title: Anthers, SAND_COLD_rep3

city: Rosario

first: Nahuel

middle: Damian

last: Gonzalez-Schain

state: Santa Fe

address: Ocampo y Esmeralda

department: Biofisica del reconocimiento molecular

country: Argentina

institute: Instituto de Biologia Molecular y Celular de Rosario

data_processing:
Evaluation and processing of raw data was performed on the commercially available CLC Genomics Workbench v.4.7.1. After trimming, the resulting high-quality reads were mapped onto the Oryza MSU7.0 database. More than 20 million reads that mapped with ≤2 mismatches were used for further analyses. The read number of each gene model was computed based on the coordinates of the mapped reads. A read was counted if any portion of that read’s coordinates were included within a gene model. As CLC Genomics Workbench v.4.7.1 distributes multi-reads at similar loci in proportion to the number of unique reads recorded and normalized by transcript length, we included both unique reads and reads that occur up to 10 times in the analysis to avoid undercount for genes that have closely related paralogs. Gene expression values were based on reads per kilobase of exon model per million mapped read (RPKM) values. To obtain statistical confirmation of the differences in gene expression, P and FDR values were computed using Baggerley’s test on expression proportions. We applied a threshold value of P<0.05 and FDR<0.05 to ensure that differential gene expression was maintained at a significant level (5%) for the individual statistical tests.
Genome_build: Oryza MSU7.0
Supplementary_files_format_and_content: Normalized means-FC-FDR.xlsx

organism: Oryza sativa

source_name: Anthers at post-meiotic stage

growth_protocol: Plants were grown in a temperature-controlled growth chambers maintained at 26/22°C day/night temperature and day/night relative humidity (RH) of 75–85% under LD (16/8 h light/dark) or heading-inductive SD conditions (10/14 h light/dark). Light intensity was set to ∼500 µmol/m2/s. Seeds were pre-germinated in seeding trays for 3-4 weeks and then seedlings were transplanted individually into pots. After 7-10 weeks, depending on the cultivar, plants were transferred to SD inductive conditions for 3 more weeks.

extract_protocol:
Spikelets from the middle part of the panicles were collected, dissected to separate the anthers and collected in tubes suspended in liquid nitrogen. Total RNA was extracted from pooled anthers by using TRIzol® (Invitrogen). Three biological replicates were collected for each treatment (Cold-stress and Control). The quality and quantity of RNA samples were assessed by gel electrophoresis and Nanodrop quantification.
RNA libraries were prepared for sequencing by using Truseq mRNA kit at IGA Technology Services (Udine, Italy).

treatment_protocol: Cold-stress (8°C) or control (24°C) treatments were applied only during the night period for one day when rice plants showed auricle distances between flag leaf and penultimate leaf (AD) that matched post-meiotic developmental stage for each cultivar.

tag: cultivar

value: SANT ANDREA

tag: phenotype

value: cold-stress susceptible

tag: stress

value: COLD (8°C)

value: Anthers at post-meiotic stage


title: Anthers, SAND_COLD_rep1

status: Public on Sep 07 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: Anthers, SAND_COLD_rep2


title: Anthers, ERY_CONTROL_rep3

value: ERYTHROCEROS HOKKAIDO

value: cold-stress tolerant

value: CONTROL (24°C)


title: Anthers, SAND_CONTROL_rep2


title: Anthers, ERY_COLD_rep3


title: Anthers, ERY_COLD_rep1


title: Anthers, SAND_CONTROL_rep1


title: Anthers, ERY_COLD_rep2


title: LNCaP R1881 0.1 Dox-1

city: Ann Arbor

first: Steven

last: Kregel

state: MI

address: 1500 E. Medical Center Drive, Room 5320 RCC

department: MCTP

country: USA

institute: University of Michigan

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.1uM Doxorubin treated 12 hours replicate-1

data_processing:
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
GRCh38
counts

molecule: polyA RNA

organism: Homo sapiens

source_name: LNCaP

extract_protocol:
The ChIP assays were performed using HighCell ChIP kit with IPure 2.0 kit elution (Diagenode) according to manufacturer's protocol. The antibodies used for ChIP assay are AR_PG-21 (Millipore Cat. # 06-680); TBP (Abcam Cat. #ab63766), and Normal Rabbit IgG Control (Diagenode). LNCaP cells were grown in charcoal-stripped serum containing media for 48 hrs followed by 12 hrs of vehicle or 1 nM R1881 and dox treatment (0.1 µM for ‘low,’ 0.4 µM for ‘medium,’ and 0.7 µM for ‘high’) for all ChIP-qPCR and ChIP-seq conditions.  ChIP-seq sample preparation for sequencing was performed according to the manufacturer's instructions (Illumina).
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
RNA-seq using cDNA based on manufacturer's instructions (Illumina)

tag: cell type

value: Prostate Adenocarcinoma

tag: passage

value: passage 30-50

tag: doxorubicin treatment

value: Low


title: LNCaP CSS-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h replicate 1


title: Anthers, ERY_CONTROL_rep1


title: Anthers, ERY_CONTROL_rep2


title: Anthers, SAND_CONTROL_rep3


title: Notch3 KO-derived T-ALL 3 (RNA-Seq)

city: Tarrytown

first: Qi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc

data_processing:
RNA-Seq reads were mapped to the mouse mm10 reference genome guided by UCSC gene models by OSA aligner implemented in ArrayStudio software from Qiagen
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrix in txt format

organism: Mus musculus

source_name: spleen

extract_protocol:
Total RNA was extracted
Total RNA was converted to mRNA libraries using KAPA Stranded mRNA-Seq kits from KAPA Biosystems following the manufacturer’s protocols

tag: strain

value: BALB/c

tag: genotype

value: spleen

tag: disease state

value: tumor

tag: donor thymus genotype

value: Notch3 knockout


title: 1123+TGF-beta-1

status: Public on Sep 08 2019

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Trizol extraction of total RNA
from purified polyA RNA

value: glioma stem-like cell (GSC)

tag: tissue source

value: brain

tag: treatment

value: 20ug/ml TGF-beta for 8 h


title: WT-derived T-ALL 202 (RNA-Seq)

value: Wild type


title: Liver from ST diet + vehicule, biological replicate #3

type: RNA

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4*44K V2 Microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k V2 array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters .  Data treatment was performed with bioconductor and Limma library. Background substraction was performed using the Normexp correction with offset =50. Quantile normalization was then applied.  Features flagged in Feature Extraction as control, as Feature Non-uniform outliers, saturating or too weak were excluded.

source_name: Liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp labeling One color : Cy3 (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted with Trizol (Life Technologies) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Liver

tag: diet

value: ST diet + vehicule

tag: age

value: 12 weeks old

tag: Sex

value: female


title: WT-derived T-ALL 110 (RNA-Seq)


title: WT-derived T-ALL 108 (RNA-Seq)


title: WT-derived T-ALL 126 (RNA-Seq)


title: Liver from ST diet + vehicule, biological replicate #1


title: Liver from ST diet + pollutants, biological replicate #4

value: ST diet + pollutants


title: Liver from HFHS diet+ vehicule, biological replicate #3

value: HFHS diet+ vehicule


title: Liver from ST diet + pollutants, biological replicate #1


title: Liver from ST diet + pollutants, biological replicate #3


title: Liver from ST diet + pollutants, biological replicate #5


title: WT-derived T-ALL 48 (RNA-Seq)


title: WT-derived T-ALL 36 (RNA-Seq)


title: WT-derived T-ALL 7 (RNA-Seq)


title: Liver from HFHS diet+ vehicule, biological replicate #1


title: WT-derived T-ALL 128 (RNA-Seq)


title: Liver from ST diet + vehicule, biological replicate #2


title: WT-derived T-ALL 120 (RNA-Seq)


title: Liver from HFHS diet+ vehicule, biological replicate #4


title: 26_HiIIA_MQexposed

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Arabidopsis thaliana

organism: Zea mays

source_name: Zea mays leaf tissue

growth_protocol: Arabidopsis plants were grown  under  controlled  environmental  conditions  with  a  14h,  22  C°/  10h,  20°C  dark  /  light  period.   Zea mays plants were grown  under  controlled  environmental  conditions with 16h,  26°C/  8h,  20°C  light/dark  period.

extract_protocol:
Total RNA was extracted from ground leaf tissue using RNeasy plant mini kit
libraries were generated with the llumina Truseq strand-specific mRNA library preparation withhout size selection.

treatment_protocol: Seven week A.thaliana old plants were exposed to M. quadrilineatus for three days. Three week Z.mays old platns were exposed to  D. maidis for three days.

tag: line

value: HillA overexpressed

value: exposed to M. quadrilineatus

value: leaf


title: Liver from ST diet + pollutants, biological replicate #2


title: Liver from HFHS diet+ vehicule, biological replicate #5


title: Liver from HFHS diet+ vehicule, biological replicate #2


title: WT-derived T-ALL 5 (RNA-Seq)

value: BALB/c


title: WT-derived T-ALL 4 (RNA-Seq)

value: spleen


title: WT-derived T-ALL 3 (RNA-Seq)

value: tumor


title: Notch3 KO-derived T-ALL 1 (RNA-Seq)

value: Notch3 knockout


title: WT-derived T-ALL 111 (RNA-Seq)


title: Notch3 KO-derived T-ALL 2 (RNA-Seq)


title: Thymus, control 4 (RNA-Seq)

source_name: thymus

value: thymus

value: normal


title: Thymus, control 6 (RNA-Seq)


title: Thymus, control 5 (RNA-Seq)


title: WT-derived T-ALL 14 (RNA-Seq)


title: Thymus, control 3 (RNA-Seq)


title: Thymus, control 2 (RNA-Seq)


title: Thymus, control 1 (RNA-Seq)


title: RNAseq_MZezh2mutant_3_3hpf_rep5

city: Nijmegen

first: Leonie

middle: M

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
RNA-seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with --quantMode geneCounts
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw gene counts (.tab)

organism: Danio rerio

growth_protocol: Zebrafish (Danio rerio), were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning, one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. (Kimmel et al., 1995).

extract_protocol:
RNA-seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit.
RNA-seq: extraction was followed by fragmentation, cDNA synthesis, and KAPA-HYPERprep library preparation.

tag: strain background

value: TU/TLF mixed background

tag: genotype/variation

value: 3.3 hours post-fertilization

value: whole embryo


title: RNAseq_Wildtype_3_3hpf_rep4

value: wildtype


title: RNAseq_MZezh2mutant_3_3hpf_rep3


title: RNAseq_Wildtype_3_3hpf_rep5


title: RNAseq_MZezh2mutant_3_3hpf_rep4


title: RNAseq_MZezh2mutant_3_3hpf_rep6


title: RNAseq_Wildtype_3_3hpf_rep3


title: RNAseq_MZezh2mutant_0hpf_rep6

value: 0 hours post-fertilization


title: RNAseq_MZezh2mutant_3_3hpf_rep7


title: RNAseq_MZezh2mutant_0hpf_rep5


title: RNAseq_Wildtype_0hpf_rep4


title: ChIPseq_MZezh2mutant_H3K4me3_rep3

library_source: genomic

data_processing:
ChIPseq: reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters
ChIPseq: aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2
ChIPseq: peaks were called using macs2 version 2.1.1 with --broad and qvalue cutoff=1e-03 relative to input track, except for Ezh2 where qvalue cutoff was 1e-02. Peaks called in the input track alone were then subtracted from the peak sets and the remaining peaks separated by less than 1kb distance were merged using bedtools subtract and merge v2.20.1.
Genome_build: GRCz10
Supplementary_files_format_and_content: peak files (.bed)

molecule: genomic DNA

source_name: whole embryo

extract_protocol:
ChIP-seq: Embryos of 24 hpf were fixed, deyolked, and homogenized using pestles and sonication to isolate the chromatin
ChIP-Seq: In the regular non-spike in experiment zebrafish chromatin was incubated with antibody overnight. For spike-in experiments zebrafish chromatin was mixed with Drosophila spike-in chromatin (Active Motif 53083) and incubated overnight with H2Aγ (Active Motif 61686) and specific antibodies. After o/n antibody incubation the chromatin was extensive washed. The resulting ChIP-DNA was used as input for KAPA-HYPERprep library preparation.

value: 24 hours post-fertilization

tag: chip antibody

value: H3K4me3 (Millipore 04-745)


title: RNAseq_Wildtype_0hpf_rep3

tag: tissue


title: BM_lncRNA_8Gy_CBLB502_ip

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with CBLB502 (i.p.)

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression   Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in  Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US),  according to the manufacturer’s instructions. After 17 hours hybridization, slides  were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara,  CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent  technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent  technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by   Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA,  US).

source_name: Bone Marrow, 12hr, 8 Gy, CBLB502 (i.p.)

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,  One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the  manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004,  QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for  a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent  technologies, Santa Clara, CA, US).

treatment_protocol: The mice were pretreated with 10mg/kg Amifostime (i.p. 0.5 hr pre-IR), 0.2mg/kg CBLB502 (i.p. 0.5 hr pre-IR) and 150mg/kg Nilestriol (i.g. 48 hr pre-IR), and then radiated with 8 Gy gamma-radiation. At 12 hr post-radiation, samples of the bone marrow or hyprothalamus (pretreated 10 mg/kg Amifostine only) were obtained from the pooled three mice per group.

value: Bone marrow

tag: gender

value: male


title: RNAseq_MZezh2mutant_0hpf_rep4


title: BM_lncRNA_8Gy_PBS_ig

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated PBS (i.g.)

source_name: Bone Marrow, 12hr, 8 Gy, PBS (i.g.)


title: HY_lncRNA_8Gy_PBS_ip

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice Hypothalamus pretreated with PBS (i.p.)

source_name: Hypothalamus, 12hr, 8 Gy, PBS (i.p.)

value: Hypothalamus


title: BM_lncRNA_8Gy_Amifostine_ip

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with Amifostine (i.p.)

source_name: Bone Marrow, 12hr, 8 Gy, Amifositine (i.p.)


title: SLR14-treated 2

city: New Haven

first: Xiaodong

last: Jiang

address: 300 Cedar Street

institute: Yale University

description: 100bp pair-end sequencing

data_processing:
Base-calling: Illumina NovaSeq6000
Btrim to trim reads; TopHat2 for alignment for cellular gene analysis
DEseq2 was used to calculate differential gene expression
Genome_build: mn10
Supplementary_files_format_and_content: excel spreadsheet DEseq2 output

source_name: YUMMER1.7 melanoma

extract_protocol:
Tumors were removed, fresh frozen on dry ice. Total RNA was extracted using the Qiagen Rneasy PowerLyzer Tissue & Cells Kit (Cat No. 15055-50)
KAPA RNA library prep kit

treatment_protocol: At day 7 post tumor cell injection, 1 mg/kg SLR14 formulated with jetPEI in 5% glucose solution was intratumorally injected (total volume = 50 ul). Injection was performed every 3 days for a total of 3 cycles

value: YUMMER1.7 melanoma

tag: days

value: day 14 post tumor cell injection


title: vehicle-treated 1

description: 100bp pair-end sequencing


title: ChIPseq_Wildtype_H3K4me3_rep3

tag: cell type


title: vehicle-treated 3

description: 100bp pair-end sequencing

tag: strain


title: vehicle-treated 2

description: 100bp pair-end sequencing


title: MNAse-seq of total chromatin in rtt109D mutant

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

institute: CNRS

description:
Mnase digest of total chromatin from asynchronous cells
rtt109D_total_tss_aligned.txt
total chromatin Mnase digest in asynchronous cells

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points  were separated by barcode and the 5bp barcode was removed from the read sequence
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 1bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the average read count value was calculated and the data were normalized to one
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: tab-delimited text files of nucleosome occupancy for every gene at indicated time points (lines),  showing every 20th bp frpm  -500bp to the end of the gene coding sequence surrounding the transcription start site (marked as tss). Occupancy data start after the GWEIGHT header.

organism: Saccharomyces cerevisiae

source_name: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a chd1 deletion

growth_protocol: Cells were grown in SCD-URA over night at 30°C to an OD of 1.0. The next day the culture was diluted to OD=0.25 and cells were allowed to double once. Cell pellets were then transferred to preheated and premixed SCD-URA+ 10μM EdU media. Thymidine (to a final concentration of 5mM) was added after 5 min incubation with EdU at 30°C and incubated for another 5 min. Cells were then pelleted and transferred into fresh media with 5mM Thymidine and 200ml aliquots were taken at indicated time points (after the Thymidine incubation) and fixed as above.

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were treated with micrococcal nuclease. EdU from isolated nascent DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads. An input DNA aliquot was set aside prior to biotinylation.
nascent and input DNA samples, were treated with calf intestinal phosphatase (NEB), blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read), and PCR amplified and size selected by gel purification. For nascent libraries, the nascent strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: cell cycle

value: asynchronous

tag: edu incubation

tag: thymidine incubation (min)


title: BM_lncRNA_8Gy_Nilestriol_ig

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with Nilestriol  (i.g.)

source_name: Bone Marrow, 12hr, 8 Gy, Nilestriol (i.g.)


title: BM_lncRNA_0Gy_Nilestriol_ig

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with Nilestriol  (i.g.)

source_name: Bone Marrow, 12hr, 0 Gy, Nilestriol (i.g.)


title: BM_lncRNA_0Gy_CBLB502_ip

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with CBLB502 (i.p.)

source_name: Bone Marrow, 12hr, 0 Gy, CBLB502 (i.p.)


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [25 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
25 min after Thymidine chase, nascent chromatin


title: RNAseq_Wildtype_0hpf_rep5


title: RNAseq_MZezh2mutant_0hpf_rep3


title: SLR14-treated 3

description: 100bp pair-end sequencing


title: BM_lncRNA_0Gy_PBS_ig

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with PBS (i.g.)

source_name: Bone Marrow, 12hr, 0 Gy, PBS (i.g.)


title: BM_lncRNA_8Gy_PBS_ip

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with PBS (i.p.)

source_name: Bone Marrow, 12hr, 8 Gy, PBS (i.p.)


title: ChIPseq_Wildtype_Rnf2_rep2

tag: genotype

value: RING1B (Cell Signaling 5694S)


title: RNAseq_MZezh2mutant_rep7

data_processing:
reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with --quantMode geneCounts
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw gene counts (.tab)

extract_protocol:
Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit.
extraction was followed by fragmentation, cDNA synthesis, and KAPA-HYPERprep library preparation for paired-end samples or Illumina TruSeq Stranded RNA Kit for single samples


title: BM_lncRNA_0Gy_Amifostine_ip

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with Amifostine (i.p.)

source_name: Bone Marrow, 12hr, 0 Gy, Amifositine (i.p.)


title: BM_lncRNA_0Gy_PBS_ip

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with PBS (i.p.)

source_name: Bone Marrow, 12hr, 0 Gy, PBS (i.p.)


title: RNAseq_MZezh2mutant_rep6


title: HY_lncRNA_8Gy_Amifostine_ip

description: lncRNA and mRNA expression after 12hr in 8 Gy-irradiated mice Hypothalamus pretreated with Amifostine (i.p.)

source_name: Hypothalamus, 12hr, 8 Gy, Amifostine (i.p.)


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [6 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
6 min after Thymidine chase, nascent chromatin


title: RNAseq_MZezh2mutant_rep5


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [8 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
8 min after Thymidine chase, nascent chromatin


title: RNAseq_MZezh2mutant_rep4


title: HY_lncRNA_0Gy_Amifostine_ip

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice Hypothalamus pretreated with Amifostine (i.p.)

source_name: Hypothalamus, 12hr, 0 Gy, Amifostine (i.p.)


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [15 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
15 min after Thymidine chase, nascent chromatin


title: RNAseq_MZezh2mutant_rep3


title: RNAseq_Wildtype_rep6

source_name: Wildtype


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [6 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
6 min after Thymidine chase, nascent chromatin


title: RNAseq_Wildtype_rep5


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [2 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
2 min after Thymidine chase, nascent chromatin


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [8 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
8 min after Thymidine chase, nascent chromatin


title: HY_lncRNA_0Gy_PBS_ip

description: lncRNA and mRNA expression after 12hr in 0 Gy-irradiated mice Hypothalamus pretreated with PBS (i.p.)

source_name: Hypothalamus, 12hr, 0 Gy, PBS (i.p.)


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [2 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
2 min after Thymidine chase, nascent chromatin


title: ChIPseq_Wildtype_Input_DNA

data_processing:
reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters
aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2
peaks were called using macs2 version 2.1.1 with --broad and qvalue cutoff=1e-03 relative to input track, except for Ezh2 where qvalue cutoff was 1e-02.
Genome_build: GRCz10
Supplementary_files_format_and_content: peak files in BED6+3 format (.bed)

extract_protocol:
Embryos of 24 hpf were fixed, deyolked, and homogenized using pestles and sonication to isolate the chromatin
In the regular non-spike in experiment zebrafish chromatin was incubated with antibody overnight. For spike-in experiments zebrafish chromatin was mixed with Drosophila spike-in chromatin (Active Motif 53083) and incubated overnight with H2Aγ (Active Motif 61686) and specific antibodies. After o/n antibody incubation the chromatin was extensive washed. The resulting ChIP-DNA was used as input for KAPA-HYPERprep library preparation.

value: AB

value: None (Input)


title: RNAseq_Wildtype_rep3


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [0 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
0 min after Thymidine chase, nascent chromatin


title: ChIPseq_MZezh2mutant_H3K4me3_rep1


title: ChIPseq_MZezh2mutant_H3K4me3_rep2


title: ChIPseq_Wildtype_H3K4me3_rep2


title: RNAseq_MZezh2mutant_rep2


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [4 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate1_tss_aligned.txt
4 min after Thymidine chase, nascent chromatin


title: RNAseq_MZezh2mutant_rep1


title: ChIPseq_Wildtype_H3K4me3_rep1


title: RNAseq_Wildtype_rep2


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [4 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
4 min after Thymidine chase, nascent chromatin


title: ChIPseq_MZezh2mutant_Rnf2_rep1


title: ChIPseq_MZezh2mutant_Rnf2_rep2


title: RNAseq_Wildtype_rep1


title: ChIPseq_Wildtype_Rnf2_rep1


title: ChIPseq_MZezh2mutant_H3K27me3_rep2

description: Spiked-in drosophila chromatin (Active Motif 53083) and anti-H2Aγ (Active Motif 61686) antibody were used according to manufacturer's protocol to validate experiment

value: H3K27me3 (Millipore 07-449); H2Aγ (Active Motif 61686)


title: ChIPseq_Wildtype_H3K27me3_rep2

value: TU/TLF mixed background


title: ChIPseq_MZezh2mutant_H3K27me3_rep1

value: H3K27me3 (Millipore 07-449)


title: BM_miRNA_8Gy_Nilestriol_ig

description: miRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with Nilestriol  (i.g.)

hyb_protocol: Each slide was hybridized with 100ng Cy3‐labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat# 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US) at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent  technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent   technologies, Santa Clara, CA, US) with default settings.

label_protocol: Total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted, pooled, and purified using miRNeasy Mini Kit (QIAGEN, GmBH, Germany) following the manufacturer’s instructions, and the RNA integrity number was verified on an Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The mice were pretreated with 10mg/kg Amifostime (i.p. 0.5 hr pre-IR), 0.2mg/kg CBLB502 (i.p. 0.5 hr pre-IR) and 150mg/kg Nilestriol (i.g. 48 hr pre-IR), and then radiated with 8 Gy gamma-radiation. At 12 hr post-radiation, samples of the bone marrow or hyprothalamus (pretreated with PBS or 10 mg/kg Amifostine) were obtained from the three mice per group.


title: BM_miRNA_8Gy_CBLB502_ip

description: miRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with CBLB502 (i.p.)

source_name: Bone Marrow, 12hr, 8 Gy, CBLB502 (i.p.)


title: HY_miRNA_0Gy_PBS_ip

description: miRNA expression after 12hr in 0 Gy-irradiated mice Hypothalamus pretreated with PBS (i.p.)


title: BM_miRNA_8Gy_Amifostine_ip

description: miRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with Amifostine (i.p.)


title: ChIPseq_Wildtype_Ezh2_rep1

value: whole embryo

value: Ezh2 (Cell Signaling 5246S)


title: ChIPseq_Wildtype_H3K27me3_rep1

value: wildtype


title: ChIPseq_Wildtype_Ezh2_rep2

value: 24 hours post-fertilization

value: Ezh2 (Cell Signaling 5246S); H2Aγ (Active Motif 61686)


title: BM_miRNA_8Gy_PBS_ig

description: miRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated PBS (i.g.)

source_name: Bone Marrow, 12hr, 8 Gy, PBS (i.g.)

value: Bone marrow


title: BM_miRNA_8Gy_PBS_ip

description: miRNA expression after 12hr in 8 Gy-irradiated mice bone marrow pretreated with PBS (i.p.)

value: male


title: ChIPseq_MZezh2mutant_Ezh2_rep1


title: HY_miRNA_0Gy_Amifostine_ip

description: miRNA expression after 12hr in 0 Gy-irradiated mice Hypothalamus pretreated with Amifostine (i.p.)

value: Hypothalamus


title: S2_inputDNA

first: Wentao

last: Yu

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science,Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Built genome index from Drosophila melanogaster genome(BDGP6)with bowtie2-build
Reads were aligned to Drosophila genome BDGP6 index with bowtie2
Converted sam files to bam files with samtools
Peaks were called from the aligned reads using MACS2 callpeak
Peaks annotation using R package ChIPseeker
Genome_build: Drosophila melanogaster genome (BDGP6)
Supplementary_files_format_and_content: fold change and p-value of peak

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were cultured in Drosophila Schneider’s Medium (Invitrogen, Carlsbad, California, United States) with 10% fetal bovine serum, 100 U/ml of penicillin, and 100 mg/ml of Streptomycin.

extract_protocol:
S2 cells were cross-linked for 15 min at 37℃ in 1 ml of 1% formaldehyde in PBS buffer. The cross-linking was stopped by adding Glycine to a final concentration of 0.125M. Cells were sonicated with a Bioruptor sonicator to yield genomic DNA fragments with an average size of about 200 bp.  protein-DNA complexes were isolated with Lola antibody. Genomic DNA was purified with a DNA purification kit (QIAGEN).
Libraries were prepared using standard Illumina protocols.

tag: cell line

value: embryo cell line


title: BM_miRNA_0Gy_Nilestriol_ig

description: miRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with Nilestriol  (i.g.)


title: Lola_S2_ChIPSeq


title: HY_miRNA_8Gy_PBS_ip

description: miRNA expression after 12hr in 8 Gy-irradiated mice Hypothalamus pretreated with PBS (i.p.)

source_name: Hypothalamus, 12hr, 8 Gy, PBS (i.p.)


title: BM_miRNA_0Gy_CBLB502_ip

description: miRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with CBLB502 (i.p.)


title: BM_miRNA_0Gy_PBS_ig

description: miRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with PBS (i.g.)


title: BM_miRNA_0Gy_Amifostine_ip

description: miRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with Amifostine (i.p.)


title: BM_miRNA_0Gy_PBS_ip

description: miRNA expression after 12hr in 0 Gy-irradiated mice bone marrow pretreated with PBS (i.p.)


title: ChIPseq_MZezh2mutant_Ezh2_rep2


title: HY_miRNA_8Gy_Amifostine_ip

description: miRNA expression after 12hr in 8 Gy-irradiated mice Hypothalamus pretreated with Amifostine (i.p.)


title: Periaortic WAT, Cold, replicate 5

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

hyb_protocol: Hybridization was performed by preparing a cRNA target solution containing 1.875 ng Cy3-labeled cRNA, 1.875 ng Cy5-labeled pool cRNA, 25 μl of 10Xblocking agent, 5 μl 25X Fragmentation Buffer in a total volume of 125 μl. The samples were incubated at 60 ºC for 30 min, and then immediately cooled on ice for one minute. After that, 125 μl 2x GEx hybridization buffer HI-RPM was added and hybridized on 2x400k G4861A whole genome Agilent arrays (Agilent Technologies, Inc., Santa Clara, CA, USA) for 17h at 65 ºC in Agilent hybridization chambers in an Agilent hybridization oven rotating at 10 rpm. After hybridization, the arrays were subsequently washed with GE wash buffer 1, for 1 min at room temperature, and GE wash buffer 2, for 1 min at approximately 37 ºC, according to manufacturers protocol (Agilent Technologies).

scan_protocol: The arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies Scanner G2505C US22502548, Agilent Tecnologies) with a Profile AgilentG3_GX_2Color.

data_processing: Data were exported into GeneMaths XT 2.12 (Applied Mathematics, Sint-Martens-Latem, Belgium) for background correction and normalization.

organism: Mustela putorius furo

source_name: periaortic white adipose tissue

label_protocol: 0.2 mg RNA of each sample was reverse transcribed using the Agilent Low Input Quick Amp Labeling kit (Agilent), according to the manufacturer’s protocol with some modifications (all materials and reagents are from Agilent Technologies, Palo Alto, CA, US). Half of the cDNA sample (5μl) was used for linear RNA amplification and labeling with Cy5 or Cy3. All reactions were performed using half of the amounts indicated by the manufacturer (van Schothorst et al., 2007). Briefly, a transcription master mix was prepared (0.375 μl nuclease-free water; 1.6 μl 5 X Transcription buffer;  0.3 μl 0.1 M DTT; 0.5 μl NTP mix; 0.115 μl T7 RNA Polymerase Blend and 0.12 cyanine 3-CTP or cyanine 5-CTP per sample) was added to 5 μl cDNA.  In vitro transcription and labeling were carried out at 40 ºC for 2 h. The labeled cRNA samples were purified using Qiagen Rneasy minispin columns (Qiagen, Venlo, The Netherlands). Dye incorporation and cRNA concentration was measured using the microarray measurement of the Nanodrop spectrophotometer (NanoDrop Technologies). Yield of each individual sample was 1.875ng and specific activity 6.0 pmol Cy3 or Cy5 per μg cRNA. All approved high quality Cy5 cRNA’s were pooled to serve as standard reference pool; the pool consisted of RNA isolated from different tissues to increase signal distribution over all probes.

extract_protocol: Total RNA from periaortic and inguinal WAT samples was extracted using Tripure Reagent (Roche Diagnostics, Barcelona, Spain). RNA samples were purified with E.Z.N.A. MicroElute RNA Clean Up (Omega Biotek, Vermont, USA), and with 3M sodium acetate and absolute ethanol. RNA yield was quantified using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom).

treatment_protocol: Male Ferrets (Mustela Putorius Furo from Cunipic, Lleida, Spain) of 3 months of age were used. Ferrets were distributed into two groups (n=7): a control group, acclimatized to room temperature (22±2ºC), and a cold group, acclimatized to 4ºC for 1 week. The animals were weighed before and after cold exposure. Cold-exposed animals were housed individually. All animals were exposed to a light/dark cycle os 12 h and had free acces to water and diet (Gonzalo Zaragoza Manresa SL, Alicante, Spain). The animals were anesthetized using 10mg/kg of Ketamine hydrochloride (Imalgène 1000, Merial Laboratorios SA, Lyon, France) and 80 mg/kg medetomidine (Domtor, Orion Pharma, Espoo, Finland), and sacrificed by exsanguination after cardiac punction. White adipose tissue depots were rapidly removed and weighed, frozen in liquid nitrogen and stored at -80ºC until RNA analysis.

value: periaortic WAT

value: 3 months

source_name: periaortic and inguinal white adipose tissue and PBMC


title: RNAseq_MZezh2mutant_3_3hpf_rep2

value: 3.3 hours post-fertilization


title: RNAseq_MZezh2mutant_3_3hpf_rep1


title: CLL cells, 603_WT

city: Aviano

first: Federico

last: Pozzo

state: PN

address: via Franco Gallini 2

department: Department of Translational Research

country: Italy

institute: Centro di Riferimento Oncologico (CRO) di Aviano IRCCS

description:
Constitutive Gene expression of CLL cells.
603_WT

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Signal were normalized using the Quantile method.

source_name: CLL Peripheral Blood (PB). Leukemic cells >90%.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from CLL cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2200 Tapestation (Agilent Technologies)

treatment_protocol: not applicable

value: whole blood

value: CLL cells

tag: mutation


title: Patient NO.27_lesion adjacent tissue_rep1

first: Chen

last: Zhang

address: NO.11, Xizhimen South Street

department: Gynecological Oncology Center

institute: Peking University People’s Hospital

description: lncRNA/mRNA expression files of lesion adjacent tissue in Patient NO.27

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Patient NO.27, lesion adjacent tissue, replicate 1

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: lesion adjacent tissue

tag: age


title: CLL cells, 2360_SF3B1

description:
Constitutive Gene expression of CLL cells.
2360_SF3B1


title: CLL cells, 1995_SF3B1

description:
Constitutive Gene expression of CLL cells.
1995_SF3B1


title: RNAseq_Wildtype_3_3hpf_rep2

value: TU/TLF mixed background


title: Periaortic WAT, Cold, replicate 6

value: periaortic and inguinal white adipose tissue and PBMC


title: Patient NO.25_lesion adjacent tissue_rep1

description: lncRNA/mRNA expression files of lesion adjacent tissue in Patient NO.25

source_name: Patient NO.25, lesion adjacent tissue, replicate 1


title: CLL cells, 1210_SF3B1

description:
Constitutive Gene expression of CLL cells.
1210_SF3B1


title: CLL cells, 2276_NOTCH

description:
Constitutive Gene expression of CLL cells.
2276_NOTCH

value: NOTCH


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course rtt109D mutant [15 min after Thymidine chase]

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase
PC_5_5_EdU_rtt109D_replicate2_tss_aligned.txt
15 min after Thymidine chase, nascent chromatin

source_name: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a chd1 deletion

value: asynchronous


title: CLL cells, 995_WT

description:
Constitutive Gene expression of CLL cells.
995_WT


title: Periaortic WAT, Cold, replicate 2


title: Periaortic WAT, Cold, replicate 4


title: CLL cells, 2147_WT

description:
Constitutive Gene expression of CLL cells.
2147_WT


title: CLL cells, 1620_SF3B1

description:
Constitutive Gene expression of CLL cells.
1620_SF3B1


title: Periaortic WAT, Cold, replicate 3


title: RNAseq_Wildtype_3_3hpf_rep1

value: wildtype

value: whole embryo


title: Periaortic WAT, Control, replicate 6


title: RNAseq_MZezh2mutant_0hpf_rep2

value: 0 hours post-fertilization


title: Patient NO.13_lesion adjacent tissue_rep1

description: lncRNA/mRNA expression files of lesion adjacent tissue in Patient NO.13

source_name: Patient NO.13, lesion adjacent tissue, replicate 1


title: Patient NO.21_lesion adjacent tissue_rep1

description: lncRNA/mRNA expression files of lesion adjacent tissue in Patient NO.21

source_name: Patient NO.21, lesion adjacent tissue, replicate 1


title: CLL cells, 338B_WT

description:
Constitutive Gene expression of CLL cells.
338B_WT


title: Periaortic WAT, Control, replicate 7


title: Patient NO.27_eutopic endometrium_rep1

description: lncRNA/mRNA expression files of eutopic endometrium in Patient NO.27

source_name: Patient NO.27, eutopic endometrium, replicate 1

value: eutopic endometrium


title: Patient NO.25_eutopic endometrium_rep1

description: lncRNA/mRNA expression files of eutopic endometrium in Patient NO.25

source_name: Patient NO.25, eutopic endometrium, replicate 1


title: CLL cells, 524_WT

description:
Constitutive Gene expression of CLL cells.
524_WT


title: RNAseq_MZezh2mutant_0hpf_rep1


title: CLL cells, 811_WT

description:
Constitutive Gene expression of CLL cells.
811_WT


title: CLL cells, 1226_WT

description:
Constitutive Gene expression of CLL cells.
1226_WT


title: Periaortic WAT, Control, replicate 5

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

value: male


title: Patient NO.13_eutopic endometrium_rep1

description: lncRNA/mRNA expression files of eutopic endometrium in Patient NO.13

source_name: Patient NO.13, eutopic endometrium, replicate 1


title: RNAseq_Wildtype_0hpf_rep1


title: Patient NO.27_ectopic endometrium_rep1

description: lncRNA/mRNA expression files of ectopic endometrium in Patient NO.27

source_name: Patient NO.27, ectopic endometrium, replicate 1

value: ectopic endometrium


title: pmiR-203-U251_Experimental_Repeat_3

city: Chicago

first: Sajani

middle: S

last: Lakka

state: IL

address: 909 S Wolcott,, College of Medicine Research Building

department: Medicine

institute: The University of Illinois at Chicago

data_processing:
Briefly, RNA-sequencing (RNA-seq) was performed by the Illumina HiSeq 4000 system using the standard pair-end sequencing protocol. Approximately 70 to 80 million 150-bp paired reads were obtained and mapped to the reference genome.
Image analysis and base calling were performed using Solexa pipeline v.18 (Off-Line Base Caller Software, v1.8).
The trimmed sequence reads (trimmed 5’, 3’-adaptor based cutadapt) were aligned to the human reference genome UCSC build hg19 (GRCh37) assembly using Hisat2 software
The transcript abundances for each sample was estimated with StringTie [28, 29], and gene and transcript level were calculated as FPKM (fragments per kilobase per million mapped reads) using R package Ballgown
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FPKM (fragments per kilobase per million mapped reads)

source_name: miR-203 expressing U251 cells

growth_protocol: Glioma Cell line U251 Cell Culture Standard Protocol

extract_protocol:
For whole transcriptome analysis, total RNA was extracted from miR-203 expressing U251 stable cell lines (pmiR-203) and pEV control samples in biological triplicate. RNA extractions were performed using RNeasy Mini Kit (Qiagen Inc., Valencia, CA) with DNase treatment on column following manufacture’s instruction.
RNA-seq library was prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific.

treatment_protocol: miR-203 expressing U251 cells were generated and total RNA was extracted from U251 pEV control samples and U251 pmiR-203 samples.

value: Human GBM Cell Type

tag: passages


title: Periaortic WAT, Cold, replicate 1

value: periaortic WAT


title: Patient NO.21_eutopic endometrium_rep1

description: lncRNA/mRNA expression files of eutopic endometrium in Patient NO.21

source_name: Patient NO.21, eutopic endometrium, replicate 1


title: CLL cells, 1110_WT

description:
Constitutive Gene expression of CLL cells.
1110_WT


title: Periaortic WAT, Control, replicate 4

value: 3 months


title: Periaortic WAT, Control, replicate 2


title: CLL cells, 1028_WT

description:
Constitutive Gene expression of CLL cells.
1028_WT


title: pmiR-203-U251_Experimental_Repeat_2


title: RNAseq_Wildtype_0hpf_rep2


title: pmiR-203-U251_Experimental_Repeat_1


title: KOHF3

city: Houston

first: Kristin

last: Eckel-Mahan

state: TX

address: 1825 Pressler St., SRB 437B

department: Institute of Molecular Medicine

institute: UT Health Sciences Center at Houston

data_processing:
Raw image data files from Illumina were transformed to Sequenced Reads by CASAVA base recognition. Raw Data was stored in FASTQ(fq) format. All sequence alignments were performed using Tophat program.
Genes were mapped using STAR sofware v2.5 and quantification was performed using HTSeq v0.6.1. Paired-end clean reads were aligned to the reference genome.
Expression levels were quanitified using HTSeq v0.6.1, which counted the read numbers mapped for each gene. FPKMs for each gene were calculated based on the length of the gene and reads count mapped to this specific gene.
Differentially expressed genes were determined using DESeq2 V2_1.6.3 and padj<0.05.  P values were adjusted using the Benjamini and Hochberg's approach for controlling the FDR.
Genome_build: GRCm38-mm10 genome served as the reference genome and was access directly from NCBI. Indexes were built using STAR.
Supplementary_files_format_and_content: Data in processed data file include Reads Per Kilobase of exon model per Million mapped reads (FPKM) for each sample.

source_name: liver

extract_protocol:
Trizol RNA extraction, per manufacturer's instructions.
Per Novogene's library construction

value: Hnf4a liver knockout

tag: treatment

value: high fat diet feeding


title: KOHF2


title: CLL cells, 1999_WT

description:
Constitutive Gene expression of CLL cells.
1999_WT

value: whole blood

value: CLL cells


title: CLL cells, B2501_SF3B1

description:
Constitutive Gene expression of CLL cells.
B2501_SF3B1


title: Periaortic WAT, Control, replicate 3


title: KOHF1


title: Periaortic WAT, Control, replicate 1


title: RNAseq_Wildtype_rep4

source_name: Wildtype

value: TU/TLF mixed background

value: 24 hours post-fertilization


title: Patient NO.21_ectopic endometrium_rep1

description: lncRNA/mRNA expression files of ectopic endometrium in Patient NO.21

source_name: Patient NO.21, ectopic endometrium, replicate 1


title: Patient NO.13_ectopic endometrium_rep1

description: lncRNA/mRNA expression files of ectopic endometrium in Patient NO.13

source_name: Patient NO.13, ectopic endometrium, replicate 1


title: Patient NO.25_ectopic endometrium_rep1

description: lncRNA/mRNA expression files of ectopic endometrium in Patient NO.25

source_name: Patient NO.25, ectopic endometrium, replicate 1


title: Inguinal WAT, Cold, replicate 6

source_name: inguinal white adipose tissue

extract_protocol: Total RNA from inguinal WAT samples was extracted using Tripure Reagent (Roche Diagnostics, Barcelona, Spain). RNA samples were purified with E.Z.N.A. MicroElute RNA Clean Up (Omega Biotek, Vermont, USA), and with 3M sodium acetate and absolute ethanol. RNA yield was quantified using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom).

treatment_protocol: Male Ferrets (Mustela Putorius Furo from Cunipic, Lleida, Spain) of 3 months of age were used. Ferrets were distributed into two groups (n=7): a control group, acclimatized to room temperature (22±2ºC), and a cold group, acclimatized to 4ºC for 1 week. The animals were weighed before and after cold exposure. Cold-exposed animals were housed individually. All animals were exposed to a light/dark cycle os 12 h and had free acces to water and diet (Gonzalo Zaragoza Manresa SL, Alicante, Spain). The animals were anesthetized using 10mg/kg of Ketamine hydrochloride (Imalgène 1000, Merial Laboratorios SA, Lyon, France) and 80 mg/kg medetomidine (Domtor, Orion Pharma, Espoo, Finland), and sacrificed by exsanguination after cardiac punction. White adipose tissues were rapidly removed and weighed, frozen in liquid nitrogen and stored at -80ºC until RNA analysis.

value: inguinal white adipose tissue

source_name: inguinal WAT mixed with other tissues

value: inguinal WAT mixed with other tissues


title: KOVC3

value: vivarium chow feeding


title: pEV-U251_Control_Repeat_3

source_name: control pEV U251 cells


title: pEV-U251_Control_Repeat_2


title: KOVC1


title: WTHF3

value: wild-type


title: LM-FZC3

city: Changsha

first: Zhipeng

last: Gao

address: Nong da road 1#

institute: Hunan Agriculture University

description: with the treatment of linalool

data_processing:
Illumina Casava1.7 software were used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.

organism: Listeria monocytogenes ATCC 19115

source_name: bacterial cells with the treatment of linalool

growth_protocol: the bacterial cells were incubated by using Brain Heart Infusion broth (BHI, Guangdong Huankai Microbial) at 37 °C.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol of Majorbio Company (Shanghai, China)
RNA libraries were prepared for sequencing Illumina TruseqTM RNA sample prep Kit

value: bacterial cells


title: pEV- U251_Control_Repeat_1


title: LM-FZC2

description: with the treatment of linalool


title: CLL cells, B2410_NOTCH

description:
Constitutive Gene expression of CLL cells.
B2410_NOTCH

source_name: CLL Peripheral Blood (PB). Leukemic cells >90%.

value: NOTCH


title: Inguinal WAT, Cold, replicate 4

value: male


title: Inguinal WAT, Cold, replicate 5


title: CLL cells, B1958_SF3B1

description:
Constitutive Gene expression of CLL cells.
B1958_SF3B1


title: Inguinal WAT, Cold, replicate 3


title: CLL cells, 2226_WT

description:
Constitutive Gene expression of CLL cells.
2226_WT


title: CLL cells, B2052_NOTCH

description:
Constitutive Gene expression of CLL cells.
B2052_NOTCH


title: CLL cells, 2298_SF3B1

description:
Constitutive Gene expression of CLL cells.
2298_SF3B1


title: CLL cells, 2546_SF3B1

description:
Constitutive Gene expression of CLL cells.
2546_SF3B1


title: WTHF1


title: WTHF2


title: WTVC3


title: LM-DZ3

description: without the treatment of linalool

source_name: bacterial cells without the treatment of linalool


title: Inguinal WAT, Cold, replicate 1

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.


title: Inguinal WAT, Cold, replicate 2


title: Inguinal WAT, Control, replicate 5


title: Inguinal WAT, Control, replicate 7


title: LM-DZ2

description: without the treatment of linalool


title: WTVC2


title: Inguinal WAT, Control, replicate 6


title: CLL cells, 1558_WT

description:
Constitutive Gene expression of CLL cells.
1558_WT


title: LM-DZ1

description: without the treatment of linalool


title: LM-FZC1

description: with the treatment of linalool


title: CLL cells, 1146_WT

description:
Constitutive Gene expression of CLL cells.
1146_WT


title: Inguinal WAT, Control, replicate 3


title: KOVC2


title: CLL cells, 2495_SF3B1

description:
Constitutive Gene expression of CLL cells.
2495_SF3B1


title: Inguinal WAT, Control, replicate 4


title: Sample_70_longRNA

status: Public on Sep 06 2019

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description:
Sperm_RNAseq
RPKMgenomic.txt

data_processing:
For long RNA samples, paired-end reads were trimmed of adaptors and low-quality bases using Trimmomatic (version 0.36) [217], using default parameters (2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15), and requiring a minimum read length of 50 bp (MINLEN:50). The TruSeq Universal adaptor (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) was used as input to Trimmomatic.
For long RNA samples, trimmed paired and unpaired reads were aligned to the consensus human ribosomal RNA (GenBank: U13369.1) using HISAT2 (version 2.0.6) and the non-default parameters (-p10 --max-seeds 30 -k 2), then aligned to the human genome (hg38) and exogenous RNA spike-in sequences, using the same HISAT2 parameters. Reads without alignments in either U13369.1, the human genome (hg38), or an exogenous RNA were further assessed for alignments to repeat sequences (RepBase, February 2017 release), using HISAT2, with the following parameters (-p10 --no-spliced-alignment --max-seeds 10 -k 3). Reads without alignments in either U13369.1, hg38, an exogenous RNA, or RepBase were aligned to bacterial and viral genomes using Kraken (version 0.10.5-beta) and Jellyfish (version 1.1.10), implementing the full Kraken library and filtering alignments with a threshold of 0.15. Read alignments to the human genome, exogenous RNAs, and U13369.1 were processed to remove duplicated reads using Picardtools MarkDuplicates (version 1.129).
For long RNA samples, RNA element (RE) discovery algorithm (REDa) was applied to genomic read alignments, and expression in Reads Per Kilobase per Million (RPKM) for the RE loci was calculated. Due to the use of REs, rather than whole transcripts, Paired-end read alignments were treated as individual (single) reads, and the common FPKM value was replace by RPKM. Depending on a read pair’s insert size and RE length, this approach ran the risk of inflating the read count for a given RE. To mitigate this risk, read counts were assessed for the forward and reverse reads separately, with the read count from single (non-paired due to mate loss during quality control) reads were added to the forward and reverse read counts. The averaged read count between the forward and reverse reads were then used for generating the RPKM values.
For small RNA libraries, reads were trimmed of adaptors and low-quality bases, followed by removal of reads smaller than 13 bp. sncRNAbench (version 10.14) was used for assigning reads to small RNA species and repeat classes, followed by a custom code for generating normalized expression values (RPM- Reads Per Million).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include RPKM values for long RNA libraries and RPM values for small RNA libraries

source_name: Ejaculated spermatozoa

extract_protocol:
Sperm samples were brought up to 1ml volume with PureSperm Buffer (Nidacon) and laid onto a 50% PureSperm (Nidacon) gradient, then centrifuged at 300xg for 20 minutes. The pellet was removed and washed in PureSperm Buffer. Each sample was added to a 2ml tube containing 500ul RLT buffer (Qiagen) with 7.5ul BME (14.3M), 100mg 0.2mm nuclease free SS beads. The sample were homogenized, 500ul Qiazol (Qiagen) added and homogenized again. 200ul chloroform (0.124M) was added and samples shaken by hand then centrifuged at 12,000xg for 20 minutes at 4⁰C and the upper aqueous layer removed. RNA was isolated from the aqueous layer using a customized Qiacube (Qiagen) protocol. RNA samples were treated with 4U Turbo DNase (Ambion) for 20 minutes at room temperature.  Samples were tested for DNA contamination by RT-PCR and intron spanning PRM1 primers. Samples still containing DNA were treated a second time and tested again by RT-PCR. The RNA samples void of DNA were quantified with a fluorescent assay as described. An aliquot of RNA (5 ng or 10 ng) of each sample was used to make cDNA with SuperScript III RT (Invitrogen). The cDNAs were used as template for RT-PCR with intron spanning PRM1 primers providing verification of RNA.
Two nanograms of RNA per sample was used with the Seqplex (Sigma-Aldrich) amplification kit prior to library construction. Fifty nanograms of Seqplex cDNA product was used with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing at a concentration of 2 nM per sample. All samples were subject to paired-end sequencing using either the NextSeq 500 (Illumina) sequencer, HiSeq 2500 (Illumina) sequencer or the HiSeq 4000 (Illumina) sequencer. One nanogram of small RNA per sample was used with the NEXTflex Small RNA-Seq Kit v2 (Bioo Scientific) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing. Samples were subject to paired-end sequencing using the MiSeq (Illumina) sequencer.

value: spermatozoa

tag: study subject

tag: visit number

tag: visit type

value: Crossover

tag: dbp level

tag: rna fraction

value: long RNA


title: Sample_71_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossback


title: Sample_38_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_36_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Baseline


title: LF82 transcripts (with DSS, Mouse#16)

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49558

data_processing:
We downloaded the reads files from the Sequencing Core’s storage, and concatenated those into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC (version 0.10.0) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads from the samples from the two strains to respective E. Coli reference genome sequence (NCBI LF82) [5, 6] using Bowtie2 (version 2.1.0). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation and differential expression analysis, using respective reference genome sequence reference transcriptome annotation. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Genome_build: GCF_000284495.1
Supplementary_files_format_and_content: Two text files of raw mapped read counts

organism: Escherichia coli LF82

source_name: Cecal content

extract_protocol:
Total RNA was extracted by combining Phenol:Chloroform:Isoamyl Alcohol (pH4.5, Ambion 9720) and LiCl precipitation (Ambion) according to the manufacturer's instructions. Then, isolated RNAs were treated with DNase (Ambion) and RNeasy (QIAGEN). Further, bacterial ribosomal RNA was depleted by Ribo-zero kit (illumina). Isolated RNA was assessed for quality using the TapeStation (Agilent).
Samples with RNA Integrity Numbers (RINs) of 8 or greater were prepped using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), NEBNext Ultra RNA Library Prep kit (NEB) and NEB Next Multiplex Adaptors for Illumina (NEB, E7335, E7500, E6609, E7600). Where (10ng up to 1μg) of total RNA was converted to mRNA using a poly A purification. The mRNA is then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA were then adenylated and adapters were ligated. One of the adapters that was ligated has a 6 nucleotide barcode that will be unique for each sample which allowed us to sequence more than one sample in each lane of the Illumina HiSeq flow cell. The products were purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems). Sixteen samples were multiplexed and pooled. They were clustered on the cBot (Illumina) and sequenced over two lanes on a 50 cycle single end on a HiSeq 2500 in High Output mode using version 4 reagents according to manufacturer’s protocols

treatment_protocol: Cecal contents (100-300mg) from E. coli mono-colonized germ-free B6 mice treated with or without 1.5 % DSS for 5 days were isolated (N=4, each group).

tag: agent

value: DSS


title: LF82 transcripts (with DSS, Mouse#15)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49557


title: WTVC1


title: LF82 transcripts (with DSS, Mouse#14)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49556


title: Sample_69_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: cell type


title: Sample_37_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_92_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: CLL cells, 1326_NOTCH

description:
Constitutive Gene expression of CLL cells.
1326_NOTCH

tag: tissue

value: whole blood


title: CLL cells, 2071_NOTCH

description:
Constitutive Gene expression of CLL cells.
2071_NOTCH

value: CLL cells


title: shSCR

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

description: MicroRNA expression data from breast cancer cells treated with shSCR.

hyb_protocol: The labeled RNA was purified and hybridized to miRNA arrays according to the Agilent manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA), and analyzed using Agilent feature extraction software version 10.7.

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent). The default 90th percentile normalization method were performed for date preprocessing.

source_name: shSCR MCF-7 Cells

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.2 ug RNA using the Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions, followed by Micro Bio-spin 6 column purification (Bio-Rad).

growth_protocol: MCF-7 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol: Total RNA was extracted from the MCF-7 cells using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were checked by optical density of NanoDrop ND-1000 and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: MCF-7 cells

value: transfection with shSCR


title: shGATA3

description: MicroRNA expression data from breast cancer cells treated with shGATA3.

source_name: shGATA3 MCF-7 Cells

value: transfection with shGATA3


title: Human atrial tissue sample in age group SR70, replication 2 [mRNA]

last: Yao

address: No 2 Anzhen Road

institute: Beijing Anzhen Hospital

data_processing:
Raw mRNA-seq reads were first inspected for overall quality by FastQC and then cleaned by Cutadapt script (Andrews et al., 2010; Martin et al., 2011).
The cleaned reads were mapped to human genome hg19/GRCh37 using the Subread aligner (Liao et al., 2013), which allows fast and efficient mapping for short reads less than 160 bp.
gene-level quantification was performed using featureCounts (Liao et al., 2014), which is a reads summarization program to efficiently count the mapped reads for genomic features (i.e., genes and exons). In this study, all human genes under genome build hg19 were retrieved via R annotation package org.Hs.eg.db.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized read counts by library size

source_name: Right atrial appendage

extract_protocol:
The total RNA was extracted from the frozen human right atrial appendages using TRIZOL reagent following the manufacturer’s protocol. The RNA yield and purity were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) and NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, USA).
For transcriptomic profiling, twelve human right atrial tissues were subjected to mRNA-seq according to the BIOPIC recommended workflow for mRNA-seq. A proportion (~2.5 μg) of twelve isolated total RNA samples was used to generate cDNA libraries using Illumina TruSeq RNA Sample Preparation v2 Kit (Lot # RS-122-2001, RS-122-2002). Each library was sequenced in one or two lanes (see below)

tag: gender

value: Male

value: aortic valve replacement


title: Human atrial tissue sample in age group SR70, replication 1 [mRNA]


title: Human atrial tissue sample in age group SR70, replication 3 [mRNA]

value: Female


title: CLL cells, B2496_NOTCH

description:
Constitutive Gene expression of CLL cells.
B2496_NOTCH


title: LF82 transcripts (without DSS, Mouse#11)

institute: University of Michigan

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49553


title: LF82 transcripts (without DSS, Mouse#12)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49554


title: LF82 transcripts (without DSS, Mouse#10)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49552


title: LF82 transcripts (without DSS, Mouse#9)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49551


title: Inguinal WAT, Control, replicate 2

value: inguinal white adipose tissue

value: 3 months

value: inguinal WAT mixed with other tissues


title: LF82 transcripts (with DSS, Mouse#13)

description:
K12_CuffDiff_rawCountsMatrix.txt
Sample_49555


title: Human atrial tissue sample in age group SR60, replication 3 [mRNA]


title: Human atrial tissue sample in age group SR60, replication 2 [mRNA]


title: Human atrial tissue sample in age group SR60, replication 1 [mRNA]


title: Inguinal WAT, Control, replicate 1

description: Cy5 samples were pooled on a equimolar basis and served as reference pool, and individual Cy3-labelled samples were hybridized against the reference pool.

value: male


title: Human atrial tissue sample in age group SR70, replication 3

data_processing:
The overall quality of raw reads was evaluated using program FastQC. Then raw reads were trimmed to remove adapter sequences using Cutadapt script.
The cleaned reads were mapped to human genomes GRCh38 by Burrows-Wheeler Aligner (BWA) with parameters (-t 15, -n 1, -o 0, -e 0, -l 8, -k 0).
The mapped reads were sorted and indexed using samtools with BAM format. The BAM data from multiple runs for the same sample were merged before miRNA quantification.
Python-based program HTSeq was used to quantify the expression level of known mature miRNAs curated in the recent human miRBase database at the time of analysis  (v21)
Raw counts were normalized with the 'TMM' method and analyzed by program edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized read counts by library size

extract_protocol:
The total RNA was extracted from the frozen human right atrial appendages using TRIZOL reagent following the manufacturer’s protocol. The RNA yield and purity were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) and NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, USA).
Genome-wide miRNA expression profiles of twelve human right atrial tissues were generated by miRNA-seq, which was carried out at the Biodynamic Optical Imaging Center (BIOPIC) in Peking University (Beijing, China). miRNA-seq followed the BIOPIC recommended protocol that was based on the NEBNext Multiplex Small RNA Library Prep Kit (Lot #E7560S). Each library was sequenced in two lanes.


title: Human atrial tissue sample in age group SR40, replication 3 [mRNA]


title: Human atrial tissue sample in age group SR40, replication 2 [mRNA]


title: Human atrial tissue sample in age group SR70, replication 2


title: Human atrial tissue sample in age group SR40, replication 1 [mRNA]


title: Human atrial tissue sample in age group SR60, replication 3


title: Human atrial tissue sample in age group SR70, replication 1


title: Human atrial tissue sample in age group SR50, replication 1 [mRNA]


title: Human atrial tissue sample in age group SR50, replication 3 [mRNA]


title: Human atrial tissue sample in age group SR50, replication 2 [mRNA]


title: Human atrial tissue sample in age group SR60, replication 2


title: Human atrial tissue sample in age group SR50, replication 3


title: Human atrial tissue sample in age group SR50, replication 2


title: Human atrial tissue sample in age group SR60, replication 1


title: Human atrial tissue sample in age group SR50, replication 1


title: Human atrial tissue sample in age group SR40, replication 3


title: D447_MDA5_12H

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

data_processing:
Bam files generated using TopHat alignment software using Illumina's Basespace
Samples were filtered with normalized read counts across all samples >1
A value of '1' was added to each of the genes across all samples.  This provides a value to genes which show no read counts and allows for appropriate calculations of fold change.  Low abundance transripts are moe influenced by highly expressed transcripts.
Genome_build: Human reference genome 38 (GRCh38)
Supplementary_files_format_and_content: The processed data file was processed using Tibco Spotfire with OmicsOffice.  This sofware utilizes Cufflinks to generate raw read counts.  Read counts were normalized using DESeq2 through R software.

source_name: Monocyte-derved DCs

extract_protocol:
Total RNA was prepared using Zymnoresearch RNA extraction kit
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 2500 in 100-base single-read reactions.

treatment_protocol: Human monocyte-derived DCs moDCs were generated from 5 donors and  treated with innate immune agonists for 12hr (RIG-I, MDA5, or IFNβ) or infected with WNV (12hpi and 24hpi). Time matched mocks were left untreated and collected at 12 and 24 hours post-treatment. RIG-I agonist- 100 ng RNA derived from the 3'UTR of Hepatitis C virus, MDA5 agonist- 100 ng high molecular weight poly-I:C, IFN- 100 IU/ml IFNb and West Nile virus(WNV)-TX lineage 1 strain.

value: Monocyte-derved DCs


title: Human atrial tissue sample in age group SR40, replication 2


title: Human atrial tissue sample in age group SR40, replication 1


title: D447_Mock_24H


title: D434_MDA5_12H


title: D434_RIG-I_12H


title: D447_Mock_12H


title: D447_IFNb_12H


title: D434_WNV_24H


title: D434_WNV_12H


title: D434_IFNb_12H


title: D447_RIG-I_12H


title: D253_Mock_24H


title: D253_Mock_12H


title: D253_IFNb_12H


title: D253_WNV_12H


title: D434_Mock_12H


title: D434_Mock_24H


title: D253_MDA5_12H


title: D125_MDA5_12H


title: D253_WNV_24H


title: D125_IFNb_12H


title: D125_RIG-I_12H


title: D447_WNV_12H


title: D125_Mock_24H


title: D253_RIG-I_12H


title: D447_WNV_24H


title: D125_WNV_24H


title: D125_WNV_12H


title: D9_WNV_12H


title: D9_MDA5_12H


title: D9_RIG-I_12H


title: D125_Mock_12H


title: D9_Mock_24H


title: D9_IFNb_12H


title: D9_WNV_24H


title: D9_Mock_12H


title: Sample_147_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: spermatozoa

value: long RNA


title: Sample_149_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossover


title: Sample_145_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Baseline


title: Sample_146_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossback


title: Sample_144_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_143_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_142_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_139_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_135_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_131_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_129_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_133_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_127_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_126_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_124_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_123_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_125_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_111_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_140_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_137_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_109_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_110_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_108_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_130_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_106_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_151_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_114_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_116_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_104_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_118_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_112_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_122_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_102_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_100_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_103_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_121_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_113_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_101_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_96_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_95_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_94_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_105_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_93_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_90_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_85_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_84_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_82_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_79_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_78_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_76_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Homo rep2 miRNA

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
miRDeep2 0.0.8 was used to count the number of  microRNAs
The numbers are then manually normalized into FPKM values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Subcutaneous adipose tissue

extract_protocol:
Trizol
TruSeq Small RNA Library Preparation (Illumina)

tag: strain

value: adipose tissue

value: 24 weeks

tag: diet

value: fed high fat high sucrose diet for 16 weeks starting from 8-week-old

value: Homo KO


title: Hete rep3 miRNA

tag: genotype

value: Hete KO


title: Hete rep2 miRNA


title: Homo rep3 miRNA


title: Homo rep1 miRNA


title: Sample_75_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: WT rep3 miRNA

value: WT


title: WT rep1 miRNA


title: WT rep2 miRNA


title: Sample_88_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_74_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_77_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_73_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Hete rep1 miRNA


title: Sample_72_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: ZT12_ALDH_p_2

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: ZT12, ALDH(+)

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: 4T1 cell was impranted in mice

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

treatment_protocol: Non treatmment

value: BALB/C

value: Tumor


title: ZT0_ALDH_p

source_name: ZT0, ALDH(+)


title: Gde3 WT_Spinal cord OPCs 3

city: Baltimore

first: Shanthini

last: Sockanathan

address: 725 North Wolfe St.

institute: The Solomon H. Snyder Department of Neuroscience Johns Hopkins University School of Medicine

data_processing:
Paired-end reads, 50 bp in length, were generated on an Illumina HiSeq 2500 system. To analyze the RNA-seq data, reads were quality checked and trimmed using the programs fastqc and fqtrim. Reads were then mapped to the mouse genome mm10 using the spliced alignment program Tophat2 v2.1.1, and assembled into transcripts using Cufflinks v2.2.1. Transcript assemblies across all samples were merged with Cuffcompare v.2.2.1, using GENCODE v.M5 as reference, to create a set of gene and transcript annotations that was later used in the differential analyses. Lastly, Cuffdiff v2.2.1 was run on each pairwise comparison to determine statistically significant differentially expressed genes (significance cutoffs: p-value <= 0.05, q-value <= 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: gtf

source_name: Gde3 WT_Spinal cord OPCs

growth_protocol: OPCs were plated on Poly-L-Lysine (0.1mg/mL) and Laminin (10µg/mL) coated plates at a density of 150,000 cells per cm2 in proliferative media containing 1mM Sodium Pyruvate, 5µM Forskolin, 10ng/mL PDGF, 10ng/mL CNTF, B27, N2, and antibiotic. OPC medium was made with freshly reconstituted growth factors, 0.22um filtered and stored at 4°C for no longer than 3 days.

extract_protocol:
OPCs were isolated from P0.5 spinal cords using Miltenyi Biotec magnetic beads for A2B5+ cells according to manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Gde3 WT

value: spinal cord

value: oligodendrocyte precursor cells (OPCs)

tag: isolation

value: A2B5+ magnetic pulldown


title: Gde3 WT_Spinal cord OPCs 2


title: ZT0_ALDH_m

source_name: ZT0, ALDH(-)


title: Gde3 KO_Spinal cord OPCs 1

source_name: Gde3 KO_Spinal cord OPCs

value: Gde3 KO


title: Sample_67_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: spermatozoa

value: long RNA


title: Gde3 WT_Spinal cord OPCs 1


title: Sample_65_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossover


title: Gde3 KO_Spinal cord OPCs 3


title: Sample_64_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Baseline


title: Sample_62_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

value: Crossback


title: Sample_60_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_59_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: V583 ΔtdcΔagdi (test) compared to V583 (reference) Replicate 1

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

description: Biological replicate 1 of 2.

hyb_protocol: Nine hundred ng of DyLight 550- and nine hundred ng of DyLight 650-labelled cDNA were mixed and hybridized for 17 h at 60°C in the E. faecalis V583 DNA microarray using the In situ Hybridization Kit Plus, the Hybridization Gasket Slide and the Agilent G2534A Microarray Hybridization Chamber (Agilent Technologies). Slides were washed using the washing buffers indicated by the manufacturer.

scan_protocol: Microarrays were scanned using a GenePix 4200A Microarray Scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Slide images were analyzed using GenePix Pro v.6.0 software. Background subtraction and LOWESS (locally weighted scatterplot smoothing) normalization were done using the standard routines provided by GENOME2D software available at http://server.molgenrug.nl/index.php/analysis-pipeline.

label: DyLigth 650

organism: Enterococcus faecalis

source_name: Enterococcus faecalis V583  delta-tdc delta-agdi

label_protocol: Total cDNA was synthesized from 20 µg of RNA using the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands). The cDNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nager, Landsmeer, The Netherlands) following the manufacturer instructions. Twenty µg of the purified cDNA was immediately labeled with DyLight 550 or DyLight 650 using the DyLight® Amine-Reactive Dyes kit (Thermo Scientific) as the manufacturer indicated. Quality and quantity of cDNA and DyLight 550 and DyLight 650 labelling were checked on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

growth_protocol: Both strains E. faecalis V583 and E. faecalis V583 ΔtdcΔagdi were grown in 30 mL of M17 culture medium (Oxoid, UK) supplemented with 0.5% glucose (w/v) (GM17) for 7 h at 37°C without aereation. After a centrifugation at 16,000 x g for 1 min at 4˚C, the supernatants were discarded and cell pellets were frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Cell pellets were resuspended in 400 µl of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and 50 µl of 10% SDS, 500 µl of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich), 500 mg of glass beads (75–150 µm) (Sigma-Aldrich), and 175 µl of Macaloid suspension (Bentone MA, Rheox Inc., Scotland, United Kingdom) were added. Cells were mechanically disrupted in a bead beater at 4˚C with two cycles of 60 s. During the shaking intervals the cells were kept on ice for 1 min. The samples were then centrifuged at 16,000 x g for 1 min at 4˚C. The upper phase was transferred to fresh tubes containing 500 µl chloroform: isoamyl alcohol (24:1) and centrifuged for 5 min at 4˚C. Total RNA was isolated with the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany) following the instructions provided by the manufacturer. The concentration and quality of the RNA was determined on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

value: V583  delta-tdc delta-agdi

tag: tyramine and putrescine producer

value: No

label: DyLigth 550

source_name: Enterococcus faecalis V583

value: Yes


title: Sample_58_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Ctrl4

first: Andrew

middle: P.

last: Lane

state: Maryland

address: 855 N Wolfe Street, Room 540

department: Department of Otolarynology

institute: Johns Hopkins School of Medicine

description: NoDox

data_processing:
Reads were demultiplexed using bcl2fastq2, Reads quality was checked for each sample using FastQC v0.10.1.
Reads were then imported into TopHat v2.1.1 for alignment into BAM files. The aligned reads were assembled with CLASS v.2.1.7
The resulted gtf files were fed to Cuffmerge  to create  a non-redundant set of transcripts. This file will be used later on, in the differential expression step. Cuffdiff v2.2.1 was run on each sample in order to obtain FPKM values. Cuffdiff was used to look for significant changes in transcript expression.
Genome_build: mm10 and gencodeM5
Supplementary_files_format_and_content: GENE_ID, Counts

source_name: Olfactory Neuroepithelium

extract_protocol:
GFP-positive cells were sorted directly into Trizol LS (Invitrogen). Completely lysed samples were treated with chloroform to separate phases. The aqueous phase containing RNA was transferred and purified using a RNeasy Micro Kit (Qiagen). On-Column DNase I digestion was conducted to remove genomic DNA contamination.
The quality of RNA from sorted cells was verified by Agilent 2100 Bioanalyzer. Three individual RNA samples for each group with high quality (RIN > 7) were enrolled for library preparation. mRNA amplification was performed using 5ng total RNA with a Clontech Smarter RNA seq v4 kit. RNA-seq libraries were prepared using Illumina Nextera library preparation kit.

value: Olfactory Neuroepithelium

value: horizontal basal stem cells


title: Dox4

description: Dox 6w

value: Krt17-EGFP; Cyp2g1-rtTA; TRE-TNF


title: Dox1

description: Dox 6w


title: Dox3

description: Dox 6w


title: Sample_57_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: V583 ΔtdcΔagdi (test) compared to V583 (reference) Replicate 3

description: Technical replicate 1 of 1.


title: ZT12_ALDH_m_2

source_name: ZT12, ALDH(-)

value: BALB/C

value: Tumor


title: Sample_66_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Ctrl2

description: NoDox


title: Sample_53_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Gde3 KO_Spinal cord OPCs 2

value: spinal cord


title: Sample_128_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_52_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_50_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Ctrl1

description: NoDox


title: Sample_49_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_42_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_45_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_43_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_41_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_44_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_40_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_39_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_34_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_33_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_31_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_30_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_120_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_27_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_26_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_25_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_24_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_23_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_22_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_28_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_21_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_19_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_17_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_16_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_12_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt