title: WT_8h

source_name: wild-type small RNAs @8 hpm

value: wild-type B2086 x CU428


title: CL1-Cal_coDel_Cross1_3h

status: Public on May 15 2018

type: SRA

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

library_source: transcriptomic

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012; Noto et al. 2015). Briefly, following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Genome_build: Tetrahymena thermophila MIC genome assembly released in 2016 was used for mapping. All information about MIC chromosome, including the Chr5, were obtained from http://ciliate.org/index.php/home/downloads/2016_mic.genome.fasta
Supplementary_files_format_and_content: Sequenced 26 to 32 nt RNAs that map uniquely to the sense and antisense strands of the 30 kb CL1 locus, 30 kb M locus, and the whole MIC chromosome 5 (Chr5) are counted, and normalized numbers (reads per million reads [RPM] for the CL1 and M loci and reads per kb per million reads [RPKM] for the Chr5) are shown in histograms with 100 nt and 50 kb bins, respectively.
Chromosome coordinates used in processed data files:
CL1: 16473376 to 16503399 of the MIC Chr2
M: 15091812 to 15121604 of the MIC Chr4
R3-R4: 15117953 to 15147831 of the MIC Chr4
note: CL1-Cal and CL1 are the same region
Bins are named with bp count (e.g. 50, 100, 150, etc for 50kb bins) indicating that 'bin 50' includes first base in region to +50.  For example:  in file 10508_CL1_Hist.txt, Bin 50 = MIC  Chr2:16473376-16473426.

molecule: total RNA

organism: Tetrahymena thermophila

source_name: CL1-Cal_coDel @3 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight.

extract_protocol:
Total RNA was extracted with TRIzol reagent . 1 mL of Trizol reagent was used to lyse1x10e6 cells.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

treatment_protocol: To induce conjugation, exponentially growing cells (~3-5x 10e5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 10e5/ml) at 30°C.

tag: strain

value: Deletion @ CL1-Cal locus in MAC


title: N001_F_sRNA_R3

city: Pamplona

first: Raul

last: Castanera

address: Campus Arrosadia, DPTO Producción Agraria

country: Spain

institute: Public University of Navarre

data_processing:
SRNA-seq: Small RNA (sRNA) raw reads were first processed to trim the adapter sequence and filter by size (17 to 30 nt) using BBduk software. Reads mapping to a custom database of ribosomal RNA (rRNA) and transfer RNA (tRNA) were also removed. The remaining sRNA reads were mapped to the reference genome using Butter 0.3.2
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq

organism: Pleurotus ostreatus

source_name: N001 dikaryotic strain (fruitbody)

extract_protocol:
Total RNA isolation for mRNA (mRNA-seq) and small RNA (sRNA-seq) sequencing was performed using a Fungal RNA E.Z.N.A Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer’s guidelines. Genomic DNA (gDNA) from the fungal samples was extracted using an E.Z.N.A Fungal DNA Mini Kit (Omega Bio-Tek, Norcross, GA)
Library preparation was performed using the Illumina TruSeq DNA Sample Prep  according to the manufacturer’s instruction

tag: tissue

value: Fruitbody


title: CL1+BTU1_Cross1_8h

source_name: CL1+BTU1 cells small RNAs @8 hpm

value: CL1 IES @ BTU1 locus in MAC


title: TWI11_cKO_Cross2_3h

source_name: TWI11 MAC+MIC KO E9xE10 @3 hpm

value: TWI11 MAC+MIC KO


title: N001_P_Bsseq.R2

library_source: genomic

data_processing:
Bs-seq:  Raw reads from bisulfite treatment were checked for quality using FastQC and aligned to the reference genome (PC15 v2.0) using the BS-Seeker2 pipeline
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq

molecule: genomic DNA

source_name: N001 dikaryotic strain (primordium)

value: Primordium


title: TWI11_cKO_Cross1_3h

source_name: TWI11 MAC+MIC KO E1xE2 @3 hpm


title: N001_P_Bsseq.R1


title: M+BTU1_Cross2_3h

source_name: M+BTU1 cells small RNAs @3 hpm

value: M IES @ BTU1 locus in MAC


title: liuqianxinA-liuqianxinB-1

city: Yangzhou

first: Chen

last: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

country: China

institute: Yangzhou University

data_processing:
Raw reads were processed using the Trimmomatic v0.32 package to remove adaptors and discard low quality reads.
The paired-end reads were aligned to the rice reference genome (MSU) by Bowtie 2  (Version: 2.2.1) with default parameters.
Aligned reads were firstly filtered by mapping quality -q 20 using samtools (Version: 0.1.16). GATK (Version: 3.5) was used to process aligned reads and call SNPs. SNPs coverage>10 were qualified to be candidate for further analysis.
Imprinted genes were identified by calculating the ratio of maternal to paternal reads at each SNP site that deviated from the expected 2:1 ratio using χ2 tests.
Supplementary_files_format_and_content: abundance measurements of imprinted genes of two interspecific crosses of rice

organism: Oryza sativa

source_name: endosperm (5 DAF)

growth_protocol: Wufeng-A and -B, Rongfeng-A and -B, Liuqianxin-A and -B, Yu6-A and -B, and wild rice were grown in Nanchang, Jiangxi Province, China. The RL-LR and WY-YW reciprocal crosses were performed in the summer of 2014. Plants were grown in a paddy field under regular conditions. The ovary donors were emasculated before flowering and moved to a growth chamber on a 14 h/10 h light-dark cycle at 30°C.

extract_protocol:
At 5 DAF, the endosperm was carefully collected with a pipette to avoid maternal tissue contamination per the method used by Luo et al. (2011). Two (WY-YW) or three (LR-RL) replicates were used for mining of imprinted genes. Each replicate was pooled with 20–30 endosperm.  RNA was extracted from endosperm or seedlings using a Plant RNA Kit (OMEGA) and treated with RNA-free DNase set (OMEGA) to remove DNA contamination per the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: hybrid

value: liuqianxinA-liuqianxinB

value: endosperm of intraspecific hybrids

tag: developmental stage

value: 5 days after fertilization


title: PAwt_whole_culture_mid_log_phase_planktonic_4h_2

type: RNA

city: Ottawa

first: Patrick

middle: Kyle

last: Taylor

state: Ontario

address: 4125 Roger Guindon Hall 451 Smyth Rd

department: Biochemistry, Microbiology, and Immunology

country: Canada

institute: University of Ottawa

hyb_protocol: Samples were shipped out and labelling protocol was carried out by Genome Quebec Innovation Centre at McGill University

data_processing: GCRMA method performed using Microarray Suite 5.0. ANOVA was used to determine significance (> 2-fold).

label: biotin

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: whole culture, planktonic growth, 4h with shaking, 37C

growth_protocol: Grown overnight at 37C in LB medium on a shaker before being sub-cultured for either biofilm or planktonic growth used for collecting samples.

extract_protocol: Trizol/phenol/chloroform extraction used to isolate total RNA from cultures. RNA then purified using commercial kits from Ambion.

tag: genotype/variation

value: wild type

tag: growth type

value: planktonic growth


title: PAwt_whole_culture_mid_log_phase_planktonic_4h_1

scan_protocol: Samples were shipped out and labelling protocol was carried out by Genome Quebec Innovation Centre at McGill University


title: M+F4_Cross2_3h

source_name: M+F4 cells small RNAs @3 hpm

value: M IES in MAC


title: M+F1_Cross2_3h

source_name: M+F1 cells small RNAs @3 hpm


title: N001_P_sRNA_R2


title: N001_P_sRNA_R3


title: M+F4_Cross1_3h


title: M+F1_Cross1_3h


title: PAwt_whole_culture_colony_biofilm_48h_2

source_name: whole culture, colony biofilm, 48h static growth, 37C 24h, room temp 24h

label_protocol: Samples were shipped out and labelling protocol was carried out by Genome Quebec Innovation Centre at McGill University

value: colony biofilm


title: N001_F_polyA_R3

data_processing:
mRNAseq: RNA-seq data were filtered for quality using FastQC and trimmed with BBDuk from the BBMap package (https://sourceforge.net/projects/bbmap/) 5 to remove sequences of adapters and low-quality reads. The resulting reads were aligned to the reference genome assembly using STAR v2.3.16 restricted to single hit mapping using the following parameters: --outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 1
Genome_build: https://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=PleosPC15_2
Supplementary_files_format_and_content: files include read count values for sRNA,  RPKM values for mRNA and methylation levels (0 to 1) for BS-seq

molecule: polyA RNA


title: CL1-Cal_coDel_Cross2_3h


title: N001_F_polyA_R1


title: N001_P_polyA_R3


title: tctED_whole_culture_mid_log_phase_planktonic_4h_2

value: tctED deletion


title: CL1+F4_Cross1_3h

source_name: CL1+F4 cells small RNAs @3 hpm

value: CL1 IES in MAC


title: CL1+F4_Cross2_3h


title: N001_P_polyA_R2


title: PAwt_whole_culture_colony_biofilm_48h_1


title: tctED_whole_culture_colony_biofilm_48h_2


title: tctED_whole_culture_colony_biofilm_48h_1


title: N001_M_Bsseq.R3

source_name: N001 dikaryotic strain (mycelium)

value: mycelium


title: CL1+F1_Cross2_3h

source_name: CL1+F1 cells small RNAs @3 hpm


title: N001_M_Bsseq.R2


title: N001_M_Bsseq.R1


title: M+_Cross2_12h

source_name: M+ cells small RNAs @12 hpm

value: M IES @ rDNA locus in MAC


title: N001_P_polyA_R1


title: N001_P_sRNA_R1


title: tctED_whole_culture_mid_log_phase_planktonic_4h_1


title: N001_M_sRNA_R3


title: N001_M_sRNA_R2


title: M+_Cross2_8h

source_name: M+ cells small RNAs @8 hpm


title: M+_Cross1_8h


title: N001_M_sRNA_R1


title: M+_Cross2_3h

source_name: M+ cells small RNAs @3 hpm


title: N001_M_polyA_R3


title: OVPool_3

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

country: USA

institute: leslie cope

data_processing:
RNA sequences were aligned to the NCBI human genome build 37 using STAR aligner (v2.3.1z).
Quantification of genes annotated in Gencode (version 18) was performed using featureCounts (v1.4.3).
DESeq2 (doi:10.1101/002832) was used to normalize feature counts.
Picard and RSeQC 50 was used to collect QC metrics (http://broadinstitute.github.io/picard/)
Genome_build: NCBI human genome build 37
Supplementary_files_format_and_content: Tab delimited text file containing Gene ID, Gene Name and counts

organism: Homo sapiens

source_name: normal ovarian tissue pool

extract_protocol:
RNA was isolated from fresh brushings,  utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.).   RNA quality was assessed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.  Briefly, 500ng of total RNA was purified by Ribo-Zero to remove rRNA and fragmented by divalent cations under elevated temperature. The fragmented RNA underwent first strand synthesis using reverse transcriptase and random primers.  Second strand synthesis created the cDNA fragments using DNA polymerase I and RNaseH.   The cDNA fragments then went through end repair, adenylation of the 3’ ends, and ligation of adapters.  The cDNA library was enriched using 10 cycles of PCR and purified.

value: normal ovarian surface brushings

tag: stic

value: No

tag: age

tag: platinumstatus

tag: recurrence

tag: vitalstatus

tag: race


title: OVPool_4


title: M+_Cross1_3h


title: OVPool_2


title: N001_M_polyA_R2


title: N001_M_polyA_R1


title: CL1+_Cross1_12h

source_name: CL1+ cells small RNAs @12 hpm

value: CL1 IES @ rDNA locus in MAC


title: CL1+_Cross2_12h


title: N001_HyB_Bsseq.R3

source_name: Dikaryon resulting from PC9 + PC15 mating


title: CL1+F1_Cross1_3h


title: PerPool_3

source_name: normal peritoneal tissue pool

value: normal peritoneal brushings


title: CL1+_Cross2_8h

source_name: CL1+ cells small RNAs @8 hpm


title: PerPool_2


title: PerPool_1


title: M+_Cross1_12h


title: N001_HyB_Bsseq.R2


title: CL1+_Cross1_8h


title: N001_HyB_Bsseq.R1


title: N001_HyB_sRNA_R3


title: FTPool_2

source_name: normal fallopian tube tissue pool

value: normal fallopian tube brushings


title: FTPool_3


title: N001_HyB_sRNA_R2


title: CL1+_Cross2_3h

source_name: CL1+ cells small RNAs @3 hpm


title: CL1+_Cross1_3h


title: FTPool_1


title: N001_HyB_sRNA_R1


title: WT_12h

source_name: wild-type small RNAs @12 hpm

value: wild-type B2086 x CU428


title: WT_3h

source_name: wild-type small RNAs @3 hpm


title: OVPool_1


title: Tim-4+CD4+ small intestine macrophages  - replicate 4 from 3 pooled mice

city: Manchester

first: Tovah

middle: N

last: Shaw

address: 46 Grafton Street

department: Division of Infection, Immunity and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

data_processing:
Bcl2fastq 2.17.1.14
Trimmomatic 0.36
star 2.5.3
Htseq-count 0.6.1p1
DESeq2
Genome_build: GRCm38.p4,gencode.vM11.annotation.gtf
Supplementary_files_format_and_content: raw counts and normalised counts(xls)

organism: Mus musculus

source_name: small intestine

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting (FACS) from the small intestine or peripheral blood of 3-4 pooled adult wild type C57/BL6 mice. Cells were sorted directly into RLT buffer (Qiagen) and stored on dry ice before storage at -80oC for subsequent RNA extraction. RNA was extracted from 120,000 – 200,000 cells using an RNeasy micro kit (Qiagen) following manufacturer’s instructions.
Strand-specific RNA-seq libraries were prepared using the Illumina workflow with the TruSeq® Stranded mRNA Sample Preparation Kit.

tag: cell type

value: Tim-4+CD4+ small intestine macrophages

value: small intestine

tag: Sex

value: male


title: N001_HyB_polyA_R2


title: InDrop_HMLE_TGFbeta_day10

city: New Haven

first: David

last: van Dijk

state: CT

address: 333 Cedar street

department: Genetics, Computer Science

institute: Yale University

description: processed data file: HMLE_TGFb.tsv.gz

data_processing:
ATAC-seq processing using Trimmomatic v0.36, bowtie2, MAPQ, samtools, MACS2, FIMO
InDrop single cell RNA-seq processing using SEQC v0.1.8rc3
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq peaks; ATACseq_peaks_motifs_meta.txt with column header information; Count matrices; cb*.txt with indrop barcodes

source_name: HMLE breast cancer cell line

growth_protocol: HMLE and all derived cell lines used in this work were cultured in MEGM (Mammary Epithelial Cell Growth Medium) media (Lonza, USA, CC-3051). Cells were cultured in round tissue culture dishes 10cm in diameter (Corning, USA) and split to a ratio of 1:7 every 2 to 3 days or once they reached 80% confluence on a plate. All cell dissociations were performed using TrypLE™ (Ambion, USA) reagent. For the ATAC-seq HMLE cells were induced with TGF-beta (5 ng/mL, replenished every day) and grown for 8 days. TGF-beta induced HMLE cells were removed from the cell culture plate with TrypLE treatment, washed twice in 1X PBS buffer, and stained with DAPI dye and Anti-Human/Mouse CD44 (PE-Cyanine 7) antibody. The stained cells were then analyzed by flow cytometry and the top 3% (n=48,000) CD44 positive cells (mesenchymal population) were FACS sorted into a collection tube. Sorted-cells were then processed according to ATAC-Seq protocol(Buenrostro et al., 2013).

extract_protocol:
All cell dissociations were performed using TrypLE™ (Ambion, USA) reagent.
scRNA-seq libraries were constructed following the InDrop protocol(Klein et al., 2015). ATAC-Seq was done following (Buenrostro et al., 2013).

treatment_protocol: EMT was induced by addition of Recombinant Human TGF-β1 (HEK293 cell derived) (PeproTech, USA 100-21) to a final concentration of 5ng/ml. EMT was also induced by overexpression of Zeb1 transcription factor. HMLE cells transfected with FUW plasmid, a tetracycline operator, and minimal CMV promoter(Brambrink et al., 2008) were used and Zeb1 gene overexpression was induced by addition of doxycycline (Sigma, D3447) to a final concentration of 1g/ml. All cells under induction were passaged once they reached 80% confluence.

tag: cell line

value: HMLE

value: breast cancer cell line

tag: cell status

value: TGFbeta induced EMT


title: InDrop_Zeb1_Dox

value: Zeb1 induced EMT


title: ATACseq_HMLE_TGFbeta


title: InDrop_HMLE_TGFbeta_day8

description: processed data file: HMLE_TGFb.tsv.gz


title: PC9_Bsseq.R3

source_name: PC9 monokaryotic strain


title: N001_HyB_polyA_R1


title: PC9_Bsseq.R2


title: Uninjected rep3

city: New York

first: Philipp

last: Niethammer

state: NY

address: 430 East 67th street

institute: MSKCC

data_processing:
The output data (FASTQ files) were mapped to the zebrafish genome GCz10 (UCSC) using the rnaStar aligner that mapped reads genomically and resolved reads across splice junctions.
A two pass -mapping method was used in which the reads were mapped twice. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions, and a second mapping pass was done (on the second pass the RemoveNoncanoncial flag was used).
After mapping, the output SAM files were post processed using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorted the file and converted it to the compressed BAM format.
The expression count matrix was then computed from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq).
The raw count matrix generated by HTSeq were then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq), which was used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: GCz10 (UCSC)
Supplementary_files_format_and_content: xls, normalized gene counts for each sample. xlsx, differentially expressed (normalized counts log2 fold change >1) genes in HypoPA vs Uninjected and IsoPA vs Uninjected

organism: Danio rerio

source_name: whole larva

growth_protocol: Adult wt casper zebrafsih and larvae were maintained according to institutional animal helthcare guidelines with the approval of the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
After homogenization, total RNA was extracted using Trizol reagent (Life technologies) according to manufacturer`s protocol.
After Quant-It quantification and quality control of Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and Truseq library preparation according to instruction provided by TruSeq Stranded mRNA Library Prep Kit (Illumina).
Samples were barcoded and run on a Hiseq 2500 in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v4 (Illumina).  An average of 42 million paired reads was generated per sample.

treatment_protocol: Wt Pseudomonas aeruginosa (PA14) resuspended in either standard or isotonic E3 were injected into the otic vesicle of 2.5-3 dpf zebrafish larvae. Uninjected zebrafish larvae served as control. ~20 larvae from each group were euthanized 1 h after injection.

tag: treatment

value: uninfected

value: whole larva

value: wt casper

tag: Stage

value: 2.5-3 days post fertilization

tag: bathing condition

value: hypotonic


title: Uninjected rep1

tag: tissue

tag: strain


title: PC9_Bsseq.R1

value: mycelium


title: IsoPA rep2

value: Pseudomonas aeruginosa infection

value: isotonic


title: IsoPA rep3


title: Uninjected rep2


title: IsoPA rep1


title: PC9_sRNA_R3


title: HypoPA rep3


title: PC9_sRNA_R2


title: HypoPA rep2


title: N001_HyB_polyA_R3


title: HypoPA rep1


title: PC9_sRNA_R1


title: PC9_polyA_R3


title: PC9_polyA_R2


title: PC9_polyA_R1


title: MR1543 vs MR1545

city: Murcia

first: Montserrat

last: Elías-Arnanz

state: Please Select

address: Campus Espinardo

department: Departamento de Genética y Microbiología

institute: University of Murcia

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Myxococcus xanthus

source_name: Vegetative cells culture OD(600nm)=0.9

label_protocol: Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)

growth_protocol: M. xanthus cells were grown to an optical density at 550 nm of 1.0 in the rich casitone-Tris (CTT) medium supplemented with required antibiotic

extract_protocol: The total RNA was extracted using three cycles of hot phenol and liquid nitrogen followed by phenol:chloroform and a final step with chloroform. Then, it was ethanol-precipitated and resuspended in water. It was then treated with DNase (Roche) and purified using QIAGEN RNeasy kit following manufacturer's instructions for both treatments.

treatment_protocol: No treatment was applied

tag: genotype

value: delta-carG ddvA::Tn5-lac


title: yu6A-wufengB-2

source_name: endosperm (5 DAF)

tag: hybrid

value: endosperm of intraspecific hybrids

tag: developmental stage

value: 5 days after fertilization


title: SYY2352 scd6∆-rep2

city: Worcester

first: Feng

last: He

state: MA

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: University of Massachusetts Medical School

description: Experiment at time period I

data_processing:
RSEM program (Li and Dewey 2011) was used to map the sequence reads to the transcriptome and to quantify individual transcript levels with settings --bowtie-m 30 --no-bam-output --forward-prob 0.
The expected read counts for individual transcripts from RSEM were considered as the number of reads mapped to each transcript and were then imported into Bioconductor DESeq package (Anders and Huber 2010) for differential expression analysis.
Genome_build: R64-2-1 S288C sacCer3 genome assembly
Supplementary_files_format_and_content: Tab-delimited text files include the estimated read counts of individual transcripts in wild-type and scd6∆ cells

organism: Saccharomyces cerevisiae

growth_protocol: Cells were all grown in YEPD media at 30°C. In each case, cells (15 ml) were grown to an OD600 of 0.7 and harvested by centrifugation. Cell pellets were frozen on dry ice and then stored at -80°C until RNA isolation.

extract_protocol:
Total RNA was extracted from yeast cells using hot phenol.
Total RNA was treated with Baseline-zero DNase (Epicenter, cat# DB0711K) to remove any genomic DNA contamination. Five micrograms of DNase-treated total RNA was then depleted of rRNAs using the Illumina yeast RiboZero Removal Kit (cat# MRZY1306) and the resulting RNA was used for RNA-Seq library preparation. Multiplex strand-specific cDNA libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (cat# RS-122-2101).

tag: strain background

tag: genotype/variation


title: PC15_Bsseq.R3

source_name: PC15 monokaryotic strain


title: SYY2353 scd6∆-rep3

description: Experiment at time period I


title: SYY2352 scd6∆-rep1

description: Experiment at time period I


title: MR1543 vs MR1544

value: delta-carD ddvA::Tn5-lac


title: DK vs MR1545

value: WT


title: MR1545 vs MR1543


title: HFY114 WT-rep3

description: Experiment at time period I

value: Wild-type


title: HFY114 WT-rep2

description: Experiment at time period I


title: MR1545 vs DK


title: yu6A-wufengB-1


title: wufengAyu6B-2


title: MR1544 vs MR1543


title: PC15_Bsseq.R2


title: wufengAyu6B-1


title: HFY114 WT-rep1

description: Experiment at time period I


title: PC15_sRNA_R2


title: PC15_sRNA_R3


title: DK vs MR1544


title: PC15_sRNA_R1


title: PC15_polyA_R1


title: PC15_Bsseq.R1


title: SCI group-rep2

city: Beijing

first: Chuan

last: Qin

address: No.95,yong an road.

department: Department of Urology

institute: Beijing Friendship Hospital, Capital Medical University

description: circular RNA expression at 3 days post-SCI in the spianl cord of rats

hyb_protocol: Array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.).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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. Analyzed data are available on the series record in the file "GSE114426_Platform.xls".

organism: Rattus norvegicus

source_name: spinal cord, SCI group, 3days after surgery, replicate 2

label_protocol: Sample labeling were performed according to the manufacturer’s protocol (Arraystar Inc.). Cyanine-3 (Cy3) labeled cRNA was prepared.Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 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.

growth_protocol: Prior to the tissue collection, rats were then housed in individual cages with sterile sawdust as bedding on a 12-hour light/dark cycle under controlled atmospheric temperature and humidity. Animals were fed with free access to food and water. Penicillin (40000 U, intramuscular injection) was administered daily for 3 days to prevent systemic infection. The bladders were emptied manually every 8 hours until the rats were killed.

extract_protocol: Briefly, total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) based on the manufacturer’s instructions. After identifying the purity and concentration of total RNA from each sample with a NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), the integrity of RNA and gDNA contamination was tested using denaturing agarose gel electrophoresis.

treatment_protocol: Rats were anesthetized at 3 days post-surgery, and a 1-cm long segment of spinal cord, including the injury epicenter, was quickly dissected and collected without transcardial perfusion in advance and was then fresh frozen in liquid nitrogen to prevent RNA degradation

value: spinal cord

tag: gender and age

value: female

tag: age

value: 11 weeks

value: Sprague-Dawley


title: SCI group-rep3

source_name: spinal cord, SCI group, 3days after surgery, replicate 3


title: PC15_polyA_R2


title: KO3

status: Public on May 14 2018

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Knock Out replicate 3_RNAseq

data_processing:
Illumina RTA was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript.
The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file containing the normalized read counts

source_name: Knock Out replicate 3_RNAseq

extract_protocol:
Forebrains from Kif20a wild-type and knock-out E12.5 embryoes were collected and total RNAs were extracted using TRIzol.
poly(A) RNA was purified and library was constructed using Illumina's TruSeq RNA-seq kit following manufacturer's recommendation

value: Forebrain

value: Neural cell

value: Embryonic day 12.5


title: S93

city: Daejeon

first: Yoonkang

last: Hur

address: 99 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Chungnam National University

description: Wild type Brassica L. cv. Kenshim X RCBr F2 generation

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Brassica rapa

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: All plants was grown in a glasshouse (16 h light/8 h dark cycle) at 22~37℃. Each plant was grown in a pot (diameter 9.5 cm, height 9 cm) filled with soil (Pu-nong Co., Kyeongju, Korea) for 6-week-old after germination.

extract_protocol: Total RNA was extracted using Isol-RNA Lysis Reagent (5prime Inc., Gaithersburg, US) and purified by NucleoSpin RNA Clean-up kit(MACHEREY-NAGEL, Germany).

tag: phenotype

value: long leaf length & leaf width


description:
Conditional Knock Out replicate 1_RNAseq
ckoMT1

source_name: Forebrain

tag: cell type

value: Kif20a knock out


title: KO2

description: Knock Out replicate 2_RNAseq

source_name: Knock Out replicate 2_RNAseq


title: Cumulus liDNaseSeq Rep1

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
The single-end 100-bp reads generated from liDNase-seq were first trimmed of low quality and adapter sequences using trim_galore (v0.4.4). Then, we mapped the obtained reads to the mm9 reference genome using Bowtie1 (v0.12.9) with parameters ‘-v 3 -m 1 -S -t’. Unmapped and Multi-mapped reads were filtered using samtools (Li et al. 2009) (v1.3.1-38-g9df6321). PCR duplicates where removed using the MarkDuplicates command from Picard tools (v2.6.0). Next, for each replicate an initial list of DHS was generated using hotspot (John et al. 2011) (v4.1.0). The most reliable peaks between replicates were then selected using the IDR method (Li et al. 2011) , available at https://github.com/nboley/idr (v2.0.4), with a cutoff of IDR < 0.05.   Overlapping DHS detected in Cumulus, 1-Cell SNCT, paternal pronuclei and the SCNT+Aphidicolin samples were merged using the findOverlapsOfPeaks function of the R/Bioconductor package ChIPpeakAnno (Zhu et al. 2010). The number of reads mapping to each peak were calculated using the summarizeOverlaps function from the R/Bioconductor  GenomicAlignments  package (Lawrence et al. 2013)  then normalized to RPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: cumulus cells

growth_protocol: All animal studies were performed in accordance with guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. The mouse strain used in this study was B6D2F1/J (BDF1) (Jackson Laboratory, 100006)

extract_protocol:
MII oocytes were collected from superovulated 8-11 week-old BDF1 females.  Cumulus cells were removed from oocytes by treatment with 300 U/ml bovine testicular hyaluronidase (Calbiochem). MII oocytes were enucleated in HEPES-buffered KSOM containing 7.5 µg/ml cytochalasin B (CB) (Chalbiochem 250233). Nuclei of cumulus cells were injected into the enucleated oocytes using a Piezo-driven micromanipulator (Primetech). After 1 hr incubation in KSOM, SCNT oocytes were activated by Ca-free KSOM containing 3mM strontium chloride (SrCl2) and 5 µg/ml CB for 1 hr and further cultured in KSOM with CB for 4 hrs. At 5 hrs post-activation (hpa), embryos were washed in KSOM. To block DNA replication, embryos were transferred to KSOM containing 3 µg/ml aphidicolin (Sigma-Aldrich) at 4 hpars  until sample collection at 12 hpa
Low-input DNase-seq libraries were prepared as previously described (Inoue et al., 2017). Embryos or nuclei collected in 1.5 ml tubes were resuspended in 36 μl lysis buffer (10 mM Tris- HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Triton X-100) and incubated on ice for 5 min. DNase I (10 U/μl, Roche) was added to the final concentration of 80 U/ml (for the GV nucleus sample) or 40 U/ml (for all the other samples) and incubated at 37 °C exactly 5 min. The reaction was stopped by adding 80 μl Stop Buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.15% SDS, 10 mM EDTA) containing 2 μl Proteinase K (20 mg/ml, Life technologies). Then 20 ng of a circular carrier DNA [a pure plasmid DNA without any mammalian genes purified with 0.5x Beckman SPRIselect beads (Beckman Coulter) to remove small DNA fragments] was added. The mixture was incubated at 50 °C for 1 hr, then DNA was purified by extraction with phenol- chloroform and precipitated by ethanol in the presence of linear acrylamide (Life technologies) overnight at -20 °C. Precipitated DNA was resuspended in 50 μl TE (2.5 mM Tris, pH 7.6, 0.05 mM EDTA), and the entire volume was used for sequencing library construction Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufactures' instruction with the exception that the adaptor ligation was performed with 0.03 μM adaptor in the ligation reaction for 30 minutes at 20 °C and that PCR amplification was performed using Kapa Hifi hotstart readymix (Kapa Biosystems) for 8-cycles. The PCR products were purified with x1.3 volume of SPRIselect beads (Beckman Coulter) and then size selected with x0.65 volume followed by x0.7 volume of SPRIselect beads and eluted in 24 μl TE. The number of cycles for the second PCR amplification was measured by qPCR using 1 μl of the 1:1,000 diluted eluent. The remaining 23 μl of the samples was then amplified with Kapa Hifi hotstart readymix (we used 7 cycles for all samples in this study). The PCR product was purified with x1.3 volume of SPRIselect beads and then size selected with x0.65 volume followed by x0.7 volume of SPRIselect beads. The DNA was eluted in 30 μl of TE. The libraries were sequenced on a Hiseq2500 with single-end 100 bp reads (Illumina).

treatment_protocol: The procedures of SCNT using cumulus cells as donors were described previously (Matoba et al., 2011). Briefly, MII oocytes were collected from superovulated 8-11 week-old BDF1 females.  Cumulus cells were removed from oocytes by treatment with 300 U/ml bovine testicular hyaluronidase (Calbiochem). MII oocytes were enucleated in HEPES-buffered KSOM containing 7.5 µg/ml cytochalasin B (CB) (Chalbiochem 250233). Nuclei of cumulus cells were injected into the enucleated oocytes using a Piezo-driven micromanipulator (Primetech). After 1 hr incubation in KSOM, SCNT oocytes were activated by Ca-free KSOM containing 3mM strontium chloride (SrCl2) and 5 µg/ml CB for 1 hr and further cultured in KSOM with CB for 4 hrs. At 5 hrs post-activation (hpa), embryos were washed in KSOM. To block DNA replication, embryos were transferred to KSOM containing 3 µg/ml aphidicolin (Sigma-Aldrich) at 4 hpars  until sample collection at 12 hpa

tag: line

value: B6D2F1/J (BDF1)

value: 8-11 weeks


description:
Conditional Knock Out replicate 3_RNAseq
ckoMT3


description:
Conditional Knockout Wild Type Control replicate 2_RNAseq
ckoWT2

value: Wild Type


description:
Conditional Knockout Wild Type Control replicate 1_RNAseq
ckoWT1


description:
Conditional Knock Out replicate 2_RNAseq
ckoMT2


title: S100

source_name: Wild type Brassica L. cv. Kenshim X RCBr F2 generation

value: long petiole length


title: sham control-rep2

description: circular RNA expression at 3 days post- laminectomy in the spianl cord of rats

source_name: spinal cord, sham control, 3days after surgery, replicate 2


title: PC15_polyA_R3

value: mycelium


title: sham control-rep1

source_name: spinal cord, sham control, 3days after surgery, replicate 1


title: Cumulus liDNaseSeq Rep2


title: SCNT+Aphidicolin 1Cell liDNaseSeq Rep2

source_name: 1-Cell Aphidicolin treatedSCNT embryos


title: SCNT+Aphidicolin 1Cell liDNaseSeq Rep1


title: SCNT 1Cell liDNaseSeq Rep1

source_name: 1-Cell SCNT embryos


title: SCNT 1Cell liDNaseSeq Rep2


title: SCI group-rep1

source_name: spinal cord, SCI group, 3days after surgery, replicate 1


title: sham control-rep3

source_name: spinal cord, sham control, 3days after surgery, replicate 3


title: S33

value: short petiole length


title: RCBr

description: Wild type Brassica L. cv. Rapid-cycling Brassica rapa.

value: relatively small leaf size and lobed leaf margin


title: KO1

description: Knock Out replicate 1_RNAseq

source_name: Knock Out replicate 1_RNAseq


title: WT1

description: Wild Type replicate 1_RNAseq

source_name: Wild Type replicate 1_RNAseq


title: WT2

description: Wild Type replicate 2_RNAseq

source_name: Wild Type replicate 2_RNAseq


title: WT3

description: Wild Type replicate 3_RNAseq

source_name: Wild Type replicate 3_RNAseq


title: S19

value: Wild-type

value: lobed leaf margin


title: MR1544 vs DK

source_name: Vegetative cells culture OD(600nm)=0.9

value: delta-carD ddvA::Tn5-lac

value: WT


title: Schlap1 Replicate C

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

data_processing:
trim-galore (0.4.1) --nextera --paired
bowtie2 -X 2000
sed '/chrM/d'
samtools view -u -q 20
deeptools/2.5.2 bamCoverage --binSize 30 --normalizeUsingRPKM  --minFragmentLength 50 --maxFragmentLength 200
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files generated using deeptools

source_name: RWPE1 Prosate Cells

growth_protocol: Cells were grown in Keratinocyte serum free media supplemented with 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02

extract_protocol:
ATAC-seq was carried out as described (Buenrostro et al 2013)
ATAC-seq libraries were created using protocol from Buenrostro et al 2013, and processed using Nextera adapter sequences for Illumina sequencing

treatment_protocol: Cells were infected with lentivirus and selected in 2.5ug/mL blasticidin for at least 1 week.

tag: cell line

value: Prosate


title: Schlap1 Replicate B


title: Lacz Replicate B


title: Lacz Replicate C


title: Lacz Replicate A


title: Schlap1 Replicate A


title: Kenshim (dataset 2)

description: Wild type Brassica L. ssp. Pekinensis

source_name: Wild type Brassica L. ssp. Pekinensis

value: relatively big leaf size and entire leaf margin


title: H3

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: hepatocytes

data_processing:
Raw reads were aligned and quanitfied using a psuedoalignment algorithm from Kallisto to generate transcripts per million for each transcript across all samples.
Data were normalized using the DESeq algorithm, and each transcript baselined to the median across all samples.
Transcripts were filtered, requiring TPM > 3 in all samples of at least 1 experimental condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited with TPM and ensembl ID

source_name: hepatocytes

extract_protocol:
Hepatocyte-derived peripheral cholangiocytes and peripheral cholangiocytes were isolated by FACS from liver nonparenchymal cells, obtained by in situ collagenase perfusion followed by sequential digestion with collagenase, accutase and trypsin, and sorted directly into extraction buffer for RNA isolation using PicoPure RNA isolation kit (Thermo Fisher Scientific); hepatocytes were isolated by FACS after in situ collagenase perfusion and sorted directly into extraction buffer for RNA isolation using PicoPure RNA isolation kit.
Libraries were prepared using Low Input Library Prep Kit v2 (Clontech).

value: Mixed (C57BL/6, FVB, CD1)

value: Liver


title: H2

description: hepatocytes


title: H1

description: hepatocytes


title: pC3

description: peripheral cholangiocytes

source_name: peripheral cholangiocytes


title: HpC4

description: hepatocyte-derived peripheral cholangiocytes


title: HpC1


title: HpC3


title: HpC2


title: pC1

description: peripheral cholangiocytes


title: WT Spleen

first: Li

last: Qiang

address: 1150 St. Nicholas Ave. Room 607A

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [Trapnell C, et al., 2009 Bioinformatics] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [Trapnell C et al., 2010 Nature Biotech] (version 2.0.2) with default settings.
We test for differentially expressed genes under various conditions using DEseq [Anders S et al., 2010 Genome Biology]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: mm8

source_name: Spleen

extract_protocol:
Treg cells were sorted into TriZol and RNA was extracted by using microRneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: Treg

value: 12-13 month old


title: WT eWAT

source_name: eWAT

value: eWAT


title: 2KR Spleen


title: pC2

description: peripheral cholangiocytes


title: 2KR eWAT


title: W5000 RNA-seq

city: Bethesda

first: Derek

last: Gildea

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

description: F2 offspring from (TRAMP x WSB/EiJ) cross

data_processing:
Basecalling performed by CASAVA-1.8.2
The 17 5'-most bases and the 3'-most base were trimmed from all RNA-seq reads
RSEM (v 1.2.20) was used to perform RNA-seq read mapping (calling Bowtie2 v. 2.2.5) and counting. RNA-seq reads were mapped to Ensembl transcripts (release 81).
Genome_build: GRCm38
Supplementary_files_format_and_content: rnaseq_tpm_counts.txt: tab-delimied text matrix of RNA-seq normalized RNA-seq read counts (TPM) for transgene positive samples.

source_name: prostate tumor tissue

extract_protocol:
total RNA was extracted from snap frozen (TRAMP x WSB/EiJ) F2 bulk tumor samples using TRIzol Reagent (Life Technologies, Inc.) according to the manufacturer’s protocol, and purified using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocol.
RNA-Seq libraries were constructed from 1 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions. The cDNAs were fragmented to ~275 bp using a Covaris E210. Libraries were  pooled together for sequencing. The pooled libraries were sequenced on multiple lanes of a HiSeq 2500 using version 4 chemistry to achieve a minimum of 43 million 126 base read pairs

tag: mouse breeding

value: (TRAMP x WSB/EiJ) F2

value: Transgene positive


title: W462 RNA-seq


title: W1796 RNA-seq


title: W4182 RNA-seq


title: W4392 RNA-seq


title: W4356 RNA-seq


title: W5001 RNA-seq


title: W5005 RNA-seq


title: W992 RNA-seq


title: W5003 RNA-seq


title: W4162 RNA-seq


title: W5002 RNA-seq


title: W1103 RNA-seq


title: W1702 RNA-seq


title: W5004 RNA-seq


title: W4417 RNA-seq


title: W4202 RNA-seq


title: W407 RNA-seq


title: W1065 RNA-seq


title: W4180 RNA-seq


title: W4362 RNA-seq


title: W4350 RNA-seq


title: W4219 RNA-seq


title: W4378 RNA-seq


title: W244 RNA-seq


title: W4517 RNA-seq


title: W4381 RNA-seq


title: W1182 RNA-seq


title: W4376 RNA-seq


title: W4414 RNA-seq


title: W4394 RNA-seq


title: W4421 RNA-seq


title: W4120 RNA-seq


title: W242 RNA-seq


title: W4064 RNA-seq


title: W4492 RNA-seq


title: W4386 RNA-seq


title: W4363 RNA-seq


title: W4360 RNA-seq


title: W4427 RNA-seq


title: W4076 RNA-seq


title: W4063 RNA-seq


title: W4181 RNA-seq


title: W4179 RNA-seq


title: W4125 RNA-seq


title: W4078 RNA-seq


title: W4065 RNA-seq


title: W4079 RNA-seq


title: W4292 RNA-seq


title: W4351 RNA-seq


title: W4178 RNA-seq


title: W4072 RNA-seq


title: W4077 RNA-seq


title: W4126 RNA-seq


title: W78022 RNA-seq


title: W1514 RNA-seq


title: W4173 RNA-seq


title: W4403 RNA-seq


title: W4419 RNA-seq


title: W4397 RNA-seq


title: W4216 RNA-seq


title: W4288 RNA-seq


title: W4226 RNA-seq


title: W353 RNA-seq


title: W1790 RNA-seq


title: W4379 RNA-seq


title: W4509 RNA-seq


title: W1462 RNA-seq


title: W4549 RNA-seq


title: W247 RNA-seq


title: W4429 RNA-seq


title: Col-0-control-r3

city: Shanghai

first: Yang

last: Zhao

state: Shanghai

address: 300 Fenglin RD

institute: Shanghai Center for Plant Stress Biology, and CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
Reads of RNA-seq data were mapped to Arabidopsis reference genome (TAIR10) using TopHat.
Differentially expressed genes (DEG) were identified using cuffdiff in Cufflinks.
We define a gene as DEG by requiring q-value < 0.05 and at least 2 fold change of expression level.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited excel files

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seedlings were grown vertically for 9 days before treatment.

extract_protocol:
Total RNA was extracted with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: These seedlings (0.05 ~ 0.1 g) were treated on filter papers.

tag: ecotype

value: wildtype

value: 9-day-old seedlings

tag: treatment

value: 1/2 MS for 24 hours


title: W4165 RNA-seq


title: W1050 RNA-seq


title: W4296 RNA-seq


title: Col-0-control-r2


title: W4422 RNA-seq


title: W897 RNA-seq


title: Col-0-control-r1


title: W4437 RNA-seq


title: W370 RNA-seq


title: W4548 RNA-seq


title: Col-0-osmotic stress-r3

value: 300 mM mannitol for 24 hours


title: Col-0-osmotic stress-r2


title: W4070 RNA-seq


title: W4183 RNA-seq


title: W4491 RNA-seq


title: W4441 RNA-seq


title: Col-0-osmotic stress-r1


title: W1154 RNA-seq


title: W4424 RNA-seq


title: W1915 RNA-seq


title: W4209 RNA-seq


title: W1052 RNA-seq


title: Sfpq homologous knock-out 3

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RNA expression value derived from Expression Console software; full-exon analysis
Raw data were processed with the Expression Console 1.2.0.20 (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed according to our previous plublication (Yamashita et al. J. Hum. Genet. 57, 368-374).  )R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: Sfpq-/- (Sfpq homologous knock-out)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Expression Kit (Ambion) and then fragmented and labeled with the WT Terminal Labelingand and Controls Kit (Affymetrix).

growth_protocol: Embryonic cerebral cortices were disected, isoalted in eppendorf tube, and quickly frozen in Liquid nitrogen.

extract_protocol: Total RNA from cerebral cortical regions of control, Sfpq+/-,and Sfpq+/- brains were extracted using Rneasy Plus Micro (Qiagen) according to the manufacturer’s instructions.

value: embryo

value: brain (cerebral cortical region)

value: Sfpq-/-


title: Col-0-ABA-r3

value: 100 microM ABA for 24 hours


title: W1512 RNA-seq


title: Col-0-ABA-r2


title: W1118 RNA-seq


title: W899 RNA-seq


title: Col-0-ABA-r1


title: W4426 RNA-seq


title: W4370 RNA-seq


title: pyl duodecuple-control-r3

value: pyl duodecuple


title: Control 3

description: RNA expression value derived from Expression Console software; full-exon analysis

source_name: wild-type

value: wild type


title: W4071 RNA-seq


title: W4487 RNA-seq


title: pyl duodecuple-control-r2


title: Nup358GLKD GROSeq Biological Repeat 2

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

data_processing:
Library strategy: GRO-seq
3’-adapter (5'-TGGAATTCTCGGGTGCCAAGG) was removed from the sequenced reads using cutadapt.
Trimmed reads were mapped to gene, transposon and piRNA cluster sequences using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) and quantified using RSEM (Li and Dewey, 2011). Expected counts from RSEM output were normalized to counts per million (CPM). CPM from two independent biological repeats of control and Nup358 GLKD were averaged, CPMNup358GLKD/CPMControl was calculated and plotted. Differential expression analysis was performed using EBSeq and FDR cutoff was set at 0.1.
Differential expression analysis was performed using EBSeq and FDR cutoff was set at 0.1.
Genome_build: dm3
Supplementary_files_format_and_content: Tab delimited text containing expected count from RSEM. Conclusions in this paper were based on these counts.

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
GRO-Seq was performed as described before (Core et al., 2008; Rozhkov et al., 2013) with the following changes. RNA fragmentation was performed using NEBNext Magnesium RNA Fragmentation Module as per manufacture instructions. Polynucleotide Kinase (PNK) treatment of RNA fragments was performed as described earlier (Gardini, 2017). Briefly, 1μl of RNase Inhibitor, Murine (NEB), 30 U of T4 PNK (NEB), 1mM ATP (ThermoFisher Scientific) and 1X PNK reaction buffer was added to purified RNA fragments and reaction was incubated at 37°C for 60 min. To this reaction, 20U of PNK and 10 mM EDTA were added and incubated at 37°C for an additional 60 min. Enzyme was heat inactivated by incubating the reaction mixture at 65°C for 20 min.
Libraries were prepared using TruSeq small RNA Library Prep Kit (Illumina) and sequenced using single-end 50bp sequencing. GRO-seq was performed twice with two independent biological repeats of control and Nup358 GLKD ovaries.

value: Adult

value: ovary

value: Nup358 germline KO


title: Control GROSeq Biological Repeat 2

value: control


title: Nup358GLKD GROSeq Biological Repeat 1


title: Control 1


title: W4508 RNA-seq


title: W4454 RNA-seq


title: Control GROSeq Biological Repeat 1


title: pyl duodecuple-control-r1


title: W4431 RNA-seq


title: Nup358GLKD Total Small RNA

data_processing:
3’-adapter (5'-TGGAATTCTCGGGTGCCAAGG) was removed from the sequenced reads using cutadapt and analyzed by piPipes using dm3 as the reference genome.
Genome_build: dm3
Supplementary_files_format_and_content: Feature Counts from piPipes. These are the sequences used as input for piPipes

extract_protocol:
Thirty μg of total RNA from Control (mat>Luciferase) and Nup358 GLKD ovaries was resolved on a 15% denaturing polyacrylamide gel containing 7M urea. Small RNAs ranging from 20-40nt were purified without oxidation step as described in Li C et al (Cell, 137, 509-521).
Small RNA sequencing libraries were prepared  using  TruSeq Small RNA Library Preparation Kit (Illumina, San Diego, CA) with one minor modification. A terminator block oligo (5’-TAC AAC CCT CAA CCA TAT GTA GTC CAA GCA/3SpC3/-3’) was added prior to 5’ adapter ligation as described in Wickersheim, M.L et al (Biotechniques,55,269-272). This step specifically blocked reverse transcription of 30nt long 2S rRNA and hence substantially reduced rRNA contamination in the final sequenced reads.   Sequencing libraries were size selected with a Pippin Prep (Sage Science, MA). Single read sequencing (1X50 cycles) was performed on a HiSeq2500 (Illumina, San Diego, CA). Sequencing was performed at Hollings Cancer Center Genomics Core Lab at Medical University of South Carolina (MUSC).


title: pyl duodecuple-osmotic stress-r3


title: Sfpq heterologous knock-out 1

source_name: Sfpq+/- (Sfpq heterologous knock-out)

value: Sfpq+/-


title: W4495 RNA-seq

value: (TRAMP x WSB/EiJ) F2


title: Control Total Small RNA


title: W4443 RNA-seq

value: Transgene positive


title: W4511 RNA-seq


title: W4434 RNA-seq


title: pyl duodecuple-osmotic stress-r2


title: pyl duodecuple-osmotic stress-r1


title: W4498 RNA-seq


title: W4218 RNA-seq


title: W7822 RNA-seq


title: pyl duodecuple-ABA-r3


title: pyl duodecuple-ABA-r1


title: W4438 RNA-seq


title: W4199 RNA-seq


title: W4471 RNA-seq


title: W4512 RNA-seq


title: Sfpq 22Rv1 Replicate B

data_processing:
STAR alignment version 2.6 quantMode GeneCounts using GENCODE v27 containing ERCC spike ins
Salmon version 0.8.2 using index with k = 23 and --gcBias --seqBias using gencode version 27 with ERCC sequences and a transcript representing the entire transcript (exons + introns) included
deeptools version 2.5.2 bamCoverage binsize = 10 filterStrand (forward/reverse) --scaleFactor (calculated from 75% of ERCC spike ins)
DESEq2 - normalized count data (sizeFactors calculated only on ERCC transcripts, applied to remaining transcripts) - output is matrix for each cell line of normalized counts fore ach transcript
Genome_build: hg38 , gencode V27
Supplementary_files_format_and_content: bigwig, normalized count data

source_name: Prostate Cancer cells

growth_protocol: Lncap or 22Rv1 cells were otbtained from ATCC and grown in RPMI1640 supplmented with 10% FCS, Penecillin, and streptomycin at 37 degrees in 5% C02

extract_protocol:
Cells were fixed in 0.3% HCHO for 30 minutes at 4 degrees before being subjected to RNA immunoprecipitation
Equal volumes of cells, and input  diluted to be similar concentration to the highest concentration of IP were supplemented with equal volumnes of ERCC spike-ins before library preparation using Kapa Ribo-depletion Hyperprep stranded RNA library kit.

tag: antibody

value: Genetex GTX114209

value: Prostate Cancer


title: W4347 RNA-seq


title: W4455 RNA-seq


title: W4513 RNA-seq


title: Sfpq heterologous knock-out 3

tag: tissue


title: Sfpq homologous knock-out 1


title: Sfpq homologous knock-out 2


title: W4399 RNA-seq


title: pyl duodecuple-ABA-r2

value: 9-day-old seedlings


title: Input Lncap Replicate B

value: Lncap


title: Input 22Rv1 Replicate B


title: W4336 RNA-seq


title: IgG Lncap Replicate B

value: Sigma I5006


title: Input Lncap Replicate A


title: Input 22Rv1 Replicate A


title: Sfpq 22Rv1 Replicate A


title: Control 2

value: embryo

value: brain (cerebral cortical region)


title: IgG 22Rv1 Replicate B


title: Brg1 Lncap Replicate B

value: Abcam ab110641


title: IgG 22Rv1 Replicate A


title: Sfpq heterologous knock-out 2


title: Brg1 22Rv1 Replicate A


title: Brg1 22Rv1 Replicate B


title: m-tartrate Exp. 2 Flask 88 - Rep 1

city: La Jolla

first: Adam

middle: M

last: Feist

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

data_processing:
Sequenced reads were mapped onto NC_000913.2 reference genome sequence using bowtie v.1.1.2 with parameters -X 1000 -n 2 -p 2 -3 3 -S.
Expression levels of each gene in units per kilobase per million fragments mapped (FPKM) were calculated using cufflinks v.2.2.1.
FPKM data was then utilized to run cuffdiff to calculate gene expression fold changes between endpoint and initial growth populations using a geomentric normalization and a false discovery rate of 0.05.
Gene expression fold changes was considered significant if the calculated q-value was smaller that 0.05.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: FPKM tracking files (cufflinks output files) include FPKM values for each sample.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell cultures

growth_protocol: All evolved populations were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with either 0.2% D-lyxose, D-2-deoxyribose, D-arabinose, or m-tartrate.

extract_protocol:
Total RNA was isolated and purified using Qiagen’s RNeasy minikit column according to the manufacturer’s specifications. Ribosomal RNA (rRNA) was removed utilizing Ribo-Zero rRNA removal kit (Epicentre) for Gram-negative bacteria.
The KAPA Stranded RNA-seq kit (Kapa Biosystems) was used for generation of paired-end, strand-specific RNA sequencing libraries.
RNA sequencing libraries were then run on an Illumina HiSeq 2500 using the ‘rapid-run mode’ with 2 x 35 paired end reads.

treatment_protocol: The cell cultures were treated with RNAprotect reagent (Qiagen).

tag: carbon source

value: m-tartrate

value: Evolved - endpoint/optimization


title: m-tartrate Exp. 1 Flask 86 - Rep 2


title: m-tartrate Exp. 2 Flask 88 - Rep 2


title: m-tartrate Exp. 1 Flask 86 - Rep 1


title: IgG Lncap Replicate A


title: IgG 22Rv1 Replicate C


title: W4489 RNA-seq

tag: genotype


title: m-tartrate Exp. 2 Flask 10 - Rep 2

value: Evolved - early/innovation


title: m-tartrate Exp. 2 Flask 10 - Rep 1


title: Brg1 Lncap Replicate A


title: m-tartrate Exp. 1 Flask 10 - Rep 2


title: D-arabionse Exp. 2 Flask 70 - Rep 2

value: D-arabinose


title: m-tartrate Exp. 1 Flask 10 - Rep 1


title: HeLa_RRP40_nuclear RNA replicate 3

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against hg19.
Uniquely mapped and properly paired reads were used for downstream analysis.
The data was quantified using Rsubread on the human GENCODE annotation v19.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: RRP40(knock down) nuclear RNA

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Nuclear RNA was extracted from fractionated cells with Trizol (Thermo Fisher Scientific). 50 μg of nuclear RNA was used for pA+ RNA purification using Oligo (dT)25 Dynabeads (Thermo Fisher Scientific) according to the manufacturer’s instructions.to the manufacturer’s manual.
libraries were prepared from ribo-depleted samples using standard Illumina protocol

treatment_protocol: siRNA transfections were performed targeting EGFP(control) and RNA exosome core factor RRP40

value: HeLa Kyoto

tag: transfected with

value: siRNA targeting RNA exosome core factor RRP40

tag: molecule subtype

value: nuclear polyA RNA


title: HeLa_RRP40_nuclear RNA replicate 2


title: CD8_Mreg_d5_donor452

city: Regensburg

first: James

middle: Alexander

last: Hutchinson

state: Bavaria

department: General Surgery

country: Germany

institute: University Hospital Regensburg

description: gene expression analysis of T7-amplified polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: CD4+ T cells isolated from 5-day co-cultures with M regs

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Human M regs and IFN-γ Mφ were generated according to published protocols (Hutchinson, JA et al. Methods Mol Bio., 2011). CD3+ T cells were isolated from PBMC by MACS-sorting according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated using RNeasy Plus kits (Qiagen) as previously described (Riquelme, P et al. Mol Ther., 2013).

treatment_protocol: Coculture of allogeneic human T cells and either M regs or IFN-γ Mφ were performed in X-Vivo serum-free medium supplemented with M-CSF.

value: CD8+ T cell

tag: days in culture

tag: co-cultivation

value: Cocultured with M reg


title: Glut1-TG rep3

city: Seattle

first: Dan

last: Shao

state: WA

address: 850 Republican Street, N130

department: Mitochondria and Metabolism Center

institute: University of Washington

description: gene expression data from Glut1-TG mouse heart

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

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

data_processing: The data were analyzed with GCOS (GeneChip Operating Software) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: left ventricle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The mice were housed at 22°C with a 12-hour light, 12-hour dark cycle with free access to water and standard chow.

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

treatment_protocol: Hearts were harvested, rinsed briefly in 1× PBS, and freeze-clamped in liquid nitrogen.

tag: gender

value: male

tag: strain

value: FVB

value: heart

value: 11-12 weeks


title: D-arabionse Exp. 2 Flask 70 - Rep 1

tag: genotype/variation


title: CD8_Mreg_d5_donor451

tag: cell type


title: CD8_Mreg_d5_donor462


title: CD8_IFNg-Mphi_d5_donor468

source_name: CD8+ T cells isolated from 5-day co-cultures with IFN-γ Mφ

value: Cocultured with IFN-γ Mφ


title: CD8_IFNg-Mphi_d5_donor427


title: CD8_Mreg_d5_donor468


title: Glut1-TG rep2

tag: age


title: CD8_control_d5_donor452

source_name: CD8+ cells kept in culture for five days without APCs

value: no


title: CD8_Mreg_d5_donor427


title: Glut1-TG rep1


title: HeLa_RRP40_nuclear RNA replicate 1


title: WT rep2

description: gene expression data from wild type mouse heart


title: CD8_control_d0_donor462

source_name: Freshly isolated human CD8+ T cells


title: CD8_IFNg-Mphi_d5_donor451


title: CD8_control_d5_donor468


title: CD8_control_d0_donor468


title: CD8_IFNg-Mphi_d5_donor452


title: CD8_control_d5_donor462


title: CD8_IFNg-Mphi_d5_donor462


title: CD8_control_d5_donor451


title: WT rep1


title: WT rep3


title: CD8_control_d5_donor427


title: D-arabionse Exp. 1 Flask 78 - Rep 2


title: CD8_control_d0_donor452


title: D-arabionse Exp. 1 Flask 78 - Rep 1


title: HeLa_EGFP_nuclear RNA replicate 2

source_name: EGFP(control) nuclear RNA

value: siRNA targeting EGFP(control)


title: HeLa_EGFP_nuclear RNA replicate 1


title: D-arabionse Exp. 1 Flask 9 - Rep 2


title: CD8_control_d0_donor451


title: D-arabionse Exp. 1 Flask 9 - Rep 1


title: D-2-deoxyribose Exp. 1 Flask 118 - Rep 2


title: D-2-deoxyribose Exp. 1 Flask 18 - Rep 2


title: D-2-deoxyribose Exp. 1 Flask 18 - Rep 1


title: D-lyxose Exp. 2 Flask 90 - Rep 2

value: D-lyxose


title: D-lyxose Exp. 2 Flask 90 - Rep 1


title: CD4_Mreg_d5_donor462

value: CD4+ T cell


title: CD4_Mreg_d5_donor468


title: D-lyxose Exp. 1 Flask 73 - Rep 2

value: Evolved - endpoint/optimization


title: CD4_IFNg-Mphi_d5_donor468

source_name: CD4+ T cells isolated from 5-day co-cultures with IFN-γ Mφ


title: D-lyxose Exp. 1 Flask 73 - Rep 1


title: CD4_Mreg_d5_donor427


title: CD4_IFNg-Mphi_d5_donor462


title: D-lyxose Exp. 1 Flask 6 - Rep 2

value: Evolved - early/innovation


title: CD4_IFNg-Mphi_d5_donor452


title: Input Sonicated Lacz replicate 2

data_processing:
Aligned to genome hg38 using bowtie2 version --sensitive
Filter using samtools -q 30  |samtools rmdup -s
samtools merge to merge bamfiles
call peaks with macs2 callpeak --qvaue 0.5 --extsize 150 --keepdup-all --fix-bimodal
convert to bigwig with deeptools/2.5.2 bamCoverage --binSize 30 --extendReads 150 --normalizeTo1x --ignoreForNormalization chrM chrX chrY
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of signal tracks and csv files of annotated peaks.

source_name: Benign Prostate Epithelial Cells (RWPE1)

growth_protocol: RWPE1 cels were grown in keratinocyte serum free media supplemented with penicillin and streptomycin at 37 degrees 5% C02

extract_protocol:
Cells were fixed in 0.3% HCHO at 4 degrees for 30 minutes before quenching with 125mM glycine. For histone modifications chromatin was prepared by sonication. For SWI/SNF chromatin was processed by Mnase digestion before overnight immunoprecipitation with antibodies against targets of interest
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing

treatment_protocol: Cell lines were generated by lentivirus infection with LACZ or SCHLAP1 expression constructs and were selected for at least 1 week in 2.5ug/mL blasticidin

tag: cell line

value: Benign Prostate Epithelial Cells

tag: input


title: CD4_control_d5_donor452

source_name: CD4+ cells kept in culture for five days without APCs


title: CD4_control_d0_donor462

source_name: Freshly isolated human CD4+ T cells


title: CD4_control_d0_donor468


title: CD4_control_d5_donor427


title: CD4_control_d5_donor462


title: Input Sonicated Lacz replicate 1


title: CD4_Mreg_d5_donor452


title: CD4_control_d5_donor468


title: CD4_control_d5_donor451


title: CD4_control_d0_donor427


title: CD4_IFNg-Mphi_d5_donor451


title: CD8_control_d0_donor427


title: CD4_control_d0_donor451


title: Snf5 Schlap1 replicate 2

value: Abcam ab192864

value: Mnase


title: CD4_control_d0_donor452


title: CD4_IFNg-Mphi_d5_donor427


title: Zta_C189V_5hmC_rep2

type: protein

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Zta(C189V)  PBM  experiment, 5hmC

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.

molecule: protein

organism: human gammaherpesvirus 4

source_name: Zta(C189V), HK design

label_protocol: 180 ng of plasmid containing DNA binding domains of Zta or Zta(C189) mutants were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: The bZIP DNA binding domain (DBD) of wild type Zta was obtained from Dr. Timothy Hughes, University of Toronto, Canada as a GST construct cloned into a modified pDEST15 MAGIC vector (N-terminal GST) vector.  Mutant constructs of Zta (C189S, C189T, C189V, and C189A) were generated via site-directed mutagenesis of the wild-type construct (GenScript)

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: bZIP

tag: protein

tag: double-stranding treatment


title: Zta_C189V_5mCG_rep2

description: Zta(C189V)  PBM  experiment, methylated

data_processing: For all 32,896 8-bp long DNA sequences (8-mers), a transformed median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.

treatment_protocol: The double stranded arrays were either methylated (5mCG) or unmethylated (C). The methylation of the double stranded microarray were performed using 10 μl of M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: probe state

value: methylated


title: Zta_C189T_5mCG_rep2

description: Zta(C189T)  PBM  experiment, methylated

source_name: Zta(C189T), HK design


title: Zta_C189S_5mCG_rep2

description: Zta(C189S)  PBM  experiment, methylated

source_name: Zta(C189S), HK design


title: Zta_C189T_5mCG_rep1

description: Zta(C189T)  PBM  experiment, methylated


title: Zta_C189A_5mCG_rep2

description: Zta(C189A)  PBM  experiment, methylated

source_name: Zta(C189A), HK design


title: Zta_C189V_5hmC_rep1

description: Zta(C189V)  PBM  experiment, 5hmC


title: Zta_C189A_5hmC_rep2

description: Zta(C189A)  PBM  experiment, 5hmC


title: Input Mnase Schlap1 replicate 2

tag: tissue

tag: antibody


title: Zta_C189A_5hmC_rep1

description: Zta(C189A)  PBM  experiment, 5hmC


title: Snf5 Schlap1 replicate 1


title: CD4_Mreg_d5_donor451

value: Cocultured with M reg


title: Input Mnase Schlap1 replicate 1


title: Zta_C189V_5mCG_rep1

description: Zta(C189V)  PBM  experiment, methylated


title: Zta_C189T_5hmC_rep1

description: Zta(C189T)  PBM  experiment, 5hmC


title: Input Sonicated Schlap1 replicate 2


title: Input Sonicated Schlap1 replicate 1


title: H3K4me3 Schlap1 replicate 2

value: Abcam ab8580

value: Sonicated


title: Zta_C189A_5mCG_rep1

description: Zta(C189A)  PBM  experiment, methylated


title: H3K4me3 Schlap1 replicate 1


title: Zta_WT_5mCG_rep1

description: Zta  PBM  experiment, methylated

source_name: Zta, HK design

value: Zta


title: Zta_C189V_C_rep2 (mCG)

description: Zta(C189V)  PBM  experiment, unmethylated


title: Zta_C189A_C_rep1 (mCG)

description: Zta(C189A)  PBM  experiment, unmethylated

value: unmethylated


title: Zta_C189S_5hmC_rep2

description: Zta(C189S)  PBM  experiment, 5hmC


title: H3K4me3 Lacz replicate 2


title: Zta_C189T_C_rep1 (mCG)

description: Zta(C189T)  PBM  experiment, unmethylated


title: Zta_WT_5mCG_rep2

description: Zta  PBM  experiment, methylated


title: Zta_C189V_C_rep1 (mCG)


title: Zta_C189A_C_rep2 (mCG)


title: Zta_C189S_C_rep1 (mCG)

description: Zta(C189S)  PBM  experiment, unmethylated


title: Zta_WT_C_rep1 (mCG)

description: Zta  PBM  experiment, unmethylated


title: Zta_C189S_C_rep2 (mCG)


title: H3K4me3 Lacz replicate 1


title: Zta_C189A_5mC_rep2

description: Zta(C189V)  PBM  experiment, 5mC


title: Zta_C189A_5mC_rep1

description: Zta(C189V)  PBM  experiment, 5mC


title: Zta_C189S_5hmC_rep1

description: Zta(C189S)  PBM  experiment, 5hmC


title: H3K4me1 Schlap1 replicate 1

value: Active Motif 39635


title: Zta_WT_C_rep2 (mCG)

description: Zta  PBM  experiment, unmethylated


title: Zta_C189T_5hmC_rep2

description: Zta(C189T)  PBM  experiment, 5hmC


title: Patient_CODE37 - Celiac Disease

city: Bari

first: Marica

last: Cariello

address: Pzza Giulio Cesare

country: Italy

institute: University of Bari

description:
6062739110_H
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in more than 1 group were excluded. Data were analyzed with parametric analysis plus False Discovery Rate, FDR.

source_name: PBMCs

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the QIAzol® Lysis Reagent, according to the manufacturer’s instructions. Quality control was performed with Biorad Experion.

tag: disease state

value: Celiac Disease

value: PBMCs


title: Zta_C189S_5mCG_rep1

description: Zta(C189S)  PBM  experiment, methylated


title: Patient_CODE38 - Celiac Disease

description:
6062739110_B
replicate 1


title: Patient_CODE40 - Celiac Disease

description:
6062739108_H
replicate 1


title: Zta_C189V_5mC_rep2

description: Zta(C189A)  PBM  experiment, 5mC


title: Zta_C189T_5mC_rep2

description: Zta(C189T)  PBM  experiment, 5mC


title: Patient_CODE36 - Celiac Disease

description:
9234921144_H
replicate 1


title: Zta_C189S_5hmC_rep3

description: Zta(C189S)  PBM  experiment, 5hmC


title: Patient_CODE31 - Celiac Disease

description:
6062739108_E
replicate 1


title: H3K4me1 Lacz replicate 2


title: Patient_CODE35 - Celiac Disease

description:
6062739108_J
replicate 1


title: Zta_C189T_5mC_rep1

description: Zta(C189T)  PBM  experiment, 5mC


title: Zta_C189V_5mC_rep1

description: Zta(C189A)  PBM  experiment, 5mC


title: Patient_CODE34 - Celiac Disease

description:
6062739108_I
replicate 1


title: Patient_CODE32 - Celiac Disease

description:
6062739108_F
replicate 1


title: H3K4me1 Schlap1 replicate 2


title: H3K27ac Schlap1 replicate 2

value: Active Motif 39133


title: H3K27ac Lacz replicate 1


title: Brm Schlap1 replicate 2

value: Cell Signaling 11966


title: Patient_CODE25 - Celiac Disease

description:
6062739110_I
replicate 1


title: Patient_CODE29 - Celiac Disease

description:
6062739108_B
replicate 1


title: Patient_CODE24 - Celiac Disease

description:
6062739110_E
replicate 1


title: Zta_C189S_5mC_rep2

description: Zta(C189S)  PBM  experiment, 5mC


title: Patient_CODE33 - Celiac Disease

description:
6062739108_G
replicate 1


title: Zta_WT_5mC_rep2

description: Zta  PBM  experiment, 5mC


title: H3K27ac Schlap1 replicate 1


title: Patient_CODE23 - Celiac Disease

description:
6062739110_D
replicate 1


title: Patient_CODE30 - Celiac Disease

description:
6062739108_C
replicate 1


title: H3K27ac Lacz replicate 2


title: Patient_CODE26 - Celiac Disease

description:
6062739110_J
replicate 1


title: Patient_CODE22 - Celiac Disease

description:
6062739110_C
replicate 1


title: Zta_WT_5mC_rep1

description: Zta  PBM  experiment, 5mC


title: Zta_C189V_C_rep2 (mC)

description: Zta(C189V)  PBM  experiment, cytosine

value: cytosine


title: Patient_CODE20 - Healthy Control

description:
9031313041_C
replicate 1

value: Healthy Control


title: H3K4me1 Lacz replicate 1

value: Benign Prostate Epithelial Cells


title: Patient_CODE21 - Celiac Disease

description:
6062739110_A
replicate 1


title: Brm Schlap1 replicate 1


title: Brg1 schlap1 replicate 2

value: Abcam ab110641


title: Zta_C189A_C_rep2 (mC)

description: Zta(C189A)  PBM  experiment, cytosine


title: Patient_CODE19 - Healthy Control

description:
9031313041_A
replicate 1


title: Brg1 Schlap1 replicate 1

value: Mnase


title: Patient_CODE14 - Healthy Control

description:
9234921127_D
replicate 1


title: Zta_C189V_C_rep1 (mC)

description: Zta(C189V)  PBM  experiment, cytosine

value: bZIP


title: Patient_CODE18 - Healthy Control

description:
9234921127_K
replicate 1


title: Patient_CODE15 - Healthy Control

description:
9234921127_G
replicate 1


title: Patient_CODE13 - Healthy Control

description:
9234921144_E
replicate 1


title: Zta_C189A_C_rep1 (mC)

description: Zta(C189A)  PBM  experiment, cytosine


title: Patient_CODE16 - Healthy Control

description:
9234921127_H
replicate 1


title: Patient_CODE17 - Healthy Control

description:
9234921127_I
replicate 1


title: CSF vaccinated_PBMCs_21dpv

city: Bareilly

first: AMIT

last: KUMAR

state: Uttar Pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

description: miRNA expression of infected cells after 9day

data_processing:
fastq files containing sequencing reads, each of control and infected samples were imported to CLC Workbench 6.1 software, where in, adapters were trimmed  from the reads. Thereafter, known miRNAs were identified by annotating the clean reads according to miRBase 11 (Bos taurus species). The counts obtained were analyzed using edgeR for identifying differentially expressed miRNAs under CSF vaccination after normalising the abundance and correcting library size using TMM values.
Supplementary_files_format_and_content: tab-delimited text files include miRNA name,  expression values (log2 fold change) and significant p-value

organism: Sus scrofa

source_name: PBMCs collected at 21st days post vaccination

extract_protocol:
Total RNA from each of the collected samples was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Multiplex Small RNA Library Prep Kit (New England Biolabs Inc.) following the manufacturer’s protocol. The quality of the libraries was assessed on Bioanalyzer and quantification was done using a Qubit 2.0 Fluorometer (Life Technologies) and by quantitative real-time PCR. Libraries wee sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Three groups of PBMCs including control and CSF vaccinated at two time points were used in the study. From all three groups blood was collected was collected and PBMCs were isloated at 0dpv, 7dpv and 21dpv. The isolated PBMCs of all three groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.

tag: infection status

value: vaccinated


title: Patient_CODE11 - Healthy Control

description:
9234921144_C
replicate 1


title: Patient_CODE9 - Healthy Control

description:
9234921141_D
replicate 1


title: Patient_CODE12 - Healthy Control

description:
9234921144_D
replicate 1


title: Zta_C189T_C_rep1 (mC)

description: Zta(C189T)  PBM  experiment, cytosine


title: Patient_CODE8 - Healthy Control

description:
9031313030_I
replicate 1


title: Unvaccinated_PBMCs Control_0dpv

description: miRNA expression of control cells after 9day

source_name: PBMCs collected at on date of vaccination (from un vaccinated 06 pigs)

value: Control


title: Patient_CODE7 - Healthy Control

description:
9031313030_A
replicate 1


title: Patient_CODE5 - Healthy Control

description:
6062739174_K
replicate 1


title: CSF vaccinated_PBMCs_7dpv

source_name: PBMCs collected at 7th days post vaccination


title: Patient_CODE3 - Healthy Control

description:
6062739174_E
replicate 1


title: Zta_WT_C_rep2 (mC)

description: Zta  PBM  experiment, cytosine


title: Patient_CODE10 - Healthy Control

description:
9234921141_E
replicate 1


title: Patient_CODE6 - Healthy Control

description:
6062739174_L
replicate 1


title: Zta_C189S_C_rep2 (mC)

description: Zta(C189S)  PBM  experiment, cytosine


title: Patient_CODE4 - Healthy Control

description:
6062739174_J
replicate 1


title: single sperm 52

status: Public on May 13 2018

type: genomic

city: Wuhan

last: Zhou

state: Hubei

address: Shizishanjie #1

department: College of animal science

institute: Huazhong Agricultural University

description:
generated in Neogen/GeneSeek (Lansing, MI, USA)
Genomic DNA extracted from single sperm was genotyped using Illumina® BovineHD Genotyping BeadChip assay

hyb_protocol: PCR products were purified and sent to Neogen/GeneSeek (Lansing, MI, USA).

data_processing:
Whole-genome amplificated DNA from single sperm were genotyped by the Illumina® BovineHD Genotyping BeadChip assay.
Coordinates in S*crossover.txt files from UMD3.1

organism: Bos taurus

source_name: semen

extract_protocol: Whole-genome amplification was performed according to the manufacturer’s protocol using a Single Cell Whole Genome Amplification Kit (Yikon Genomics, Shanghai, China) based on the MALBAC (Multiple Annealing and Looping Based Amplification Cycles) technology.

treatment_protocol: Sperm cells were obtained from semen samples stored in liquid nitrogen. Frozen semen was thawed in 37 ºC water for 30-45 seconds. Sperms were diluted by PBS+1%BSA and washed twice. Then the sperms were further diluted to a proper resolution using PBS+1%BSA on a petri-dish, and active single sperms were picked up manually by pipetting into a reaction tube under micromanipulator.

value: sperm


title: single sperm 56

scan_protocol: PCR products were purified and sent to Neogen/GeneSeek (Lansing, MI, USA).


title: single sperm 50

label_protocol: PCR products were purified and sent to Neogen/GeneSeek (Lansing, MI, USA).


title: single sperm 53


title: Zta_C189S_C_rep1 (mC)

description: Zta(C189S)  PBM  experiment, cytosine


title: single sperm 55


title: single sperm 54


title: single sperm 49


title: Zta_C189T_C_rep2 (mC)

description: Zta(C189T)  PBM  experiment, cytosine


title: single sperm 48


title: Patient_CODE1 - Healthy Control

description:
6062739174_B
replicate 1


title: single sperm 47


title: Patient_CODE2 - Healthy Control

description:
6062739174_D
replicate 1


title: single sperm 51


title: Zta_WT_C_rep1 (mC)

description: Zta  PBM  experiment, cytosine


title: single sperm 44


title: single sperm 45


title: single sperm 46


title: single sperm 42


title: single sperm 43


title: single sperm 40


title: single sperm 38


title: single sperm 41


title: single sperm 39


title: Zta_C189T_C_rep2 (mCG)


title: single sperm 36


title: single sperm 37


title: single sperm 34


title: single sperm 28


title: single sperm 30


title: single sperm 27


title: single sperm 31


title: single sperm 33


title: single sperm 35


title: single sperm 23


title: single sperm 25


title: single sperm 22


title: single sperm 26


title: single sperm 24


title: single sperm 21


title: single sperm 18


title: single sperm 19


title: single sperm 17


title: single sperm 16


title: single sperm 14


title: single sperm 15


title: single sperm 13


title: single sperm 12


title: single sperm 10


title: single sperm 32


title: single sperm 29


title: single sperm 9


title: CD4+CCR7-CD38- (Non Activated) From Volunteer P1 (Alpha)

city: Oxford

first: Margarida

last: Rei

address: Headley Way

institute: University of Oxford

description: P1-CCR7-CD38-(Non Activated)-alpha

data_processing:
Library strategy: Amplicon sequencing
MiGeC software version 1.2.6 was used to align and assemble TCR clonotypes, using UMI information for correction of sequencing errors.
VDJtools software version 1.1.4 was used to convert files to VDJtools format for post-processing.
Supplementary_files_format_and_content: Tab-delimited clonotype table with statistics, CDR3 sequence, and VDJ segment id. Alpha files contain TCRalpha chain information. Beta files contain TCRbeta chain information.

source_name: volunteer challenged with Salmonella Paratyphi A

extract_protocol:
Upon FACS sorting, RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (Ambion), following the manufacturer’s instructions.
RNA was reversed transcribed using a template-switch oligo with a 6bp unique molecular identifier and primers designed for the constant regions of Trac and Trbc genes. TCR amplification was achieved by performing two rounds of nested PCR using primers specific for the constant region of the TCRs. A final PCR was performed to add the Illumina adaptors. Libraries were sequenced on Illumina MiSeq. The R1 reads contain the unique molecular identifier (UMI) tag (atcaacgcagagtacatggNNNNNNgg).

value: Peripheral Blood Mononuclear Cells

tag: time point

value: 4 days after diagnosis of enteric fever

tag: cell population

value: FACS sorted CD4+CCR7- CD38- T cells

tag: number of cells

tag: sequencing primer

value: Alpha (primers specific for the Trac gene)


title: CD4+CCR7-CD38- (Non Activated) From Volunteer P1 (Beta)

description: P1-CCR7-CD38-(Non Activated)-beta

value: Beta (primers specific for the Trbc gene)


title: single sperm 6


title: single sperm 8


title: single sperm 7


title: CD4+CCR7- CD38+(Activated) From Volunteer P1 (Beta)

value: FACS sorted CD4+CCR7- CD38+ T cells


title: CD4+CCR7- CD38+(Activated) From Volunteer P1 (Alpha)


title: CD4+CCR7-CD38- (Non Activated) From Volunteer T4 (Beta)

description: T4-CCR7-CD38-(Non Activated)-beta

source_name: volunteer challenged with Salmonella Typhi


title: single sperm 5


title: single sperm 20


title: single sperm 3


title: single sperm 4


title: CD4+CCR7-CD38- (Non Activated) From Volunteer T4 (Alpha)

description: T4-CCR7-CD38-(Non Activated)-alpha


title: Round spermatid sample from 23 dpp Sox30 knockout mice-2

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs in FPKM

source_name: testes

extract_protocol:
RNA isolation and sequencing library construction were conducted by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Haploid cells were sorted from total testicular cells from 23 dpp mice stained with Hoechst dye using FACS

tag: background strain

tag: gender

value: male

tag: genotype

value: Sox30 knockout

value: testes

value: Round spermatid


title: single sperm 2

tag: cell type


title: single sperm 1


title: CD4+CCR7- CD38+(Activated) From Volunteer T4 (Alpha)


title: CD4+CCR7- CD38+(Activated) From Volunteer T4 (Beta)


title: single sperm 11


title: Round spermatid sample from 23 dpp Sox30 knockout mice-1

tag: age


title: Round spermatid sample from 23 dpp wildtype mice-1

value: wild type


title: Rend-WT_168_Bsub_exo

status: Public on May 12 2018

city: Cambridge

first: Aaron

middle: James

last: DeLoughery

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

description: exo treated mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.2.1.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_000964.3

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Overnight cultures were diluted to OD590 0.0003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol: 5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using Trizol (ThermoFisher) and cleaned up and DNase treated using RNAeasy kit (QIAGEN). RNA was then treated with 5'-monophosphate specific nuclease (Epicentre). Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

tag: strain

value: subspecies 168

tag: media

value: LB


title: Rend-rny_Bsub_MSgg_stat

description: mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.2.1.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_000964.4

growth_protocol: Overnight cultures were diluted to OD590 0.003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 2.5.

extract_protocol: 5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using Trizol (ThermoFisher) and cleaned up and DNase treated using RNAeasy kit (QIAGEN). Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 90 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: subspecies 3611

value: MSgg


title: Rend-yaaT_Bsub_MSgg_exp

description: mRNA

growth_protocol: Overnight cultures were diluted to OD590 0.003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.6.

value: subspecies 3610


title: Rend-yaaT_Bsub_MSgg_stat

description: mRNA


title: Zta_C189S_5mC_rep1

description: Zta(C189S)  PBM  experiment, 5mC

tag: dbd

value: bZIP

tag: protein

tag: double-stranding treatment


title: Rend-WT_Bsub_MSgg_stat

description: mRNA

value: subspecies 3100


title: Rend-ymcA_Bsub_MSgg_exp

description: mRNA


title: Rend-ylbF_Bsub_MSgg_stat

description: mRNA


title: Rend-ylbF_Bsub_MSgg_exp

description: mRNA


title: Rend-WT_Bsub_MSgg_exp

description: mRNA


title: Rend-rny_Bsub_LB_exp

description: mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.2.1.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_000964.3 and KF365913.1

growth_protocol: Overnight cultures were diluted to OD590 0.003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol: 5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using Trizol (ThermoFisher) and cleaned up and DNase treated using RNAeasy kit (QIAGEN). Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: Round spermatid sample from 23 dpp wildtype mice-2

tag: tissue


title: Rend-ylbF_Bsub_LB_exp

description: mRNA


title: Rend-ymcA_Bsub_LB_exp

description: mRNA


title: Rend-yaaT_Bsub_LB_exp

description: mRNA


title: Rend-WT_Bsub_LB_exp

description: mRNA


title: Rend-ylbF_StaphHG003

description: mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.2.1.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_007795.1

organism: Staphylococcus aureus

growth_protocol: Overnight cultures were diluted to OD590 0.003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.5.

value: subspecies HG003

value: TSB


title: Rend-WT_StaphHG003

description: mRNA


title: LiSa2_HAase24h_1

city: Los Angeles

first: William

middle: Juster

last: Sullivan

state: California

address: 354-06 BSRB, 615 Charles E. Young Drive S

department: Biological Chemistry

institute: University of California, Los Angeles

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Normalized data were not generated for this study. CEL files were used as input into the GSEA software: http://software.broadinstitute.org/gsea/index.jsp. The data tables associated with sample records were generated from the supplementary CHP files located at the foot the page. Although these files were not used in the analysis performed by the submitter, they have been provided for public use.

label: biotin (Affymetrix standard labeling)

label_protocol: Affymetrix standard protocol

growth_protocol: LiSa-2 liposarcoma cells were grown in standard 10cm plates with DMEM/F12 supplemented with 10% bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit using manufacturer's guidelines

treatment_protocol: Cells were treated with bovine testicular hyaluronidase (HAase, 400ug/mL) or PBS control for times indicated

tag: cell line

value: liposarcoma

tag: treatment

value: HAase, 400ug/mL, 24h


title: LiSa2_PBS_3

value: PBS


title: LiSa2_HAase24h_3


title: LiSa2_HAase6h_1

value: HAase, 400ug/mL, 6h


title: LiSa2_PBS_1