title: SHB_1

city: Vestec by Prague

first: Jakub

last: Rohlena

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i.

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Reads were aligned against the reference Human genome version GRCh38 and count table were generated to annotation version GRCh38.87 using STAR (version 2.5.2b). As a count tables were used second column of generated tab.
Normalized number of reads was generated by DESeq2 using default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample

growth_protocol: the cells were collected at 70% confluency in full culture media.

extract_protocol:
RNAzol followed by LiCL repurification
RNA libraries were prepared for sequencing using Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: no treatment applied

tag: cell line

tag: modification

value: SDHB knockout

tag: biological replicate


title: SH1_3

status: Public on Apr 16 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: SDHB knockout SDHA knockdown


title: SHB_3


title: wild type mouse GV stage oocytes, biological rep 2

type: RNA

city: La Tronche

first: Christophe

last: Arnoult

address: rond-point de la Chantourne

department: Institute for Advanced Biosciences

country: France

institute: INSERM U1209 CNRS UMR5309

description: gene expression data from wild type mouse GV stage oocytes

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45°C on GeneChip mouse ClariomD arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned with the Affymetrix Genechip Scanner 7G.

data_processing: The data have been normalized with Expression Console from Affymetrix and annotation and analyses have been performed with TAC.3 software from Affymetrix.

label: biotin

organism: Mus musculus

source_name: wild type mouse oocytes at GV stage

label_protocol: 250 pg RNA were labeled using the Affymetrix WT pico kit

growth_protocol: Mice were stimulated with 5 UI PMSG and GV oocytes were collected 44 hours later. For MII oocytes, 48 hours after PMSG injection, mice were stimulated with 5 UI HCG and MII oocytes were collected 12 hours later.

extract_protocol: Total RNAs were purified with the Norgen Biotek Corp - Single cell Purification kit following the manufacturer's protocol. The GV samples contained a total of 20 to 32 oocytes; the MII samples a total of 28 to 46 oocytes.

treatment_protocol: Follicular cells were removed by incubating GV or MII oocytes with hyaluronidase (0.1 mg/ml) for 10 min. Remaining follicular attached cells were then removed mechanically with a micropipette. Follicular cell-free oocytes were then collected by aspiration.

tag: tissue

value: oocytes, follicular cell free

tag: oocyte stage

value: GV

tag: genotype

value: wild type mouse

tag: age

value: 44 hours post PMSG


title: SH1_1


title: UA159 galactose replicate 2

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

country: USA

institute: University of Rochester Medical Center

data_processing:
Barcodes were trimmed, low quality and short sequences (<100bp) were filtered using BBDuk (https://sourceforge.net/projects/bbmap) implemented in Geneious version 11 (https://www.geneious.com).
Expression values for each mRNA sample were generated by mapping of paired reads onto the annotated reference genome of S. mutans UA159 resulting in 175 to 275X mean coverage per sample (range of 4.2 to 6.4M reads mapped per sample).
Expression level counts and differential expression calculations in triplicate between conditions were performed using Geneious version 11 (https://www.geneious.com) using DESeq2 normalization. DESeq2 uses a model based on the negative binomial distribution with variance and mean linked by local regression (36).
Genome_build: Streptococcus mutans UA159
Supplementary_files_format_and_content: treR_RNAseq Processed data.xlsx:  Excel file containing the output prior to statistical analysis from all of the samples (UA159 vs. ∆treR) for each gene in the genome

organism: Streptococcus mutans

source_name: Streptococcus mutans UA159 parent strain

growth_protocol: all strains of Streptococcus mutans were grown to mid-log phase in TY medium supplemented with the indicated sugar at 37˚C in a 5%(v/v) CO2/95% air atmosphere

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy Power Microbiome Kit according to the manufacturer's instructions, mRNA was purified using the Zymo RNA Clean and Concentrator Kit
cDNA libraries from rRNA-depleted RNA were generated using random-primed cDNA synthesis methods according to the ScriptSeq v2 RNASeq Library preparation protocol (Epicentre, Madison, WI).  Prior to second strand cDNA synthesis, the di-tagged cDNA was purified using the Agencourt AMPure XP system (Beckman Coulter, Brea, CA).  ScriptSeq index primers were added to the libraries which were then PCR amplified for 15 cycles.

tag: growth media

tag: strain

value: wild type


title: SHB_2


title: UA159 galactose replicate 3


title: 15_S2_16:00

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

description:
Biopsy from subject 15 at time (h) 16:00
norm_reads_count.txt

data_processing:
Demultiplexing was done using bcl2fastq software
Paired-end reads were mapped to the Homo sapiens genome (GRCh38/hg38) using STAR (Dobin et al. 2013) with parameters “—alignIntronMin 20 –alignIntronMax 1000000 – GTF (option –sjdbGTFfile) and adapter clipping.
Mapped reads were quantified in intronic and exonic regions. For each gene, we defined a gene body by merging all the respective transcripts using BEDtools (Quinlan and Hall 2010). A region was defined as exonic if it occurs in a least one of the transcripts while an intronic region had to be shared between all the transcripts. We assigned uniquely mapping paired-reads to exonic regions (exon/exon and complete exon reads) or intronic regions (intron-exon and complete intron reads) considering reads orientation.
Intronic and exonic reads count were normalized using EdgeR (Robinson et al. 2010) by the library scaling factor from the exonic regions and the respective intronic and exonic length (rpkm()).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample at the pre-mRNA and mRNA levels (introns, exons).

source_name: biopsys  from the vastus lateralis

growth_protocol: 10 healthy volunteers were recruited for the in vivo study (see Table S1 for donor characteristics). One week prior to the scheduled laboratory visit, participants had to adhere to a consistent daily feeding and sleeping routine. Participants arrived in the laboratory at 19:00 h on the day prior to the testing day and ingested one standardized meal that first evening. Participants remained for the duration of their stay in a semi-recumbent position. During the waking hours of the testing day they were given mixed-macronutrient meal-replacement solutions at hourly intervals (Resource, Nestlé, CH) to ensure energy balance. The laboratory was free from natural light and with artificial lighting standardized to 800 lux in the direction of gaze, ambient temperature maintained between 20-25°C and noise levels tightly regulated. Participants were not permitted to sleep during waking hours when lights were on (i.e. 07:00-22:00 h) and wore eye masks whilst trying to sleep during lights-out (i.e. 22:00-07:00 h)

extract_protocol:
Six 100 mg biopsy samples were acquired from the vastus lateralis muscle at 4-hour intervals (12:00, 16:00, 20:00, 24:00, 04:00 & 08:00 h) and immediately snap frozen under liquid nitrogen. Samples were taken from each leg in alternating and ascending order with skin incisions separated by 2-3 cm
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded Total LT Sample Prep Kit (Illumina) with the Ribo-Zero Gold depletion set

treatment_protocol: Anesthetic administration (1% lidocaine w/o epinephrine) and skin/fascia incisions for this procedure (Bergstrom 1962) were completed within the hour prior to sleep such that night-time samples could be acquired with minimal discomfort.

value: vastus lateralis

tag: time


title: ∆treR glucose replicate 3

source_name: Streptococcus mutans ∆treR strain

value: delta-treR


title: MDA_1

value: Parental, not modified


title: SH1_2


title: 15_S1_12:00

description:
Biopsy from subject 15 at time (h) 12:00
norm_reads_count.txt


title: ∆treR glucose replicate 2


title: ∆treR glucose replicate 1


title: UA159 glucose replicate 3


title: UA159 glucose replicate 1


title: UA159 glucose replicate 2


title: SNSseq_10d_exp3_F4

status: Public on Apr 15 2018

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

description: ssDNA

library_source: genomic

data_processing:
Library strategy: SNS-Seq
Alignment: bowtie with parameters -v 3 -m 1
Removing of duplicates with samtools rmdup
Filtering of mitochondria and chloroplast
Conversion from .mpileup to .wig
Differential expression with Cuffdiff

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Arabidopsis seedlings were grown on Murashige and Skoog (MS) plates supplemented with 1% (w/v) sucrose and 1% (w/v) agar in a 16h:8h light/dark regime at 22°C, for either 4 or 10 days.

extract_protocol:
Nuclei were isolated and enriched by percoll gradients. After lysis, genomic DNA was extracted, denatured and fractionated in a sucrose gradient. Short nascent strands were purified by Lambda exonuclease digestion. ssDNA was converted to dsDNA using a slow annealing strategy.
DNA libraries were prepared using Ovation Ultralow V1 library prep kits (NuGen). RNA libraries were prepared using TruSeq Stranded mRNA library prep kit and NeoPrep (Illumina)

value: Whole seedling

tag: ecotype

tag: developmental stage

value: 10 day-old


title: SNSseq_10d_exp3_F3

description: ssDNA


title: SNSseq_10d_exp3_F5+F6+F7

description: ssDNA


title: SNSseq_10d_exp2_F4

description: ssDNA


title: SNSseq_10d_exp2_F5+F6+F7

description: ssDNA


title: gDNA_10d_exp2_exp3

description: genomic DNA

data_processing:
Alignment: bowtie with parameters -v 3 -m 1
Removing of duplicates with samtools rmdup
Filtering of mitochondria and chloroplast
Conversion from .mpileup to .wig
Differential expression with Cuffdiff


title: gDNA_10d_exp1

description: genomic DNA


title: RNAseq_4d_exp2

description: mRNA

value: 4 day-old


title: SNSseq_10d_exp1_F4

description: ssDNA


title: gDNA_4d_exp1

description: genomic DNA


title: SNSseq_10d_exp2_F3

description: ssDNA


title: gDNA_4d_exp2_exp3

description: genomic DNA


title: SNSseq_4d_exp3_F4

description: ssDNA


title: SNSseq_4d_exp3_F3

description: ssDNA


title: RNAseq_4d_exp1

description: mRNA


title: SNSseq_4d_exp2_F5+F6+F7

description: ssDNA


title: SNSseq_4d_exp2_F3

description: ssDNA


title: SNSseq_4d_exp2_F4

description: ssDNA


title: SNSseq_4d_exp1_F4

description: ssDNA


title: M5886

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 250ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by quantile normalization first, followed by global linear scaling. For this latter approach, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 20. All of those normalized gPS values that fell below this intensity border were substituted by the respective surrogate value of 20.

source_name: Tnaive (immunisation, pLN, d25)

label_protocol: 25 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification), except that reaction volumes were halved. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies). Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to a subset of total RNA sample.

extract_protocol: Total RNA was extracted by use of the RNeasy Micro Kit (Qiagen).

value: perpheral lymph node

tag: gender

value: mixed, 8-15 mice

value: 8-14 weeks

tag: rna input amount

value: 25 ng


title: M5888

source_name: Treg (immunisation, pLN, d25)


title: SNSseq_4d_exp1_F3

description: ssDNA


title: M5880

source_name: Tnaive (immunisation, pLN, d12)


title: M5883

source_name: TFR (GL7+/-, immunisation, pLN, d12)


title: M5887

source_name: TFH (GL7+, immunisation, pLN, d25)


title: M5889

source_name: TFR (GL7+/-, immunisation, pLN, d25)


title: M5882

source_name: Treg (immunisation, pLN, d12)


title: M5881

source_name: TFH (GL7+, immunisation, pLN, d12)


title: SNSseq_10d_exp1_F3

description: ssDNA


title: SNSseq_4d_exp3_F5+F6+F7

description: ssDNA


title: Control 2

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

description: RNA was extracted from PBMCs of BALB/C mice that did not undergo foot shock.

hyb_protocol: Samples were hybridized using the Affymetrix® GeneChip® WT Terminal Labeling and Hybridization kit suited for the Ambion® WT Expression Kit.

scan_protocol: The GeneChip Scanner 3000 7G was used for scanning.

data_processing:
Data were processed using Affymetrix Power Tools (APT Release 1.14.3) software using the RMA-sketch algorithm and median polish quantification on 6,553,600 probes (536989 probe-sets). A detection above background (DABG) p-value was calculated for each probeset; only probesets that passed the DABG threshold (~452k) are included in the Sample data table.

probe group file: MJAY_r2.pgf

source_name: PBMCs, untreated control

label_protocol: Samples were labeled using the Affymetrix® GeneChip® WT Terminal Labeling and Hybridization kit suited for the Ambion® WT Expression Kit.

growth_protocol: PBMCs were extracted from stressed and non-stressed (control) mice.

extract_protocol: Mice exhibiting the maximal stress markers (maximal circulation glucocorticoids) were selected for the stress group. RNA was extracted from 5 stressed and 5 control BALB/C mice. The RNA was processed through the Ambion® WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays.

treatment_protocol: Mice in the stress group underwent unpredictable repeated foot shocks. Mice in the control group were untreated.

value: BALB/C

tag: treatment

value: peripheral blood mononuclear cells (PBMCs)


title: Stress 5

description: RNA was extracted from PBMCs of BALB/C mice following unpredictable repeated foot shocks.

source_name: PBMCs, following unpredictable repeated foot shocks, stress group

value: stress


title: Control 4


title: Stress 3


title: Stress 4


title: Stress 1


title: Stress 2


title: Control 1


title: Stress 5-restain


title: Control 3


title: MDA_2


title: Control 5


title: Sample1_exp6_chip4_rep1

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description:
exp6_matrix_chip4.txt
Adult gonads

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Nasonia vitripennis

source_name: Testes collected from yellow body red-eye stage males

label_protocol: DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.

growth_protocol: Ovaries collected from females 24 hours after eclosion; testes collected from male pupa.

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Samples were prepared at 25º C as follows: Approximately 200 N. vitrirpennis (AsymCX) virgins were collected as black pupa. When eclosed, half of them were provided with males and were allowed to mate overnight, and the other half were kept as virgins. Virgin setting result in all-male progeny whereas mated females produced ~89.5% female progeny under the design used here. Females were provided 15- 20 Sarchophaga bullata hosts in groups of 20 females for 24 hrs to induce production of eggs. The hosts were then removed and females were left overnight (~18 hrs). To collect embryos, individual females were given access to a host at one end (to restrict the oviposition site) and allowed to lay eggs for 6-10 hrs before being removed. Embryos were then harvested immediately (early embryos), 18 hrs later (late embryos), or 51 hrs later (1st instar larvae). All embryos and larvae were collected in an RNase-free environment. The host was cracked open and the "cap" removed to expose embryos. Dissecting needles were used to gently scrape embryos from the surface of the host and transfer them into a 1.5 ml tube pre-chilled on dry ice. Samples were stored at -80º C. If at anytime the host was punctured or embryos were exposed to host hemolymph, they were discarded. Estimates of the number of embryos per replicate (three per life stage/sex) were recorded; early embryos ranged from 300-900, late embryo 140-500, 1st instar larvae 245-520. Since sex cannot be determined at larval stage, some of the mated female hostings were allowed to mature to adulthood then males and females were counted to determine the sex ratio. Early larvae showed an average of 82.9% females and late larvae had an average of 84.2%. Pupae collections were made among the progeny of mated females provided with hosts for 48 hrs. They were sorted by sex and stage (early yellow, red-eye, half black, and black pupae). Equal numbers (S20) of pupae from each stage were then pooled prior to RNA extraction. Males and females were extracted separately. Male reproductive tracts (testes, seminal vesicles, and accessory glands) were dissected in phosphate buffered saline (PBS) from and transferred with a small amount of PBS into a tube on dry ice. A total of 60 testes per replicate were dissected (10 each yellow/red, salt & pepper, and black pupal stages). Female reproductive tracts (30 per replicate) were removed from 1-3 days post eclosion virgin females and transferred to a tube on dry ice.

tag: Sex

value: male

value: pupa

value: testes

value: AsymCX

source_name: Ovaries collected from adult females 24 hours after eclosion

value: female

value: adult

value: ovaries


title: Sample3_exp3_chip4_rep3

source_name: 1st instar male larva; 51-61 hours post laying; 245-520 individuals per replicate

growth_protocol: 51-61 hours post laying; 245-520 individuals per replicate; Male Samples are 100% male, Female Samples are on average 82.9 to 84.2 percent female based on sexing of individuals from matching

value: 1st instar larva

value: whole body

source_name: 1st instar female larva; 51-61 hours post laying; 245-520 individuals per replicate


title: Sample1_exp4_chip4_rep1

source_name: Male pupa collected at the yellow body red-eye stage

growth_protocol: Collected at the yellow body red-eye stage; sexed at the time of collection

source_name: Female pupa collected at the yellow body red-eye stage


title: Sample2_exp5_chip4_rep2

source_name: Adult males collected 24 hours after eclosion

growth_protocol: collected 24 hours after eclosion; sexed at the time of collection

source_name: Adult females collected 24 hours after eclosion


title: Sample1_exp2_chip4_rep1

source_name: Late male embryos; 18-28 hours post laying; 140-500 individuals per replicate

growth_protocol: 18-28 hours post laying; 140-500 individuals per replicate; Male Samples are 100% male, Female Samples are on average 82.9 to 84.2 percent female based on sexing of individuals from matching

value: late embryos

source_name: Late female embryos; 18-28 hours post laying; 140-500 individuals per replicate


title: Sample3_exp4_chip4_rep3


title: Sample1_exp3_chip4_rep1


title: Sample2_exp2_chip4_rep2


title: Sample2_exp4_chip3_rep2


title: Sample3_exp2_chip4_rep3


title: Sample3_exp1_chip4_rep3

source_name: Early male embryos; 0-10 hours post laying; 300-900 individuals per replicate

growth_protocol: 0-10 hours post laying; 300-900 individuals per replicate; Male Samples are 100% male, Female Samples are on average 82.9 to 84.2 percent female based on sexing of individuals from matching

value: early embryos

source_name: Early female embryos; 0-10 hours post laying; 300-900 individuals per replicate


title: Sample3_exp5_chip4_rep3


title: Sample2_exp1_chip4_rep2


title: Sample3_exp5_chip3_rep3


title: Sample2_exp3_chip4_rep2


title: Sample3_exp6_chip4_rep3

description:
exp6_matrix_chip4.txt
Adult gonads


title: Sample1_exp5_chip4_rep1


title: Sample1_exp1_chip4_rep1


title: Sample2_exp6_chip3_rep2

description:
exp6_matrix_chip3.txt
Adult gonads


title: Sample2_exp6_chip4_rep2

description:
exp6_matrix_chip4.txt
Adult gonads


title: Sample3_exp6_chip3_rep3

description:
exp6_matrix_chip3.txt
Adult gonads


title: Sample2_exp4_chip4_rep2


title: Sample1_exp5_chip3_rep1


title: Sample1_exp6_chip3_rep1

description:
exp6_matrix_chip3.txt
Adult gonads


title: Sample2_exp5_chip3_rep2


title: Sample3_exp4_chip3_rep3


title: Sample1_exp4_chip3_rep1


title: Sample2_exp3_chip3_rep2


title: Sample1_exp3_chip3_rep1


title: Sample3_exp3_chip3_rep3


title: Sample3_exp2_chip3_rep3


title: Sample1_exp2_chip3_rep1


title: Sample2_exp1_chip3_rep2


title: Sample3_exp4_chip2_rep3


title: Sample3_exp5_chip2_rep3

growth_protocol: Collected 24 hours after eclosion; sexed at the time of collection


title: Sample1_exp2_chip2_rep1


title: Sample3_exp2_chip2_rep3


title: Sample2_exp2_chip3_rep2


title: Sample2_exp2_chip2_rep2


title: Sample2_exp4_chip2_rep2


title: Sample3_exp3_chip2_rep3


title: Sample1_exp4_chip2_rep1


title: Sample1_exp6_chip2_rep1

description:
exp6_matrix_chip2.txt
Adult gonads


title: KH_1KO_L7: IL-2-KO rep 3

city: Merced

first: Katrina

last: Hoyer

state: California

address: 5200 North Lake Road

institute: University of California, Merced

description: 1.1x10^6 cells

data_processing:
Illumina software used for basecalling.
Adapter contamination removal and quality trimming were performed using Atropos v. 1.1.17  with Python v3.6.2. Trimming was performed with -q20 and removing pairs if any read after traimming was less than 20bp.
Rsubread v1.28.1 was used to map read pairs to the GRCm38/mm10 NCBI build 38.1 (GCF_000001635.20) genome reporting up to 10 equally likely mapping location for each read pair.
Read summarization was performed on the gene level using featureCounts using annotations from a modified version of the RefSeq top level feature annotations for GRCm38/mm10 NCBI build 38.1 containing only protein coding genes
Multi-mapping reads were treated as fractional counts when mapping to several genes, reads mapping across more than one gene and read pairs where ends mapped to different chromosomes,  were discarded. Before performing differential expression analysis genes that had less than one count per million in at least three samples were discarded, and the remaining gene counts were normalized using TMM
Differential expression analysis was performed in a linear model framework using limma v3.34.9  using Voom transformed read counts. Genes were considered differential expressed if their p-value was < 0.05 after the false discovery rate was controlled  using the Benjamini Hochberg procedure.
Read mapping, summarization, and differential expression analysis were performed using R v3.4.3. Differential expressed genes were annotated with their biological process Gene Ontology group using Panther 13.1 using the GO Ontology database released on 2018-02-02.
Genome_build: GRCm38/mm10 NCBI build 38.1 (GCF_000001635.20)
Supplementary_files_format_and_content: tab-delimited text file containing TMM normalized counts per million for each sample

source_name: peripheral lymph nodes

extract_protocol:
Lymph nodes were extracted and pooled if indicated. CD8 T cells were isolated by cell sorting on an ARIA II. Sorted cells were pelleted and flash frozen to send on dry ice to Expression Analysis Inc. for RNA extraction using the Illumina TrueSeq Stranded Total RNA extraction kit.
Illumina TrueSeq Stranded Total RNA Sample Preparation Kit

value: BALB/c

value: 12 days of age

value: peripheral lymph nodes


title: Sample3_exp1_chip2_rep3


title: Sample1_exp1_chip3_rep1


title: KH9KO_L8: IL-2-KO rep 2

description: 42.6x10^6 cells


title: KH10KO_L1: IL-2-KO rep 1

description: 26.7x10^6 cells


title: Sample3_exp6_chip2_rep3

description:
exp6_matrix_chip2.txt
Adult gonads


title: KH_3KO_L5: IL-2-KO rep 4

description: 0.4x10^6 cells


title: KH_6WT_L6: WT rep 4

description: 1.3x10^6 cells from 2 pooled mice

value: WT


title: KH_4WT_L3: WT rep 3

description: 1.3x10^6 cells from 3 pooled mice


title: Sample2_exp6_chip2_rep2

description:
exp6_matrix_chip2.txt
Adult gonads


title: KH_2WT_L2: WT rep 2

description: 28.7x10^6 cells from 5 pooled mice


title: Sample1_exp1_chip2_rep1


title: clsy3-2,4-2_rep3_smRNA-seq

status: Public on Apr 14 2018

city: San Diego

first: Julie

last: Law

state: CALIFORNIA

address: 10010 N Torrey Pines Rd, La Jolla

institute: Salk Institute for Biological Studies

description: Sample 93

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: The adapter sequences in the de-multiplexed smRNA sequencing reads were trimmed using cutadapt (v1.9.1) and reads longer than 15nt were kept for further analyses. The trimmed smRNA reads were then mapped to Arabidopsis genome (TAIR10) using ShortStack (v3.8.1), allowing 1 mismatch (--mismatches 1) and employing either the multi-mapping mode (--mmap f) or the unique mode (-mmap n). Subsequently, a custom JSON filter was employed to keep only perfectly matching reads and reads with a single mismatch at their 3’ terminus, as such mismatches were recently identified as a feature of Pol-IV-dependent RNAs.
Core 24nt siRNA cluster calling: The smRNA reads passing this custom filter were then used to call small RNA clusters using ShortStack using the --mincov 20 and --pad 100 options. The number of 21-24nt of the smRNA clusters identified are presented in Table 3. To facilitate further analysis, the smRNA reads passing the JOSN filter (bam file form) were used to generate a “Tag Directory” using the makeTagDirectory script from the HOMER (Hypergeometric Optimization of Motif EnRichment) package. The Tag Directory was then split into sub-TagDirectory by smRNA size (20-25nt) using a custom perl script (splitTagDirectoryByLength.dev2.pl).
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

growth_protocol: Arabidopsis used in this study were in the Columbia-0 (Col) ecotype and unless otherwise specified, plants were grown in Salk green houses with long day conditions at ~22°C.

extract_protocol:
4 un-opened flower buds (stage 12 and younger) from individual mutant plants as well as 3 individual wild-type (WT) controls were collected, frozen in liquid nitrogen and kept at -80°C until use. Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. These total RNAs then were enriched for small RNAs through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The resulting small RNAs were used for library preparation using NEBnext Multiplex Small RNA Library Prep Set for Illumina (Cat# E7300) following the manual. The final library products were further purified by running 8% polyacrylamide gels and performed size-selection from 140-160nt as described above. The purified libraries were equally pooled and submitted for single-end 50 bp (SE50) sequencing on HiSeq 2500 (Illumina) at the Next Generation Sequencing Core of the Salk Institute for Biological Studies.

value: Columbia

value: stage 12 and younger flower buds

tag: molecule subtype

value: small RNA


title: Sample2_exp1_chip2_rep2

value: male


title: Sample2_exp6_chip1_rep2

description:
exp6_matrix_chip1.txt
Adult gonads

value: pupa

value: testes


title: Sample2_exp5_chip2_rep2

value: AsymCX

value: female


title: clsy3-2_rep3_smRNA-seq

description: Sample 91


title: Sample1_exp3_chip2_rep1


title: Sample3_exp1_chip3_rep3


title: Sample3_exp6_chip1_rep3

description:
exp6_matrix_chip1.txt
Adult gonads

value: adult

value: ovaries


title: Sample2_exp3_chip2_rep2

value: 1st instar larva

value: whole body


title: clsy2-1_rep2_smRNA-seq

description: Sample 87


title: clsy1-7,2-1_rep1_smRNA-seq

description: Sample 86


title: WT_7_rep3_smRNA-seq

description: Sample 89


title: Sample1_exp5_chip2_rep1


title: Sample1_exp6_chip1_rep1

description:
exp6_matrix_chip1.txt
Adult gonads


title: NRPD1-3xFLAG,clsy3-1,4-1_IP_2

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: ChIP sequencing data were aligned to TAIR10 reference genome using bowtie (v1.1.0)30 allowing 2 mismatches (-v 2) and including multi-mapping reads (--all --best --strata).
ChIP Enrichment Relative to Wild-type: ChIP enrichment relative to wild-type controls at the identified siRNA clusters were visualized using deepTools (v2.4.0). Briefly the sorted bam files derived from bowtie mapping were compared to WT controls using the bamCompare tools (reference-point --referencePoint center --ratio=log2) and the resulting bigwig files were used to generate a data matrix using the computeMatrix tool (reference-point --referencePoint center -a 5000 -b 5000 –bs=20).  Finally, the data was plotted using the plotHeatmap or plotProfile tools.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: stage 12 and younger flower buds

extract_protocol:
2.0g of un-opened flower buds (stage 12 and younger) for each genotype were collected and ground to a fine powder in liquid nitrogen and crosslinked in 1% formaldehyde (Sigma, Cat# F8775) for 20min at room temperature with slow rotation. The chromatin was then fragmented to ~500bp by sonication and the lysate was incubated with the anti-Flag M2 Magnetic beads (Sigma, Cat# M8823) at 4°C for 2h. The beads were washed 5 times, for 5min at 4°C and then the crosslinking was reversed by incubation at 65°C overnight and further purified using the phenol:Chloroform:Isoamyl Alcohol kit (Thermo scientific, Cat# 17908).
The resulting DNA then was used for library preparation with NEBNext Ultra II DNA Library Prep Kit (NEB, Cat# 7645). The ChIP libraries were sequenced in SE50 mode on a HiSeq2500 machine.


title: Sample3_exp5_chip1_rep3


title: WT_6_rep3_smRNA-seq

description: Sample 88


title: KH7WT_L4: WT rep 1

description: 115x10^6 cells from 5 pooled mice


title: NRPD1-3xFLAG,shh1-1_IP_2


title: NRPD1-3xFLAG,clsy1-7,2-2,3-1,4-1_IP_2


title: NRPD1-3xFLAG_IP_1


title: NRPD1-3xFLAG_IP_2


title: NRPD1-3xFLAG_input_2


title: NRPD1-3xFLAG_input_1


title: Sample1_exp5_chip1_rep1


title: clsy4-1_rep2_smRNA-seq

description: small RNA


title: Sample2_exp4_chip1_rep2


title: clsy3-1_rep2_smRNA-seq

description: small RNA


title: suvh4,5,6_rep1_smRNA-seq

description: small RNA


title: WT_IP_1

value: wild-type


title: nrpd1-4_rep2_smRNA-seq

description: small RNA


title: atxr5,6_rep1_smRNA-seq

description: small RNA


title: Sample3_exp4_chip1_rep3


title: WT_IP_2


title: clsy1-7_rep2_smRNA-seq

description: small RNA


title: met1-3_rep2_smRNA-seq

description: small RNA


title: WT_5_rep2_smRNA-seq

description: small RNA


title: NRPD1-3xFLAG,clsy2-2_IP_1


title: ddm1-2_rep1_smRNA-seq

description: small RNA


title: NRPD1-3xFLAG,clsy4-1_IP_1


title: WT_4_rep2_smRNA-seq

description: small RNA


title: cmt2-7_rep1_smRNA-seq

description: small RNA


title: Sample2_exp5_chip1_rep2


title: drm1-2,2-2_rep1_smRNA-seq

description: small RNA


title: met1-3_rep1_smRNA-seq

description: small RNA


title: shh1-1,clsy3-1,4-1_rep1_smRNA-seq

description: small RNA


title: Sample1_exp4_chip1_rep1


title: shh1-1,clsy1-7,2-1_rep1_smRNA-seq

description: small RNA


title: clsy4-2_rep3_smRNA-seq

description: Sample 92


title: NRPD1-3xFLAG,clsy3-1_IP_1


title: NRPD1-3xFLAG,clsy1-7,2-2_IP_2


title: shh1-1_rep1_smRNA-seq

description: small RNA


title: cmt3-11_rep1_smRNA-seq

description: small RNA


title: MET1-3wt_rep1_smRNA-seq

description: small RNA


title: clsy1-7,2-2,3-1,4-1_rep1_smRNA-seq

description: small RNA


title: clsy1-7,2-1,3-1,4-1_rep1_smRNA-seq

description: small RNA


title: MET1-3wt_rep2_smRNA-seq

description: small RNA


title: Sample3_exp2_chip1_rep3

value: late embryos


title: clsy2-2,4-1_rep1_smRNA-seq

description: small RNA


title: clsy1-7,3-1_rep1_smRNA-seq

description: small RNA


title: shh1-1,clsy1-7_rep1_smRNA-seq

description: small RNA


title: clsy3-1_rep1_smRNA-seq

description: small RNA


title: clsy3-1,4-1_rep1_smRNA-seq

description: small RNA


title: clsy2-2,3-1_rep1_smRNA-seq

description: small RNA


title: Sample1_exp3_chip1_rep1


title: clsy1-7,4-1_rep1_smRNA-seq

description: small RNA


title: clsy1-7_rep1_smRNA-seq

description: small RNA


title: Sample3_exp3_chip1_rep3


title: clsy1-7,2-2_rep1_smRNA-seq

description: small RNA


title: Sample2_exp3_chip1_rep2


title: clsy2-2_rep1_smRNA-seq

description: small RNA


title: Sample2_exp2_chip1_rep2


title: WT_2_rep1_smRNA-seq

description: small RNA


title: nrpd1-4_rep2_mRNA-seq

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: mRNA-seq reads were mapped to TAIR10 reference genome using STAR (v2.5.0c) allowing 2 mismatches (--outFilterMismatchNmax 2) and including only uniquely mapped reads (--outFilterMultimapNmax 1).
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

extract_protocol:
4 un-opened flower buds (stage 12 and younger) were collected from the same individual plants as used for the smRNA-seq and MethylC-seq analyses and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Ultra RNA Library Prep Kit (NEB, Cat# E7530). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.


title: nrpd1-4_rep1_mRNA-seq


title: clsy3-1,4-1_rep2_mRNA-seq


title: clsy1-7,2-2,3-1,4-1_rep1_mRNA-seq


title: WT_3_rep1_smRNA-seq

description: small RNA


title: clsy3-1,4-1_rep1_mRNA-seq


title: clsy1-7,2-2,3-1,4-1_rep2_mRNA-seq


title: clsy4-1_rep2_mRNA-seq


title: clsy1-7,2-2_rep1_mRNA-seq


title: clsy4-1_rep1_mRNA-seq


title: clsy3-1_rep1_mRNA-seq


title: clsy2-2_rep2_mRNA-seq


title: clsy2-2_rep1_mRNA-seq


title: Sample2_exp1_chip1_rep2

value: early embryos


title: WT_1_rep1_smRNA-seq

description: small RNA


title: clsy1-10_rep3_smRNA-seq

description: Sample 90


title: WT_3_rep2_mRNA-seq


title: clsy1-7,2-2_rep2_mRNA-seq


title: WT_2_rep2_mRNA-seq


title: clsy1-7_rep2_mRNA-seq


title: WT_1_rep1_mRNA-seq


title: WT_3_rep1_mRNA-seq


title: shh1-1_MethylC-seq

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Mapping and call methylation: MethylC-seq reads were analyzed using BS-seeker2 (v2.0.8). Briefly, reads were mapped against the C-to-T converted TAIR10 reference genome or the chloroplast genome using the bs_seeker2-align.py script with the bowtie aligner, allowing 2 mismatches (-m 2). The mapped reads were further the duplication reads using MarkDuplicates of picard (v2.16.0) and the retained reads were then used to calculate the methylation level at each cytosine using the bs_seeker2-call_methylation.py script, requiring a minimum coverage of 4 reads (-r 4). From these analyses, the mapability, coverage, global percent CG, CHG, and CHH methylation levels, and non-conversion rates for each library were determined (See Table 5). In addition, wiggle (wig) files showing the percent CG, CHG and CHH methylation for each genotype at single nucleotide resolution were generated using a custom perl script (BSseeker2_2_wiggleV2.pl) based on the BSseeker2 CGmap output files.
Methylation levels: From these analyses, the mapability, coverage, global percent CG, CHG, and CHH methylation levels, and non-conversion rates for each library were determined (See Table 5).
DMR calling: To call differentially methylated regions (DMRs) several custom perl scripts were used (BSseeker2_methylCall_2cytosineFormat.pl and Cytosine_2_100bp_v7.pl). These scripts identified DMRs in the CG, CHG or CHH contexts based on pair-wise comparisons between each mutant and three independent WT data sets in 100bp non-overlapping bins using the following criteria:  (1) only bins with ≥ 4 cytosines in the specified context were included, (2) only bins in which there was sufficient coverage in both genotypes being compared were included (i.e. ≥4 reads over the required 4 cytosines in the specific context), and (3) only bins with a fold change of 40%, 20% or 10% methylation in the CG, CHG, and CHH contexts, respectively, with an adjusted p value of ≤0.01 relative to all three WT controls were called as DMRs.
Genome_build: TAIR10
Supplementary_files_format_and_content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation

extract_protocol:
0.1g of un-opened flower buds (stage 12 and younger) were collected from the same individual plants as used for the smRNA-seq analyses and genomic DNA was isolated using the DNeasy Plant Mini Kit (Qiagen, Cat# 69104).
2.0μg purified genomic DNA then was sonicated using the Covaris S2 Sonicator and fragments that smaller than 500bp were retained using Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) for MethylC-seq libraries. These DNA ends were repaired using the End-It DNA End-Repair Kit (Epicentre, Cat# ER81050) and purified by Sera-Mag Magnetic SpeedBeads. The end-repaired DNA was adenylated at 3’ end using the polymerase activity of Klenow Fragment (3’à5’ exo, NEB, Cat# M0212) and followed by purification of Sera-Mag Magnetic SpeedBeads. These DNA were then ligated to the methylated adapter in NEXTflex Biosulfite-Seq Barcode Kit (BIOO Scientific, Cat# 511911) using T4 DNA ligase (NEB, Cat# M0202). The ligated DNA was performed the C-to-T bisulfite conversion using MethylCode Bisulfite Conversion Kit (Life Tech Cat# MECOV50). The resulting DNA was amplified for 4 cycles, purified, pooled and sequenced with SE50 using HiSeq 2500.


title: nrpd1-4_MethylC-seq


title: WT_1_rep2_mRNA-seq


title: clsy1-7,2-2,3-1,4-1_MethylC-seq


title: clsy1-7_rep1_mRNA-seq


title: clsy3-1_MethylC-seq


title: clsy4-1_MethylC-seq


title: clsy1-7,2-2_MethylC-seq


title: Sample3_exp1_chip1_rep3


title: Sample1_exp2_chip1_rep1


title: clsy2-2_MethylC-seq


title: clsy4-1_rep1_smRNA-seq

description: small RNA


title: clsy1-7_MethylC-seq


title: WT_3_MethylC-seq


title: WT_2_MethylC-seq


title: clsy3-1,4-1_MethylC-seq


title: WT_2_rep1_mRNA-seq


title: WT_1_MethylC-seq


title: HL-60_shLUC_RNA_PMA16_rep2

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

description: ribodepleted RNA

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq): BWA
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: HL-60 cell line

growth_protocol: HL-60 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of super calf serum (GEMcell) and 2 mM of L-glutamine.

extract_protocol: NEBNext Ultra Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: HL-60 cells were differentiated with 100 nM Phorbol 12-myristate 13-acetate (PMA) in growing medium

tag: cell line

value: PMA treated (16h)


title: M5_INTS13_shNAB2-2

source_name: in vitro differentiated monocytes (from bone marrow CD34+ cells)

growth_protocol: Monocytes were differentiated fromCD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3, 50 ng/ml M-SCF and 25 ng/ml GM-CSF, and collected at day 5

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

tag: chip antibody

value: INTS13, Bethyl A303-575A

tag: cell type

value: bone marrow CD34+ derived monocytes (day5)

tag: infection

value: shRNA against NAB2 (NAB2 KD)


title: HL-60_shNAB2-1_RNA_PMA16

description: ribodepleted RNA

extract_protocol: NEBNext Ultra II Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)


title: HL-60_shLUC_RNA_PMA16_rep1

description: ribodepleted RNA


title: macrophages_INTS13

source_name: in vitro differentiated macrophages

growth_protocol: Macrophages were differentiated from monocytes in IMDM supplemented with 10%FBS and 25 ng/ul GM-CSF

value: monocytes-derived macrophages


title: JURKAT_INTS13_CTRL

source_name: JURKAT cell line

growth_protocol: Jurkat cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of super calf serum (GEMcell) and 2 mM of L-glutamine.

value: Jurkat

value: untreated


title: M5_INTS13_shEGR1

treatment_protocol: Monocytes were differentiated fromCD34+ cells in StemSpan SFEM medium supplemented with 100 ng/ml SCF, 10 ng/ml IL-3, 50 ng/ml M-SCF and 25 ng/ml GM-CSF

value: shRNA against EGR1 (EGR1 KD)


title: monocytes_INTS13

source_name: circulating monocytes

value: circulating monocytes


title: monocytes_NAB2

value: NAB2, ThermoFisher PA5-27925


title: JURKAT_INTS13_PMA

treatment_protocol: Jurkat cells were differentiated with 100 nM Phorbol 12-myristate 13-acetate (PMA) in growing medium

value: PMA (16h)


title: HL-60_INTS13_shNAB2-2

value: shRNA against shNAB2 (NAB2 KD)


title: HL-60_INTS13_shLUC_rep2

value: shRNA against shLUC


title: HL-60_H3K27Ac_PMA48

value: H3K27Ac, Abcam ab4279

value: PMA treated (48h)


title: HL-60_H3K27Ac_PMA_rep2


title: HL-60_INTS13_shNAB2-1


title: macrophages_NAB2

treatment_protocol: Macrophages were differentiated from monocytes in IMDM supplemented with 10%FBS and 25 ng/ul GM-CSF


title: HL-60_shNAB2-2_RNA_PMA16

description: ribodepleted RNA


title: IPIMEL274.T1.rna.live

city: San Francisco

first: Saurabh

last: Asthana

state: CA

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

data_processing:
Reads were aligned with RSEM
Alignment quality was assessed using Picard tools.
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM genes results files with estimated read counts and TPM expression

molecule: polyA RNA

source_name: melanoma biopsy

extract_protocol:
50,000 total live cells, determined by staining with the Zombie Aqua fixable viability dye (BioLegend, 423102), were directly sorted into lysis buffer by fluorescence activated cell sorting (FACS) to isolate RNA. RNA was isolated using the Dynabeads mRNA DIRECT purification kit (ThermoFisher Scientific 61011) following the manufacturer’s suggested protocol.
Isolated RNA was converted into amplified cDNA using the Ovation RNA-Seq System V2 kit (NuGen 7102-A01) and cDNA was converted into RNAseq libraries using the Nextera XT DNA Library Prep kit (Illumina FC-131-2001), following the manufacturer’s suggested protocol. RNAseq library quality was checked using a Bioanalyzer HS DNA chip (Agilent) and pooled.

tag: condition

value: melanoma


title: fl/fl repl 1

first: Robbert

last: Hoogeboom

address: 123 Coldharbour lane

institute: King's College London

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 mm10, GRCm38 whole genome using bowtie
Reads were quantified using Tophat and Cufflinks
Genome_build: mm10, GRCm38
Supplementary_files_format_and_content: Tab-delimited text file lists average RPKM values of biological triplicates and statistics.

source_name: Follicular B cells

extract_protocol:
RNA was isolated using TriZol, followed by further purification using RNEasy mini kit from Qiagen. RNA was amplified using Ovation RNA-Seq system V2 (NuGen).
Libraries were prepared using TruSeq Nano DNA kit (Illumina)

tag: genotype


title: fl/fl repl 2


title: fl/fl repl 3


title: IPIMEL253.T1.rna.live


title: IPIMEL212.T1.rna.live


title: wt/fl repl 2


title: IPIMEL149.T1.rna.live


title: wt/fl repl 1


title: wt/fl repl 3


title: HL-60_H3K27Ac_CTRL_rep2

value: H3K27ac, Abcam ab4279


title: IPIMEL221.T1.rna.live


title: KO-H3K27Me ChIP 1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic (parameters used were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”)
Surviving paired reads were then aligned against the mouse reference genome (GRCm38.p4) using Bowtie2
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
Processed alignments were then used in macs2 with BAM files of ChIP samples as treatments (-t) and the input sample BAM as control.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: bigwig

source_name: connective tissue

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
50 ug total fragmented chromatin were mixed with 5 ug antibody overnight at 4 degree with rotation. The chromatin-antibody complex were then precipitated with protein A/G magnetic beads (Thermo Fisher Scientific). After washes with low salt wash buffer (20mM Tris, 2mM EDTA, 50mM NaCl, 0.01% SDS and 1% SDS), high salt wash buffer (same composition, 250 mM NaCl) and LiCL-wash buffer (10mM Tris, 1mM EDTA, 250 mM LiCl, 1% NP40 and 1% sodium deoxycholate), precipitated chromatin was eluted in 200µl of elution buffer (10µl 20% SDS, 20µl 1M NaHCO3 and 170µl dH2O). Reverse cross linking was done by adding 8 ul 5M NaCl and incubate at 65 deg overnight. 1 ul 10 mg/ml RNase A was added to the tube for 30 mins incubation at 37°C. Then 4µl 0.5M EDTA, 8µl 1M Tris-HCl and 1µl 20 mg/ml Proteinase K was added for 2h incubation at 42°C. The released DNA was purified using QIAquick PCR purification kit (Qiagen).
Purified DNA from two replicates were pooled for library preparation using TruSeq Nano DNA Library Prep Kit (Illumina) according to the manufacturer's instructions

tag: strain/background

value: BALB/c

tag: genotype/variation

value: Actb -/-

tag: age

value: 10.5 day old embryos

value: Mouse embryonic fibroblast


title: IPIMEL113.T1.rna.live


title: WT-H3K27Me ChIP 1

value: Actb +/+


title: HL-60_H3K27Ac_PMA24

value: H3K27Ac,Abcam ab4279

value: PMA treated (24h)


title: KO-H3K27Me ChIP 2


title: IPIMEL108.T1.rna.live


title: IPIMEL069.T1.rna.live


title: IPIMEL085.T1.rna.live


title: IPIMEL056.T1.rna.live


title: RNA-seq_DR8dex2_rep1

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using hisat2 software.
Reads were counted by Htsseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) derived from hESCs and primary human MSCs were cultured in MEM (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) from 1x106 cells per duplicate and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: ES-derived  mesenchymal stem cell

tag: passage


title: RNA-seq_WT_ rep1

value: WT


title: RNA-seq_WT_ rep2


title: IPIMEL131.T1.rna.live


title: RNA-seq_DR8dex2_rep2


title: WT-H3K27Me ChIP 2


title: nrpd1-4_rep1_smRNA-seq

description: small RNA

tag: ecotype

value: Columbia

tag: tissue

value: stage 12 and younger flower buds


title: NRPD1-3xFLAG,clsy1-7_IP_1


title: Sample1_exp1_chip1_rep1

value: male

tag: developmental stage

value: early embryos

value: whole body

tag: strain

value: AsymCX

value: female


title: PAM_finistere_10h_RNA_125

city: Jouy-en-Josas

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

description: Gene expression 10 h after infection in total RNA from Finistere infected sample

hyb_protocol: Subsequently, for each sample 600 ng of Cy3-labeled cRNA (specific activity > 9.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes in a volume of 25 µl containing 25x of Agilent Fragmentation Buffer and 10x of Agilent Blocking Agent. Afterwards, 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array following the recommended protocol. After hybridization, microarrays were washed 1 minute at room temperature with the GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C using the GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides (scan area 61x21.6 mm).

data_processing:
The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).
Data were normalized using intra-array median substraction and log2 transformation

organism: Sus scrofa

source_name: PAM, finistere, 10h, RNA, 125

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies), and the starting RNA amounts varied according to the type of sample under analysis. In the case of total RNAs 50 ng were used, while in the case of Co-IP RNAs 10 ng were used. In both cases specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: Batches of around 10^9 porcine alveolar macrophages (PAMs) were collected by lung lavage from each of four 7 weeks old SPF pigs and conserved in liquid nitrogen in fetal bovine serum (FBS) containing 10 % DMSO until start of experiment.For each experimental condition, 10^8 PAMs were pre-incubated at 37°C with 5% CO2 for 24h in 175 cm2 flask in RPMI 1640 medium supplemented with 15% of gamma irradiated FBS, 5% of serum collected from SPF pigs, 2 mM of L-Glutamine and 200 U/ml of penicillin-streptomycin.

extract_protocol: Total RNAs and RISC boundd RNAs were extracted and purified using TRIzol LS Reagent according to the manufacturer’s recommendations (Life Technologies, Carlsbad, CA, USA). Total RNAs and RISC bounded RNAs were further purified using the RNeasy Minelute clean up kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations. RNA yield and purity were monitored using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Pico kits (Agilent Technologies, Santa Clara, USA). RNA quality was evaluated using the RNA Integrity Number (RIN).

treatment_protocol: RISC immunoprecipitation was carried out using monoclonal anti-pan-Argonaute antibody 2A8 (Millipore) that recognizes Ago1, Ago2, Ago3 and Ago4 proteins. Cells were washed three times in cold PBS 1X / 5 mM EDTA and immediately lysed using the lysis buffer of the Pierce IP classic kit (Pierce) supplemented with protease inhibitor (Roche) and RNase inhibitor (Thermo scientific). Lysed cells were stored at -80°C until use for immunoprecipitation of miRNP complexes. For immunoprecipitation of miRNP complexes from the lysed cells, agarose resin were pre-incubated five hours at 4°C with polyclonal rabbit anti-mouse IgG (Jackson Immunoresearch) to increase their avidity and over-night at 4°C with Anti-pan Ago clone 2A8. The cell lysate was then incubated with the antibodies-protein A\G Plus agarose resin complex followed by washing five times with IP lysis/wash buffer from the IP classic kit (Pierce).

value: PAM

tag: virus vs control

value: Finistere

tag: total rna vs immunoprecipitated

value: RNA

tag: individual


title: PAM_finistere_10h_RNA_126

source_name: PAM, finistere, 10h, RNA, 126


title: PAM_finistere_7h_RNA_124

description: Gene expression 7 h after infection in total RNA from Finistere infected sample

source_name: PAM, finistere, 7h, RNA, 124

value: 7 h


title: PAM_finistere_10h_RNA_124

source_name: PAM, finistere, 10h, RNA, 124


title: PAM_finistere_10h_RNA_123

source_name: PAM, finistere, 10h, RNA, 123


title: PAM_finistere_7h_RNA_125

source_name: PAM, finistere, 7h, RNA, 125


title: PAM_control_10h_RNA_126

description: Gene expression 10 h after infection in total RNA from control sample

source_name: PAM, control, 10h, RNA, 126

value: control


title: PAM_finistere_7h_RNA_123

source_name: PAM, finistere, 7h, RNA, 123


title: PAM_finistere_7h_RNA_126

source_name: PAM, finistere, 7h, RNA, 126


title: PAM_control_10h_RNA_124

source_name: PAM, control, 10h, RNA, 124


title: PAM_control_10h_RNA_125

source_name: PAM, control, 10h, RNA, 125


title: STI -, clinical manifestations of PID + #23

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R

source_name: human blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Alpha and beta globin mRNA was removed from total RNA using Globinclear (Ambion/ThermoFisher Scientific). Quality control was performed with Agilent Bioanalyser.

value: Whole blood

tag: Sex

tag: disease state

value: normal histology


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #2

value: chronic endometritis + chlamydia


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #6


title: STI -, clinical manifestations of PID + #19


title: STI -, clinical manifestations of PID + #24


title: STI -, clinical manifestations of PID + #27


title: STI -, clinical manifestations of PID + #25


title: STI -, clinical manifestations of PID + #22


title: 5 uM methyl viologen

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description:
MV5_sequence
processed data file: All_Normalized_Expression_Levels.csv

data_processing:
Fastq files were examined with FastQC to confirm high quality as well as the lack of sequences from the adaptor present in the reads.
Reads from all samples were aligned to the genomes of Thermosynechococcus elongatus BP-1 (NCBI: NC_004113) and Meiothermus ruber strain A (NCBI: NZ_JXOP01000000.1) using the Burrows Wheeler Aligner (BWA) with the default settings.
Gene counts were determined using HT-seq.
Raw counts were normalized using DESeq2.
Genome_build: Thermosynechococcus elongatus BP-1 (NC_004113.1), Meiothermus ruber strain A (NZ_JXOP01000000.1).
Supplementary_files_format_and_content: All_Normalized_Expression_Levels.csv: Comma-separated text file contains normalized log2 gene expression values for all genes of T. elongatus and M. ruber that were expressed in at least one of 20 conditions.

organism:
Meiothermus ruber
Thermosynechococcus vestitus BP-1

growth_protocol: T. elongatus BP1 and M. ruber strain A cells cultured under batch conditions in BG-11 medium.

extract_protocol:
SV Total RNA Isolation System (Promega, Madison, WI).
Libraries were prepared for Illumina sequencing using the Ovation Universal RNA seq system (NuGEN, San Carlos, CA).
cDNA sequencing took place on an Illumina NextSeq 500 using 75-bp single end reads.

treatment_protocol: Each treatment was carried out for 4 hours.

tag: meiothermus ruber strain

value: A

tag: culture type

value: Planktonic

tag: condition type

value: Batch

tag: treatment

value: 5 uM methyl viologen


title: 250 mM NaCl

description:
Na250_sequence
processed data file: All_Normalized_Expression_Levels.csv

source_name: T. elongatus BP1 and M. ruber strain A cells

value: 250 mM NaCl


title: STI -, clinical manifestations of PID + #20


title: STI -, clinical manifestations of PID + #18


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #4


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #3


title: PAM_control_10h_RNA_123

source_name: PAM, control, 10h, RNA, 123


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #5


title: STI -, clinical manifestations of PID + #26


title: endo CT+ (low burdern), chronic endometritis, clinical manifestations of PID - #1


title: STI -, clinical manifestations of PID + #14


title: STI -, clinical manifestations of PID + #16


title: STI -, clinical manifestations of PID + #21


title: clsy3-1_rep2_mRNA-seq

source_name: stage 12 and younger flower buds

value: Columbia

value: stage 12 and younger flower buds

tag: genotype


title: Methyl viologen and Iron

description:
MV5F_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: Methyl viologen and Iron


title: STI -, clinical manifestations of PID + #17

value: female


title: 50 mM NaCl

description:
Na50_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: 50 mM NaCl


title: C source: Lactate

description:
L5_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: C source:Lactate


title: STI -, clinical manifestations of PID + #15


title: C source: Acetate

description:
A5_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: C source:Acetate


title: C Source: Glucose

description:
G5_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: C Source:Glucose


title: PAM_control_7h_RNA_125

description: Gene expression 7 h after infection in total RNA from control sample

source_name: PAM, control, 7h, RNA, 125

value: PAM

value: control

value: 7 h

value: RNA


title: STI -, clinical manifestations of PID + #13

value: Whole blood

value: normal histology


title: PAM_control_7h_RNA_124

source_name: PAM, control, 7h, RNA, 124


title: 5x more Iron

description:
F5_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: A

value: Planktonic

value: Batch

value: 5x more Iron


title: STI -, clinical manifestations of PID + #8


title: STI -, clinical manifestations of PID + #12


title: PAM_control_7h_RNA_126

source_name: PAM, control, 7h, RNA, 126


title: STI -, clinical manifestations of PID + #10


title: No agitation

description:
STAT_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: No agitation


title: PAM_control_7h_RNA_123

source_name: PAM, control, 7h, RNA, 123


title: STI -, clinical manifestations of PID + #11


title: PAM_finistere_10h_IP_126

description:
RISC-bound RNA
Gene expression 10 h after infection in RISC-bound RNA from Finistere infected sample

source_name: PAM, finistere, 10h, IP, 126

value: Finistere

value: IP


title: PAM_finistere_10h_IP_124

source_name: PAM, finistere, 10h, IP, 124


title: PAM_finistere_10h_IP_123

source_name: PAM, finistere, 10h, IP, 123


title: No Irradiance

description:
DARK_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: No Irradiance


title: pH:9

description:
pH9_sequence
processed data file: All_Normalized_Expression_Levels.csv


title: STI -, clinical manifestations of PID + #9

value: female


title: STI -, clinical manifestations of PID + #5


title: STI -, clinical manifestations of PID + #6


title: PAM_finistere_10h_IP_125

source_name: PAM, finistere, 10h, IP, 125


title: STI -, clinical manifestations of PID + #4


title: STI -, clinical manifestations of PID + #2


title: STI -, clinical manifestations of PID + #3


title: PAM_finistere_7h_IP_125

description:
RISC-bound RNA
Gene expression 7 h after infection in RISC-bound RNA from Finistere infected sample

source_name: PAM, finistere, 7h, IP, 125


title: STI -, clinical manifestations of PID + #1


title: Temperature:60C

description:
60c_sequence
processed data file: All_Normalized_Expression_Levels.csv


title: CT +, clinical manifestations of PID + #16

value: chlamydia


title: CT +, clinical manifestations of PID + #17


title: CT +, clinical manifestations of PID + #15


title: PAM_finistere_7h_IP_126

source_name: PAM, finistere, 7h, IP, 126


title: Temperature: 40C

description:
40c_sequence
processed data file: All_Normalized_Expression_Levels.csv


title: N source: Urea

description:
NU_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: N source:Urea


title: pH:6

description:
pH6_sequence
processed data file: All_Normalized_Expression_Levels.csv


title: N source: Ammonia

description:
NH4_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: N source:Ammonia


title: STI -, clinical manifestations of PID + #7


title: No Nitrate

description:
NN_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: No Nitrate


title: No Iron

description:
NF_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: No Iron


title: CT +, clinical manifestations of PID + #13


title: CT +, clinical manifestations of PID + #11


title: PAM_control_10h_IP_125

description:
RISC-bound RNA
Gene expression 10 h after infection in RISC-bound RNA from control sample

source_name: PAM, control, 10h, IP, 125

value: PAM

value: control


title: CT and MG +, clinical manifestations of PID + #9

value: Whole blood

value: chlamydia + mycoplasma genitalium


title: PAM_finistere_7h_IP_123

source_name: PAM, finistere, 7h, IP, 123

value: 7 h


title: CT +, clinical manifestations of PID + #12


title: PAM_control_10h_IP_126

source_name: PAM, control, 10h, IP, 126


title: CT +, clinical manifestations of PID + #5

source_name: human blood


title: PAM_finistere_7h_IP_124

source_name: PAM, finistere, 7h, IP, 124


title: GC +, clinical manifestations of PID + #6

value: gonorrhea


title: CT +, clinical manifestations of PID + #4


title: CT and GC +, clinical manifestations of PID + #1

value: chlamydia + gonorrhea


title: CT and MG +, clinical manifestations of PID + #10


title: PAM_control_7h_IP_126

description:
RISC-bound RNA
Gene expression 7 h after infection in RISC-bound RNA from control sample

source_name: PAM, control, 7h, IP, 126


title: GC +, clinical manifestations of PID + #2


title: PAM_control_10h_IP_124

source_name: PAM, control, 10h, IP, 124


title: Standard

description:
S_sequence
processed data file: All_Normalized_Expression_Levels.csv

source_name: T. elongatus BP1 and M. ruber strain A cells

value: A

value: Planktonic

value: Batch

value: Standard


title: CT+, clinical manifestations of PID + #3

value: female


title: High glucose-2 (H2)

city: Urla

first: sukru

last: gulec

state: İzmir

address: Gülbahçe Mah., İzmir Yüksek Teknoloji Enstitüsü,

department: Food Engneering

country: Turkey

institute: Izmir Institute of Technology

description: replicate 2

scan_protocol: illumina iScan - Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio Software (v.1.9.0)

source_name: Colon Carcinoma Cell Line

label_protocol: Standard Illumina hybridization protocol

growth_protocol: Cell were growth on collagen coated inserts for 21 days.

extract_protocol: Total RNA was isolated by RNAzol reageant from high glucose and control groups. Quality of RNAs were analyzed by bioanalyzer and then genome-wide mRNA array was performed.

treatment_protocol: Cells were growth at least 3 passages under high or low glucose conditions. The cells were incubated for 21 days under indicated conditions.

tag: gender

value: Male

value: 72 years

tag: cell line


title: High glucose-3 (H3)

description: replicate 3

tag: age


title: High glucose-1 (H1)

description: replicate 1


title: Control-3 (C3)

description: replicate 3


title: Lenti-sh Ctl

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

data_processing:
Using a HiSeq SBS sequencing kit version 4, Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Trimmomatic ver 0.36 was used to remove sequence adapters and low-quality bases and quality control was checked by FastQC ver 0.11.5
Sequencing alignment was performed by STAR ver 2.5.3a.
The differential expression profiles of RNA-seq were analyzed by the edgeR-based R (ver 3.4.1) pipeline
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts, fold change, FDR between two conditions generated by edgeR

source_name: primary hepatocytes

growth_protocol: Primary hepatocytes pooled from five C57BL/6 mice in each group were plated in M199 media + 10% fetal bovine serum.

extract_protocol:
RNA from the hepatocytes was isolated with the RNeasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols. The cDNA library was sequenced using an Illumina HiSeq2000 (Illumina, San Diego, CA) to produce paired-end 100 bp reads.

treatment_protocol: Twenty-four h after plating, the hepatocytes were infected with control lentivirus or lentivirus expressing JMJD3 shRNA for 48 h followed by treatment with 5 mM glucose and 10 μM Fsk for 6 h to mimic fasting.

tag: cells

value: Primary hepatocytes

value: wild type


title: CT +, clinical manifestations of PID + #14

value: chlamydia

tag: tissue


title: PAM_control_7h_IP_124

source_name: PAM, control, 7h, IP, 124

value: PAM

value: IP


title: No Sulfate

description:
NS_sequence
processed data file: All_Normalized_Expression_Levels.csv

value: No Sulfate


title: PAM_control_7h_IP_125

source_name: PAM, control, 7h, IP, 125

value: control


title: Lenti-sh JMJD3

value: JMJD3 down-regulated


title: Control-2 (C2)

description: replicate 2


title: Zebrafish 3 hpf whole embryo injected with TUT47MO (Exp. ID: rs2)

status: Public on Apr 13 2018

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow.
Sequenced reads from RNA-seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31.
The gene-level quantifications were performed using RSEM with the default options for strand-specific and paired-end RNA-seq. The "rs1a" set of our libraries was between-sample normalized using RUV-seq 1.10.0. The standard workflow suggested by RUV-seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead, we first chose a subset of spike-in RNAs that have ≥ 256 “expected counts” of reads in at least 90% of samples. Then, the counts were normalized by the RUVg algorithm (k = 1). The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike-in reads in our second RNA-seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike-in sequences were significantly out of the linear correlations between any two samples. As a workaround, we picked the internal controls from the first set to find genes that express more than 500 normalized reads with ≤ 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike-in RNAs for processing counts by the modified indirect RUVg approach.
Genome_build: GRCz10
Supplementary_files_format_and_content: comma-separated text file include RUVg-normalized (rs1a and rs1b) or TPM-normalized (rs2) values for each sample.

organism: Danio rerio

source_name: Zebrafish whole embryo

growth_protocol: Zebrafish embryos were obtained by the natural mating of wild-type AB strain and grown in embryo medium at 28.5˚C. Embryos were staged according to standard morphological criteria.

extract_protocol:
For each sample, embryos were collected and total RNA was extracted with TRIzol (Invitrogen). The samples were spiked in with ERCC RNA Spike-In Mix (Ambion) for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 (Agilent).
Ribosomal RNA was depleted from total RNA using Ribo-Zero Gold kit (Epicentre). RNA- seq libraries were constructed using TruSeq stranded total RNA library prep kit (Illumina) and sequenced in Illumina Nextseq 500 v2  to yield paired-end 76nt reads.

treatment_protocol: Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild-type zebrafish embryos at 1-cell stage.

tag: hour post fertilization

tag: morpholino

value: TUT4 (translation-blocking), TUT7 (translation-blocking)

value: AB


title: Zebrafish 5 hpf whole embryo injected with TUT47MO (Exp. ID: rs2)

tag: strain


title: Zebrafish 5 hpf whole embryo injected with ConMO (Exp. ID: rs2)

value: Control


title: Zebrafish 3 hpf whole embryo injected with ConMO (Exp. ID: rs2)


title: PAM_control_10h_IP_123

source_name: PAM, control, 10h, IP, 123

tag: virus vs control

tag: total rna vs immunoprecipitated


title: Flavedo_EV_2h [EV d0 D ]

city: Valencia

first: Ana

last: Rodríguez

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología de cítricos

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP)

description: Gene expression 2h after P. citricarpa inoculation

hyb_protocol: Hybridization and washing steps were performed with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers (Agilent), respectively.

scan_protocol: The slides were scanned at 5 µm resolution using the double scanning in an Agilent G2565AA microarray scanner. Analysis was performed with the Feature Extraction software 9.5.1 and comparisons with the GeneSpring 11.5 software.

data_processing: Control features spotted on the array were removed, and only those for which the “IsWellAboveBG” parameter was 1 in the three replicates were selected. A Student’s t test analysis was performed to identify significantly expressed genes with a false discovery rate adjustment according to Benjamini and Hochberg’s method.

organism: Citrus sinensis

source_name: Fruit of EV sweet orange fruit inoculated with Phyllosticta citricarpa rep3

label_protocol: 100 ng of RNA were amplified and labelled in a one-color experimental design with the Agilent Low Input Quick Amp Labelling Kit and assessing for labelling and hybridization efficiencies with an Agilent Spike-In Kit. A 2100 Bioanalyzer (Agilent) was used for evaluating total RNA before and after labelling.

growth_protocol: Orange transformants used in this study were generated previously and trees are being grown currently at the Instituto Valenciano de Investigaciones Agrarias (IVIA) in Villarreal, Spain (39°56’40.4’’N, 0°08’11.0’’W and elevation of 67 m). Transgenic antisense (AS1, AS7) and empty-vector (EV) control orange fruit (Citrus sinensis) cv. ‘Navelina’ were harvested at maturity stage (November to February in the Mediterranean region). The experiments were performed with P. citricarpa isolate LGMF6 transformed with the GFP reporter gene (Figueiredo et al., 2010) deposited in the collection of the Laboratório de Genética de Microrganismos in the Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil. Isolate was cultured on potato dextrose agar (PDA, Difco, Detroit, MI, USA) for 21 days at 25°C, with photoperiod of 12 h light/dark.

extract_protocol: Total RNA was obtained from the peels of P. citricarpa-inoculated fruit using the RNAeasy kit and cleaned up with the RNeasy mini kit (Qiagen) following manufacturer instructions.

treatment_protocol: Fruit were inoculated in four equatorial points by injecting into the peel 5 µL of a 106 conidia/mL suspension of P. citricarpa. Inoculated fruit were kept into sealed plastic trays in a security chamber at 25 ºC and 80% RH in a P-2 laboratory.

value: flavedo (peel) of sweet orange fruit

value: EV

tag: agent

value: Phyllosticta citricarpa LGMF6  transformed with the GFP reporter gene

tag: time point

value: 2h after P. citricarpa inoculation


title: Flavedo_EV_2h [EV d0 C ]

source_name: Fruit of EV sweet orange fruit inoculated with Phyllosticta citricarpa rep2


title: Flavedo_AS7_8d [AS7 d8 H ]

description: Gene expression 8d after P. citricarpa inoculation

source_name: Fruit of AS7 sweet orange fruit inoculated with Phyllosticta citricarpa rep3

value: 8d after P. citricarpa inoculation


title: Flavedo_AS7_8d [AS7 d8 G ]

source_name: Fruit of AS7 sweet orange fruit inoculated with Phyllosticta citricarpa rep2


title: Flavedo_AS7_2h [AS7 d0 A ]

source_name: Fruit of AS7 sweet orange fruit inoculated with Phyllosticta citricarpa rep1


title: Flavedo_EV_8d [EV d8 C ]


title: Flavedo_EV_8d [EV d8 A ]

source_name: Fruit of EV sweet orange fruit inoculated with Phyllosticta citricarpa rep1


title: Flavedo_AS7_8d [AS7 d8 E ]


title: Flavedo_AS1_8d [AS1 d8 A ]

source_name: Fruit of AS1 sweet orange fruit inoculated with Phyllosticta citricarpa rep1


title: Flavedo_EV_8d [EV d8 B ]


title: Flavedo_AS1_2h [AS1 d0 B ]

source_name: Fruit of AS1 sweet orange fruit inoculated with Phyllosticta citricarpa rep2


title: Flavedo_EV_2h [EV d0 A ]


title: PAM_control_7h_IP_123

source_name: PAM, control, 7h, IP, 123

value: 7 h

tag: individual


title: Flavedo_AS7_2h [AS7 d0 E ]


title: Flavedo_AS1_2h [AS1 d0 A ]


title: Flavedo_AS1_2h [AS1 d0 E ]

source_name: Fruit of AS1 sweet orange fruit inoculated with Phyllosticta citricarpa rep3


title: Zebrafish 3 hpf whole embryo injected with TUT47MO (Exp. ID: rs1b)


title: Zebrafish 6 hpf whole embryo injected with TUT47MO (Exp. ID: rs1b)


title: Flavedo_AS1_8d [AS1 d8 C ]


title: Zebrafish 6 hpf whole embryo injected with ConMO (Exp. ID: rs1b)


title: Flavedo_AS1_8d [AS1 d8 B ]


title: Zebrafish 3 hpf whole embryo injected with ConMO (Exp. ID: rs1b)


title: Zebrafish 4 hpf whole embryo injected with TUT47MO (Exp. ID: rs1a)


title: Zebrafish 6 hpf whole embryo injected with TUT47MO (Exp. ID: rs1a)


title: Flavedo_AS7_2h [AS7 d0 D ]


title: Zebrafish 6 hpf whole embryo injected with TUT4MO (Exp. ID: rs1a)

value: TUT4 (translation-blocking)


title: Zebrafish 2 hpf whole embryo injected with TUT47MO (Exp. ID: rs1a)


title: Zebrafish 2 hpf whole embryo injected with TUT7MO (Exp. ID: rs1a)

value: TUT7 (translation-blocking)


title: Zebrafish 4 hpf whole embryo injected with TUT4MO (Exp. ID: rs1a)


title: clsy2-2_rep2_smRNA-seq

description: small RNA

source_name: stage 12 and younger flower buds

extract_protocol:
4 un-opened flower buds (stage 12 and younger) from individual mutant plants as well as 3 individual wild-type (WT) controls were collected, frozen in liquid nitrogen and kept at -80°C until use. Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. These total RNAs then were enriched for small RNAs through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The resulting small RNAs were used for library preparation using NEBnext Multiplex Small RNA Library Prep Set for Illumina (Cat# E7300) following the manual. The final library products were further purified by running 8% polyacrylamide gels and performed size-selection from 140-160nt as described above. The purified libraries were equally pooled and submitted for single-end 50 bp (SE50) sequencing on HiSeq 2500 (Illumina) at the Next Generation Sequencing Core of the Salk Institute for Biological Studies.

tag: ecotype

value: Columbia

value: stage 12 and younger flower buds


title: Zebrafish 4 hpf whole embryo injected with TUT7MO (Exp. ID: rs1a)


title: Zebrafish 2 hpf whole embryo injected with TUT4MO (Exp. ID: rs1a)


title: Zebrafish 6 hpf whole embryo injected with ConMO (Exp. ID: rs1a)


title: Zebrafish 4 hpf whole embryo injected with ConMO (Exp. ID: rs1a)


title: Zebrafish 2 hpf whole embryo injected with ConMO (Exp. ID: rs1a)


title: LtfCre/+ Foxa2f/f GD 4 rep 2

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
Adapters were trimmed from reads using cutadapt (version 1.11) and quality trimmed to a sliding window quality score of 30 and minimum length of 20 bp with fqtrim software.
Reads were mapped to the reference genome (GRCm38.p5) using Hisat2 mapper.
FeatureCounts tool was used to determine the number of reads that mapped to genes using Ensembl gene annotations.
Differential gene expression analysis was performed using the edgeR-robust method.
Genome_build: GRCm38.p5

source_name: Uterus

growth_protocol: Floxed Foxa2 (Foxa2f/f) mice were crossed with PgrCre or LtfiCre mice to generate conditional knockout animals. Gestational time points were obtained by the mating of 8- to 10-wk-old C57BL/6J wildtype or Foxa2 conditional knockout females with CD-1 male mice with the day of vaginal plug observation considered GD 1. After rescue of implatation, the implantation sites on the morning of GD 5 were visualized by intravenous injection of 1% Evans blue dye (Sigma-Aldrich) before necropsy.

extract_protocol:
Uteru were removed, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For rescue of implantation, FOXA2-deficient mice received i.p. injections of recombinant mouse LIF (10 μg in saline; catalog #554008, BioLegend) on GD 4 at 1000 h and 1800 h.

value: Uterus

tag: lif

value: No

value: LtfiCre/+ Foxa2f/f

tag: gestational day


title: PgrCre/+ Foxa2f/f GD 6 rep 3

value: Yes

tag: genotype

value: PgrCre/+ Foxa2f/f


title: LtfCre/+ Foxa2f/f GD 4 rep 3


title: Control GD 6 rep 1

value: control


title: PgrCre/+ Foxa2f/f GD 6 rep 1


title: PgrCre/+ Foxa2f/f GD 6 rep 4


title: Control GD 6 rep 3


title: Control GD 6 rep 2


title: LtfCre/+ Foxa2f/f GD 4 rep 4


title: Control GD 6 rep 4


title: Control-1 (C1)

description: replicate 1

source_name: Colon Carcinoma Cell Line

tag: gender

value: Male

value: 72 years


title: LtfCre/+ Foxa2f/f GD 4 rep 1


title: PgrCre/+ Foxa2f/f GD 4 rep 4


title: PgrCre/+ Foxa2f/f GD 6 rep 2


title: PgrCre/+ Foxa2f/f GD 4 rep 3


title: PgrCre/+ Foxa2f/f GD 4 rep 2


title: Zebrafish 6 hpf whole embryo injected with TUT7MO (Exp. ID: rs1a)

value: AB


title: Control GD 4 rep 1


title: Control GD 4 rep 4


title: Control GD 4 rep 2


title: Control GD 4 rep 3


title: PgrCre/+ Foxa2f/f GD 4 rep 1


title: FFPE, patient 1, 10 hours tissue lysis

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression data from human hippocampus (formalin-fixed paraffin-embedded)

hyb_protocol: Fragmented and labelled samples were hybridized to GeneChip Human Gene 2.0 ST Arrays.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G (with AGCC v3.1.1 software)

data_processing: The data were analyzed with Affymetrix Expression Console software (v1.4.1) using RMA-Sketch algorithm for data normalization. FF, FFPE_3h and FFPE_10h datasets were normalized together. Normalization was done to gene level as well as to exon level.

label: Biotin

source_name: Formalin-fixed paraffin-embedded human hippocampus; patient 1

label_protocol: Biotinylated cRNA samples were prepared using the Affymetrix GeneChip WT Pico Reagent Kit from 2 ng total RNA.

extract_protocol: Total RNA was isolated using the High Pure FFPE RNA Micro Kit (Roche) according to the manufacturer's instructions.

tag: diagnosis

value: epileptic patient suffering from Rasmussen encephalitis

value: hippocampus


title: FFPE, patient 3, 10 hours tissue lysis

source_name: Formalin-fixed paraffin-embedded human hippocampus; patient 3


title: FF, patient 3

description: Gene expression data from human hippocampus (fresh frozen)

source_name: Fresh frozen human hippocampus; patient 3

extract_protocol: Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.


title: DMN_M_2ppm_15d_1

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Agilent Mouse miRNA arrays (G4472A) were hybridized, washed and scanned on an Agilent Microarray Scanner following manufacturer instructions.

scan_protocol: Arrays ware scanned on an Agilent Microarray Scanner. Images from the scanner were processed using Agilent Feature Extraction Software v10.5.1.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: Dimethylnitrosamine, male, 14 days

label_protocol: 100 ng Total RNA (diluted to 50ng/µl) were labelled using miRNA complete labelling (PCp-Cy3) and hybridization kit (Agilent# 5190-0456).

growth_protocol: CD-1 male and female mice were orally treated with a set of genotoxic carcinogens (CIDB, DMN and MDA), nongenotoxic carcinogens (DCB, PB and PBO), non-hepatocarcinogens (CFX, Praz and Prop) and a group of undefined compounds (CPA, Wy-14643 and TAA) over a period of 3 and 14 days.

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany). RNA integrity was checked using the Agilent Bioanalyzer.

treatment_protocol: After 3 and 14 days of compound treatment mice were anaesthetized in isoflurane and exsanguinated from the heart and subjected to necropsy. The left lateral liver lobe was extracted and snap frozen under -80°C conditions.

value: male

value: liver

tag: treatment short name

value: DMN

tag: treatment

value: Dimethylnitrosamine

tag: treatment duration

value: 14 days

tag: treatment dose

value: 2 mg/kg/d

tag: treatment group

tag: corresponding control


title: DMN_M_2ppm_15d_5

tag: strain

tag: tissue


title: DMN_M_2ppm_4d_4

source_name: Dimethylnitrosamine, male, 3 days

value: 3 days


title: CIDB_F_2500ppm_4d_1

source_name: C.I. Direct Black, female, 3 days

value: female

value: CIDB

value: C.I. Direct Black

value: 25 mg/kg/d


title: CO_F_G65_15d_2

source_name: Corn Oil, female, 14 days

value: CO

value: Corn Oil


title: CO_F_G64_4d_1

source_name: Corn Oil, female, 3 days


title: CO_F_G64_4d_3


title: CIDB_F_2500ppm_15d_3

source_name: C.I. Direct Black, female, 14 days


title: CIDB_F_2500ppm_4d_3


title: CIDB_F_2500ppm_4d_4


title: DMN_M_2ppm_15d_3


title: CO_F_G65_15d_1


title: CO_F_G64_4d_4


title: CO_F_G65_15d_4


title: CO_F_G64_4d_2


title: CO_F_G65_15d_3


title: CIDB_F_2500ppm_15d_4


title: FFPE, patient 2, 10 hours tissue lysis

source_name: Formalin-fixed paraffin-embedded human hippocampus; patient 2


title: FFPE, patient 3, 3 hours tissue lysis


title: FFPE, patient 1, 3 hours tissue lysis


title: DMN_M_2ppm_4d_2


title: FFPE, patient 2, 3 hours tissue lysis


title: DMN_M_2ppm_4d_3


title: DMN_M_2ppm_15d_4


title: CIDB_F_2500ppm_4d_2


title: FF, patient 1

source_name: Fresh frozen human hippocampus; patient 1


title: FF, patient 2

source_name: Fresh frozen human hippocampus; patient 2


title: DMN_M_2ppm_4d_1


title: CIDB_M_2500ppm_15d_4

source_name: C.I. Direct Black, male, 14 days


title: CO_M_G65_15d_2

source_name: Corn Oil, male, 14 days


title: CO_M_G64_4d_3

source_name: Corn Oil, male, 3 days


title: CIDB_M_2500ppm_4d_4

source_name: C.I. Direct Black, male, 3 days


title: CO_M_G65_15d_4


title: CIDB_M_2500ppm_4d_2


title: PB_F_80ppm_15d_1

source_name: Phenobarbital, female, 14 days

value: PB

value: Phenobarbital

value: 8 mg/kg/d


title: CIDB_M_2500ppm_4d_3


title: CO_M_G64_4d_4


title: CIDB_M_2500ppm_4d_1


title: CIDB_M_2500ppm_15d_1


title: PB_F_80ppm_15d_4


title: CO_M_G64_4d_1


title: CO_M_G64_4d_2


title: CIDB_M_2500ppm_15d_2


title: CIDB_M_2500ppm_15d_3


title: PB_F_80ppm_15d_2


title: PB_F_80ppm_4d_4

source_name: Phenobarbital, female, 3 days


title: TAA_F_20ppm_15d_3

source_name: Thioacetamid, female, 14 days

value: TAA

value: Thioacetamid


title: PB_F_80ppm_4d_2

value: liver


title: CO_M_G65_15d_3

value: male


title: TAA_F_20ppm_15d_4


title: PB_F_80ppm_4d_1


title: TAA_F_20ppm_4d_4

source_name: Thioacetamid, female, 3 days


title: PB_F_80ppm_4d_3


title: TAA_F_20ppm_15d_2


title: TAA_F_20ppm_15d_1


title: CO_M_G65_15d_1


title: PB_F_80ppm_15d_3


title: TAA_F_20ppm_4d_2


title: TAA_F_20ppm_4d_3


title: TAA_F_20ppm_4d_1


title: PBO_F_600ppm_15d_2

source_name: Piperonylbutoxide, female, 14 days

value: PBO

value: Piperonylbutoxide

value: 6 mg/kg/d


title: PBO_F_600ppm_15d_1

value: 14 days


title: PBO_F_600ppm_15d_4

value: female


title: WY_F_200ppm_15d_2

source_name: Wy-14643, female, 14 days

value: WY

value: 2 mg/kg/d


title: CMC_F_G40_4d_4

source_name: Carboxymethyl Cellulose, female, 3 days

value: CMC

value: Carboxymethyl Cellulose

value: 3 days


title: WY_F_200ppm_4d_2

source_name: Wy-14643, female, 3 days


title: PBO_F_600ppm_4d_1

source_name: Piperonylbutoxide, female, 3 days


title: CMC_F_G41_15d_2

source_name: Carboxymethyl Cellulose, female, 14 days


title: CMC_F_G41_15d_4


title: WY_F_200ppm_15d_3


title: PBO_F_600ppm_4d_4


title: WY_F_200ppm_4d_4


title: CMC_F_G41_15d_1


title: CMC_F_G40_4d_2


title: CMC_F_G41_15d_3


title: PBO_F_600ppm_15d_3


title: WY_F_200ppm_15d_1


title: WY_F_200ppm_4d_3


title: WY_F_200ppm_4d_1


title: CMC_F_G40_4d_1


title: CMC_F_G40_4d_3


title: WY_F_200ppm_15d_4


title: PB_M_80ppm_15d_5

source_name: Phenobarbital, male, 14 days

value: PB


title: PBO_F_600ppm_4d_3


title: PB_M_80ppm_15d_3

value: Phenobarbital


title: PB_M_80ppm_15d_2

value: 8 mg/kg/d


title: PBO_F_600ppm_4d_2


title: PB_M_80ppm_15d_1


title: PB_M_80ppm_4d_4

source_name: Phenobarbital, male, 3 days


title: PB_M_80ppm_4d_2


title: TAA_M_20ppm_15d_2

source_name: Thioacetamid, male, 14 days

value: TAA


title: TAA_M_20ppm_4d_1

source_name: Thioacetamid, male, 3 days

value: Thioacetamid


title: TAA_M_20ppm_15d_3

value: liver


title: TAA_M_20ppm_4d_3

value: male


title: TAA_M_20ppm_15d_1


title: WY_M_200ppm_15d_6

source_name: Wy-14643, male, 14 days


title: TAA_M_20ppm_4d_4


title: TAA_M_20ppm_4d_2


title: WY_M_200ppm_15d_4


title: TAA_M_20ppm_15d_4


title: PBO_M_600ppm_4d_2

source_name: Piperonylbutoxide, male, 3 days

value: PBO


title: PBO_M_600ppm_15d_3

source_name: Piperonylbutoxide, male, 14 days

value: Piperonylbutoxide


title: PBO_M_600ppm_15d_2

value: 6 mg/kg/d


title: PBO_M_600ppm_15d_1

value: 14 days


title: PBO_M_600ppm_4d_1


title: WY_M_200ppm_4d_1

source_name: Wy-14643, male, 3 days


title: WY_M_200ppm_4d_3


title: WY_M_200ppm_4d_2


title: WY_M_200ppm_4d_4


title: WY_M_200ppm_15d_3


title: PBO_M_600ppm_4d_4


title: CMC_M_G41_15d_4

source_name: Carboxymethyl Cellulose, male, 14 days


title: PB_M_80ppm_4d_1


title: PB_M_80ppm_4d_3


title: CMC_M_G41_15d_3


title: WY_M_200ppm_15d_1


title: PBO_M_600ppm_15d_4


title: CMC_M_G41_15d_2


title: PBO_M_600ppm_4d_3


title: CMC_M_G41_15d_1


title: CMC_M_G40_4d_2

source_name: Carboxymethyl Cellulose, male, 3 days


title: CMC_M_G40_4d_4


title: CMC_M_G40_4d_3


title: CMC_F_G23_15d_4

value: female


title: CMC_M_G40_4d_1


title: Praz_F_5ppm_15d_3

source_name: Prazosin, female, 14 days

value: Praz

value: Prazosin

value: 5 mg/kg/d


title: Prop_F_80ppm_15d_3

source_name: Propranolol, female, 14 days

value: Prop

value: Propranolol


title: CMC_F_G23_15d_3

value: CMC

value: Carboxymethyl Cellulose


title: Prop_F_80ppm_15d_5

value: 8 mg/kg/d


title: CFX_F_250ppm_15d_2

source_name: Cefuroxime, female, 14 days

value: CFX

value: Cefuroxime

value: 25 mg/kg/d


title: CFX_F_250ppm_15d_1

value: liver


title: Prop_F_80ppm_15d_4


title: CFX_F_250ppm_15d_3


title: Praz_F_5ppm_15d_4


title: Praz_F_5ppm_15d_1


title: Praz_F_5ppm_15d_2


title: CMC_F_G23_15d_2


title: Praz_M_5ppm_15d_3

source_name: Prazosin, male, 14 days

value: male


title: Praz_M_5ppm_15d_4


title: Praz_M_5ppm_15d_1


title: Praz_M_5ppm_15d_2


title: Prop_M_80ppm_15d_2

source_name: Propranolol, male, 14 days


title: Prop_M_80ppm_15d_3


title: Prop_M_80ppm_15d_4


title: Prop_F_80ppm_15d_1


title: CFX_M_250ppm_15d_3

source_name: Cefuroxime, male, 14 days


title: CFX_M_250ppm_15d_4


title: CMC_F_G23_15d_1

source_name: Carboxymethyl Cellulose, female, 14 days


title: CFX_F_250ppm_15d_4


title: CFX_M_250ppm_15d_2


title: CMC_M_G23_15d_3


title: CMC_M_G23_15d_2


title: MDA_F_75ppm_4d_2

source_name: Methylendianiline, female, 3 days

value: MDA

value: Methylendianiline

value: 3 days

value: 75 mg/kg/d


title: CFX_M_250ppm_15d_1

value: 14 days


title: DCB_F_600ppm_4d_4

source_name: 1,4-Dichlorobenzene, female, 3 days

value: female

value: DCB

value: 6 mg/kg/d


title: DCB_F_600ppm_4d_2


title: DCB_F_600ppm_15d_1

source_name: 1,4-Dichlorobenzene, female, 14 days


title: DCB_F_600ppm_4d_3


title: Prop_M_80ppm_15d_1

value: Prop

value: Propranolol


title: DCB_F_600ppm_4d_1


title: CPA_F_160ppm_15d_6

source_name: Cyproterone Acetate, female, 14 days

value: CPA

value: Cyproterone Acetate

value: 16 mg/kg/d


title: CPA_F_160ppm_15d_1


title: CPA_F_160ppm_15d_2


title: CPA_F_160ppm_4d_4

source_name: Cyproterone Acetate, female, 3 days


title: CPA_F_160ppm_4d_3


title: CPA_F_160ppm_4d_2


title: MDA_F_75ppm_4d_1


title: MDA_F_75ppm_15d_5

source_name: Methylendianiline, female, 14 days


title: MDA_F_75ppm_15d_3


title: MDA_F_75ppm_4d_3


title: MDA_F_75ppm_15d_6


title: MDA_F_75ppm_4d_4


title: DCB_F_600ppm_15d_3


title: DCB_F_600ppm_15d_4


title: MDA_F_75ppm_15d_4


title: CMC_M_G23_15d_4

value: CMC

value: Carboxymethyl Cellulose


title: CMC_M_G23_15d_1

value: liver


title: DCB_F_600ppm_15d_2


title: CPA_F_160ppm_4d_1


title: CO_F_G77_15d_5

source_name: Corn Oil, female, 14 days

value: CO

value: Corn Oil


title: CO_F_G77_15d_3


title: CO_F_G77_15d_4


title: CPA_F_160ppm_15d_5


title: CO_F_G77_15d_2


title: CO_F_G76_4d_4

source_name: Corn Oil, female, 3 days


title: CO_F_G76_4d_3


title: CO_F_G76_4d_2


title: CO_F_G76_4d_1


title: MDA_M_75ppm_15d_4

source_name: Methylendianiline, male, 14 days

value: male

value: MDA

value: Methylendianiline


title: MDA_M_75ppm_15d_3

value: 14 days

value: 75 mg/kg/d


title: MDA_M_75ppm_15d_2


title: MDA_M_75ppm_4d_3

source_name: Methylendianiline, male, 3 days

value: 3 days


title: MDA_M_75ppm_4d_4


title: MDA_M_75ppm_4d_1


title: MDA_M_75ppm_4d_2


title: MDA_M_75ppm_15d_1


title: DCB_M_600ppm_15d_4

source_name: 1,4-Dichlorobenzene, male, 14 days

value: DCB

value: 6 mg/kg/d


title: DCB_M_600ppm_15d_3


title: DCB_M_600ppm_15d_2


title: DCB_M_600ppm_4d_4

source_name: 1,4-Dichlorobenzene, male, 3 days


title: DCB_M_600ppm_15d_5


title: DCB_M_600ppm_4d_3


title: DCB_M_600ppm_4d_2


title: DCB_M_600ppm_4d_1


title: CPA_M_160ppm_15d_2

source_name: Cyproterone Acetate, male, 14 days


title: CPA_M_160ppm_4d_2

source_name: Cyproterone Acetate, male, 3 days


title: CPA_M_160ppm_15d_1


title: CPA_M_160ppm_4d_3