seq

value: embryonic fibroblasts


title: mouse_mef_7day_control_H3K27me3_ChIP_2

description: H3K27me3 ChIP

value: no


title: mouse_liver_0-3M_control_H3K4me3_ChIP_2

description: H3K4me3 ChIP


title: mouse_mef_7day_control_H3K27me3_ChIP_1

description: H3K27me3 ChIP

value: 7 days


title: mouse_liver_0-3M_dox_H3K4me3_ChIP_2

description: H3K4me3 ChIP


title: mouse_liver_0-3M_dox_H3K27me3_ChIP_2

description: H3K27me3 ChIP


title: mouse_liver_0-3M_dox_H3K4me3_ChIP_1

description: H3K4me3 ChIP


title: mouse_liver_0-3M_control_input_ChIP

description: ChIP input


title: YKL-06-102_rep1

description:
RNA-seq after 6h YKL-06-102 (200 nM) treatment
YKL_1

value: AML

value: TGACCA


title: BSJ-03-123_rep1

description:
RNA-seq after 6h BSJ-03-123 (200 nM) treatment
BSJ_1

value: CAGATC


title: mouse_liver_0-3M_dox_input_ChIP

description: ChIP input


title: DMSO_rep2

description:
RNA-seq after 6 h DMSO (0.1%) treatment
DMSO_2

value: CGATGT


title: DMSO_rep1

description:
RNA-seq after 6 h DMSO (0.1%) treatment
DMSO_1

value: ATCACG


title: BSJ-03-123_rep2

description:
RNA-seq after 6h BSJ-03-123 (200 nM) treatment
BSJ_2

value: ACTTGA


title: mouse_liver_0-3M_control_H3K27me3_ChIP_1

description: H3K27me3 ChIP


title: mouse_liver_0-3M_control_H3K27me3_ChIP_2

description: H3K27me3 ChIP


title: DMSO_rep3

description:
RNA-seq after 6 h DMSO (0.1%) treatment
DMSO_3

value: TTAGGC


title: mouse_mef_7day_dox_H3K27me3_ChIP-BS_2

description: H3K27me3 immunoprecipitation + bisulfite sequencing

value: yes


title: mouse_mef_7day_dox_H3K27me3_ChIP-BS_1


title: mouse_mef_7day_control_H3K27me3_ChIP-BS_2


title: mouse_mef_7day_control_H3K27me3_ChIP-BS_1


title: HFD-apoE4-CNS-ChP-6

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

description: growth protocol: HFD

hyb_protocol: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: Central nervous system

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 24h IVT

growth_protocol: Maintained under normal mouse chow (ND) or under high fat diet (HFD)

extract_protocol: Qiagen RNEasy Lipid Tissue Mini kit, standard protocol

treatment_protocol: Fresh-frozen nervous system tissues were isolated by laser capture microdissection and taken up in Trizol

tag: strain

value: Choroid plexus

value: humanized ApoE4-Knockin

tag: gender

value: female

tag: age

value: 78 weeks


title: HFD-apoE4-CNS-ChP-2

description: growth protocol: HFD

tag: genotype

value: male


title: HFD-apoE4-CNS-ChP-4

description: growth protocol: HFD


title: mouse_liver_0-3M_control_H3K4me3_ChIP_1

description: H3K4me3 ChIP

value: liver

value: 3 months

value: H3K4me3  (Millipore, 07-473)


title: HFD-apoE4-CNS-ChP-5

description: growth protocol: HFD


title: HFD-apoE4-CNS-ChP-3

description: growth protocol: HFD


title: HFD-apoE3-CNS-ChP-6

description: growth protocol: HFD

value: humanized ApoE3-Knockin


title: HFD-apoE4-CNS-ChP-1

description: growth protocol: HFD


title: HS_+Rapa

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

data_processing:
bases called by Illumina software
aligned to sacCer3 by Tophat
quantified by htseq-count
Genome_build: saccer3
Supplementary_files_format_and_content: .txt files with normalized counts

organism: Saccharomyces cerevisiae

extract_protocol: Phenol/chloroform; Illumina tru-seq

tag: perturbation

value: 10' 39ºC/+ rapamycin


title: HFD-apoE3-CNS-ChP-5

description: growth protocol: HFD


title: mouse_mef_1day_dox_H3K27me3_ChIP-BS_1

value: embryonic fibroblasts

value: 1 day

value: H3K27me3 (Millipore 07-449)


title: mouse_mef_1day_control_H3K27me3_ChIP-BS_2

value: no


title: NHS_+Rapa

value: 30ºC/+ rapamycin


title: mouse_mef_1day_dox_H3K27me3_ChIP-BS_2


title: NHS_noRapa

value: 30ºC/- rapamycin


title: mouse_mef_1day_control_H3K27me3_ChIP-BS_1


title: HFD-apoE3-CNS-ChP-3

description: growth protocol: HFD


title: HFD-apoE3-CNS-ChP-4

description: growth protocol: HFD


title: HS_noRapa

value: 10' 39ºC/- rapamycin


title: HFD-apoE3-CNS-ChP-2

description: growth protocol: HFD

value: Choroid plexus


title: apoE4-CNS-ChP-4

description: growth protocol: ND

value: humanized ApoE4-Knockin


title: HFD-apoE3-CNS-ChP-1

description: growth protocol: HFD


title: apoE4-CNS-ChP-6

description: growth protocol: ND

value: female


title: apoE4-CNS-ChP-2

description: growth protocol: ND

value: 78 weeks


title: apoE4-CNS-ChP-1

description: growth protocol: ND

value: male


title: apoE3-CNS-ChP-6

description: growth protocol: ND


title: apoE4-CNS-ChP-5

description: growth protocol: ND


title: apoE3-CNS-ChP-1

description: growth protocol: ND


title: apoE4-CNS-ChP-3

description: growth protocol: ND


title: apoE3-CNS-ChP-3

description: growth protocol: ND


title: pGATA23::slr-1-GR_DMSO_6h_2

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Center for Organismal Studies

institute: Heidelberg University

data_processing:
Reads were mapped onto the Arabidopsis thaliana genome (TAIR10) and numbers of reads per transcripts computed using STAR (version 2.5.2b) with options: --runThreadN 36 --quantMode TranscriptomeSAM GeneCounts
Subsequent analysis of differentially expressed genes was performed in R using the DEseq2 package (Love, M. I. et al. Genome Biology 15, (2014))
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include counts values per transcript for each Sample

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 4d after germination under 16h light/8h dark conditions to 10µM NPA for 22h and shifted to plates containing 10µM NPA and 10µM DEX or DMSO control for 2h.

extract_protocol:
Root samples were flash frozen in liquid nitrogen, RNA was extracted with the Universal RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were then transferred to plates containing 10µM IAA, and 10µM DEX and DMSO control. Root tissue was harvested at 0, 2, 4 and 6 h after transfer onto auxin plates. All sampling points were performed in triplicate. For each sample, app. 200 segments of the lower two-thirds of the seedling roots were pooled.

tag: treatment

value: DMSO

tag: replicate


title: apoE3-CNS-ChP-4

description: growth protocol: ND


title: apoE3-CNS-ChP-2

description: growth protocol: ND


title: apoE3-CNS-ChP-5

description: growth protocol: ND


title: pGATA23::slr-1-GR_DMSO_6h_3


title: pGATA23::slr-1-GR_DMSO_6h_1


title: JEV infected, 60 hour post infection, biological replicate 3

city: kuala lumpur

first: Shu Pin

last: Yu

state: kuala lumpur

address: Kuala Lumpur

department: Pathology

country: Malaysia

institute: University Malaya

description: Gene expression data of relatively late time point

hyb_protocol: Following fragmentation, 12µg biotinylated cRNA were  hybridized for 16 hour at 45℃ at a rotation speed of 60 rpm onto Affymetrix Human PrimeView arrays. Genechips were washed and stained in the Affymetrix Fluidics station 400

scan_protocol: Genechips were scanned using  Affymetrix GeneChip Scanner 3000 with Affymetrix AGCC scan control software

data_processing: Data were analyzed with Affymetrix customized softwares: Expression Console and Transciptome Analysis Console, v3, following Affymetrix default settings and normalized using Robust Multichip Average (RMA)

source_name: JEV infected SK-N-MC cells, 60 hour

label_protocol: 100 ng total RNA were processed and label using  Affymetrix GeneChip 3' IVT Plus kits

growth_protocol: Post JEV infection, SK-N-MC cells were cultured in Dulbecco modified eagle medium (DMEM) supplemented with 5% FBS

extract_protocol: Total RNA were extracted using RNeasy Plus Mini kit, QIAGEN following manufacturer's protocol

treatment_protocol: SK-N-MC cells were infected with JEV at MOI 10 on the following day post seeding. Unbound innoculums were removed prior to further incubation in 36℃. Mock infections were achieved by replacement of viruses with equal amounts of medium and cells were treated the same as of infected cells. Total RNA were extracted at 48 hour and 60 hour post infection.

value: SK-N-MC

value: human neuroepithelioma cells

tag: time post infection

value: 60 hour

tag: pathogen

value: Japanese Encephalitis Virus


title: no infection, 60 hour post infection, biological replicate 3

source_name: no infection SK-N-MC cells, 60 hour


title: JEV infected, 60 hour post infection, biological replicate 2


title: no infection, 60 hour post infection, biological replicate 1


title: pGATA23::slr-1-GR_DMSO_4h_3


title: no infection, 60 hour post infection, biological replicate 2


title: Zf_70d_F_GSC_A

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Trimming using TrimGalore ! (v0.4.2), Quality threshold 20, hard trimming 10bp
Reads were aligned against Zebrafish genome version 10 (GRCz10) using Bismark (v0.19.0)
CpG calls were extracted using bismark_methylation_extractor tool from Bismark software
Genome_build: GRCz10
Supplementary_files_format_and_content: Processed files contain individual CpG calls obtained by Bismark

organism: Danio rerio

source_name: Germinal stem cells

growth_protocol: Fish in different developmental stages were dissociated with 500 μL TrypLETM Express (ThermoFisher, 12604021) and continuous pipetting every 15 minutes for 60 min at room temperature (RT). eGFP positive and negative cells were obtained using a FACSAria sorter (BD)

extract_protocol:
Total nucleic acids were purified using the Bio-On-Magnetic-Beads (BOMB) approach (Oberacker et al., 2018). Briefly, a guanidine isothiocyanate lysis buffer was used to homogenize cells, and then was combined with TE-diluted Sera-Mag Magnetic SpeedBeads (GE Healthcare, GEHE45152105050250) and isopropanol in volumetric ratio of 2:3:4 (beads:lysate:isopropanol). Beads were captured with a neodymium magnet and washed once with isopropanol, twice with 70% ethanol and resuspended in milliQ water.
Bisulfite-converted genomic libraries were preparing using a modified post-bisulfite adapter tagging method. Briefly, bisulfite treatment was performed according to the EZ Methylation Direct Mag Prep kit (Zymo, D5044) instruction manual. To synthethise the first strand, we used converted DNA and 5’-biotinylated adaptor primers bearing a seven random nucleotides at its 3’ end (BioP5N7, biotin- ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNN). The first strand product was purified using streptavidin coated magnetic beads (ThermoFisher, 11205D) and alkaline denaturation.  Second strand DNA was synthesized using the immobilized first strand DNA and another adaptor primer also bearing seven random nucleotides at its 3’ end (P7N7, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNN). Second strand DNA was eluted, amplified by 15 cycles of PCR and size selected by PEG-diluted SPRI beads. During PCR, unique molecular barcodes and sequences required for Illumina flow-cells binding were added to libraries using 1X HiFi HotStart Uracil+ Mix (KAPA, KK2801 and 10 μM indexed Truseq-type oligos). Library integrity was assessed on an Agilent 2100 Bioanalyzer and sequenced on a 250 bp single-end run on Illumina MiSeq.
Post-bisulfite adaptor tagging (PBAT)

tag: line

value: vas:eGFP (Krøvel AV et al., 2002)

tag: day post fertilisation

tag: number of fish

tag: Sex

value: Female


title: Zf_70d_F_GSC_B


title: Zf_70d_F_GSC_C


title: JEV infected, 48 hour post infection, biological replicate 1

description: Gene expression data of early infection

source_name: JEV infected SK-N-MC cells, 48 hour

value: 48 hour


title: JEV infected, 48 hour post infection, biological replicate 2

description: Gene expression data of early infection


title: Zf_70d_F_Control_C

source_name: Whole embryo eGFP -


title: JEV infected, 60 hour post infection, biological replicate 1


title: pGATA23::slr-1-GR_DMSO_4h_2


title: JEV infected, 48 hour post infection, biological replicate 3

description: Gene expression data of early infection


title: Zf_70d_F_Control_B


title: pGATA23::slr-1-GR_DMSO_4h_1


title: pGATA23::slr-1-GR_DMSO_2h_3


title: Cg Wt 200 mM NaCl Vs 200 mM glutarate replicate 3

city: Bielefeld

first: Fernando

last: Pérez-García

address: Universitaetsstr. 25

institute: University of Bielefeld

description: Technical replicate 3 of 3

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were up- or downregulated in WT with 200 mM glutarate in both replicates were taken into account for further analysis (p-value < 0.05, mRNA value > 2).

organism: Corynebacterium glutamicum

source_name: Growth of C. glutamicum in minimal medium supplemented with 200mM of glutarate

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: BHI seed culture was inoculated from an agar plate and grown overnight. The cells were harvested by centrifugation (4000 x g, 10 min) and washed once with CGXII medium lacking the carbon source. Finally, 50 mL of CGXII medium containing 4% of glucose, the necessary supplements, and either 200 mM NaCl or 200 mM glutarate was inoculated to an OD600 of 1.0. Cells were grown until mid-exponential phase (OD between 15 and 26) and were spilled in two falcons (half filled with ice) and centrifuged (4000 x g, 10 minutes, 4ºC). Supernatant was discarded and cells were kept at -80ºC.

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: 200 mM NaCl or 200 mM glutarate were added to CGXII medium  from the beginning of the growth

source_name: Growth of C. glutamicum in minimal medium supplemented with 200mM of NaCl


title: CRZ2_ChIP_Lower array

type: genomic

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description:
Sample 2
Background strain is BWP17 carrying a homozygous deletion of CRZ2 and expressing TAP-tagged or untagged CRZ2 alleles under the control of the tetracycline derivative-inducible promoter.

hyb_protocol: The labeled DNA was speed-vaced and the pellets were resuspended in 104 µl of H2O. 26 µl of Agilent 10X blocking agent and 130 µl of Agilent 2X Hybridization Buffer were added for a total of 260 µl hybridization mix. Samples were heated at 95ºC for 3 minutes and incubated immediately at 37ºC during 30 min. 245 µl were dispensed onto each of the 2x400k Agilent gaskets. The hybridization chambers were assembled and rotated overnight at 65ºC as per the manufacturer's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol.

data_processing: Data were quantile normalized using CisGenome version 1.0 (Hongkai et al. 2005 Bioinformatics, 21: 3629-3636).

organism: Candida albicans

source_name: Candida albicans untagged strains, treated with 40 µg/ml doxycycline for 4h in YPD medium at 30ºC, immunoprecipitated DNA

label_protocol: The IP DNA (40 µl out of 50 µl) fragments were blunted with T4 DNA polymerase and ligated to unidirectional linkers. The DNA was amplified by ligation-mediated PCR in the presence of aminoallyl-modified dUTP. Labeling was carried out post-PCR using monoreactive Cy dye N-hydroxysuccinimide esters (Cy5/Cy3 monoreactive dye packs; Amersham Biosciences) that react specifically with the aminoallyl-modified dUTP [5-(3-aminoallyl)-2′ deoxyuridine-5′-triphosphate; Sigma-Aldrich]. Labeled IP DNA from the tagged strain (Cy5) and the untagged control strain (Cy3) were mixed and hybridized to C. albicans tiling arrays.

growth_protocol: Cells were grown overnight in 2 ml YPD at 30°C, diluted to an OD600 nm of 0.3 in YPD medium supplemented with 40 µg/ml doxycycline and re-grown for 4h at 30ºC.

extract_protocol: PTET-TAP-CRZ2 (Tagged) and PTET-CRZ2 (untagged control) were grown overnight in 2 ml YPD at 30°C, diluted to an OD600 nm of 0.3 in YPD medium supplemented with 40 g/ml doxycycline and grown during 4 hours at 30°C. Cultures were treated with 1% formaldehyde (cross-linking) and snap-frozen in liquid nitrogen. Total cell extracts were prepared by bead beating using a FastPrep-24 instrument (MP Biomedicals) with 10 runs during 40 seconds each at 5.5 m/sec and 1 minute on ice in between. Soluble chromatin fragments were prepared by sonicating the extracts 6 times during 20 sec at power 8 (knob position) for an output signal amplitude of 15 (Microns, Peak to Peak) using a probe sonicator (MSE), yielding a majority of ~200-500 bp DNA fragments. Immunoprecipitation was conducted overnight at 4ºC with 500 µl of clarified sonicated extracts and 40 µl of IgG-coated magnetic beads (Dynabeads Pan mouse IgG, Invitrogen, cat# 11041, lot# 120572900), previously prehybed overnight with PBS-0.1% BSA at 4ºC. The concentration of the purified immunoprecipitated (IP) DNA was ranging between 31 pg/µl and 147 pg/µl in 50 µl TE (10 mM Tris [pH 8.0], 1 mM EDTA).

tag: genotype/variation

value: doxycycline

tag: chip antibody

value: mouse IgG

source_name: Candida albicans strains expressing a TAP-tagged version of the CRZ2 gene placed under the control of a doxycycline-inducible promoter, treated with 40 µg/ml doxycycline for 4h in YPD medium at 30ºC, immunoprecipitated DNA


title: Zf_70d_F_Control_A


title: CRZ2_ChIP_Upper array

description:
Sample 1
Background strain is BWP17 carrying a homozygous deletion of CRZ2 and expressing TAP-tagged or untagged CRZ2 alleles under the control of the tetracycline derivative-inducible promoter.


title: Zf_70d_M_GSC_C

value: Male


title: no infection, 48 hour post infection, biological replicate 3

description: Gene expression data of early infection

source_name: no infection SK-N-MC cells, 48 hour

tag: cell line

tag: tissue


title: no infection, 48 hour post infection, biological replicate 1

description: Gene expression data of early infection


title: no infection, 48 hour post infection, biological replicate 2

description: Gene expression data of early infection


title: pGATA23::slr-1-GR_DMSO_2h_2


title: Lu3010

city: Boston

first: Vadim

last: Gladyshev

address: 77 avenue louis pasteur

institute: BWH

data_processing:
The reads were trimmed using Trim Galore v0.4.1 with the parameters: --rrbs --paired
The filtered reads were mapped to the mouse genome (GRCm38/mm10) using Bismark v0.15.0 with the default parameters to obtain methylation levels and coverage per site
Genome_build: mm10
Supplementary_files_format_and_content: Bismark Coverage (tab delimeted methylation status data)

source_name: Lung

extract_protocol:
DNA was isolated from 3-10 of frozen tissue
Libraries were prepared using Reduced Representation Bisulfite Sequencing. Five to seven samples were pooled together using Illumina's TrueSeq Nano DNA LT adaptors.

tag: strain

tag: age,months

value: Wild Type

value: Lung


title: Cg Wt 200 mM NaCl Vs 200 mM glutarate replicate 1

description: Technical replicate 1 of 3


title: pGATA23::slr-1-GR_DMSO_2h_1


title: Zf_70d_M_GSC_A


title: Lu3004

tag: gender


title: pGATA23::slr-1-GR_DMSO_1h_2

tag: genotype


title: Lu3009


title: pGATA23::slr-1-GR_DMSO_1h_1


title: Zf_70d_M_Control_C


title: pGATA23::slr-1-GR_DMSO_1h_3


title: Zf_70d_M_Control_B


title: Zf_70d_M_Control_A


title: Zf_50d_F_GSC_C

tag: presumptive sex


title: pGATA23::slr-1-GR_DMSO_0h_3

tag: treatment


title: Cg Wt 200 mM NaCl Vs 200 mM glutarate replicate 2

description: Technical replicate 2 of 3


title: Lu3003


title: Lu2010


title: pGATA23::slr-1-GR_DMSO_0h_2

tag: replicate


title: Lu2006


title: Zf_70d_M_GSC_B


title: Zf_50d_F_GSC_B


title: Lu2005


title: Zf_50d_F_GSC_A


title: Lu3008


title: Lu2004


title: YKL-06-102_rep2

description:
RNA-seq after 6h YKL-06-102 (200 nM) treatment
YKL_2

tag: cell type

value: AML

tag: barcode

value: ACAGTG


title: pGATA23::slr-1-GR_DEX_6h_3

value: DEX


title: Lu2003


title: pGATA23::slr-1-GR_DEX_6h_2


title: Zf_50d_F_Control_C

tag: line

value: female


title: Lu1208


title: pGATA23::slr-1-GR_DMSO_0h_1

value: DMSO


title: Lu1209


title: Lu1207


title: Zf_50d_M_GSC_C

tag: day post fertilisation

value: male


title: Zf_50d_F_Control_A

tag: number of fish


title: Zf_50d_F_Control_B


title: pGATA23::slr-1-GR_DEX_4h_3


title: pGATA23::slr-1-GR_DEX_4h_2


title: pGATA23::slr-1-GR_DEX_6h_1


title: Zf_50d_M_GSC_B


title: pGATA23::slr-1-GR_DEX_4h_1


title: Lu1203


title: Zf_50d_M_Control_C


title: pGATA23::slr-1-GR_DEX_2h_3


title: pGATA23::slr-1-GR_DEX_2h_2


title: Zf_50d_M_Control_B


title: Lu0609


title: Lu0610


title: pGATA23::slr-1-GR_DEX_2h_1


title: pGATA23::slr-1-GR_DEX_1h_3


title: Zf_50d_M_Control_A


title: Lu0608


title: Zf_45d_F_GSC_C


title: pGATA23::slr-1-GR_DEX_1h_2


title: Lu0607


title: pGATA23::slr-1-GR_DEX_1h_1


title: Zf_45d_F_GSC_A


title: Zf_45d_F_GSC_B


title: Zf_45d_F_Control_B


title: Lu1204


title: L3009

source_name: Liver

value: Liver


title: Zf_45d_F_Control_C


title: pGATA23::slr-1-GR_DEX_0h_2


title: pGATA23::slr-1-GR_DEX_0h_3


title: pGATA23::slr-1-GR_DEX_0h_1


title: Zf_45d_F_Control_A


title: L3010


title: Zf_45d_M_GSC_C


title: Zf_50d_M_GSC_A


title: L3008


title: Lu0603


title: L3003


title: pGATA23::shy2-2-GR_DMSO_6h_2


title: pGATA23::shy2-2-GR_DMSO_6h_3


title: L2010


title: Zf_45d_M_GSC_B


title: pGATA23::shy2-2-GR_DMSO_6h_1


title: L2006


title: pGATA23::shy2-2-GR_DMSO_4h_3


title: Zf_45d_M_GSC_A


title: L2005


title: L2004


title: Zf_45d_M_Control_C


title: pGATA23::shy2-2-GR_DMSO_4h_2


title: Zf_45d_M_Control_B


title: pGATA23::shy2-2-GR_DMSO_4h_1


title: Zf_45d_M_Control_A


title: L2003


title: L1208


title: L1209


title: pGATA23::shy2-2-GR_DMSO_2h_3


title: Zf_40d_F_GSC_C


title: Zf_40d_F_GSC_B


title: L1207


title: L1203


title: Zf_40d_F_GSC_A


title: pGATA23::shy2-2-GR_DMSO_2h_1


title: pGATA23::shy2-2-GR_DMSO_1h_3


title: L1204


title: L1003


title: pGATA23::shy2-2-GR_DMSO_1h_1


title: pGATA23::shy2-2-GR_DMSO_1h_2


title: Zf_40d_F_Control_B


title: pGATA23::shy2-2-GR_DMSO_0h_3


title: Zf_40d_F_Control_A


title: Zf_40d_M_GSC_C


title: L0610


title: pGATA23::shy2-2-GR_DMSO_0h_2


title: L0609


title: L0608


title: pGATA23::shy2-2-GR_DMSO_0h_1


title: Zf_40d_M_GSC_B


title: Zf_40d_M_GSC_A


title: pGATA23::shy2-2-GR_DEX_6h_3


title: pGATA23::shy2-2-GR_DMSO_2h_2


title: L0607


title: Zf_40d_M_Control_B


title: pGATA23::shy2-2-GR_DEX_6h_2


title: Zf_40d_M_Control_C


title: pGATA23::shy2-2-GR_DEX_6h_1


title: H3009

source_name: Heart

value: Heart


title: pGATA23::shy2-2-GR_DEX_4h_2


title: L0603


title: pGATA23::shy2-2-GR_DEX_4h_3


title: Zf_40d_F_Control_C


title: Zf_40d_M_Control_A


title: H3010


title: Zf_35d_F_GSC_B


title: Zf_35d_F_GSC_C


title: pGATA23::shy2-2-GR_DEX_4h_1


title: pGATA23::shy2-2-GR_DEX_2h_2


title: H3003


title: Zf_35d_F_GSC_A


title: Zf_35d_F_Control_C


title: pGATA23::shy2-2-GR_DEX_2h_1


title: H3008


title: H2006


title: Zf_35d_F_Control_A


title: pGATA23::shy2-2-GR_DEX_1h_3


title: H3004


title: Zf_35d_F_Control_B


title: H2005


title: Zf_35d_M_GSC_C


title: pGATA23::shy2-2-GR_DEX_1h_2


title: Zf_35d_M_GSC_B


title: H2004


title: pGATA23::shy2-2-GR_DEX_1h_1


title: H2003


title: pGATA23::shy2-2-GR_DEX_2h_3


title: Zf_35d_M_Control_C


title: Zf_35d_M_GSC_A


title: pGATA23::shy2-2-GR_DEX_0h_2


title: pGATA23::shy2-2-GR_DEX_0h_3


title: H1208


title: H2010


title: H1209


title: pGATA23::shy2-2-GR_DEX_0h_1


title: H1207


title: Zf_28d_GSC_E

tag: Sex

value: Pooled male and female


title: Zf_28d_GSC_D

value: vas:eGFP (Krøvel AV et al., 2002)


title: H1003


title: Zf_28d_GSC_C


title: H1204


title: 35% ethanol_2ml/kg_1005_RNASeq

city: North Chicago

first: Rita

last: Ciurlionis

address: 1 North Waukegan Road

institute: Abbvie

data_processing:
base calling and quality scoring Real-Time Analysis RTA v2
bcl2fastQ Conversion Software v2.0
reads trimmed to quality score of 2
read alignment software OSA4 (Omicsoft Aligner 4)
Genome_build: rat reference genome (Rat B6.0), Ensembl.R83
Supplementary_files_format_and_content: raw counts

organism: Rattus norvegicus

source_name: 35% ethanol_2ml/kg, liver left lateral lobe

extract_protocol:
Qiazol extraction of total RNA with subsequent DNase treatment was performed according to the manufacturer's instructions.
75 ng total RNA of each sample was used with Illumina TruSeq Stranded mRNA Library Prep Kit using standard Illumina protocols

tag: agent

value: 35% ethanol

tag: dose

value: liver left lateral lobe


title: methylenedianiline_100mg/kg_4001_RNASeq

source_name: methylenedianiline_100mg/kg, liver left lateral lobe

value: methylenedianiline


title: Zf_28d_GSC_B


title: methylenedianiline_100mg/kg_4003_RNASeq


title: H0609


title: Zf_28d_GSC_A


title: H0610


title: methylenedianiline_100mg/kg_4005_RNASeq


title: 35% ethanol_2ml/kg_1001_RNASeq


title: 35% ethanol_2ml/kg_1003_RNASeq


title: H0608


title: Zf_35d_M_Control_B


title: Zf_35d_M_Control_A


title: Zf_28d_Control_C


title: H0607


title: H0603


title: diclofenac_10mg/kg_4005_RNASeq

source_name: diclofenac_10mg/kg, liver left lateral lobe

value: diclofenac


title: Zf_28d_Control_A


title: diclofenac_10mg/kg_4003_RNASeq


title: Zf_28d_Control_B


title: diclofenac_10mg/kg_4001_RNASeq


title: H1203

value: Male


title: Br3010

source_name: Cortex

value: Wild Type

value: Cortex


title: Br3009


title: acetaminophen_1000mg/kg_3003_RNASeq

source_name: acetaminophen_1000mg/kg, liver left lateral lobe

value: acetaminophen


title: Br3008


title: Zf_25d_GSC_A


title: Zf_25d_GSC_B


title: Br3004


title: Br3003


title: acetaminophen_1000mg/kg_3001_RNASeq


title: corn oil_2ml/kg_2001_RNASeq

source_name: corn oil_2ml/kg, liver left lateral lobe

value: corn oil


title: corn oil_2ml/kg_2003_RNASeq


title: Br2010


title: corn oil_2ml/kg_2005_RNASeq


title: Zf_25d_Control_B


title: Zf_25d_Control_A


title: Br2006


title: water_10ml/kg_1003_RNASeq

source_name: water_10ml/kg, liver left lateral lobe

value: water


title: Zf_21d_GSC_C

source_name: Germinal stem cells


title: Br2005


title: water_10ml/kg_1001_RNASeq


title: CCl4_1582mg/kg_4005_RNASeq

source_name: CCl4_1582mg/kg, liver left lateral lobe


title: Zf_25d_GSC_C


title: acetaminophen_1000mg/kg_3005_RNASeq


title: CCl4_1582mg/kg_4003_RNASeq


title: Br1209


title: Zf_21d_GSC_B


title: Br2003


title: Br2004


title: Zf_21d_GSC_A


title: Zf_21d_Control_C

source_name: Whole embryo eGFP -


title: CCl4_1582mg/kg_4001_RNASeq


title: Zf_21d_Control_B


title: ANIT_100mg/kg_3005_RNASeq

source_name: ANIT_100mg/kg, liver left lateral lobe

value: ANIT


title: Zf_21d_Control_A


title: Zf_25d_Control_C


title: ANIT_100mg/kg_3003_RNASeq


title: ANIT_100mg/kg_3001_RNASeq


title: Br1204


title: Br1203


title: corn oil_5ml/kg_1003_RNASeq

source_name: corn oil_5ml/kg, liver left lateral lobe


title: corn oil_5ml/kg_1001__RNASeq


title: Br0608


title: Br0603


title: Br0607


title: Zf_14d_Control_A


title: Zf_14d_Control_C


title: HR rehydrated2

city: Beijing

first: Chih Ta

last: Lin

address: No.20 Nanxincun, Xiangshan

department: CAS Key Laboratory of Photosynthesis and Molecular Physiology

country: China

institute: Institute of Botany Chinese Academy of Sciences

description:
R-2
replicate2

data_processing:
HiSeq Software Suite was used for reads collection
The raw paired reads were trimmed and quality controlled by Seqprep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters.
Then clean data from the samples (Haberlea rhodopensis) were used to do RNA de novo assembly with Trinity (http://trinityrnaseq.sourceforge.net/), Grabherr et al, 2011, Nat. Biotechnol.
Supplementary_files_format_and_content: GeneID, length, FPKM values and annotation results are listed in FPKM_annot.xls

organism: Haberlea rhodopensis

source_name: leaf

growth_protocol: Haberlea rhodopensis in vitro propagated plants (Djilianov et al. 2005) were transferred to standard soil-sand-gravel mixture in pots (6 cm diameter) and grown for about a year under controlled environment at 22-24 °C, a 16-h photoperiod, 60% relative humidity, and a photon flux density of 36 µmol m-2 s-1.

extract_protocol: Plant leaves (0.4g) were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in 2ml Eppendorf tubes and total RNA was isolated following the protocol of GeneMATRIX Universal RNA kit (EURx Ltd., Gdansk, Poland).

treatment_protocol: Dehydration was induced by withholding water of pot plants. They were fully desiccated for 8 days. After 10 days at full dry state, rehydration was started by watering the plants. They recovered for a week.   In vivo fast fluorescence-based approach was applied for collection of plant leaf simples, according to established relation between leaf water content and photosynthetic performance at stress and recovery (Mladenov et al. 2015)  Handy PEA (Hansatech Instrument Ltd., King's Lynn, Norfolk, PE30 4NE, UK) device was used for measurement of the prompt chlorophyll a fluorescence on plants in light-adapted state. The SOM developed as a result in previous study (Mladenov et al. 2015) was applied and plant samples were collected at five points responding to the fallowing relative water content (RWC): fully hydrated (fresh) leaves - F (90% RWC), two stages of dehydration (D75, 75% RWC) and (D20, 20% RWC), fully desiccated leaves (DT, 6% RWC) and recovery (R, 90% RWC).  Mature, fully expanded leaves from the middle of rosettes with similar size and appearance were used in all measurements. At least 4 independent plants were used for each sampling point.

value: leaf

tag: water stress

value: Rehydrated after fully dehydrated

tag: rwc


title: Zf_14d_Control_B


title: Zf_11d_GSC_C


title: Zf_11d_GSC_A


title: Br1207

tag: strain

tag: tissue


title: Br1208

tag: gender

tag: age,months


title: Zf_14d_GSC_B


title: HR rehydrated1

description:
R-1
replicate1


title: Zf_14d_GSC_A


title: HR fully dried2

description:
DT-2
replicate2

value: Fully dehydrated


title: Zf_11d_Control_C


title: HR fully dried1

description:
DT-1
replicate1


title: Zf_11d_Control_A


title: Br0609

tag: genotype


title: Zf_11d_GSC_B


title: corn oil_5ml/kg_1005_RNASeq

value: male


title: HR 20%RWC2

description:
D20-2
replicate2

value: Extensively dehydrated


title: Br0610


title: HR 20%RWC1

description:
D20-1
replicate1


title: Zf_14d_GSC_C

value: vas:eGFP (Krøvel AV et al., 2002)

value: Pooled male and female


title: HR 75%RWC1

description:
D75-1
replicate1

value: Slightly dehydrated


title: Zf_07d_GSC_C


title: Zf_07d_GSC_B


title: Zf_11d_Control_B


title: Zf_07d_Control_C


title: Zf_07d_Control_B


title: Untreated control2

description:
F-2
replicate2

value: Untreated


title: Untreated control1

description:
F-1
replicate1


title: Zf_07d_Control_A


title: HR 75%RWC2

description:
D75-2
replicate2


title: Zf_04d_GSC_C


title: Zf_04d_GSC_A


title: Al3

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

hyb_protocol: Equal amounts of RNA, isolated from each of the six plants per treatment, were pooled, resulting in a total of 24 samples (6 treatments x 4 experimental replicates). RNA was hybridized on custom 12x135K microarrays (Roche NimbleGen, Basel, Switzerland), using one array per sample (pooled treatment).

scan_protocol: Standard procedures were followed.

data_processing: Data were transferred to the Bioconductor framework (limma, Smyth 2004) for final statistical processing (normalisation using Loess and Aquantile). A linear model that treats the non-infested control plants as a common reference was fitted to the processed data. Relative transcript levels and associated Benjamini-Hochberg false discovery rate-adjusted P-values were identified via empirical Bayes statistics. Significant differentially expressed genes were identified by applying a P-value and log2 fold change (FC) cutoff of 0.05 and 0.585, respectively.

label: Cy3 and Cy5

organism: Solanum lycopersicum

source_name: leaf material

label_protocol: Preparation, labeling, purification, hybridization and scanning was carried out by the MicroArray Department (MAD) of the University of Amsterdam (Amsterdam, the Netherlands) according to the manufacturer’s specifications (Roche NimbleGen).

growth_protocol: Tomato (S. lycopersicum cv. Castlemart) and bean (P. vulgaris cv. Speedy) plants were germinated and grown in a greenhouse (25/18 °C day/night temperature, 16 light (L)/8 dark (D) photoperiod, 50-60% relative humidity (RH)). Experiments were carried out in a climate room (25 °C, 16L/8D photoperiod, 60% RH, 300 µmol m-2 s-1), to which plants were transferred seven days in advance.

extract_protocol: Total RNA was isolated from tomato tissue using the hot phenol method (Verwoerd et al., 1989). RNA integrity was checked by agarose-gel electrophoresis and a NanoDrop spectrophotometer (ND-1000; Thermo Fisher Scientific, Waltham, MA, USA) was subsequently used to assess RNA quantity and purity.

treatment_protocol: Mites were transferred to 21-day-old tomato plants and infested leaflets were harvested seven days later, following previously described procedures (Glas et al., 2014; Alba et al., 2015), with minor modifications. Briefly, plants were infested either with one species of mite (T. urticae, T. evansi, or A. lycopersici), or simultaneously with a combination of two species (T. urticae plus T. evansi, or T. urticae plus A. lycopersici).   Tetranychid mite infestations were performed by individually transferring adult females, randomly collected from the rearing population, with a fine brush to each of three leaflets per plant. For single infestations, each leaflet received 15 spider mites so that in total each plant was infested with 45 spider mites.   Russet mite infestations were performed by transferring mites on small pieces (ca. 0.5 cm²) of leaflet, cut out from well-infested rearing-plants, to each of three leaflets per plant. These leaflet pieces were cut out while using a stereo microscope to ensure each of them contained approximately 250 mobile stages of russet mites. For single infestations, each plant was thus infested with approximately 750 russet mites.   For the dual infestation treatments, each of three leaflets received either 15 T. urticae + 15 T. evansi (in total 90 spider mites per plant), or 15 T. urticae + approximately 250 A. lycopersici (in total 45 spider mites and 750 russet mites per plant).

tag: infested with

value: Aculops lycopersici


title: Zf_04d_GSC_B


title: Zf_07d_GSC_A


title: Al4


title: InfectedVehicle_3

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description:
Ribominus RNA
Exp#5-R

data_processing:
Base calling was performed using RTA version 1.18.64.
Demultiplexing and fastq file generation were conducted using bcl2fastq.
RNA-seq reads were trimmed using Cutadapt (version 1.14) to remove sequencing adapters, prior to mapping to a custom h19+KSHV (NC_009333.1) reference genome with STAR (version 2.5.2b) in two-pass mode with parameters: first pass parameters (--outSAMstrandField None --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesIn $r1 $r2 --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix $sampleName --chimSegmentMin 20 --outSAMtype BAM Unsorted), second pass parameters (--outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbFileChrStartEnd pass1.uniq.sj.out.tab --chimSegmentMin 20 --outSAMtype BAM Unsorted)
For annotation, the GENCODE Human v19 reference gene annotation (GTF) combined with the KSHV gene annotation were used.
The chimeric alignments were detected using the –chimSegmentMin parameter by the STAR aligner. These chimeric alignments were used by CIRCexplorer version 1.1.1 for detecting circRNAs. circRNAs with at least 5 reads mapping to the head-to-tail splice junction in one sample were used for quantitative analyses.
For the identification of viral circular RNAs, total RNA treated or not treated with RNase R were aligned by STAR with two-pass alignment for accurate mapping to novel splicing junctions. The chimeric alignments were used to detect viral circRNAs with CIRCExplorer2.3.
Genome_build: hg19 (GRCh37) + KSHV (NC_009333.1)
Supplementary_files_format_and_content: bed files containing back-splice junctions from the second pass of STAR.

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: Primary cells, HUVEC

growth_protocol: HUVEC cells were grown in EGM2 media.

extract_protocol:
Total RNA was purified using miRNeasy System (Qiagen).
Total RNA samples were depleted of ribosomal RNA using RiboMinus Eukaryote System v2 (ThermoFisher). Ribo-depleted RNA was treated with 6 U of RNase R (Epicenter Biotechnologies) at 37° for 15 min. Libraries were generated using TruSeq Stranded Total RNA System (Illumina).
Paired-end 150bp RNA-Seq sequencing reads.

treatment_protocol: Some conditions included RNase R treatment of the purified RNA.

tag: human cell type

value: HUVEC

tag: virus infection

value: KSHV

tag: rnase treatment

value: no

tag: time point

value: 2 days post infection


title: InfectedVehicle_4

description:
Ribominus RNA
Exp#6-R


title: InfectedVehicle_2

description:
Ribominus RNA
Exp#4-R


title: HK3RV

description:
Ribominus RNA
Exp#2+R

value: yes

value: 7 days post infection


title: Tu+Al4

value: Tetranychus urticae + Aculops lycopersici


title: InfectedVehicle_1

description:
Ribominus RNA
Exp#3-R


title: Zf_04d_Control_C

tag: line

tag: day post fertilisation


title: Al1


title: Zf_04d_Control_B

tag: number of fish

tag: Sex


title: Al2


title: HK3MV

description:
Ribominus RNA
Exp#2-R


title: Tu+Al3


title: Tu+Al2


title: Zf_04d_Control_A


title: Tu+Al1


title: Tu4

value: Tetranychus urticae


title: Tu3


title: Tu2


title: Tu1


title: Tu+Te3

value: Tetranychus urticae + Tetranychus evansi


title: Tu+Te2


title: HK1RV

description:
Ribominus RNA
Exp#1+R


title: HK1MV

description:
Ribominus RNA
Exp#1-R


title: LP rep2

city: zhanjiang

first: ying

middle: bin

last: xue

state: Guangdong

address: Haida Road #1, Mazhang District

department: College of Chemistry and Environment

institute: Guangdong Ocean University

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Remove contaminated Reads (the number of bases contaminated with Reads is greater than 5 bp. For double-stranded sequencing, if one end is affected Connector contamination, then remove both ends of the Reads). Remove low-quality Reads (Quality Q ≤ 19 bases in Reads account for more than 50% of total bases. For double-stranded sequencing, If one end has low quality Reads, both ends will be removed). Remove Reads containing more than 5% of N (for double-ended sequencing, if the ratio of N at one end is greater than 5%, both ends will be removed Reads)
Bowtie2 v2.2.3 was used for building the genome index,and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Screening DEGs using DESeq2 v1.6.3.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample .

organism: Glycine max

source_name: Nodule

extract_protocol:
Total RNA of nodules was isolated using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. The quantity and purity of total RNA was checked using a Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nodule

tag: phosphorus conccentration

value: 25 mM


title: Zf_02d_GSC_B


title: Zf_02d_GSC_A


title: Tu+Te4


title: LP rep3


title: Zf_02d_GSC_C


title: HP rep3


title: Tu+Te1


title: Zf_02d_Control_B


title: Zf_02d_Control_A


title: HP rep2


title: Te4

value: Tetranychus evansi


title: Zf_01d_GSC_C

value: vas:eGFP (Krøvel AV et al., 2002)


title: C4

value: no mites, control


title: Zf_02d_Control_C

value: Pooled male and female


title: Te1


title: Te3


title: LP rep1


title: HP rep1


title: Zf_01d_GSC_B


title: WT_Microarrays_CD4+Treg3_LN

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

hyb_protocol: Incubated for 17 hours at 45°C.

scan_protocol: Affymetrix Command Console software with Affymetrix 7G scanner.

data_processing:
Raw CEL files were preprocessed and normalized using Affymetrix Expression Console (version 1.4.1.46) and resulting data were analyzed with the Affymetrix Transcriptome Analysis Console (version 3.1.0.5).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: WT CD4+ Treg

label_protocol: GeneChip WT Pico Reagent Kit (biotin); A reverse transcription priming method that primes the entire length of RNA. The kit generates amplified and biotinylated sense-strand DNA targets from total RNA. Product is fragmented and labeled for hybridization.

extract_protocol: 50,000 RFP+ Treg or RFPneg Tconv cells from Foxp3-RFP+/+ Il2ramut/mut or WT reporter mice were flow-sorted (Aria III). Pelleted cells were stored in 700 micrL of TRIzol (Life Technologies) at-80C until RNA extraction. Total RNA was extracted using the RNAeasy Micro kit with RNase-Free DNase Set (Qiagen) according to the manufacturer protocol. The quality score and quantity of purified RNA was assessed with a Bioanalyzer RNA 6000 Pico Chip (Agilent). Total RNA was then converted to cDNA, amplified and hybridized to Affymetrix Mouse Transcriptome Array 1.0 Pico.

treatment_protocol: Naïve steady state mice of 6- 8 weeks old were bred in our SPF facility and lymph nodes used as a source of donor T cells.

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: 6-8 weeks

value: female

value: Lymph nodes

tag: cell type

value: Foxp3+ CD4+ regulatory T (Treg)


title: Il2ramut/mut_Microarrays_CD4+Treg3_LN

source_name: Il2ramut/mut CD4+ Treg

tag: tissue


title: C3


title: Il2ramut/mut_Microarrays_CD4+Treg1_LN


title: Il2ramut/mut_Microarrays_CD4+Treg2_LN


title: WT_Microarrays_CD4+Treg2_LN


title: C1


title: Zf_01d_Control_C


title: WT_Microarrays_CD4+Treg1_LN


title: Il2ramut/mut_Microarrays_CD4+Tconv2_LN

source_name: Il2ramut/mut CD4+ Tconv

value: conventional T (Tconv) cells


title: Zf_01d_GSC_A


title: Te2


title: Il2ramut/mut_Microarrays_CD4+Tconv1_LN


title: C2


title: Zf_01d_Control_A


title: Zf_01d_Control_B


title: Susceptible soybean stem 48 hours post infection biological replicate 2

status: Public on Nov 19 2018

city: Madison

first: Mehdi

last: Kabbage

state: Wisconsin

address: Department of Plant Pathology, 583 Russell Labs 1630 Linden Dr

department: Department of Plant Pathology

institute: University of Wisconsin Madison

data_processing:
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread. The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were generated using the featureCounts tool from subread.
Next, we performed additional QC at gene level, including number of genes detected, percentage of reads belonging to the top genes, normalization for RNA composition, and grouping and correlation between samples. Click here to view full QC report at gene level.
R Limma package was used for differential expression analysis. See section 3 above for further technical details.
Based on expression changes, we further carried out analyses to detect enriched functions
genome build: The Soybean genome (Reference_Gmax_275_v2.0.fa), gene annotations (Annotation_Gmax_275_Wm82.a2.v1.gene.gff3,originally downloaded from phytozome). Soybean chloroplast (NC_007942) and mitochondrion (NC_020455)
processed data files format and content: excel file include RPKM values for each Sample and comparison statistics for the designated conditions.
In this table, S1 is "S 0", S2 is "S 24 hpi", S3 is "S 48 hpi", S5 is "S 96 hpi"; R1 is "R 0", R2 is "R 24 hpi", R3 is "R 48 hpi", R5 is "R 96 hpi"; I, II III indicate biological replicates

source_name: Stem tissue

growth_protocol: Soybean seedlings and plants were maintained in the greenhouse or growth chamber at 24 ± 2◦C with 16 h light/8 h dark photoperiod cycle. S. sclerotiorum strain 1980 was grown at room temperature on potato dextrose agar (PDA).

extract_protocol:
Total RNA was extracted from the stem tissues and fungal material using a Trizol protocol. Samples were cleaned using the RNeasy Plant Mini Kit protocol (RNeasy Plant Mini Kit, Qiagen, Hilden, Germany). RNA concentration and purity were determined by Nanodrop and sample quality was assessed using an Agilent Bioanalyzer 2100 and a RNA 6000 Nano Kit.
RNA from each sample was randomly fragmented, and individually indexed libraries were prepared using the TruSeq RNA Sample Preparation v2 kit according to the manufacturer’s instructions  protocol. Library was quantified with Qubit HS DNA kit. The quality of the library was checked with an Agilent Bioanalyzer 2100 and an Agilent DNA 1000 kit.

treatment_protocol: Inoculations were performed using the cut petiole method as described by (Ranjan et al. 2017). Plant tissue was sampled by cutting horizontally above and below (1.5 cm) the node of the first trifoliate with a clean straight-edge razor. Tissue samples were collected at 24, 48, and 96 h post inoculation (hpi) and immediately frozen in liquid nitrogen prior to RNA extraction. For control non inoculated stem tissues were collected for R and S line

tag: infection time

tag: plant phenotype

value: susceptible


title: Susceptible soybean stem 24 hours post infection biological replicate 3


title: Susceptible soybean stem 48 hours post infection biological replicate 1


title: Susceptible soybean stem 96 hours post infection biological replicate 1


title: Susceptible soybean stem 96 hours post infection biological replicate 2


title: Susceptible soybean stem 48 hours post infection biological replicate 3


title: Susceptible soybean stem 96 hours post infection biological replicate 3


title: Susceptible soybean stem 24 hours post infection biological replicate 1


title: Susceptible soybean stem 24 hours post infection biological replicate 2


title: non infected susceptible soybean stem biological replicate 2


title: non infected susceptible soybean stem biological replicate 1


title: RAW264.7-IL13-72h

city: Hangzhou

first: Rong

last: Dong

state: Zhejiang

address: No.886 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

description:
To screen for the functional lncRNAs involved in macrophages M2 polarization, we utilized the cellular model of IL13-driven macrophage M2 polarization. RAW264.7 cells were treated with IL13 (10 ng/ml) for 72 hours.
RAW2647 cells were obtained from the Cell Bank of the China Science Academy (Shanghai, China).

hyb_protocol: Pre-hybridization:   1) Assembled  CustomArray™ microarray with Hybridization Cap and Clips.  2) Fill the hybridization chambers with nuclease-free water. Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation.  3) Incubate at 65°C for 10min.  4) Remove the microarray from the incubator and bring to room temperature. Remove the adhesive tape and aspirate the water out of the hybridization chambers.  5) Fill the hybridization chambers with Pre-hybridization Solution. Mix gently by pipetting. A small air bubble can be introduced to improve the mixing process if the arrays are rotated. Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape.  6) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation. Hybridization:   1) Prepare the hybridization solution with labeled RNA target.  2) Denature the hybridization solution at 95°C for 3 minutes, and then cool for 20 seconds on ice. Remove the hybridization solution from ice and keep it at room temperature.  3) Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.  4) Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.  5) Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting. A small air bubble will form, and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.  6) Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue, and cover the solution portals with adhesive tape.  7) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation. Hybridization washing:   1) Remove the microarray from the hybridization oven. Remove the adhesive tape and pipet the hybridization solution out of the chambers.  2) Using the Wash solution 1, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 1 from the hybridization chambers.  3) Using the Wash solution 2, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 2 from the hybridization chambers.  4) Using the Wash solution 3, rinse the hybridization chambers, fill the chambers,and incubate the array for 3 minutes at room temperature. Remove the Wash solution 3 from the hybridization chambers.  5) Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix4000B (Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it, taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: The raw signal is normalized with quantile normalization method. Standard selection criteria to identify differentially expressed genes are established at P < 0.05.

source_name: RAW264.7 cells were treated with IL13 (10 ng/mL) for 72 hours

label_protocol: The platinum complex of ULS molecule was used to form coordinative bound with the N7 position of guanine. Labeling efficiency can be calculated by the concentration of CyDye and RNA measured by K5500 micro-spectrophotometer. For good microarray result, labeling efficiency should be between 1.0~3.6.

growth_protocol: RAW264.7 cells were cultured in DMEM medium containing 10% FBS and 100U per ml of penicillin-streptomycin in a 5% CO2 humidified incubator at 37°C.

extract_protocol: 1. For proper amount of cells, add 1mL of TRIzol reagent and mix by briefly vortex. Stand for 5 mins at room temperature. If a lot of insoluble material exists after homogenization and room-temperature incubation, remove by centrifugation at 12,000Xg for 10 mins at 4ºC. Transfer the supernatant to a fresh tube.  2. Add 200ul chloroform for 1ml mixture and vortex for 15 sec. Then stand for 5 mins at room temperature.  3. Centrifuge the mixture for 15 min at ≥12000xg at 4ºC.  4. Transfer the aqueous phase (the upper layer containing RNA) to a fresh tube.  5. Add equal volume of 100% Isopropanol to the aqueous phase, mix by inverting the tube several times.  6. Incubate at ‐20ºC for ≥30 min.  7. Centrifuge at 13000 rpm for 15 min at 4ºC.  8. Wash the pellet with 80% EtOH, invert the tube several times. Centrifuge at 7500 rpm for 5 min at -4ºC.  9. Carefully discard the supernatant without touching the pellet, dry the pellet at room temperature.  10. Dissolve the pellet with 20‐30ul DEPC-treated H2O, based on the size of the pellet. RNA solution should be stored at -80ºC.

treatment_protocol: RAW264.7 was seeded in 6-well plates at a density of 2×10^5/well and stimulated with 10 ng/ml IL13 for indicated times.

tag: cell line

tag: treatment

tag: time


title: RAW264.7-IL13-48h

description:
To screen for the functional lncRNAs involved in macrophages M2 polarization, we utilized the cellular model of IL13-driven macrophage M2 polarization. RAW264.7 cells were treated with IL13 (10 ng/ml) for 48 hours.
RAW2647 cells were obtained from the Cell Bank of the China Science Academy (Shanghai, China).

source_name: RAW264.7 cells were treated with IL13 (10 ng/mL) for 48 hours


title: WT_Microarrays_CD4+Tconv2_LN

source_name: WT CD4+ Tconv


title: resistant soybean stem 48 hours post infection biological replicate 1

value: resistant


title: RAW264.7-IL13-24h

description:
To screen for the functional lncRNAs involved in macrophages M2 polarization, we utilized the cellular model of IL13-driven macrophage M2 polarization. RAW264.7 cells were treated with IL13 (10 ng/ml) for 24 hours.
RAW2647 cells were obtained from the Cell Bank of the China Science Academy (Shanghai, China).

source_name: RAW264.7 cells were treated with IL13 (10 ng/mL) for 24 hours


title: resistant soybean stem 96 hours post infection biological replicate 2


title: resistant soybean stem 24 hours post infection biological replicate 3


title: resistant soybean stem 96 hours post infection biological replicate 3


title: RAW264.7-Control

description:
To screen for the functional lncRNAs involved in macrophages M2 polarization, we utilized the cellular model of IL13-driven macrophage M2 polarization. RAW264.7 cells without treatment were regarded as control group.
RAW2647 cells were obtained from the Cell Bank of the China Science Academy (Shanghai, China).

source_name: RAW264.7 cells were untreated


title: resistant soybean stem 96 hours post infection biological replicate 1


title: resistant soybean stem 48 hours post infection biological replicate 3


title: BMDMs-Control

hyb_protocol: Pre-hybridization:  1) Assembled CustomArray™ microarray with Hybridization Cap and Clips. 2) Fill the hybridization chambers with nuclease-free water. Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation. 3) Incubate at 65°C for 10min. 4) Remove the microarray from the incubator and bring to room temperature. Remove the adhesive tape and aspirate the water out of the hybridization chambers. 5) Fill the hybridization chambers with Pre-hybridization Solution.Mix gently by pipetting. A small air bubble can be introduced to improve the mixing process if the arrays are rotated. Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape. 6) Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation. Hybridization:  1) Prepare the hybridization solution with labeled RNA target. 2) Denature the hybridization solution at 95°C for 3 minutes, and then cool for 20 seconds on ice. Remove the hybridization solution from ice and keep it at room temperature. 3) Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed. 4) Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers. 5) Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting. A small air bubble will form, and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven. 6) Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue, and cover the solution portals with adhesive tape. 7) Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation. Hybridization washing:  1) Remove the microarray from the hybridization oven. Remove the adhesive tape and pipet the hybridization solution out of the chambers. 2) Using the Wash solution 1, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue. Remove the Wash solution 1 from the hybridization chambers. 3) Using the Wash solution 2, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue. Remove the Wash solution 2 from the hybridization chambers. 4) Using the Wash solution 3, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperatrue. Remove the Wash solution 3 from the hybridization chambers. 5) Repeat step one more time for a total of two washings with the Wash solution 3.

source_name: BMDMs were untreated

growth_protocol: Six-week-old C57BL/6 mice were sacrificed and soaked in 75% ethanol. Bone marrow cells were cultured in DMEM containing 10% FBS and 50 ng/ml M-CSF for three days to obtain BMDMs.

treatment_protocol: BMDMs were seeded in 6-well plates at a density of 2×10^5/well and stimulated with 10 ng/ml IL13 for indicated times.

tag: strain/background

value: 6 weeks

value: bone marrow-derived macrophages (BMDMs)


title: resistant soybean stem 24 hours post infection biological replicate 1


title: non infected resistant soybean stem biological replicate 3


title: resistant soybean stem 24 hours post infection biological replicate 2


title: non infected susceptible soybean stem biological replicate 3


title: non infected resistant soybean stem biological replicate 1


title: EV RNA, dcl234 triple mutant, Replicate 1

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Leaf EV RNA

data_processing:
Read quality control usinf FastQC
Adaptor trimming and chopping using Cutadapt with a minimum size of 10 and a maximum size of 34
Genome alignment using Bowtie and Arabidopsis TAIR10 genome
sequeces are then formated to tag-count format
Genome_build: The Arabidopsis Information Resource (TAIR) v10
Supplementary_files_format_and_content: Final trimmed and cropped output file in tag-count format

source_name: Leaf EV RNA

growth_protocol: Arabidopsis seeds were surfaced sterilized using 50% bleach, plated on half-strength Murashige and Skoog medium containing 0.8% agar. The seeds were placed at 4*C for 2 days before being moved to short day conditions (9 hour days, 22*C, 150 uEm-2s-1). After one week, seedlings were transferred to ProMix-B soil and grown for 6 weeks before harvest.

extract_protocol:
RNA was extracted using Trizol (Invitrogen #15596026)
Libraries were constructed following manufacturer's instructions using NEBNext (NEB #E7330S)

treatment_protocol: Vesicles were isolated from the apoplastic wash of Arabidopsis rosettes as described in Rutter and innes 2017 (DOI:10.1104/pp.16.01253)

tag: genotype

value: dcl234 triple mutant

tag: replicate

value: Leaf

tag: rna fraction

value: Extracellular vesicle RNA


title: WT_Microarrays_CD4+Tconv 1_LN


title: resistant soybean stem 48 hours post infection biological replicate 2


title: Leaf TotalRNA, dcl234 triple mutant, Replicate 1

description: Leaf total RNA

source_name: Leaf total RNA

value: Total RNA


title: Supernatant RNA, dcl234 triple mutant, Replicate 1

description: Leaf Supernatant RNA

source_name: Leaf Supernatant RNA

value: Supernatant RNA


title: Supernatant RNA, dcl234 triple mutant, Replicate 2

description: Leaf Supernatant RNA


title: Leaf TotalRNA, dcl234 triple mutant, Replicate 2

description: Leaf total RNA


title: EV RNA, dcl234 triple mutant, Replicate 2

description: Leaf EV RNA


title: non infected resistant soybean stem biological replicate 2


title: EV RNA, Col-0, Replicate 3

description: Leaf EV RNA

data_processing:
Read quality control usinf FastQC
Adaptor trimming and chopping using Cutadapt with a minimum size of 10 and a maximum size of 34
Genome alignment unig Bowtie and Arabidopsis TAIR10 genome
sequences are then formated to tag-count format
Genome_build: The Arabidopsis Information Resource (TAIR) v10
Supplementary_files_format_and_content: Final trimmed and cropped output file in tag-count format

tag: ecotype

value: Columbia 0


title: EV RNA, Col-0, Replicate 2

description: Leaf EV RNA


title: Supernatant RNA, Col-0, Replicate 3

description: Leaf Supernatant RNA


title: Supernatant RNA, Col-0, Replicate 1

description: Leaf Supernatant RNA


title: Leaf TotalRNA, Col-0, Replicate 3

description: Leaf total RNA


title: Supernatant RNA, Col-0, Replicate 2

description: Leaf Supernatant RNA


title: Leaf TotalRNA, Col-0, Replicate 2

description: Leaf total RNA


city: München

first: Marlies

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description:
MOCR-HeLa-NS-CTCF-10sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 5 sec R1T1

data_processing:
Library strategy: CUT&RUN (Cleavage under targets and Release using nuclease)
Reads were mapped to hg19 using bowtie2. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
PCR duplicates, ChrM etc were removed to obtain bam files of valid reads. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files of valid reads were converted to bed files and separated by reads longer than 120bp and smaller than 120bp for further downstream analysis using HOMER. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
These cut and run bed files were only used to make signal aggregation plots on functional elements using HOMER.
For correct use of no antibody control files, files should be match to the cut&run experiment done at the same time. CTCF matches with NoAb R1 and R2, H2A.Z matches with NoAb R2 and R3 and H3K4Me1 and Me3 match with NoAb R3 and R4.
Genome_build: hg19
Supplementary_files_format_and_content: bed files of all valid reads of combined replicates for further processing using HOMER

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each CUT&RUN library 500,000 cells were used
CUT&RUN was performed according to published protocol (Skene and Henikoff, Elife, 2017), with minor changes. See supplemental methods in Oomen et al 2018 for more information

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using Thymidine treatment and Nocodazole (mitotic cells). See supplemental methods for more information

tag: protocol

value: CUT&RUN

tag: enzyme

value: MNase

value: Human adenocarcinoma cells

value: HeLa-S3 (CCL-2.2)


description:
MOCR-HeLa-NS-CTCF-1min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 30 sec R1T1


title: Leaf TotalRNA, Col-0, Replicate 1

description: Leaf total RNA


description:
MOCR-HeLa-NS-CTCF-30min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 30 min R1T1


description:
MOCR-HeLa-MC-CTCF-10sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 10 sec R1T1


description:
MOCR-HeLa-MC-CTCF-1min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 1 min R1T1


description:
MOCR-HeLa-MC-CTCF-30sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 30 sec R1T1


title: EV RNA, Col-0, Replicate 1

description: Leaf EV RNA


description:
MOCR-HeLa-NS-CTCF-10min-combined_R1_R2.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 10 min R1T1


description:
MOCR-HeLa-MC-CTCF-30min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 30 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 30 sec R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-30sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 30 sec R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa non sync cell Cut&Run no antibody control 1 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-1min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 1 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


description:
MOCR-HeLa-MC-CTCF-10min-combined_R1_R2.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 10 min R1T1


description:
MOCR-HeLa-MC-CTCF-5min-R1T1S1_2.bam.quality.sort.unique.bam.sort.bam.unique.sam.gz.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run on CTCF 5 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 10 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-10min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 10 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa non sync cell Cut&Run no antibody control 5 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 5 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: BMDMs-IL13

source_name: BMDMs were treated with IL13 (10 ng/mL) for 24 hours


title: HeLa Mitotic Cell Cut&Run no antibody control 30 sec R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-30sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 30 sec R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


description:
MOCR-HeLa-NS-CTCF-5min-R1T1S1_2.bam.quality.sort.unique.bam.sort.bam.unique.sam.gz.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 1 min R1T1


title: HeLa non sync cell Cut&Run no antibody control 30 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-NS-NoAb-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run no antibody control 30 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa Mitotic Cell Cut&Run no antibody control 10 sec R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-10sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 10 sec R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


description:
MOCR-HeLa-NS-CTCF-30sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa non sync cell Cut&Run on CTCF 10 sec R1T1


title: HeLa Mitotic Cell Cut&Run no antibody control 1 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-1min-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 1 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa Mitotic Cell Cut&Run no antibody control 5 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-5min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 5 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa Mitotic Cell Cut&Run no antibody control 30 min R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-30min-R1_R2.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 30 min R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: HeLa Mitotic Cell Cut&Run no antibody control 0 sec control R1T1 (match with CTCF R1)

description:
MOCR-HeLa-MC-NoAb-0sec-R1T1S1.bam.quality.sort.unique.bam.no_blacklist.bam.no_norm.bed.gz (in CUT_and_RUN_BED_files.tar.gz)
HeLa Mitotic Cell Cut&Run no antibody control 0 sec control R1T1 (match with CTCF R1, processed files combine replicates R1 and R2 for CTCF)


title: T47D-NC

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description: This sample is of T47D transfected with lentivirus of negtive control.

hyb_protocol: Microarray hybridization was performed at 65°C for 17 hours on NimbleGen 12x135k Whole Human Genome Oligonucleotide Microarray (HG18) in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Axon GenePix 4000B (Molecular Devices) and uploaded into NimbleScan (v2.5), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

label_protocol: cDNA samples were amplified, Cy3-labeled with NimbleGen one-color DNA labeling kit following manufacturer’s protocol. Microarray hybridization was performed at 65°C for 17 hours to NimbleGen whole human genome 12x135K microarrays in NimbleGen Hybridization System.

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37o C and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: T47D cells transfected with lentivirus are referred as T47D-NC and T47D-shTRPS1.

value: breast cancer cell line T47D