title: MCF-7.Untreated.C

description: cell line


title: MMTV-Neu.180161.Entinostat.6wk.aCGH

status: Public on Dec 10 2018

type: genomic

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: aCGH

hyb_protocol: hybridized to Agilent 244k CGH arrays (model G4415A)

scan_protocol: scanned on Agilent scanner (model G2505B)

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

molecule: genomic DNA

organism: Mus musculus

source_name: DNA reference - UCSC mm7/NCBI release 35 (August 2005)

label_protocol: labeled according to the direct incorporation method (Agilent)

extract_protocol: genomic DNA isolated using Dneasy kit (Qiagen)

treatment_protocol: 4 different treatments: Untreated, 3 week treatment, 6 week treatment, and Entinostat Progression

tag: characteristics

value: reference:DNA reference

tag: cell line

value: MMTV-Neu

tag: treatment

value: Entinostat 6wks


title: Ecoli_MG1655(Δpnp)_T5_rep2

type: RNA

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description:
the cells were in stationary phase, the sampling was performed 5 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 29

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing:
Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used. Only a normalization between arrays according to an invariant probeset intensities was performed. For each strain, a set of probes in the background for which the ranks were roughly invariant across all twelve arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.
After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

molecule: total RNA

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

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit

growth_protocol: The laboratory strain E. coli K12 MG1655 and two mutant strains E. coli MG1655(Δrnr) and E. coli MG1655(Δpnp) were grown in baffled flasks in LB medium at 37 °C and 180 rpm. Initial pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Cultures were performed in triplicate.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively. Total RNA extraction profiles were checked to be similar for all the three tested strains.

treatment_protocol: Three hours after the stationary phase of growth was reached, samples were collected for transcriptomic analysis; this time point was also the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit the initiation of transcription, and cells were harvested at three different time points after this addition. Cultures were performed in triplicate. Samples were taken at either at 0’, 2’, 8’ and 15’, or 0’, 5’, 10’ and 18’ or 0’, 3’, 12’ and 30’ min after rifampicin addition. Samples were immediately frozen in liquid nitrogen upon collection.

tag: genotype/variation

value: {delta}pnp

tag: sampling time point

value: 5 minutes after rifampicin addition

tag: repetition

value: repetition 2


title: aorta_lpgds-ko_biological rep4

city: Philadelphia

first: Emanuela

last: Ricciotti

state: PA

address: 3400 Civic Center Blvd.

department: Department of Pharmacology/Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

hyb_protocol: Hybridization was carried out at the Penn Microarray Facility. Microarray MOE430v2 was used.

scan_protocol: Data were collected at the Penn Microarray Facility.

data_processing: The data were quantified and normalized using GCRMA. WT2 sample was excluded from further analysis. Q-values were calculated using PaGE (http://www.ncbi.nlm.nih.gov/pubmed/15797908) which uses a T-statistic based permutation test, and was run in unpaired mode.

label: biotin

source_name: aorta from Ptgds knockout mouse

label_protocol: Labeling was carried out at the Penn Microarray Facility.

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule and fed a chow diet.

extract_protocol: Total RNA was isolated from aorta using the Qiagen miRNEasy protocol with DNAse treatment. RNA was eluted in 30 ul nuclease-free water. 1 ul was used for RNA OD determination. 1 ul was used to make a 1:10 dilution to run on an Agilent Bioanalyzer Pico chip.

treatment_protocol: Mice were euthanized and aorta were extracted.

tag: strain

tag: Sex

value: male

tag: tissue

value: aorta

value: Ptgds-/-


title: Ecoli_MG1655(Δpnp)_T15_rep1

description:
the cells were in stationary phase, the sampling was performed 15 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 27

value: 15 minutes after rifampicin addition

value: repetition 1


title: Ecoli_MG1655(Δpnp)_T0_rep2

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 28

value: before rifampicin addition


title: MCF-7.Entinostat.B

description: cell line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

organism: Homo sapiens

source_name: Human Reference B

extract_protocol: Total RNA isolated by stratagene

tag: sample type

value: Human Reference B

source_name: Breast cancer, Cell_lines, Entinostat-treated

value: Treated by Entinostat for 72 hours at the IC50 doses


title: aorta_lpgds-ko_biological rep5


title: MMTV-Neu.179063.Entinostat.6wk.aCGH

description: aCGH


title: aorta_wt_biological rep2

description: No processed data for this sample. This sample was excluded from the analysis.

source_name: aorta from wild type mouse

value: wild type


title: MCF-7.Entinostat.A

description: cell line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: MMTV-Neu.177754.Entinostat.6wk.aCGH

description: aCGH


title: Gametocytes of P.falciparum 3D7 in Day 2

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of Cy5- and Cy3-labelled cDNA samples were hybridised on a P. falciparum 8×15K Agilent gene expression microarray for 16 hours at 65°C in an Agilent hybridisation oven (G2545A) (Painter et al., 2013).

scan_protocol: Slides were scanned using the GenePix scanner 4000B and GenePix pro 6.0 software (Molecular Devices).

data_processing: All the samples were Loess normalized within arrays and quantile normalized between arrays using Limma package of R. Probes showing weak signals were ignored at the threshod of forground intensity < 1.5 background intensity for both Cy5 and Cy3 channels.

organism: Plasmodium falciparum

label_protocol: All the cDNA samples were equally Cy5- and Cy3-labelled (1 mg each)

growth_protocol: P. falciparum 3D7/HP1-GFP-DD ON parasites were cultured at 5% haematocrit, 4 nM WR99210 and 625 nM Shield-1 as described (Brancucci et al., 2014). Growth synchronisation was achieved by repeated treatment with 5% D-sorbitol (Lambros and Vanderberg, 1979). Gametocytogenesis was triggered by removing Shield-1 from the growth medium of ring stage cultures (4-12 hpi), which leads to activation of pfap2-g and the consequential commitment to sexual development in over 50% of schizonts (Brancucci et al., 2014). The RBCs from a 150 ml ring stage culture (5-6% parasitaemia) were pelleted and washed once in medium lacking Shield-1. After addition of 15 ml uninfected RBCs (packed cell volume (PCV)) and 450 ml growth medium lacking Shield-1, 15 equal 30 ml cultures of 3D7/HP1-GFP-DDOFF parasites were prepared (1.75% parasitaemia) (day -1). After schizogony (day 0) and re-invasion, these cultures reached 6-8% total ring stage parasitaemia with approximately half of all parasites representing sexually committed ring stages (day 1). Note that PfHP1-depleted sexual ring stages differentiate normally into stage V gametocytes over the following 8 to 10 days, whereas PfHP1-depleted asexual ring stages enter cell cycle arrest at the late ring/early trophozoite stage (Brancucci et al., 2014). This highly enriched early gametocyte bulk culture was used to isolate total RNA daily from day 1 to 12 to cover the entire gametocyte differentiation period (one 30 ml culture aliquot each was harvested for days 1 to 9; two 30 ml culture aliquots each were harvested for days 10 to 12)

extract_protocol: Total parasite RNA from the day 1 sample was harvested directly from the mixture of asexual and sexual ring stage parasites. For each of the eleven consecutive time points (days 2 to 12; early stage I to mature stage V gametocytes) total RNA was harvested from MACS column-enriched gametocyte samples. RNA extraction and cDNA synthesis was carried out as described (Bozdech et al., 2003).

tag: transgenic line

value: HP1 transgenic line

tag: time point

source_name: Reference pool

tag: reference

value: Mixture of asexual stages from ring to schizont


title: MMTV-Neu.178267.Entinostat.3wk.aCGH

description: aCGH

value: reference:DNA reference

value: Entinostat 3wks


title: Ecoli_MG1655(Δpnp)_T8_rep1

description:
the cells were in stationary phase, the sampling was performed 8 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 26

value: 8 minutes after rifampicin addition


title: BT474.Untreated.C

description: cell line

source_name: Breast cancer, Cell_lines, Untreated

value: Untreated for 72 hours


title: DPN 2

type: SRA

city: Oxford

first: Haifei

last: Shi

state: OH

address: 700 E High Street

department: Biology

institute: Miami University

library_source: transcriptomic

data_processing:
Single-end sequencing reads were aligned to the human genome (ENSEMBL GRCh38.p10) using using standard Illumina sequence analysis pipeline
Differential gene expression analysis was performed by DESeq2
Expression data were normalized with DESeq2
differentially expressed genes (|log2 fold change| > 1.5; Padj < 0.01)
Genome_build: gene transcripts were mapped to human genome (ENSEMBL GRCh38.p10)

source_name: Liver

growth_protocol: HepG2 cells from American Type Culture Collection, maintained in phenol red-free DMEM supplemented with heat-inactivated and charcoal-stripped FBS and antibiotics.

extract_protocol:
RNA extraction using RNeasy Mini Kit (Qiagen, Foster City, CA, USA)
Libraries were sequenced as single-end 50 bp on Illumina NextSeq2000 sequencing system at University of Cincinnati. Approximately 27-30 millions of reads were retrieved from each sample
Automated, strand-specific library preparation method using PrepX RNA-Seq samples and a library preparation kit (WaferGen Biosystems, Fremont, CA, USA) with Apollo 324 NGS automated library prep system (WaferGen Biosystems)

treatment_protocol: 1 × 10^5 /ml cells were seeded, and when 70%-80% confluent, medium was starved in 0.1% FBS 16 hours before treatment. DMSO, 17β E2 PPT, DPN (1 microM) treat for 48 hours.

value: Hepatocellular Carcinoma

value: DPN


title: Ecoli_MG1655(Δpnp)_T0_rep1

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 25

value: {delta}pnp


title: DPN 1


title: BT474.Untreated.B

description: cell line


title: aorta_wt_biological rep5

value: male

value: aorta


title: MMTV-Neu.178113.Entinostat.3wk.aCGH

description: aCGH

value: MMTV-Neu


title: aorta_lpgds-ko_biological rep1

value: Ptgds-/-


title: aorta_lpgds-ko_biological rep2


title: Ecoli_MG1655(Δrnr)_T3_rep3

description:
the cells were in stationary phase, the sampling was performed 3 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 22

value: {delta}rnr

value: 3 minutes after rifampicin addition

value: repetition 3


title: Ecoli_MG1655(Δrnr)_T0_rep3

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 21

value: before rifampicin addition


title: aorta_wt_biological rep4

value: wild type


title: BT474.Untreated.A

description: cell line

value: Human Reference B


title: Ecoli_MG1655(Δrnr)_T30_rep3

description:
the cells were in stationary phase, the sampling was performed 30 minutes after rifampicin addition .It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 24

value: 30 minutes after rifampicin addition


title: Ecoli_MG1655(Δrnr)_T12_rep3

description:
the cells were in stationary phase, the sampling was performed 12 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 23

value: 12 minutes after rifampicin addition


title: PPT 2

value: PPT


title: aorta_wt_biological rep3


title: aorta_wt_biological rep1


title: MMTV-Neu.177757.Entinostat.3wk.aCGH

description: aCGH

value: reference:DNA reference

value: Entinostat 3wks


title: Ecoli_MG1655(Δrnr)_T18_rep2

description:
the cells were in stationary phase, the sampling was performed 18 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 20

value: 18 minutes after rifampicin addition

value: repetition 2


title: MMTV-Neu.177755.Entinostat.3wk.aCGH

description: aCGH


title: BT474.Entinostat.C

description: cell line

value: Treated by Entinostat for 72 hours at the IC50 doses


title: PPT 1

value: Hepatocellular Carcinoma


title: BT474.Entinostat.B

description: cell line


title: MMTV-Neu.179059.Untreated.aCGH

description: aCGH

value: MMTV-Neu

value: Untreated


title: E2 2

value: estradiol


title: E2 1


title: MMTV-Neu.175389.Untreated.aCGH

description: aCGH


title: BT474.Entinostat.A

description: cell line


title: Ecoli_MG1655(Δrnr)_T5_rep2

description:
the cells were in stationary phase, the sampling was performed 5 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 18

value: {delta}rnr

value: 5 minutes after rifampicin addition


title: MMTV-Neu.180265.Untreated.aCGH

description: aCGH


title: Control 2

value: DMSO


title: Ecoli_MG1655(Δrnr)_T15_rep1

description:
the cells were in stationary phase, the sampling was performed 15 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 16

value: 15 minutes after rifampicin addition

value: repetition 1


title: Control 1


title: MMTV-Neu.180264.Untreated.aCGH

description: aCGH


title: MMTV-Neu.176661.Untreated.aCGH

description: aCGH


title: Ecoli_MG1655(Δrnr)_T0_rep2

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 17

value: before rifampicin addition


title: Ecoli_MG1655(Δrnr)_T10_rep2

description:
the cells were in stationary phase, the sampling was performed 10 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 19

value: 10 minutes after rifampicin addition


title: AB33 sporidia RNAseq replicate 2

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

data_processing:
Basic quality checks were applied to all sequenced reads using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, RNA-Seq reads were trimmed based on sequencing quality (Phred score) using Flexbar (version 3.0.3; Dodt et al., Biology, 2012 [DOI:10.3390/biology1030895]). Specifically, adapter sequences were removed (TruSeq Universal Adapter) and reads were trimmed at the first position with a Phred score < 20. Trimmed reads were removed if the remaining read length was less than 20 nt.
Trimmed reads were mapped to the U. maydis genome and its gene annotation using STAR (version 2.5.3a; Dobin et al., Bioinformatics, 2013 [DOI:10.1093/bioinformatics/bts635]), allowing up to five mismatches with soft-clipping. Only uniquely mapped reads were kept for further analysis.
Genome_build: All bioinformatics analyses are based on the U. maydis 521 genome sequence (original PEDANT database name p3_t237631_Ust_maydi_v2GB) and the associated gene annotation (version p3_t237631_Ust_maydi_v2GB.gff3; both downloaded from ftp://ftpmips.gsf.de/fungi/Ustilaginaceae/Ustilago_maydis_521/).
Supplementary_files_format_and_content: BAM files contain all reads mapped to the U. maydis genome.

molecule: polyA RNA

organism: Mycosarcoma maydis

source_name: fungal sporidia

growth_protocol: The conditions used for cultivation of U. maydis are described in Brachmann et al., Mol Genet Genomics, 2004 (DOI: 10.1007/s00438-004-1047-z). Starting cultures were grown in CM-glc medium.

extract_protocol:
RNA was extracted using the RNeasy Mini kit following the manufacturer’s instructions for preparation of total RNA from yeast (Qiagen, Hilden, Germany). To this end, AB33 sporidia and hyhae 6 h.p.i. were opened in a Retsch ball mill (3 balls, d=4 mm ; MM400; Retsch, Haan, Germany) 4 times for 5 min at 30 Hz while keeping samples frozen using liquid nitrogen. The resulting cell powder was resolved in 450 µl RLT buffer (+ß-mercapthoethanol) and centrifuged at 13,000 rpm for 2 min at 4°C. The supernatant was transferred to a new reaction tube, mixed with 1 Vol. 70 % EtOH and then added to the RNeasy spin column. All following processing steps were performed according to manufacturer’s instructions.
TruSeq RNA Library Prep kit v2 (Illumina, San Diego, CA, USA) was used for cDNA library generation.

treatment_protocol: For the RNA-Seq experiments, 20 ml cultures of lab strain AB33 and derivates were grown to an OD600 of 0.5 in CM-glc medium. For control AB33 sporidia, 4 ml of the cultures directly harvested. The remainder of the cultures was shifted to nitrate minimal medium supplemented with 1% glucose (NM-glc) to induce filamentous growth. At 6 hours post induction (h.p.i.), 4 ml of the shifted cultures were harvested.

tag: genetic background

value: a2 Pnar:bW2bE1

tag: growth state

value: sporidial growth

tag: culture medium

value: NM-glc

tag: technique

value: RNA-Seq


title: AB33 filaments RNAseq replicate 1

source_name: fungal hyphae

value: induced filamentous growth (6 hours post induction)

value: CM-glc


title: AB33 filaments RNAseq replicate 2


title: AB33 filaments RNAseq replicate 3


title: Ecoli_MG1655(Δrnr)_T8_rep1

description:
the cells were in stationary phase, the sampling was performed 8 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 15

value: 8 minutes after rifampicin addition


title: MMTV-Neu.179065.Untreated.aCGH

description: aCGH

tag: characteristics

value: reference:DNA reference

value: MMTV-Neu


title: HEK293T psi-pri-miR-9-2

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

data_processing:
Adaptor removal using custom scripts. Described in Gu et al. Cell (2012)
miRNA mapping based on custom motifs, QuagmiR.
Genome_build: miRBase21
Supplementary_files_format_and_content: tsv files reporting number of reads, length, 5' fidelity, trimming and tailoring events.

growth_protocol: HEK293T and HeLa cells were maintained in DMEM high glucose (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone), 100 U/ml penicillin-streptomycin (Gibco) at 37℃. Cells were tested to be free of mycoplasma contamination.

extract_protocol:
Phenol-cholorphorm total RNA extraction
5µg of total RNA was ligated with RNA 3’ adaptor using T4 RNA Ligase 2 - truncated (NEB), in the presence of RNase Inhibitor (NEB). RNA 5’ adaptor was ligated using T4 RNA Ligase 1 - high concentration (NEB) and 10 mM ATP. Ligated small RNAs were reverse transcribed using SuperScript ® IV Reverse Transcriptase (Thermo-Fisher). Small RNA library cDNA was amplified and indexed using Phusion® High-Fidelity DNA polymerase (NEB). Constructs were purified in a 6% (w/v) native acrylamide gel based on the expected product size and purified by ethanol precipitation.

treatment_protocol: Transfections were performed using PolyJet™ DNA Transfection Reagent (SignaGen) according to the manufacturer's instructions.

tag: construct

tag: cell line


title: HEK293T psi-pri-miR-9-1 2


title: Ecoli_MG1655_T30_rep3

description:
the cells were in stationary phase, the sampling was performed 30 minutes after rifampicin addition .It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 12

tag: genotype/variation

value: wild type

value: 30 minutes after rifampicin addition

value: repetition 3


title: AB33 sporidia RNAseq replicate 3


title: AB33 sporidia RNAseq replicate 1


title: input-72h-dmsoa-i42_S24

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Alignment was performed using bowtie2 v2.3.4.1
Peak calling was performed using MACS2 v2.1.0
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Genome_build: Hg19 containing an artificial contigs consisting of SF9 genome
Supplementary_files_format_and_content: BigWig of samples normalised to SF9 reads

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was constructed using the NEB Ulra II DNA library prep kit

tag: kdm inhibitor

value: DMSO

tag: chip antibody

value: none (input)


title: Ecoli_MG1655_T12_rep3

description:
the cells were in stationary phase, the sampling was performed 12 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 11

tag: sampling time point

value: 12 minutes after rifampicin addition

tag: repetition


title: HEK293T psi-pri-miR-9-1


title: Ecoli_MG1655_T3_rep3

description:
the cells were in stationary phase, the sampling was performed 3 minutes after rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 10

value: 3 minutes after rifampicin addition


title: Ecoli_MG1655_T0_rep3

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the third of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 9

value: before rifampicin addition


title: Ecoli_MG1655(Δrnr)_T0_rep1

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 13

value: {delta}rnr

value: repetition 1


title: Ecoli_MG1655(Δrnr)_T2_rep1

description:
the cells were in stationary phase, the sampling was performed 2 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 14

value: 2 minutes after rifampicin addition


title: input72h-55a-i39_S21


title: HEK293T psi-pri-miR-9-2-scaffold


title: input-72h-36a-i41_S23


title: HEK293T psi-pri-miR-9-1-scaffold


title: Ecoli_MG1655_T5_rep2

description:
the cells were in stationary phase, the sampling was performed 5 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 6

value: 5 minutes after rifampicin addition

value: repetition 2


title: Ecoli_MG1655_T10_rep2

description:
the cells were in stationary phase, the sampling was performed 10 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 7

value: 10 minutes after rifampicin addition


title: Ecoli_MG1655_T18_rep2

description:
the cells were in stationary phase, the sampling was performed 18 minutes after rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 8

value: 18 minutes after rifampicin addition


title: HEK293T U6-sh-miR-9-alt


title: input-72h-34a-i40_S22


title: HEK293T U6-sh-miR-9-can


title: input-72h-32a-i38_S20


title: HeLa CMV-pri-miR-9-1-bulged-stem

source_name: HeLa

value: HeLa


title: HeLa CMV-pri-miR-9-1-perfect-stem


title: 72h-dmso-A-i18_S12


title: Ecoli_MG1655_T15_rep1

description:
the cells were in stationary phase, the sampling was performed 15 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 4

value: 15 minutes after rifampicin addition


title: input-72h-25a-i37_S19


title: HeLa CMV-pri-miR-9-F1-LS2-TL2


title: Ecoli_MG1655_T2_rep1

description:
the cells were in stationary phase, the sampling was performed 2 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 2

value: wild type


title: Ecoli_MG1655_T8_rep1

description:
the cells were in stationary phase, the sampling was performed 8 minutes after rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 3

value: 8 minutes after rifampicin addition


title: 72h-55a-i15_S9


title: 72h-36A-i17_S11


title: Ecoli_MG1655_T0_rep2

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 5


title: 93-11 rep2

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

country: China

institute: Chinese Academy of Agricultrual Sciences

data_processing:
Methylated cytosines were extracted from aligned reads using the Bismark methylation extractor with default parameters
Genome_build: NIP-BRI and 93-11-BRI
Supplementary_files_format_and_content: gff files for each sample.

organism: Oryza sativa

source_name: seedling

growth_protocol: Rice plants were grown on Yoshida solution in a growth chamber under short day (SD) condition (10 h light/14 h dark) with a light intensity of 800 μmol m-2 s-1

extract_protocol:
3-week-old NIP and 9311  seedlings were harvested and total DNA were extracted using the DNeasy  Plant Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was removed by Ribo-zeroTM Rrna Removal Kit (Epicentre),
KAPA’s Illumina library creation kit (KAPA Biosystems) was used to construct the library and sequencing was done on IlluminaHiSeq X Ten platform.

tag: cultivar

tag: age


title: Ecoli_MG1655_T0_rep1

description:
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the first of three biological replicates used in this experiment, each from separate cultures.
SAMPLE 1


title: 93-11 rep1


title: HeLa CMV-pri-miR-9-F2-LS1-TL2


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 5, replicate 1

city: University Park

first: Zhao

last: SU

address: 354 N. Frear

institute: The Penn State University

description: Gene expression data from Arabidopsis anac019-1 (SALK_096295) unopen flower buds sampled 5 days later from drought-treated plants

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by using robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) with the R/Bioconductor package affy. and then converted to logarithm base 2.

organism: Arabidopsis thaliana

source_name: Arabidopsis anac019-1 (SALK_096295) inflorescence sampled 5 days later from drought-treated plant

label_protocol: Standard Affymetrix protocol.

growth_protocol: Seeds were directly sown into pots containing 100g soil mixture of Metro-Mix 360 soil (Sun Gro Horticulture Canada Ltd) and Turface profile greens grade (Profile Products LLC) in 3:2 ratio by volume, with a maximum water-holding capacity of 100g (defined as 100% soil moisture). Seeds were stratified in a cold room for 2 d at 4 ℃ in the dark. After stratification, the pots with seeds were transferred into a Conviron growth chamber (Conviron Inc), which was set at our normal conditions (22 ℃, 16h day/8h night photoperied, ~300 μmol m-2 s-1 photon flux, 60% humidity) until just after flowering (bolting) when some of the plants were subjected to drought stress.

extract_protocol: Total RNA was isolated from unopened flower buds using RNeasy columns following instructions from the manufacturer (Qiagen, Valencia, CA, USA).

treatment_protocol: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

tag: tissue

value: Unopen flower buds

tag: genotype

value: Arabidopsis at day 30 after seed germination


title: HeLa CMV-pri-miR-9-F2-LS2-TL1


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 4, replicate 2

description: Gene expression data from Arabidopsis anac019-1 (SALK_096295) unopen flower buds sampled 4 days later from drought-treated plants

source_name: Arabidopsis anac019-1 (SALK_096295) inflorescence sampled 4 days later from drought-treated plant

value: Arabidopsis at day 29 after seed germination


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 4, replicate 1


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 3, replicate 2

description: Gene expression data from Arabidopsis anac019-1 (SALK_096295) unopen flower buds sampled 3 days later from drought-treated plants

source_name: Arabidopsis anac019-1 (SALK_096295) inflorescence sampled 3 days later from drought-treated plant

value: Arabidopsis at day 28 after seed germination


title: NIP rep2

value: Nipponbare


title: HeLa CMV-pri-miR-9-F2-LS1-TL1


title: 72h-32a-i14_S8


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 3, replicate 1


title: 72h-25a-i13_S7


title: NIP rep1


title: anac019-1 (SALK_096295) inflorescence, drought-treated, day 5, replicate 2


title: HeLa CMV-pri-miR-9-F1-LS2-TL1


title: ddm1a-1/ddm1b-1 rep3

data_processing:
Alignment: TopHat v2.0.9 using default settings; expression levels: Cufflinks v2.1.1 using default settings
Genome_build: NIP-BRI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Leaf

growth_protocol: Rice plants were grown in field

extract_protocol:
3-week-old wild-type and mutant leaves were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was removed by Ribo-zeroTM Rrna Removal Kit (Epicentre),
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library and sequencing was done on Illumina Hiseq HiSeq X Ten platform.

tag: variety


title: HeLa CMV-pri-miR-9-F1-LS1-TL2


title: 72h-34a-i16_S10


title: ddm1a-1/ddm1b-1 rep2


title: HeLa CMV-pri-miR-9-3


title: HeLa CMV-pri-miR-9-2


title: WT (NIP) rep3


title: ddm1a-1/ddm1b-1 rep1


title: aorta_lpgds-ko_biological rep3

tag: strain

tag: Sex

value: male

value: aorta

value: Ptgds-/-


title: Sple-P26

city: Blacksburg

first: Rujuan

last: Dai

state: VA

address: IDRF 127c,, 245 duck pond drive

department: biomedical science

institute: Virginia Tech

description: Among gene expression codeset profiling 561 genes, 547 immunology-related mouse genes+14 internal reference controls were added

hyb_protocol: According to the manufactuer's protocol.  http://academicdepartments.musc.edu/cohr/l-cohr/nanostring/geneassaymanual.pdf

scan_protocol: Cartrige were placed into the nCounter Digital Analyzer for direct digital counting

data_processing: The raw data in .RCC file were uploaded to nSolver Nanostring software 3.0 and processed with default quality control settings, and then for data normalization and expression analysis.

label: digital molecular barcode

source_name: splenocytes

extract_protocol: Total RNAs were extracted from splenocytes with miRNeasy Mini Kit. On-column DNase digestion with RNase-free DNase (Qiagen) was performed to remove residual amounts of DNA contamination in the isolated RNA

tag: gender

value: female

tag: treatment

value: Placebo control


title: Sple-P22

label_protocol: According to the manufactuer's protocol.  http://academicdepartments.musc.edu/cohr/l-cohr/nanostring/geneassaymanual.pdf


title: HSC_6 Empty_methylation

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

description:
SAMPLE 24
overexpression

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: Cord blood 6

growth_protocol: Cord blood samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit number: EK 187-08). CD34+ HSPCs were isolated from cord blood and cultured in StemSpan Serum-Free Expansion Medium supplemented with 10 μg/mL heparin, 20 ng/mL thrombopoietin, 10 ng/mL stem cell factor, 10 ng/mL fibroblast growth factor 1 and 100 U/mL penicillin/streptomycin.

extract_protocol: Genomic DNA was isolated using the NucleoSpin Tissue kit (Macherey-Nagel) acording to the manufacturers instructions.

treatment_protocol: For knockdown (KD) or overexpression (OE) of specific transcripts the HSPCs were lentivirally infected 1 day after isolation and selected with 2.5 µg/mL puromycin at day 2 post infection. To knockdown DNMT3A transcripts we designed short hairpin RNAs (shRNAs) to target transcript-specific exons: exon 5 of  transcript 1+3 (ENSE00001486208), exon 2 of  transcript 2 (ENSE00001486123), and exon 4  of  transcript 4 (ENSE00001559474). In brief, forward and reverse oligonucleotides (Metabion, Planegg, Germany) were joined and ligated into the pLKO.1 vector (Addgene, Cambridge, MA, USA) that drives shRNA expression from the human U6 promoter and carries the puromycin resistance gene. For constitutive overexpression of DNMT3A transcripts the sequences of the transcripts were amplified from cDNA of human blood cells with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA, USA) using exon-specific primers.

tag: cell type

value: CD34+ HSCs

tag: primary tissue

value: cord blood

tag: dnmt3a transcript

value: Control


title: HeLa CMV-pri-miR-9-1

tag: construct

tag: cell line

value: HeLa


title: Sple-EE14

value: 17alpha-ethinyl estradiol (EE)


title: HSC_6 OE Tr.4_methylation

description:
SAMPLE 23
overexpression

label_protocol: Standard Infinium HD Methylation Assay protocol

value: DNMT3A transcript 4


title: HeLa CMV-GFP

value: CMV-GFP


title: HSC_5 Empty_methylation

description:
SAMPLE 20
overexpression

source_name: Cord blood 5


title: Sple-E2

description: nCounter Immunology Panel. Among gene expression codeset profiling 561 genes, 547 immunology-related mouse genes+14 internal reference controls were added

value: 17-beta estradiol (E2)


title: Sple-EE11


title: HSC_6 OE Tr.2_methylation

description:
SAMPLE 22
overexpression

value: DNMT3A transcript 2


title: HEK293T CMV-pri-miR-9-1-perfect-stem


title: HEK293T CMV-pri-miR-9-1-bulged-stem


title: IP2 Nipponbare

data_processing:
Raw data were trimmed with Skewer to remove adapters and low-quality bases. Reads with more than 15% N, more than 50% low-quality base or less than 18 nt were filtered out. BWA was used to align reads to Nip-BRI. After alignment, 6mA enriched regions were called with MASC2 with the cutoffs FDR <0.05, fold change >2.
Genome_build: Nip-BRI
Supplementary_files_format_and_content: Wig files were generated using the MACS2. Scores represent pileup normalized to 1M reads.

source_name: Whole plant

growth_protocol: Rice plants were grown on Yoshida solution in a growth chamber under short day (SD) condition (10 h light/14 h dark) with a light intensity of 800 μmol m-2 s-1。

extract_protocol:
Genomic DNA was extracted from 3-week-old wild-type Oryza sativa Nipponbare and sonicated to produce fragments of ~250 bp. Fragmented DNA was incubated for 2 h at 4 °C with anti-6mA polyclonal antibody (Synaptic Systems) in immunoprecipitation buffer (10 mM sodium phosphate, 2 mM potassium phosphate, 137 mM NaCl, 2.7 mM KCl, 0.05% Triton X-100, pH 7.4). The mixture was then immunoprecipitated by incubation with Protein A/G Plus-Agarose (Santa Cruz) that was pre-bound with bovine serum albumin (BSA) at 4 °C for additional 2 h. After extensive washing, bound DNA was eluted from the beads in elution buffer (50 mM Tris, pH 8.0, 1% SDS, 10 mM EDTA) at 65 °C, treated with proteinase K and purified using QIAquick PCR Purification Kit (Qiagen).
DNA quality was monitored on agarose gels and Qubit® DNA Assay in  Qubit® 2.0Flurometer (Life Technologies). Three libraries (two biological replicates for 6mA IP and one biological replicates for input) were prepared with NEBNext DNA library prep kit (NEB) following manufacturer’s instructions, Size selection and gel purification, followed by PCR amplification. Library concentration was quantified by Qubit®2.0 Flurometer (Life Technologies) and the insert size was determined by Agilent Bioanalyzer 2100 system (Agilent).

value: Whole plant

tag: developmental stage

tag: ip antibody

value: 6mA (202003, Synaptic Systems)


title: Sple-E1


title: HEK293T CMV-pri-miR-9-F1-LS2-TL2


title: HSC_6 OE Tr.1+3_methylation

description:
SAMPLE 21
overexpression

value: DNMT3A transcripts 1+3


title: HSC_5 OE Tr.4_methylation

description:
SAMPLE 19
overexpression


title: Input Nipponbare

value: Nipponbare


title: SA53_32_R3

city: Belo Horizonte

first: Henrique

middle: César Pereira

last: Figueiredo

state: Minas Gerais

address: Av. Antônio Carlos 6627, Caixa Postal 567, Pampulha

country: Brazil

institute: AQUACEN - National Reference Laboratory for Aquatic Animal Diseases

description: Gene expression of Streptococcus agalactiae after incubation at 32 ºC

hyb_protocol: The cRNA fragmentation and hybridization were performed using Agilent Gene Expression Hybridization kit according to the manufacturer’s instructions. For this, 600 ng of Cy3-labeled cRNA, with specific activity ? 16.2 pmol Cy3/ng was fragmented at 60 ºC for 30 min in a mix composed by 5 mL of 10X Blocking agent, 1 mL of 25X Fragmentation Buffer and nuclease-free water to reach a final volume of 25 mL. After fragmentation, 25 mL of 2X GEx Hybridization Buffer were added in each replicate, which were centrifuged at 21,900 x g for 2 min. Next, 45 µL of hybridization solution were dispensed into a custom-made Agilent slide (8 x 60K) formulated based on the library of 4673 non-redundant genes (Agilent.SingleColor.72627) of 9 fish GBS strains (SA07, SA20, SA53, SA288, SA289, SA320, 138P, GD201008_001, ZQ0910) for microarray-based gene expression analysis. The slide was incubated at 65 ºC for 18 h at 10 rpm in a hybridization oven (Agilent Technologies). Then, the slides were washed in two buffers (Gene Expression Wash Buffer 1 and 2, both Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slide was scanned using Agilent DNA Microarray Scanner (Agilent Technologies) using default parameters.

data_processing: The data obtained from array images were extracted using Agilent Features Extraction software version 11.5 (Agilent Technologies), using the protocol GE1_1105_Oct12_2_Back Subtract_2 to obtain background subtracted.

organism: Streptococcus agalactiae

source_name: Bacteria, 32 ºC, replicate 3

label_protocol: A total of 50 ng of RNA of each biological replicate was amplified and Cy3-labeled using the Agilent Quick Amp Labeling kit (Agilent Technologies) along with RNA Spike-in controls according to Agilent One-Color Microarray-Based Expression Analysis protocol (Agilent Technologies).

growth_protocol: The SA53 strain was streaked onto 5 % sheep blood agar and incubated at 28 ºC for 48 h. Then, colonies were pickep up, inoculated in triplicate culture of 100 mL BHI broth (“Brain Heart Infusion”, Himedia, Mumbai, India) with 0.05 % (v/v) Tween 80 (BHIT), incubated at 32 ºC or 22 ºC under low agitation and harvested at the mid-exponential phase of bacterial growth (OD600 = 0.2). Two aliquots of 50 mL of each biological replicate were harvested for RNA extraction.

extract_protocol: The bacterial pellet resuspended in RNAlater was centrifuged at 12,000 x g for 10 min at 4 ºC and the pellets were lysed mechanically using pestle. Total RNA was extracted using TRIzol RNA Isolation Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. The extracted RNA of each replicate was treated with Turbo DNA-free kit (Ambion, Carlsbad, USA), quantified using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, USA) and its quality and integrity was evaluated using TapeStation 2200 (Agilent Technologies, Santa Clara, USA). RIN values ranging from 7.7 to 9.1 were used.

treatment_protocol: a culture volume of 50 mL of each biological triplicate was immediately centrifuged at 12,000 x g for 30 min at 4 ºC. Bacterial pellets obtained were resuspended in 2 mL of RNAlater (Life Technologies, Carlsbad, USA), incubated at room temperature for 5 min, and posteriorly stored at -70 ºC overnight.

tag: temperature


title: IP1 Nipponbare

tag: cultivar


title: Input 93-11

data_processing:
Raw data were trimmed with Skewer to remove adapters and low-quality bases. Reads with more than 15% N, more than 50% low-quality base or less than 18 nt were filtered out. BWA was used to align reads to 93-11-BRI. After alignment, 6mA enriched regions were called with MASC2 with the cutoffs FDR <0.05, fold change >2.
Genome_build: 93-11-BRI
Supplementary_files_format_and_content: Wig files were generated using the MACS2. Scores represent pileup normalized to 1M reads.

extract_protocol:
Genomic DNA was extracted from3-week-old wild-type Oryza sativa 93-11and sonicated to produce fragments of ~250 bp. Fragmented DNA was incubated for 2 h at 4 °C with anti-6mA polyclonal antibody (Synaptic Systems) in immunoprecipitation buffer (10 mM sodium phosphate, 2 mM potassium phosphate, 137 mM NaCl, 2.7 mM KCl, 0.05% Triton X-100, pH 7.4). The mixture was then immunoprecipitated by incubation with Protein A/G Plus-Agarose (Santa Cruz) that was pre-bound with bovine serum albumin (BSA) at 4 °C for additional 2 h. After extensive washing, bound DNA was eluted from the beads in elution buffer (50 mM Tris, pH 8.0, 1% SDS, 10 mM EDTA) at 65 °C, treated with proteinase K and purified using QIAquick PCR Purification Kit (Qiagen).
DNA quality was monitored on agarose gels and Qubit® DNA Assay in  Qubit® 2.0Flurometer (Life Technologies). Four libraries (two biological replicates for 6mA IP and one biological replicates for input) were prepared with NEBNext DNA library prep kit (NEB) following manufacturer’s instructions, Size selection and gel purification, followed by PCR amplification. Library concentration was quantified by Qubit®2.0 Flurometer (Life Technologies) and the insert size was determined by Agilent Bioanalyzer 2100 system (Agilent).


title: HEK293T CMV-pri-miR-9-F2-LS2-TL1


title: HEK293T CMV-pri-miR-9-F2-LS1-TL2


title: IP2 93-11


title: SA53_32_R2

source_name: Bacteria, 32 ºC, replicate 2


title: HSC_5 OE Tr.1+3_methylation

description:
SAMPLE 17
overexpression


title: WT (NIP) rep2

tag: age

tag: genotype/variation

value: wild type


title: IP1 93-11

tag: tissue


title: HSC_4 OE Tr.2_methylation

description:
SAMPLE 14
overexpression

source_name: Cord blood 4


title: HSC_5 OE Tr.2_methylation

description:
SAMPLE 18
overexpression


title: HEK293T CMV-pri-miR-9-F1-LS2-TL1


title: SA53_22_R3

description: Gene expression of Streptococcus agalactiae after incubation at 22 ºC

source_name: Bacteria, 22 ºC, replicate 3


title: SA53_32_R1

source_name: Bacteria, 32 ºC, replicate 1


title: SA53_22_R2

source_name: Bacteria, 22 ºC, replicate 2


title: HSC_4 OE Tr.1+3_methylation

description:
SAMPLE 13
overexpression


title: HEK293T CMV-pri-miR-9-F2-LS1-TL1


title: SA53_22_R1

source_name: Bacteria, 22 ºC, replicate 1


title: HSC_4 Empty_methylation

description:
SAMPLE 16
overexpression


title: HEK293T CMV-pri-miR-9-F1-LS1-TL2


title: HSC_3 Scramble_methylation

description:
SAMPLE 12
knockdown

source_name: Cord blood 3


title: WT (NIP) rep1

tag: variety


title: Rrm4 iCLIP replicate 1

description:
co-purified RNA
peaks_Rrm4.bed

data_processing:
Basic quality checks were applied to all sequenced reads using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, iCLIP reads were filtered based on sequencing quality (Phred score) in the barcode region, keeping only reads with at most one position with a Phred score < 20 in the experimental barcode (positions 4 to 7) and without any position with a Phred score < 17 in the random barcode (positions 1 to 3 and 8 to 9). The reads were then de-multiplexed based on the experimental barcode at positions 4 to 7 using Flexbar (version 2.4) without allowing mismatches (Dodt et al., Biology, 2012 [DOI:10.3390/biology1030895]). The following analysis steps were applied to all individual samples: Remaining adapter sequences were trimmed from the read ends using Flexbar (version 2.4) allowing one mismatch in 10 nt, requiring a minimal overlap of 1 nt between read and adapter as well as removing all reads with a remaining length of less than 24 nt (including the 9-nt barcode). The first 9-nt of each read containing the barcode were trimmed off and added to the read name in the fastq file.
Filtered and trimmed reads were mapped to the U. maydis genome and its gene annotation using STAR (version 2.4.0h; Dobin et al., Bioinformatics, 2013 [DOI:10.1093/bioinformatics/bts635]), allowing up to two mismatches without soft-clipping. Only uniquely mapped reads were kept for further analysis.
After mapping and filtering, duplicate reads were marked using the dedup function from bamUtil (version 1.0.7; https://github.com/statgen/bamUtil)  and removed if carrying an identical random barcode and hence representing technical duplicates. The nucleotide position upstream of each aligned read was considered as the 'crosslink nucleotide', with each read counted as individual 'crosslink event'.  The crosslink events were collected in bigWig files, separately for each immunoprecipitated RNA-binding protein, replicate and strand.
In order to identify putative RBP binding sites, peak calling was performed on merged replicates for each RBP using ASPeak (Kucukural et al., Bioinformatics, 2013 [DOI: 10.1093/bioinformatics/btt428]). The predicted peaks were centred on the summit (i.e. the first position with highest number of crosslink events within the peak) and then extended to 9 nt. Overlapping peaks were merged and newly centred as described above. In order to account for reproducibility, we required each binding site to be detected by at least 5 crosslink events from each biological replicate. We further removed all Rrm4 and Grp1 binding sites that overlapped by at least 1 nt with any of 88 reproducible Gfp binding sites.
In order to facilitate comparisons between binding sites, crosslink events from both replicates were summed up within each binding site and represented as ‘signal-over-background’ (SOB). Background for each gene was as the number of crosslink events outside the binding sites divided by the number of nucleotides in the gene that harbour such background crosslink events. Only binding sites associated with the top 25% of the SOB distribution for each RBP were taken into consideration for further analyses. This procedure yielded a total of 6,412 and 6,478 binding sites in 3,262 and 3,165 target transcripts for Rrm4 and Grp1, respectively.
Genome_build: All bioinformatics analyses are based on the U. maydis 521 genome sequence (original PEDANT database name p3_t237631_Ust_maydi_v2GB) and the associated gene annotation (version p3_t237631_Ust_maydi_v2GB.gff3; both downloaded from ftp://ftpmips.gsf.de/fungi/Ustilaginaceae/Ustilago_maydis_521/).
Supplementary_files_format_and_content: bigWig files show all detected crosslink events (separately on plus and minus strand) for each protein (Gfp, Grp1-Gfp and Rrm4-Gfp) and replicate. bed files specify the coordinates of 6,412, 6,478 and 88 binding sites for Rrm4, Grp1 and Gfp, respectively.

source_name: fungal hyphae

extract_protocol:
The iCLIP protocol was performed as described in Huppertz et al., Methods, 2014 (DOI:10.1016/j.ymeth.2013.10.011). (i) The initial two-step Tap tag purification (König et al., EMBO J, 2009 [DOI:10.1038/emboj.2009.145]) was switched to single-step purification using Rrm4-Gfp-expressing strains and Gfp-trap immunoprecipitation (Rothbauer et al., Mol Cell Proteomics, 2008 [DOI:10.1074/mcp.M700342-MCP200], ChromoTek, Martinsried, Germany). (ii) For UV-C crosslinking, cells were irradiated continuously in a single session. (iii) RNase I (1/10 dilution, 16 minutes, 37°C) was used for the controls (Figure 4A). The addition of DNase and RNase I was omitted from the samples used for iCLIP library preparation.     After 6 h, hyphae were harvested by centrifugation at 7,500 rpm for 10 min at 4°C and the pellet resuspended in 15 ml ice-cold PBS. For UV-C crosslinking, the cell suspension was split into 3x 5 ml and kept on ice. Cells were irradiated with 200 mJ/cm2 at 254 nm (Biolink UV-Crosslinker; Vilber-Lourmat), pooled in a 50 ml tube, and hyphae were harvested by centrifugation at 7,500 rpm for 10 min at 4°C. Hyphae were resuspended in 6 ml lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Nonidet P-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with proteinase inhibitors per 10 ml lysis buffer: 2× Complete protease inhibitor EDTA-free (Roche), 1 mM DTT (GERBU), 1 mM PMSF (Sigma), 0.75 µg/µl Heparin (Sigma), 5.25 µl ng/µl Pepstatin A (Sigma) and 15 µl SUPERase-In (20 U/µL; Thermo Fisher Scientific). The cell lysis was performed in a Retsch ball mill (d=12 mm ; MM400; Retsch, Haan, Germany) 3 times for 10 min at 30 Hz while keeping samples frozen using liquid nitrogen. All following steps were performed at 4°C. The cell lysate was harvested by centrifugation at 7,500 rpm for 10 min at 4°C. The respective cell lysates were pooled, and the protein-RNA complexes were purified by using 60 µl GFP-Trap®_MA beads (Chromotek) (Rothbauer et al., Mol Cell Proteomics, 2008 [DOI:10.1074/mcp.M700342-MCP200]). The beads were washed 3 times with 500 µl ice-cold lysis buffer (without inhibitors). The cell lysate was added to the prepared magnetic beads and incubated for 1 h at 4°C. All following washing steps of the beads were performed with 900 µl of the respective buffer. The beads were washed 3 times with high-salt wash buffer and 4 times with PNK buffer.
3´ end RNA dephosphorylation, L3 adapter ligation, 5´ end phosphorylation, SDS-PAGE and nitrocellulose transfer were performed as described in Huppertz et al., Methods, 2014 (DOI:10.1016/j.ymeth.2013.10.011) with minor changes implemented. 50% instead of 20% of the sample were radioactively labelled for 10 min at 37°C and the labelled beads were washed once with PNK buffer before they were combined with the unlabelled beads. The beads were diluted in 80 µl 1× NuPAGE LDS loading buffer (Invitrogen NP0007) with 0.1 M DTT. The protein-RNA complexes were separated at 180 V for 70 min on a 4-12% NuPAGE Bis-Tris gel (1x MOPS running buffer, NP0001, Invitrogen) and transferred onto a nitrocellulose membrane. The same nitrocellulose membrane was used to detect Rrm4-Gfp, Grp1-Gfp and Gfp by using an anti-GFP antibody (clones 7.1 and 13.1; Sigma) as first antibody.  A mouse IgG HRP conjugate (H+L; Promega, Madison, WI) was used as a secondary antibody. Activity was detected using the AceGlow blotting detection system (Peqlab, Erlangen, Germany). Labelled RNA was detected by overnight exposure of X-ray films (Fujifilm, Düsseldorf, Germany) at -80°C. All following steps were performed as described in Huppertz et al., Methods, 2014 (DOI:10.1016/j.ymeth.2013.10.011). To avoid overamplification of the cDNA library, the optimal PCR cycle number was tested for individual protein in each experiment (PCR cycler MJ Research, PTC-200). For all Grp1 and Gfp replicates, 18 PCR cycles were determined, and for the Rrm4 sample, 18 and 22 PCR cycles were determined for the two replicates, producing PCR products of around 150 nt (cDNA insert = 20-30 nt; L3 adapter, RT-primer and P3/P5 Solexa primers = 128 nt).

treatment_protocol: For the induction of filamentous growth of lab strain AB33 and derivates, 150 ml cultures were grown to an OD600 of 0.5 in CM-glc medium and shifted to nitrate minimal medium supplemented with 1% glucose (NM-glc). iCLIP and RNA-Seq experiments were performed 6 hours post induction (h.p.i.).

tag: strain

tag: genetic background

value: a2 Pnar:bW2bE1 rrm4-gfp

tag: technique

value: iCLIP

tag: ip-ed protein

tag: ip reagent

value: GFP-Trap_MA beads (Chromotek, Code:gtma-20, Lot#:50911001A)

value: fungal hyphae


title: HSC_4 OE Tr.4_methylation

description:
SAMPLE 15
overexpression

tag: cell type

value: CD34+ HSCs

tag: primary tissue

value: cord blood


title: HEK293T CMV-pri-miR-9-2

tag: construct


title: Sple-P22 [miRNA]

description: Assay includes probes for the following: 578 mouse miRNAs, 33 viral miRNAs, 6 positive miRNA assay controls, 8 negative miRNA assay controls, 4 mRNA housekeeping controls, and 3 non-mammalian miRNA spike-in probes.

tag: gender

value: female

tag: treatment

value: Placebo control


title: Sple-P26 [miRNA]


title: HEK293T CMV-pri-miR-9-3

tag: cell line


title: HEK293T CMV-pri-miR-9-1


title: KDcatUrine

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequencing adaptors (mainly 3’ adaptors and contaminants of 5’ adaptors), and reads having too short inserts (< 14nt) or no inserts were trimmed with an in-house script.
The trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie 1.0.0 with the option –m 10000, which allows reads to be aligned onto the multiple locations in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.5 software (Agilent Technologies, Santa Clara, CA).
The read counts allocated for the small RNA feature of mm10 (version 2013.10.09) were quantified using a Trimmed Mean of M-value (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: An excel format file (XLS) includes TMM quantification values and gene annotations of all samples (known genes, novel genes, and mature miRNAs).

organism: Felis catus

source_name: kidney disease

extract_protocol:
Total RNA was extracted from the Urine Exosome using Urine Exosome RNA Isolation Kit (Cat. 47200).
Total RNA obtained from each sample was subjected to a sequencing library construction procedure using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s protocols.

tag: material

value: Urine Exosome

tag: sample type

value: 1 pool sample of 45 cats


title: Rrm4 iCLIP replicate 2

description:
co-purified RNA
peaks_Rrm4.bed


title: HCcatUrine

source_name: normal renal function

value: 1 pool sample of 43 cats


title: Grp1 iCLIP replicate 2

description:
co-purified RNA
peaks_Grp1.bed

value: a2 Pnar:bW2bE1 grp1-gfp


title: Sple-EE14 [miRNA]

value: 17alpha-ethinyl estradiol (EE)


title: Grp1 iCLIP replicate 1

description:
co-purified RNA
peaks_Grp1.bed


title: Gfp iCLIP replicate 2

description:
co-purified RNA
peaks_Gfp.bed

value: a2 Pnar:bW2bE1 gfp

value: Gfp


title: Nip_3w

data_processing:
Library strategy: SMRT sequencing
After quality control, the Canu (Canu) assembler was used for the de novo assembly of the SMRT sequencing reads. To polish the assembly results, the Pilon (v1.22) algorithm (using default parameters, www.broadinstitute.org/software/pilon/) was used to correct errors using 129× illumina short reads. Then we constructed the pseudo-chromosomes for Nip-BRI according to the gene order syntenic relationship between Nip-BRI and MSU7 using Quota-align  and ALLMAPS.  The PacBio SMRT Analysis 2.3.0 was used to detect 6mA base modifications using default parameters. In detail, each of the raw data in bax.h5 format were first aligned to genome using pbalign in base modification identification mode. After alignment by loadChemistry.py and loadPulses scripts, the polymerase kinetics information was loaded. Then cmph5tools were used to merge and sort the two post-aligned datasets. Afterwards the 6mA modification was identified using ipdSummary.py script. To control for potential false positives, after detecting kinetic signatures, 6mA sites were filtered using the criteria of RQ > 20 and per-strand coverage ≥ 25×. Additionally, the upper limit of 6mA site coverage was also considered as previous report (Mondo et al., 2017).
Genome_build: Nip-BRI
Supplementary_files_format_and_content: The gff file is the PacBio standard analysis protocol result for DNA modification containing the 6mA sites information, genome locus, strand, coverage, IPD ratio and context sequence

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
Then the magnetic beads (Pacific Biosciences, Cat. 100-265-900) were used to purify DNA, followed by washing steps. Finally, DNA was eluted from beads. The amount and quality of native DNA were examined by gel electrophoresis, Nanodrop (OD 260/280, 1.8-2.0; OD 260/230, 2.0-2.2) and Qubit DNA Assay Kit (Life Technologies).  The 20 kb libraries for SMRT sequencing were constructed according to the standard protocol of SMRT RSII platform. Briefly, DNA was fragmented and purified, then the SMRTbell Template Prep kit 1.0 (Pacific Biosciences, Cat. 100-259-100) was used for the library construction. Size selection was performed using Bluepippin to recover fragments longer than 10 kb. The libraries were then purified using AMPure PB magnetic beads (Pacific Biosciences) and quantified using Qubit Fluorometry before the sequencing step. Sequencing was performed on 75  PacBio RSII cells with P6/C4 chemistry.

value: Whole plant

tag: cultivar

value: Nipponbare

tag: developmental stage


title: Sple-EE11 [miRNA]


title: Gfp iCLIP replicate 1

description:
co-purified RNA
peaks_Gfp.bed

tag: tissue


title: HSC_3 KD Tr.4_methylation

description:
SAMPLE 11
knockdown

tag: dnmt3a transcript

value: DNMT3A transcript 4


title: 93-11_3w

data_processing:
Library strategy: SMRT sequencing
After quality control, the Canu (Canu) assembler was used for the de novo assembly of the SMRT sequencing reads. To polish the assembly results, the Pilon (v1.22) algorithm (using default parameters, www.broadinstitute.org/software/pilon/) was used to correct errors using 41× illumina short reads. Then we constructed the pseudo-chromosomes for Nip-BRI according to the gene order syntenic relationship between 93-11-BRI and Shuhui498 using Quota-align  and ALLMAPS.  The PacBio SMRT Analysis 2.3.0 was used to detect 6mA base modifications using default parameters. In detail, each of the raw data in bax.h5 format were first aligned to genome using pbalign in base modification identification mode. After alignment by loadChemistry.py and loadPulses scripts, the polymerase kinetics information was loaded. Then cmph5tools were used to merge and sort the two post-aligned datasets. Afterwards the 6mA modification was identified using ipdSummary.py script. To control for potential false positives, after detecting kinetic signatures, 6mA sites were filtered using the criteria of RQ > 20 and per-strand coverage ≥ 25×. Additionally, the upper limit of 6mA site coverage was also considered as previous report (Mondo et al., 2017).
Genome_build: 93-11-BRI
Supplementary_files_format_and_content: The gff file is the PacBio standard analysis protocol result for DNA modification containing the 6mA sites information, genome locus, strand, coverage, IPD ratio and context sequence

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
Then the magnetic beads (Pacific Biosciences, Cat. 100-265-900) were used to purify DNA, followed by washing steps. Finally, DNA was eluted from beads. The amount and quality of native DNA were examined by gel electrophoresis, Nanodrop (OD 260/280, 1.8-2.0; OD 260/230, 2.0-2.2) and Qubit DNA Assay Kit (Life Technologies).  The 20 kb libraries for SMRT sequencing were constructed according to the standard protocol of SMRT RSII platform. Briefly, DNA was fragmented and purified, then the SMRTbell Template Prep kit 1.0 (Pacific Biosciences, Cat. 100-259-100) was used for the library construction. Size selection was performed using Bluepippin to recover fragments longer than 10 kb. The libraries were then purified using AMPure PB magnetic beads (Pacific Biosciences) and quantified using Qubit Fluorometry before the sequencing step. Sequencing was performed on 64  PacBio RSII cells with P6/C4 chemistry.


title: Sple-E2 [miRNA]

tag: strain

value: 17-beta estradiol (E2)


title: HCdogUrine

organism: Canis lupus familiaris

value: 1 pool sample of 37 dogs


title: HSC_2 KD Tr.2_methylation

description:
SAMPLE 6
knockdown

source_name: Cord blood 2

value: DNMT3A transcript 2


title: HSC_1 Scramble_methylation

description:
SAMPLE 4
knockdown

source_name: Cord blood 1

value: CD34+ HSCs

value: Control


title: HSC_3 KD Tr.1+3_methylation

description:
SAMPLE 9
knockdown

value: cord blood

value: DNMT3A transcripts 1+3


title: HCT116-Treated-Replicate 3-Repeat-Batch2

status: Public on Dec 09 2018

first: Bala

last: Davient

address: 60 Nanyang Dr

institute: Singapore Centre for Environmental Life Sciences Engineering

data_processing:
All samples had a sequencing depth of more than 24 million reads. These reads were processed using the CLC Genomics Workbench Version 11.0.1 (CLC Bio, Aarhus, Denmark).
The default settings were used unless otherwise stated. All reads were trimmed with a quality score of 0.05.
Using the ‘RNA-Seq Analysis’ function, the trimmed reads were mapped onto the human genome GRCh38 downloaded from the Ensemble database.
The maximum number of hits for a read was set to 1. Gene hits were annotated with GRCh38.92 from the Ensemble database.
A negative binomial test was executed using the workbench’s ‘Differential Expression for RNA-Seq’ tool to establish differentially expressed genes (DEGs).
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel Worksheets (.xlsx) include Gene Name (based on GRCh38.92 annotation from Ensemble), Ensemble ID,  Log2Fold Change, Fold Change, P-value and FDR p-value

source_name: Colon

growth_protocol: HSAEC, A549, HCT116 cells, and the Airway Epithelial Cell Basal Medium (AECBM) with associated growth factors were purchased from the American Type Culture Collection (Manassas, VA, USA). Phosphate buffered saline (PBS) without calcium and magnesium, high glucose Dulbecco’s modified Eagles media (DMEM) with added L-glutamine, sodium pyruvate, and phenol red, were purchased from GE Healthcare Life Sciences (Logan, UT, USA). Heat-inactivated foetal bovine serum (FBS) of South American origin and Trypsin-EDTA (0.25%) with phenol red were purchased from Gibco (Waltham, MA, USA). HSAEC cells were cultured with 8mL AECBM while both A549 and HCT116 cells were cultured with 8mL DMEM supplemented with 10% FBS, which henceforth will be referred to as complete media, in a 75cm2 culture flask. After 72 hours of culture on weekdays and 96 hours over the weekends, cell confluency reached approximately 70% and 90%, respectively. Sub-cultures were conducted at a seed density of 1.0 x 104 cells/cm2 for A549 cells while 0.5 x 104 cells/cm2 for both HSAEC and HCT116 cells. Sub-culture seed densities were estimated based upon total cells enumerated with a haemocytometer without live-dead staining. No antibiotics were used in all cultures. All culture vessels were incubated in a humidified atmosphere at 37oC with 5% CO2. All incubations mentioned henceforth will be referring to these conditions. For the actual RNA-seq experiment, HSAEC, A549 and HCT116 at passage number P8 were cultured as technical triplicates in 25cm2 culture vessels, and after two more passages, each cell line was considered to have biological triplicates of n = 3. At 90% confluency, HSAEC and A549 cells were split at a seed density of 3.0 x 104 cells/cm2, while HCT116 cells were split at 6.0 x 104 cells/cm2 into 6-well plates.

extract_protocol:
Cells were gently agitated on an orbital shaker at 80 revolutions per minute for 10 minutes. A lysis cocktail comprised of 10µL 1% β-mercaptoethanol, 20µL proteinase K, and 800µL RLT buffer, which was a component in the RNeasy Mini Kit (Qiagen), was homogenized with cells in each well. The RNA extraction was conducted according to instructions in the RNeasy Mini Kit. Additionally, a 30 minutes on-column DNase I treatment was performed.   DNA contamination was further minimized with TURBO™ DNase treatment. Next, RNA was purified with the Angencourt RNAClean XP Kit. RNA integrity was verified using the RNA ScreenTape with analysis on the Agilent 2200 TapeStation (Agilent). Using the Qubit™ dsDNA HS and RNA HS Assay Kits, total RNA was quantified fluorometrically via the Qubit™ Fluorometer 2.0 (Invitrogen).
mRNA was purified with the Illumina® TruSeq® Stranded messenger RNA Sample Prep Kit

treatment_protocol: After 24 hours of incubation in 3mL of AECBM or complete media, the spent media was replaced with 3mL of either 1.0µM PG (treatment) or 0.05% DMSO (control). Cells were incubated for another 24 hours and thereafter, the media was replaced with 1mL of RNAprotect Cell Reagent.

value: Treated; 1.0uM PG

value: Epithelial

tag: status

value: Cancer (carcinoma)


title: HCT116-Unreated-Replicate 2-Repeat-Batch2

value: Untreated; 0.05% DMSO


title: HCT116-Treated-Replicate 1-Repeat-Batch2


title: HCT116-Unreated-Replicate 3-Repeat-Batch2


title: HSC_3 KD Tr.2_methylation

description:
SAMPLE 10
knockdown


title: HSC_2 Scramble_methylation

description:
SAMPLE 8
knockdown


title: HSC_2 KD Tr.4_methylation

description:
SAMPLE 7
knockdown


title: HCT116-Unreated-Replicate 1-Repeat-Batch2


title: A549-Treated-Replicate 3-Repeat-Batch2

description: BALA009-(DEG)A549TreatmentvsControl.xlsx

source_name: Lung

value: Cancer (adenocarcinoma)


title: MIA PaCa-2_Saline_rep2

first: Yanbo

last: Zheng

address: 1# Tiantan Xili

institute: Institute of Medicinal Biotechnology

description: Gene expression after saline-treated xenograft

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: MIA PaCa-2, Saline, replicate 2

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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: MIA PaCa-2 cells (1×107) were suspended in 200 μL saline and inoculated subcutaneously (s.c.) in the right armpit of NIH (nu/nu) athymic mice (18–22 g). After 3 weeks, tumors were dissected and pieces of tumor tissue (2 mm3 in size) were transplanted s.c. by a trocar into mice.

extract_protocol: Three days after the last administration, mice were sacrificed and tumor tissues were used for gene expression analysis.Total RNA was extracted from tumor tissues using TRIzol reagent (Invitrogen).

treatment_protocol: When the tumor size reached about 100 mm3 (day 7), mice were divided with 3 mice per group and treated orally with saline or DBDx , once daily, 5 consecutive days a week for 3 weeks.

value: MIA PaCa-2 xenograft

value: Human pancreatic carcinoma cell line MIA PaCa-2


title: MIA PaCa-2_DBDx_rep3

description: Gene expression after DBDx-treated xenograft

source_name: MIA PaCa-2, DBDx, replicate 3


title: KDdogUrine

value: Urine Exosome

value: 1 pool sample of 47 dogs


title: MIA PaCa-2_Saline_rep3

source_name: MIA PaCa-2, Saline, replicate 3


title: A549-Treated-Replicate 1-Repeat-Batch2


title: A549-Treated-Replicate 2-Repeat-Batch2


title: A549-Unreated-Replicate 1-Repeat-Batch2


title: A549-Unreated-Replicate 3-Repeat-Batch2


title: A549-Unreated-Replicate 2-Repeat-Batch2


title: MIA PaCa-2_Saline_rep1

source_name: MIA PaCa-2, Saline, replicate 1


title: HCT116-Treated-Replicate 2

description: BALA014_(DEG)_HCT116_Treatment_vs._Control

tag: disease


title: HCT116-Treated-Replicate 1


title: HSC_1 KD Tr.2_methylation

description:
SAMPLE 2
knockdown


title: HCT116-Unreated-Replicate 2


title: HSC_1 KD Tr.4_methylation

description:
SAMPLE 3
knockdown

value: DNMT3A transcript 4


title: HSC_2 KD Tr.1+3_methylation

description:
SAMPLE 5
knockdown


title: A549-Treated-Replicate 3

description: BALA014 _(DEG)_A549_Treatment_vs._Control


title: HCT116-Unreated-Replicate 3


title: A549-Treated-Replicate 2


title: A549-Unreated-Replicate 2


title: A549-Treated-Replicate 1


title: HSAEC-Treated-Replicate 2

description: BALA014_(DEG)_Normal_Cell_Treatment_Vs._Control

value: Normal, immortalized

value: HSAEC


title: A549-Unreated-Replicate 1


title: SC_SC.24

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

institute: University of Texas Southwestern Medical Center

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence (mm10 from UCSC)
Uniquely mapped reads were quantified using HTSeq python suite based on gencode.vM17.annotation.gtf from Gencode based on protein coding genes and gene body
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited text file for count data

extract_protocol:
nuclear extraction protocol: 5000-10000 flow cytometry sorted PreCFU-E and CFU-E from Scf FL/FL, Scf KO/FL and Scf KO/FL;Lepr-Cre mice
FANS protocol: c-Kit+ bone marrow cells were enriched with anti-APC paramagnetic beads after staining with anti-c-Kit APC-eFluor780 antibody (eBioscience). Cells were then stained with lineage antibodies (CD2, CD3, CD5, CD8, Ter119, B220, Gr1) (Tonbo Biosciences), CD105 (BD Biosciences), CD150 (Biolegend), CD41 (Biolegend), CD16/32 (Biolegend) and Sca1 (eBioscience)
total RNA extraction protocol: Total RNA was extracted with RNeasy Micro Kit (Qiagen). Total RNA was extracted following the kit instructions, and RNA integrity and concentration were measure using a Bioanalyzer. Samples with RIN values equal or higher than 9.4 were used for library generation.
Two to six ng of total RNA were used to generate a cDNA library using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).

tag: genotype/variation

tag: Sex

value: M

value: colony-forming unit erythroid (CFU-E)

tag: sample id

tag: replicate

value: C


title: SC_SC.25

tag: cell type

value: A


title: SC_SC.23

value: F

value: B


title: SC_SC.27


title: HSC_1 KD Tr.1+3_methylation

description:
SAMPLE 1
knockdown

value: CD34+ HSCs

tag: primary tissue

value: cord blood

value: DNMT3A transcripts 1+3


title: HCT116-Unreated-Replicate 1

tag: treatment

value: Untreated; 0.05% DMSO

value: Epithelial

value: Cancer (carcinoma)


title: HSAEC-Unreated-Replicate 3

tag: cell line


title: HSAEC-Unreated-Replicate 2


title: SC_SC.22


title: SC_SC.26


title: HSAEC-Treated-Replicate 3

value: Treated; 1.0uM PG


title: SC_SC.20


title: Sple-E1 [miRNA]

description: Assay includes probes for the following: 578 mouse miRNAs, 33 viral miRNAs, 6 positive miRNA assay controls, 8 negative miRNA assay controls, 4 mRNA housekeeping controls, and 3 non-mammalian miRNA spike-in probes.  Based on miRBase v.15

source_name: splenocytes

tag: gender

value: female

value: 17-beta estradiol (E2)


title: SC_SC.21


title: A549-Unreated-Replicate 3

value: Cancer (adenocarcinoma)


title: HCT116-Treated-Replicate 2-Repeat-Batch2


title: MIA PaCa-2_DBDx_rep1

source_name: MIA PaCa-2, DBDx, replicate 1

value: MIA PaCa-2 xenograft

value: Human pancreatic carcinoma cell line MIA PaCa-2


title: HSAEC-Treated-Replicate 1

value: Normal, immortalized

value: HSAEC


title: SC_SC.19

value: M

value: colony-forming unit erythroid (CFU-E)

value: A


title: SC_SC.17

value: F

value: PreCFU-E

value: B


title: SC_SC.18

value: C


title: SC_SC.15


title: SC_SC.14


title: SC_SC.16


title: IDD4-GFP_1_Input

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were processed using Trimmomatic to remove adapter contents and low quality bps.
ChipSeq reads were mapped to TAIR10 genome using bowtie2.
RNAseq reads were mapped to TAIR10 genome using TOPHAT.
Chipseq peaks were calculated using MACS2.
RNSeq diffential expression was done using cufflinks package.
Genome_build: TAIR10
Supplementary_files_format_and_content: wiggle, excel

source_name: 14 day-old seedlings

growth_protocol: 14 day-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC

extract_protocol:
The whole 14 day-old seedlings were used for total RNA extraction. ChIP assays were performed on 14 day-old in half MS-grown seedlings using Anti-GFP antibody - ChIP Grade (Abcam) and RNA polymerase II (Santa Cruz) antibodies. Briefly, after plant material fixation in 1% (v/v) formaldehyde, the tissues were homogenised, and the nuclei were isolated and lysed. Cross-linked chromatin was sonicated using a water bath Bioruptor UCD-200 (Diagenode; 15-s on/15-s off pulses, 15 times). The complexes were immunoprecipitated with antibodies overnight at 4°C with gentle shaking and incubated for 1 h at 4°C with 50 μL of Dynabeads Protein A (Invitrogen).
mRNA library generation followed by paired end sequencing (Hiseq4000). NEB ChIP-seq Library Prep Master Set for Illumina
Sequencing was performed on each library to generate 101-bp paired-end reads on Illumina HiSeq Genome Analyzer platform.

treatment_protocol: 1µM flg22 treatment for 1 hour

value: ColO, pUBI10::IDD4:GFP

tag: antibody

value: input

value: 14 day-old seedlings


title: IDD4-GFP_3_IP

value: anti-GFP


title: IDD4-GFP_1_IP


title: IDD4-GFP_3_Input


title: UBQ10_GFP_IP_Rep2

value: ColO, pUBI10::GFP


title: IDD4-GFP_4_IP


title: SC_SC.12


title: HSAEC-Unreated-Replicate 1

value: Untreated; 0.05% DMSO

value: Epithelial


title: SC_SC.13


title: SC_SC.10


title: UBQ10_Input_Rep2


title: IDD4-GFP_4_Input


title: DD1 (IDD4-DD)

value: ColO, pUBI10::IDD4-DD:RFP

tag: transgene info

value: The introduced transgene expresses a nucleotide-modified IDD4 ORF that codes for a phospho-modified IDD4 version (Serine-73 and Threonine-130 were replaced by Aspartic acid (D))


title: DD2 (IDD4-DD)


title: AA1 (IDD4-AA)

value: ColO, pUBI10::IDD4-AA:RFP

value: The introduced transgene expresses a nucleotide-modified IDD4 ORF that codes for a phospho-modified IDD4 version (Serine-73 and Threonine-130 were replaced by Alanine (A))


title: SC_SC.11


title: HCT116-Treated-Replicate 3

value: Treated; 1.0uM PG

value: Cancer (carcinoma)


title: AA2 (IDD4-AA)


title: OX2 (IDD4ox)


title: EGLKO4

city: St. Louis

first: Guoyan

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

description: outlier by Robust PCA statistics

data_processing:
adapter trimming using cutadapt version 1.16
sequence quality control using PRINSEQ version 0.20.4
RNA-seq reads were aligned to the GENCODE release 16 with STAR version 2.5.3a.
Gene counts were derived from the number of uniquely aligned unambiguous reads using HTSeq version 0.6.1
differentially expressed genes were identified using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: feature count tables generated using HTSeq

source_name: EGL

growth_protocol: Brain tissue was taken from SnoN conditional knockout and wild-type mice maintained under standard housing conditions.

extract_protocol:
Total RNA was extracted from cerebellum of P6 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. The EGL from the central lobules of P6 mice cerebellum was micro-dissected and RNA was extracted using RNeasy Plus Micro Kit with gDNA eliminator column.
After Agilent BioAnalyzer quality control, intact RNA was used for library using NEBNext Ultra RNA library preparation kit for Illumina (E7530).

value: cerebellum

tag: tissue region

value: EGL

tag: genotype

value: knockout


title: EGLKO8

tag: tissue


title: A1 (WT)

value: ColO


title: EGLKO5

tag: strain


title: EGLKO2

value: wild type


title: R3H180

city: Jena

first: Vito

last: Valiante

address: Beutenbergstrasse 11A

department: Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses

institute: Leibniz-Institute for Natural Product Research and Infection Biology

description: processed data file: counts.csv

data_processing:
Basecalls performed using CASAVA.
Reads were trimmed with btrim.
Trimmed reads were mapped to the reference genome with tophat1.
Mapped reads were counted using htseq-count.
Genome_build: Aspergillus_fumigatusa1163
Supplementary_files_format_and_content: counts.csv: Comma-delimited text file includes counts for each gene per sample.

organism:
Pseudomonas aeruginosa PAO1
Aspergillus fumigatus A1163

source_name: Fungal mycelium and heat-inactivated bacteria

growth_protocol: 10^8/ml Aspergillus fumigatus conidia were inoculated in 100 ml AMM medium and pre-cultivated for 12 h at 37° C in shaking conditions (200 rpm). Total mycelium was filtered, washed, and then transferred into 100 ml of fresh AMM.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer instructions.
Enrichment of mRNA by poly(A) attached to magnetic beads and subsequent cDNA library construction (performed by LGC Genomics Berlin).
100 bp paired-end read.

treatment_protocol: 10^9 untreated or heat-inactivated Pseudomonas cells were added to pre-cultivated A. fumigatus.

value: Fungal mycelium

tag: cultivation condition

value: Heat-inactivated Pseudomonas

tag: time point

value: 180 min


title: A2 (WT)

tag: genotype/variation

value: 14 day-old seedlings


title: R3H90

description: processed data file: counts.csv

value: 90 min


title: R1H180

description: processed data file: counts.csv


title: R2H180

description: processed data file: counts.csv


title: R2H90

description: processed data file: counts.csv


title: R3H45

description: processed data file: counts.csv

value: 45 min


title: idd4c_flg22

value: Salk_148352C; IDD4 mutant


title: R1H90

description: processed data file: counts.csv


title: EGLKO3


title: idd4b_flg22


title: R1H45

description: processed data file: counts.csv


title: idd4a_flg22


title: R3P180

description: processed data file: counts.csv

source_name: Fungal mycelium and bacteria

value: Co-cultivation


title: EGLWT5


title: EGLWT3


title: EGLWT1


title: OX1 (IDD4ox)

value: ColO, pUBI10::IDD4:GFP


title: EGLWT6


title: EGLWT7


title: EGLWT2

description: outlier by Robust PCA statistics


title: WTc_flg22


title: EGLKO6


title: R2P180

description: processed data file: counts.csv


title: R2H45

description: processed data file: counts.csv


title: WTb_flg22


title: R1P180

description: processed data file: counts.csv


title: MIA PaCa-2_DBDx_rep2

source_name: MIA PaCa-2, DBDx, replicate 2

value: MIA PaCa-2 xenograft

value: Human pancreatic carcinoma cell line MIA PaCa-2


title: idd4c

value: untreated


title: R3P90

description: processed data file: counts.csv


title: P6WT1_RNA

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of genes, identifiers, and counts for each sample

source_name: Cerebellum

extract_protocol:
Total RNA was extracted from the cerebellum of mice at P6 using Trizol (Invitrogen) according to the manufacturer’s instructions.
Single-end short read sequencing libraries were prepared using the NEBNext Ultra RNA library preparation kit for Illumina (E7530)
RNA-seq was performed by GTAC on their standard pipeline, using an Illumina HiSeq 3000

tag: Sex

value: Female

value: Cerebellum

tag: age

value: 6 days


title: P6WT2_RNA

value: Male


title: WTa_flg22

value: ColO


title: P6KO2_RNA

value: SnoN cKO


title: R3A180

description: processed data file: counts.csv

organism: Aspergillus fumigatus A1163

source_name: Fungal mycelium

value: Fungal mycelium

value: Fungus alone


title: idd4b

value: 14 day-old seedlings


title: HaCat small RNA sequencing

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
base calling filtering and dimultiplexing using BaseCaller
Absolute quantification of human tRNA-derived fragments (tRFs) (in house bash script)
Genome_build: tRFdb human tRFs (http://genome.bioch.virginia.edu/trfdb/)
Supplementary_files_format_and_content: tRFs counts

source_name: Immortalized human keratinocyte cell

growth_protocol: DMEM 10% FBS

extract_protocol:
miRVANA RNA Isolation Kit
Total RNA-Seq Kit v2
Protocol for small RNA sequencing

treatment_protocol: No treatment

value: HaCaT


title: R2A180

description: processed data file: counts.csv

value: 180 min


title: idd4a

value: Salk_148352C; IDD4 mutant


title: R1P90

description: processed data file: counts.csv

value: Co-cultivation

value: 90 min


title: R3A90

description: processed data file: counts.csv


title: R2A90

description: processed data file: counts.csv


title: R1A90

description: processed data file: counts.csv


title: R1A180

description: processed data file: counts.csv


title: R3A45

description: processed data file: counts.csv

value: 45 min


title: WTc


title: WTb


title: R2P45

description: processed data file: counts.csv


title: P6KO3_RNA


title: P6KO1_RNA


title: P6WT3_RNA

value: wild type


title: R1P45

description: processed data file: counts.csv


title: R1A45

description: processed data file: counts.csv


title: R2A45

description: processed data file: counts.csv


title: R2P90

description: processed data file: counts.csv


title: RNA-Seq MEFs FLDD 1h TNF

status: Public on Dec 08 2018

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing: RNA-Seq data were aligned to hg38 or mm10 using RNA STAR using a gffread filtered gencode annotation file. Normalized reads were obtained using cufflinks.

source_name: MEFs

growth_protocol: HeLa and MEF cells were cultured in DMEM (Life Technologies) supplemented with FCS and Penicillin/Streptomycin.

extract_protocol:
For RNA-Seq cells were harvested and total RNA was isolated using the NucleoSpin RNA Kit (Macherey-Nagel).  For ChIP-Seq samples were crosslinked using Formaldehyde, Sonicated and chromatin was extracted using the p65 Antibody. DNA was purified NucleoSpin Gel and PCR Clean UP Kit with buffer NTB (Macherey-Nagel).
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded total RNA LT kit (Illumina). ChIP-Seq libraries were prepared from purified ChIP DNA with the Microplex Library Preparation Kit (Diagenode)

treatment_protocol: HeLa cells and MEFs were stimulated with TNFα (20 ng/ml) for 60 min

value: Mouse Embryonic Fibroblasts (MEFs)

value: p65 KO, FLDD p65 rescue

tag: tnf stimulation

value: 1h TNF


title: RNA-Seq MEFs FLDD 0h TNF

value: 0h TNF


title: RNA-Seq MEFs ev 1h TNF

value: p65 KO, empty vector rescue


title: RNA-Seq MEFs wt 1h TNF

value: p65 KO, wt p65 rescue


title: RNA-Seq MEFs wt 0h TNF


title: RNA-Seq MEFs E39I 0h TNF

value: p65 KO, E38I p65 rescue


title: RNA-Seq MEFs E39I 1h TNF


title: WTa

value: ColO

value: untreated


title: RNA-Seq MEFs ev 0h TNF


title: R3P45

description: processed data file: counts.csv

value: Fungal mycelium


title: S. pombe SPCC645.10 #3

city: Madison

first: Melanie

last: Preston

state: WI

address: 433 Babcock Dr

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
Illumina Casava1.9 software used for basecalling
Use custom Python script (extract tails.py) to identify unique tails added to tRNA reporter from every .fastq file in a directory.
Use custom Python script (analyzeTails.py) to compile nucleotide composition of tails added to tRNA reporter at each tail length and normalize to dataset size
Use custom Perl script to calculate the total percent of each nucleotide in added tails
Genome_build: N/A
Supplementary_files_format_and_content: txt file contains columns of sequence of the end of the reporter tRNA, tail sequence, and # times observed

organism: Saccharomyces cerevisiae BY4741

source_name: S. pombe SPCC645.10 #3

growth_protocol: BY4741 yeast were co-transformed using standard methods with a plasmid expressing the reporter tRNA and a plasmid expressing the rNTase of interest, or vector controls, and selected on synthetic yeast medium lacking uracil and leucine (SD-Ura-Leu).  Cultures were inoculated with single colonies, grown to saturation, and then diluted to 0.1 OD600/mL and grown to log phase (0.8-1 OD600/mL).  Cells were spun down in pellets of 25 OD600 (approximately 5 x 108 cells) and stored at -80°C until RNA extraction

extract_protocol:
RNA was extracted from 25 OD of yeast corresponding to each sample by modification of a previously described method.  Briefly, to each sample, 0.5 g of 0.5 mm acid washed beads (Sigma-Aldrich), 0.5 mL of RNA ISO buffer (500 mM NaCl, 200 mM Tris-Cl pH 7.5, 10 mM EDTA, 1 % SDS) and 0.5 mL of phenol-chloroform-isoamyl alcohol pH 6.7 (PCA, Fisher Scientific) was added.  Samples were lysed with 10 cycles that each consisted of vortexing for 20 seconds and incubation on ice for 30 seconds.  1.5 volumes (relative to starting amount of ISO Buffer) of RNA ISO Buffer and of PCA were added, and samples were centrifuged at 4°C to separate phases. The aqueous layer was transferred to a pre-spun phase-lock gel (heavy) tube (5PRIME/Quantabio); an equal volume of PCA was added and mixed prior to centrifugation at room temperature to separate phases.  The aqueous layer was transferred to 2 new tubes for ethanol precipitation with 2 volumes of 100% ethanol followed incubation at -80°C for 1 hour to overnight. Precipitated RNA was pelleted by centrifugation at 4°C.  Each pellet was dissolved in 25 μL nuclease-free water and combined into 1 tube per sample.  Co-purifying DNA was digested with 20 U of Turbo DNase (Invitrogen) at 37°C for 4 hours, and RNA was cleaned up with the GeneJET RNA Purification Kit (Thermo Scientific), and eluted with 50 μL of DEPC-treated water.
Total RNA (100 ng) was ligated with 20 pmol of a 5ʹ adenylated primer containing a 7-nucleotide random DNA sequence (random heptamer), Illumina TruSeq adapter sequence and a 3ʹ dideoxycytidine (5ʹ-A(pp) NNNNNNN TGGAATTCTCGGGTGCCAAGG ddC-3ʹ) using 200 U of T4 RNA ligase 2, truncated KQ (New England BioLabs) in a 20μL reaction with 16°C overnight incubation.  This ligation added the random heptamer and Illumina TruSeq adapter sequence to the 3ʹ end of the RNAs in the sample.  Half of the ligation reaction (10 μL) was reverse transcribed using 5 pmol of Illumina RNA RT primer (5ʹ-GCCTTGGCACCCGAGAATTCCA-3ʹ) and ImProm-II Reverse Transcriptase (Promega Corporation) with 1.5 mM MgCl2 and 0.5 mM dNTPs, according to manufacturer’s instructions.  Samples were then PCR-amplified with a forward primer consisting of Illumina-specific sequences and sequence (underlined),  specific to the tRNA reporter   (5ʹ-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATCGAGGATCACCCATGTCGCAG-3ʹ) and a reverse Illumina RNA PCR Primer with various indices used for multiplexing, using GoTaq Green PCR Master Mix (Promega Corporation). PCR products were run on an 8% polyacrylamide 8M urea gel and gel extracted. Resulting samples for each sequencing run were combined in equimolar amounts and run on an Illumina HiSeq2000 or HiSeq2500 (2x50 bp or 2x100 bp), to produce approximately 1 x 106 reads per sample.

tag: rntase expressed

value: S. pombe SPCC645.10

tag: trna reporter expressed

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: S. pombe SPCC645.10 #2

source_name: S. pombe SPCC645.10 #2


title: S. pombe SPCC645.10 #1

source_name: S. pombe SPCC645.10 #1


title: S. pombe SPAC1093.04 #5

source_name: S. pombe SPAC1093.04 #5

value: S. pombe SPAC1093.04


title: S. pombe SPAC1093.04 #4

source_name: S. pombe SPAC1093.04 #4


title: S. pombe SPAC1093.04 #2

source_name: S. pombe SPAC1093.04 #2


title: S. pombe Cid16 #3

source_name: S. pombe Cid16 #3

value: S. pombe Cid16


title: S. pombe SPAC1093.04 #1

source_name: S. pombe SPAC1093.04 #1


title: S. pombe Cid14 #3

source_name: S. pombe Cid14 #3

value: S. pombe Cid14


title: S. pombe Cid16 #2

source_name: S. pombe Cid16 #2


title: S. pombe Cid16 #1

source_name: S. pombe Cid16 #1


title: S. pombe Cid11 #1

source_name: S. pombe Cid11 #1

value: S. pombe Cid11


title: S. pombe Cid14 #2

source_name: S. pombe Cid14 #2


title: S. pombe Cid11 #3

source_name: S. pombe Cid11 #3


title: S. pombe Cid13 #2

source_name: S. pombe Cid13 #2

value: S. pombe Cid13


title: S. pombe Cid12 #5

source_name: S. pombe Cid12 #5

value: S. pombe Cid12


title: S. pombe Cid12 #6

source_name: S. pombe Cid12 #6


title: S. pombe Cid13 #1

source_name: S. pombe Cid13 #1


title: S. pombe Cid12 #2

source_name: S. pombe Cid12 #2


title: S. pombe Cid11 #2

source_name: S. pombe Cid11 #2


title: S. cerevisiae Cca1 #1

source_name: S. cerevisiae Cca1 #1

value: S. cerevisiae Cca1


title: S. cerevisiae Cca1 #2

source_name: S. cerevisiae Cca1 #2


title: S. pombe Cid12 #3

source_name: S. pombe Cid12 #3


title: S. pombe Cid14 #1

source_name: S. pombe Cid14 #1


title: S. pombe Cid13 #4

source_name: S. pombe Cid13 #4


title: S. pombe Cid12 #1

source_name: S. pombe Cid12 #1


title: S. cerevisiae Cca1 #3

source_name: S. cerevisiae Cca1 #3


title: S. pombe SPAC1093.04 #3

source_name: S. pombe SPAC1093.04 #3


title: S. pombe Cid12 #4

source_name: S. pombe Cid12 #4


title: S. pombe Cid1 #1

source_name: S. pombe Cid1 #1

value: S. pombe Cid1


title: S. pombe Cid13 #3

source_name: S. pombe Cid13 #3


title: N. crassa NCU08022.7 #3

source_name: N. crassa NCU08022.7 #3

value: N. crassa NCU08022.7


title: N. crassa NCU11050.7 #3

source_name: N. crassa NCU11050.7 #3

value: N. crassa NCU11050.7


title: N. crassa NCU11050.7 #4

source_name: N. crassa NCU11050.7 #4


title: S. pombe Cid1 #2

source_name: S. pombe Cid1 #2


title: N. crassa NCU11050.7 #1

source_name: N. crassa NCU11050.7 #1


title: N. crassa NCU11050.7 #2

source_name: N. crassa NCU11050.7 #2


title: N. crassa NCU05588.7 #1

source_name: N. crassa NCU05588.7 #1

value: N. crassa NCU05588.7


title: N. crassa NCU08022.7 #1

source_name: N. crassa NCU08022.7 #1


title: N. crassa NCU08022.7 #2

source_name: N. crassa NCU08022.7 #2


title: N. crassa NCU04364.7 #4

source_name: N. crassa NCU04364.7 #4

value: N. crassa NCU04364.7


title: H. sapiens TUT7 #3

source_name: H. sapiens TUT7 #3

value: H. sapiens TUT7


title: H. sapiens TUT4 #7

source_name: H. sapiens TUT4 #7

value: H. sapiens TUT4


title: N. crassa NCU04364.7 #1

source_name: N. crassa NCU04364.7 #1


title: N. crassa NCU00538.7

source_name: N. crassa NCU00538.7

value: N. crassa NCU00538.7


title: N. crassa NCU04364.7 #3

source_name: N. crassa NCU04364.7 #3


title: H. sapiens TUT4 #6

source_name: H. sapiens TUT4 #6


title: H. sapiens TUT1 #1

source_name: H. sapiens TUT1 #1

value: H. sapiens TUT1


title: H. sapiens TUT4 #2

source_name: H. sapiens TUT4 #2

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: H. sapiens TUT4 #1

source_name: H. sapiens TUT4 #1


title: H. sapiens TUT4 #4

source_name: H. sapiens TUT4 #4


title: H. sapiens TUT7 #4

source_name: H. sapiens TUT7 #4


title: H. sapiens TUT1 #3

source_name: H. sapiens TUT1 #3


title: H. sapiens TUT1 #2

source_name: H. sapiens TUT1 #2


title: H. sapiens TUT4 #5

source_name: H. sapiens TUT4 #5


title: H. sapiens TUT7 #2

source_name: H. sapiens TUT7 #2


title: H. sapiens TUT7 #1

source_name: H. sapiens TUT7 #1


title: H. sapiens TUT4 #3

source_name: H. sapiens TUT4 #3


title: H. sapiens TENT4B #4

source_name: H. sapiens TENT4B #4

value: H. sapiens TENT4B


title: H. sapiens TENT4B #2

source_name: H. sapiens TENT4B #2


title: H. sapiens TENT4B #1

source_name: H. sapiens TENT4B #1


title: H. sapiens TENT4A #3

source_name: H. sapiens TENT4A #3

value: H. sapiens TENT4A


title: N. crassa NCU05588.7 #2

source_name: N. crassa NCU05588.7 #2


title: H. sapiens TENT4A #2

source_name: H. sapiens TENT4A #2


title: H. sapiens TENT4B #3

source_name: H. sapiens TENT4B #3


title: H. sapiens TENT2 #2

source_name: H. sapiens TENT2 #2

value: H. sapiens TENT2


title: H. sapiens MTPAP #2

source_name: H. sapiens MTPAP #2

value: H. sapiens MTPAP


title: H. sapiens TENT2 #1

source_name: H. sapiens TENT2 #1


title: N. crassa NCU04364.7 #2

source_name: N. crassa NCU04364.7 #2


title: H. sapiens MTPAP #1

source_name: H. sapiens MTPAP #1


title: tRNA reporter only #3

source_name: tRNA reporter only #3

value: Empty vector


title: tRNA reporter only #1

source_name: tRNA reporter only #1


title: Empty vector

source_name: Empty vector


title: C. elegans ZK863.4 #4

source_name: C. elegans ZK863.4 #4

value: C. elegans ZK863.4


title: H. sapiens TENT4A #1

source_name: H. sapiens TENT4A #1


title: C. elegans ZK863.4 #3

source_name: C. elegans ZK863.4 #3


title: C. elegans ZK863.4 #2

source_name: C. elegans ZK863.4 #2