title: 3bp_substitution_offtarget_1

data_processing:
Library strategy: 3 bp substitution cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the mutagenized subset of the S. cerevisiae HAS1pr-TDA1pr region using Bowtie2. The read alignments were scored for the number of substitutions, insertions, and deletions, and the frequency of each substitution and the total number of reads were calculated.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "mutcounts.txt" include the 1) set of mutations, 2) the total number of mutations, 3) the number of substitutions, 4) the number of deletions, 5) the number of insertions, 6) the number of reads with this set of mutations. tab-delimited text files ending in "subcounts.txt" include the number of reads with each substitution and the total number of reads. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

value: DpnII


title: validation_ko_genomic_2

status: Public on Aug 05 2018

type: SRA

city: Stanford

first: Seungsoo

last: Kim

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

country: USA

institute: Stanford University

description:
fixed-locus_ko_barcodes.fa
validation_ko_associations.txt

library_source: genomic

data_processing:
Library strategy: fixed-locus trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed to a fixed length of 25 bp and mapped to the set of possible barcodes using Bowtie2. Barcodes were associated with gene knockouts based on programmed barcode associations.
Genome_build: Barcode file fixed-locus_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include an identifier for each barcoded construct, the systematic name of the gene knockout, and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping. tab-delimited text files ending in "associations.txt" include the gene knockout (including "r" for replicates) and the systematic gene name.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.

treatment_protocol: Cells were crosslinked by addition of 37% formaldehyde to a 1% final concentration, for 20 minutes at room temperature, and then quenched by addition of 2.5M glycine, incubation for 5 minutes, and a TBS (Tris-buffered saline) wash.

tag: growth conditions

value: saturated in YPD

tag: restriction enzyme

value: EcoRI-HF


title: 3bp_substitution_genomic_2


title: P187_08_Cln3_dex7-8_1070_light_NaCl

status: Public on Aug 17 2018

type: RNA

city: Cologne

first: Thomas

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

country: Germany

institute: University of Cologne

description: total retina transcripts from Cln3_dex7-8 light plus Nacl

hyb_protocol: 15 µg of fragmented cRNA was hybridized to Affymetrix mouse Clariom S arrays

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 Blank7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression Console and Genomatix Software using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Retina from Cln3_dex7-8 light plus Nacl

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

growth_protocol: All experimental procedures were in compliance with the German law on animal protection and the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research.

extract_protocol: Retinas were removed and RNA was harvested using Qiagen RNeasy Kit.

treatment_protocol: Wild type littermates and Cln3Δex7/8 mice were dark-adapted for 16 h before light exposure. To test low light and high light conditions, pupils were dilated with 2.5 % Phenylephrin and 1 % Tropicamid under dim red light and the mice were placed into aluminum foil-coated cages. A light intensity of 10,000 lux for 30 min for low light conditions and a light intensity of 15,000 lux for 60 min were used for high light conditions, respectively. Mice of both genotypes without light exposure served as controls. Then mice were then kept in dark-reared conditions over night. For the therapy study with minocycline only Cln3Δex7/8 mice and low light conditions were used. Minocycline (45 mg/kg dissolved in 0.9 % NaCl solution, Sigma) was injected intraperitoneally starting one day before light exposure and then daily until one day before the final experiment. Cln3Δex7/8 mice were injected with the same volume and frequency of 0.9 % NaCl solution as a solvent control

tag: tissue

value: retina

tag: treatment

value: light plus Nacl

tag: strain

value: Cln3 delta ex7/8


title: 3bp_substitution_offtarget_2


title: P187_04_Cln3_WT_1084_highlight

description: total retina transcripts fromCln3 WT high light

source_name: Retina from Cln3 WT high light

value: high light

value: Balb/c


title: validation_ko_genomic_1


title: 3bp_substitution_genomic_1


title: interactor_ko_genomic_2

description:
fixed-locus_ko_barcodes.fa
interactor_ko_associations.txt


title: fixed-locus_ko_offtarget_1

description:
fixed-locus_ko_barcodes.fa
fixed-locus_ko_associations.txt


title: validation_ko_3C_3


title: fixed-locus_ko_offtarget_2


title: 3bp_substitution_3C_2


title: fixed-locus_ko_genomic_3


title: fixed-locus_ko_genomic_2


title: 3bp_substitution_3C_1


title: validation_ko_3C_1


title: fixed-locus_ko_3C_2


title: fixed-locus_ko_genomic_1


title: error-prone_genomic_1

description: error-prone.fa

data_processing:
Library strategy: error-prone PCR cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the mutagenized subset of the S. cerevisiae HAS1pr-TDA1pr region using Bowtie2. The read alignments were scored for the number of substitutions, insertions, and deletions, and the frequency of each substitution and the total number of reads were calculated.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "mutcounts.txt" include the 1) set of mutations, 2) the total number of mutations, 3) the number of substitutions, 4) the number of deletions, 5) the number of insertions, 6) the number of reads with this set of mutations. tab-delimited text files ending in "subcounts.txt" include the number of reads with each substitution and the total number of reads. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.


title: error-prone_genomic_2

description: error-prone.fa


title: in-gene_ko_offtarget_2

data_processing:
Library strategy: in-gene trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were mapped to the set of possible barcodes using Bowtie2.
Genome_build: Barcode file in-gene_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include an identifier for each barcoded construct, the systematic name of the gene knockout, and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping.


title: error-prone_3C_1

description: error-prone.fa


title: error-prone_offtarget_1

description: error-prone.fa


title: in-gene_ko_genomic_2


title: in-gene_ko_genomic_1


title: fixed-locus_ko_3C_3


title: fixed-locus_ko_3C_1


title: error-prone_3C_2

description: error-prone.fa


title: subsequences_genomic_2

data_processing:
Library strategy: subsequences cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the S. cerevisiae HAS1pr-TDA1pr region, or the mutagenized subset thereof using Bowtie2. For subsequences, read coverage was calculated using bedtools.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "cov.txt" include the raw read coverage at each position within the HAS1pr-TDA1pr region. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.


title: subsequences_offtarget_1


title: in-gene_ko_3C_1


title: subsequences_genomic_1


title: subsequences_3C_2


title: subsequences_3C_1


title: validation_ko_3C_2


title: YMD3920_saturated_Sau3AI

description:
ScSu.32000.bed
Surep-rDNA.bed

data_processing:
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20) trimmed of adapter sequences and then trimmed up to the ligation junction (if present), excluding read pairs in which either read was shorter than 20 bp after trimming.
Reads were independently mapped using bowtie2 2.2.3 using the parameter set --very-sensitive. Reads were mapped to a combined reference containing both species references, where if secondary mappings were present the best alignment must have a score ≥ 10 greater than the next best alignment. Only read pairs in which both reads mapped with MAPQ ≥ 30 were used.
PCR duplicates (with identical fragment start and end positions) were removed, as were read pairs mapping within 1 kb of each other or in the same restriction fragment, which represent either unligated or invalid ligation products.
The genome was then binned into 32 kb fragments (except the last fragment of each chromosome), and the number of read pairs mapping to each 32 kb genomic bin was counted based on the position of the restriction sites that were ligated together. Due to gaps in the reference genomes of S. uvarum, some repetitive sequences were only represented once and therefore artifactually mapped uniquely; therefore, reads mapping to annotated repetitive sequences were masked from further analysis. The resulting matrices were then normalized by excluding the diagonal (interactions within the same genomic bin), filtering out rows/columns with an average of less than 1 read per bin, and then multiplying each entry by the total number of read pairs divided by the column and row sums.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD and Saccharomyces uvarum (bayanus var. uvarum) from saccharomycessensustricto.org, with minor modifications as described in Kim et al, eLife 2017.
Supplementary_files_format_and_content: tab-delimited text files ending in "matrix.txt" include the raw read counts and normalized interaction frequencies for each pair of 32 kb genomic bins; those ending in "rowsums.txt" include the raw sums across each row of these matrices. BED files include either the genomic regions included in each matrix bin or those masked from the matrices.

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme Sau3AI or HindIII, gap-filled in using biotinylated dCTP, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
Libraries were prepared according to manufacturer's instructions using the KAPA Hyper Prep kit.


title: YMD3920_exponential_Sau3AI

description:
ScSu.32000.bed
Surep-rDNA.bed

value: exponential growth in YPD


title: error-prone_offtarget_2

description: error-prone.fa


title: Fig3_2NoAb_50cells

status: Public on Jul 20 2018

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
library strategy: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol:
The CUT&RUN protocol was modified from Skene and Henikoff (eLife 2017), who made their modified protocol available online (http://blocks.fhcrc.org/steveh/papers/CUT&RUN_protocol.htm). Mouse ES cells were counted using a TC-10 cell counter (Biorad) and diluted manually to respective cell amounts. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were washed with 1mL cold PBS. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were resuspended in 1mL cold nuclear extraction (NE) buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% TritonX-100, 20% glycerol, freshly added protease inhibitors). Cells were pelleted at 600g for 3min at 4°C, the supernatant was discard and cells were resuspended in 600uL NE buffer. During the cell washes, Concanavalin A beads (Polysciences) were prepared. For 500,000 cells 200uL bead slurry were used, for 50,000 cells 150uL bead slurry were used, for 5,000 cells, 100uL bead slurry were used, for 500 cells and 50 cells 50uL bead slurry were used, and for 10 cells 20uL bead slurry were used. Beads were withdrawn and transferred to a microfuge tube containing 3X volume cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Beads were washed twice in 1mL cold Binding buffer and resuspended in 300uL binding buffer. Extracted nuclei were added to beads with gentle vortexing and incubated for 10 minutes at room temperature. After nuclei binding, cytosolic fraction was discarded and beads were blocked with 1mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) which was added with repeated gentle pipetting and incubated for 5 minutes at room temperature. Supernatant was discarded and nuclei/beads were washed in 1mL cold Wash Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250uL cold Wash Buffer. Primary antibody was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:100. Samples were incubated with rotation at 4°C for 2 hours. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 250uL cold Wash Buffer. ProteinA-MNase (kindly provided by Steven Henikoff) was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:400. Samples were incubated with rotation at 4°C for 1 hour. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 150uL cold Wash Buffer. Samples were equilibrated to 0°C on ice water for 5-10 minutes. 3uL 100mM CalC2 was added during gentle vortexing, samples were flicked quickly to mix and returned to 0C on ice water. After 5 minutes of digestion, reactions were stopped with addition of 150uL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen, 10pg/mL yeast spike-in DNA). Samples were incubated at 37°C for 20 minutes to activate RNase and release fragments. Samples were centrifuged at 16,000g for 5minutes and supernatants were transferred to a new microfuge tube while pellets and beads were discarded. Following addition of 3uL 10% SDS and 2.5uL 20m/gmL ProteinaseK, samples were mixed by inversion and incubated at 70°C for 10 minutes. DNA was cleaned using PCI followed by chloroform extraction, and precipitated with glycogen and ethanol. DNA was pelleted with a high speed spin at 4C, washed, air dried for ~5 minutes and resuspended in 36.5uL 0.1XTE.
Libraries were prepared using a modification of the Henikoff available protocol. DNA end-repair, phosphorylation, and A-tailing was performed in a single reaction, as follows. T4 DNA Polymerase (NEB) was diluted 1:20. 5uL 10X T4 DNA ligase buffer (NEB), 2.5uL 10mM dNTPs, 1.25uL 10mM ATP, 3.13uL 40% PEG4000, 0.63uL T4 PNK (NEB), 0.5uL diluted T4 DNA Polymerase, and 0.5uL Taq polymerase (homemade) was added to 36.5uL of CUT&RUN enriched DNA. Samples were incubated at 12°C for 15 minutes, 37°C for 15 minutes, followed by 72°C for 20 minutes in a thermocycler. Samples were put on ice immediately and the following adapter ligation reaction was performed. PE inline Illumina adapters were used for these experiments. 55uL of 1X Quick ligase buffer (NEB), 5uL Quick ligase (NEB), and 5uL of 1.5uM adapter mix was added to 50uL of A-tailed DNA and samples were incubated at 20°C for 15 minutes in a thermocycler. Immediately following adapter ligation, samples were cleaned using Ampure XP beads (Beckman Coulter). Beads were warmed to room temperature during adapter ligation and 38uL well-mixed beads were added to libraries. Samples were mixed thoroughly and incubated for 15 minutes at room temperature. Following solution clearing on a magnetic rack, supernatants were discarded and beads were washed two times with 200uL 80% EtOH. Samples were briefly spun, residual liquid was discarded, and beads were allowed to air dry for ~5 minutes. DNA was eluted from beads by resuspending beads in 30uL 10mM Tris-HCL pH 8.0 and incubation at room temperature for 2 minutes. Following solution clearing on a magnetic rack, 27.5uL DNA was transferred to a 0.2mL PCR tube and library enrichment was performed. Libraries were enriched for 14-19 cycles of PCR, with the following conditions. 10uL 5X KAPA buffer, 1.5uL 10mM dNTPs, 5uL 20uM PE PCR 1.0, 20uM PE PCR 2.0, 1uL KAPA hotstart HiFi polymerase (KAPA) was added to 27.5uL of library DNA. The following PCR program was used to enrich the samples: 98°C 45 seconds, 98°C 15 seconds, 60°C 10 seconds, steps two and three were repeated specified number of times, 72°C 1 minute. Following library enrichment, samples were loaded on an agarose gel and DNA corresponding to 150-700 bases was extracted using the Qiagen extraction buffer and Econospin columns. Size distribution of libraries was determined using a Fragment analyzer, and libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Unfixed nuclei were bound to Concanavalin A beads (Polysciences, Inc), washed, followed by successive addition of primary antibody followed by proteinA-MNase. Cleavage of MNase was initiated by calcium chloride addition and chelated by EDTA. Fragments were released and deep sequencing libraries were prepared.

tag: cell type

value: E14 mouse embryonic stem cells (ESCs)

tag: secondary antibody

value: proteinA-MNase kindly provided by Steven Henikoff, used at 1:400


title: in-gene_ko_offtarget_1


title: Fig3_NoAb_50cells


title: Fig3_2NoAb_50000cells


title: subsequences_offtarget_2


title: IMR90_CigS2

status: Public on Jul 18 2018

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

description: ATACseq

data_processing:
After removing adaptors using Trimmomatic, 50bp paired-end ATAC-Seq reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 with default parameters.
After filtering reads from mitochondrial chromosome M and sex chromosome Y, we included properly paired reads with high mapping quality (MAPQ score > 10, qualified reads) through SAMTools for further analysis. Duplicate reads were removed using Picard tools MarkDuplicates program.
ATAC-Seq peak regions of each sample were called using MACS2 with parameters --nomodel --shift -100 --extsize 200. The blacklisted regions in human were excluded from peak regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
For each of retina and RPE samples, the fragments were counted across each peak region using HTSeq.
Using Tophat and Cufflinks with default parameters, raw data were mapped to the hg19 genome assembly, and gene expression FPKM (Fragments Per Kilobase Of Exon Per Million) were obtained.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Peak files in narrowPeak format following columns: chromosome, start, stop, name, length of peak region, strand, integer score for display, fold-change, -log10(pvalue), -log10(qvalue), relative summit position to peak start. FPKM files for gene expression.

organism: Homo sapiens

source_name: cell line

extract_protocol:
Chromatin was extracted and processed for Tn5-mediated tagmentation and adapter incorporation, according to the manufacturer’s protocol (Nextera DNA sample preparation kit, Illumina®) at 37 °C for 30 minutes. Reduced-cycle amplification was carried out in presence of compatible indexed sequencing adapters. Total cellular RNA was purified using the Qiagen RNAeasy Mini kit and samples with RNA integrity number ≥ 7 were further processed. total RNA was denatured at 65°C for 5 minutes, cooled on ice, purified and incubated at 80°C for two minutes. The eluted mRNA was fragmented at 94°C for 8 min and converted to double stranded cDNA, end repaired, A-tailed, and ligated with indexed adaptors.
The quality of the libraries was assessed by DNA-based fluorometric assay (Thermo Fisher ScientificTM) and automated capillary electrophoresis (Agilent Technologies, Inc.). Up to 3 samples per lane were pooled and run on a HiSeq2500 Illumina sequencer with a paired-end read of 50bp. The quality of the libraries was also assessed by RNA-based fluorometric assay (Thermo Fisher ScientificTM) and automated capillary electrophoresis (Agilent Technologies, Inc.).

treatment_protocol: Fresh postmortem eyes were processed within 14 hours after death when obtained from Eye Banks (Portland, USA) and National Disease Research Interchange (Philadelphia, USA). For each eye, we separated the retina and RPE from other tissues and  obtained a punch (6 mm diameter) of retina or RPE tissue in each of macular and peripheral regions. Biopsy punches of fresh retina and RPE tissues were re-suspended in cold PBS.

tag: type of cell line

value: Cigarrete smoking

tag: replicate


title: in-gene_ko_3C_2


title: EP1_HDAC11

description: ATACseq

value: HDAC11 overexpression


title: EP1_Ctrl

description: ATACseq

value: Control


title: IMR90_Ctrl

description: ATACseq


title: IMR90_CigS1

description: ATACseq


title: Fig3_NoAb_50000cells


title: MG_1

status: Public on Jul 17 2018

city: Qingdao

first: xiao

last: fan

address: Nanjing Road 106

country: China

institute: Yellow Sea Fisheries Research Institute

data_processing:
Quality control by fastQC
Reads mapping to the reference genome using Bismark
Estimating methylation level
Supplementary_files_format_and_content: tab-delimited text files include methylated site for each Sample.

organism: Saccharina japonica

source_name: entire body

extract_protocol:
A total amount of 5.2 microgram genomic DNA be coped with RNAase and spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation.
Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system

tag: age

value: 2 momths

tag: developmental stage

value: male gametophyte


title: EP1_CigS2

description: ATACseq


title: FG_1

value: female gametophyte


title: EP1_Empty

description: ATACseq

value: Control with empty vector


title: FG_3


title: MG_2


title: SP_2

value: 4 months

value: sporophyte


title: FG_2


title: phyB c-term deletion red rep3

status: Public on Jul 14 2018

city: Austin

first: Inyup

last: Paik

state: TX

address: NHB 2.616, Stop A5000 100 East 24th St.

department: Molecular Biosciences

institute: UT Austin

description:
phyB_delta_C_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

library_source: transcriptomic

data_processing:
FastQC
Bowtie2
Tophat
HTseq
DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Total_Count.txt: Tab-delimited text file includes raw counts after HTseq.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings

growth_protocol: Total five genotypes: Col-0, cop1-4, spaQ, phyAphyB/phyB FL, and phyAphyB/phyB ΔC plants were used for mRNA sequencing analysis.

extract_protocol:
Total RNA was isolated using sigma plant total RNA kit (Sigma, Cat.# STRN250).
NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB Cat.# E7370S) was used to generate mRNA sequencing library according to the manufacturer’s instruction.

treatment_protocol: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days before treated for 3 hours of white light and 21 hours of dark incubation to induce germination. After initial 24 hours, seeds were further treated with far-red light (10 µmole/s2/m2) to inactivate phytochrome activity. After additional two days in the dark, seedlings were either collected (dark sample) or treated with 1 hour of continuous red light (red sample) (8 µmole/s2/m2).

tag: ecotype/background

tag: genotype/variation

value: phyB C-terminal deletion

value: Seedlings

value: 3 days

value: 1h red light


title: EP1_CigS1

description: ATACseq


title: phyB c-term deletion red rep1

description:
phyB_delta_C_R_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB c-term deletion red rep2

description:
phyB_delta_C_R_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: MG_3


title: phyB c-term deletion dark rep3

description:
phyB_delta_c_D_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: dark control


title: phyB full length red rep3

description:
phyB_FL_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: phyB full length


title: phyB full length red rep2

description:
phyB_FL_R_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB full length red rep1

description:
phyB_FL_R_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB full length dark rep3

description:
phyB_FL_D_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: SP_1


title: phyB c-term deletion dark rep2

description:
phyB_delta_c_D_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB c-term deletion dark rep1

description:
phyB_delta_c_D_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB full length dark rep2

description:
phyB_FL_D_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: spaQ red rep2

description:
spaQ_R_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: spaQ


title: spaQ red rep1

description:
spaQ_R_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: phyB full length dark rep1

description:
phyB_FL_D_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: SP_3


title: Col-0 red rep3

description:
Col_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: WT


title: cop1 red rep1

description:
cop1_R_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: C1.13_control_vHPC

status: Public on Jul 04 2018

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were trimmed for adaptors and aligned to mouse genome GRCm38/mm10 using STARv 2.5.0c with default settings.
Aligned reads were annotated to gene exons with HTSeq v0.6.11 using GTF release 86 (update 2016-10), using non-stranded union model for vHPC and stranded intersection-nonempty for mPFC and BNST.
Count matrixes for mPFC, BNST, vHPC were TMM and voom normalized with limma and batch adjusted with ComBat.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log(CPM) values, normalization was done separately for each brain region.

source_name: ventral hippocampus

growth_protocol: Mice (Charles River Laboratories, Sulzfeld, Germany) were housed in groups in a temperature and humidity controlled facility on a 12h light/dark cycle for the acclimatization period. All mice had ad libitum access to food and water throughout the experiment (except for the durations of behavioral tests). Animal procedures were approved by the Regional State Administration Agency for Southern Finland (license numbers ESAVI-3801-041003-2011 and ESAVI/2766/04.10.07/2014) and carried out in accordance to directive 2010/63/EU of the European Parliament and of the Council, and the Finnish Act on the Protection of Animals Used for Science or Educational Purposes (497/2013).

extract_protocol:
Brain regions were dissected on a sterile chilled petri dish within 7 minutes and tissue was flash-frozen in liquid N2. Total RNA was extracted with TriReagent (Molecular Research Center, Inc.) and RNA integrity was controlled with Bioanalyzer (Agilent). The rRNA was depleted with either Ribo-Zero Gold rRNA Removal Kit (Illumina; mPFC and vHPC) or custom designed Insert dependent adaptor cleavage (InDA-C) primers (BNST).
Sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), and Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits.

treatment_protocol: Mice were killed by cervical dislocation between 8 am and 11 am to avoid circadian differences in gene expression, and the order was counterbalanced across experimental conditions.

tag: age on dissection

value: 8  weeks

tag: Sex

value: male

tag: csds phenotype

value: control


title: Tomato

status: Public on Jun 25 2018

city: Chengdu

first: Juan

last: Xiao

state: Sichuan

address: Huimin road No.211, Wenjiang

department: Institute of Animal Genetics and Breeding, College of Animal Science and Technology

institute: Sichuan Agricultural University

description:
microRNA
miRNA-derived exosome-like nanoparticles in Tomato.

data_processing:
Original sequence was subjected to a series of stringent filters (such as removing low quality reads, repeated sequences and adaptor sequences) and called clean data.
The filtered reads were identified by matching with all known plant mature miRNAs deposited in the miRBase21.0 (November 2016) database (http://www.mirbase.org/index.shtml) with no more than 2 mismatch.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files; Identified miRNAs in each library with count reads and normalized data.

organism: Solanum lycopersicum

source_name: Exosome-like nanoparticles

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: First, the peel of edible plants with more Juice was cut away, then the fleshes were wrapped with gauze and squeezed by hand, while less Juice of edible plants with PBS were ground in a mixer to obtain the juice. Subsequently, the collected juice was sequentially centrifuged at 1,200g for 20 min, 3,000g for 20 min, and followed by centrifugation (10,000g , 60 min, 4°C) in a Sorvall Lynx 6000 (Fisher Scientific) to remove large particles and cellular debris. Afterwards, it was filtered through filtrator of 1μm (Millipore Corp., Bedford, MA), and the supernatant was centrifuged at 150,000 × g for 90 min at 4 °C in a LE-80 ultracentrifuge (Beckman Coulter; Palo Alto, CA) to pellet EPDELNs, the final fraction was resuspended in 250ul of PBS.

value: Tomato fruit


title: Coconut

description:
microRNA
miRNA-derived exosome-like nanoparticles in Coconut.

organism: Cocos nucifera

value: Coconut fruit


title: Soybean

description:
microRNA
miRNA-derived exosome-like nanoparticles in Soybean.

organism: Glycine max

value: Soybean fruit


title: Pear

description:
microRNA
miRNA-derived exosome-like nanoparticles in Pear.
Pyrus spp

organism: Pyrus

value: Pear fruit


title: Hami melon

description:
microRNA
miRNA-derived exosome-like nanoparticles in Hami melon.
Cucumis melo var

organism: Cucumis melo

value: Hami melon fruit


title: Kiwi

description:
microRNA
miRNA-derived exosome-like nanoparticles in Kiwi.

organism: Actinidia chinensis

value: Kiwifruit


title: Lima bean

description:
microRNA
miRNA-derived exosome-like nanoparticles in Pea.

organism: Lathyrus oleraceus

value: Lima bean fruit


title: spaQ red rep3

description:
spaQ_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: Seedlings


title: Orange

description:
microRNA
miRNA-derived exosome-like nanoparticles in Orange.

organism: Citrus reticulata

value: Orange fruit


title: Ginger

description:
microRNA
miRNA-derived exosome-like nanoparticles in Ginger.

organism: Zingiber officinale

value: Ginger rhizome


title: Col-0 red rep1

description:
Col_R_1
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: 3 days

value: 1h red light


title: Blueberry

description:
microRNA
miRNA-derived exosome-like nanoparticles in Blueberry.
Vaccinium Spp

organism: Vaccinium

value: Blueberry fruit


title: cop1 red rep2

description:
cop1_R_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: cop1 red rep3

description:
cop1_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt


title: Grapefruit

description:
microRNA
miRNA-derived exosome-like nanoparticles in Grapefruit.
Citrus paradisi

organism: Citrus x paradisi

value: Grapefruit fruit


title: A3 d65 rep2

status: Public on Jun 12 2018

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

hyb_protocol: The quality and quantity of human total RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 500ng of total RNA was then prepared for hybridisation to the Illumina HumanHT-12 Expression Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).

scan_protocol: After RNA integrity verification using RNA LabChip and BioAnalyzer2100 (Agilent Technologies, USA), RIN=10 RNA samples were used for Illumina HT-12 microarray hybridization and iSCAN analysis (performed by AGRF-Melbourne).

data_processing: The data were background corrected and log2-tranformed. Data was then quantile-normalised using lumi (version 2.10.0) in R version 2.15.3.

source_name: Neuronal differentiation culture

label_protocol: A total hybridisation volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Illumina HumanHT-12 Expression Beadchip. A total of 12 different labelled samples can be loaded into 12 individual arrays per beadchip.  The chip was then hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.  Upon completion of the washing, the chips were then coupled with Cy3 and scanned in the Illumina iScan Reader.  The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis.

extract_protocol: Total RNA from triplicates of day 45 and 65 neuronal differentiation cultures (Chamber et al. 2009; Briggs et al., 2013) was prepared using direct lysis on the plate with TriZOL reagent (LifeTechnologies), followed by total RNA isolation using PureLink RNA kit (Ambion/LifeTech) with on-column DNase treatment (as per manufacturer’s instructions).

value: Neuronal differentiation culture

tag: cell line

value: Day 65

tag: description

value: APP copy number-corrected DS Clone A3 Day 65


title: C18 d65 rep3

value: DS Clone C18 Day 65


title: A3 d65 rep3


title: C79 d65 rep2

value: Euploid Clone C79 Day 65


title: A3 d65 rep1


title: neural progenitor C79 d45 rep3

value: Day 45

value: Euploid Clone C79 Day 45


title: C79 d65 rep1


title: C87 d65 rep1

value: Euploid Clone C87 Day 65


title: C18 d65 rep2


title: neural progenitor A3 d45 rep2

value: APP copy number-corrected DS Clone A3 Day 45


title: neural progenitor C79 d45 rep2


title: C87 d65 rep3


title: neural progenitor A3 d45 rep1


title: C79 d65 rep3


title: C18 d65 rep1


title: neural progenitor C87 d45 rep3

value: Euploid Clone C87 Day 45


title: neural progenitor C79 d45 rep1


title: C87 d65 rep2


title: neural progenitor C87 d45 rep1


title: C11 d65 rep2

value: DS Clone C11 Day 65


title: neural progenitor A3 d45 rep3


title: C86 d65 rep1

value: Euploid Clone C86 Day 65


title: neural progenitor C87 d45 rep2


title: C86 d65 rep3


title: neural progenitor C18 d45 rep3

value: DS Clone C18 Day 45


title: C11 d65 rep3


title: neural progenitor C18 d45 rep1


title: C86 d65 rep2


title: C11 d65 rep1


title: neural progenitor C86 d45 rep1

value: Euploid Clone C86 Day 45


title: neural progenitor C86 d45 rep3


title: neural progenitor C11 d45 rep1

value: DS Clone C11 Day 45


title: neural progenitor C86 d45 rep2


title: Col-0 red rep2

description:
Col_R_2
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt

value: WT

value: Seedlings

value: 3 days

value: 1h red light


title: Venous blood_B_W505

status: Public on Jun 01 2018

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

description: Gene expression 30 days after brutal weaning in mare blood.

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions.

scan_protocol: Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software.

data_processing:
The fluorescence signal was extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters.
Raw data (median of pixels intensity) were filtered, log2 transformed, corrected for batch effects (washing and labeling serials) and normalized using quantile method.

organism: Equus caballus

source_name: Venous blood, brutal, mare W505

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of  total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNA clean-up using Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).

treatment_protocol: 5ml venous blood were collected from the 32 mares, 30 days after weaning, using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.

tag: breed

value: Welsh Pony

value: whole blood

value: mare

tag: gender

value: female

tag: weening type

value: brutal

tag: time after weaning

value: 30 days

tag: horse id


title: Venous blood_B_W536

source_name: Venous blood, brutal, mare W536

tag: tissue


title: Venous blood_B_W486

source_name: Venous blood, brutal, mare W486


title: Venous blood_B_W551

source_name: Venous blood, brutal, mare W551


title: Venous blood_B_W635

source_name: Venous blood, brutal, mare W635


title: Venous blood_P_W652

description: Gene expression 30 days after progressive weaning in mare blood.

source_name: Venous blood, progressive, mare W652

value: progressive


title: Venous blood_P_W660

source_name: Venous blood, progressive, mare W660


title: Venous blood_P_W661

source_name: Venous blood, progressive, mare W661


title: Venous blood_P_W641

source_name: Venous blood, progressive, mare W641


title: Venous blood_P_W625

source_name: Venous blood, progressive, mare W625


title: Venous blood_B_W560

source_name: Venous blood, brutal, mare W560


title: Venous blood_B_W587

source_name: Venous blood, brutal, mare W587


title: Venous blood_P_W637

source_name: Venous blood, progressive, mare W637


title: Venous blood_P_W620

source_name: Venous blood, progressive, mare W620


title: Venous blood_B_W543

source_name: Venous blood, brutal, mare W543


title: Venous blood_P_W636

source_name: Venous blood, progressive, mare W636


title: Venous blood_P_W657

source_name: Venous blood, progressive, mare W657


title: Venous blood_B_W567

source_name: Venous blood, brutal, mare W567


title: Venous blood_B_W640

source_name: Venous blood, brutal, mare W640


title: neural progenitor C11 d45 rep3

source_name: Neuronal differentiation culture

tag: cell type

value: Neuronal differentiation culture

value: Day 45


title: Venous blood_B_W645

source_name: Venous blood, brutal, mare W645


title: Venous blood_P_W542

source_name: Venous blood, progressive, mare W542


title: Venous blood_P_W601

source_name: Venous blood, progressive, mare W601


title: Venous blood_B_W613

source_name: Venous blood, brutal, mare W613


title: Venous blood_B_W631

source_name: Venous blood, brutal, mare W631


title: Venous blood_B_W594

source_name: Venous blood, brutal, mare W594


title: Venous blood_B_W588

source_name: Venous blood, brutal, mare W588


title: Venous blood_P_W621

source_name: Venous blood, progressive, mare W621


title: Venous blood_P_W552

source_name: Venous blood, progressive, mare W552


title: Venous blood_P_W654

source_name: Venous blood, progressive, mare W654


title: Venous blood_D95_B_W710

description: Gene expression 95 days after brutal weaning in foal blood.

source_name: Venous blood, 95 days, brutal, foal W710

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of DNase pre-treated (0.2μl DNase 10X, 0.4μl 10X Buffer DNase, 0.4μl RNasin 40U/μl, 3μl total RNA) total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNA clean-up using Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

treatment_protocol: 5ml venous blood were collected from the 32 foals, 30 and 95 days after weaning, using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.

value: foal

value: 95 days


title: Venous blood_B_W515

source_name: Venous blood, brutal, mare W515


title: Venous blood_D30_P_W712

description: Gene expression 30 days after progressive weaning in foal blood.

source_name: Venous blood, 30 days, progressive, foal W712


title: Venous blood_D30_B_W701

description: Gene expression 30 days after brutal weaning in foal blood.

source_name: Venous blood, 30 days, brutal, foal W701


title: Venous blood_D30_P_MW534

source_name: Venous blood, 30 days, progressive, foal MW534

value: male


title: Venous blood_D30_B_MW533

source_name: Venous blood, 30 days, brutal, foal MW533


title: Venous blood_D30_P_W696

source_name: Venous blood, 30 days, progressive, foal W696


title: Venous blood_D95_P_MW534

description: Gene expression 95 days after progressive weaning in foal blood.

source_name: Venous blood, 95 days, progressive, foal MW534


title: Venous blood_D95_P_MW540

source_name: Venous blood, 95 days, progressive, foal MW540


title: Venous blood_D95_B_MW533

source_name: Venous blood, 95 days, brutal, foal MW533


title: Venous blood_D30_B_W711

source_name: Venous blood, 30 days, brutal, foal W711


title: Venous blood_D95_B_W701

source_name: Venous blood, 95 days, brutal, foal W701


title: Venous blood_D95_P_W712

source_name: Venous blood, 95 days, progressive, foal W712


title: Venous blood_D30_B_W710

source_name: Venous blood, 30 days, brutal, foal W710


title: Venous blood_D95_B_W711

source_name: Venous blood, 95 days, brutal, foal W711


title: Venous blood_D95_P_W696

source_name: Venous blood, 95 days, progressive, foal W696


title: Venous blood_D95_P_MW543

source_name: Venous blood, 95 days, progressive, foal MW543


title: Venous blood_D95_B_MW545

source_name: Venous blood, 95 days, brutal, foal MW545


title: Venous blood_D30_B_W706

source_name: Venous blood, 30 days, brutal, foal W706


title: Venous blood_D95_B_W706

source_name: Venous blood, 95 days, brutal, foal W706


title: Venous blood_D95_P_W699

source_name: Venous blood, 95 days, progressive, foal W699


title: Venous blood_D30_B_MW545

source_name: Venous blood, 30 days, brutal, foal MW545


title: Venous blood_D95_P_W709

source_name: Venous blood, 95 days, progressive, foal W709


title: Venous blood_D30_B_MW541

source_name: Venous blood, 30 days, brutal, foal MW541


title: Venous blood_D30_P_MW543

source_name: Venous blood, 30 days, progressive, foal MW543


title: Venous blood_D30_P_W699

source_name: Venous blood, 30 days, progressive, foal W699


title: Venous blood_D30_P_MW540

source_name: Venous blood, 30 days, progressive, foal MW540


title: Venous blood_D30_P_W709

source_name: Venous blood, 30 days, progressive, foal W709


title: Venous blood_D95_P_W700

source_name: Venous blood, 95 days, progressive, foal W700


title: Venous blood_P_W544

source_name: Venous blood, progressive, mare W544


title: Venous blood_D95_B_MW541

source_name: Venous blood, 95 days, brutal, foal MW541


title: Venous blood_D30_P_W700

source_name: Venous blood, 30 days, progressive, foal W700


title: Venous blood_D95_B_W698

source_name: Venous blood, 95 days, brutal, foal W698


title: Venous blood_D30_B_W698

source_name: Venous blood, 30 days, brutal, foal W698


title: Venous blood_D30_P_W694

source_name: Venous blood, 30 days, progressive, foal W694


title: Venous blood_D95_P_W694

source_name: Venous blood, 95 days, progressive, foal W694


title: Venous blood_D95_B_W697

source_name: Venous blood, 95 days, brutal, foal W697


title: Venous blood_D30_B_W697

source_name: Venous blood, 30 days, brutal, foal W697


title: Venous blood_D30_B_MW536

source_name: Venous blood, 30 days, brutal, foal MW536


title: Venous blood_D95_B_MW542

source_name: Venous blood, 95 days, brutal, foal MW542


title: Venous blood_D95_P_MW537

source_name: Venous blood, 95 days, progressive, foal MW537


title: Venous blood_D95_B_MW536

source_name: Venous blood, 95 days, brutal, foal MW536


title: Venous blood_D95_P_MW539

source_name: Venous blood, 95 days, progressive, foal MW539


title: Venous blood_D30_P_MW537

source_name: Venous blood, 30 days, progressive, foal MW537


title: Venous blood_D30_P_MW539

source_name: Venous blood, 30 days, progressive, foal MW539


title: Venous blood_D30_B_MW542

source_name: Venous blood, 30 days, brutal, foal MW542


title: Venous blood_D30_B_W708

source_name: Venous blood, 30 days, brutal, foal W708


title: Venous blood_D95_B_W708

source_name: Venous blood, 95 days, brutal, foal W708


title: Venous blood_D95_P_W702

source_name: Venous blood, 95 days, progressive, foal W702


title: Venous blood_D30_B_MW531

source_name: Venous blood, 30 days, brutal, foal MW531


title: Venous blood_D95_P_W705

source_name: Venous blood, 95 days, progressive, foal W705


title: Venous blood_D30_P_W702

source_name: Venous blood, 30 days, progressive, foal W702


title: Venous blood_D95_P_MW538

source_name: Venous blood, 95 days, progressive, foal MW538


title: Venous blood_D95_B_W695

source_name: Venous blood, 95 days, brutal, foal W695


title: Venous blood_D30_B_W695

source_name: Venous blood, 30 days, brutal, foal W695


title: Venous blood_D30_P_W705

source_name: Venous blood, 30 days, progressive, foal W705


title: Venous blood_D95_B_MW544

source_name: Venous blood, 95 days, brutal, foal MW544


title: Venous blood_D95_P_MW530

source_name: Venous blood, 95 days, progressive, foal MW530


title: Venous blood_P_W524

source_name: Venous blood, progressive, mare W524


title: Venous blood_D30_B_MW544

source_name: Venous blood, 30 days, brutal, foal MW544


title: Venous blood_D95_B_W703

source_name: Venous blood, 95 days, brutal, foal W703


title: Venous blood_D30_P_MW530

source_name: Venous blood, 30 days, progressive, foal MW530


title: Venous blood_D95_B_MW531

source_name: Venous blood, 95 days, brutal, foal MW531


title: Pam3csk4 acute, rep2

status: Public on May 30 2018

description:
No processed data for this sample because it failed quality control
Pam3csk4_2
Gene expression after toll-like receptor ligand stimulation of macrophages

hyb_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray.  The hybridized array was then washed and scanned and data was extracted from the scanned image  using Feature Extraction version 10.7 (Agilent Technologies).

data_processing: Data were pre-processed using limma R/Bioconductor package including RMA background correction, quantile normalisation and log2 transformation. Control probes were removed after normalisation. Detection threshold (log2) for Stemformatics graphing uses 95th percentile of negative control probe expression as per limma recommendation. Median expression is median (log2) of above-threshold expression of all non-control probes.

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml, 4hours, replicate 2

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to  fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following  the manufacturerâ€™s protocol.

growth_protocol: Bone marrow derived macrophages were isolated from female 6 - 8 week C57BL/6 mice and differentiated for 7 days in L929 conditioned growth medium

extract_protocol: Total RNA was extracted using Rneasy mini kit in combination with Qiashredders and a DNase step according to the manufacturers instructions (Qiagen).

treatment_protocol: BMDMs were left untreated or stimulated with each ligand for 24 hours prior to wahing with phosphate buffered saline and the addition of fresh medium. Cells were then stimulted/re-stimulated with the appropriate TLR ligand for 4 hours prior to RNA extraction. Untreated cells were left untreated.

tag: background strain

value: bone marrow

value: macrophages

tag: strain


title: Venous blood_D30_P_MW538

source_name: Venous blood, 30 days, progressive, foal MW538

tag: developmental stage


title: Venous blood_D30_P_W707

source_name: Venous blood, 30 days, progressive, foal W707


title: LPS tolerance, rep3

description:
No processed data for this sample because it failed quality control
LPSTolerance_3
Gene expression after toll-like receptor ligand stimulation of macrophages

scan_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray.  The hybridized array was then washed and scanned and data was extracted from the scanned image  using Feature Extraction version 10.7 (Agilent Technologies).

source_name: Bone marrow derived macrophage, LPS 100ng/ml pre-treatment, LPS 100ng/ml 4hours, replicate 3


title: Venous blood_D30_B_W703

source_name: Venous blood, 30 days, brutal, foal W703


title: Venous blood_D95_P_W707

source_name: Venous blood, 95 days, progressive, foal W707


title: Poly IC acute, rep1

description:
PolyIC_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml, 4hours, replicate 1


title: Pam3csk4 tolerance, rep1

description:
Pam3csk4Tolerance_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml pre-treatment, Pam3csk4 100ng/ml 4hours, replicate 1


title: Poly IC acute, rep3

description:
PolyIC_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml, 4hours, replicate 3


title: Poly IC tolerance, rep1

description:
PolyICTolerance_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml pre-treatment, Poly I:C 10ug/ml 4hours, replicate 1


title: CpG tolerance, rep2

description:
CpGTolerance_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM pre-treatment, CpG 100uM 4hours, replicate 2


title: Poly IC tolerance, rep2

description:
PolyICTolerance_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml pre-treatment, Poly I:C 10ug/ml 4hours, replicate 2


title: Pam3csk4 tolerance, rep2

description:
Pam3csk4Tolerance_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml pre-treatment, Pam3csk4 100ng/ml 4hours, replicate 2


title: CpG acute, rep1

description:
CpG_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM, 4hours, replicate 1


title: Pam3csk4 tolerance, rep3

description:
Pam3csk4Tolerance_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml pre-treatment, Pam3csk4 100ng/ml 4hours, replicate 3


title: Pam3csk4 acute, rep1

description:
Pam3csk4_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml, 4hours, replicate 1


title: CpG acute, rep2

description:
CpG_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM, 4hours, replicate 2


title: Poly IC acute, rep2

description:
PolyIC_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml, 4hours, replicate 2


title: CpG acute, rep3

description:
CpG_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM, 4hours, replicate 3


title: Pam3csk4 acute, rep3

description:
Pam3csk4_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Pam3csk4 100ng/ml, 4hours, replicate 3


title: CpG tolerance, rep3

description:
CpGTolerance_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM pre-treatment, CpG 100uM 4hours, replicate 3


title: CpG tolerance, rep1

description:
CpGTolerance_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, CpG 100uM pre-treatment, CpG 100uM 4hours, replicate 1


title: Poly IC tolerance, rep3

description:
PolyICTolerance_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, Poly I:C 10ug/ml pre-treatment, Poly I:C 10ug/ml 4hours, replicate 3


title: LPS acute, rep3

description:
LPS_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, LPS 100ng/ml, 4hours, replicate 3


title: B9

status: Public on Apr 26 2018

city: Changsha

first: Yang

address: 87 Xiangya Road

department: Xiangya Hospital

institute: Central South University

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include tag count and TPM values for each Sample

organism: Rattus norvegicus

growth_protocol: Sprague-Dawley rats (male, 180g-220g) were cared in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health (NIH Publication No. 85-23, revised 1996). The Committee on the Use and Care of Animals of Central South University (CSU) (201403164) has approved animal protocols. Rats accessed to water and food freely under a room temperature at 25°C and a 12 h light-dark cycle.

extract_protocol:
After deeply anesthetized and saline perfused at days 21, brain tissue surrounding the hemorrhagic region (the right globus pallidus) was harvested for following detections. Total RNAs were extracted according to the manufacturer’s instruction (Qiagen, USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

treatment_protocol: Animals were randomly assigned into the sham operated group (sham), ICH group (ICH) and ICH+BYHWD-treated group (BYHWD). animals were anesthetized with pentobarbital (65 mg/kg). Afterward, the rats were pronely fixed on a stereotactic frame (Stoelting Co., Chicago, IL). After making a scalp incision, we drilled a small cranial burr near the right coronal suture (1.4 mm posterior and 3.2 mm lateral to bregma). Then collagenase type VII (0.5 U dissolved in 2.5 μl saline) was slowly injected into the right globus pallidus (5.6 mm deep) at an even speed in 2 minutes. The needle was kept in place for another 5 minutes then withdrawn to prevent backflow. Finally, the burr hole was filled with bone wax, and the scalp sutured closed. Sham rats underwent the same procedure but with 2.5 μl saline infusion instead. For BYHWD group, intragastrical administration of Buyang Huanwu Decoction (4.36 g/kg) was performed once a day for 21days.

tag: strain background

value: Sprague–Dawley

tag: age

value: post operation day 21

tag: group

value: intracerebral hemorrhage (ICH) treated with Buyang Huanwu Decoction (BYHWD)

value: Brain tissue around the right globus pallidus

tag: molecule subtype

value: tress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF)


title: LPS tolerance, rep2

description:
LPSTolerance_2
Gene expression after toll-like receptor ligand stimulation of macrophages

organism: Mus musculus

source_name: Bone marrow derived macrophage, LPS 100ng/ml pre-treatment, LPS 100ng/ml 4hours, replicate 2


title: Untreated, rep3

description:
UT_3
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage no treatment replicate 3


title: Untreated, rep1

description:
UT_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage no treatment replicate 1


title: LPS tolerance, rep1

description:
LPSTolerance_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, LPS 100ng/ml pre-treatment, LPS 100ng/ml 4hours, replicate 1


title: KRAS_CL cell, biological rep3

status: Public on May 16 2018

city: Frederick

first: NA-YOUNG

last: SONG

state: MD

address: 1050 Boyles Street

institute: NCI

hyb_protocol: 15 ug of biotinylated cRNA were fragmented and hybridized for 16 hr at 45C on mouse Genome Array mo430 2.0.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450, were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed using Affymetrix Expression Console and normalized to 150.

source_name: lung adenocarcinoma-associated macrophages from C57BL/6 mouse intratracheally injected with KRAS_CL cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA (IVT Express 15402 or IVT Plus 18737)

growth_protocol: All mice used in this study were cared for in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of the National Institute of Health (NIH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The mice were intratracheally injected with Kras_CL or Kras IKKa low cells. At 1.5 months post injection, the mice were euthanized and lung tissues were collected for macrophage isolation.

tag: genotype/variation

value: wild type

value: lung

tag: treatment

value: Kras-CL


title: LPS acute, rep2

description:
LPS_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, LPS 100ng/ml, 4hours, replicate 2

value: female


title: KRAS IKKa low cell, biological rep1

source_name: lung adenocarcinoma-associated macrophages from C57BL/6 mouse intratracheally injected with KRAS IKKa low cells

value: Kras IKKa


title: KRAS IKKa low cell, biological rep3


title: KRAS_CL cell, biological rep2


title: KRAS IKKa low cell, biological rep2


title: KRAS_CL cell, biological rep1


title: Untreated, rep2

description:
UT_2
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage no treatment replicate 2


title: LPS acute, rep1

description:
LPS_1
Gene expression after toll-like receptor ligand stimulation of macrophages

source_name: Bone marrow derived macrophage, LPS 100ng/ml, 4hours, replicate 1


title: IMR90_0Gy_24h_III

status: Public on Mar 31 2018

type: genomic

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

institute: Bundeswehr Institute for Radiobiology

description: meDIP

hyb_protocol: Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; Agilent-069114).

scan_protocol: Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.3 March 2014; Agilent® G2505C; Scan Control Version A.8.1.3; resolution 3 µm; 16 bit TIFF; no XDR; Images were quantified using Agilent Feature Extraction Software (version 12.0).

data_processing: Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: IMR90, 0Gy, 24h, methylated

label_protocol: Samples were labeled with Cy3 and reference DNA (GM12878) was labeled with Cy5 according to manufacturer's protocol (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014). Dye swaps were also performed.

growth_protocol:
Human lymphoblastoid cells (GM12878, suspension cells) and primary human lung fibroblasts (IMR-90, adherent cells) were obtained from Corriell Institute for medical Research (Camden, New Jersey, USA). Cells were cultivated at 37°C / 5% CO2 in RPMI-1640 2mM L-glutamine and Eagle's Minimum Essential Medium, respectively.
For each timepoint and dose, 10 million cells were irradiated with an x-ray beam at room temperature with 240 kV tube current (YXLON Maxishot; Hamburg, Germany) filtered with 3 mm beryllium. Absorbed dose was measured with a PTW Unidos dosimeter (PTW Freiburg GmbH, Germany). Dose rate was 1 Gy/min at 13 mA. No fresh medium was added to cells after irradiation. Sham irradiated samples were treated the very same way, apart from not being irradiated (e.g. taken out of the incubator for the same time span, brought to the same room).

extract_protocol: DNA was randomly sheared using the Covaris M220 according to the manufacturers’ protocol (Covaris protocol truChIP™ Chromatin Shearing Reagent Kit, PN 010179, Rev C 15 August 2013) with the following parameters: average incident power= 10 W; Peak Incident power= 50 W; Duty factor= 20 %; Cycles/Burst= 200; Duration=80 s. The optimal fragment length of 300-500 bp was verified by gel electrophoreses. The methylated portion of the genome was enriched by immunoprecipitation employing the MagMeDIP kit (Magnetic Methylated DNA Immunoprecipitation kit, Diagenode, Version 1 08.10). In brief, for each sample, 1 µg of sheared DNA was denatured at 95°C for 3 min in a thermocycler. After denaturation, samples were immediately put on ice for 10 min and 5% of each sample were removed for later use as an input control. Immunoprecipitation with monoclonal antibody against 5-methyl cytidine and magnetic beads was done overnight at 4°C on a rotating wheel. The next day, magnetic beads with bound complexes of antibody and methylated DNA were washed for three times and DNA was detached from the beads with proteinase K. Immunoprecipitated DNA as well as input control DNA were purified using the QiaQuick PCR-purification kit (QIAGEN®, QIAquick®). Amplification of DNA was performed with the GenomePlex® Complete Whole Genome Amplification (WGA) Kit according to the protocol (Sigma-Aldrich; Version WGA2, 02/12-1) apart from omitting the fragmentation step.

tag: cell line

value: primary lung fibroblast cell line

value: 0Gy X-ray radiation

tag: timepoint

tag: sample type

value: methylated gDNA

source_name: IMR90, 0Gy, 24h, input

value: matching control gDNA


title: IMR90_0Gy_48h_III

description: meDIP

source_name: IMR90, 0Gy, 48h, methylated

source_name: IMR90, 0Gy, 48h, input


title: IMR90_0Gy_120h_III

description: meDIP

source_name: IMR90, 0Gy, 120h, methylated

source_name: IMR90, 0Gy, 120h, input


title: IMR90_0Gy_120h_II

description: meDIP


title: IMR90_0Gy_0h

description: meDIP

hyb_protocol: Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; SurePrint G3 Human Genome CGH Microarray 2x400K, 5.3 kb spacing).

source_name: IMR90, 0Gy, 0h, methylated

value: methylated DNA

source_name: IMR90, 0Gy, 0h, input


title: IMR90_0Gy_6h_III

description: meDIP

source_name: IMR90, 0Gy, 6h, methylated

source_name: IMR90, 0Gy, 6h, input


title: IMR90_2Gy_48h

description: meDIP

source_name: IMR90, 2Gy, 48h, methylated

source_name: IMR90, 2Gy, 48h, input


title: GM12878_4Gy_24h

description: meDIP

source_name: GM12878, 4Gy, 24h, methylated

value: lymphoblastoid cell line


title: GM12878_4x0.5Gy_96h

description: meDIP

source_name: GM12878, 4x0.5Gy, 96h, methylated


title: IMR90_2Gy_24h

description: meDIP

source_name: IMR90, 2Gy, 24h, methylated

source_name: IMR90, 2Gy, 24h, input


title: GM12878_4Gy_48h

description: meDIP

source_name: GM12878, 4Gy, 48h, methylated


title: IMR90_0Gy_24h_II

description: meDIP

source_name: IMR90, 0Gy, 24h, methylated


title: IMR90_0Gy_48h_II

description: meDIP


title: IMR90_0Gy_120h_I

description: meDIP


title: IMR90_0Gy_1h_II

description: meDIP

source_name: IMR90, 0Gy, 1h, methylated

source_name: IMR90, 0Gy, 1h, input


title: IMR90_0Gy_6h_I

description: meDIP


title: IMR90_0Gy_24h_I

description: meDIP

source_name: IMR90, 0Gy, 24h, input


title: IMR90_0Gy_6h_II

description: meDIP


title: GM12878_2Gy_24h

description: meDIP

source_name: GM12878, 2Gy, 24h, methylated


title: IMR90_4Gy_24h_DS

description: meDIP

source_name: IMR90, 4Gy, 24h, methylated

source_name: IMR90, 4Gy, 24h, input


title: IMR90_0Gy_0h_III

description: meDIP

source_name: IMR90, 0Gy, 0h, methylated

source_name: IMR90, 0Gy, 0h, input


title: IMR90_0.5Gy_24h_III

description: meDIP

source_name: IMR90, 0.5Gy, 24h, methylated

value: 0.5Gy X-ray radiation

source_name: IMR90, 0.5Gy, 24h, input


title: GM12878_2Gy_48h

description: meDIP

source_name: GM12878, 2Gy, 48h, methylated


title: IMR90_4Gy_48h_DS

description: meDIP

source_name: IMR90, 4Gy, 48h, methylated

source_name: IMR90, 4Gy, 48h, input


title: GM12878_0Gy_0h

description: meDIP

source_name: GM12878, 0Gy, 0h, methylated

source_name: GM12878, 0Gy, 0h, input


title: IMR90_4x0.5Gy_96h_DS

description: meDIP

source_name: IMR90, 4x0.5Gy, 96h, methylated

source_name: IMR90, 4x0.5Gy, 96h, input


title: IMR90_0Gy_48h_I

description: meDIP

source_name: IMR90, 0Gy, 48h, methylated

source_name: IMR90, 0Gy, 48h, input


title: IMR90_0.5Gy_120h_DS_II

description: meDIP

source_name: IMR90, 0.5Gy, 120h, methylated

source_name: IMR90, 0.5Gy, 120h, input


title: IMR90_0Gy_0h_I

description: meDIP


title: IMR90_0.5Gy_120h_I

description: meDIP


title: IMR90_0.5Gy_48h_I

description: meDIP

source_name: IMR90, 0.5Gy, 48h, methylated

source_name: IMR90, 0.5Gy, 48h, input


title: GM12878_0.5Gy_120h_III

description: meDIP

source_name: GM12878, 0.5Gy, 120h, methylated


title: IMR90_0.5Gy_24h_DS_I

description: meDIP


title: IMR90_0.5Gy_24h_II

description: meDIP


title: IMR90_0Gy_1h_I

description: meDIP

source_name: IMR90, 0Gy, 1h, methylated

source_name: IMR90, 0Gy, 1h, input


title: IMR90_0.5Gy_6h_DS_I

description: meDIP

source_name: IMR90, 0.5Gy, 6h, methylated

source_name: IMR90, 0.5Gy, 6h, input


title: IMR90_0.5Gy_48h_III

description: meDIP


title: IMR90_0Gy_0h_II

description: meDIP

source_name: IMR90, 0Gy, 0h, methylated

source_name: IMR90, 0Gy, 0h, input


title: IMR90_0.5Gy_1h_III

description: meDIP

source_name: IMR90, 0.5Gy, 1h, methylated

source_name: IMR90, 0.5Gy, 1h, input


title: IMR90_0.5Gy_6h_II

description: meDIP


title: IMR90_0.5Gy_120h_III

description: meDIP


title: IMR90_0.5Gy_1h_DS_II

description: meDIP


title: IMR90_0.5Gy_6h_III

description: meDIP


title: IMR90_0.5Gy_48h_DS_II

description: meDIP


title: GM12878_0.5Gy_48h_III

description: meDIP

source_name: GM12878, 0.5Gy, 48h, methylated


title: IMR90_0.5Gy_1h_I

description: meDIP


title: GM12878_0.5Gy_120h_I

description: meDIP


title: GM12878_0.5Gy_24h_III

description: meDIP

source_name: GM12878, 0.5Gy, 24h, methylated


title: GM12878_0.5Gy_24h_II

description: meDIP


title: GM12878_0.5Gy_24h_I

description: meDIP


title: GM12878_0.5Gy_6h_III

description: meDIP

source_name: GM12878, 0.5Gy, 6h, methylated


title: GM12878_0.5Gy_48h_I

description: meDIP


title: GM12878_0.5Gy_48h_II

description: meDIP


title: IMR90_0Gy_1h_III

description: meDIP


title: GM12878_0.5Gy_6h_I

description: meDIP


title: GM12878_0.5Gy_120h_II

description: meDIP


title: GM12878_0.5Gy_1h_II

description: meDIP

source_name: GM12878, 0.5Gy, 1h, methylated


title: GM12878_0.5Gy_6h_II

description: meDIP


title: GM12878_0.5Gy_1h_I

description: meDIP


title: GM12878_0Gy_120h_I

description: meDIP

source_name: GM12878, 0Gy, 120h, methylated


title: GM12878_0Gy_48h_I

description: meDIP

source_name: GM12878, 0Gy, 48h, methylated


title: GM12878_0.5Gy_1h_III

description: meDIP


title: GM12878_0Gy_24h_I

description: meDIP

source_name: GM12878, 0Gy, 24h, methylated


title: GM12878_0Gy_120h_II

description: meDIP


title: GM12878_0Gy_48h_III

description: meDIP


title: GM12878_0Gy_120h_III

description: meDIP


title: GM12878_0Gy_6h_I

description: meDIP

source_name: GM12878, 0Gy, 6h, methylated

source_name: GM12878, 0Gy, 6h, input


title: GM12878_0Gy_48h_II

description: meDIP


title: GM12878_0Gy_1h_III

description: meDIP

source_name: GM12878, 0Gy, 1h, methylated

source_name: GM12878, 0Gy, 1h, input


title: GM12878_0Gy_1h_II

description: meDIP


title: GM12878_0Gy_6h_II

description: meDIP


title: GM12878_0Gy_1h_I

description: meDIP


title: GM12878_0Gy_24h_III

description: meDIP


title: GM12878_0Gy_0h_III

description: meDIP

source_name: GM12878, 0Gy, 0h, methylated

source_name: GM12878, 0Gy, 0h, input


title: GM12878_0Gy_6h_III

description: meDIP


title: GM12878_0Gy_0h_II

description: meDIP


title: ColonCancer058

status: Public on Mar 30 2018

city: Kobe

first: Yuichiro

last: Yoshida

address: 4-4-4 Takatsukadai Nishi-ku

department: central research laboratories

country: Japan

institute: Sysmex corporation

description: Frozen sections with tumor burden > 60% were prepared from each specimen and subjected to DNA microarray measurement/gene mutation analysis.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data was normalized with Microarray Suite (MAS) 5.0 in the Expression console (Affymetrix).

label: biotin

source_name: Frozen tissue of primary colon cancer

label_protocol: Approximately 100ng of total RNA was processed to produce biotinylated cRNA targets using 3’IVT express kit (Affymetrix)

extract_protocol: Total RNA was extracted from cancer tissue using RNeasy Mini Kit (QIAGEN).

tag: disease state

value: primary colorectal tumor

tag: Stage

value: N

value: Y

value: MSS

tag: risk group

value: high-risk


title: ColonCancer057

value: low-risk


title: ColonCancer059


title: GM12878_0Gy_0h_I

description: meDIP


title: ColonCancer054


title: ColonCancer056

value: MSI


title: ColonCancer053


title: ColonCancer052


title: ColonCancer051


title: ColonCancer050


title: ColonCancer055


title: ColonCancer049


title: ColonCancer048


title: ColonCancer044


title: ColonCancer042


title: ColonCancer045


title: ColonCancer040


title: ColonCancer047


title: ColonCancer041


title: ColonCancer039


title: ColonCancer046


title: ColonCancer037


title: ColonCancer043


title: ColonCancer036


title: ColonCancer035


title: ColonCancer032


title: ColonCancer031


title: ColonCancer027


title: ColonCancer029


title: ColonCancer038


title: ColonCancer023


title: ColonCancer024


title: ColonCancer020


title: ColonCancer026


title: ColonCancer028


title: ColonCancer030


title: ColonCancer034


title: ColonCancer033


title: ColonCancer025


title: ColonCancer019


title: ColonCancer022


title: ColonCancer018


title: ColonCancer012


title: Sample_scr_nucleus_m6A_rep2

status: Public on Mar 14 2018

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
library strategy: m6A-seq
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.

growth_protocol: E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.

extract_protocol:
Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
m6A-seq: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody.
RNA-seq: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.
RIP-seq: RNA was fragmented and subject to immunoprecipitation with a anti-Zc3h13 specific antibody.

value: scr

value: murine embryonic stem cell

tag: antibody

value: Rabbit anti-m6A (Synaptic, 202003)

value: nucleus RNA


title: ColonCancer010


title: ColonCancer011


title: ColonCancer013


title: AMD5_RPE_PerR

status: Public on Mar 05 2018

data_processing:
After removing adaptors using Trimmomatic, 50bp paired-end ATAC-Seq reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 with default parameters.
After filtering reads from mitochondrial chromosome M and sex chromosome Y, we included properly paired reads with high mapping quality (MAPQ score > 10, qualified reads) through SAMTools for further analysis. Duplicate reads were removed using Picard tools MarkDuplicates program.
ATAC-Seq peak regions of each sample were called using MACS2 with parameters --nomodel --shift -100 --extsize 200. The blacklisted regions in human were excluded from peak regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
For each of retina and RPE samples, the fragments were counted across each peak region using HTSeq.
Using Tophat and Cufflinks with default parameters, raw data were mapped to the hg19 genome assembly, and gene expression FPKM (Fragments Per Kilobase Of Exon Per Million) were obtained.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Peak files in narrowPeak format following columns: chromosome, start, stop, name, length of peak region, strand, integer score for display, fold-change, -log10(pvalue), -log10(qvalue), relative summit position to peak start.
Supplementary_files_format_and_content: FPKM files for gene expression.
Supplementary_files_format_and_content: Retina_ATACSeq_peak_counts.txt: Tab-delimited text file; For a description of the file's contents, see the peak_counts_annotation.txt file.
Supplementary_files_format_and_content: RPE_ATACSeq_peak_counts.txt: Tab-delimited text file; For a description of the file's contents, see the peak_counts_annotation.txt file.

source_name: Fresh postmortem eye

extract_protocol:
Chromatin was extracted and processed for Tn5-mediated tagmentation and adapter incorporation, according to the manufacturer’s protocol (Nextera DNA sample preparation kit, Illumina®) at 37 °C for 30 minutes. Reduced-cycle amplification was carried out in presence of compatible indexed sequencing adapters. Total cellular RNA was purified using the Qiagen RNeasy Mini kit and samples with RNA integrity number ≥ 7 were further processed. Total RNA was denatured at 65°C for 5 minutes, cooled on ice, purified and incubated at 80°C for two minutes. The eluted mRNA was fragmented at 94°C for 8 min and converted to double stranded cDNA, end repaired, A-tailed, and ligated with indexed adaptors.
The quality of the libraries was assessed by DNA-based fluorometric assay (Thermo Fisher ScientificTM) and automated capillary electrophoresis (Agilent Technologies, Inc.). Up to 3 samples per lane were pooled and run on a HiSeq2500 Illumina sequencer with a paired-end read of 50bp. The quality of the libraries was also assessed by RNA-based fluorometric assay (Thermo Fisher ScientificTM) and automated capillary electrophoresis (Agilent Technologies, Inc.).

treatment_protocol: Fresh postmortem eyes were processed within 14 hours after death when obtained from Eye Banks (Portland, USA) and National Disease Research Interchange (Philadelphia, USA). For each eye, we separated the retina and RPE from other tissues and obtained a punch (6 mm diameter) of retina or RPE tissue in each of macular and peripheral regions. Biopsy punches of fresh retina and RPE tissues were re-suspended in cold PBS.

tag: donor

value: Donor 5

tag: gender

value: Female

tag: interval

tag: disease status

value: Late AMD

tag: eye

value: Right

tag: tissue

value: RPE

tag: location

value: Periphery


title: ColonCancer003

value: primary colorectal tumor


title: ColonCancer014

value: N


title: ColonCancer016

value: Y


title: ColonCancer017

value: MSS


title: ColonCancer021


title: AMD4_RPE_MacR

value: Donor 4

tag: age

value: Early AMD

value: Macula


title: ColonCancer009

value: high-risk


title: ColonCancer007

value: MSI

value: low-risk


title: ColonCancer015


title: AMD3_RPE_PerR

value: Donor 3


title: ColonCancer005


title: AMD2_RPE_PerR

value: Donor 2

value: Male


title: GM12878_0Gy_24h_II

description: meDIP

tag: cell type

value: lymphoblastoid cell line

value: 0Gy X-ray radiation

value: methylated gDNA

value: matching control gDNA


title: ColonCancer001

value: primary colorectal tumor


title: ColonCancer008

value: N


title: AMD5_RPE_MacR

value: Donor 5

value: Female

value: Late AMD

value: Right

value: RPE


title: AMD2_RPE_PerL

value: Left

value: Periphery


title: AMD1_RPE_PerR

value: Donor 1


title: AMD2_RPE_MacL

value: Macula


title: AMD1_RPE_MacR


title: NOR4_RPE_PerR

value: Donor 4

value: Healthy


title: ColonCancer004

value: Y

value: MSS

value: low-risk


title: NOR3_RPE_PerR

value: Donor 3

value: Male


title: NOR4_RPE_MacR


title: AMD1_RPE_MacL


title: ColonCancer002

value: primary colorectal tumor

value: N


title: NOR4_RPE_PerL


title: AMD2_RPE_Right_exp

value: Donor 2

value: Early AMD


title: NOR2_RPE_PerL

value: Female


title: NOR4_RPE_MacL

value: RPE


title: NOR2_RPE_PerR

value: Right


title: AMD2_Retina_Right_exp

value: Retina

value: Periphery


title: NOR2_RPE_Mac

value: Pooled

value: Macula


title: AMD2_RPE_Left_exp

value: Late AMD

value: Left


title: AMD5_Retina_PerL

value: Donor 5


title: AMD5_Retina_MacR


title: AMD5_Retina_MacL


title: AMD4_Retina_MacR

value: Donor 4


title: AMD4_Retina_PerR_Rep2


title: AMD2_Retina_MacR


title: ColonCancer006

value: MSS

value: low-risk


title: AMD2_Retina_PerL

value: Male


title: AMD3_Retina_PerR

value: Donor 3


title: AMD2_Retina_MacL

value: Donor 2


title: AMD2_Retina_Left_exp


title: AMD1_Retina_PerR

value: Donor 1


title: AMD1_Retina_MacL

value: Female


title: AMD1_Retina_MacR


title: NOR4_Retina_PerL

value: Healthy


title: NOR5_Retina_PerR

value: Right


title: NOR4_Retina_MacR

value: Retina


title: NOR4_Retina_PerR

value: Periphery


title: NOR2_Retina_Mac

value: Pooled


title: NOR2_Retina_Per


title: NOR1_Retina_PerL


title: NOR1_Retina_PerR


title: NOR4_Retina_MacL

value: Macula


title: AMD4_Retina_PerR_Rep1

value: Early AMD


title: NOR1_Retina_MacR


title: AMD2_Retina_PerR


title: NOR3_Retina_MacR


title: KYSE850_KHSRP_KD_2_miR

status: Public on Feb 22 2018

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

hyb_protocol: Probes were hybridized to Agilent array (G4872A) using miRNA Hybridization Kit at 55°C for 20 hours with rotation. Then, the slides were washed by Gene Expression Wash Buffer 1 at room temperature for 5 minutes and by Gene Expression Wash Buffer 2 at 37°C for 5 minutes.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: Data were processed by the Agilent GeneSpring GX software (ver. 12.6). Total gene signal from GeneView data files extracted with default settings in Agilent Feature Extraction was used as signal for miRNAs.

source_name: KYSE850 esophageal squamous cell carcinoma, treated with KHSRP siRNA

label_protocol: 100 ng of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol. Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase, denatured with dimethyl sulfoxide and labeled with Cyanine 3-pCp using T4 RNA ligase using the miRNA Labeling Kit.

extract_protocol: RNA was prepared using the NucleoSpin miRNA Kit (Takara, Shiga, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

value: Esophageal squamous cell carcinoma cell line

tag: genotype/variation

value: KHSRP knockdown


title: KYSE850_KHSRP_KD_1_miR

tag: cell line


title: KYSE850_control_2_miR

source_name: KYSE850 esophageal squamous cell carcinoma, treated with control siRNA

value: Control


title: KYSE850_control_1_miR


title: AMD3_RPE_MacR

value: RPE


title: mRNA_OvarianCancer_rep24

status: Public on Aug 31 2017

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Fastq files were generated by CASAVA-1.8.2 from Illumina Hiseq output.
Fastq files were mapped to hg19 reference genome by bowtie2 to generate bam files.
Expression level is quantified by RSEM-1.3.0.
Genome_build: hg19
Supplementary_files_format_and_content: Rsem.genes.results file has columns named TPM and FPKM. Each columns represent Transcripts Per Million mapped reads and Fragments Per Kilobase of transcript and Million mapped reads for each gene.

molecule: polyA RNA

source_name: mRNA from fresh frozen ovarian cancer

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
cDNA library was prepared with Ilumina TruSeq Stranded mRNA Library Preparation Kit

value: primary tumor from ovarian cancer patient

value: female


title: mRNA_OvarianCancer_rep26


title: mRNA_OvarianCancer_rep25


title: mRNA_OvarianCancer_rep27


title: mRNA_OvarianCancer_rep28


title: mRNA_OvarianCancer_rep23


title: mRNA_OvarianCancer_rep22


title: KYSE850_control_1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Oligo Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.6 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).


title: AMD5_RPE_MacL

value: Donor 5

value: Late AMD

value: Left


title: KYSE850_KHSRP_KD_1


title: KYSE850_KHSRP_KD_4


title: hESCs_3

status: Public on Jan 16 2018

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadStation 500 using the standard Illumina scanning protocol.

data_processing: The data were log2-transformed and normalised using quantile normalisation with R/Bioconductor package lumi.

source_name: embryonic stem cells

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

growth_protocol: Human ES cell were maintained under sterile conditions in a humidified incubator in a 5% CO2-95% air atmosphere at 37 degree Celsius. In a routine culture cells were maintained on Matrigel in conditioned media.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Qiagen), and DNase digestion (RNase-free DNase Set, Qiagen) has been applied on the columns during isolation.

treatment_protocol: The derivation of HLCs from the hESCs followed protocols described by Hay et al. and Agarwal et al. Differentiation was initiated when cells reached 50-60% confluence. RNA samples were extracted after each step of the differentiation protocol in order to ex-amine the activation of endoderm and hepatocyte-associated genes. On day 18 functional tests were performed.

value: embryonic stem cells


title: KYSE850_control_2


title: KYSE850_KHSRP_KD_2


title: KYSE850_control_4


title: KYSE850_control_3


title: fMSC

status: Public on Jan 12 2018

description:
fMSC_1
Replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array.

data_processing: The data were normalised using RMA normalisation from R/Bioconductor.

source_name: Fetal mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol:
Amniotic fluid samples were washed with PBS (Gibco; Thermo Fisher Scientific, Darmstadt, Germany) and centrifuged at 300xg for 5min. The supernatant was discarded and the pellet washed again with PBS. The pellet was dissolved in Ammonium chloride to lyse the remaining erythrocytes. Thereafter, the cell solution was incubated at 4°C for 20min and centrifuged again. This procedure was repeated until the pellet had a clear colour. Afterwards the cells were cultured in Chang C Medium (Irvine Scientific, CA, USA) containing 88% αMEM (Minimum Essential Medium Eagle – Alpha Modified; Sigma), 10% FBS, 1% GlutaMAX, 1% Penicillin/Streptomycin (all Gibco), 10% Chang B Basal Medium and 2% Chang C supplement (Irvine Scientific) at 37°C.
Pluripotent stem cells (iPS-cells and human embryonic stem cells H1, H9 (#WA01, #WA09)) were cultured in StemMACS iPS-Brew XF, human (Milteny Biotech) and penicillin/streptomycin (Thermo Fisher Scientific). Passaging of pluripotent stem cells was carried out with a splitting ratio of 1:6. Cell culture dishes coated with Matrigel (BD) were used to culture iPS-cells and hESCs. MSC, iPSC and ESC culture was carried out at 37°C and 5% CO2 in a humidified atmosphere.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following the manufacturer's protocol. The quality of the RNA was checked with a NanoDropTM spectrophotometer (Thermo Scientific).

treatment_protocol: Retroviral-based reprogramming of HFF cells together with 8-Br-cAMP and VPA treatment was performed to create the HFF-iPSC line B4 [Wang, Adjaye; 2011]. In brief, pMXs-based retroviral vectors each encoding the transcription factors OCT4, SOX2, KLF4 and c-MYC were used. Transfection was done into Phoenix Ampho cells with the use of Fugene transfection reagent (Roche Diagnostics, Basel, Switzerland). To generate iPSC from HFF1, cells were incubated for 24h with the viral supernatants supplemented with 4 ug/ml polybrene (Sigma, St. Louis, USA). This procedure was repeated after 24h. The cells were maintained on irradiated MEF feeder cells in human ES cell culture medium and supplemented with different concentrations of 8-Br-cAMP (Biaffin GmbH &Co KG, Kassel, Germany) and VPA (CALBIOCHEM, San Diego, USA).

value: Fetal mesenchymal stem cells


title: AF-MSC2

description:
AF_MSC_2
Replicate 1

source_name: Mesenchymal stem cells derived from AF2

value: Mesenchymal stem cells derived from AF2


title: hESCs_1

description: Replicate 1


title: mRNA_OvarianCancer_rep18


title: mRNA_OvarianCancer_rep20


title: hESCs_2

description: Replicate 2


title: H9

description:
H9
Replicate 1

source_name: Embryonic stem cells

value: Embryonic stem cells


title: AF-MSC1

description:
AF_MSC_1
Replicate 1

source_name: Mesenchymal stem cells derived from AF1

value: Mesenchymal stem cells derived from AF1


title: iPSC

description:
B4_HFF_iPS
Replicate 1

source_name: Induced pluripotent stem cells from human foreskin fibroblasts (HFF)

value: Induced pluripotent stem cells from HFF


title: mRNA_OvarianCancer_rep14


title: mRNA_OvarianCancer_rep16


title: mRNA_OvarianCancer_rep17


title: mRNA_OvarianCancer_rep19


title: mRNA_OvarianCancer_rep11


title: mRNA_OvarianCancer_rep15


title: mRNA_OvarianCancer_rep12


title: mRNA_OvarianCancer_rep9


title: mRNA_OvarianCancer_rep8


title: mRNA_OvarianCancer_rep6


title: mRNA_OvarianCancer_rep7


title: H1

description:
H1
Replicate 1


title: mRNA_OvarianCancer_rep10


title: mRNA_OvarianCancer_rep3


title: mRNA_OvarianCancer_rep2


title: mRNA_OvarianCancer_rep5


title: mRNA_OvarianCancer_rep4


title: mRNA_OvarianCancer_rep1


title: AMD5_Retina_PerR

value: Female

value: Right

value: Retina

value: Periphery