title: Leaves from Non Inoculated-Wounded (NIW) plants 8 wpi rep 2

city: Davis

first: Mélanie

last: Massonnet

state: California

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

data_processing:
For the stem sample L-NINW_8W_B, reads were randomized using fastq-sample program v0.8 (https://github.com/dcjones/fastq-tools) into 17M reads due to much greater coverage compared with the other samples
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Adapter contamination removal was done with Scythe v.0.991
Bowtie2 v.2.2.327 was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal.
Counts of uniquely mapped reads (mapping quality Q > 30) were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Neofusicoccum parvum UCD646So strain predicted transcriptome (NCBI; accession: NP_UCD646So.CDS.fasta linked as supplementary file at foot of GSE85079 record) was combined with the predicted transcriptome of V. vinifera cv. ‘PN40024’ (version V1 from http://genomes.cribi.unipd.it/grape/)
Supplementary_files_format_and_content: Vitis_Np_local_distal_counts.txt: tab delimited text file, raw read counts determined by mapping the trimmed sequencing reads

organism: Vitis vinifera

growth_protocol: The experiment was conducted on potted Vitis Vinifera cv. ‘Cabernet Sauvignon’ clone 19 plants, propagated in 10 x 10-cm pots from green cuttings 12 months before inoculation as described by Travadon et al. (2013). In total, 252 plants were arranged in a completely randomized design and were grown under greenhouse conditions [natural sunlight photoperiod, 25 ± 1°C (day), 18 ± 3°C (night)].

extract_protocol:
Total RNA was isolated using a Cetyltrimethyl Ammonium Bromide extraction protocol described in Blanco-Ulate et al. (2013)
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Grapevine plant inoculations included three treatments consisting of three biological replicates with four plants each. The first treatment consisted of inoculated wounded (IW) plants that were inoculated with 20 µl of the prepared inoculum of N. parvum UCD646So (Travadon et al., 2013) and the second treatment consisted of non-inoculated wounded (NIW) plants that received 20 µl of sterile PDB (mock-inoculum). A power drill was used to wound the woody stem (2 x 3 mm) at 1 cm below the uppermost node. After wounding and administering the fungal inoculum or mock-inoculum, the wound was sealed with Vaseline (Unilever, Greenwich, CT) and Parafilm (American National Can, Chicago, IL). A third treatment consisted of non-inoculated non-wounded (NINW) control plants that were neither wounded nor inoculated. Leaves and stems were collected for all three treatments at seven time points: 0 hours post-inoculation (hpi), 3 hpi, 24 hpi, 2 weeks post-inoculation (wpi), 6 wpi, 8 wpi and 12 wpi.

tag: cultivar

value: Cabernet Sauvignon clone FPS 19

tag: treatment

value: Non Inoculated-Wounded (NIW)

tag: time point

value: 8 wpi

value: leaf tissue


title: Leaves from Non Inoculated-Wounded (NIW) plants 12 wpi rep 3

status: Public on Aug 17 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

value: 12 wpi

tag: tissue


title: UMCG-TT-17 Responder

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

description: Processed data file: MBD2 R vs NR promoter -2000 - +500bp exon_Count Data.xlsx

library_source: genomic

data_processing:
Data were mapped using BOWTIE.
For each nucleotide, the amount of mapped fragments was considered (= coverage).
Data files were compressed by merging neighbouring nucleotides with equal coverages into single rows, with indication of start and end position of nucleotides with that specific coverage.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MBD2_R_vs_NR_promoter_-2000_-_+500bp_exon_Count_Data.xlsx: Excel file with columns containing resp. region id, version, Ensembl gene id, Entrez Gene id, gene label, gene description, chromosome, begin position, end position (nucleotide), location, location info, middle difference and amount of mapped fragments perl sample for the promoter region (-2000 bps and +500 bps of TSS).

molecule: genomic DNA

organism: Homo sapiens

source_name: Ovarian tumor, responder

extract_protocol:
DNA extracted using Qiagen Blood and Tissue Kit according to manufacturer's instructions.
Libraries were prepared using standard multiplexed paired-end ChIP-seq protocol (Illumina). In summary, 500 ng of DNA per sample was fragmented by ultrasound mediated DNA shearing (Covaris S2, Covaris, Woburn, Massachusetts, USA) set to obtain fragments with an average length of 200bp. We employed the MethylCap kit (Diagenode AF-100-0048, Liège, Belgium) to obtain methylated DNA fragments using the highest salt concentration single elution step option. This was followed by the library preparation for the enriched DNA, which was performed with a modified 'multiplexed paired-end ChIP protocol' (Illumina, San Diego, California, USA). Therefore, the NEBNext® DNA Sample Prep Master Mix Set 1 (New England BioLabs (NEB) E6040, Ipswich, Massachusetts, USA) was combined with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001). Per sample, 22µl of the prepared sample was subjected to PCR (21 cycles) following the Illumina Library Amplification Index Protocol. After purification (QIAquick PCR Purification columns, Qiagen), elution and concentration (evaporation), the libraries were pooled and denatured (NaOH), followed by Illumina HiSeq 2000 sequencing (multiplexed paired-end run, 2 times 45 cycles) of 10pM/pool.

tag: disease

value: High-grade serous ovarian cancer (HGSOC)

value: Ovarian tumor

tag: response to platinum-based chemotherapy

value: Extreme responder


title: Leaves from Non Inoculated-Wounded (NIW) plants 8 wpi rep 3


title: ChIP Tbx6

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
ChIP-Seq
in vitro differentiated presomoitic mesoderm

data_processing:
For RNA-Seq, reads were mapped with TopHat2 (version 2.1.0) (Kim et al., 2013) using bowtie (version 1.1.2) (Langmead et al., 2009), providing refSeq annotations in gtf format (UCSC) and the options --no-coverage-search --no-mixed --no-discordant -g1 --library-type (“fr-firststrand” or “fr-secondstrand” for libraries generated using the TotalScript and Scriptseq kits respectively). Reads that were called to be spliced and containing ambiguous strand information (e.g. containing both XS:A:+ and XS:A:- tags) were removed together with their respective mates. For visualization, wiggle tracks were generated with BEDTools (version 2.23.0) (Quinlan and Hall, 2010), normalized towards the sample with the lowest read count, converted into bigwig format and loaded into the Integrated Genome Browser (Freese et al., 2016). For calculation of FPKM’s, we used Cuffdiff, part of Cufflinks (version 2.2.1) (Trapnell et al., 2012), with the options -u --no-effective-length-correction -b.
ChIP-Seq data was using bowtie version 1.1.2. To estimate the fragment size distribution of the libraries and determine the maximum length cutoff, we performed an initial mapping of a limited number of reads using the options -y -m 1 -S -I 100 -X 500. The final mapping was performed using the same options and the determined maximum length parameter (-X). Paired-end reads were combined in a bed file by generating the original fragment using a custom perl script, duplicates were removed and .wig files were generated using BEDtools.
For ATAC-Seq, reads were trimmed to 50bp length and adapters were detected and removed using fastq-mcf of ea-utils  (https://expressionanalysis.github.io/ea-utils, version 1.04.738). Those reads in which the adapter sequences were not found, were further trimmed by 5bp (to account for potentially undetected but present short adapter sequences) and paired-end mapped using bowtie ((Langmead, et al., 2009) version 1.1.2), allowing a maximum fragment size of 2000bp. Possible PCR duplicates were removed using Picard (https://broadinstitute.github.io/picard, version 1.103). Reads for which the adapter sequences were found and removed were independently mapped from their mates to the mm10 genome (containing chromosomes 1-19, X, Y and M) using bowtie and supplying the options -y -m 1 –S.. After merging the resulting output files, the samtools ((Li, et al., 2009), version 1.2) fixmate function was used to combine corresponding reads into mates. Only those properly mapped mates with a maximum fragment length of 2000bp were filtered and potential PCR duplicates were removed using Picard. The resulting pairs were combined with the previously mapped reads, resulting in the final alignment file. Inspection of the data revealed 35 regions in the genome, mostly repetitive and on average 18kb in size, displaying mapping artefacts (Buenrostro, et al., 2015). We used samtools to remove reads, together with their corresponding mates, falling into these regions. Due to the repetitive nature of the Y chromosome and non-informative mitochondrial genome, reads mapped to either of them were filtered out. Paired-end reads were combined in a bed file by generating the original fragment using a custom perl script, duplicates were removed and .wig files were generated using BEDtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing read density for ATAC-Seq and ChIP-Seq
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each RNA-Seq sample for refseq genes

organism: Mus musculus

source_name: in vitro differentiated ES cells

growth_protocol: Presomitic mesoderm differentiation was carried out as described (Sudheer, et al., 2016) using CHIR99021 and high levels of FGF2 (250ng/ml for 2 days), following the conversion to EpiSCs.

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in LB1 (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA pH8, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer with a tight pestle with 3x 15 strokes, with short resting times on ice in between. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 10mM Tris pH 8) per cell pellet. After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA, 10mM Tris pH8, 100mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C coldroom with tubes chilled in ice water. After sonication, 150ul of triton X-100 was added per tube, transferred to two 1.5ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50ul as an input control, the chromatin was distributed into 1.5ml aliquots, snap frozen and stored at -80C until use.  The input was reverse-crosslinked with the addition of 50ul 2x elution buffer (100mM Tris pH8, 20mM EDTA pH8, 2% SDS) and overnight (13h-15h) incubation at 65°C. The next day, 100ul of TE buffer were added to dilute the SDS of the elution buffer and RNA was digested using RNase A at a 0.2ug/ml final concentration at 37°C for 2 hours. Proteins were digested with the addition of 0.2ug/ml proteinase K and incubation at 55°C for 2 hours. The DNA was purified with two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH8) isolations and subsequent MinElute (Qiagen) purification. Purification was performed according to manufacturer’s recommendations, except that the columns were washed 2x with PE and air dried for at least 10 minutes before elution with EB. The input DNA was quantified using a NanoPhotometer (Implen) and the shearing was verified by running 600ng of DNA on a 1.5% agarose gel. For sonication to be considered successful and sonicated chromatin to be usable for ChIP, the bulk DNA of the input had to be located between 100bp-500bp.
For ChIP, 50µl or 100ul (for β-catenin) of protein-coated Dynal beads (Life Technologies) were washed 3x using 1ml of blocking solution (PBS containing 0.5% BSA), resuspended in 500µl of blocking solution together with approximately 5µg or 10 µg (for β-catenin) antibody and rotated overnight at 4°C. The antibodies used were a goat polyclonal anti-T (Santa Cruz, sc-17743), a goat polyclonal anti-Sox2 (R&D Systems, AF2018), a rabbit polyclonal anti-β-catenin (Invitrogen, 71-2700) and a rabbit polyclonal anti-Tbx6 (this paper). The next day, three further washes using 1ml blocking buffer were performed and the beads were resuspended in 100µl blocking buffer. Chromatin equivalent to approximately 25x106 or 50x106 (for β-catenin) cells was added and rotated overnight at 4°C. The following day, washing steps (6, 8 and 9 washes for Tbx6, Sox2 / β-catenin and T respectively) were performed using 1ml RIPA buffer (50mM Hepes pH7.6, 500mM LiCl, 1mM EDTA pH8, 1% NP-40, 0.7% Na-Deoxycholate) containing 1x complete protease inhibitors without EDTA and finally with 1ml of TEN (10mM Tris pH8, 1mM EDTA pH8, 50mM NaCl). The immunoprecipates were eluted in two subsequent steps using 100µl of 1x elution buffer (50mM Tris pH8, 10mM EDTA pH8, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. The eluates were combined and incubated overnight (13h-15h) at 65°C under agitation. The next day, 200µl of TE were added to dilute the SDS of the elution buffer and the ChIPs were purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-Seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the following modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 15µl of resuspension buffer (RSB, Illumina). In the case of Tbx6, 14µl of the eluate were used for PCR pre-amplification in order to convert adapters into double-stranded DNA. After the addition of 1µl primer mix (25mM each, Primer 1: 5’- AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21µl of RSB. Libraries were directly amplified for 18 cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips.

treatment_protocol: Crosslinking was performed directly on differentiating cells in growth medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) for 10 minutes at room temperature, with the dishes placed on a shaker. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Dishes were placed on ice or in a 4°C cold room and washed twice with cold PBS. Cells were scraped and washed off using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~30-50x106 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.

tag: strain

tag: developmental stage


title: Leaves from Non Inoculated-Wounded (NIW) plants 12 wpi rep 2


title: Leaves from Non Inoculated-Wounded (NIW) plants 6 wpi rep 3

value: 6 wpi


title: Leaves from Non Inoculated-Wounded (NIW) plants 8 wpi rep 1


title: Leaves from Non Inoculated-Wounded (NIW) plants 6 wpi rep 1


title: Leaves from Non Inoculated-Wounded (NIW) plants 6 wpi rep 2


title: UMCG-TT-15 Non-responder

source_name: Ovarian tumor, non-responder

value: Non-responder


title: Leaves from Non Inoculated-Wounded (NIW) plants 2 wpi rep 3

value: 2 wpi


title: Leaves from Non Inoculated-Wounded (NIW) plants 2 wpi rep 2


title: Leaves from Non Inoculated-Wounded (NIW) plants 24 hpi rep 2

value: 24 hpi


title: Leaves from Non Inoculated-Wounded (NIW) plants 24 hpi rep 3


title: Leaves from Non Inoculated-Wounded (NIW) plants 2 wpi rep 1


title: UMCG-TT-12 Non-responder


title: UMCG-TT-13 Non-responder


title: Leaves from Non Inoculated-Wounded (NIW) plants 12 wpi rep 1


title: Leaves from Non Inoculated-Wounded (NIW) plants 3 hpi rep 2

value: 3 hpi


title: Leaves from Non Inoculated-Wounded (NIW) plants 3 hpi rep 1


title: Leaves from Non Inoculated-Wounded (NIW) plants 0 hpi rep 3

value: 0 hpi


title: Leaves from Non Inoculated-Wounded (NIW) plants 3 hpi rep 3


title: UMCG-TT-11 Responder


title: UMCG-TT-9 Non-responder


title: Leaves from Non Inoculated-Wounded (NIW) plants 0 hpi rep 1


title: UMCG-TT-8 Non-responder


title: Leaves from Non Inoculated-Wounded (NIW) plants 0 hpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 3

value: Non Inoculated-Non Wounded (NINW)


title: UMCG-TT-6 Non-responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 1


title: UMCG-TT-5 Non-responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 3


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 2


title: UMCG-TT-3 Responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 1


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 3


title: UMCG-TT-16 Responder


title: UMCG-TT-2 Non-responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 3


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 1


title: UMCG-TT-1 Responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 3


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 1


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 3


title: Leaves from Non Inoculated-Wounded (NIW) plants 24 hpi rep 1


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 2


title: UMCG-TT-7 Responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 1


title: UMCG-TT-4 Responder


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 2


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 3


title: MDA_ROR1kd_1

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Göttingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed with STAR RNA-Seq aligner version 2.3.1y, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.5.
The transcriptome was generated with RSEM from Ensembl reference genome version 37.72.
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-separated text file include expected counts for each Sample

source_name: Ror1 knock-down MDA-MB-231 cell-line

growth_protocol: The human breast cancer cell line MDA-MB231 was purchased from ATCC (Rockville, USA) and was cultured in RPMI-1640 media (PAA, Coelbe, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FCS; Sigma, Munich, Germany).

extract_protocol:
RNA was isolated using Trizol reagent including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina (SR; 50 bp; 35 million reads per sample).

treatment_protocol: For ROR1 knockdown, MDA-MB231 cells were co-transfected with the packaging plasmids pMD2.G (Addgene plasmid 12259) and pCMVΔR8.2 (Addgene plasmid 12263, both provided by Didier Trono, École Polytechnique Fédéral de Lausanne, Lausanne, Switzerland) and either the pGIPZ shCTL or shROR1 vector (Thermo Scientific, Schwerte, Germany) through calcium phosphate precipitation. Virus-containing supernatants were concentrated using the lentiviral enrichment reagent (MoBiTech, Göttingen, Germany) and cells transfected with a MOI of 5.0. Stable expression was achieved by selecting for puromycin (2 µg/ml) resistance.

tag: cell line

tag: cell type

value: breast cancer


title: MDA_ctl_3

source_name: Control MDA-MB-231 cell-line (with empty vector)


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 1


title: Leaves from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 1


title: Leaves from Inoculated-Wounded (IW) plants 12 wpi rep 1

value: Inoculated-wounded (IW)


title: Leaves from Inoculated-Wounded (IW) plants 12 wpi rep 2

value: Cabernet Sauvignon clone FPS 19


title: MDA_ROR1kd_3


title: MDA_ctl_2


title: Leaves from Inoculated-Wounded (IW) plants 8 wpi rep 2


title: Leaves from Inoculated-Wounded (IW) plants 6 wpi rep 3


title: MDA_ROR1kd_2


title: MDA_ctl_1


title: Leaves from Inoculated-Wounded (IW) plants 2 wpi rep 2


title: Leaves from Inoculated-Wounded (IW) plants 2 wpi rep 3


title: Leaves from Inoculated-Wounded (IW) plants 24 hpi rep 2


title: Leaves from Inoculated-Wounded (IW) plants 24 hpi rep 1


title: Leaves from Inoculated-Wounded (IW) plants 24 hpi rep 3


title: Leaves from Inoculated-Wounded (IW) plants 6 wpi rep 1


title: Leaves from Inoculated-Wounded (IW) plants 12 wpi rep 3


title: Leaves from Inoculated-Wounded (IW) plants 3 hpi rep 2


title: Woody stem from Non Inoculated-Wounded (NIW) plants 12 wpi rep 3

value: Non Inoculated-Wounded (NIW)

value: stem tissue


title: Leaves from Inoculated-Wounded (IW) plants 0 hpi rep 3

value: leaf tissue


title: Leaves from Inoculated-Wounded (IW) plants 2 wpi rep 1


title: Leaves from Inoculated-Wounded (IW) plants 3 hpi rep 3


title: Woody stem from Non Inoculated-Wounded (NIW) plants 12 wpi rep 2

value: 12 wpi


title: Leaves from Inoculated-Wounded (IW) plants 0 hpi rep 1


title: Leaves from Inoculated-Wounded (IW) plants 0 hpi rep 2


title: Leaves from Inoculated-Wounded (IW) plants 6 wpi rep 2


title: Leaves from Inoculated-Wounded (IW) plants 3 hpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 12 wpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 8 wpi rep 3

value: 8 wpi


title: Woody stem from Non Inoculated-Wounded (NIW) plants 8 wpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 6 wpi rep 2


title: Woody stem from Non Inoculated-Wounded (NIW) plants 6 wpi rep 3


title: Leaves from Inoculated-Wounded (IW) plants 8 wpi rep 3


title: Woody stem from Non Inoculated-Wounded (NIW) plants 6 wpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 2 wpi rep 3


title: Woody stem from Non Inoculated-Wounded (NIW) plants 2 wpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 2 wpi rep 2


title: Woody stem from Non Inoculated-Wounded (NIW) plants 24 hpi rep 3


title: Quiescent Serum Starvation 2

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Reads were demultiplexed using bcl2fastq 1.8.4 with 1 mismatch allowed
Sequencing reads were mapped against the human genome build GRCh37.75 using tophat 2.0.12 with parameters --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were calculated using a custom script that uses the same strategy as HTSeq-count with union mode
Genes that have zero expression across all samples are removed from the dataset.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: The file readcounts.txt contains the absolute gene expressions values for each of the samples.

molecule: total RNA

source_name: Quiescent Serum Starvation

growth_protocol: Cells were propagated in DMEM (GIBCO) supplemented with 9% fetal bovine serum.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor and hTERT were cultured in 0% FBS DMEM medium for 10 days before harvesting in trizol (quiescent).
Cells were maintained for 9 days after the treatment specified in Treatment

value: diploid embryonic lung fibroblasts

tag: day treament

tag: cutured in

value: 0% FBS DMEM medium for 10 days (quiescent)


title: Cycling Control Serum 3

source_name: Cycling Control Serum

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor and hTERT were cultured in 9% FBS DMEM medium for 10 days before harvesting in trizol (cycling)
Cells were maintained for 9 days after the treatment specified in Treatment

value: 9% FBS DMEM medium for 10 days (cycling)


title: Quiescent Serum Starvation 3


title: Woody stem from Non Inoculated-Wounded (NIW) plants 8 wpi rep 2


title: Cycling Control Serum 2


title: Woody stem from Non Inoculated-Wounded (NIW) plants 3 hpi rep 3


title: Quiescent Serum Starvation 1


title: BRAF Senescence Bypass Day 10 Rep 3

description: X2947_18_ST.BRAF_Day_9_R_3_8.7.2014__C_CGATGTA

source_name: BRAF Senescence Bypass Day 10

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the SV40 small T antigen, were transduced with pBabe-puro-BRAFE600 (OIS bypass). The infected population was selected using puromycin 1μg/ml. Ten days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment

tag: transduced with

value: pBabe-puro-BRAFE600 (OIS bypass)

value: 10days after transduction


title: Woody stem from Non Inoculated-Wounded (NIW) plants 24 hpi rep 2

value: 24 hpi


title: Woody stem from Non Inoculated-Wounded (NIW) plants 0 hpi rep 2


title: Woody stem from Non Inoculated-Wounded (NIW) plants 24 hpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 0 hpi rep 1


title: Woody stem from Non Inoculated-Wounded (NIW) plants 3 hpi rep 2

value: 3 hpi


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 2


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 2


title: Cycling Control Serum 1


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 3


title: Woody stem from Non Inoculated-Wounded (NIW) plants 0 hpi rep 3

value: 0 hpi


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 3

value: Non Inoculated-Non Wounded (NINW)


title: BRAF OIS Day 10 Rep 3

description: X2947_17_PBH.BRAF_Day_9_R_3_8.7.2014__C_ATCACGA

source_name: BRAF OIS Day 10

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with pBabe-puro-BRAFE600 (OIS). The infected population was selected using puromycin 1μg/ml. Ten days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment

value: pBabe-puro-BRAFE600 (OIS)


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 3

value: 6 wpi


title: Woody stem from Non Inoculated-Wounded (NIW) plants 3 hpi rep 1

value: Cabernet Sauvignon clone FPS 19


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 12 wpi rep 1


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 8 wpi rep 1


title: Cycling Day 10 Rep 3

description: X2947_16_PBH.vector_Day_9_R_3_8.7.2014__B_CCGTCCC

source_name: Cycling Day 10

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with  empty vector (cycling). The infected population was selected using puromycin 1μg/ml. Ten days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment

value: empty vector (cycling)


title: Leaves from Inoculated-Wounded (IW) plants 8 wpi rep 1

value: Inoculated-wounded (IW)


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 2

value: stem tissue


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 6 wpi rep 1


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 3

value: 2 wpi


title: Cycling Day 4 Rep 3

description: X2947_13_PBH.vector_Day_4_R_3_8.2.2014__B_ACAGTGA

source_name: Cycling Day 4

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with  empty vector (cycling). The infected population was selected using puromycin 1μg/ml. Four days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment

value: 4days after transduction


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 3


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 1


title: BRAF OIS Day 4 Rep 3

description: X2947_14_PBH.BRAF_Day_4_R_3_8.2.2014__B_GCCAATA

source_name: BRAF OIS Day 4

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the (pBabe-hygro) empty vector, were transduced with pBabe-puro-BRAFE600 (OIS). The infected population was selected using puromycin 1μg/ml. Four days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment

value: diploid embryonic lung fibroblasts


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 2


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 1


title: Cycling Day 10 Rep 2

description: X2947_10_PBH.vector_Day_9_R_2_8.2.2014__B_CGATGTA


title: Woody stem from Inoculated-Wounded (IW) plants 12 wpi rep 2

value: 12 wpi


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 2


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 2


title: BRAF Senescence Bypass Day 10 Rep 2

description: X2947_12_ST.BRAF_Day_9_R_2_8.2.2014__B_TGACCAA


title: BRAF Senescence Bypass Day 4 Rep 3

description: X2947_15_ST.BRAF_Day_4_R_3_8.7.2014__B_CAGATCA

source_name: BRAF Senescence Bypass Day 4

treatment_protocol:
Human diploid fibroblast Tig3 cells expressing the ecotropic receptor, hTERT, and the SV40 small T antigen, were transduced with pBabe-puro-BRAFE600 (OIS bypass). The infected population was selected using puromycin 1μg/ml. Four days after transduction, cells were harvested in Trizol.
Cells were maintained for 9 days after the treatment specified in Treatment


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 24 hpi rep 1


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 1


title: Cycling Day 4 Rep 2

description: X2947_7_PBH.vector_Day_4_R_2_28_7_2014__A_CAGATCA


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 0 hpi rep 3


title: BRAF Senescence Bypass Day 4 Rep 2

description: X2947_9_ST.BRAF_Day_4_R_2_28_7_2014__B_ATCACGA


title: BRAF OIS Day 10 Rep 2

description: X2947_11_PBH.BRAF_Day_9_R_2_8.2.2014__B_TTAGGCA


title: BRAF Senescence Bypass Day 10 Rep 1

description: X2947_6_ST.BRAF_Day_9_R_1_26_7_2014__A_GCCAATA


title: Woody stem from Inoculated-Wounded (IW) plants 8 wpi rep 2

value: 8 wpi


title: BRAF OIS Day 10 Rep 1

description: X2947_5_PBH.BRAF_Day_9_R_1_26_7_2014__A_ACAGTGA


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 2 wpi rep 2


title: Woody stem from Inoculated-Wounded (IW) plants 6 wpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 6 wpi rep 2


title: Woody stem from Non Inoculated-Non Wounded (NINW) plants 3 hpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 12 wpi rep 1


title: BRAF OIS Day 4 Rep 2

description: X2947_8_PBH.BRAF_Day_4_R_2_28_7_2014__A_CCGTCCC


title: BRAF Senescence Bypass Day 4 Rep 1

description: X2947_3_ST.BRAF_Day_4_R_1_21_7_2014__A_TTAGGCA

value: pBabe-puro-BRAFE600 (OIS bypass)


title: Woody stem from Inoculated-Wounded (IW) plants 12 wpi rep 3


title: Cycling Day 10 Rep 1

description: X2947_4_PBH.vector_Day_9_R_1_26_7_2014__A_TGACCAA

value: 10days after transduction


title: Woody stem from Inoculated-Wounded (IW) plants 2 wpi rep 2


title: Woody stem from Inoculated-Wounded (IW) plants 6 wpi rep 1


title: Woody stem from Inoculated-Wounded (IW) plants 2 wpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 2 wpi rep 1


title: Woody stem from Inoculated-Wounded (IW) plants 8 wpi rep 3


title: Cycling Day 4 Rep 1

description: X2947_1_PBH.vector_Day_4_R_1_21_7_2014__A_ATCACGA


title: BRAF OIS Day 4 Rep 1

description: X2947_2_PBH.BRAF_Day_4_R_1_21_7_2014__A_CGATGTA


title: Woody stem from Inoculated-Wounded (IW) plants 8 wpi rep 1


title: Woody stem from Inoculated-Wounded (IW) plants 3 hpi rep 1


title: Woody stem from Inoculated-Wounded (IW) plants 24 hpi rep 2

value: 24 hpi


title: Woody stem from Inoculated-Wounded (IW) plants 3 hpi rep 2

value: 3 hpi


title: Woody stem from Inoculated-Wounded (IW) plants 24 hpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 3 hpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 24 hpi rep 1


title: Woody stem from Inoculated-Wounded (IW) plants 0 hpi rep 2

value: 0 hpi


title: Woody stem from Inoculated-Wounded (IW) plants 0 hpi rep 3


title: Woody stem from Inoculated-Wounded (IW) plants 0 hpi rep 1


title: MCF7_ROR2_WNT5A_2

description: Non stranded mRNA-Seq

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed with STAR RNA-Seq aligner version 2.4.0a, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.5.
The transcriptome was generated with RSEM from Ensembl reference genome version 37.73.
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: hs37 (primary assembly of GRCh37 plus the EBV genome)
Supplementary_files_format_and_content: tab-delimited text file include expected counts for each Sample

source_name: MCF-7 cells

growth_protocol: The human breast cancer cell line MCF-7 was purchased from ATCC (Rockville, USA) and was cultured in RPMI-1640 media (PAA, Coelbe, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FCS; Sigma, Munich, Germany).

extract_protocol:
RNA was isolated using Trizol reagent and including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina (SR; 50 bp; 35 million reads per sample).

treatment_protocol: For ROR2 over-expression, the plasmids pcDNA 3.1/Zeo(+) (Invitrogen, Paisley, UK) and pcDNA hsROR2 were introduced into MCF-7 cells using the Nanofectin transfection reagent (PAA, Colbe, Germany). Stable expression was achieved by selecting for zeomycin (100 µg/ml) resistance. For stimulation experiments the cells were treated for 24h with WNT5a (100 ng/ml, R&D systems) prior to cell lysis.

value: ER-positive breast cancer cell line MCF-7

value: ROR2 overexpression construct with stimulation with recombinant WNT5A


title: MCF7_ROR2_3

description: Non stranded mRNA-Seq

value: ROR2 overexpression construct


title: MCF7_ROR2_WNT5A_1

description: Non stranded mRNA-Seq


title: Abemaciclib tumor 12

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Data were analyzed, with all the default parameters, by Torrent Suite (Thermo Fisher) for base caliing, alignment, and filtering,  and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt file includes read counts for all Samples.

source_name: Murine mammary carcinoma

growth_protocol: Mice were induced with doxycyclin at age 6 weeks. Once tumors were established, mice were randomized to two groups with equal mean tumor volume.

extract_protocol:
Tumor tissue was snap frozen w hours after the 12th dose of treatment. Total RNA was extracted using the Macherey Nagel RNA Plus kit
cDNA libraries were constructed using the Ion AmpliSeq AmpliSe DNA and RNA Library kit with custome primers(Thermo Fisher)
An Ion AmpliSeq™ Custom Panel was designed by the manufacturer (thermo Fisher) using Ion AmpliSeq™ Designer for targeted amplification of 3826 mouse genes ,  A short amplicon (~110 bp) is amplified for each target

treatment_protocol: Control vehicle or abemaciclib 90mg/kg daily by gavage

value: mammary tumor

tag: agent

value: abemaciclib


title: MCF7_ROR2_WNT5A_3

description: Non stranded mRNA-Seq


title: Abemaciclib tumor 11


title: Abemaciclib tumor 10


title: MCF7_ROR2_2

description: Non stranded mRNA-Seq


title: Abemaciclib tumor 9


title: Abemaciclib tumor 8


title: Abemaciclib tumor 7


title: Abemaciclib tumor 6


title: MCF7_ROR2_1

description: Non stranded mRNA-Seq


title: MCF7_WNT5A_3

description: Non stranded mRNA-Seq

value: control empty vector (pcDNA) with stimulation with recombinant WNT5A


title: MCF7_WNT5A_2

description: Non stranded mRNA-Seq


title: Abemaciclib tumor 5


title: Abemaciclib tumor 3


title: Abemaciclib tumor 4


title: MCF7_WNT5A_1

description: Non stranded mRNA-Seq


title: Abemaciclib tumor 1


title: Control tumor 11

value: control


title: Abemaciclib tumor 2


title: MCF7_ctl_2

description: Non stranded mRNA-Seq

value: control empty vector (pcDNA)


title: Control tumor 7


title: Control tumor 10


title: MCF7_ctl_3

description: Non stranded mRNA-Seq


title: Control tumor 9


title: Control tumor 8


title: Control tumor 5


title: Control tumor 6


title: Control tumor 3


title: Control tumor 2


title: MCF7_ctl_1

description: Non stranded mRNA-Seq


title: Control tumor 4


title: H3K27me3_Hypoxia

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

country: South Korea

institute: POSTECH

data_processing:
Illumina Casava 1.8 Software was used for basecalling
Sequenced reads were trimmed for adaptor sequences and masked for low-quality sequences using cutadapt v1.0 with parameter -q 20
Trimmed reads were mapped to hg19 whole genome using BOWTIE2 v.2.0.6 with parameter -q -p 16 --end-to-end --sensitive --phred 33
Duplicated reads were marked with Picard v1.76
Low quality and duplicated reads were removed with Samtools with parameter -b -F1028 -q 5
Reads per kilobase of target per megabase of library (RPKM) were calculated for all genes. Briefly, location data for all gene was acquired from ensembl (v76, Grch38). The number of reads falling in this locations were counted and normalized by the size lf the gene length and by size of the library.
Peaks were called using MACS v1.4  with following setting -f BAM -g hs --tsize=101 -p 1e-3 --nomodel --keep-dup=1 --call-subpeaks --bdg
Genome_build: GrCh 38
Supplementary_files_format_and_content: MACS_peaks.xlsx: Peaked region obtained by MACS

source_name: adipocyte-derived stem cells (hADSCs)

growth_protocol: Human Adipose-Derived Stem Cells were purchased from Invitrogen (Carlsbad, CA), which are isolated from human adipose tissue collected during liposuction procedures.

extract_protocol:
The cells were lysed by radioimmunoprecipitation assay (RIPA) buffer and the cell lysates were collected by centrifugation. Immunoprecipitated DNA was isolated with selected antibodies.
Libraries were prepared according to Illumina's instructions. Briefly, 10 ng of DNA was end-repaired using a combination of Klenow polymerase and T4 polynucleotide kinase to yield a protruding 3-d'A' overhang. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 100~500 bp were band isolated from an agarose gel. The purified DNA was captured on agilent bioanalyzer. Libraries were sequencedHiSeq 2000 platform following the manufacturer's protocols.

treatment_protocol: For hypoxia samples, the cells were incuabated in hypoxic condition (<0.5%) for 48 hours.

tag: o2 concentration


title: Control tumor 1


title: H3K9me3_Hypoxia


title: H3K4me3_Hypoxia


title: H3K9me3_Normoxia


title: H3K4me3_Normoxia


title: Enriched KO 60min IL-7

city: New Haven

first: Huabing

last: Li

state: CONNECTICUT

address: 1 Gilbert Street, S570

department: Immunobiology

institute: Yale University School of Medicine

description: Biochemically enriched RNA (rRNA depleted)

data_processing:
Sequencing reads were aligned used STAR (version 2.4.2a) to align RNA-Seq reads simultaneously to the M. musculus and S. pombe genomes (mm10/PomBase v22) and transcriptomes (UCSC mm10 and Ensembl Fungi v22).
HTSeq-count (version 0.6.1p1) was used to quantify annotated M. musculus and S. pombe transcripts for total RNA (-t gene) and mRNA (-t exon).
Normalized expression values for bedGraph files to S. pombe spike-ins by multiplying raw FPKM's by the ratio of total S. pombe reads in each sample to total S. pombe reads in input WT 0min IL-7.
Genome coverage tracks were generated using IGVTools (version 2.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph files (normalized using S. pombe spike-ins) for forward and reverse strands for each sample are separated.

source_name: CD4+CD25-CD45RBhi naïve T cells, Mettl3(-/-)

growth_protocol: The naïve T cells were isolated from Mettl3 WT and KO mice with StemCell Naïve T cell isolation kits. The pure naïve T cells were resuspended in PBS+2%FBS in 1.5mL tubes, with or without IL-7 addition / s4U labeling at 37℃ incubator.

extract_protocol:
Cells were resuspended in TRIzol reagent, flash frozen, and stored overnight at -80°C. Cell lysates were chloroform extracted once and total RNA purified by isopropanol precipitation. Total RNA was sheared to ~200 bp and purified using the RNeasy Mini Kit. s4U-RNA was biotinylated with MTSEA-biotin-XX, and excess biotin was removed by chloroform extraction and RNeasy Mini Kit. Biotinylated RNA was enriched on Dynabeads Streptavidin C1 beads, and eluted by the addition of DTT. Enriched fractions were purified by ethanol precipitation.
10 ng input and RNA collected from eluted fractions were used for Smarter Stranded RNA-Seq Pico Input Mammalian library preparation (Clontech) with rRNA depletion. Input and enriched samples were multiplexed with Illumina bar codes and sequenced using single-end 1x75-nt cycles on an Illumina HiSeq instrument.

treatment_protocol: WT and Mettl3(-/-) cells were IL-7 stimulated (as above) for 0, 15, 30, 45, 60, or 75 min and labeled with 250 uM s4U for the last 15 min of stimulation, followed by PBS wash, trypsinization, and harvest.

tag: strain/background

tag: genotype/variation

value: Mettl3 KO

value: Naive T cells

tag: il-7 stimulation

tag: s4u feed

value: 250 uM, 15 minutes


title: Enriched KO 30min IL-7


title: Control 52 (C6)

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description:
processed data file: Processed data PPCD evHCEnC.xls
Sample name: Sample 13

data_processing:
The FASTQ files containing the RNA-sequencing data were uploaded to the Partek Flow servers for alignment to the hg38 genome using the TopHat2 aligner, which output the results in BAM files
The BAM files were uploaded to the Partek Genomics Suite software and the reads and read-depth were transformed to reads per kilobase per million (RPKM) values, a normalized quantity that accounts for gene size.
These data were annotated using the Ensemble 82 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 82 gene symbol ID in the first column. Sample names are given on the first row with RPKM values for each gene running down the column.

source_name: ex vivo corneal endothelium

growth_protocol: Cultured cells were either grown in F99 or Human Endothelial SFM.

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.

tag: diagnosis

value: healthy control

value: cornea

value: endothelial

tag: immortalization

tag: culture medium


title: Control 57 (C5)

description:
processed data file: Processed data PPCD evHCEnC.xls
Sample name: Sample 12

tag: tissue


title: Enriched KO 0min IL-7


title: PPCD CDDL 286 (P5)

description:
processed data file: Processed data PPCD evHCEnC.xls
Sample name: Sample 10

value: Posterior Polymorphous Corneal Dystrophy (PPCD)


title: HEK293T and NIH/3T3 cell mixture (sciRNA-seq with three levels indexing)

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sciRNAseq with three levels indexing

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2)
RT barcode (10bp) and UMI (8bp) sequence in Read1 is attached to the read name of Read2. Reads not matching to the expected RT barcodes were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.
Trimmed reads were mapped to the human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758) or a chimeric reference genome of hg19, mm10 and PRJNA13758, using STAR/v 2.5.2b (38) with default settings and gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse, WormBase PRJNA13758.WS253.canonical_gene set for C.elegans).
Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end-coordinate.
Mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index (ED < 2, including insertions and deletions).
To generate digital expression matrices, we calculated the number of strand-specific UMIs mapping to the exonic and intronic regions of each gene, for each cell; generally, fewer than 3% of total UMIs strand-specifically mapped to multiple genes. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.
Genome_build: human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758)
Supplementary_files_format_and_content: Processed data file is a sparsematrix in R: each row corresponds to genes, and each column corresponds to single cell, number in the matrix is the UMI count data.

organism:
Homo sapiens
Mus musculus

source_name: cell line

growth_protocol: All cultured cell lines were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin).

extract_protocol:
All cell lines were trypsinized, spun down at 300xg for 5 min (4°C). and washed once in 1X PBS. L2 stage worms were disscociated with SDS-DTT solution and pronase to generate single cell suspension. Detailed protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
library construction protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."

treatment_protocol: For c.elegans, a synchronized L2 population was obtained by two cycles of bleaching gravid adults to isolate fertilized eggs allowing the eggs to hatch in the absence of food to generate a population of starved L1 animals.

value: HEK293T and NIH/3T3


title: PPCD CDDL 290 (P6)

description:
processed data file: Processed data PPCD evHCEnC.xls
Sample name: Sample 11


title: Enriched WT 45min IL-7

source_name: CD4+CD25-CD45RBhi naïve T cells, WT

value: WT


title: H3K27me3_Normoxia


title: Enriched WT 15min IL-7


title: DMSO [CC4]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: danRer7
Supplementary_files_format_and_content: excel files include FPKM values for each Sample ...

organism: Danio rerio

source_name: sox10:GFP+ cells from zebrafish embryos

extract_protocol:
Total RNA was extracted using Trizol LS according to the manufacturer's instructions.
Libraries were prepared using the Ribogone kit (Clontech) and the SMARTer Universal Low RNA Kit (Clontech) according to the manufacturer’s instructions. Libraries were analyzed on a Fragment Analyzer (Advanced Analytical) and quantified using the Qubit (Invitrogen) prior to sequencing on the Illumina HiSeq 2500.

treatment_protocol: Zebrafish embryos were treated with 10 micromolar CAPE or vehicle (DMSO) control in E3 embryo medium at 2 ss and sox10:GFP+ cells were sorted at 17 ss.

value: sox10:GFP transgenic

tag: developemental stage

value: embryo

tag: treated with

value: 10 micromolar CAPE

value: sox10:GFP+ cells

tag: molecule subtype

value: rRNA depleted RNA


title: CAPE [CC5]

value: DMSO control

tag: cell type


title: CAPE_17ss

data_processing:
All zebrafish ATAC-Seq datasets were aligned to build version UCSC danRer7 of zebrafish human genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: danRer7
Supplementary_files_format_and_content: bed file of called peaks

extract_protocol:
Cells (12,000-40,000) were pelleted at 500 rcf for 5 minutes at 4°C, washed once in ice cold PBS, and permeabilized in 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360.
Libraries were prepared using the Nextera DNA Preparation Kit (Illumina) with a transposase reaction time of 30-45 minutes and purified with the MinElute PCR Purification Kit (Qiagen). Quantitative PCR was used to estimate the total number of cycles needed for library amplification. Libraries were analyzed on a Fragment Analyzer (Advanced Analytical) and quantified using the Qubit (Invitrogen) prior to sequencing on the Illumina HiSeq 2500.

treatment_protocol: Zebrafish embryos were treated with 10 micromolar CAPE or vehicle (DMSO) control in E3 embryo medium at 2 ss and sox10:GFP+ cells were sorted at 17 or 20 ss.

tag: somite stage (ss)


title: Input KO 60min IL-7

description: Total RNA (rRNA depleted)


title: Lin37 rescue clone 632-2 sample 2

city: Leipzig

first: Gerd

last: Müller

address: Semmelweisstrasse 14

department: Medical School

institute: University of Leipzig

description:
Sample name: 632-2_Lin37-rescue_2
rRNA depleted RNA
biological replicate of 632-2_Lin37-rescue_1

data_processing:
Illumina’s HiSeq Control  Software (HCS) used for basecalling.
adapter was clipped using cutadapt with a minimum length of 12 with AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC as adapter for mate 1 and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT as adapter for mate 2
Segemehl 0.2.0 was used for alignment to mm10 genome assembly with default parameters and split read mapping enabled
RPKMs on gencode vM5 were computed using rnacounter 1.5.2 with default parameters except -nh flag enabled
Insert sizes for non-split reads computed with CollectInsertSizeMetrics.jar form picard-tools 1.89
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing RPKM values for each sample

source_name: NIH3T3 mouse fibroblasts

growth_protocol: Cells were maintained in DMEM containing 10% FCS.

extract_protocol:
RNA was extracted with the qiagen Rneasy kit
100 ng of total RNA were fragmented by adding fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier. Fragmented RNA was further processed using the Ovation Human FFPE RNA-Seq Library Systems (Nugen) according to the instructions of the manufacturer. The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems).

treatment_protocol: Cells were cultivated in DMEM containing 0% FCS for 60h prior to RNA extraction

tag: cell line

tag: genotype

value: Lin37 rescue

tag: cell cycle stage

value: G0 / quiescent


title: Enriched WT 0min IL-7


title: Input KO 30min IL-7

description: Total RNA (rRNA depleted)

value: Mettl3 KO


title: Lin37 rescue clone 632-2 sample 1

description:
Sample name: 632-2_Lin37-rescue_1
rRNA depleted RNA


title: DMSO_20ss


title: DMSO_17ss


title: Lin37 knockout clone 632-2 sample 3

description:
Sample name: 632-2_Lin37-KO_3
rRNA depleted RNA
technical replicate of 632-2_Lin37-KO_2

value: Lin37 knockout


title: Enriched KO 15min IL-7

value: Naive T cells

value: 250 uM, 15 minutes


title: Input KO 15min IL-7

description: Total RNA (rRNA depleted)


title: Enriched WT 60min IL-7


title: K5

city: Scarborough

first: Robert

last: Koza

state: Maine

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

data_processing:
Instrument Control Software 1.2.0-0.r26064 was used for basecalling. No adjusted parameters
The alignment of sequence tags back to a reference genome will be performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was installed, modified to meet stringent mapping criteria.
Raw count files were analyzed and normalized by the R/Bioconductor program DE-Seq31 and significance and predictive analyses were performed using SAM and PAM respectively.
P-values were adjusted for false discovery rate using the Benjamini-Hochberg method and pairwise analyses of samples was performed using Bioconductor edgeR version 3.2.3.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene IDs and normalized values for each sample

source_name: Mest+/-_epididymal adipose tissue

extract_protocol:
Epididymal adipose tissue was rapidly excised, flash frozen in liquid nitrogen and crushed into a homeogeneous powder prior to isolation of RNA.  RNA was isolated using TRI Reagent with modifications to remove DNA using Qiagen RNAeasy columns and RNAase-free DNAseI. Quality and quantity of RNA was determined using an Agilent 2100 Bioanalyzer.
RNA will be transcribed into cDNA via priming at the poly A+ tail. Double-stranded cDNA will be digested with NlaIII restriction enzyme and ligated to adaptors containing an EcoP15L restriction site. Digestion with EcoP15L, ligation of "bar code" oligonucleotides that specifically label each sample, and subsequent PCR amplification will yield a library for sequencing where each gene will be represented by a 3'-expression tag.

tag: strain

value: Mest+/-; paternal knockout

tag: age

value: 16 weeks

value: epididymal adipose tissue


title: K3

tag: genotype/variation


title: K4


title: Enriched WT 75min IL-7

tag: strain/background

tag: il-7 stimulation


title: Input KO 0min IL-7

description: Total RNA (rRNA depleted)

tag: s4u feed


title: Input WT 60min IL-7

description: Total RNA (rRNA depleted)


title: Input WT 75min IL-7

description: Total RNA (rRNA depleted)


title: Lin37 knockout clone 632-2 sample 1

description:
Sample name: 632-2_Lin37-KO_1
rRNA depleted RNA


title: K2


title: CAPE_20ss


title: Lin37 rescue clone 411-27 sample 2

description:
Sample name: 411-27_Lin37-rescue_2
rRNA depleted RNA
biological replicate of 411-27_Lin37-rescue_1


title: K1


title: Input WT 30min IL-7

description: Total RNA (rRNA depleted)


title: Lin37 knockout clone 411-27 sample 2

description:
Sample name: 411-27_Lin37-KO_2
rRNA depleted RNA
biological replicate of 411-27_Lin37-KO_1


title: Lin37 rescue clone 632-2 sample 3

description:
Sample name: 632-2_Lin37-rescue_3
rRNA depleted RNA
technical replicate of 632-2_Lin37-rescue_2


title: Lin37 rescue clone 411-27 sample 1

description:
Sample name: 411-27_Lin37-rescue_1
rRNA depleted RNA


title: Input WT 45min IL-7

description: Total RNA (rRNA depleted)


title: C5

source_name: WT_epididymal adipose tissue

value: wildtype


title: Lin37 knockout clone 411-27 sample 1

description:
Sample name: 411-27_Lin37-KO_1
rRNA depleted RNA


title: C6


title: Input WT 0 min IL-7

description: Total RNA (rRNA depleted)

value: WT

value: 0 min


title: Input WT 15min IL-7

description: Total RNA (rRNA depleted)


title: C4


title: Lin37 knockout clone 632-2 sample 2

description:
Sample name: 632-2_Lin37-KO_2
rRNA depleted RNA
biological replicate of 632-2_Lin37-KO_1


title: Input_ChIPseq

city: Beijing

first: Guojia

last: Xie

address: No.38, Xueyuan Rd

country: China

institute: PKUHSC

data_processing:
Base-Calling was conducted by CASAVA software.
ChIP Seq reads were aligned to the hg19 genome assembly by Bowtie2.
Peaks were called by MACS14 with the thresholds of fragments size=300 and P-Value<1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS14, bed file represents the binding coordinates in the whole genome of UTX

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 107 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by polyclonal antibodies against UTX. The DNA was purified with the Qiagen PCR purification kit.
The 1st strand cDNA was synthesized with random primer flanked by 7 nt sequence to track infromation. The 2nd strand DNA was generated with N6 adaptor. The resulting DNA libraries were amplified with Phusion High-Fidelity DNA Polymerase.


title: Sbi._R.07020_60DAP_internode_4.3

city: college station

first: brian

middle: adam

last: mckinley

state: tx

address: 2128 tamu

department: biochemistry and biophysics

institute: texas A&M University

data_processing:
Read alingement to sorghum bicolor referance genome (CLC Genomics Workbench)
Qauntification of expression (CLC Genomics Workbench)
Statistical analysis of differential expression using the edge test (edgeR plugin for CLC Genomics Workbench)
Gene functional analysis and k-means clustering (Mapman)
Genome_build: Sorghum bicolor BTx623 V3.1
Supplementary_files_format_and_content: csv, RPKM data

organism: Sorghum bicolor

source_name: Internode 4

growth_protocol: For microscopic and RNA-seq analysis of successive sub-apical internodes of sorghum stems, the photoperiod sensitive bioenergy genotype R.07020 was grown in a growth chamber for 60 days under long day conditions (14 h photoperiod) to prevent floral induction. The growth chamber’s temperature was 310C/220C day/night and at constant 50% relative humidity. The light in the growth chamber was supplied with fluorescent lamps at a light intensity of ~350 µMol m-2 s -1 of photosynthetically active radiation (PAR).

extract_protocol:
RNA was extracted using TRIzol according to the manufacturer’s protocol (Invitrogen). About three µg of total RNA was used for RNA-seq library preparation using TruSeq™ RNA Sample Prep Kit v2 (Illumina, Inc.). RNA-seq library quality was assessed using a Bioanalyzer and sequenced on an Illumina HiSeq 2500 at the Texas A&M University Genomics and Bioinformatics Service Center.
The sequence template was prepped using the True-seq V2 kit from illumina which isolates polyadenylated RNA and preps it for sequencing.

treatment_protocol: Plants wereharvesteed at 60 days after planting.  The top four succesive internodes below the apical dome were exicsed at the node thereby seperating each internode individually.  The develpomental progression of internode represents the treatment in this expeirment.

tag: line

value: internode


title: Enriched WT 30min IL-7


title: UTX_ChIPseq


title: Sbi._R.07020_60DAP_internode_4.2


title: pHCEnC ZEB1 siRNA 72hr 193

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 9

source_name: primary corneal endothelial cells

value: cornea

value: endothelial

tag: immortalization

tag: culture medium


title: C2

tag: tissue


title: Sbi._R.07020_60DAP_internode_4.1


title: pHCEnC ZEB1 siRNA 72hr 187

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 8


title: C1


title: C3


title: Sbi._R.07020_60DAP_internode_3.2

source_name: Internode 3


title: pHCEnC ZEB1 siRNA 72hr 175

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 7


title: pHCEnC ZEB1 siRNA 24hr 191

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 6


title: Sbi._R.07020_60DAP_internode_3.1


title: pHCEnC ZEB1 siRNA 24hr 185

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 5


title: Sbi._R.07020_60DAP_internode_2.3

source_name: Internode 2


title: H111 ntrC mutant rep3

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome (Carlier et al 2014) using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample (CLC exported)

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System
Nugen

value: ntrC mutant

tag: growth

value: planktonic cells, OD600 equal 0.5

tag: medium

value: minimal medium shift experiment (15 mM to 0.3 mM)


title: H111 ntrC mutant rep2


title: H111 ntrC mutant rep1


title: Sbi._R.07020_60DAP_internode_3.3


title: pHCEnC ZEB1 siRNA 24hr 173

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 4

tag: cell type


title: Sbi._R.07020_60DAP_internode_2.1


title: Sbi._R.07020_60DAP_internode_2.2


title: H111 wt  rep1

value: wt


title: H111 wt  rep2


title: Sbi._R.07020_60DAP_internode_1.3


title: pHCEnC CNTL siRNA 24hr 172

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 1


title: pHCEnC CNTL siRNA 24hr 190

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 3


title: Sbi._R.07020_60DAP_internode_1.2


title: c.elegans cells (L2 stage) and HEK293T cell mixture (experiment 1)

description: sci-RNA-seq with mixture of c.elegans cells and HEK293T cells

organism:
Caenorhabditis elegans
Homo sapiens

source_name: whole c.elegans (L2 stage) + cell line

value: A C. elegans strain (RW12139 stIs11435(unc-120::H1-Wcherry;unc-119(+));unc-119(tm4063)) carrying an integrated Punc-120::mCherry gene in a wild type background was used

value: HEK 293T


title: FASTmC_Lmic

city: Poznan

first: karolina

last: susek

address: Strzeszynska

country: Poland

institute: Institute of Plant Genetics, Polish Academy of Sciences

description: DNA methylation

data_processing:
FASTmC, a non-referenced based approach to estimate the levels of DNA methylation
linear models were created for each sequence context from the DNA methylation levels that were obtained from a reference-based alignment using methylpy
Genome_build: non-referenced based approach
Supplementary_files_format_and_content: bulk levels of mCG, mCHG and mCHH (Processed data FASTmC.xlsx)

organism: Lupinus micranthus

source_name: leaves

extract_protocol:
Genomic DNA was extracted using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s recommendations
MethylC-seq libraries for each species was prepared according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR.; MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc. 2015;10(3):475-83. doi: 10.1038/nprot.2014.114.

tag: accession no.

value: leaves


title: McrA-deleted-rep1

city: Nagoya

first: Tomohiro

last: Akashi

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Advanced Medical Science

country: Japan

institute: Nagoya University Graduate School of Medicine

description: Carries mutation that activates secondary metabolite production.

data_processing:
Illumina Miseq Control Software used for basecalling.
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to  Aspergillus nidulans genome using HISAT v1.
Genome_build: A_nidulans_FGSC_A4_version_s10-m03-r26
Supplementary_files_format_and_content: tab-delimited text files with abundance measurements (raw counts).

organism: Aspergillus nidulans

source_name: Liquid culture

growth_protocol: Spores were inoculated in a glucose minimum medium supplemented with uridine, uracil, pyridoxine, and riboflavin (1,000,000 spores in 150 ml), and incubated at 37 degree for 1day.

extract_protocol:
Mycelia cultured in liquid media were harvested, flash frozen in liquid nitrogen, and RNA was recovered using Sepazol reagent. NEB directional RNA Sample Prep Kit was used with polyA-RNA for the construction of sequencing libraries.
Directional RNA libraries were prepared for sequencing using standard NEB protocols

value: Strain LO8158

tag: culture

value: Glucose minimal medium, 1 day culture

value: mcrA-


title: McrA-deleted-rep2

tag: genotype


title: c.elegans cells (L2 stage) and HEK293T cell mixture  (experiment 2)

tag: cell line


title: FASTmC_Llut

description: DNA methylation

organism: Lupinus luteus

tag: cultivar variety

value: cv. ‘Talar’


title: FASTmC_Lcos

description: DNA methylation

organism: Lupinus cosentinii


title: WT_H2O2

city: Seoul

first: Seon Ah

last: Cheon

address: 84 Heukseok-ro

institute: Chung-Ang University

data_processing:
Quality-filtered sequence reads were mapped to the reference genome sequence of C. neoformans (http://www.broadinstitute.org) using the CLC Genomics Workbench 5.5 (CLC bio).
The relative transcript abundance was calculated by counting the reads per kilobase of exon model per million mapped sequence reads (RPKM).
Genome_build: CNA3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cryptococcus neoformans H99

source_name: WT at oxidative stress condition

growth_protocol: For non-stress samples, cells were cultivated in YPD medium up to the early exponential growth phase for non-stress samples. For oxidative stress samples, cells were incubated in YPD medium containing 1 mM H2O2  for 1 h for oxidative stress samples.

extract_protocol:
total RNAs were extracted using RNeasy mini kit (Qiagen) and the quantity and quality of the total RNA were evaluated using RNA electropherograms (Agilent 2100 Bioanalyzer) and the RNA integrity number (RIN).
10 ug of total RNAs were used to prepare sequencing libraries with the illumina mRNA-Seq sample preparation kit (illumina).

treatment_protocol: 1 mM H2O2 treatment for 1 hour for oxidative stress condition

value: wild-type

tag: growth condition


title: FASTmC_Lpil

description: DNA methylation

organism: Lupinus pilosus


title: gsb1_H2O2

source_name: gsb1 at oxidative stress condition


title: H111 wt  rep3

tag: genotype/variation


title: WT-rep3

tag: strain

value: Strain LO1362

value: mcrA+


title: gsb1_YPD

source_name: gsb1 at non-stress condition

value: YPD


title: WT-rep2


title: FASTmC_Lang

description: DNA methylation

organism: Lupinus angustifolius

value: cv. ‘Sonet’


title: McrA-deleted-rep3


title: pHCEnC CNTL siRNA 24hr 184

description:
processed data file: Processed data ZEB1 KD pHCEnC.xls
Sample name: Sample 2

value: cornea

value: endothelial


title: FASTmC_Ldig

description: DNA methylation

organism: Lupinus digitatus


title: RR474;protein: NGT_NHA-Shu-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

status: Public on Aug 16 2017

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

description: piRNAs

data_processing:
Reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200). Only reads which are at least 15 nucleotides in length were left for subsequent analysis.
Reads were then aligned to the desired reporter sequence using bowtie allowing no mismatches.
Genome_build: Reads were mapped to the reporter sequences.
Supplementary_files_format_and_content: The files contain mapping of the reads (piRNAs) to the reporter sequence.

organism: Drosophila melanogaster

source_name: fly germ cells

growth_protocol: For expression in the Drosophila ovarian somatic cell (OSC) cultures, we used the pAC5.1 vector (Life Technologies) driving expression from the fly actin promoter. For expression of either HA-tag (pAC-HA) or N-HA-tag fusions (pAC-NHA), the pAC5.1 vector was further modified to add the necessary coding sequences. The HA tag is for detection of the expressed protein and theN-peptide is for artificially tethering the fusion protein to a transcript containing BoxB sequences. OSCs were cultured in 75 cm flasks and grown to 80% confluence. Approximately 3.5x106 cells were used for each electroporation reaction using Cell Line Nucleofector Kit V (Lonza, Cat No. VCA-1003) and were plated in 6-well plate.  For creating transgenic fly lines, the coding sequences for NHA- or HA-tagged fusions of Armi, Yb or Shu, and the point mutant versions were inserted into the pUASp_attB_delK10 plasmid containing the white+ gene marker. These were used for site-specific integration (BestGene, Inc) in the Drosophila genome using the PhiC31 (ΦC31) integrase-mediated transgenesis system.

extract_protocol:
piRNAs present in PIWI, Aub or Ago3 complexes were isolated using indicated antibodies.
Sequencing libraries  were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. The synthesized libraries were resolved on agarose gel and fragments of around 120 bp (corresponding to piRNAs) sequenced on Illumina HiSeq platform (EMBL Heidelberg Gene core facility).

treatment_protocol: For fly ovarian soma expression, a recombinant line carrying the ovarian soma-specific driver traffic jam-Gal4 (tj-Gal4) (gift of A. Pelisson), and the UASp- Reporter-5BoxB was created by classical meiotic recombination in the y[1]w[1118] genetic background. Then homozygous females yw;tj-Gal4,UASp- Reporter-5BoxB were crossed with males from each line carrying the transgene expressing one of the various fusion proteins: UASp-NHA-Armi-WT, UASp-NHA-ArmiDQAG, UASp-NHA-ArmiGNT, UASp-HA-Armi-WT, UASp-NHA-Yb or UASp-NHA-Shu. The resulting F1 female progeny of the following genotype: yw;tj-Gal4,UASp- Reporter-5BoxB/+;UASp-Fusion protein/+ was selected and analyzed for piRNA expression or protein expression in the ovaries.  For fly ovarian germ line expression, each transgene allowing for the expression of fusion proteins were individually combined with the ovarian germline driver line NGT-Gal4 (gift of J. Brennecke) by classical genetic crosses using balancers of the second (CyO) and third (TM6b) chromosomes from a multiple balanced line y[1],w[1118]; If/CyO; Sb/TM6b. Females yw;NGT-Gal4/(CyO); UASp-fusion protein/(TM6b) carrying or not CyO and TM6b balancers (to avoid dominant partial sterility induced by the expression of some of the transgenes) were then crossed with  UASp- Reporter-5BoxB gene and the resulting F1 progeny carrying the three transgenes (yw;NGT-Gal4/UASp- Reporter-5BoxB;UASp-fusion protein/+) was selected and analyzed for piRNA expression or protein expression in the ovaries.  Alternatively, in a second set of experiments, a homozygous, fully viable and fertile recombinant line yw;NGTGal4,UASp- Reporter-5BoxB was created by meiotic recombination and crossed with each of the UASp-fusion protein lines. The resulting progeny of the following genotype yw;NGT-Gal4,UASp- Reporter-5BoxB/+; UASp-fusion protein/+ was analyzed for piRNA or protein expression in the ovaries with similar results.

value: germ cells

tag: tethered protein

tag: reporter

tag: ip antibody

value: PIWI (rabbit polyclonal;PMID:26166577)


title: RR466;protein: NGT_NHA-Yb-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs

value: Aub (rabbit polyclonal;PMID:26166577)


title: WT-rep1


title: RR473;protein: NGT_NHA-Yb-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

description: piRNAs


title: WT_YPD

source_name: WT at non-stress condition


title: RR467;protein: NGT_NHA-Shu-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs


title: Sbi._R.07020_60DAP_internode_1.1

tag: line

value: internode


title: RR468;protein: NGT_NHA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

description: piRNAs


title: RR475;protein: NGT_NHA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs

value: Ago3 (rabbit polyclonal;PMID:26166577)


title: RR463;protein: NGT_NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs


title: RR477;protein: NGT_NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs


title: RR461;protein: NGT_NHA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs


title: RR462;protein: NGT_NHA-Armi-DQ;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs


title: RR464;protein: NGT_HA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Aub IP

description: piRNAs


title: RR476;protein: NGT_NHA-Armi-DQ;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs


title: RR480;protein: NGT_NHA-Yb-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs


title: RR471;protein: NGT_HA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

description: piRNAs


title: FASTmC_Lalb

description: DNA methylation

organism: Lupinus albus

value: cv. ‘Boros’

value: leaves


title: RR459;protein: Tj_NHA-Shu-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs

source_name: fly follicle cells

value: follicle cells


title: RR469;protein: NGT_NHA-Armi-DQ;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

description: piRNAs


title: RR449;protein: Tj_NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR456;protein: Tj_NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR450;protein: Tj_HA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR458;protein: Tj_NHA-Yb-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR478;protein: NGT_HA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs


title: RR451;protein: Tj_NHA-Yb-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR452;protein: Tj_NHA-Shu-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR457;protein: Tj_HA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR454;protein: Tj_NHA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR481;protein: NGT_NHA-Shu-wt;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;Ago3 IP

description: piRNAs


title: RR447;protein: Tj_NHA-Armi-wt;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR346;protein: HA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs

source_name: OSC

value: ovarian somatic cell culture

value: HA-Armi


title: RR455;protein: Tj_NHA-Armi-DQ;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR448;protein: Tj_NHA-Armi-DQ;reporter 1356:Luc-5BoxB-LacZ;fly follicle cells ;PIWI IP

description: piRNAs


title: RR470;protein: NGT_NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;fly germ cells;PIWI IP

description: piRNAs


title: RR334;protein: HA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR347;protein: NHA-LacZ;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs

value: NHA-LacZ


title: RR341;protein: NHA-LacZ;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR335;protein: NHA-LacZ;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR345;protein: NHA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs

value: NHA-Armi


title: RR339;protein: NHA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR333;protein: NHA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR337;protein: HA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR343;protein: HA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR331;protein: HA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR332;protein: NHA-LacZ;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR344;protein: NHA-LacZ;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR338;protein: NHA-LacZ;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR330;protein: NHA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR336;protein: NHA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR284;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR278;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR329;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR328;protein: HA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: HA-Shu


title: RR318;protein: HA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR342;protein: NHA-Armi;reporter Uint:Luc-5BoxB-LacZ with Us at specific places;OSC;PIWI IP

description: piRNAs


title: RR282;protein: HA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR281;protein: NHA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: NHA-Shu


title: RR340;protein: HA-Armi;reporter Uless:Luc-5BoxB-LacZ with U-depleted regions;OSC;PIWI IP

description: piRNAs


title: RR268;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR293;protein: HA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: HA-Yb


title: RR277;protein: HA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR292;protein: NHA-Yb_D-A;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR291;protein: NHA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: NHA-Yb


title: RR319;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR276;protein: NHA-Yb_D-A;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR266;protein: NHA-Yb_D-A;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR275;protein: NHA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR274;protein: HA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: HA-Piwi


title: RR289;protein: NHA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: NHA-Piwi


title: RR264;protein: HA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: PIWI (rabbit polyclonal;PMID:26166577)


title: RR273;protein: NHA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR265;protein: NHA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR327;protein: NHA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR290;protein: HA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR288;protein: HA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR283;protein: HA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR262;protein: HA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR326;protein: HA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR317;protein: NHA-Shu;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR323;protein: NHA-ArmiDel3;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR313;protein: NHA-ArmiDel3;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR321;protein: NHA-ArmiDel1;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR263;protein: NHA-Piwi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR267;protein: HA-Yb;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR325;protein: NHA-ArmiDQ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: NHA-ArmiDQ


title: RR314;protein: NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: NHA-Armi-GNT


title: RR324;protein: NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR315;protein: NHA-ArmiDQ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR286;protein: NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR260;protein: NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR310;protein: NHA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR320;protein: NHA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR270;protein: NHA-Armi-GNT;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR269;protein: NHA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR259;protein: NHA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR316;protein: HA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR311;protein: NHA-ArmiDel1;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR252;protein: none;reporter 1358:Luc-piRNA2-LacZ;OSC;PIWI IP

description: piRNAs


title: RR250;protein: none;reporter 1357:Luc-piRNA1-LacZ;OSC;PIWI IP

description: piRNAs


title: RR246;protein: none;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: RR251;protein: none;reporter 1357:Luc-piRNA1-LacZ;OSC;PIWI IP

description: piRNAs


title: cep1 mutant

first: Hui

address: Qinghua East Road No.35

department: Biochemistry and Molecular Biology

institute: Beijing Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: NCBI

organism: Arabidopsis thaliana

source_name: mature stem

growth_protocol: All the plants grew in greenhouse at 20 oC (16h light, 8h dark).

extract_protocol:
Total RNA was isolated from the main stem of different developmental stage of Arabidopsis plant, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: non-treatment

value: stem

tag: Stage

value: 25 days after flowering

value: cep1 mutant


title: RR242;protein: none;reporter 1347:Luc-LacZ;OSC;PIWI IP

description: piRNAs


title: RR248;protein: none;reporter 1347:Luc-LacZ;OSC;PIWI IP

description: piRNAs


title: RR245;protein: none;reporter 1355:Luc-Flam718-LacZ;OSC;PIWI IP

description: piRNAs


title: RR249;protein: none;reporter 1347:Luc-LacZ;OSC;PIWI IP

description: piRNAs


title: RR243;protein: none;reporter 1347:Luc-LacZ;OSC;PIWI IP

description: piRNAs


title: wild type

tag: tissue

value: wild type


title: RR247;protein: none;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs

value: ovarian somatic cell culture


title: Chromera_infected_48h_rep1

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

institute: CSIRO

description:
48_Sydney_Chromera_1/48H_matrix.TMM.fpkm.matrix
48_Sydney_Chromera_1/48H_matrix.counts.matrix

data_processing:
Illumina reads were mapped onto Acropora digitifera transcriptome (http://marinegenomics.oist.jp/coral/viewer/download?project_id=3) using BOWTIE version 0.12.7
Transcripts abundance was estimated using RSEM version 1.1.17
Differential expression was performed using the R package edgeR comparining Chromera-infected samples to control at 4, 12, and 48h post infection
Genome_build: Acropora digitifera reference transcriptome assembly Shinzato et al 2011; http://marinegenomics.oist.jp/coral/viewer?project_id=3
Supplementary_files_format_and_content: matrix.TMM.fpkm.matrix: count matrix containing normalised expression values (FPKM;Fragments Per Kilobase of transcript per Million)
Supplementary_files_format_and_content: matrix.counts.matrix.txt : raw count matrix

organism: Acropora digitifera

source_name: coral larvae

growth_protocol: After Acropora digitifera spawning in Okinawa, coral larvae were reared in 0.2 uM FSW under ambient conditions

extract_protocol:
total RNA was extracted using TRIZOL reagent
RNA-Seq libraries were prepared using TruSeq sample preparation kit (Illumina)

treatment_protocol: Chromera was inoculated and larvae were snap frozen in liquid Nitrogen for RNA isolation at 4, 12, 48 h post infection

tag: time point


title: Chromera_infected_48h_rep3

description:
48_Sydney_Chromera_3/48H_matrix.TMM.fpkm.matrix
48_Sydney_Chromera_3/48H_matrix.counts.matrix


title: Negative_control_48h_rep2

description:
48_Negative_control_2/48H_matrix.TMM.fpkm.matrix
48_Negative_control_2/48H_matrix.counts.matrix


title: Negative_control_48h_rep3

description:
48_Negative_control_3/48H_matrix.TMM.fpkm.matrix
48_Negative_control_3/48H_matrix.counts.matrix


title: Negative_control_48h_rep1

description:
48_Negative_control_1/48H_matrix.TMM.fpkm.matrix
48_Negative_control_1/48H_matrix.counts.matrix


title: RR253;protein: none;reporter 1358:Luc-piRNA2-LacZ;OSC;PIWI IP

description: piRNAs


title: RR285;protein: NHA-Armi;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: Chromera_infected_12h_rep1

description:
12_Chromera_1/12H_matrix.TMM.fpkm.matrix
12_Sydney_Chromera_1/12H_matrix.counts.matrix


title: Chromera_infected_12h_rep2

description:
12_Symbiodinium_CladeB_2/12H_matrix.TMM.fpkm.matrix
12_Sydney_Chromera_2/12H_matrix.counts.matrix


title: RR244;protein: none;reporter 1355:Luc-Flam718-LacZ;OSC;PIWI IP

description: piRNAs


title: Negative_control_12h_rep3

description:
12_Negative_control_3/12H_matrix.TMM.fpkm.matrix
12_Negative_control_3/12H_matrix.counts.matrix


title: Chromera_infected_04h_rep3

description:
Sydney_Chromera_3/04H_matrix.TMM.fpkm.matrix
Sydney_Chromera_3/04H_matrix.counts.matrix


title: Chromera_infected_04h_rep2

description:
Sydney_Chromera_2/04H_matrix.TMM.fpkm.matrix
Sydney_Chromera_2/04H_matrix.counts.matrix


title: Negative_control_12h_rep2

description:
12_Negative_control_2/12H_matrix.TMM.fpkm.matrix
12_Negative_control_2/12H_matrix.counts.matrix


title: Chromera_infected_48h_rep2

description:
48_Sydney_Chromera_2/48H_matrix.TMM.fpkm.matrix
48_Sydney_Chromera_2/48H_matrix.counts.matrix


title: Chromera_infected_12h_rep3

description:
12_Symbiodinium_CladeB_3/12H_matrix.TMM.fpkm.matrix
12_Sydney_Chromera_3/12H_matrix.counts.matrix


title: RR294;protein: NHA-LacZ;reporter 1356:Luc-5BoxB-LacZ;OSC;PIWI IP

description: piRNAs


title: Negative_control_04h_rep2

description:
Negative_control_2/04H_matrix.TMM.fpkm.matrix
Negative_control_2/04H_matrix.counts.matrix


title: Negative_control_04h_rep1

description:
Negative_control_1/04H_matrix.TMM.fpkm.matrix
Negative_control_1/04H_matrix.counts.matrix


title: iWAT_FGF [GAR1143]

city: Garching

first: Martin

last: Jastroch

address: Parkring 13

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm10 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain raw read count; they have two columns where the first column specifies the gene name and the second the actual read count

organism: Mus musculus

source_name: iWAT

extract_protocol:
Total RNA was extracted from inguinal WAT, BAT, muscle and hypothalamus of WT, FGF21 KO, UCP1 KO and dKO mice (n=5-6) using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies). Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq2500 platform.

treatment_protocol: All mice were bred, born and weaned at 30°C. At the age of 10 to 12 weeks, mice were transferred to a temperature-controlled (+/- 0.5°C) climate chamber and kept for 12 days at 18°C followed by 3 weeks at 5°C. Afterwards, mice were euthanized after 2-3 hours food withdrawal, and serum and tissue samples were collected.

value: iWAT


title: iWAT_FGF [GAR1145]


title: Chromera_infected_04h_rep1

description:
Sydney_Chromera_1/04H_matrix.TMM.fpkm.matrix
Sydney_Chromera_1/04H_matrix.counts.matrix


title: iWAT_DKO [GAR1140]


title: iWAT_FGF [GAR1144]


title: iWAT_DKO [GAR1136]


title: iWAT_FGF [GAR1142]


title: iWAT_UCP [GAR1134]


title: iWAT_UCP [GAR1132]


title: iWAT_DKO [GAR1135]


title: iWAT_UCP [GAR1133]


title: iWAT_FGF [GAR1141]


title: iWAT_DKO [GAR1137]


title: iWAT_DKO [GAR1139]


title: iWAT_UCP [GAR1131]


title: iWAT_UCP [GAR1130]


title: Negative_control_04h_rep3

description:
Negative_control_3/04H_matrix.TMM.fpkm.matrix
Negative_control_3/04H_matrix.counts.matrix


title: iWAT_WT [GAR1124]


title: iWAT_WT [GAR1125]


title: iWAT_WT [GAR1127]


title: iWAT_WT [GAR1123]


title: iWAT_WT [GAR1128]


title: BAT_FGF [GAR1122]

source_name: BAT

value: BAT


title: iWAT_DKO [GAR1138]


title: BAT_FGF [GAR1121]


title: BAT_FGF [GAR1120]


title: BAT_FGF [GAR1119]


title: BAT_DKO [GAR1115]


title: P12_Ctrl_m6A_miCLIP_Rep2

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

data_processing:
Basecalls performed by Casava using default settings
Method of pre-processing for reads was performed essentially as previously reported[Moore et al. 2014; PMID: 24407355].Adaptor was trimmed by fastx_clipper from fastx_toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads shorter than 24 nt would be discarded. After trimmed, reads without barcode marker sequence or within large fragment (length > 60) will be discarded to eliminate unspecific RNA tags.
Remained reads were mapped to the zebrafish mouse genomes (version Zv9mm9) with BWA (v0.7.10)44 and allowed <=0.06 error rate (substitutions, insertions, or deletions) per read (bwa aln -n 0.06 -q 20) as online CTK Documentation (https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation).
To identify the m6A locus, the mode of mutation calling was performed as previously reported with minor modification [Linder et al. 2015; PMID: 26121403].
Genome_build: mm9
Supplementary_files_format_and_content: m6A site location in bed format

source_name: mouse testes

growth_protocol: The mice used in this study were B6D2F1 (C57BL/6×DBA2), DBA2 and C57BL6 strains.

extract_protocol:
For miCLIP-seq, mRNA was isolated from the control mouse testes at 12 days post-partum (P12). For all samples, the RNA integrity was checked using an Agilent Bioanalyzer 2100
For m6A-miCLIP-seq, the immunoprecipitated m6A-containing RNAs were subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403].All the libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.
CLIP-seq

value: mouse testes

value: control mouse testes

tag: passage

value: P12 (12 days post-partum)


title: BAT_DKO [GAR1113]


title: P12_Ctrl_m6A_miCLIP_Rep1

tag: cell type


title: BAT_DKO [GAR1114]