title: JD02 [miRNA-seq]


title: WT8-568

status: Public on Mar 03 2020

type: SRA

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38 mouse reference genome using STAR aligner (Dobin et al., Bioinformatics, 2013) and reads were counted using featureCounts (Liao et al., Bioinformatics, 2014)
Differential gene expression analysis was performed using limma-voom through the Degust interface (v0.20), and trimmed mean of M-values (TMM) normalisation was performed (Robinson and Oshlack, Genome Biology, 2010).
FDR values were assigned to each gene and a cut-off of FDR<0.01 was used to select differentially expressed genes.
edgeR_3.18.1
limma_3.32.7
Genome_build: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: Grhl2 WT_first pharyngeal arch

extract_protocol:
First pharyngeal arches were removed, flash frozenon liquid nitrogen and total RNA isolated using QIAGEN micro Rneasy kit (#74004) with on-column Dnase digestion.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library preparation (RiboZero) protocol using 500 ng RNA.

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue

value: first pharyngeal arch


title: myco_con_4

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4).
Trimmed reads were mapped to mm10 and hg19 using STAR aligner (version 2.6) separately; then, ambiguous reads which mapping to both mm10 and hg19 were assigned to mm10, hg19 or discarded using tool –“Disambiguate"
Subread featureCounts (version 1.4.6) was applied for gene quantification based on GENCODE annotation release (GRCh37,p13)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count and log2 transformed DESeq2 normalized counts for each sample

organism: Homo sapiens

source_name: tumor

growth_protocol: Clean (no bacteria) or M. hyorhinis-infected HCT116 cells were grown in RPMI1640 with 10% FBS and pen/strep.

extract_protocol:
RNA was extracted using RNAeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA with Ribo-Zero kit.

treatment_protocol: 2*10e6 clean (no bacteria) or M. hyorhinis-infected (Mycoplasma) HCT116 cells were xenografted into nude mice.  Treatment with 15 mg/Kg STF118804 or vehicle control twice daily by subcutaneous injections was initiated when the tumor reached 200 mm3 and continued for two weeks or till tumor reached 1000 mm3. Then mice were sacrificed, tumor RNA isolated and analyzed by RNAseq.

tag: cell line

tag: cancer type

value: colon adenocarcinoma

tag: infection

value: Mycoplasma Hyorhinis

tag: protocol

value: xenografted into nude mice

tag: treatment

value: vehicle

value: xenograft tumor


title: WT5-566


title: myco_con_5


title: Hu1_ret_rep2_nuclei_RNA

city: Seattle

first: Timothy

middle: J

last: Cherry

state: WA

department: Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

description:
total nuclear RNA
Hu1_ret_rep2_nuclei_RNA

data_processing: QUANTIFICATION AND STATISTICAL ANALYSIS: Sequence read data processing (ATAC_Seq, ChIP_Seq): Read processing and alignment: Demultiplexed FASTQ files were trimmed with Trimmomatic (version 0.33) using the parameter SLIDINGWINDOW:5:30 (Bolger et al., 2014). Trimmed reads were indexed and aligned to the human or mouse genomes (Human GRCh38/hg38 assembly December 2013; Mouse GRCm38/mm10 assembly, December 2011) using the Burrows_Wheeler Aligner (bwa) tool (Li and Durbin, 2010) with the parameters: bwa aln  _q 0  _t 4  _n 2  _k 2  _l 32  _e _1  _o 0 and bwa samse  _n 5. Tag directories of reads were created using HOMER (version 4.6) makeTagDirectory (Heinz et al., 2010). Peak calling: High confidence peaks across concordant biological replicates were identified via ENCODE’s Irreproducible Discovery Rate (IDR) pipeline using a 1% IDR threshold (Landt et al., 2012). For each set of replicates, bam files of reads were pooled and 2 pseudoreplicate files were generated by samtools view with the parameters _h _b _s 1.5 and _h _b _2.5. Peaks in biological replicate, pooled replicate, and pseudoreplicate samples were called over pooled input samples using MACS2 (version 2.1.1) (Zhang et al., 2008) with the parameters –nomodel _g <hs or mm> _p 1e_1 –extsize 200, where hs or mm refers to human or mouse genomes. An optimal final set of IDR_filtered peaks was obtained from the peak caller and used as the final high_confidence peak set for further analyses and the centers of these peaks were used as summits for analyses with HOMER. Sequence read data processing (Total RNA Nuc_Seq): Read processing and alignment: Reads were trimmed to 70bp and aligned to the human genome (Human GRCh38/hg38 assembly December 2013) using the Burrows_Wheeler Aligner (bwa) tool. Two sets of target sequences were provided and incorporated into the bwa index in addition to the usual 23 chromosomal targets: (1) the human mitochondrial genome (GenBank accession NC_012920.1); and (2) a set of ~10 million short (≤138bp) exon_exon splice_junction sequences (see below). For RNA_seq data, a third set of 92 short (< 2.1kb) spike_in oligos representing a wide range of reference concentrations (ERCC RNA Spike_In Mix, Life Technologies; Mix 2) was also incorporated into the index. Typically ~90% of all reads were mappable, allowing up to 2 mismatches, and of these ~70_85% were mapped uniquely. Multiple reads whose 5ʹ ends were assigned to the same locus were not flattened to a single count. The splice_junction target sequences were based on the NCBI RefSeq database for GRCh38. For each annotated transcript, we noted all subsets of two or more exons, not necessarily adjacent, that could be spliced together to produce a sequence at least as long as the read length. Each of these sequences were then trimmed to the maximum number of bases such that a read mapping to the sequence would necessarily cross these ordered exons’ splice junction(s). This procedure produced a library of all unique sets of exons whose intragenic splice junctions could possibly be covered by a read of the given length, based on the RefSeq annotation of exonic loci. Aligned reads thus had the opportunity to align either to genomic (chromosomal) sequences or to exon_junction_crossing sequences found only in mature mRNA. Expression level quantification: An in_house software tool, MAPtoFeatures (Gray et al., 2014), was used to quantify expression levels for individual genes as follows. A database of genic features (CDSs and UTRs) was constructed from ~103,000 genomic transcripts annotated in RefSeq for GRCh38. Merged genes were constructed by unioning all exons in all transcripts assigned to each distinct gene; the resulting segments defined the gene’s exonic coordinates used here (with the gaps between them defining introns). Genes with zero CDS exons were labeled ‘‘noncoding’’. These 24,644 genes were supplemented with 37 mitochondrial genes and 1,752 additional noncoding genes specified by the loci of all ribosomal RNA genes obtained from RepeatMasker (where the options Variations and Repeats, rmsk.repFamily=‘‘rRNA’’ yielded 414 LSU_rRNA_Hsa; 74 SSU_rRNA_Hsa; ,1264 5S). The purpose of this step was to allow the filtering out of reads stemming from transcription of repeats and rRNA genes, which tend to get populated to inconsistent degrees from sample to sample depending on the variable quality of rRNA depletion. Reads that aligned uniquely were then queried for their intersection with the exonic ranges of any of the above 26,433 genes, including exon_exon splice junctions. The total number of read bases that overlapped an exonic range was divided by the range’s length to give an average exonic read density (i.e., coverage). All reads were assigned to genes or to intergenic regions. However, only those reads not assigned to noncoding genes counted towards the total normalization count N, which ultimately afforded a more stable comparison of expression levels between samples than simply using the total number of reads. All read densities were normalized to a reference total of 10 million reads and a reference read length of 35 bp through multiplication by the factor (107/N)*(35 bp/70 bp). (Division of these normalized densities by 0.35 yields expression levels in alternative units of reads per kilobase of transcript per million mapped reads, RPKM.) For downstream analyses, genes with a normalized exon density value of 0 in any replicate at any timepoint were discarded to remove lowly expressed genes. Sequence read data processing (Single_nucleus RNA_Seq): inDrops sequencing_data processing: Transcripts were processed according to a previously published pipeline (Hrvatin et al., 2018; Klein et al., 2015). Briefly, this pipeline was used to build a custom transcriptome from the Ensembl GRCh38 genome and annotation with Bowtie 1.1.1 (Langmead et al., 2009), after filtering the annotation gtf file (gencode.v17. annotation.gtf filtered for feature_type=‘gene’, gene_type=‘protein_coding’ and gene_status=‘KNOWN’). Read quality control and mapping against this transcriptome were then performed. Finally, unique molecular identifiers were used to reference sequence reads back to individual captured molecules, thus yielding values denoted UMIFM counts. All steps of the pipeline were run with default parameters unless explicitly specified. Quality control for cell inclusion: Our initial dataset contained ~30,000 cells with more than 1,000 reads assigned to each cell. All mitochondrially encoded genes were removed from the dataset. Cells with fewer than 400 or more than 15,000 unique_molecular_identifier counts were next excluded, thus yielding 4,763 high quality cells isolated from three donors. Dimensionality reduction and clustering: All 4,763 cells were combined into a single dataset. The Seurat R package (Macosko et al., 2015; Satija et al., 2015) was used to cluster cells. The data were log normalized and scaled to 10,000 transcripts per cell. Variable genes were identified with the MeanVarPlot() function, which calculates the average expression and dispersion for each gene, then bins genes and calculates a z score for dispersion within each bin. The following parameters were used to set the minimum and maximum average expression and the minimum dispersion: x.low.cutoff=0.0125, x.high.cutoff=3, y.cutoff=0.5. Next, PCA was carried out, and the top 20 principal components were retained. The clustering resolution was set to 0.6. This method resulted in 14 initial clusters across 4,763 cells. Quantifying bioreplicate correlations: To validate the reproducibility of our epigenomic and transcriptomic assays, we compared the correlation of bioreplicates performed on distinct samples for ATAC_Seq/DNase_Seq, H3K27ac ChIP_Seq and total RNA Nuc_Seq experiments. For each assay, we found a high degree of correlation between samples of the same tissue type (Figure S1A). As expected, retinal and macular samples

source_name: Adult human retina

extract_protocol:
METHOD DETAILS: DNA accessibility: ATAC_Seq: Flash_frozen tissue was thawed by addition of 700ul of lysis buffer (10 mM Tris_HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP_40), homogenized by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, and transferred back to original 1.5mL LoBind tube (Eppendorf). Dounce was washed with an additional 700ul ice cold lysis buffer and buffer was transferred to tube with sample for a final volume of 1.4mL. Sample was then centrifuged in a microcentrifuge at 4C for 10min at 500 rcf. The pellet was re_eluted in 1.4mL ice cold lysis buffer, transferred to a pre_chilled dounce, homogenized again 12x with tight pestle, and transferred back to 1.5mL LoBind tube. Nuclei were counted on a hemocytometer and the volume of lysis buffer/nuclei suspension needed for 20,000 nuclei was aliquoted into a separate 1.5mL LoBind tube. Samples were centrifuged along with tube containing remaining nuclei (for nuclear localized RNA) at 4C for 5min at 500g (RCF). The supernatant was removed from samples and remaining nuclei. Subsequent ATAC libraries were generated with 20,000 nuclei per sample using the Nextera DNA library prep kit (FC_121_1030; Illumina, San Diego, CA USA) according to the protocol described in (Buenrostro et al., 2013; Buenrostro et al., 2015). DNase I_Seq: Sequence files from the ENCODE Consortium (Consortium, 2012) for human retinal pigment epithelium (ENCBS420ENC, ENCBS893GDP), embryonic human retina (ENCSR820ICX, ENCSR474GZQ, ENCSR621ENC), and 8 week mouse retina (ENCSR000CNW) described in (Wilken et al., 2015) were analyzed in parallel with ATAC_Seq data. Chromatin immunoprecipitation: Crosslinking: Flash frozen human or mouse tissue was homogenized in crosslinking buffer (10 mM HEPES_NaOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA) containing 1% formaldehyde (added immediately before crosslinking) by trituration 10x with a p1000 pipet set to 500ul, dounced in an ice cold RNase_free 2mL glass dounce 10x with a loose pestle and 10x with tight pestle, transferred back to original 1.5mL LoBind tube (Eppendorf), and incubated while rotating gently at room temperature for 10 min. Crosslinks were quenched by addition of glycine to a final concentration of 0.125 M and incubated while rotating gently at room temperature for 5 min. Cells were pelleted by centrifugation 5 min at 1,350 g at 4C. Cell pellets were resuspended once with cold PBS and re_spun for 5 min at 1,350 g at 4C. Nuclei prep: Crosslinked cell pellets were resuspended in cold 5mL L1 buffer (50 mM HEPES_NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X_100, 0.5% NP_40, 10% glycerol, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) by pipetting and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 5mL L2 by pipetting (10mM Tris_HCl pH 8.0, 200mM NaCl, protease inhibitors; 10 mM sodium butyrate added for H3K27ac ChIPs) and rotated vertically at 4C for 10 min. Pellets were spun for 5 min at 1,350 g at 4C, and the supernatants were aspirated. Pellets were resuspended in cold 1.5 mL LB3 (10mM Tris_HCl pH 8.0, 100mM NaCl, 1mMEDTA, 0.5mMEGTA, 0.1% sodium deoxycholate, 0.5% N_lauroylsarcosine, protease inhibitors; 10mM sodium butyrate added for H3K27ac ChIPs) by pipetting and transferred to polystyrene tubes (Thermo Fisher 352099) for sonication. Sonication: Nuclei pellets were sonicated (Bioruptor Plus, Diagenode) in polystyrene tubes on high power with 36 cycles of 30 sec ‘‘on’’, 45 sec ‘‘off’’. After sonication, Triton X_100 was added to 1% final concentration and sonicated chromatin was centrifuged at 16,000 g for 5 min at 4C. The supernatant was used for preclearing and ChIP. All subsequent steps were performed using DNA LoBind tubes (Eppendorf). Preclearing and antibody_bead coupling: Protein A Dynabeads (Life Technologies) were washed twice with blocking buffer (0.1% BSA in LB3 + 1% Triton X_100) and aliquoted for preclearing and antibody_bead coupling. Antibodies were coupled to beads in 1.8 mL of blocking buffer by vertical rotation at 4C for 4 hr. In parallel, each sample of sonicated chromatin was incubated with an equivalent volume of washed bead slurry for preclearing. Each ChIP was performed in 1.8 mL LB3 + 1% Triton X_100 and rotated vertically at 4C for 16 hr. For input samples, 1% of sample was saved for de_crosslinking and DNA purification. Washes and elution: For each wash, beads were rotated vertically in wash buffer at 4C for 5 min. Beads were washed twice with low salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X_100, 2 mM EDTA, 20 mM Tris_HCl pH 8.0, 500 mM NaCl), twice with lithium chloride wash buffer (0.25 M LiCl, 1% NP_40, 0.5% sodium deoxycholate, 1 mM EDTA, 10 mM Tris_HCl pH 8.0), and once with TE (50 mM Tris, 10 mM EDTA). Beads were then incubated at 65C in 200 mL of TE + 1% SDS per sample for 30 min with vortexing every 10 min. Eluted protein_DNA complexes were separated from the beads and incubated at 65C for 16 hr to reverse crosslinks. Purification of immunoprecipitated DNA: Elutions were incubated with 10mg RNase A for 1 hr at 37C, followed by 140 mg proteinase K for 2_3 hr at 55C with shaking. DNA was extracted with 1 volume of 25:24:1 phenol_chloroform_isoamyl alcohol and purified with a Qiagen PCR purification kit. ChIP DNA concentrations were determined by Qubit dsDNA HS Assay Kit (Thermo Fisher). Gene expression: Total RNA Nuc_seq: To determine RNA expression in adult human retina, macula and RPE nuclei, RNA was extracted from excess nuclei (~80M) from the ATAC nuclear preparation protocol using Trizol (ThermoFisher; 15596026). Prior to RNA extraction, an equal amount of ERCC spike_in control RNA (Mix 2) was added to each sample, following the manufacturer’s specifications. RNA was extracted using the Qiagen RNeasy Mini Kit with on_column DNase I digestion (Qiagen 79254). Single Nucleus RNA_seq: Generation of single_nucleus suspensions were prepared by isolating nuclei from flash frozen human retina as described above and purified using an iodixanol gradient (Optiprep; Sigma_Aldrich, St. Louis, MO, USA) with RNase_inhibitor. After gradient centrifugation, the nuclei were washed in dissociation solution (Hrvatin et al., 2018; Klein et al., 2015) containing 0.04% BSA and were resuspended in dissociation solution containing 0.04% BSA and 15% Optiprep for single_nucleus RNA sequencing using a modified inDrops protocol (Klein et al., 2015).
Library preparation and sequencing: ATAC_seq: ATAC_Seq libraries were prepared as described above and sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads. ChIP_seq: 2_40 ng of each ChIP sample was used to prepare libraries with the NuGEN Ovation Ultralow Library System v2 kit per manufacturer’s protocol. Libraries were sequenced on the Illumina NextSeq 500 platform with 75 bp single_end reads, or 2 x 150 bp paired_end reads.Total RNA Nuc_seq: RNA_seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (E7420L, NEB) and either NEB rRNA depletion kit (E6310, NEB) or Qiagen GeneRead rRNA Depletion Nano kit (180211, Qiagen). Spike_in RNA (Fisher 4456740) were used for sample_to_sample normalization. Samples were then sequenced on the Illumina NextSeq 500 platform with 2x 150 bp paired_end reads. Single_nucleus RNA_seq: Single_nucleus RNA sequencing (inDrops): One or two libraries of approximately 3,000 cells were collected from each donor retina. inDrops was performed as previously described (Klein et al., 2015; Zilionis et al., 2017), generating indexed libraries that were then pooled and sequenced on the NextSeq 500 (Illumina) platform.

tag: donor apparent sex

value: Male

tag: donor age

tag: donor apparent race

value: caucasian

tag: postmortem interval

tag: chip_seq antibody


title: Hu1_ret_ChIP_input

library_source: genomic

molecule: genomic DNA


title: JD17

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
The raw sequences were quality assessed using fastqc; no primer removal was required.
Zebrafish transcripts details and sequences were obtained from Ensembl release (Rel84, March 2016); a total of 57264 transcript models were obtained.
Alignments (end-to-end, --very-sensitive settings) to the reference transcript set were performed using bowtie2, with a requirement for concordant read pair mapping was applied, and all other alignments discarded.  Alignments were stored in indexed BAM files, and transcript counts extracted for each transcript using samtools idxstats.
Raw "tag counts" per sample were scale normalised to the sample with the lowest number of alignments, and counts converted to log2; "abundance normalised" data were not further quantile normalised for linear model fitting purposes.
Pairwise comparisons of the two sample groups (e.g. cases relative to controls) were performed on the normalised tag counts using linear modeling (Bioconductor limma package).
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text of annotated raw transcript counts

organism: Danio rerio

source_name: 30 pooled larvae (5dpf)_triptolide for 6 h

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5 °C

extract_protocol:
Total RNA was extracted from pooled zebrafish larvae (30 larvae per sample) for qPCR and RNA-sequencing. Larvae were fixed in Qiazol after which they were disrupted using a tissue disruptor. Subsequently, total RNA was extracted using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) eluted in 30 µl RNAse free water.
RNA libraries were prepared for each sample with the Truseq Stranded Total RNA Sample Prep LT Kit. Libraries were checked for size, purity and concentration with a high sensitivity DNA chip on the Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: 5 dpf larvae (N = 30) were treated per 50 ml dish for 6 h with a TP concentration of 0 µM (8 dishes) or 1.6 µM (8 dishes)

tag: strain

value: WIK

value: triptolide (1.6μM) for 6 h

value: 30 pooled larvae


title: WT3-588


title: myco_con_2


title: Hu1_ret_nuclei_RNA

description:
total nuclear RNA
Hu1_ret_nuclei_RNA


title: JD14


title: myco_con_1


title: WT1-568


title: JD12


title: JD15


title: Hu1_ret_ATAC_rep2


title: clean_STF_4

value: no bacteria


title: JD11


title: Hu1_ret_ChIP_H3K27ac

value: Female


title: WT1-566


title: clean_STF_3


title: Hu1_ret_ATAC


title: KO3-604

source_name: Grhl2 KO_first pharyngeal arch


title: clean_STF_2


title: JD08

source_name: 30 pooled larvae (5dpf)_vehicle


title: Hu1_mac_nuclei_RNA

description:
total nuclear RNA
Hu1_mac_nuclei_RNA

source_name: Adult human macula


title: KO2-568


title: JD13


title: Hu1_mac_ATAC


title: JD07


title: clean_STF_1


title: clean_con_5


title: KO1-628


title: clean_con_4


title: JD05


title: KO1-588


title: KO2-566


title: JD06


title: Hu1_retina_1_snRNA

description:
single nucleus polyA RNA
Hu1_retina_1_snRNA
Hu1_Hu4_Hu8_single_nuclei_rawcount_matrix.txt

molecule: polyA RNA


title: T148_CCR8plus_ICOSplus

city: Rozzano

first: Simone

last: Puccio

state: Milan

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCm38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9 R version 3.4.4
Genome_build: GRCh38.p12

source_name: FACS sorted Tumor Infiltrating Regulatory T cells ICOS positive CCR8 positive

extract_protocol:
Max of 20.000 cells was sorted by BD FACSARIA III and RNA was immediately after extracted using Direct-zol RNA Micro prep (Zymo research, Catalog #R2061) according to manufacturer instructions.
SMART-Seq© v4 Ultra© Low Input RNA Kit for Sequencing (Clontech-Takara)

tag: cell type

value: Tumor infiltrating cells

value: lung cancer

tag: marker

value: ICOSpositive


title: Hu1_retina_1_rep2_snRNA

description:
single nucleus polyA RNA
Hu1_retina_1_rep2_snRNA
Hu1_Hu4_Hu8_single_nuclei_rawcount_matrix.txt


title: clean_con_3


title: T148_CCR8minus_ICOSminus

source_name: FACS sorted Tumor Infiltrating Regulatory T cells ICOS negative CCR8 negative

value: ICOSnegative


title: JD04


title: JD03


title: 72h: control4

type: RNA

city: Tokyo

first: Sayaka

last: Katagiri

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression after 72hr in non-treated bone in calvaria

hyb_protocol: cRNAs were analyzed by hybridization onto an Agilent SurePrint G3 Unrestricted Gene Expression 8 × 60 K Microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Fluorescence signals from the hybridized microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies) according to the manufacturer’s instructions.

data_processing:
Raw microarray data were extracted using Feature Extraction Software (ver. 11.0.1.1; Agilent Technologies).
Microarray data were quantile normalized and log2-transformed (Shippy et al., 2006) using R (ver. 3.6.0).

organism: Rattus norvegicus

source_name: calvaria, non-treated

label_protocol: The Agilent Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, California, USA) was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray (Cy3) analysis according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, California, USA) with NucleoSpin RNA (TaKaRa Bio, Shiga, Japan). cDNA was synthesized using a PrimeScript RT Master Mix (TaKaRa Bio) according to the manufacturer’s instructions.

treatment_protocol: Rectangular bone defect (8 × 3 mm area) was prepared by a few strokes of bur drilling (mean feed speed: approximately 0.75 mm/s) or 3 strokes (chisel contact tip, panel setting: 220 mJ/pulse and 20 Hz, output energy: 127 mJ/pulse, energy density at tip end: 20.2 J/cm2/pulse, feed speed: approximately 2 mm/s, pulse duration: 200 µs). In controls, periosteum was removed without bone ablation.

value: bone

tag: age

value: 10 weeks old


title: JD02


title: HfadR

city: Tianjin

first: Lixia

last: Fang

address: 135 Yaguan Road, Jinnan District

country: China

institute: Tianjin University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome(https://www.ncbi.nlm.nih.gov/nuccore/CP001509.3?report=fasta) and gene model annotation files (https://www.ncbi.nlm.nih.gov/nuccore/CP001509.3?report=genbank) were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.(Langmead, B. and S.L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: CP001509.3
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample.

organism: Escherichia coli BL21(DE3)

source_name: Escherichia coli BL21(DE3)

extract_protocol:
Total RNA was extracted using the RNAprep pure Cell/Bacteria Kit (Tiangen) following lysozyme treatment. RNA degradation and contamination were monitored on 1 % agarose gels. RNA concentration was measured by Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and RNA integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies, CA, USA). rRNA is removed using a Ribo-zero kit that leaves the mRNA. A total of 3 μg RNA was used as an input per sample.
Sequencing libraries were generated using a NEBNext®UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s instructions, and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.

value: HfadR

tag: phase

value: the early stationary phase


title: LihfA

value: LihfA


title: T141_CCR8minus_ICOSminus


title: 72h: laser4

description: Gene expression after 72hr in laser ablated bone in calvaria

source_name: calvaria, laser ablated


title: JD01

tag: developmental stage

value: vehicle


title: control (Control)

value: control (Control)


title: T140_CCR8plus_ICOSplus

tag: tissue


title: JD16


title: 72h: bur4

description: Gene expression after 72hr in bur drilled bone in calvaria

source_name: calvaria, bur drilled


title: C03_rat pineal gland at night

city: Changchun

first: bao

last: yuan

address: 5333 Xi'an Road

institute: Jilin University

data_processing:
For circRNA, the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA) was used for rRNA removal. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNAPolymerase Iand RNaseH. Remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. AMPure XP Beads (Beckman Coulter, Beverly, USA) were used to select insert fragments of preferentially 150~200bpin length. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer.
At last, PCR products of circRNA were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.After Clean Reads was obtained, it was sequenced with the rat genome to obtain the location information on the rat genome and the unique sequence characteristics of the sequencing sample. The reads that are mapped to a specific rat genome are called Mapped reads, and the corresponding Data is called Mapped Data.We use CIRI (CircRNA Identifier) tools and find_circ software to identification circRNA29,30. The intersect of the results of the two methods will be the final prediction.The expression of circRNA was determined by the number of junction reads identify by CIRI tools and find_circ software.
Differential expression analysis of two conditions/groups was performed using the DESeq R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 and absolute value of log2(Fold change) >2 found by DESeq were assigned as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: CIRI and find_circ was uesd to predicted circRNA expression.TPM was uesd to calibrate the circRNA expression.

source_name: pineal gland

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen). RNA degradation and contamination, especially DNA contamination, were monitored on 1.5% agarose gels. RNA concentrations and purity were measured using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of an Agilent Bioanalyzer 2100 System (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three rats were anesthetized and sacrificed under dark conditions (under red light) from 04:00 to 05:00 and were considered the dark group; these rats were named C04, C05 and C06 . Another three rats were anesthetized and sacrificed in bright sunlight from 16:00 to 17:00 and were considered the light group; these rats were named C01, C02 and C03 .

tag: time

value: pineal gland

value: post natal week 8


title: OfadR

value: OfadR


title: clean_con_1

tag: cell line

tag: cancer type

value: colon adenocarcinoma

value: xenografted into nude mice

value: xenograft tumor


title: T141_CCR8plus_ICOSplus

value: Tumor infiltrating cells


title: C02_rat pineal gland at night


title: 72h: control3


title: C06_rat pineal gland during day time


title: 72h: bur3


title: BR

city: ST CATHARINES

first: Shasha

last: Hu

state: Ontario

address: 1812 Sir Isaac Brock Way

department: Biological department

country: Canada

institute: Brock University

description: PD

data_processing:
FastQC is used data quality control software.
Trimmomatic software was used for raw data Trimming to remove the sequencing adapter and low quality data of the sequencing data, and the clean data obtained was used for subsequent analysis. 1. Filter the low-quality reads; 2. Filter the sequence in which the N's content greater than 5% of the total length of the sequence; 3. Filter the sequence in which the bases with quality less than 20 greater than 50% of the total length of the sequence; 4. Filter the sequence containing the adapter; 5. Filter the reads that are shorter than 36 nt after trimming; 6. Filter the reads that cannot form paired.
Bsmap software was used to map the methylation data to the reference genome Metarhizium robertsii strain ARSEF 2575
Genome_build: Metarhizium robertsii strain ARSEF 2575 (JELW01) MR2010_11_27
Supplementary_files_format_and_content: bedgraph

organism: Metarhizium robertsii ARSEF 2575

source_name: fungal biomass

growth_protocol: PDA (potato dextrose agar) plate at 27℃

extract_protocol:
CTAB DNA extraction
The genomic DNA was randomly interrupted to 200-400 bp using Covaris M220; End-repairing the DNA fragment after interrupted, adding A tail, and ligating the sequencing linker in which all cytosines are methylated; followed by Bisulfite treatment (using EZ DNA Methylation Gold Kit, Zymo Research), after treatment, C which has not undergone methylation becomes U (changes to T after PCR amplification), and methylated C remains unchanged, and finally PCR amplification is performed to obtain a final WGBS library

tag: sample type

value: recovery of condiation

tag: phenotype

value: recovery of fungal virulence


title: T124_CCR8plus_ICOSplus

value: lung cancer

value: ICOSpositive


title: C01_rat pineal gland at night


title: Mr lc-2575

description: WD

value: phenotypically degenerated strain (low conidiation)

value: low fungal virulence


title: T111_CCR8plus_ICOSplus


title: T124_CCR8minus_ICOSminus

value: ICOSnegative


title: In vitro plant material, Ultrasonicated 1 week

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

data_processing:
Trimmed the adapters from the FASTQ files with TrimGalore 0.5.0
FastQC 0.11.5 was used for the QC
Trimmed data files were aligned to the reference genome with HISAT2 v2.1.0
Processed date files were generated with the SeqMonk v1.42.0
Genome_build: SolTub 3.0 from Ensembl (GCA_000226075.1)
Supplementary_files_format_and_content: raw counts

organism: Solanum tuberosum

source_name: in vitro plant material

growth_protocol: Single-node segments with a single leaf were cut from 4-w-old in vitro potato plantlets (cv. Desirée) and used for the experiment. The culture conditions, medium and vessels used were the same as in our earlier study on the effects of ultrasonication on the antioxidant defense system and subsequent growth and development of in vitro potato (Dobránszki et al. 2017).

extract_protocol:
Total RNA was purified from the 10 potato samples as three biological replicates each that were pooled using the Direct-zol™ kit (Zymo Research, Irvine, CA, USA) with TRIzol reagent based on the manufacturer’s protocol.
Using the Illumina TruSeq Stranded mRNA kit, mRNA was first randomly fragmented by adding fragmentation buffer, then cDNA was synthesized with an mRNA template and a random hexamer primer, after which a custom second-strand synthesis buffer, dNTPs, RNase H and DNA polymerase I were added to initiate second-strand synthesis. The second step involved terminal repair, A ligation and sequencing adaptor ligation, after which the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Freshly cut explants were placed into 50 ml glass beakers (90 explants / 40 ml liquid MS / beaker) and ultrasonicated in an ultrasonicator (Elmasonic X-tra 30 H; ElmaSchmidbauer GmbH, Singen, Germany). Ultrasonicated and non-ultrasonicated (treatment control) explants were placed on shoot regeneration medium (Murashige and Skoog 1962) medium without plant growth regulators and subcultured for 4 w. Both ultrasonicated and non-ultrasonicated plant material was sampled at 0 h, 24 h, 48 h, 1 w and 4 w after ultrasonication.

value: stem; plantlet

value: 1 week after ultrasonication

tag: treatment

value: Ultrasonicated


title: C05_rat pineal gland during day time

value: pineal gland


title: T111_CCR8minus_ICOSminus


title: In vitro plant material, Ultrasonicated 48 hours

value: 48 hours after ultrasonication


title: C04_rat pineal gland during day time

value: post natal week 8


title: In vitro plant material, Ultrasonicated 24 hours

value: stem

value: 24 hours after ultrasonication


title: 72h: bur2

value: bone

value: 10 weeks old


title: mRNA_sgRNA4.9_24hr_PFA_2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
Phosphonoformic acid (PFA) is a viral DNA replication inhibitor.
mrna_sgUS2_sg4.9_24h_PFA_human_rpkm.xlsx
mrnamrna_sgUS2_sg4.9_24h_PFA_viral_rpkm.xlsx

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human or mouse and and the matching herpesvirus genome.
All remaining reads were aligned to the human/ mouse transcriptome (canonical known genes).
Wig files were then generated by summing the numbers of reads obtained from each position in the human/mouse genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19 + NC_006273.2 + mm10 + NC_004065.1

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Human foreskin fibroblast

extract_protocol:
Cells were lysed and RNA was extracted using Tri Reagent (Sigma).
mRNA was isolated using polyA selection kit (Ambion) and then fragmented. Fragments were then dephosphorylated, ligated with a 3' barcoded adapter, reverse transcribed and ligated with a 5' barcoded adapter. The resulting barcoded cDNA was PCR amplified.

tag: cells

value: primary

value: Merlin


title: 72h: laser3


title: In vitro plant material, Ultrasonicated 4 weeks

value: 4 weeks after ultrasonication


title: In vitro plant material, Ultrasonicated 0 hour

value: 0 hour after ultrasonication


title: 72h: control1


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked yH2A rep2

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

institute: University of Sussex

data_processing:
FASTQ files were generated by Illumina basespace   (https://basespace.illumina.com/home/index).
The resulting sequences were aligned to S. cerevisiae reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) and to S. pombe (Downloaded from https://www.pombase.org/downloads/genome-datasets (9/4/2018)) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Unaligned reads from S. cerevisiae were aligned to S. pombe genome and unaligned reads from S. cerevisiae were aligned to S. pombe genome to aquire unique reads using samtools (http://samtools.sourceforge.net/) and bowtie2  (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):
BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
The data then was sorted into 50 bp bins and used for meta data analysis using custom made R programs
H2AP enrichment data over H2AP was normalized by multiplying each value by OR= Enrichment over input in S. cerevisiae genome/enrichment over input in S. pombe genome
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Genome_build: Schizosaccharomyces pombe (pombase (9/4/2018))
Supplementary_files_format_and_content: wig files contained normalised realtive H2AP enrichment over H2A

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol: Sacchamromyces cerevisiae top2-td cell cultures for alpha factor release experiments were prepared as described previously -S. A. Schalbetter, S. Mansoubi, A. L. Chambers, J. A. Downs, J. Baxter, Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proceedings of the National Academy of Sciences. 112, E4565-70 (2015).  Schizosaccharomyces pombe cells were induced for 2h as described in  Adam T. Watson, Petra Werler, Antony M. Carr, Regulation of gene expression at the fission yeast Schizosaccharomyces pombe urg1 locus, Gene, Volume 484, Issues 1-2, 2011, Pages 75-85, ISSN 0378 1119, https://doi.org/10.1016/j.gene.2011.05.028.

extract_protocol:
S. cereviseae pellets from 50 ml culture were resuspended in 500 μl SDS buffer (1% SDS, 10 mM EDTA, 5M Tris HCl, cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)). Aliquots of S. pombe cell pellets were resuspended in 250 µl SDS buffer, and 1/1000 volume of the original S. cerevisiae culture (corresponding to 1:10 S. pombe to S. cerevisiae ratio) was added to each S. cerevisiae samples.  Cells were lysed in a FASTPREP machine, 5 rounds of 1 min at 6.5 power, with 200 μl of 0.5 mm silica beads. Lysate was spun out and IP buffer (0.1% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM TRIS HCl (pH8), cOmplete Tablets, Mini EDTA-free EASYpack (Roche), PhosSTOP (Roche)) was added to a final volume of 1 ml. Samples were sonicated using the Focused-Ultrasonicator (Covaris, M220) (Average incident power - 7.5 Watts, Peak Incident Power - 75 Watts, Duty Factor - 10 %, Cycles/Burst - 200, Duration - 20 min). The sample was centrifuged for 20 min at 13,000 rpm at 4°C. Supernatant was then diluted to 1:10 (5 ml total).  50 μl protein A Dynabeads (Invitrogen, 10002D) and 50 μl protein G Dynabeads (Invitrogen, 10004D), were washed 3 times in IP buffer followed by adding to the sample and incubating for 2 h at 4°C. Supernatant was split, with 2X 2 ml being taken to 15 ml Falcon tubes, and 1 ml being kept at -20°C as an input sample. To the two 2 ml samples antibody was added, either H2A 1:500 (active motif) or 1.6 μg/ml yH2A (Abcam), and these were placed on a rotating wheel at 4°C for 15 - 20 h.   A preparation of Dynabeads (Invitrogen), Protein A (30 μl) and Protein G (30 μl), was washed 3 times in IP buffer. This was added to each sample and incubated at 4°C for 4 h. Supernatant was removed and beads were washed at 4°C for 6 min in TSE-150 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 150 mM NaCl), followed by TSE-500 (1% Triton-X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris HCl (pH8), 500 mM NaCl), followed by LiCl wash (0.25 M LiCl, 1% NP-40, 1% dioxycholate, 1 mM EDTA, 10 mM Tris HCl (pH8)) and finally Tris-EDTA (TE pH8). Elution was carried out in 400 μl elution buffer, for 30 min at room temperature. At the same time 50 μl from the input sample was added to 150 μl of elution buffer. 20 μl of 5 M NaCl and 10 μl of 10 mg/ml proteinase K (Invitrogen) was then added to the input, and 40 μl and 20 μl to the IP samples respectively. These were incubated at 65°C overnight. Then 10 μl of DNase-free RNase (Roche) was added to the input and 20 μl to the IP samples, and they were left at 37°C for 30 min. All DNA was purified with a Qiagen PCR pufirication kit and eluted in 50 μl. DNA amount was measured using the Qubit 2.0 Fluorometer (Life technologies) as per the manufacturer’s instructions.
Libraries were prepared using the NEBnext Ultra II library kit (NEB) as per the manufacturers instructions. PCR enrichment required 13 cycles. PCR purification was carried out using AMPure XP beads.

treatment_protocol: Cultures were fixed at 25°C  in  YP  + 1%  formaldehyde  (Sigma)  for  45  min. 125 mM glycine was then added for 5 min. Cells were washed with PBS before being pelleted and frozen in liquid nitrogen.

tag: s. cerevisiae strain

tag: s. cerevisiae genotype

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5’ upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)

tag: s. pombe strain

tag: s. pombe genotype

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

value: 120 min after alpha factor release

tag: chip antibody

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: mRNA_sgUS2_24hr_PFA_2

tag: strain


title: In vitro plant material, Control 4 weeks

value: stem; plantlet

tag: age

value: 4 weeks after subculture

value: Control


title: 72h: laser1


title: In vitro plant material, Control 1 week

value: 1 week after subculture


title: 72h: control2


title: Cow 813 CONTROL embryo #5 EX

city: Wilrijk

first: Karolien

middle: LJ

last: Desmet

state: Antwerpen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

data_processing:
RNAseq read pairs were mapped against the Bos Taurus UMD3.1 genome using CLC Genomics Workbench (version 9, Qiagen). Read pairs uniquely mapping to genes were used to obtain a gene count table for further processing.
Differential analysis was then performed using the DESeq2 R package version 1.10.1 .
Four samples were excluded from further analysis as they were identified as strong outliers in a preliminary principle component analysis on the normalized DESeq2 data. These four samples had a poor sequencing quality measures according to the quality control results from the sequencing run, each with more than 50% uncalled bases and less than 1 million mapped reads. Embryos where the ED could not be dissected from EXT were not included in the RNAseq analysis as well. This was limited to the spherical embryos.
Differential expression within the remaining samples was established in a DESeq2 model based on a Negative Binomial distribution. The samples were divided by origin, namely ED and EXT for further analysis. Gene dispersion estimates were based on all samples of each origin, regardless of treatment or morphology. Genes with less than one average read per sample were excluded from the analysis.
An FDR of 10% was used as a cut-off for differential expression and reported P-values were Benjamini-Hochberg corrected.
Genome_build: Bos Taurus UMD3.1 genome
Supplementary_files_format_and_content: abundance measurements

organism: Bos taurus

source_name: bovine day 14 embryo

growth_protocol: A total of 2141 embryos were produced among the three treatment groups (7 replicates). Grade I cumulus-oocyte complexes (COCs) were matured in groups of 50-60 in 500 μl serum-free maturation medium (containing TCM199 supplemented with 0.75% w/v FA-free BSA, 0.4 mM glutamine, 0.2 mM sodium pyruvate, 0.1 mM cysteamine, 50 mg/ml gentamycin and 20 ng/ml murine epidermal growth factor) in 4-well plates for 24 h in humidified air with 5% CO2 at 38.5°C. Oocytes were randomly divided in equal groups between treatment-specific maturation media. After IVM, COCs were co-incubated in groups of 100-120 with spermatozoa at a final concentration of 106/ml for 22 h at 38.5°C in 500 μl fertilization medium (containing 114 mM NaCl, 3.1 mM KCl, 0.3 mM Na2HPO4, 2.1 mM CaCl2-2H2O, 0.4 mM MgCl2-6H2O, 25 mM bicarbonate, 1 mM sodium pyruvate, 36 mM sodium lactate, 2 μl/ml phenol red, 6 mg/ml FA-free BSA, 50 μg/ml gentamycin and 0.72U/ml heparin) in 4-well plates in a humidified 5% CO2 incubator at 38.5°C. Presumptive zygotes were cultured in groups of 25 ± 4 in 75 μl droplets of modified synthetic oviductal fluid (mSOF) medium supplemented with 5% fetal bovine serum in 96-well plates in a modular incubator (5% CO2, 5% O2 and 90% N2 at 38.5 °C) until the day of transfer. Cows were randomly assigned to receive embryos from the BASAL and HIGH PA treatment group following a crossover design. Cows were synchronized in groups of four. Two cows received embryos from the BASAL group and two cows received HIGH PA embryos. One of the cows was used once for CONTROL embryos. Embryo transfer (ET) was performed into the uterine horn ipsilateral to the CL on day 7.7. Equal proportions of normal and expanded blastocysts (n = 8 blastocysts per recipient cow), per treatment and per replicate, were transferred to the synchronized cows. At day 14 p.i., conceptuses were transcervically flushed and recovered, morphologically assessed and dissected into ED and EX. A total of 53 samples (EX and ED) were used for RNA/DNA extraction, representative for the pool of recovered day 14 embryos, the embryo morphology, the recipient cows (embryos from one of the eight cows were excluded for RNA sequencing) and replicates.

extract_protocol:
Total RNA was isolated from individual ED and EXT samples using the Allprep DNA/RNA micro and mini kit (Qiagen), respectively, according to the manufacturer’s protocol.
Sequencing libraries were prepared using the TruSeq® Stranded mRNA HT Sample Preparation kit (Illumina, California, US), following the manufacturer's Low Sample protocol.
12 samples per lane, 2x 50BP paired end

treatment_protocol: oocytes were exposed during IVM to the following conditions: i) CONTROL: FA-free and solvent-free medium, ii) BASAL: physiological NEFA concentrations (72 μM total NEFA containing 28 μM SA, 23 μM PA, and 21 μM OA) in 0.45 % absolute ethanol, iii) HIGH PA: a combination of physiological concentrations of SA (28 µM) and OA (21 µM) and an elevated concentration of PA equivalent to that measured in follicular fluid during lipolytic conditions (150 μM) in 0.45 % absolute ethanol.

tag: individual

value: extraembryonic tissue

value: CONTROL

value: day 14 embryo

tag: morphology

value: ovoid

tag: Sex

value: female


title: 72h: bur1

tag: tissue

value: bone

value: 10 weeks old


title: mRNA_sgRNA4.9_24hr_PFA_1

value: primary

value: Merlin


title: mRNA_sgUS2_24hr_PFA_1


title: 24h: control4

description: Gene expression after 24hr in non-treated bone in calvaria


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked yH2A rep1

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5’ upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)

tag: time


title: T140_CCR8minus_ICOSminus

tag: cell type

value: Tumor infiltrating cells

value: lung cancer

tag: marker

value: ICOSnegative


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked H2A rep2

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

value: 120 min after alpha factor release


title: Cow 66 PA embryo #1 EX+ED

value: embryonic disc + extraembryonic tissue

value: HIGH PA

tag: developmental stage

value: male


title: 72h: laser2


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked H2A rep1


title: In vitro plant material, Control 24 hours

value: stem

value: 24 hours after subculture

tag: treatment

value: Control


title: H18

city: Galveston

first: Anna

last: Nia

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

data_processing:
STAR alignment program, version 2.5.3a, with the recommended ENCODE options (Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013;29(1):15-21 doi: 10.1093/bioinformatics/bts635published Online First: Epub Date]|.) -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: comma-seperated text file which includes raw transcript expression counts (with corresponding ENSEMBL ID) for each sample

source_name: Left liver lobes

extract_protocol:
Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA)
rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500.

tag: treatment type

value: Non-Irradiated Control

value: 9 months

tag: biological replicate


title: 24h: laser4

description: Gene expression after 24hr in laser ablated bone in calvaria

value: bone

value: 10 weeks old


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked input rep2

tag: s. cerevisiae strain

tag: s. cerevisiae genotype


title: In vitro plant material, Control 0 hour

value: immediately after subculture


title: Cow 66 PA embryo #2 EX+ED

value: day 14 embryo

value: spherical


title: 24h: bur4

description: Gene expression after 24hr in bur drilled bone in calvaria


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked yH2A rep2

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5’ upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)

tag: s. pombe strain

tag: s. pombe genotype

value: 80 min after alpha factor release

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: 24h: control3


title: Ribo_S2

city: Daejeon

first: Yongjae

last: Lee

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description:
Sample 22
Ribo_DESeq2.txt

data_processing:
Library strategy: Ribo-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome. Also, the random 3’-overhanging (N2) sequences in reads of Term-seq library were trimmed.
The reads were aligned to the S. avermitilis genome (BA000030) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
The 3' end position of Term-Seq reads located within intergenic regions including up to 10 bp downstream to gene were regarded as potential transcription termination sites (TTS). The positions were clustered together based on the distance from adjacent positions (< 10 bp). Within each cluster, the read count of each position was assumed to follow normal distribution and read count enriched positions were deduced by calculating modified z-score. Z(x)=(r(x)-μ(r(x)))/(σ(x)), where, μ(r(x))=1/(N(x)-1)(-r(x)+∑_(y∈C(x))▒r(y) ), σ(x)=√(μ(〖r(x)〗^2 )-〖μ(r(x))〗^2 ). Z(x) is modified z-score at position x, r(x) is the read count of evaluated position x. μ(r(x)) and σ(x) is the mean and standard deviation of read counts of other positions in the cluster except the evaluated position, respectively. N(x) is the length of the cluster containing position x and C(x) is the set of positions within the cluster containing position x. The positions with read count less than 3 or modified z-score less than 3 were discarded. All the procedures above were conducted separately for each biological replicate. Among the remaining potential TTSs, the reproducible positions with the highest read count within the intersecting region of clusters from two biological replicate was selected as TTS. For example, if genomic positions from 3 to 25 were clustered together for one replicate and genomic positions from 13 to 42 were clustered together for another replicate, potential TTS with highest read count within the genomic positions from 13 to 25 was selected as TTS.
Genome_build: BA000030
Supplementary_files_format_and_content: tab-delimited text files include TSS, TTS or normalized expression values for each sample

organism: Streptomyces avermitilis

source_name: cell culture

growth_protocol: The mycelium of S. avermitilis MA4680 was maintained in 25% glycerol. Cells were first recovered in 50 mL R5- media with 8 g glass beads (3 ± 0.3 mm diameter) at 30 oC, 250 rpm. R5- medium consists of 5.73 g/L TES (pH 7.2), 103 g/L sucrose, 10 g/L glucose, 5 g/L yeast extract, 10.12 g/L MgCl2∙6H2O, 0.25 g/L K2SO4, 0.1 g/L casamino acids, 0.08 mg/L ZnCl2, 0.4 mg/L FeCl3∙6H2O, 0.02 mg/L CuCl2∙2H2O, 0.02 mg/L MnCl2∙4H2O, 0.02 mg/L Na2B4O7∙10H2O, and 0.02 mg/L (NH4)6Mo7O24∙4H2O. The inoculum was then transferred to fresh R5- media with 8 g glass beads for main culture. Cells were harvested at 13, 17, 19.5 and 33.5 hours after inoculation for early exponential phase (E), transition phase (T), late-exponential phase (L) and stationary phase (S), respectively.

extract_protocol:
The cell pellet was washed with polysome buffer (20 mM Tris-HCl pH 7.4, 140 mM NaCl, 5mM MgCl2, and 33.5 ug/mL thiostrepton) and resuspended with lysis buffer (475 uL Polysome buffer, 25 uL Triton X-100, and 6 uL DNase I (New England Biolabs)). The cell suspension was frozen with liquid nitrogen and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and soluble supernatant was recovered. Ribosome unprotected RNA was digested by treating RNase I (Invitrogen) by incubating at 37 oC for 45 minutes. After RNase I digestion, RNase activity was inactivated by treating SUPERase-In (Invitrogen) and monosome was recovered using Sephacryl S-400 column (GE Healthcare Life Science). Ribosome protected RNA was recovered using phenol:chloroform:isoamyl alcohol = 25:24:1 solution and rRNA was removed with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer’s instructions. After rRNA depletion, RNA was resolved on a 15% TBE-urea gel and 26-34 nt RNA fragments were size-selected. The size-selected RNA was eluted in 300 mM sodium acetate pH 5.2, 1 mM EDTA and 0.25% SDS. The eluted RNA was further purified with ethanol precipitation.
Library was constructed with NEB Next small RNA library prep set (New England Biolabs) according to the manufacturer’s instructions. The constructed libraries were amplified and indexed using Phusion High-Fidelity DNA Polymerase (Thermo) for Illumina sequencing. The amplification step was monitored on a CFX96 Real-Time PCR Detection System (Bio-Rad) to be stopped before the PCR reaction was fully saturated. The amplified libraries were further size-selected on 2% agarose gel with MinElute Gel Extraction Kit (Qiagen).

treatment_protocol: Thiostrepton was treated to cell culture for 5 minutes before harvesting the cells.

tag: strain

tag: growth phase

value: stationary phase (S)


title: In vitro plant material, Control 48 hours

value: stem; plantlet

tag: age

value: 48 hours after subculture


title: Cow 25 PA embryo  #1 EX

tag: individual

value: extraembryonic tissue

value: HIGH PA

tag: morphology

value: female


title: Cow 12 PA embryo #1 EX

tag: tissue

tag: Sex

value: not determined


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked H2A rep2

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

tag: time

tag: chip antibody


title: 24h: bur3


title: 24h: laser3


title: Cow 813 CONTROL embryo #4 EX

value: CONTROL

tag: developmental stage

value: tubular

value: male


title: Ribo_L2

description:
Sample 20
Ribo_DESeq2.txt

value: late-exponential phase (L)


title: Ribo_S1

description:
Sample 21
Ribo_DESeq2.txt


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked yH2A rep1


title: 24h: control2

value: bone

value: 10 weeks old


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked H2A rep1

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100    UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)    Leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3    trp1-1::SDM-pFA6a-GAL1-SMC2-K39I-6HA, TRP1    smc2-td SMC2 5’ upstream-100 to -1 replaced with kanMX-tTA (tetR-VP16) -tetO2 -Ub -DHFRts -3xHA extended linker)   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)


title: 24h: laser2


title: Cow 12 BASAL embryo #2 EX

tag: treatment

value: BASAL

value: day 14 embryo


title: GAL1_SMC2_K38I_smc2-td top2-td 120 min spiked input rep1

value: 120 min after alpha factor release


title: 24h: bur2


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked input rep2

value: 80 min after alpha factor release


title: GAL1_SMC2_K38I_smc2-td top2-td 80 min spiked input rep1


title: Cow 72 BASAL embryo #2 EX


title: Cow 12 BASAL embryo #1 EX

value: ovoid


title: Ribo_T2

description:
Sample 18
Ribo_DESeq2.txt

value: transition phase (T)


title: Cow 13 BASAL embryo #1 EX

value: extraembryonic tissue


title: scc1_73 top2-td 120 min spiked yH2A rep2

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker   scc1-73    pRS316

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: 24h: control1


title: Ribo_E2

description:
Sample 16
Ribo_DESeq2.txt

value: mid-exponential phase (M)


title: scc1_73 top2-td 120 min spiked H2A rep2

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1


title: 24h: laser1


title: scc1_73 top2-td 120 min spiked input rep2


title: Cow 07 BASAL embryo #1 EX

value: tubular


title: 24h: bur1


title: RNA_S2

description:
Sample 14
RNA_DESeq2.txt

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome. Also, the random 3’-overhanging (N2) sequences in reads of Term-seq library were trimmed.
The reads were aligned to the S. avermitilis genome (BA000030) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
The 3' end position of Term-Seq reads located within intergenic regions including up to 10 bp downstream to gene were regarded as potential transcription termination sites (TTS). The positions were clustered together based on the distance from adjacent positions (< 10 bp). Within each cluster, the read count of each position was assumed to follow normal distribution and read count enriched positions were deduced by calculating modified z-score. Z(x)=(r(x)-μ(r(x)))/(σ(x)), where, μ(r(x))=1/(N(x)-1)(-r(x)+∑_(y∈C(x))▒r(y) ), σ(x)=√(μ(〖r(x)〗^2 )-〖μ(r(x))〗^2 ). Z(x) is modified z-score at position x, r(x) is the read count of evaluated position x. μ(r(x)) and σ(x) is the mean and standard deviation of read counts of other positions in the cluster except the evaluated position, respectively. N(x) is the length of the cluster containing position x and C(x) is the set of positions within the cluster containing position x. The positions with read count less than 3 or modified z-score less than 3 were discarded. All the procedures above were conducted separately for each biological replicate. Among the remaining potential TTSs, the reproducible positions with the highest read count within the intersecting region of clusters from two biological replicate was selected as TTS. For example, if genomic positions from 3 to 25 were clustered together for one replicate and genomic positions from 13 to 42 were clustered together for another replicate, potential TTS with highest read count within the genomic positions from 13 to 25 was selected as TTS.
Genome_build: BA000030
Supplementary_files_format_and_content: tab-delimited text files include TSS, TTS or normalized expression values for each sample

extract_protocol:
Harvested cells were washed with polysome buffer (20 mM Tris-HCl pH 7.5, 140 mM NaCl, 5 mM MgCl2), and then resuspended with lysis buffer (0.3 M sodium acetate pH 5.2, 10 mM EDTA, 1% Triton X-100). The cell suspension was then frozen with liquid nitrogen, and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and the supernatant was stored at -80 oC until used for RNA extraction. RNA was extracted by mixing with equal volume of phenol:chloroform:isoamyl alcohol = 25:24:1 solution. The mixture was then centrifuged and upper aqueous phase was recovered. The RNA was purified with ethanol precipitation. The purified RNA was treated with DNase I (New England Biolabs) to remove any genomic DNA contamination. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer's instructions.
The RNA-Seq libraries (Sample 7 to 14) were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina) based on manufacturer's instructions.

value: stationary phase (S)


title: Ribo_E1

description:
Sample 15
Ribo_DESeq2.txt


title: Ribo_L1

description:
Sample 19
Ribo_DESeq2.txt

value: late-exponential phase (L)


title: Ribo_T1

description:
Sample 17
Ribo_DESeq2.txt


title: 6h: control4

description: Gene expression after 6hr in non-treated bone in calvaria

value: bone


title: Cow 66 BASAL embryo #1 EX

value: male


title: Cow 813 BASAL embryo #3 EX

value: female


title: RNA_S1

description:
Sample 13
RNA_DESeq2.txt


title: 6h: laser4

description: Gene expression after 6hr in laser ablated bone in calvaria

value: 10 weeks old


title: Cow 813 PA embryo #3 EX

value: HIGH PA

value: day 14 embryo


title: Cow 13 PA embryo #2 EX


title: 6h: control3


title: RNA_T2

description:
Sample 10
RNA_DESeq2.txt


title: RNA_L1

description:
Sample 11
RNA_DESeq2.txt


title: RNA_L2

description:
Sample 12
RNA_DESeq2.txt


title: scc1_73 top2-td 80 min spiked yH2A rep2

value: 80 min after alpha factor release


title: Cow 07 PA embryo #5 EX

value: ovoid


title: scc1_73 top2-td 120 min spiked input rep1

value: 120 min after alpha factor release


title: Cow 72 PA embryo #2 EX

value: extraembryonic tissue


title: 6h: laser3


title: RNA_T1

description:
Sample 9
RNA_DESeq2.txt

value: transition phase (T)


title: scc1_73 top2-td 80 min spiked H2A rep2

value: Mat a ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100   UBR1::GAL1-10-Ubiquitin-M-LacI    fragment-Myc-UBR1 (HIS3)   leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3   top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker   scc1-73    pRS316


title: RNA_E2

description:
Sample 8
RNA_DESeq2.txt

value: mid-exponential phase (M)


title: 6h: bur3

description: Gene expression after 6hr in bur drilled bone in calvaria


title: Cow 13 BASAL embryo #2 EX

value: BASAL


title: scc1_73 top2-td 120 min spiked H2A rep1

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1


title: scc1_73 top2-td 80 min spiked input rep2


title: scc1_73 top2-td 120 min spiked yH2A rep1

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: 6h: bur4


title: 6h: control2


title: Cow 813 CONTROL embryo #1 EX

value: CONTROL

value: tubular


title: 6h: laser2

value: bone


title: 6h: bur2


title: Cow 813 CONTROL embryo #2 EX

value: male


title: Term2

description:
Sample 6
Term.txt

data_processing:
Library strategy: Term-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome. Also, the random 3’-overhanging (N2) sequences in reads of Term-seq library were trimmed.
The reads were aligned to the S. avermitilis genome (BA000030) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
The 3' end position of Term-Seq reads located within intergenic regions including up to 10 bp downstream to gene were regarded as potential transcription termination sites (TTS). The positions were clustered together based on the distance from adjacent positions (< 10 bp). Within each cluster, the read count of each position was assumed to follow normal distribution and read count enriched positions were deduced by calculating modified z-score. Z(x)=(r(x)-μ(r(x)))/(σ(x)), where, μ(r(x))=1/(N(x)-1)(-r(x)+∑_(y∈C(x))▒r(y) ), σ(x)=√(μ(〖r(x)〗^2 )-〖μ(r(x))〗^2 ). Z(x) is modified z-score at position x, r(x) is the read count of evaluated position x. μ(r(x)) and σ(x) is the mean and standard deviation of read counts of other positions in the cluster except the evaluated position, respectively. N(x) is the length of the cluster containing position x and C(x) is the set of positions within the cluster containing position x. The positions with read count less than 3 or modified z-score less than 3 were discarded. All the procedures above were conducted separately for each biological replicate. Among the remaining potential TTSs, the reproducible positions with the highest read count within the intersecting region of clusters from two biological replicate was selected as TTS. For example, if genomic positions from 3 to 25 were clustered together for one replicate and genomic positions from 13 to 42 were clustered together for another replicate, potential TTS with highest read count within the genomic positions from 13 to 25 was selected as TTS.
Genome_build: BA000030
Supplementary_files_format_and_content: tab-delimited text files include TSS, TTS or normalized expression values for each sample

extract_protocol:
Harvested cells were washed with polysome buffer (20 mM Tris-HCl pH 7.5, 140 mM NaCl, 5 mM MgCl2), and then resuspended with lysis buffer (0.3 M sodium acetate pH 5.2, 10 mM EDTA, 1% Triton X-100). The cell suspension was then frozen with liquid nitrogen, and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and the supernatant was stored at -80 oC until used for RNA extraction. RNA was extracted by mixing with equal volume of phenol:chloroform:isoamyl alcohol = 25:24:1 solution. The mixture was then centrifuged and upper aqueous phase was recovered. The RNA was purified with ethanol precipitation. The purified RNA was treated with DNase I (New England Biolabs) to remove any genomic DNA contamination. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer's instructions.
500~900 ng of the rRNA-depleted RNA was mixed with 1 mL of 150 mM amino-blocked DNA adaptor (5'-p-NNAGATCGGAAGAGCGTCGTGT-3'), 2.5 uL of 10x T4 RNA ligase 1 buffer, 2.5 uL of 10 mM ATP, 2 uL of DMSO, 9.5 uL of 50% PEG8000, and 2.5 uL of T4 RNA ligase 1 (New England BioLabs). The mixture was incubated at 23 oC for 2.5 hours and purified with Agencourt AMPure XP beads (Beckman Coulter) and eluted with 9 uL DEPC-treated water. Then the RNA-adaptor ligates were fragmented using fragmentation buffer (Ambion) by incubating at 72 oC for 90 seconds. After fragmentation, the product was purified with Agencourt AMPure XP beads and eluted with 8 uL DEPC-treated water. The fragmented RNA was reverse transcribed using 1 uL of 10 uM reverse transcription primer (5'-TCTACACTCTTTCCCTACACGACGCTCTTC-3') with SuperScript III Reverse Transcriptase (Invitrogen) according to the manufacturer’s instructions. After reverse transcription, the cDNA was purified with Agencourt AMPure XP beads and eluted with 5 uL DEPC-treated water. The purified cDNA was subjected to another adaptor ligation as above, with increased incubation time (8 hours) and different amino-blocked adaptor sequence (5'-p-NNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3'). After adaptor ligation, the product was purified using Agencourt AMPure XP beads and indexed by PCR for 10 cycles with Phusion High-Fidelity DNA Polymerase using forward (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCT-3') and reverse (5'-CAAGCAGAAGACGGCATACGAGATNNNNNN (6 nt index) GTGACTGGAGTTCAGAC-3') primers.


title: scc1_73 top2-td 80 min spiked input rep1


title: TSS_TAP_untreated2

description:
Sample 4
TSS.txt

data_processing:
Library strategy: dRNA-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome. Also, the random 3’-overhanging (N2) sequences in reads of Term-seq library were trimmed.
The reads were aligned to the S. avermitilis genome (BA000030) with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
The 3' end position of Term-Seq reads located within intergenic regions including up to 10 bp downstream to gene were regarded as potential transcription termination sites (TTS). The positions were clustered together based on the distance from adjacent positions (< 10 bp). Within each cluster, the read count of each position was assumed to follow normal distribution and read count enriched positions were deduced by calculating modified z-score. Z(x)=(r(x)-μ(r(x)))/(σ(x)), where, μ(r(x))=1/(N(x)-1)(-r(x)+∑_(y∈C(x))▒r(y) ), σ(x)=√(μ(〖r(x)〗^2 )-〖μ(r(x))〗^2 ). Z(x) is modified z-score at position x, r(x) is the read count of evaluated position x. μ(r(x)) and σ(x) is the mean and standard deviation of read counts of other positions in the cluster except the evaluated position, respectively. N(x) is the length of the cluster containing position x and C(x) is the set of positions within the cluster containing position x. The positions with read count less than 3 or modified z-score less than 3 were discarded. All the procedures above were conducted separately for each biological replicate. Among the remaining potential TTSs, the reproducible positions with the highest read count within the intersecting region of clusters from two biological replicate was selected as TTS. For example, if genomic positions from 3 to 25 were clustered together for one replicate and genomic positions from 13 to 42 were clustered together for another replicate, potential TTS with highest read count within the genomic positions from 13 to 25 was selected as TTS.
Genome_build: BA000030
Supplementary_files_format_and_content: tab-delimited text files include TSS, TTS or normalized expression values for each sample

extract_protocol:
Harvested cells were washed with polysome buffer (20 mM Tris-HCl pH 7.5, 140 mM NaCl, 5 mM MgCl2), and then resuspended with lysis buffer (0.3 M sodium acetate pH 5.2, 10 mM EDTA, 1% Triton X-100). The cell suspension was then frozen with liquid nitrogen, and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and the supernatant was stored at -80 oC until used for RNA extraction. RNA was extracted by mixing with equal volume of phenol:chloroform:isoamyl alcohol = 25:24:1 solution. The mixture was then centrifuged and upper aqueous phase was recovered. The RNA was purified with ethanol precipitation. The purified RNA was treated with DNase I (New England Biolabs) to remove any genomic DNA contamination. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer's instructions.
About 700 ng of rRNA-depleted RNA was incubated in 1x RNA 5' polyphosphatase (TAP) (Epicentre) reaction buffer and 1 U of SUPERase-In (Invitrogen) at 37 oC for 1 hour without TAP. After ethanol precipitation, 5 pmol of 5' RNA adaptor (5'-ACACUCUUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated to the purified RNA with T4 RNA ligase (Thermo) in 1x RNA ligase buffer and 0.1 mg/mL BSA by incubating at 37 oC for 90 minutes. The adaptor-ligated RNA was then purified using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The purified product was reverse-transcribed using SuperScript III Reverse Transcriptase (Invitrogen) and purified using Agencourt AMPure XP beads. The purified cDNA was amplified and indexed using Phusion High-Fidelity DNA Polymerase (Thermo) for the Illumina sequencing. The amplification step was monitored on a CFX96 Real-Time PCR Detection System (Bio-Rad) to be stopped before the PCR reaction was fully saturated. Finally, the amplified library was purified using Agencourt AMPure XP beads, and the concentration of the library was measured with Qubit 2.0 fluorometer (Invitrogen). The size distribution of the library was checked with gel electrophoresis on 2% agarose gel.


title: scc1_73 top2-td 80 min spiked H2A rep1


title: Term1

description:
Sample 5
Term.txt


title: 6h: control1

value: 10 weeks old


title: Cow 07 BASAL embryo #2 EX


title: 6h: laser1


title: Cow 813 BASAL embryo #4 EX

value: female


title: 6h: bur1


title: scc1_73 top2-td 80 min spiked yH2A rep1


title: top2-td 120 min spiked input rep2

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)  pRS316


title: top2-td 120 min spiked yH2A rep2


title: top2-td 120 min spiked yH2A rep1


title: TSS_TAP_treated2

description:
Sample 2
TSS.txt

extract_protocol:
Harvested cells were washed with polysome buffer (20 mM Tris-HCl pH 7.5, 140 mM NaCl, 5 mM MgCl2), and then resuspended with lysis buffer (0.3 M sodium acetate pH 5.2, 10 mM EDTA, 1% Triton X-100). The cell suspension was then frozen with liquid nitrogen, and lysed by grinding using mortar and pestle. The cell lysate was centrifuged at 4 oC for 10 minutes at 16,000 g and the supernatant was stored at -80 oC until used for RNA extraction. RNA was extracted by mixing with equal volume of phenol:chloroform:isoamyl alcohol = 25:24:1 solution. The mixture was then centrifuged and upper aqueous phase was recovered. The RNA was purified with ethanol precipitation. The purified RNA was treated with DNase I (New England Biolabs) to remove any genomic DNA contamination. Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) according to the manufacturer's instructions.
About 700 ng of rRNA-depleted RNA was incubated in 1x RNA 5' polyphosphatase (TAP) (Epicentre) reaction buffer and 1 U of SUPERase-In (Invitrogen) at 37 oC for 1 hour with 1 U of TAP. After ethanol precipitation, 5 pmol of 5' RNA adaptor (5'-ACACUCUUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated to the purified RNA with T4 RNA ligase (Thermo) in 1x RNA ligase buffer and 0.1 mg/mL BSA by incubating at 37 oC for 90 minutes. The adaptor-ligated RNA was then purified using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The purified product was reverse-transcribed using SuperScript III Reverse Transcriptase (Invitrogen) and purified using Agencourt AMPure XP beads. The purified cDNA was amplified and indexed using Phusion High-Fidelity DNA Polymerase (Thermo) for the Illumina sequencing. The amplification step was monitored on a CFX96 Real-Time PCR Detection System (Bio-Rad) to be stopped before the PCR reaction was fully saturated. Finally, the amplified library was purified using Agencourt AMPure XP beads, and the concentration of the library was measured with Qubit 2.0 fluorometer (Invitrogen). The size distribution of the library was checked with gel electrophoresis on 2% agarose gel.


title: Cow 12 BASAL embryo #4 EX

value: day 14 embryo


title: RNA_E1

description:
Sample 7
RNA_DESeq2.txt


title: top2-td 120 min spiked H2A rep1


title: Mtb6230_snc1#3

city: Dallas

first: Igor

middle: M

last: Dozmorov

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Raw data was processed with normalization method  based on the use of “internal standards”, that characterize some aspects of the system’s behavior, such as technical variability. The two-step normalization procedure and the Associative analysis functions are presented in our publications (Dozmorov, I. and I. Lefkovits, Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res, 2009. 37(19): p. 6323-39). These algorithms are also obtainable from an R package diffGeneAnalysis, available as a part of Bioconductor packages (http://www.bioconductor.org/packages/2.5/bioc/html/diffGeneAnalysis.html).
Genome_build: hg38
Supplementary_files_format_and_content: excel,expression profiles

organism: Mycobacterium tuberculosis

growth_protocol: Bacterial culture at stationary phase was used

extract_protocol:
Cells were lyzed in qiazol and bead beating was done
6 bacterial libraries were made using Epicentre bacteria kit according to the manufacturer's instructions. 1.3pM loading was done according to pico. Libraries were sequenced with Nextseq550 sequencing platform with primers such as 5´-AGTCAA-3´, 5´-AGTTCC-3´, 5´-ATGTCA-3´ for first three samples and 5´-CCGTCC-3´, 5´-GTAGAG-3´, 5´-GTCCGC-3´ for last three samples.

treatment_protocol: SncRNA-1  or ctl vector exogenously expressed

tag: strain background

tag: genotype/variation

value: sncRNA-1 vector

tag: cell type

value: bacterial cell culture


title: Cow 13 PA embryo #1 EX

value: extraembryonic tissue

value: HIGH PA


title: Mtb6230_snc1#2


title: top2-td 120 min spiked H2A rep2

tag: s. cerevisiae strain

tag: s. cerevisiae genotype

value: 120 min after alpha factor release


title: Cow 66 BASAL ebmryo #2 EX

value: ovoid


title: TSS_TAP_treated1

description:
Sample 1
TSS.txt


title: Cow 07 PA embryo #1 EX


title: Mtb6230_snc1#1


title: Cow 813 BASAL embryo #1 EX

value: BASAL


title: Cow 07 PA embryo #3 EX


title: top2-td 120 min spiked input rep1

tag: s. pombe strain

tag: s. pombe genotype

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1


title: Cow 72 PA embryo #1 EX


title: top2-td 80 min spiked yH2A rep2

value: 80 min after alpha factor release

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: top2-td 80 min spiked H2A rep2


title: top2-td 80 min spiked input rep2


title: Cow 25 BASAL embryo #1 EX

value: tubular


title: Mtb6230_ctl#3

value: control


title: Mtb6230_ctl#2


title: Mtb6230_ctl#1


title: top2-td 80 min spiked yH2A rep1


title: stage4_SAM rep3

city: cologne

first: Udhaya

last: Ponraj

state: NRW

department: Department of chromosome biology

country: Germany

institute: Max Planck Institute for Plant Breeding research

description: 1X150 bp single end

data_processing:
NGS analysis package: CLC genomics server 9.1.1 was used for processing and mapping reads. Data was further analysed using CLC genomics workbench 12.0
data-filtering: FASTQC was used to assess quality of reads. CLC genomics server was used to trim low quality sequences and ambiguous nucleotides using following parameters- Ambiguous trim = Yes, Ambiguous limit = 2, Quality trim = Yes, Quality limit = 0.05
read mapping: Reads were mapped to the latest annotation of the Arabis alpina genome V5 with the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Maximum number of hits for a read = 10.
adundance measurement: reads counts were normalised for differences in gene and library size using RPKM
differential expression analysis: Fold change between the two developmental stages of buds was calculated in CLC genomics workbench. The resulting candidate list was filtered for genes with statistically significant difference in expression of atleast two-fold at FDR adjusted p-value <0.05
Genome_build: Arabis alpina genome http://arabis-alpina.org/refseq.html/Arabis_alpina.MPIPZ.V5.chr.all.fasta.gz
Supplementary_files_format_and_content: excel file including geneIds, total mapped reads, normalised counts RPKM, TPM, CPM, average counts, DE test results including Fold Chnage, logFold change, FDR

organism: Arabis alpina

source_name: Shoot apical meristem

growth_protocol: All the experiments were performed using A. alpina Pajares accession (Wang et al., 2009). A. alpina seeds were stratified on wet filter paper for 4 days at 4°C in dark and then transferred to soil in a Bronson growth chamber (LD) with day-time temperature of 24°C and a night-time temperature of 18°C. Cold treatments were performed at 4°C in LD condition (16h light, 8h darkness) for seven weeks. Young buds with single leaf primordium and their corresponding shoot apical meristem including one leaf primordium were harvested. For each sample three biological replicates were prepared except for stage1_AB (two replicates). 120-150 buds and SAMs were harvested per replicate.

extract_protocol:
Total RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma Aldrich), following protocol A and on-column DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Pajares

value: Shoot apical meristem

value: after seven weeks of cold treatment


title: Cow 813 CONTROL embryo #1 ED

value: embryonic disc

value: CONTROL

value: male


title: Cow 813 CONTROL embryo #2 ED

value: day 14 embryo


title: top2-td 80 min spiked H2A rep1

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  top2-td TOP2 5’ upstream -100 to -1 replaced with kanMX-tTA (tetR-VP16)-tetO2  - Ub - DHFRL80P-ts - Myc -linker)  pRS316


title: Cow 66 BASAL embryo #2 ED


title: Cow 07 BASAL embryo #2 ED


title: stage4_SAM rep2

description: 1X150 bp single end


title: stage3_SAM rep3

description: 1X150 bp single end

value: after four weeks of cold treatment


title: stage4_SAM rep1

description: 1X150 bp single end


title: top2-td 80 min spiked input rep1


title: degron background wt 120 min spiked yH2A rep2

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  pRS316

value: 120 min after alpha factor release


title: degron background wt 120 min spiked H2A rep2


title: stage3_SAM rep2

description: 1X150 bp single end


title: 5 Control mouse [blood]

city: morgantown

middle: A

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

institute: CDC/NIOSH

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled on to the microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). For both mRNA and lncRNA - All Targets Value (Entities where at least 5 out of 10 samples have flags in Present or Marginal)Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.1).

label_protocol: Mouse LncRNA Microarray V3.0, designed by ArrayStar Inc, was employed to perform global profiling of mouse protein-coding (~24,881) transcripts. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was extracted from whole blood using the PAXgene™ Blood RNA System Kit following manufacturer's guidelines. Briefly, the samples were removed from -80°C and incubated at room temperature for 2 hours to ensure complete lysis. After that the tubes were centrifuged for 10 min at 5000 g, the supernatant decanted and 500 μL of RNase-free water added to the pellet. After washing with RNase-free water, the pellet was dissolved in 350 μl resuspension buffer and incubated with 300 μl binding buffer and 40 μl proteinase K for 10 min at 55°C in a shaker-incubator. The lysate was transferred into a PAXgene shredder spin column and centrifuged (18000 g for 3 min). The flow-through fraction was mixed with 350 μl ethanol and transferred to a PAXgene RNA spin column. After washing the column with washing buffer 1, samples were incubated with 10 μl of DNase I for 15 min. The columns were washed with washing buffer and RNA eluted with 40 μl elution buffer. The RNA yield was estimated by measuring absorbance at 260 nm in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA purity was calculated from the ratio of absorbance at 260 nm and 280 nm, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: strain

value: female

tag: age

value: 3 months

value: vehicle control

value: whole blood


title: stage3_SAM rep1

description: 1X150 bp single end


title: 3 Control mouse [blood]


title: 4 Control mouse [blood]


title: Cow 813 BASAL embryo #4 ED

tag: individual

value: BASAL

tag: morphology

value: tubular


title: 2 Control mouse [blood]

tag: Sex

tag: tissue


title: degron background wt 120 min spiked input rep2

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1

tag: time

tag: chip antibody


title: degron background wt 120 min spiked yH2A rep1

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: 1 Control mouse [blood]

tag: treatment


title: 4 Mouse exposed to 40 µg of MWCNT [blood]

value: 40 µg of MWCNT


title: 5 Mouse exposed to 40 µg of MWCNT [blood]


title: 1 Mouse exposed to 40 µg of MWCNT [blood]


title: 3 Mouse exposed to 40 µg of MWCNT [blood]


title: 2 Mouse exposed to 40 µg of MWCNT [blood]


title: stage2_SAM rep3

description: 1X150 bp single end

value: Pajares

value: Shoot apical meristem

tag: developmental stage

value: eight weeks old plant


title: Cow 12 BASAL embryo #4 ED

value: embryonic disc

value: day 14 embryo

value: male


title: stage2_SAM rep2

description: 1X150 bp single end


title: Cow 13 PA embryo #1 ED

value: HIGH PA


title: Cow 813 BASAL embryo #1 ED


title: Cow 07 PA embryo #1 ED

value: ovoid


title: Cow 07 PA embryo #3 ED


title: degron background wt 120 min spiked input rep1

value: Mat a ade2-1 his3-11 leu2-3  trp1-1 ura3-1 can1-100  UBR1::GAL1-10-Ubiquitin-M-LacI   fragment-Myc-UBR1 (HIS3)  leu2-3::pCM244 (CMVp-tetR’-SSN6, LEU2) x3  pRS316

value: 120 min after alpha factor release


title: degron background wt 120 min spiked H2A rep1


title: degron background wt 80 min spiked H2A rep2

value: 80 min after alpha factor release


title: stage1_SAM rep2

description: 1X150 bp single end

value: four weeks old plant


title: stage1_SAM rep1

description: 1X150 bp single end


title: stage1_SAM rep3

description: 1X150 bp single end


title: stage2_SAM rep1

description: 1X150 bp single end


title: stage4_AB rep3

description: 1X150 bp single end

source_name: Axillary bud

value: Axillary bud

value: after seven weeks of cold treatment


title: Cow 72 BASAL embryo #2 ED

value: BASAL

value: tubular


title: degron background wt 80 min spiked H2A rep1

value: h-urg1::Purg1lox-HO, LEU-HOcs-his3+-λ-EU2, leu1-32, his3-D1


title: Cow 12 BASAL embryo #2 ED

value: female


title: stage4_AB rep2

description: 1X150 bp single end

value: Pajares


title: degron background wt 80 min spiked yH2A rep1

value: yH2A (1.6 μg/ml final concentration, Abcam, ab181447)


title: degron background wt 80 min spiked input rep2


title: Cow 813 CONTROL embryo #4 ED

value: embryonic disc

value: CONTROL