title: EC_WT_24h

city: Boston

first: Satoshi

last: Kimura

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital

description: total tRNA

data_processing:
3’ linker sequences and one nucleotide at the 5’ end was trimmed
Bowtie v. 1.2.2 with default settings was used for mapping reads to reference tRNA sequences retrieved from tRNAdb (http://trnadb.bioinf.uni-leipzig.de/DataOutput/Search)
Two sequences in V. cholerae (tdbD00003706, tdbD00008082) and three sequences in E. coli (tdbD00007320, tdbD00010329, and tdbD00011810) were eliminated from the reference sequences due to extremely low coverage.
Mpileup files were made using the samtools mpileup command without any filtration (option, -A –ff 4 -x -B -q 0 -d 10000000 -f).
The frequency of misincorporation was calculated in each mpileup file. 5’ end termini of the mapped reads were piled up using the bedtools genomecov command (-d -5 -ibam).
To calculate the termination frequency, the number of 5’ termini at any given position was divided by the total number of mapped termini at the given position along with all upstream positions (5’ side).
genome build: Sequencing data of Vibrio cholerae and Escherichia coli are mapped to VCtRNA.fa and ECtRNAs.fa, respectively. These reference files are available at https://drive.google.com/open?id=1EsilghrGGcKp2cwND6Q1oPLk_cI2cWww
processed data files format and content: Tab-delimited text files containing frequencies of RT-signatures (misincorporation and termination) observed in tRNAs. Each row and column represents species and positions of tRNAs, respectively.

organism: Escherichia coli

extract_protocol:
Bacterial cells in a culture medium or cecal fluid were harvested by centrifugation. Total RNA was immediately extracted from cell pellets with Trizol according to the manufacture’s instruction.
The tRNA fraction was cut out from 10% TBE-Urea gels and recovered by isopropanol precipitation. tRNA fraction (250 ng) was deacylated in 500 ul of 100 mM Tris-HCl pH 9.0 at 37 °C for 1 hr and recovered by isopropanol precipitation. After dephosphorylation with alkaline phosphatase from calf intestine (New England Biolabs), tRNAs were ligated to 100 pmol of 5’ adenylated and 3’ end-blocked DNA oligo (3’ linker) using truncated T4 RNA ligase at 25 °C for 2.5 hr in 25% PEG 8000. The ligated product was purified on a 10 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific) as above. Half of the recovered ligated tRNAs were reverse transcribed with 5 pmol TGIRT-III (InGex) in 100 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 450 mM NaCl, 5 mM MgCl2, 5 mM DTT, 1 mM dNTPs, and 1.25 pmol primer (ocj485) at 60 °C for 1 hr. After the elimination of template RNAs by alkali treatment, cDNA was purified on a 10 % TBE-Urea polyacrylamide gel. The single stranded cDNA was then circularized using 50 U of CircLigase II(Epicenter) at 60 °C for 1 hr, followed by addition of another 50 U of CircLigase II for an additional 1 hr at 60 °C. cDNA was amplified using Phusion DNA polymerase (New England Biolabs) with o231 primer and index primers. After 12-18 rounds of PCR amplification, the product was gel purified from an 8 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific).

tag: growth phase

value: stationary phase

value: WT


title: 14-0115

status: Public on May 15 2020

type: SRA

city: Hershey

first: Elizabeth

middle: Anne

last: Proctor

state: PA

address: 500 University Dr

department: Neurosurgery

country: USA

institute: Pennsylvania State University

library_source: transcriptomic

data_processing:
Gene expression was mapped using the STAR/RSEM pipeline, using Mus musculus GRCm38.93 as a reference (available for download in GTF format from Ensembl).
We estimated variance-mean dependence in count data and tested for differential expression based on a model using the negative binomial distribution with the DESeq package in R from the Bioconductor repository.
From the 48 original samples, 6 outliers were identified by principal component analysis (PCA), and later confirmed by quality control to be contaminated or feature low read counts. These samples were excluded from further analysis.
Genome_build: Mus musculus GRCm38.93
Supplementary_files_format_and_content: CSV: log2-scaled gene transcript abundance

molecule: total RNA

organism: Mus musculus

source_name: kidney

growth_protocol: Male C57BL/6J mice (Jackson Laboratories, Bar Harbor, ME) weighing 23.4 ± 0.1 g were individually housed in Nalgene polycarbonate cages (11.5 in x 7.5 in x 5 in) fitted with HEPA-filter cage tops and Shepherds Specialty Blend bedding (ScottPharma, Marlborough, MA) under standard laboratory conditions (25 ± 2 °C; 12:12 hour light-dark cycle, lights on at 0600 h). Rodent laboratory chow (Harlan Teklad 7012; Madison, WI) and water were provided ad libitum. Each cage was supplied with a Nalgene Mouse House (Nalgene Nunc, Rochester, NY), maple wood product (Product #W0002; Bio-Serv, Frenchtown, NJ), and stainless steel ring attached to the wire lid for environmental enrichment. Clean cages, fresh food and water were provided weekly.  All procedures were approved by the Institutional Animal Care and Use Committee at the United States Army Research Institute of Environmental Medicine. In conducting this research, the investigators adhered to the Guide for the Care and Use of Laboratory Animals in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility.

extract_protocol:
Qiagen RNeasy with DNase
Kapa mRNA Hyperprep

treatment_protocol: under isoflurane anesthesia, mice were intraperitoneally implanted with radiotelemetry transmitters (1.1 g, model G2 Emitter; Starr Life Sciences Corp., Inc., Oakmont, PA) to measure body core temperature (Tc; ± 0.1 °C) and general activity (counts). Surgical analgesia was provided with a subcutaneous buprenorphine injection (0.05 mg/kg) just prior to surgery, and again 24 and 48 hours post-procedure. The mice recovered from surgery in approximately 7-10 days as assessed by return to pre-surgical body weight, normal food and water consumption, and stable circadian Tc and activity rhythms9. Tc and activity were continuously monitored at 1-minute intervals throughout recovery and experimentation using the VitalView system (Starr Life Sciences Corp., Inc., Oakmont, PA).

tag: Sex

value: Male

tag: strain

tag: stress

value: control

tag: injection

value: saline

tag: time point

value: 1 day


type: RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in the liver tissue of the 4 g group, 2 days after the SARA challenge, Cattle No. 19

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: 4 g group_2 days after the SARA challenge

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 500 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the rumen epithelium using Trizo (Invitrogen) according to the manufacturer's instructions.

tag: breed

value: Holstein

tag: animal id

value: Cattle No. 19

tag: sample group

value: 4 g group

value: 2 days after the SARA challenge

tag: tissue

value: Liver tissue


title: Control LNA rep3

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Raw reads were assessed for Phred quality scores using FASTQC program and low bases and adaptor sequences were trimmed off using Fqtrim retaining only reads of 75 bass length. Then, clean reads were aligned against the human reference genome (GRCh38.p10 assembly) with Gencode v27 annotation (gencode.v27.annotation.gtf.gz) using STAR v2.5.1b. STAR was run in two-pass mode allowing alignment to the transcriptome coordinates by setting the option --quantMode to TranscriptomeSAM.
Next, the expression levels in read counts, TPM, and FPKM units were then estimated at both genes and isoforms levels by running RSEM on the alignment files in default parameters.
Differentially expressed genes and isoforms upon DSCAM-AS1 silencing as compared to the control condition were identified using the DESeq2 R package (v1.26.0) in default parameters. The expression at isoform level was summarized to gene-level using the tx-import bioconductor package and the resulting count matrices were provided to DESeq2. Prior to DE analysis, lowly expressed genes and isoforms were discarded from the analysis and only genes or isoforms with more than 10 normalized read counts in at least one condition (3 out of 6 samples) were considered for further downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene-level or isoform-level raw read counts for each sample.
Supplementary_files_format_and_content: tab-delimited text files include gene-level or isoform-level TPM read counts for each sample.

organism: Homo sapiens

source_name: Breast cancer cell lines

growth_protocol: MCF-7 cells were routinely grown in DMEM (Life Technologies, 31053–028) supplemented with 10% heat-inactivated FBS (Euroclone, ECS0180L) and 2 mM L-glutamine (ThermoFisher Scientific, 25030–024). Batches of human cell lines were purchased from ATCC. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Total RNA used for downstream RNA-seq analysis was isolated from MCF-7 cells using the RNeasy Mini Kit, according to the manufacture’s protocol (Qiagen, 74104).
RNA quality check (RNA integrity number (RIN) > 8) was achieved with Fragment Analyzer (Advanced Analytical Technologies, Inc, Ankeny, IA, USA) and quantified with Qubit (Qubit™ RNA HS Assay Kit, ThermoFisher Scientific,Waltham, MA, USA;Q32852). Two ug of RNA were polyA+ selected and RNA-Seq libraries were constructed using Illumina TruSeq RNA sample prep kit (TruSeq™ RNA Sample Prep Kit v2-Set B, Illumina, RS-122-2002). Paired-end (PE) cluster generation was performed using cBot on Flow Cell v3 (TruSeq PE Cluster Kit v3-cBot-HS, Illumina, PE-401-3001). Sequencing of libraries was performed on the HiSeq sequencing system (Illumina, San Diego, CA, USA).

treatment_protocol: MCF-7 cells were detached and transfected in suspension with LNAs (20 nM final concentration) using Lipofectamine3000 (ThermoFisher Scientific, L3000015), according to the manufacturer's protocol. Custom-designed LNA GapmeRTM from Exiqon were used to target all the DSCAM-AS1 lncRNA isoforms (LNA_1 5'-ATGGCAGTTGGAGGAG-3', LNA_2 5'-ACAGAGAAGGACATGG-3' and LNA_3 5'-AAGTAGCTTCATCTTT-3'); Negative control A - LNA longRNA GapmeR™ was used as a control LNA (5'-AACACGTCTATACGC-3'; Exiqon, 300611-00). Experiments were performed 48 hours after LNA transfection.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: treatment

value: Control LNA


title: p35S-6GP2-3

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description: polysomal RNA from PPV infected 6-week-old leaf tissue

data_processing:
Reads were mapped to the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Map to reads tool and parameters (            Masking mode = No masking            Match score = 1            Mismatch cost = 2            Cost of insertions and deletions = Linear gap cost            Insertion cost = 3            Deletion cost = 3            Length fraction = 0.5            Similarity fraction = 0.8            Global alignment = No            Auto-detect paired distances = Yes            Non-specific match handling = Ignore            Output mode = Create reads track            Create report = No            Collect un-mapped reads = No - CLC Bio, Aarhus, Denmark)
Low frequency variants were called against the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Low frequency variant caller tool and parameters (            Required significance (%) = 1.0            Ignore positions with coverage above = 100,000            Restrict calling to target regions = Not set            Ignore broken pairs = Yes            Ignore non-specific matches = Reads            Minimum coverage = 10            Minimum count = 2            Minimum frequency (%) = 0.5            Base quality filter = No            Read direction filter = No            Relative read direction filter = Yes            Significance (%) = 1.0            Read position filter = No            Remove pyro-error variants = No            Create track = Yes            Create annotated table = No            Create report = No - CLC Bio, Aarhus, Denmark)
Variants were filtered on  CLC Genomics with the following parameters (Criteria = 'Forward/reverse balance < .7501',           Criteria = 'Forward/reverse balance > .2499999',           Criteria = 'Reference allele contains no' - - CLC Bio, Aarhus, Denmark)
Amino acid changes were identified using the CLC genomics Workbench Amino Acid Changes tool with parameters (CDS track = PPV Penn7 (CDS)            Sequence track = PPV Penn7 (Genome) protein cistrons            mRNA track = Not set            Filter synonymous variants = No            Genetic code = 1 Standard            Filter CDS regions with no variants = No
Genome_build: PPV-D isolate Penn7 (GenBank accession EF640935)
Supplementary_files_format_and_content: tab-delimited text files include Chromosome, Region, Type, Reference, Allele, Reference allele, Length, Linkage, Zygosity, Count, Coverage, Frequency, Probability, Forward read count, Reverse read count, Forward/reverse balance, Average quality, Read count, Read coverage, # unique start positions, # unique end positions, BaseQRankSum, Read position test probability, Read direction test probability, Homopolymer length, Homopolymer, QUAL, Coding region change, Amino acid change, Amino acid change in longest transcript, Coding region change in longest transcript, Other variants within codon, and Non-synonymous.

molecule: polyA RNA

organism: Prunus domestica

source_name: 6 week old Prunus domesitica L leaves

growth_protocol: Transgenic plum trees expressing promoter:His6FLAG-RPL18 were maintained in the plant biosafety level 3 containment facility at the USDA facility at Fort Detrick, Frederick, MD, USA. Plants in the quarantine greenhouse were subjected to a cycle of 60 days of cold dormancy (4°C) followed by 84-90 days of growth at normal greenhouse temperatures (27°C). Leaf samples were collected at two, four, six, and twelve weeks post cold induced dormancy over two consecutive vegatative growth periods

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Samples were centrifuged at 16,000 g for 15 min at 4°C. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. The polysome fraction was pelleted by centrifuging the samples at 170,000 g for 18 h at 4 °C. The pellet was resuspended in 1 mL of PEB. 50 μl of Anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO, USA) was added to the resuspended pellet and incubated at 4°C overnight with gentle rocking. The beads were recovered using their magnetic property and were washed four times in wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Polysome-RNA complexes were eluted by treatment of the magnetic beads with 100 μl of Elution Buffer (100 μl wash buffer, 10 μl of 5 mg/mL FLAG3 peptide—Sigma Chemical Company, St. Louis, MO USA, 0.5 μl of 2 U/ml RNAse OUT—Thermo Fisher Scientific Cleveland, OH, USA). RLT buffer plus β-mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) was added to the eluted complexes. A 0.5 × volume of 100% ethanol was then added, and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 2000 and with the Qubit RNA Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA). Quality of the RNA was analyzed using an RNA ScreenTape assay (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: PPV_D isolate Penn7 (EF640935) was used in this study. A Myzus persicae aphid colony was maintained inside containment and transmissions were conducted using symptomatic P. persica cv. GF 305 peach leaves as the inoculum source for aphid transmission to P. domestica L. transgenic plant lines.

tag: cultivar

value: Prunus domestica L 'President'

tag: developmental stage

value: 6 weeks GP2

tag: genotype

tag: infection status

value: PPV infected


title: p35S-6GP2-2


title: Arid2_R

city: Campinas

first: Mariana

middle: Vargas

last: Cruz

state: Sao Paulo

address: 400 Avenida Candido Rondon

department: Department of Plant Biology

country: Brazil

institute: UNICAMP

description: sampled under field conditions

data_processing:
Illumina Off-line Base Caller 1.9.4 software used for basecalling.
*.qseq.txt files were converted to *.fastq files using the Illumina 'qseq_to_fastq.pl' program
Sequenced reads were demultiplexed using the following script: paste -d '' <(echo; sed -n '1,${n;p;}' s_1_2.fastq | sed G) s_1_1.fastq | sed '/^$/d' | fastx_barcode_splitter.pl --bol --bcfile barcodes_lane_1.txt --prefix s_1_1
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequences (using the NGS QC Toolkit, with phred score > 20 for at least 70% of the read length), then used for the de novo assembly of the first transcriptome of the species (using the Qiagen CLC Genomics Workbench, with kmer size = 45, insert size = 300-500 and the remaining default parameters)
The de novo assembled transcriptome was filtered for misassembled, contaminant and redundant transcripts, and the non-redundant species specific transcriptome was used as reference in the analyses
Reads were mapped to the reference transcriptome using bowtie v0.12.2 with parameters bowtie --seed 1 -m 1 --best
Data normalization was done using the bioconductor edgeR method to estimate dispersions.
To detect DET, we used the edgeR exact test for negative binomial distribution, with an adjusted P-value threshold of 0.05
Genome_build: Avicennia_germinans_ref_transcriptome.fasta (de novo assembled non-redundant reference transcriptome of Avicennia germinans)
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads that mapped to a single transcript in the reference transcriptome

organism: Avicennia germinans

source_name: root

growth_protocol: germinated and grown under field conditions, transferred to 3L pots filled with mangrove soil and acclimated for 72 hours

extract_protocol:
Samples were harvested and immediatelly stored in a RNA stabilizaing solution (RNAlater, Ambion) and RNA was extracted using the protocol developed by Oliveira et al., 2015 (DOI: http://dx.doi.org/10.4238/2015.December.28.32). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina barcode sequences: Eq4_L: CGATGT; Eq5_L: TGACCA; Eq6_L: ACAGTG; St1_L: GCCAAT; St2_L: CAGATC; St4_L: CTTGTA; Eq4_S: CGATGT; Eq5_S: TGACCA; Eq6_S: ACAGTG; St1_S: GCCAAT; St2_S: CAGATC; St4_S: CTTGTA; Eq4_F: CGATGT; Eq5_F: TGACCA; Eq6_F; ACAGTG; St1_F: GCCAAT; St2_F: CAGATC; St4_F: CTTGTA

treatment_protocol: acclimated for 72 hours in pots filled with mangrove soil, under shadowed and well watered conditions

tag: geographical position

tag: sampling date

value: August 19th, 2013

tag: sampling time

value: seedling


title: 14-0113

tag: Sex

tag: strain

tag: stress

value: heat

value: poly I:C

value: Tcmax


title: 14-0106

value: Male

value: control

tag: injection

tag: time point


title: RNA-seq ST-d21NiTSC rep2

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

data_processing:
Demultiplexed FASTQ files are single-end reads per sample with UMI barcode are added to the read name.
We used STAR (v2.5.2b) to align the reads to  GRCh37 Ensembl reference genome (v87). Read deduplication based on UMIs was performed with je markdupes (v1.2).
and transcript read counts calculated with featureCounts (v1.5.2) against GRCh37 Ensembl annotation.
Genome_build: GRCh37
Supplementary_files_format_and_content: Each sample gene (rows) read counts matrices are gzipped TSV files.

source_name: human fibroblasts

growth_protocol: To generate iTSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched either to TSC media for d8 iTSCs,  or to naive media for d21N iTSCs, 21-28 days after transduction, cells were passaged and expanded. STs and EVTs were performed as previously described, For the differentiation of iTSCs into ST,  iTSCs were seeded at a density of 1 x 105 cells per well onto a 6-well plate pre-coated with 2.5 μg/ml Collagen IV (Sigma) and cultured in 2 ml of ST differentiation medium [DMEM/F-12, GlutaMAX (ThermoFisher) supplemented with 0.3% BSA (Sigma), 4% KSR (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1mM 2-mercaptoethanol (ThermoFisher), 0.5% Pen-Strep (ThermoFisher), 2.5 μM Y27632 (Abcam) and 2 μM forskolin (Selleckchem)].  Media were replaced daily for the initial 4 days, and cells were analysed on day 6. For the differentiation of iTSCs into EVT,  iTSCs were seeded at a density of 0.75 x 105 cells per well onto a 6-well plate pre-coated with 1 μg/ml Col IV (Sigma) and cultured in 2 ml of EVT differentiation medium [DMEM/F-12, GlutaMAX (ThermoFisher) supplemented with 0.3% BSA (Sigma), 4% KSR (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1mM 2-mercaptoethanol (ThermoFisher), 0.5% Pen-Strep (ThermoFisher), 2.5 μM Y27632 (Abcam), 100 ng/ml NRG1 (Cell Signaling) and 7.5 μM A83-01 (Sigma). Shortly after suspending the cells in the EVT differentiation medium, Matrigel (Corning) was overlaid to a 2% final concentration. On day 3 of differentiation, EVT differentiation medium without hNRG1 (Cell Signaling) and Matrigel (Corning) was added to a final concentration of 0.5%. On day 6 of differentiation, EVT differentiation media were replaced without hNRG1 (Cell Signaling) or KSR (ThermoFisher), and Matrigel (Corning) was added to 0.5% final concentration. The cells were cultured for an additional 2 days before analyses were performed.

extract_protocol:
RNA extraction was performed using the RNeasy micro kit (Qiagen, Cat#74004) from ∼2–20 × 104 cells with QIAcube (Qiagen). The concentrations of RNA were measured by a Qubit RNA HS Assay Kit (ThermoFisher, Cat#Q32855) on a Qubit 2.0 Fluorometer (ThermoFisher).
RNA-seq was performed with a multiplexing approach, using an 8 bp sample index69 and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template-switching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Sequencing was performed on the NextSeq550 (Illumina), using the V2 High output kit (Illumina, #TG-160-2005) in accordance with the Illumina Protocol 15046563 v02, generating 2 reads per cluster composed of a 19 bp R1 and a 72 bp R2.

value: STs


description: Gene expression in the liver tissue of the 0 g group, 2 days after the SARA challenge, Cattle No. 19

source_name: 0 g group_2 days after the SARA challenge

tag: breed

value: Holstein

tag: animal id

value: Cattle No. 19

tag: sample group

value: 0 g group


title: p35S-6GP2-1


title: Arid1_R

description: sampled under field conditions


title: p35S-6GP1-Total-3

description: Total RNA from PPV infected 6-week-old leaf tissue

value: 6 weeks GP1


title: 14-0092

value: saline


title: RNA-seq ST-d21NiTSC rep1

tag: cell type


title: Arid3_L

description: sampled under field conditions

source_name: leaf


title: p35S-PostBuds-1

description: polysomal RNA from PPV infected Post-CID Bud tissue

source_name: Post-CID Buds of Prunus domesitica L leaves

value: Post-CID Buds


title: RNA-seq ST-d8iTSC rep2


title: 14-0101

value: 1 day


title: p35S-6GP1-Total-2

value: Prunus domestica L 'President'


title: 14-0091

value: 100 ug poly I:C


title: RNA-seq ST-d8iTSC rep1


title: EC_WT_log

state: Massachusetts

description: total tRNA

tag: growth phase

value: log phase

value: WT


title: Arid2_L

description: sampled under field conditions

value: August 19th, 2013

value: seedling


title: Arid1_L

description: sampled under field conditions


title: Arid3_R

description: sampled under field conditions


title: p35S-6GP1-3

tag: cultivar

value: PPV infected


title: 14-0090

value: Male

value: heat

value: Tcmax


title: p35S-6GP1-2

tag: developmental stage


title: Arid2_S

description: sampled under field conditions

source_name: stem


title: 14-0065

value: control


title: Arid3_S

description: sampled under field conditions


title: p35S-6GP1-1

tag: genotype


title: Marmoset_Kidney_H3K4me3_1

city: Utrecht

first: Menno

middle: P

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
Genome_build: Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw

molecule: genomic DNA

organism: Callithrix jacchus

extract_protocol: TruSeq DNA sample preparation kit (Illumina)

tag: tissue

value: Kidney

tag: chip antibody


title: RNA-seq EVT-d8iTSC rep4

value: EVTs


title: 14-0059


title: p35S-4GP2-3

description: polysomal RNA from PPV infected 4-week-old leaf tissue

source_name: 4 week old Prunus domesitica L leaves

value: 4 weeks GP2

tag: infection status


title: Arid1_S

description: sampled under field conditions

tag: geographical position

tag: sampling date

tag: sampling time


title: RNA-seq EVT-d21NiTSC rep3


title: RNA-seq EVT-d8iTSC rep3


title: RNA-seq d21NiTSC-P10 rep3

value: iTSCs


title: RNA-seq d21NiTSC-P10 rep1


title: OP3

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

country: China

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

data_processing:
Quality control of sequencing readswas performed using FastQC (v0.11.5).
Reads were aligned to the NCBI m37 reference genome by TopHat (v2.1.1)
Gene counts of each sample were obtained through using HTSeq
R-package DESeq2 was performed to normalize gene counts
Genome_build: NCBI m37
Supplementary_files_format_and_content: text file with log2 DESeq2-normalized counts

source_name: IL27RA positive hematopoietic stem cells of old mouse

extract_protocol:
Fifty HSCs were sorted by FACS into wells of a 96-well polymerase chain reaction plate containing lysis buffer, and amplify the cell sample directly with the Smart-Seq2 method.
(1) amplified products cDNA was used as input for the library construction of single cell transcriptome. (2) Fragment the sample cDNA into 300bp by Bioruptor®Sonication System. (3) Perform terminal repair, addition of A, and ligation of sequencing adapters to the fragmented cDNA. Amplify the sequencing adapter products by PCR and distinguish each sample by adding different index tags. (4) Perform electrophoresis with the PCR amplification products in 2% agarose gels and extract the 350~450bp DNA from the gel through CWBIO Gel Extraction Kit. Dissolve the DNA for the final library.

tag: strain

value: bone marrow

value: IL27RA+ HSC

tag: age

value: 28 months


title: OP2


title: Humid2_R

description: sampled under field conditions


title: p35S-6GP1-Total-1

value: Prunus domestica L 'President'

value: 6 weeks GP1


title: p35S-4GP2-2


title: RNA-seq EVT-d21NiTSC rep4


title: p35S-4GP2-1


title: RNA-seq EVT-d21NiTSC rep2


title: Humid1_R

description: sampled under field conditions


title: p35S-4GP1-3

value: 4 weeks GP1


title: OP1


title: 14-0075

tag: Sex

tag: stress

tag: injection

value: saline

tag: time point

value: 1 day


title: RNA-seq EVT-d21NiTSC rep1

tag: cell type


title: Humid2_L

description: sampled under field conditions

value: August 19th, 2013

value: seedling


title: p35S-4GP1-2

value: PPV infected


title: Humid3_R

description: sampled under field conditions


title: RNA-seq EVT-d8iTSC rep2


title: RNA-seq EVT-d8iTSC rep1


title: ON2

source_name: IL27RA negative hematopoietic stem cells of old mouse

value: IL27RA- HSC


title: p35S-2GP2-3

description: polysomal RNA from PPV infected 2-week-old leaf tissue

source_name: 2 week old Prunus domesitica L leaves

value: 2 weeks GP2


title: ON1

source_name: IL27RA negative hematopoietic stem cells of young mouse


title: p35S-4GP1-1


title: p35S-2GP2-1


title: YP1

source_name: IL27RA positive hematopoietic stem cells of young mouse

value: 2 months


title: YP2


title: Humid2_S

description: sampled under field conditions


title: Humid3_L

description: sampled under field conditions


title: RNA-seq d21NiTSC-P10 rep2


title: p35S-2GP2-2


title: YP3


title: Humid3_S

description: sampled under field conditions


title: ON3


title: Eq6_F

description: sampled under field conditions

data_processing:
Illumina Off-line Base Caller 1.9.4 software used for basecalling.
*.qseq.txt files were converted to *.fastq files using the Illumina 'qseq_to_fastq.pl' program
Sequenced reads were demultiplexed using the following script: paste -d '' <(echo; sed -n '1,${n;p;}' s_1_2.fastq | sed G) s_1_1.fastq | sed '/^$/d' | fastx_barcode_splitter.pl --bol --bcfile barcodes_lane_1.txt --prefix s_1_1
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequences (using the NGS QC Toolkit, with phred score > 20 for at least 70% of the read length), then used for the de novo assembly of the first transcriptome of the species (using the Qiagen CLC Genomics Workbench, with kmer size = 45, insert size = 300-500 and the remaining default parameters)
The de novo assembled transcriptome was filtered for misassembled, contaminant and redundant transcripts, and the non-redundant species specific transcriptome was used as reference in the analyses
Reads were mapped to the reference transcriptome using bowtie v0.12.2 with parameters bowtie --seed 1 -m 1 --best
Data normalization was done using the bioconductor edgeR method to estimate dispersions.
To detect DET, we used the edgeR exact test for negative binomial distribution, with an adjusted P-value threshold of 0.05
Genome_build: Avicennia_schaueriana_transcriptome.fasta; De novo assembled non-redundant reference transcriptome of Avicennia schaueriana
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads that mapped to a single transcript in the reference transcriptome

organism: Avicennia schaueriana

source_name: flower

extract_protocol:
Samples were harvested under field conditions, stored in a RNA stabilizaing solution (RNAlater, Ambion) and RNA was extracted using the protocol developed by Oliveira et al., 2015 (DOI: http://dx.doi.org/10.4238/2015.December.28.32). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina barcode sequences: Eq4_L: CGATGT; Eq5_L: TGACCA; Eq6_L: ACAGTG; St1_L: GCCAAT; St2_L: CAGATC; St4_L: CTTGTA; Eq4_S: CGATGT; Eq5_S: TGACCA; Eq6_S: ACAGTG; St1_S: GCCAAT; St2_S: CAGATC; St4_S: CTTGTA; Eq4_F: CGATGT; Eq5_F: TGACCA; Eq6_F; ACAGTG; St1_F: GCCAAT; St2_F: CAGATC; St4_F: CTTGTA

value: adult flowering tree

tag: temperature at sampling moment

value: 30.1 celsius

tag: relative humidity at sampling moment

tag: solar irradiance at sampling moment (kj/square meters)


title: p35S-2GP1-Total-2

description: Total RNA from PPV infected 2-week-old leaf tissue

tag: cultivar

tag: developmental stage

value: 2 weeks GP1

tag: genotype


title: RNA-seq Primed-P10 rep2

value: Primed iPSCs


title: RNA-seq d8iTSC-P10 rep2

value: iTSCs


title: Humid1_S

description: sampled under field conditions


title: RNA-seq d8iTSC-P10 rep1


title: Humid1_L

description: sampled under field conditions


title: Eq5_F

description: sampled under field conditions

value: 28.3 celsius


title: YN2

tag: tissue

value: bone marrow


title: p35S-2GP1-Total-1

value: Prunus domestica L 'President'

tag: infection status


title: Eq4_F

description: sampled under field conditions

tag: geographical position

tag: sampling date

value: 28.5 celsius


title: RNA-seq Primed-P10 rep1


title: p35S-2GP1-3

description:
polysomal RNA from PPV infected 2-week-old leaf tissue
Analysis produced no results due to low 10-fold coverage


title: p35S-2GP1-Total-3


title: RNA-seq Fibroblast-D0 rep2

value: human fibroblasts


title: St4_F

description: sampled under field conditions

tag: sampling time

value: 20.9 celsius


title: YN1

tag: strain

tag: age


title: RNA-seq Fibroblast-D0 rep1


title: St2_F

description: sampled under field conditions

value: 18.3 celsius


title: St1_F

description: sampled under field conditions

value: 19 celsius


title: RNA-seq t2iLGoY-P10 rep1

value: Naive iPSCs


title: p35S-2GP1-2

value: PPV infected


title: SN_RNA-seq_P3N

data_processing:
Basecalls performed using CASAVA version 1.8.2
To align single nucleus sequencing experiments, a custom “premRNA” reference was created (see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references for details) to account for both mature and unspliced RNA. In summary, a premRNA GTF was generated first by extracting the transcript rows from the annotation file to then replace the feature type to exon (which is the feature type used for UMI counting). Cellranger mkref was run to create a reference using the modified GTF annotation file and the  hg19 genome (GRCh37, CellRanger reference version 1.2.0, genome build GRCh37.p13, which contained the Sendai virus KLF4, MYC and SeV sequences as extra chromosomes, also accounted for as extra annotations on the annotation file).
Sequencing single nucleus samples were aligned to the created custom reference and UMI counting were performed using cellranger count (v3.0.2, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/what-is-cell-ranger).
Genome_build: hg19
Supplementary_files_format_and_content: Gene/cell read counts matrices are contained in compressed Market Exchange Format (MEX) for sparse matrices. Feature, in this case genes, and cell barcodes  are gzipped TSV files, corresponding to row and column indices of count matrices respectively. For more information, please refer to: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=10, c-MYC MOI=10, KLF4 MOI=12. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed and naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time.

extract_protocol:
Nuclei were prepared using the ‘Frankenstein’ protocol for nuclei isolation from fresh and frozen tissue followed by 10x Genomics that can be found in https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-3fkgjkw/abstract.
Samples were processed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: human naive induced pluripotent stem cells

tag: passages

value: Passage 3


title: RNA-seq t2iLGoY-P10 rep2


title: SN_RNA-seq_D24N

value: human naive intermediates

value: Passage 0


title: SN_RNA-seq_P20N

value: Passage 20


title: Eq6_S

description: sampled under field conditions

value: adult flowering tree

value: 30.1 celsius


title: ATAC_D21N_iTSC_rep_2

data_processing:
ATAC sequencing reads (pair-end 51nt reads) were adaptor-trimmed and filtered by base quality and length using Cutadapt v 1.852 using -a CTGTCTCTTATACACATCT, -A CTGTCTCTTATACACATCT, -q 20, and --minimum-length 18 options. Read pairs passing filters were mapped to the complete human genome [hg19 human genome (UCSC version, December 2011)] using Bowtie2 with -X 2000, --no-mixed and --no-discordant options.
Mapped sample reads were filtered for multi-mappers (mapping quality < 10) and reads mapped to mitochondrial DNA using Jvarkit’s samjs. PCR duplicates were discarded using Picard’s (http://broadinstitute.github.io/picard) MarkDuplicates tool. Sequencing reads aligned to known genomic blacklisted regions were also not considered for further analysis
Peak calling was performed on each biological replicate with MACS2 callpeak subcommand using --nomodel -f BAM --keep-dup all --gsize hs --shift -100 --extsize 200 --SPMR -B options. For downstream analysis we use an “intersect and rescue” approach. This approach consisted of intersecting each time point and reprogramming media biological replicates peak sets (bedtools intersect), subcommand (-wa -wb -F/-f 0.3) and then filtering those peaks with a fold change over background of more than 5 fold change (FC) and at least 3 FC in the other replicate. This created two intersection peaksets (major to 5 FC in replicate 1 and major to 3 FC in replicate 2 and vice versa), which were then combined and merged with bedtools merge (a minimum of 1 bp overlap). The union peakset of both replicates for each timepoint and reprogramming media was then reduced by merging all peaks within 100 bp. Finally, a consensus peak set of all time points and reprogramming media was created using bedtools merge as described above.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files are the output of macs2 callpeaks. Format is is BED6+4 (details about the format can be found at https://genome.ucsc.edu/FAQ/FAQformat.html#format12 and https://github.com/taoliu/MACS/). Macs2 specific columns are: 5th display integer score (int(-10*log10qvalue)), 7th fold change at peak summit relative to background, 8th  -log10pvalue at peak summit, 9th -log10qvalue at peak summit and 10th relative peak summit position to peak start. Detailed information can be found at MACS webiste (https://github.com/taoliu/MACS/).  BigWig files were created using UCSCs bedGraphToBigWig from the normalised bedgraph file output from MACS2.

growth_protocol: To generate iTSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched either to TSC media for d8 iTSCs,  or to naive media for d21N iTSCs, 21-28 days after transduction, cells were passaged and expanded.

extract_protocol:
iTSCs were isolated by FACS (see Methods) and ~65k cells were washed and lysed in ATAC-seq lysis buffer (10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 10 mM Tris pH 7.4). The transposition reaction was then carried out by using 22.5 μl of UltraPure Distilled Water (ThermoFisher, Cat#10977-015), 25 μl of Tagment DNA Buffer (Illumina, Cat#15027866) and 2.5 μl of Tagment DNA Enzyme 1 (Illumina, Cat#15027865) for each sample, and then incubated for 30 min at 37°C, followed by immediate purification using a MinElute Reaction Cleanup Kit (Qiagen, Cat#28204) according to the manufacturer’s instructions.
11 μl of transposed DNA, 25μl of the NEBNext High-Fidelity 2x PCR Master Mix (Cat#M0541S) and 1.25μM of the adaptor sequences as published previously were used in a 50 μl PCR reaction. PCR parameters were: 72°C for 5 min, 98°C for 30 s and 9 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The prepared libraries were purified using a MinElute PCR purification kit (Qiagen, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s specifications, where library fragments ranging from 200 to 700 bp were selected and sequenced on an Illumina HiSeq 1500 in 2x51 cycle paired-end mode

value: iTSCs


title: SN_RNA-seq_D20N


title: Eq5_S

description: sampled under field conditions

value: 28.3 celsius


title: Marmoset_Liver_Input

value: Liver


title: p35S-12GP2-3

description: polysomal RNA from PPV infected 12-week-old leaf tissue

source_name: 12 week old Prunus domesitica L leaves

value: Prunus domestica L 'President'

value: 12 weeks GP2


title: p35S-12GP2-2


title: SN_RNA-seq_D16N


title: Eq4_S

description: sampled under field conditions

value: 28.5 celsius


title: ATAC_D8_iTSC_rep_2


title: YN3

value: bone marrow

value: IL27RA- HSC

value: 2 months


title: SN_RNA-seq_D12N


title: p35S-12GP1-3

value: 12 weeks GP1

value: PPV infected


title: p35S-2GP1-1

value: 2 weeks GP1


title: ATAC_D21N_iTSC_rep_1


title: St2_S

description: sampled under field conditions

value: 18.3 celsius


title: ATAC_D8_iTSC_rep_1


title: SN_RNA-seq_P20P

value: human primed induced pluripotent stem cells


title: St4_S

description: sampled under field conditions

value: 20.9 celsius


title: p35S-12GP1-2


title: St1_S

description: sampled under field conditions

value: adult flowering tree

value: 19 celsius


title: Eq6_L

description: sampled under field conditions

value: 30.1 celsius


title: Eq5_L

description: sampled under field conditions

value: 28.3 celsius


title: SN_RNA-seq_D16P

value: human primed intermediates

value: Passage 0


title: p35S-12GP1-1

value: Prunus domestica L 'President'


title: SN_RNA-seq_D20P


title: Eq4_L

description: sampled under field conditions

value: 28.5 celsius


title: SN_RNA-seq_D12P


title: St4_L

description: sampled under field conditions


title: nrpd1 rep1 (Bisulfite-seq)

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Bisulfite treated sequenced reads were mapped to TAIR10 genome assembly using Bismark v 0.19.0  bismark with parameters -N 1 -q --bowtie2 --sam -p 20
Context-dependent (CpG/CHG/CHH/CX) methylation were extracted using bismark_methylation_extractor with parameters --paired-end --no_overlap --report --bedGraph --buffer_size 20G --cytosine_report --CX --comprehensive
Genome_build: TAIR10
Supplementary_files_format_and_content: Bw format files for each chromosome for each cytosine context (CG, CHG, CHH or CX) with following tab-separated information: Chromosome, start coordinate, stop coordinate,and methylation level (methylated cytosines sequenced/total cytosines sequenced).

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 23ºC

extract_protocol:
Genomic DNA of the two-week-old seedlings was extracted and converted by bisulfite
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bisulfite treatment

tag: seedlings

value: Arabidopsis seedlings


title: not1 rep2 (Bisulfite-seq)


title: SN_RNA-seq_D8

value: human fibroblasts intermediates


title: WT rep2 (Bisulfite-seq)

value: wild type (C24)


title: SN_RNA-seq_D4


title: St2_L

description: sampled under field conditions


title: nrpd1 rep2 (Bisulfite-seq)


title: St1_L

description: sampled under field conditions


title: SN_RNA-seq_D24P


title: not1 rep1 (Bisulfite-seq)


title: Nucleus Pulposus, MCT4KO.animal3

city: Philadelphia

first: Makarand

last: Risbud

address: 1015 Walnut Street

institute: Thomas Jefferson University

description: Gene expression of nucleus pulposus tissue from the intervertebral discs of a 14 month-old MCT4 KO mouse

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Quality Control of the experiment was performed by Expression Console Software v 1.4.1. Chp files were generated by sst-rma normalization from Affymetrix .cel file using Expression Console Software.

label: biotin

source_name: MCT4 KO C57BL/6 mice Nucleus Pulposus

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: MCT4+/− mice were purchased from Taconic Bioscience. The animals were backcrossed for 10 generations to C57Bl/6N (Taconic) mice and MCT4+/− mice were used for breeding to obtain knock out and wild-type littermates. Genotype was confirmed by PCR. Mice were kept in a 12:12 light/dark cycle and provided with ad libitum food and drinking water at Thomas Jefferson University.

extract_protocol: Nucleus pulposus tissue was dissected from lumbar and caudal discs of 13-14 month-old WT and MCT4 KO mice and immediately placed in RNAlater® Reagent (INVITROGEN). 3-4 mice per genotype were sacrificed for RNA isolation and NP tissue pooled from single animal served as an individual sample. NP tissue was collected in RNAlater® Reagent and homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971). Total RNA was extracted from the tissue lysates using RNeasy® Mini kit (Qiagen).

value: Nucleus Pulposus


title: SN_RNA-seq_D0

value: human fibroblasts

value: Passage 5


title: Nucleus Pulposus, WT.animal4

description: Gene expression of nucleus pulposus tissue from the intervertebral discs of a 13 month-old wild-type mouse

source_name: Wild-type C57BL/6 mice Nucleus Pulposus

value: WT


title: Nucleus Pulposus, MCT4KO.animal1


title: Nucleus Pulposus, WT.animal3


title: Nucleus Pulposus, MCT4KO.animal2


title: Nucleus Pulposus, WT.animal2


title: Kidney_DKD+enarodustat_rep9

status: Public on May 14 2020

city: Tokyo

first: Sho

last: Hasegawa

address: 7-3-1, Hongo, Bunkyo-ku

department: Division of Nephrology and Endocrinology

institute: University of Tokyo

description: Gene expression of renal tissue in DKD+enarodustat group

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction Software 11.5.1.1(Agilent). Raw data were processed with the R package limma in Bioconductor to perform background correction and data normalization using the quantile normalization method.

source_name: Renal tissue, DKD+enarodustat, replicate 9

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Total RNA from renal tissue was isolated using GenElute Mammalian Total RNA Miniprep Kit (RTN70, Sigma-Aldrich). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Renal tissue

tag: gender

value: male


title: Kidney_DKD+enarodustat_rep7

source_name: Renal tissue, DKD+enarodustat, replicate 7


title: Nucleus Pulposus, WT.animal1


title: Kidney_DKD+enarodustat_rep8

source_name: Renal tissue, DKD+enarodustat, replicate 8


title: WT rep1 (Bisulfite-seq)


title: Kidney_DKD+enarodustat_rep6

source_name: Renal tissue, DKD+enarodustat, replicate 6


title: Kidney_DKD+enarodustat_rep2

source_name: Renal tissue, DKD+enarodustat, replicate 2


title: Kidney_DKD_rep6

description: Gene expression of renal tissue in DKD group

source_name: Renal tissue, DKD, replicate 6


title: Kidney_DKD+enarodustat_rep1

source_name: Renal tissue, DKD+enarodustat, replicate 1


title: Kidney_DKD+enarodustat_rep3

source_name: Renal tissue, DKD+enarodustat, replicate 3


title: Kidney_Sham_rep6

description: Gene expression of renal tissue in sham group

source_name: Renal tissue, Sham, replicate 6


title: Kidney_DKD_rep5

source_name: Renal tissue, DKD, replicate 5


title: GP2_V282M_2

city: Nagoya

first: Masahiro

last: Nakatochi

state: Aichi

address: 1-1-20 Daiko-Minami, Higashi-ku

institute: Nagoya University

data_processing:
Individual libraries within the samples were demultiplexed using bcl2fastq.
FastQC was used for read and alignment quality assessment.
Trimmomatic was used for removing adaptor sequence and low-quality sequence.
TopHat2 was used for read alignment.
GFOLD was used for expression count.
Genes with coding lengths <200 bp or <10 mean reads in either the GP2_V282M or GP2_WT groups were excluded.
The reads were aligned to NCBI37 Human reference genome and mapping to the human transcriptome.
Genome_build: NCBI37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: PATU 8988S was treated

growth_protocol: PATU 8988S was maintained with RPMI 1640 plus 10% fetal bovine serum at 37C in a 5% CO2 cell culture incubator.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit.
1µg of total RNA were used for library generation using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

tag: cell line

value: PATU 8988S


title: GP2_V282M_1


title: Kidney_DKD_rep9

source_name: Renal tissue, DKD, replicate 9


title: Kidney_DKD_rep2

source_name: Renal tissue, DKD, replicate 2


title: Kidney_Sham_rep4

source_name: Renal tissue, Sham, replicate 4


title: Kidney_Sham_rep3

source_name: Renal tissue, Sham, replicate 3


title: Kidney_DKD_rep3

source_name: Renal tissue, DKD, replicate 3


title: Kidney_Sham_rep2

source_name: Renal tissue, Sham, replicate 2


title: GP2_WT_2


title: Kidney_DKD+enarodustat_rep5

source_name: Renal tissue, DKD+enarodustat, replicate 5


title: Kidney_DKD+enarodustat_rep4

source_name: Renal tissue, DKD+enarodustat, replicate 4


title: Kidney_DKD_rep7

source_name: Renal tissue, DKD, replicate 7


title: Kidney_Sham_rep1

source_name: Renal tissue, Sham, replicate 1


title: BXD2-WT_#1_single_cell_VDJseq(BCR)

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: B cells and T cells from spleen of BXD2-WT_#1

data_processing:
Raw data were processed with the Cell Ranger pipeline(v.3.0.2).
Sequencing reads were aligned using STAR aligner
The cellranger-vdj pipeline was applied for single cell V(D)J BCR data
Genome_build: mm10

extract_protocol:
Single cells and beads containing barcoded DNA oligos were captured into oil droplets by 10xChromium controller using 10xGenomics 5' VDJ reagent kits. Individual cells were lyzed immediately, mRNA were released, and reverse transcription was performed by plyT primers according to 10xGenomics 5' VDJ standard protocol. Single-stranded cDNA was then captured in the each oil droplet by the barcoded DNA oligos carried by the beads.
Barcoded single cell cDNA were pooled and preamplified, 5' biased transcriptome libraries and BCR libraries were constructed according to the standard protocol of 10xGenomics 5' VDJ reagent kits.

value: Female

value: spleen


title: BXD2-WT_#2_single_cell_VDJseq(BCR)

description: B cells and T cells from spleen of BXD2-WT_#2


title: BXD2-p19-/-_#3_single_cell_VDJseq(BCR)

description: B cells and T cells from spleen of BXD2-p19-/-_#3

value: Male


title: Kidney_DKD_rep4

source_name: Renal tissue, DKD, replicate 4


title: BXD2-p19-/-_#2_single_cell_VDJseq(BCR)

description: B cells and T cells from spleen of BXD2-p19-/-_#2


title: Kidney_DKD_rep8

source_name: Renal tissue, DKD, replicate 8


title: Kidney_Sham_rep5

source_name: Renal tissue, Sham, replicate 5


title: GP2_WT_1


title: BXD2-p19-/-_#1_single_cell_VDJseq(BCR)

description: B cells and T cells from spleen of BXD2-p19-/-_#1


title: BXD2-WT_#2_single_cell_RNAseq

source_name: B cells and T cells from spleen of BXD2-WT_#2


title: BXD2-WT_#1_single_cell_RNAseq

source_name: B cells and T cells from spleen of BXD2-WT_#1


title: BXD2-p19-/-_#1_single_cell_RNAseq

source_name: B cells and T cells from spleen of BXD2-p19-/-_#1


title: Nodscid1217

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

data_processing:
The 10x Genomics Cell Ranger Suite (version 2.0.2) was used to perform sample demultiplexing, barcode processing, alignment and generation of digital gene expression matrix. For samples Nodscid1074, Nodscid1214 and Nodscid1216 two sequencing runs were merged following Cell Ranger pipeline, i.e. specifying multiple fastq files to be considered together. Reads were aligned first to the mouse reference genome (mm10), second to the human one (GRCh38). In this way, two separate gene expression matrices were constructed for each sample. Default parameters were used.
We then chose to consider the raw gene-barcode matrices and filter out empty barcodes with the function emptyDrops (R package dropletutils). Barcodes representing cells were chosen with FDR < 0.01. For each sample, we merged the human-aligned matrix with the mouse-aligned one. Each sample has cells annotated as “human”, “mouse” and “hybrid”, when the cells has reads aligning to both human and mouse transcriptomes. Moreover, we kept both transcriptome annotations as “mm10-” or “GRCh38-” plus the gene symbol.
Processed data files are gene expression matrices with genes by rows, cells by colums. Gene expression is measured in UMI counts. Processed data files still have to undergo quality filtering and normalization, as specified below.
In particular, we filtered out cells with percent.mito > 0.6 and cells expressing less than 800 different genes. UMI counts were finally log-normalized.
Genome_build: mm10, GRCh38
Supplementary_files_format_and_content: Digital gene expression matrix for each sample. Files provided in tab-delimited format.

source_name: Orthotopically transplanted BT-16 cells

growth_protocol: BT-16 cells (RRID: CVCL_M156) were cultured as suspension cells in NSC growth medium (DMEM:F12/Ham, 1% Pen/Strep, 1x B27 supplement, 10 ng/ml recombinant murine EGF and 10 ng/ml recombinant murine bFGF). BT-16 cells grew as sphere forming and gravity assays were performed to ensure additional sphere enrichment. Cells were dissociated with StemPro Accutase and seeded as single cells for experiments.

extract_protocol:
Fresh tumor tissues were isolated macroscopically and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. Vital cells were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp). For samples Nodscid1074, Nodscid1214 and Nodscid1216 we sequenced the same library at two subsequent time points, to improve saturation.

treatment_protocol: After detection of tumor presence, mice were treated in adaptation to the European Rhabdoid Registry (EU-RHAB) to assess potential therapy-resistant ATRT. Corresponding dosages and application times were modified in the mice as described in the literature (Kwak et al., 2015) (Seitz et al., 2007) (Némati et al., 2010) (Alyamkina et al., 2015) and all chemotherapeutics were administered intraperitoneally. One day after the first MRI scan, Doxorubicin (4 mg/kg bodyweight) was administered, followed by a combined dose of Vincristine (0.5 mg/kg), Cyclophosphamide (150 mg/kg) and Actinomycin-D (0.5 mg/kg), and a single dose of Vincristine seven and eight days after Doxorubicin administration, respectively. Two weeks after, mice were scanned by MRI. A day later, a combined dose of Ifosfamide (90 mg/kg), Carboplatin (25 mg/kg) and Etoposide (12 mg/kg) was administered, and a dose of Ifosfamide and Etoposide was given the following day. After 14 days without chemotherapy treatment, a third MRI was performed.

value: 23 weeks

value: NOD/SCID

tag: tumor localisation

value: Striatum (anteroposterior:0 mm; lateral:2.5 mm; dorso-ventral:3 mm)

tag: treatment

value: chemotherapy treatment


title: Nodscid1214

value: 19 weeks

value: no treatment


title: Rosini1225

data_processing:
The 10x Genomics Cell Ranger Suite (version 2.0.2) was used to perform sample demultiplexing, barcode processing, alignment (mm10) and generation of digital gene expression matrix. For samples Rosini1192 and Rosini1225 two sequencing runs were merged following Cell Ranger pipeline, i.e. specifying multiple fastq files to be considered together. Default parameters were used.
Processed data files are gene expression matrices with genes by rows, cells by colums. Gene expression is measured in UMI counts. Processed data files still have to undergo quality filtering and normalization, as specified below.
Each gene expression matrix was loaded in R separately, retaining genes expressed in at least 3 cells, and cells expressing at least 50 genes. To account for inter-sample heterogeneity, different upper thresholds on nUMI were chosen (RosiniD3_48 = 50,000; Rosini1145 = 20,000; Rosini1225 = 40,000; all others = no threshold). Moreover, we excluded cells expressing less than 200 genes or having a percentage of mitochondrial genes greater than 40%. Finally we chose an upper limit for nGenes for samples RosiniD3_48 (= 6,000), Rosini1192 (=3,400) and Rosini1237 (= 3,400).
After quality filtering, UMI counts were log-normalized.
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix for each sample. Files provided in tab-delimited format.

source_name: MYC subgroup-specific ATRT

extract_protocol:
Fresh tumor tissues were isolated macroscopically and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. Vital cells were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp). For samples Rosini1192 and Rosini1225 we sequenced the same library at two subsequent time points, to improve saturation.

value: 27 weeks

value: Rosa26-creERT2::Smarcb1 fl/fl

value: Cerebrum basal


title: Nodscid1074


title: Rosini1237

source_name: SHH subgroup-specific ATRT

value: 16 weeks

value: Striatum/subventricular zone


title: Rosini1192

value: 14 weeks


title: Nodscid1216

value: 18 weeks


title: Rosini1132_eye

value: Trigeminal nerve


title: RosiniD3_48

value: 12 weeks


title: WT-Control

city: Kobe

first: Naoki

last: Kuramoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Diabetes and Endocrinology, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: rma-gene-full-Signal

source_name: 10days after operation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The plantaris muscle was isolated 10 days after surgery and subjected to various assays.

extract_protocol: Total RNA was extracted from mouse skeletal muscle with the use of the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: The gastrocnemius and soleus muscles of both lower limbs were surgical removed from anesthetized mice.  As a control, sham surgery was undergone.

value: plantaris muscle

value: male

value: wild type

tag: agent

value: control(sham)


title: BAM15 Vehicle RNAseq3

city: Baton Rouge

first: John

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: GRCm38.84 mm10
Supplementary_files_format_and_content: tab-delimited text containing raw counts and DESeq2 normalized counts

source_name: C2C12 cell lysate

growth_protocol: C2C12 myoblasts were grown to confluence in high-glucose DMEM supplemented with 10% FBS. At confluence they were induced to differentiate by switching the media supplementation to 2% horse serum.

extract_protocol:
Qiagen Rneasy kit
Quant-Seq  3' mRNA-Seq Library Prep Kit; indexed and pooled samples, 50bp forward read

treatment_protocol: Myotubes were treated with 20uM BAM15 in DMSO or vehicle for 16 hours.

tag: differentiated cell type

value: fully differentiated myotubes


title: Rosini1145

extract_protocol:
Fresh tumor tissues were isolated macroscopically and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. Vital cells were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp). For samples Rosini1192 and Rosini1225  we sequenced the same library at two subsequent time points, to improve saturation.

value: 21 weeks


title: E14 cells, iPCR_1

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: UTSC

description: inverse PCR

data_processing:
[Processing inverse PCR reads]  The paired-end reads were pre-processed by custom Python scripts. The forward read consists of the barcode, a fixed 20 nucleotide watermark sequence used for identification, the NlaIII restriction site and some mouse genome sequence ligated to the NlaIII site. The reverse read consists of the last 25 nucleotides of pT2 and the mouse genome sequence at the insertion site of the transposon. We used seeq version 1.1 (https://github.com/ezorita/seeq) allowing up to three errors (mismatches and indels) to identify the watermark and isolate the barcode sequence. Reads were discarded if the watermark was not found or if the barcode was not between 14 and 24 nucleotides long. We removed the first 25 nucleotides of the reverse read and cut the sequence at the first NlaIII site, if any. The reads for which this sequence was shorter than 20 nucleotides were discarded. The genomic sequences thus obtained were mapped in the mouse genome release mm9 using the GEM mapper build 1.376 (Marco-Sola et al. 2012) with options `-q ignore --unique-mapping`. The reason for not using the more recent mouse release mm10 was that the chromatin from Juan et al. (2016) were only available in release mm9. After mapping, the barcodes were clustered using Starcode (Zorita, Cuscó, and Filion 2015) allowing up to two errors (options `-d2 --print-clusters`). This removes potential sequencing errors and consolidates the barcode sequences.   The barcodes were assigned to a genomic location using custom Python scripts. Unmapped genomic sequences were discarded and sequences mapping to multiple locations were flagged as such. For each barcode, we collected all the insertion sites that totalled at least 10% of the reads and we computed their diameter, equal to the maximum of their pairwise genomic distances (infinite for two sites on different chromosomes or if one of them maps to multiple locations). If the diameter was greater than 30 nucleotides, the barcode was discarded for being used in reporters mapping to different locations. Otherwise, the barcode was kept and its location was attributed to the most frequent insertion site (they are usually within 1-2 nucleotides of each other because of small mapping artefacts).
[Processing UMI-amplicon reads]  Paired-end reads were preprocessed using custom Python scripts. The forward read consists of the barcode, the watermark sequence and the right half of the second F segment . The reverse read consists of the UMI and the left half of the first F segment. Both reads extend the mid point of the F segment by three nucleotides. If the reporter is uncut or repaired by NHEJ, forward and reverse reads do not overlap. If the reporter is repaired by SSA, forward and reverse reads overlap because there is only one F segment. We can thus isolate the reads from reporters that went through SSA by ensuring that the nucleotides in the mismatch position are reverse-complement of each other in the forward and reverse reads. Thus, we used seeq with up to 10 errors to identify the half F segments and isolate the nucleotides in mismatch position on the forward and reverse reads, together with the barcode and the UMI. Barcodes and UMIs were clustered with Starcode allowing up to 2 errors (options `-d2 --print-clusters`) and the repair events were quantified for each barcode. The barcode–UMI pairs with only one read per run were discarded. After this operation, UMIs that were associated with more than one barcode were discarded. The remaining UMIs were classified as NHEJ or SSA as explained above, and those classified as SSA were further split into A/T or G/C. This provided for each barcode the full list of events reported by UMIs. Barcodes with more UMIs reporting NHEJ than SSA and those with only one UMI were removed. Barcodes that passed all these criteria in the control experiments without I-SceI induction were removed. The global proportion of remaining UMIs reporting A/T versus G/C was used a measure of repair bias.
Genome_build: mm9
Supplementary_files_format_and_content: mapped_repair.txt.gz

source_name: ES cells

growth_protocol: mESCs were grown at 37 °C under a 95% air and 5% CO2 atmosphere on gelatin in serum/LIF medium composed of GMEM (Sigma, G5154) supplemented with 15% FBS (HyClone™), 1X MEM Non-Essential Amino Acids (Gibco, 11140 - 050), 1X GlutaMax (Gibco, 35050 - 061), 1mM Sodium Pyruvate (Gibco, 11360-070), 0.1 mM 2-Mercaptoethanol (Thermo Fisher, 31350-010) and 1,000 U/ml LIF ESGRO® (Merck Millipore, ESG1106). mESCs were passaged every 2 d with a 1:8 dilution. Cells were tested yearly for mycoplasma contamination.

extract_protocol:
Genomic DNA from transfected cells was extracted using DNeasy Blood and Tissue Kit (Qiagen, #69504)
Inverse PCR: 10 μg genomic DNA from transfected mESCs were digested using 10 μl 10 U/μL NlaIII (NEB, #R0125S) in a 50 μL final volume for 3 hours at 37 °C. The reaction was heat-inactivated at 65 °C for 20 minutes. The reaction was diluted to a final volume of 1.8 mL in 1X T4 ligase buffer (Thermo Fisher Scientific, #EL0013) to favor self-ligation events, and ligation was carried out with 600 U of T4 ligase (Thermo Fisher Scientific, #EL0013) at 16°C overnight. After ligation, samples were precipitated by ethanol, pellets were resuspended in water and column-purified (QIAGEN, QIAquick PCR purification kit #28104) eluting with 100 uL EB.  Non circularized templates were eliminated by 2 h digestion at 37°C with Plasmid-safe DNAse (Epicentre, #E3101K), the enzyme was inactivated by heating for 30 minutes at 70°C. The product was column-purified (QIAGEN, QIAquick PCR purification kit #28104). The backbone of the TRIP reporters contains a I-CeuI site outside the transposable cassette, taking advantage of this, non integrated plasmids were cut by 2 h digestion at 37 °C with I-CeuI restriction enzyme (NEB, R0699S) in a total volume of 70 ul  followed by 20 minutes heat inactivation at 65 °C. All enzymatic reactions were carried out in the recommended manufacturer's buffer. For the first round of nested PCR, 10μL of I-CeuI-digestion products was mixed in 50 μL standard Phusion polymerase reaction mix (Thermo Fisher Scientific, F530S) in GC buffer, with 0.1 μM primers IR1,2 (annealing to IR/DR sequence). The cycling conditions were as follows: 98 °C for 5 min; 98°C for 20 s, 60°C for 1 min and 72°C for 5 min (1 cycle); 98°C for 20 s, 60°C for 1 min and 72°C for 2 min (20 cycles); and 72°C for 5 min. Products of the reaction were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880), and eluted in 40 μL of water . For the second round of nested PCR, 37 μL of the products was diluted to 50 μL of standard Phusion polymerase reaction mix in GC buffer with 0.1 μM primer M1 (annealing to the Illumina PE1.0 primer) and one of indexing primers M2,3. The cycling conditions were as follows: 98°C for 2 min; 98°C for 20 s, 60°C for 1 min and 72°C for 1 min (10 cycles); and 72°C for 5 min. Primers M2,3 added the Illumina PE2.0 primer and one of indices to the amplicons. Products of the reaction were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880), and eluted in 40 μL of water. PCR products ran as a smear on agarose gel. The smears were specific, because they failed to appear when the mESCs were not transfected. To eliminate I-SceI sites that were not cut during DSB induction and limit the size of PCR extension, 2 μg genomic DNA from mESCs (both, with DSB induction and control without the induction) were digested using 1 μl 100 U/μL XbaI (NEB, #R0145T) and 4 μl 5 U/μL I-SceI (NEB, #R0694L) in a 50 μL final volume for 3 hours at 37 °C. Digested DNA was column-purified (QIAGEN, QIAquick PCR purification kit #28104).
UMI-amplicons: To eliminate I-SceI sites that were not cut during DSB induction and limit the size of PCR extension, 2 μg genomic DNA from mESCs (both, with DSB induction and control without the induction) were digested using 1 μl 100 U/μL XbaI (NEB, #R0145T) and 4 μl 5 U/μL I-SceI (NEB, #R0694L) in a 50 μL final volume for 3 hours at 37 °C. Digested DNA was column-purified (QIAGEN, QIAquick PCR purification kit #28104).  UMI-LA 500 ng of genomic DNA obtained after I-SceI/XbaI digestion was used as a template in a 50 μL of Q5 DNA polymerase reaction mix (NEB, M0491S), using 50 nM of a UMI-containing primer U1 in the following cycling conditions: 98°C for 4 min; 98°C for 30s, 60°C for 1 min and 72°C for 1 min (50 cycles); and 72°C for 5 min. Products of linear amplification were purified using Agencourt AM Pure XP beads (Beckman Coulter, A63880), and eluted in 40 μL of water. Linear amplification was repeated 4 times for every sample to account for the technical variability.
UMI-PCR: 500 ng of genomic DNA obtained after I-SceI/XbaI digestion was used as a template in a 50 μL of Q5 DNA polymerase reaction mix (NEB, M0491S), using 50 nM of primers U1 and U2 in the following cycling conditions: 98°C for 1 min; 98°C for 20s, 60°C for 1 min and 72°C for 4 min (6 cycles); and 72°C for 10 min. Products of UMI-PCR were purified using Agencourt AM Pure XP beads (Beckman Coulter, A63880), and eluted in 40 μL of water. UMI-PCR was repeated 4 times for every sample to account for the technical variability.

treatment_protocol: To integrate the construct into the genome of mouse ES cells, 1 million cells in 6-well plates were transfected with 2 μg of plasmid pT2_FF together with 2 μg of plasmid pCMV(CAT)T7-SB100x and 2 μg of plasmid pcDNA3.1-mCherry using Lipofectamine 2000 (Thermo Fisher, #11668027). After 24 h, mCherry-positive cells were FACS sorted. Pools of 20,000 cells were plated on 24-well plates and grown for two weeks, transferring to 100 mm dishes when the cultures reached a density of 5x106 cells/mL. Two independent cell pools of 20,000 cells were prepared for each construct. To generate the mismatches, pools of mouse ES cells harboring integrated transposons were transfected with 5 μg of plasmid pCBASceI using Lipofectamine 2000 (Thermo Fisher, #11668027). The growth medium was changed after 16 h later. 24 h and 48 h post transfection, cells were collected using Trypsin-EDTA (Gibco, #25200056), washed with PBS, and used for genomic DNA isolation.

tag: cell type

value: ES cells

tag: construct

value: iPCR


title: KO-SA

tag: tissue

tag: genotype

value: operation(synergist ablation)


title: WT-SA


title: BAM15 Vehicle RNAseq4


title: BAM15 Vehicle RNAseq2


title: Rosini1132_lateral

value: 19 weeks

value: Rosa26-creERT2::Smarcb1 fl/fl

value: Cerebellum lateral


title: BAM15 Vehicle RNAseq6


title: BXD2-p19-/-_#2_single_cell_RNAseq

source_name: B cells and T cells from spleen of BXD2-p19-/-_#2

value: Female

value: spleen


title: BXD2-p19-/-_#3_single_cell_RNAseq

source_name: B cells and T cells from spleen of BXD2-p19-/-_#3

value: Male


title: Nodscid1073

value: 23 weeks

value: NOD/SCID

value: Striatum (anteroposterior:0 mm; lateral:2.5 mm; dorso-ventral:3 mm)

value: chemotherapy treatment


title: KO-Control

value: plantaris muscle

value: male


title: BAM15 RNAseq 6

value: fully differentiated myotubes


title: Tumor_p53_4946

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Tumor-bearing pancreas

growth_protocol: Autochthonous pancreatic tumors were generated in genetically-engineered mice and isolated at signs of morbidity requiring euthanasia.

extract_protocol:
Tumors were flash frozen and mechanically ground by mortar in pestle in liquid nitrogen. Total RNA was isolated using a Qiagen All prep kit per manufacturer's instruction. RNA quality and purity was assessed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing with the Illumina Neoprep library preparation system per manufacturer's instructions.

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. AAV-GFP was administered to select mice (see Description) via intramuscular injection but did not alter tumor or weight phenotypes of mice.

value: Pdx1-Cre; KrasLSL-G12D/WT; p53fl/fl (KPC)


title: BAM15 RNAseq 5


title: BAM15 Vehicle RNAseq5


title: Tumor_p53_5254


title: Tumor_p53_4337

value: Pdx1-Cre; KrasLSL-G12D/WT; p53R172H/fl (KPC)


title: BAM15 RNAseq 2


title: BAM15 RNAseq 4


title: BAM15 RNAseq 3


title: BAM15 Vehicle RNAseq1


title: Tumor_p53_1529

value: Pdx1-Cre; KrasLSL-G12D/WT; p53R172H/WT (KPC)


title: BAM15 RNAseq 1


title: Tumor_p53_7075


title: Tumor_p53_4163

value: Pdx1-Cre; KrasLSL-G12D/WT; MADM11-GT,p53WT/MADM11-TG-p53KO (KPC)


title: Tumor_Non_ob_5063

value: Pdx1-Cre; KrasLSL-G12D/WT (KC)


title: Tumor_p53_4164


title: Tumor_Non_ob_5771


title: Tumor_Non_ob_4872


title: Tumor_Non_ob_5773


title: Tumor_Non_ob_5794


title: Tumor_Non_ob_5849


title: Tumor_Non_ob_5436


title: Tumor_p53_4908


title: Tumor_Non_ob_5279


title: Tumor_ob_5985

description: Treated with AAV-GFP

value: Pdx1-Cre; KrasLSL-G12D/WT; ob/ob (KCO)


title: Tumor_ob_6017

description: Treated with AAV-GFP


title: Tumor_ob_4080


title: Tumor_ob_4011


title: Tumor_p53_4350


title: Tumor_ob_3512


title: Tumor_ob_3137


title: Tumor_ob_5907

description: Treated with AAV-GFP


title: Tumor_ob_6540

description: Treated with AAV-GFP


title: Tumor_ob_2372


title: Tumor_ob_4221


title: Tumor_ob_6741

description: Treated with AAV-GFP


title: Tumor_ob_6696

description: Treated with AAV-GFP


title: Tumor_ob_4457


title: NS180319_WT3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Beads-purified mouse glomeruli.
processed data file: table_featurecounts_GLO.txt

data_processing:
Mapping was performed with STAR_2.4.0a versus mm10 following Encode RNA-seq options –outFilterIntronMotifs RemoveNoncanonicalUnannotated –alignMatesGapMax 1000000 –outReadsUnmapped Fastx –alignIntronMin 20 –alignIntronMax 1000000 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMultimapNmax 20
Read count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with –primary -g gene_name -p -s 1 -M -C options.
Quality control of RNAseq count data was assessed using in-house R scripts. Low expressed genes were filtered out, then normalization and statistical analysis were performed using Bioconductor package DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: table_featurecounts_GLO.txt: Matrix text file with raw read count. Rows are genes, columns are samples.

source_name: renal glomerulus

extract_protocol:
RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer instructions.
Libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA kit (Illumina). Libraries were then quantified with Qubit ds DNA HS assay kit (Invitrogen) and pooled. 4nM of this pool were loaded on a NextSeq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry.

tag: strain/background

value: mixed C57/BL6x129/SVxBALB/c

tag: genotype/variation

value: WT

value: renal glomerulus

value: 6 months


title: Tumor_ob_6473


title: Tumor_ob_7148


title: NS161202_DH


title: p35S-12GP2-1

data_processing:
Reads were mapped to the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Map to reads tool and parameters (            Masking mode = No masking            Match score = 1            Mismatch cost = 2            Cost of insertions and deletions = Linear gap cost            Insertion cost = 3            Deletion cost = 3            Length fraction = 0.5            Similarity fraction = 0.8            Global alignment = No            Auto-detect paired distances = Yes            Non-specific match handling = Ignore            Output mode = Create reads track            Create report = No            Collect un-mapped reads = No - CLC Bio, Aarhus, Denmark)
Low frequency variants were called against the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Low frequency variant caller tool and parameters (            Required significance (%) = 1.0            Ignore positions with coverage above = 100,000            Restrict calling to target regions = Not set            Ignore broken pairs = Yes            Ignore non-specific matches = Reads            Minimum coverage = 10            Minimum count = 2            Minimum frequency (%) = 0.5            Base quality filter = No            Read direction filter = No            Relative read direction filter = Yes            Significance (%) = 1.0            Read position filter = No            Remove pyro-error variants = No            Create track = Yes            Create annotated table = No            Create report = No - CLC Bio, Aarhus, Denmark)
Variants were filtered on  CLC Genomics with the following parameters (Criteria = 'Forward/reverse balance < .7501',           Criteria = 'Forward/reverse balance > .2499999',           Criteria = 'Reference allele contains no' - - CLC Bio, Aarhus, Denmark)
Amino acid changes were identified using the CLC genomics Workbench Amino Acid Changes tool with parameters (CDS track = PPV Penn7 (CDS)            Sequence track = PPV Penn7 (Genome) protein cistrons            mRNA track = Not set            Filter synonymous variants = No            Genetic code = 1 Standard            Filter CDS regions with no variants = No
Genome_build: PPV-D isolate Penn7 (GenBank accession EF640935)
Supplementary_files_format_and_content: tab-delimited text files include Chromosome, Region, Type, Reference, Allele, Reference allele, Length, Linkage, Zygosity, Count, Coverage, Frequency, Probability, Forward read count, Reverse read count, Forward/reverse balance, Average quality, Read count, Read coverage, # unique start positions, # unique end positions, BaseQRankSum, Read position test probability, Read direction test probability, Homopolymer length, Homopolymer, QUAL, Coding region change, Amino acid change, Amino acid change in longest transcript, Coding region change in longest transcript, Other variants within codon, and Non-synonymous.

source_name: 12 week old Prunus domesitica L leaves

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Samples were centrifuged at 16,000 g for 15 min at 4°C. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. The polysome fraction was pelleted by centrifuging the samples at 170,000 g for 18 h at 4 °C. The pellet was resuspended in 1 mL of PEB. 50 μl of Anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO, USA) was added to the resuspended pellet and incubated at 4°C overnight with gentle rocking. The beads were recovered using their magnetic property and were washed four times in wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Polysome-RNA complexes were eluted by treatment of the magnetic beads with 100 μl of Elution Buffer (100 μl wash buffer, 10 μl of 5 mg/mL FLAG3 peptide—Sigma Chemical Company, St. Louis, MO USA, 0.5 μl of 2 U/ml RNAse OUT—Thermo Fisher Scientific Cleveland, OH, USA). RLT buffer plus β-mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) was added to the eluted complexes. A 0.5 × volume of 100% ethanol was then added, and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 2000 and with the Qubit RNA Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA). Quality of the RNA was analyzed using an RNA ScreenTape assay (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

tag: cultivar

value: Prunus domestica L 'President'

tag: developmental stage

value: 12 weeks GP2

tag: infection status

value: PPV infected


title: NS180319_GLO_DH

tag: age


title: NS161202_WT


title: NS180319_GLO_FRA

value: kFRA (LCDD)


title: NS171018_GLO_FRA


title: NS180319_WT2


title: NS170411_FRA


title: NS171018_GLO_DH


title: NS171018_GLO_WT


title: NS171018_PC_WT3

description: processed data file: table_featurecounts_PC.txt

data_processing:
Mapping was performed with STAR_2.4.0a versus mm10 following Encode RNA-seq options –outFilterIntronMotifs RemoveNoncanonicalUnannotated –alignMatesGapMax 1000000 –outReadsUnmapped Fastx –alignIntronMin 20 –alignIntronMax 1000000 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMultimapNmax 20
Read count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with –primary -g gene_name -p -s 1 -M -C options.
Quality control of RNAseq count data was assessed using in-house R scripts. Low expressed genes were filtered out, then normalization and statistical analysis were performed using Bioconductor package DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: table_featurecounts_PC.txt: Matrix text file with raw read count. Rows are genes, columns are samples.

source_name: plasma cells

value: spleen CD138+ plasma cells

value: 3 months


title: NS161202_FRA


title: NS170411_DH


title: NS171018_PC_WT2


title: NS171018_PC_WT1


title: NS171018_PC_FRA3


title: NS171018_PC_FRA2


title: NS171018_PC_DH2


title: NS171018_PC_DH1


title: B2449_CTR

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Read Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.7.1. Using FastX 0.0.14 and ShortRead 1.24.0, we filtered subsequently small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N) and low quality reads (more than 50% of the bases < Q25). With Bowtie2 v2.2.4 we identified and removed reads that mapped to the spiked-in PhiX.
Alignment: Processed reads were aligned with STAR v2.4.1d to the reference genome of Mus musculus (GRCm38), as downloaded from the Genome Reference Consortium. Default STAR parameter settings were used, except for ‘outSAMprimaryFlag=OneBestScore’, ‘twopassMode=Basic’, ‘alignIntronMin=50’, ‘alignIntronMax=500000’, ‘outSAMtype=BAM’, SortedByCoordinate. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: Transcript coordinates were extracted from the GRC reference annotation with Gffread from the Cufflinks v2.1.1 suite and merged to gene coordinates with mergeBed from the Bedtools v2.17.0 toolkit. GC content and gene length were derived from the gene coordinates. The numbers of aligned reads per gene were summarized using featureCounts 1.4.6 with parameters ‘Q=0’, ‘s=2’, ’t=exon’ and ‘g=gene_id’. We removed 31,537 genes for which all samples had less than 1 count-per-million. As such, we continued with raw counts for 15,446 genes. Raw counts were further corrected within samples for GC-content and between samples using full quantile-normalization, as implemented in the EDASeq package from Bioconductor.
Identifying differential gene expression: With the EdgeR 3.8.6 package, a negative binomial generalized linear model (GLM) was fitted against the normalized counts. We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate.
Genome_build: GRCm38
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

source_name: mouse with ID B2449 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl

growth_protocol: Mice were housed in a specific pathogen-free animal facility under standard 12h-light/dark cycles with water and chow ad libitum.

extract_protocol:
RNA from tail epidermis was extracted with the Mammalian Total RNA Miniprep kit (GenElute from SIGMA)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1 microgram of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NextSeq 500 instrument (High Output, 75 bp, Single Reads, v2) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: Mice were euthanized with an overdose of nembutal. Tail skin was incubated for 5h with 10 mg/ml dispase at 4°C and next, epidermis was separated from dermis.

value: 8 weeks

tag: strain

value: K14-Cre/+ Ppp1r8 fl/+


title: NS180319_WT1


title: NS171018_PC_DH3


title: B2401_KO

source_name: mouse with ID B2401 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl

value: K14-Cre/+ Ppp1r8 fl/-


title: B2402_CTR

source_name: mouse with ID B2402 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl


title: B2396_KO

source_name: mouse with ID B2396 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl


title: B2447_KO

source_name: mouse with ID B2447 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl


title: B2339_CTR

source_name: mouse with ID B2339 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl


title: QXT94

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
Library strategy: gDNA capture-seq
R1 and R2 reads were mapped to the mm9 genome separately, each both in under settings that only allows non-duplicated, uniquely mappable reads (Bowtie -m 1 --best --strata; samtools rmdup -s) and under settings that allows multimapping and duplicated reads (Bowtie --best).
Of the multimapping reads, only reads that overlap (min. 50% of read) with RLTRETN, MMETn-int, ETnERV-int, ETnERV2-int or ETnERV3-int repeats were kept.
Non-duplicated and uniquely mappable reads whose paired read partners were overlapping ETn repeats were then clustered (as bed files) using bedtools (bedtools merge -i -n -d 1000) to receive a list of all potential annotated and non-annotated new ETn insertions.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with clustered ETn-paired reads

source_name: tail

extract_protocol:
Genomic DNA was purified from Proteinase K digested lysates using the gDNA Clean & Concentrator kit (Zymo)
Libraries were constructed and enriched using the SureSelectQXT Target Enrichment kit (Agilent) and custom RNA capture probes complementary to ETn LTRs.

value: tail

tag: mouse id

tag: Sex

value: F

value: Chr4-cl WT

tag: ancestry


title: QXT99

value: M

value: Chr4-cl KO/KO


title: QXT103

source_name: testes

value: testes

value: C6733 (replicate)


title: NS171018_PC_FRA1

value: mixed C57/BL6x129/SVxBALB/c


title: QXT107

value: H03387 (replicate)

value: Chr4-cl KO/KO (F2)


title: QXT98


title: QXT96


title: QXT92

value: Chr4-cl KO/WT


title: QXT106

value: C5731 (replicate)


title: QXT93

source_name: tail (adult)

value: tail (adult)


title: QXT101


title: QXT97


title: QXT102


title: QXT95


title: QXT100


title: B2398_CTR

source_name: mouse with ID B2398 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl


title: QXT91

source_name: kidney

value: kidney


title: QXT90

source_name: blood

value: blood


title: QXT87


title: QXT88

source_name: testis

value: testis


title: QXT85


title: Kidney_DKD_rep1

source_name: Renal tissue, DKD, replicate 1

value: Renal tissue

tag: gender

value: male


title: QXT104

value: tail

value: C7415 (replicate)

value: F


title: QXT86

value: M


title: QXT84

value: Chr4-cl WT


title: B2341_KO

source_name: mouse with ID B2341 from strain Tg(KRT14-cre)1Amc/J;Ppp1r8tm1Ave;Ppp1r8tm1.1Itl

value: 8 weeks

value: K14-Cre/+ Ppp1r8 fl/-


title: QXT105

value: C5734 (replicate)

value: Chr4-cl KO/KO


title: QXT83


title: QXT82


title: QXT81


title: QXT79


title: QXT89

source_name: brain

value: brain


title: QXT76

value: Chr4-cl KO/WT


title: QXT69


title: QXT74


title: QXT72


title: QXT70


title: QXT66


title: QXT77


title: QXT65


title: QXT80


title: QXT78


title: QXT71


title: QXT68