title: H3R17me2a

city: Smithville

first: Yue

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

data_processing:
Base calling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Sequenced DNA reads were mapped to human genome hg19 using bowtie (version 0.12.8) and only the reads that were mapped to unique position were retained.To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
The original peak calling for CARM1/MED12/H3R17me2a was done by MACS (version 1.4.2) using total input DNA as control. The window size was set to 300 bp and the p-value cutoff was 1e-6. The peaks overlapping DAC Blacklisted Regions and Duke Excluded Regions downloaded from UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were removed. Then the peaks from the three factors were merged (allowing at least 1bp overlap) to form a highly confident superset of peaks. For each peak from the superset, if it overlapped the peaks of one of the factors called at p-value 1e-4, it was marked as occupied by the corresponding factor.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.txt: Chr (chromosome of the peak); Start (start position of the peak); End (end position of the peak); IsCARM1 (if the peak occupied by CARM1); IsMED12 (if the peak occupied by MED12); IsH3R17me2a (if the peak occupied by H3R17me2a)

source_name: MCF7 cells

growth_protocol: MCF-7 cells were cultured in 15 cm plates in phenol red DMEM high glucose supplemented with 10% FBS, 1% NEAA, and 1% pen/strep.

extract_protocol:
The starting materials are two 15 cm plates of MCF-7 cells for each ChIP. When cells reached a >90% confluent monolayer, 1% formaldehyde was added in culture media to fix cells for 10 minutes at 37°C. Cells were washed twice using ice cold PBS and then pelleted for nuclei purification using Nuclei Isolation Kit (Sigma, Nuc 101). Nuclei were lysed with SDS lysis buffer and chromatin was sonicated using a Bioruptor (Diagenode, B01020001) at high power with 6 pulses of 30 seconds sonication and 30 seconds rest to obtain DNA fragments of optimum size (between 200 bp and 1 kb). The remaining steps were performed using the protocol from Chromatin Immunoprecipitation (ChIP) Assay Kit (Millipore, 17-295). The eluted DNA was further purified using the QIAquick PCR Gel Extraction Kit (Qiagen,28706 ) for ChIP-seq analysis.
The Illumina compatible indexed libraries were prepared using KAPA Library preparation kit, as per the manufacturer’s instructions. In brief, DNA was fragmented to a median size of 150bp by sonication. Fragmented DNA ends were polished and 5′-phosphorylated. After addition of 3′-A to the ends, indexed Y-adapters were ligated and the samples were PCR amplified. The resulting DNA libraries were quantified and validated by qPCR, then sequenced 6 samples per lane on Illumina’s HiSeq2000 sequencer using the 36 nt single-read format. The resulting BCL files containing the sequence data were converted into “.fastq.gz” files and individual sample libraries were demultiplexed using CASAVA 1.8.2 with no mismatches.

treatment_protocol: No treatment performed

value: Breast Cancer MCF-7 cells

tag: passages

tag: chip antibody

value: H3R17me2a (Millipore, 07-214)


title: ATAC-seq Mphase rep2_NextSeq

status: Public on Sep 05 2018

type: SRA

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
ATAC-seq with synchronized M-phase T98G cells, rep2
processed data file:
ATAC-seq_processed_data.txt

library_source: genomic

data_processing:
Basecalls performed using HiSeq Control and Real-Time Analysis Software
Reads were aligned to hg19 using Rbowtie through the R package QuasR. For chromatin fraction sequencing and input, default parameters were used.  For ATAC-seq, adapter sequences were first trimmed using cutadapt.  Subsequently, one bp was trimmed from the 3' end of each read, as bowtie1 will not align perfectly overlapping forward and reverse reads. Default parameters for mapping paired-end reads were used with the QuasR package in the R environment, except for:  alignmentParameter="-m 3 -k 1 --best --strata --maxins 2000 --tryhard"
Mitochondrial reads were removed from ATAC-seq bam files using samtools: (ex..) samtools idxstats G1_rep1.bam | cut -f 1 | grep -v chrM | xargs samtools view -b G1_rep1.bam > G1_rep1_NoMito.bam
Peaks in ATAC-seq datasets were called using macs2 and subsequently merged for G1 an mitotic datasets. The following command parameters were used in macs2: -f BAM -g hs --nomodel --broad
Reads were counted in peaks and scaled down to the smallest library size before comparison.
Genome_build: hg19
Supplementary_files_format_and_content: Text file is tab-delimited containing merged ATACseq peak locations, scaled counts for each replicate, average log2(M/G1) for each peak as well as the standard deviation for this change. "NoMito" means no mitochondrial sequence included. Wig files are provided for the Chromatin fraction sequencing samples.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DMEM supplemented with 10% FCS and 2.5mM L-glutamine.  Cells were passaged every 2-3 days, depending on density

extract_protocol:
For input and chromatin fractions, nuclear prep was carried out followed by sonication to solubilize chromatin. Crosslinks were reversed overnight at 65⁰ and DNA was was isolated by phenol/chloroform followed by ethanol precipitation
ATAC-seq libraries were prepared as described in Buenrostro 2015.  Input and chromatin fractions were prepared using the NEBnext kit as per manufacturers intstructions.

treatment_protocol: G1 synchronization was achieved by serum starvation for 72 hours.  Sphase synchronization was obtained by serum starvation for 72 hours followed by a 22 hour release into 20% serum media. Mphase populations were enriched by starvation for 48 hours, followed by a 36 release into nocodazole containing media.  Mitotic cells were harvested by shaking.

tag: cell cycle stage

value: Mitosis

tag: cell line

tag: cell type

value: glioblastoma

tag: platform

value: NEXT seq


title: CARM1

last: Lu

country: USA

value: CARM1 (Epicypher, 13-0006)


title: ATAC-seq Mphase rep1_NextSeq

description:
ATAC-seq with synchronized M-phase T98G cells, rep1
processed data file:
ATAC-seq_processed_data.txt


title: MED12


title: Input


title: ATAC-seq Mphase rep3_NextSeq

description:
ATAC-seq with synchronized M-phase T98G cells, rep3
processed data file:
ATAC-seq_processed_data.txt


title: TC32_siFLI1_rep1

city: Bethesda

first: Suntae

last: Kim

state: MD

address: Bldg 37, room 6128

department: Genetics Branch

institute: CCR, NCI, NIH

description: TC32 cells treated with siFLI1, replicate 1

library_source: transcriptomic

data_processing:
Poly-A selected RNA libraries were prepared and sequenced on an Illumina HiSeq2000
RNA-Seq reads were aligned to the hg19 reference genome using TopHat v2.0.13
FPKM values was calculated using Cufflinks and ucsc genome browser gene level coordinates.
Differential gene expression were determined using Cuffdiff
Genome_build: hg19

molecule: total RNA

growth_protocol: TC32 cell lines were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

extract_protocol:
RNA was extracted with Maxwell® 16 LEV simplyRNA Cells Kit. RNA quantity was measured usind the Nanodrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate whole transcriptome profiles of each cells, total RNA was purified from untransfected or siRNA-transfected each cells (4x105 cells at plating in six-well plates) 48 hours post siRNA-transfection.

value: Ewing sarcoma

tag: transfected with


title: TC32_siEWSR1_rep1

description: TC32 cells treated with siEWSR1, replicate 1


title: TC32_siNeg_rep2

description: TC32 cells treated with siNeg, replicate 2

value: siNeg


title: TC32_siEWSR1_rep2

description: TC32 cells treated with siEWSR1, replicate 2


title: TC32_siNeg_rep1

description: TC32 cells treated with siNeg, replicate 1


title: TC32_siFLI1_rep2

description: TC32 cells treated with siFLI1, replicate 2


title: eCLIP_C2C12diff_input

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

description: Whole-cell RNA

data_processing:
3' barcodes and adapter sequences were removed using standard eCLIP scripts.
Reads were trimmed, filtered for repetitive elements, and aligned to the mm9 reference sequence using STAR.
PCR duplicate reads were removed based on the read start positions and randomer sequence.
Bigwig files for genome browser display were generated based on the location of the second of the paired end reads.
Peaks were identified using encode_branch version of CLIPPER (Lovci et al. 2013) using the parameter -s mm9
Peaks were normalized against size matched input by calculating fold enrichment of reads in IP versus input, and were designated as significant if the number of reads in IP was greater than in the input, with a Bonferroni corrected Fisher exact p-value smaller than 10^–5
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed and bigwig

organism: Mus musculus

source_name: Differentiated C2C12 cells

growth_protocol: C2C12 cells were grown in DMEM supplemented with 20% FBS and 1x penicillin-streptomycin. For differentiation, confluent cells were passaged in differentiation media (DMEM supplemented with 5% horse serum, 1x penicillin-streptomycin, and 1x ITS) for 8-10 days.

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al. 2016) with minor modifications. Briefly, confluent cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 13 mL of PBS in 15 cm plates; these cells were then spun down, flash frozen in liquid nitrogen, and stored at –80ºC. Nuclear isolation was performed as previously described (Kung et al. 2015), followed by further digestion by Bioruptor, RNase I, and Turbo DNase as specified in the original eCLIP protocol. Overnight immunoprecipitation was performed using 2 mg Protein G Dynabeads per 10 µg antibody, and appropriate antibodies for TDP-43 (5 µg/IP), or IgG (Novus NB810-56910, 5 µg/IP). Following end repair and 3′ adaptor ligation (using X1A and X1B adaptors as previously described), size selection was carried out using Nupage 4-12% Bis-Tris protein gels followed by overnight transfer at 30V to nitrocellulose membranes.
Protein-RNA complexes on nitrocellulose were then digested with Proteinase K (Roche) and reverse transcribed using SuperScript IV (Thermo Fisher). These cDNAs were then prepared for sequencing as described using Illumina TruSeq HT dual indexed primers, and sequenced on an Illumina HiSeq 2500 for high-output 2x150 bp run.

value: differentiated C2C12

tag: antibody

value: none (input)


title: E13_Ctrl_3

first: Xiying

last: Fan

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

description: Oligo(dT) selected RNA

data_processing:
Libraries are sequenced by Illumina HiSeq 2000 and 2500.
Raw reads are alligned to mouse genome version mm10 though Tophat 2 (RNA-seq) or Bowtie 2 (ATAC-seq, ChiP-seq)
Gene count data are generated using Htseq count function.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, .bedgraph

molecule: polyA RNA

source_name: Dermis

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension. Epidermal cells isolated by FACS of GFP positive cells. Dermal cells isolated by FACS through CD140a antibody staining.
SMARTer Directional cDNA Library Construction Kit and NEBNext® Ultra™ Directional RNA Library Prep Kit ; ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013; ChiP-seq, protocol described in Wang et al., RNA, 2013.

tag: age

value: Embryonic day 13

tag: tissue

value: Dermis

tag: genotype

value: {delta}Np63 -GFP KI-Het


title: CLN3-1

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

data_processing:
Read Cleaning: Reads were cleaned in R using ShortRead::TrimEnds, removing bases from each end until the remainging read has bases p-values all over 0.1.  Afterwards reads shorter than 25bp were removed.
Read Alignment: Reads were aligned to the TAIR10 genome using Tophat2 using default parameters except -g 1, specifying to only retain reads with one valid alignment
Read Counting: Reads were counted in R using GenomicAlignments::summarizeOverlaps with the TAIR10 gff as input and the counting mode of 'union'
FPKM calculations: psuedo-counts (generated from edgeR's library size normalization) were divided by the gene length (in kb) found in the TAIR 10 gff.
Differential Expression: Differential expression was carried out using edgeR with the global coefficient of variation.  Genes with less than 50 counts in any biological replicate had their log2 fold changes set to zero, along with genes with absolute log2 fold changes less than 0.5
Genome_build: TAIR10
Supplementary_files_format_and_content: raw_read_counts.txt is a tab delimated text file with genes along the rows and libraries across the columns.  Each column is named by the sample which it belongs to followed by a underscore and the lane of the illumina chip which the reads were obtained.  Genes are represented by their AGI numbers.  The value for each gene-sample combination is the non-normalized feature counts obtained from summarizeOverlaps

organism: Arabidopsis thaliana

source_name: Columbia-0 leaf tissue

growth_protocol: Seedlings were plated on 1/4 strength MS media and stratified at 4C in the dark for 48hr.  Seedlings grew on the plates for 11d before being transferred to minimal hydroponic media for 22 days.  Hydroponic media was airated with a bubble stone.  Plants were grown in a growth chamber with 16 hours light and 8 hours dark with 40% RH and XC.

extract_protocol:
RNA was first isolated by pulverizing 3-4 plants with a LN2 cooled mortar and pestle.  A Qiagen RNeasy Plant Kit was used to isolate RNA.  DNA was digested using Ambion Turbo DNase.  All protocols were followed according to manufacturers protocol
cDNA libraries were constructed using Illumina TruSeq kits according to manufacturers protocol

treatment_protocol: Plants were transferred from minimal media to minimal media with 20uM CdCl2 for 72 hours before being harvested.  Treatment and harvest were both performed at 11:00am.

value: Leaf

tag: treatment

value: Replete media

tag: biological replicate

tag: technical replicate


title: eCLIP_C2C12diff_TDP43_A

description: Whole-cell RNA

tag: antibody vendor

value: Bethyl

tag: antibody catalog number


title: eCLIP_C2C12diff_TDP43_B

description: Whole-cell RNA


title: eCLIP_C2C12_IgG

description: Whole-cell RNA

source_name: C2C12 cells

value: IgG

value: Novus


title: E13_Ctrl_2

description: Oligo(dT) selected RNA


title: E13_Ctrl_1

description: Oligo(dT) selected RNA


title: eCLIP_C2C12_TDP43_B

description: Whole-cell RNA


title: eCLIP_C2C12_input

description: Whole-cell RNA


title: E13_kO_3

description: rRNA removal RNA

source_name: Epidermis

value: Epidermis

value: {delta}Np63 -GFP KI-KO


title: eCLIP_C2C12_TDP43_A

description: Whole-cell RNA


title: E13_kO_2

description: rRNA removal RNA


title: E13_KO_1

description: rRNA removal RNA


title: E13_Het_3

description: rRNA removal RNA


title: eCLIP_C2C12diff_IgG

description: Whole-cell RNA


title: E13_Het_2

description: rRNA removal RNA


title: E13_Het_1

description: rRNA removal RNA


title: E9_Het_1

description: rRNA removal RNA

value: Embryonic day 9


title: E9_Het_4

description: rRNA removal RNA


title: E9_Het_2

description: rRNA removal RNA


title: 09020: NE-Infused 4

city: Tucson

first: Sean

middle: W

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

data_processing:
Tophat (v2.0.1)  -a 15 -m 1 -I 50000 -g 9 -N 3 -rgl 4 --red 7 -rred 0
cufflinks (v2.1.1) -G -b oar3174.fa -u -N -F 0.05  Annotation- Ensembl Ovis_aries.Oar_v3.1.74.gtf
cuffmerge -G
cuffdiff -N -u -c 24 --library-type fr-unstranded -b oar3174.fa --max-bundle-frags 25000000
Genome_build: Ensemble release 74 Ovis_aries.Oar_v3.1.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: gene_exp.diff - cuffdiff gene level statistics
Supplementary_files_format_and_content: gene_id.repFPKM.txt - table of gene ID, locus and FPKM values  from cuffdiff genes.FPKM_tracking

organism: Ovis aries

source_name: Isolated fetal pancreatic islets

growth_protocol: Columbia-Rambouillet crossbred ewes carrying singleton pregnancies.

extract_protocol:
Islets were isolated and handpicked then frozen at -80C for RNA extraction with Qiagen Microprep RNAeasy
mRNA was selected and double-stranded cDNA libraries with ligated sequencing adapters was constructed with the Illumina TruSeq RNA Sample Prep Kit. Cluster generation was conducted with Illumina TruSeq 100bp PE (paired end) cluster kit

treatment_protocol: Control fetuses received an intravenous infusion of diluent (0.3% ascorbic acid in 0.9% saline). NE fetuses received an intravenous infusion of NE (Norepinephrine Bitartrate, Bedford Labs) for 7 days at preset rates for each day of treatment (day 1 at 1 µg/min, days 2-4 at 2 µg/min, and days 5-7 at 4µg/min).

value: Isolated fetal pancreatic islets

tag: gestational age (days)

tag: fetal sex

value: male

tag: fetal weight (kg)


title: 09028: NE-Infused 3

value: female


title: 09027: Saline-Control 2


title: 09031: NE-Infused 1


title: 10027: Saline-Control 4


title: 10024: Saline-Control 1


title: 10026: Saline-Control 3


title: 10002: NE-Infused 2


title: Ter119pos_PRMT5_WT_A

status: Public on Sep 04 2018

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description: RSEM.gene.results.txt

data_processing:
Base calling using Illumina RTA 2.4.11
Reads mapped to GRCm38/mm10 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Estimated counts were obtained from RSEM.gene.results
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file contains aggragated raw RSEM expected gene level counts for all samples .

source_name: E14.5 Fetal Liver Cells

extract_protocol:
RNA was harvested using Trizol (Invitrogen #15596-026).
RNA-Seq library prep was carried out using the Illumina TruSeq Total Stranded kit (RS-122-2201) with Ribo-Zero rRNA reduction following manufacturer’s standard protocol without modification.

tag: genotype/variation

tag: mouse #


title: GAP-2/3 A

city: Rome

first: Andrea

last: Cipriano

state: Italy

address: Piazzale Aldo Moro 5

department: Biologia e Biotecnologue C. Darwin

country: Italy

institute: La Sapienza

data_processing:
Base-Calling with Casava
RNA-Seq data were analyzed using RAP using: FASTQC, NGSQC Toolkit, Bowtie 2, TopHat2, Cufflinks and Cuffdiff. Default parameters were used for the  analyses, except for: library type (fr-firststrand), mate inner distance (set to 30), standard deviation of inner distance (set to 60), and minimum read length (set to 30).
Genome_build: mm9
Supplementary_files_format_and_content: text file containg per sample gene FPKMs
Base-Calling with Casava
Reads were pre-processed with Trimmomatic and Cutadapt  to trim the 5' and 3' adapters and to remove the first five nucleotides,  whose average quality score was lower than that the other nucleotides. Low complexity reads were then removed using the DUST algorithm included in the PRINSEQ suite.
The procedure adopted by Chu was used to find EVEN and ODD common peaks (mm9 assembly, MACS14 bw=300. Fold enrichment/input > 2, average  coverage > 10 and Pearson correlation > 0.3). BEDTools was used to identify the overlapping lacZ peaks (obtained with MACS14 using the input as background). Peaks with fold enrichment/input 25  times lower than that of the overlapping lacZ peaks and with more than 50% of the length covered by repeats were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: BED file containing ChIRP peaks position and score (fold change over Input). This peaks are not filtered based on overlap with lacZ peaks and repeats.

source_name: in vitro differentiated myotubes

extract_protocol:
Cells were lysed using Trizol and RNA was extracted using qiagen RNA extraction kit.
TruSeq Stranded mRNA Library Prep Kit
The crosslinked chromatin was sonicated and the Charme RNA, together with the co-precipitated DNA, was purified.
NuGEN Ovation Ultralow Library System v2

tag: condition

value: Charme depleted 2days in vitro differentiated Myotubes using GAP-2/3

tag: library strategy

value: RNA-Seq


title: GAP-Scr A

value: Control GAP-scr 2days in vitro differentiated Myotubes


title: Ter119pos_PRMT5_KO_B

description: RSEM.gene.results.txt

value: PRMT5fl/fl; Vav-cre


title: Ter119pos_PRMT5_KO_A

description: RSEM.gene.results.txt


title: lacZ

value: Chromatin belonging to 2 days in vitro differentiated myotubes pulled down using  control LacZ probes set

value: ChIP-Seq (ChIRP-Seq)


title: GAP-2 A

value: Charme depleted 2days in vitro differentiated Myotubes using GAP-2


title: even

value: Chromatin belonging to 2 days in vitro differentiated myotubes pulled down using charme even probes set


title: GAP-2 B


title: GAP-Scr B


title: GAP-2/3 B


title: Input

value: Chromatin belonging to 2 days in vitro differentiated myotubes


title: odd

value: Chromatin belonging to 2 days in vitro differentiated myotubes pulled down using charme odd probes set


title: Ter119neg_PRMT5_WT_A

description: RSEM.gene.results.txt


title: Ter119neg_PRMT5_KO_B

description: RSEM.gene.results.txt


title: Ter119neg_PRMT5_WT_B

description: RSEM.gene.results.txt


title: Ter119pos_PRMT5_WT_B

description: RSEM.gene.results.txt


title: CLN3-2

value: Leaf

value: Replete media


title: mnr_RNA_seq_30

status: Public on Sep 03 2018

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were used to identify and quantify novel and known miRNAs with miRDeep v2.0.0.5 Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N. 'Discovering microRNAs from deep sequencing data using miRDeep', Nature Biotechnology, 26, 407-415 (2008) and R (maanova) Wu H, Yang mbH, Churchill KSwifG, Kerr K and Cui. X. maanova: Tools for analyzing Micro Array experiments. R package version 1.34.1, http://research.jax.org/faculty/churchill.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files of absolute and normalized read counts

organism: Papio anubis

source_name: MNR_fetal frontal cortex tissue

extract_protocol:
Qiagen miRNeasy mini
Small RNA libraries were prepared from the enriched fractions with Illumina Small RNA Prep Kit v1.5 following the manufacturer’s instructions.

treatment_protocol: Animals were fed Purina Monkey Diet 5038, which is a complete life-cycle diet for Old World primates. Biscuits contained stabilized vitamin C as well as all other required vitamins. Its basic composition was crude protein not <15%, crude fat not <5%, crude fiber not >6%, ash not >5%, and added minerals not >3%. At the start of the feeding period, ad libitum-fed CTR baboons were given 60 biscuits in their feeding tray. At the end of the 2-h feeding period, baboons were returned to the group cage. The biscuits remaining in the tray, on the cage floor, and in the pan beneath the cage were counted. Females in the maternal NR group were fed 70% of the CTR diet eaten by contemporaneous CTR animals on a per-kilogram basis.

tag: Sex

value: day 165 gestation

tag: sample group

value: maternal nutrient restricted (MNR)

value: frontal cortex tissue


title: mnr_RNA_seq_29

value: male

tag: age


title: mnr_RNA_seq_28

value: female

tag: tissue


title: mnr_RNA_seq_31


title: mnr_RNA_seq_27


title: mnr_RNA_seq_24

source_name: control_fetal frontal cortex tissue

value: control


title: mnr_RNA_seq_22


title: mnr_RNA_seq_21


title: mnr_RNA_seq_26


title: mnr_RNA_seq_25


title: mnr_RNA_seq_23


title: mnr_RNA_seq_20


title: Ter119neg_PRMT5_KO_A

description: RSEM.gene.results.txt


title: MV4-11 AC-4-130_2

city: Vienna

first: Tobias

last: Suske

state: Vienna

address: Veterinärplatz 1

department: Functional Cancer Genomics

country: Austria

institute: University of Veterinary Medicine

data_processing:
read alignment software STAR, version STAR_2.5.0b, default settings, genome version GRCh38.p10
expression level estimation with featureCounts (version 1.5.0-p1), Command:"featureCounts" "-T" "5" "-t" "exon" "-g" "gene_id" "-s" "0" "-a" "NCBI_GRCh38_entrez.gtf" "-o" "fname_sorted.out" "fname.sorted.bam"
expression level estimation and statistical calculations with DESeq2 (1.16.1): Genes with low expression were filtered out if the size factor normalized row count was <= 1. The functions ‘DESeq()’ and ‘results()’ were then applied with default parameters.
Genome_build: human genome GRCh38.p10
Supplementary_files_format_and_content: *.out files are tab separated featureCounts output files  *.geneID files are the geneID and counts columns from the *out files  *.id_csv are the DESeq2 files containing differential regulation data of control vs treatment triplicates from either MOLM13 or MV4 cells

source_name: human AML cell line

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MV4-11 and MOLM-13 cells were treated in triplicates with 5 µM AC-4-130 or DMSO (Ctrl) for 24 h

tag: cell type

tag: genotype

value: FTL3-ITD; MLL-AF4


title: MV4-11 AC-4-130_1

tag: treatment


title: MV4-11 DMSO_2

value: DMSO


title: MV4-11 DMSO_3


title: MV4-11 DMSO_1


title: MV4-11 AC-4-130_3


title: MOLM-13 AC-4-130_1

value: FTL3-ITD; MLL-AF9


title: MOLM-13 DMSO_3


title: MOLM-13 DMSO_2


title: MOLM-13 DMSO_1


title: MOLM-13 AC-4-130_2


title: MOLM-13 AC-4-130_3


title: Huh7 3.6

city: Rotterdam

first: Wenhui

last: Wang

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

description: RNA isolation date 9/18/2016

data_processing:
The Illumina single-end reads were trimmed to remove the TrueSeq adapter sequences using Trimmomatic (v.0.33).
The reads were mapped to the human reference genome build hg38 with the RNA-seq aligner STAR (v2.4.2a) and the Homo sapiens GENCODE v23 annotation.
Raw counts were measured with summarizeOverlaps function from the Bioconductor GenomicAlignments package (v1.12.1) using the setting mode union.
The differentially expressed genes were called with a generalized linear model using a negative binomial distribution and accounting for the different cell lines (Huh6 and Huh7). The calculations were performed by the DESeq2 package (v1.16.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Id  and read count

source_name: liver cancer Huh7 cells

growth_protocol: Huh6 and  Huh7 cell lines were transfected in 6-well plates using 7.5 µl FuGENE® HD Transfection Reagent (E2311, Promega) and 2 µg of each pX330 plasmid per well together with 0.2 µg GFP expression construct. GFP expression was used to select the cells that received high levels of the pX330 CRISPR/Cas9 constructs. After incubation at 37°C for 24 h, single cells were prepared for fluorescence activated cell sorting to a 96-well plate. After single cell sorting, Huh7 cells were maintained in DMEM supplemented with either 20% FCS or 25% Huh7-conditioned medium. Huh6 and PLC/PRF/5 were cultured in complete DMEM medium.

extract_protocol:
RNA was isolated with the Machery-NucleoSpin RNA II kit (BIOKE, Leiden, The Netherlands)
RNA-seq was performed at GATC Biotech (Konstanz, Germany) according to manufacture's instructions (Illumina). Briefly, the mRNA was enriched using oligo-dT magnetic beads, followed by fragmentation (about 200 bp). Then the first strand of cDNA was synthesized using random hexamer-primer and the second strand was further synthesized in a reaction buffer including dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was purified with magnetic beads. Then, the 3’-end single nucleotide A (adenine) was added and adapters were ligated to the fragments which were enriched by PCR amplification.

value: STRAP CON


title: Huh7 3.4

description: RNA isolation date 9/18/2016

value: STRAP KO


title: Huh7 3.12

description: RNA isolation date 9/18/2016


title: Huh7 3.1

description: RNA isolation date 9/18/2016


title: Huh7 3.15

description: RNA isolation date 9/18/2016


title: Cor4U_5Gy_3

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

country: Germany

institute: Bundeswehr Institute for Radiobiology

data_processing:
FastQ files (three biological replicates with matching sham data) were aligned using STAR (version 2.5, ) and hg19 as reference genome. Resulting .bam files were indexed using samtools (version 1.5, ) and visualized with IGV genome viewer for descriptive analysis.
For differential gene expression transcript quantification was performed using salmon (version 0.8.1) with matching reference transcriptome and .bam files from the alignment step
Resulting count data was summarized into matrices using tximport (version 1.4.0) and analyzed for differential gene expression using DESeq2 (version 1.16.1). For FPKM value validation we used a python-script (RSeQC).
For differential analysis standard setting of DESeq2 were applied and genes were assumed to be significantly expressed between treated and untreated groups when matching following criteria: p £ 0.05, padj (multiple comparison analysis) £ 0.1 and log2 fold change (FPKM) >1. Results were exported with DESeq2 and reporting tools (version 2.1.16.0) in R (version 3.4.1).
Network analysis and visualization of differentially expressed genes were performed by using an open source online tool as described elsewhere. Only genes with standard deviation ≥ 3 across all experiments were considered for hierarchical clustering. Average linkage clustering with Euclidian distance metrics was used as clustering algorithm. Hierarchical clustering was done with Cluster3 and results were visualized in Java TreeView
Genome_build: hg19
Supplementary_files_format_and_content: .txt whitespace delimited Ensbl-ID and log2 transformed DESeq2-calculated FPKM values of all samples. Table is sorted in accordance to the highest variances within groups.

source_name: hiPSC-CMs (Cor4U)

growth_protocol: In brief, cells were portioned into two 25 ml fibronectin coated culture flasks and stored in an incubator.

extract_protocol:
Cells were washed two times with phosphate buffered saline and centrifuged at 6,000 rpm for 2 min after incubation for additional 48 h prior to RNA isolation. Isolation was performed with the RNeasy Mini kit (Qiagen, RNeasy Mini Handbook 06/2012) following the manufacturer’s protocol. RNA concentration was determined by means of a Qubit 3.0 Fluorometer (Thermo Scientific, Waltham, MA, USA) and quality was assessed using Bioanalyzer (Agilent 2100 Bioanalyzer, Agilent, Santa Clara, CA, USA).
Library preparation of RNA samples was performed with the NEBNext® Ultra II Directional RNA Library Kit for Illumina (rRNA Depletion Kit, New England Biolabs Inc., Ipswich, MA, USA, protocol version 1.0 4/17). 500 ng RNA was used as input. In brief, rRNA was depleted and cDNA synthesis was executed before adapter ligation using appropriate primer design (NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1), Ipswich, MA, USA, protocol 2016). DNA fragment length was determined with Agilent Bioanalyzer (Agilent 2100 Bioanalyzer, Agilent, Santa Clara, CA, USA) and concentration was measured with a Qubit 3.0 Fluorometer (Thermo Scientific, Waltham, MA, USA).

treatment_protocol: After four days, cells were irradiated with 5 Gy x-ray irradiation. X-ray beam at room temperature with 240 kV tube current (YXLON Maxishot; Hamburg, Germany) filtered with 3 mm beryllium. Absorbed dose was measured with a PTW Unidos dosimeter (PTW Freiburg GmbH, Germany). Dose rate was 1 Gy min-1 at 13 mA. Sham irradiated samples were treated the very same way, e.g. brought to the same room and taken out of the incubator for the same time span. Medium was changed every day. Three biological replicates were used for treatment and sham control group. 48 h after irradiation cells were collected and washed with PBS twice. Cells were immediately stored at -80 °C after being shock frozen in liquid nitrogen.

value: iPSC-derived cardiomyocytes

value: 48h incubation after irradiation


title: Cor4U_5Gy_2


title: Huh6 1.26

description: RNA isolation date 9/18/2016

source_name: liver cancer Huh6 cells


title: Huh6 1.36

description: RNA isolation date 9/18/2016


title: Huh6 1.33

description: RNA isolation date 9/18/2016


title: Huh6 1.23

description: RNA isolation date 9/18/2016


title: Huh7 3.11

description: RNA isolation date 9/18/2016


title: Huh6 1.11

description: RNA isolation date 9/18/2016


title: Huh6 1.4

description: RNA isolation date 9/18/2016


title: Cor4U_5Gy_1


title: 6 days after DEN 6 month-old 3

status: Public on Sep 01 2018

city: Jerusalem

first: Jacob

last: Rachmilewitz

address: Ein -Kerem

country: Israel

institute: Hadassah Hebrew University medical center

description:
processed data header: D6_6M_3
DESeq2_final-2.xls

data_processing:
Raw reads were quality-trimmed at both ends, with a quality threshold of 32.
Adapter sequences were removed with cutadapt (version 1.7.1l), using parameters -O 1 --match-read-wildcards -m 15.
Reads were further filtered using the fastq_quality_filter program of the FASTX package (version 0.0.13), with parameters -q 20 -p 90.
Processed reads were mapped to the mouse transcriptome and genome using TopHat (v2.0.13), with parameters -G genes.gtf -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 4 genome processed.fastq.
Quantification was done with the Cufflinks package (v2.2.1), using the cuffquant and cuffnorm programs with parameters -b genome.fa -u -M mask.gtf, where genes of type IG, TR, Mt, rRNA, tRNA, miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA, piRNA, vaultRNA, ribozyme, artifact and LRG_gene were masked.
Normalization and differential expression were done with the DESeq2 package (version 1.10.1), for genes with at least two counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with the following columns: A-H, general gene details taken from the results of a BioMart query; I-X, raw counts in each sample; Y-AN, normalized counts in each sample; AO, mean normalized expression; AP-CJ, standard columns of DESeq2 results for each comparison; CK-CT, significance columns (yes/no) for each comparison according to padj<0.1.

source_name: Liver

growth_protocol: Mice were purchased from Harlan were grown under SPF condtions until sacrifies

extract_protocol:
Total RNA was isolated from liver samples using Trizol reagent (Life Technologies, Paisley, UK) and purified using MaXtract High Density (QIAGEN, Redwood City, CA). RNA yield and quantity was determined using a Nanodrop spectrophotometer ND-1000 (Thermo scientific, Wilmington, DE). The RNA quality was tested using a ND-1000 V3.7.1, according to the manufacturer’s instructions and assigned an RNA integrity number (RIN). Only samples with a RNA integrity number (RIN) of 8 or greater were employed.
Each sample represents equal amount of total RNA from three mice that were pooled prior to library construction. RNAseq libraries were constructed in the center for Genomic Technologies using Trueseq RNA Library preparation kit according to Illumina protocol and sequenced with the Illumina Nextseq 500 System to an average depth of around 30 million reads.

treatment_protocol: For the induction of DNA damage in vivo, 1 and 6-month-old C57BL/6 male mice (Harlan, Israel) were injected intraperitoneally (i.p.) with diethylnitrosamine (DEN; 25 mg/Kg body wt; Sigma-Aldrich; St. Louis, MO). Mice were sacrificed 2 and 6 days after injection and liver tissues were snap frozen in liquid nitrogen.

tag: strain

value: Wild type

value: 6 month

value: DEN; 25 mg/Kg body wt

tag: time point

value: 6 days after injection


title: Cor4U_0Gy_2

value: 48h incubation after sham irradiation


title: Cor4U_0Gy_1


title: wt24_2

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

institute: Medical University of Innsbruck

data_processing:
Whole workflow was performed using a protocol from Trapnell et al., Nature protocols, 2012. Sequenced reads ẃere mapped to FGSC_A4 whole genome using TopHat v2.1.1 with parameters -p8 -G (including features as .gff file in version s10-m04-r06)
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated by using Cufflinks v2.2.1 with parameters -p8 -u -N.
Cuffdiff v2.1.1 was used to produce per sample FPKM expression levels and estimate differential expression between the sample groups.
Supplementary_files_FPKM_tracking: .txt file includes FPKM values for each Sample
Genome_build: Aspergillus nidulans FGSC_A4 genome (version s10-m04-r06)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Aspergillus nidulans

source_name: Aspergillus nidulans TIB10

growth_protocol: Fungal strains were grown as shaking cultures in liquid glucose minimal media supplemented with biotin at 37 °C

extract_protocol:
Total RNA was extracted from snap frozen fungal mycelia with TRI reagent following the manufacturer's protocol
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries with 1 µg total RNA as input

treatment_protocol: Fungal strains were grown for 24 h and 60 h to achieve 2 time points

value: wild type

tag: growth time


title: 2 days after DEN 6 month-old 1

description:
processed data header: D2_6M_1
DESeq2_final-2.xls

value: 2 days after injection


title: STG 1

status: Public on Sep 02 2018

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 3333 Burnet Ave

department: Heart Institute

institute: Cincinnati Children's Hospital

data_processing:
Illumina OLB1.9.4. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.0.13
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated Tophat/Cufflinks v 2.1.1.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values for each Sample ...

source_name: Heart

extract_protocol:
Hearts were removed and RNA was harvested using Trizol reagent. 1 ug of total RNA from each heart was extracted for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12 weeks

value: heart

value: alphaMHCMerCreMer+/-


title: DTG 1


title: DTG 2


title: 6 days after DEN 6 month-old 2

description:
processed data header: D6_6M_2
DESeq2_final-2.xls


title: STG 2


title: 2 days after DEN 6 month-old 3

description:
processed data header: D2_6M_3
DESeq2_final-2.xls


title: Control 3 6 month-old-1

description:
processed data header: C_6M_1
DESeq2_final-2.xls

value: control


title: 6 days after DEN 3 weeks-old 3

description:
processed data header: D6_3W_3
DESeq2_final-2.xls

value: 3-4 weeks


title: Control 3 6 month-old-2

description:
processed data header: C_6M_2
DESeq2_final-2.xls


title: wt24_3


title: 6 days after DEN 3 weeks-old 1

description:
processed data header: D6_3W_1
DESeq2_final-2.xls


title: 2 days after DEN 3 weeks-old 3

description:
processed data header: D2_3W_3
DESeq2_final-2.xls


title: Cor4U_0Gy_3


title: 2 days after DEN 3 weeks-old 2

description:
processed data header: D2_3W_2
DESeq2_final-2.xls


title: Control 3 weeks-old-2

description:
processed data header: C_3W_2
DESeq2_final-2.xls


title: Control 3 weeks-old-1

description:
processed data header: C_3W_1
DESeq2_final-2.xls


title: 2 days after DEN 3 weeks-old 1

description:
processed data header: D2_3W_1
DESeq2_final-2.xls


title: 2 days after DEN 6 month-old 2

description:
processed data header: D2_6M_2
DESeq2_final-2.xls


title: Cry_KO2_Liver_ZT22_male

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:
Cry_KO_Exon_ZT_22_2
Processed data file: raw_exon_CryKO_male.txt

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i
A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene, all exons of the respective annotated protein-coding transcripts were considered.
Genome_build: mm10
Supplementary_files_format_and_content: raw_exon_CryKO.txt: Tab-delimited text file includes raw counts of fragments.

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al., 2006) with classical methods using guanidium thiocyanate lysis buffer.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Prep Kit with the Ribo-Zero Gold depletion set (Illumina) following the manufacturer’s protocol. We used 250 ng total RNA as starting material and performed 11 PCR cycles from library amplification (optimal cycle determined with the same method as the small RNA, see above). Samples were pooled by 24, denatured, spiked with 3% PhiX and loaded onto a paired-end read flow cell v3 at a final concentration of 11 pM for a paired-end 100 cycles run, strictly following Illumina’s recommendations. Sequencing depth was equivalent to 3 samples per lane.

value: male

value: Liver

value: 12-16 weeks

tag: gut microbiome status

value: conventional raised

tag: zeitgeber time


title: 6 days after DEN 6 month-old 1

description:
processed data header: D6_6M_1
DESeq2_final-2.xls


title: wt24_1


title: Cry_KO1_Liver_ZT22_male

description:
Cry_KO_Exon_ZT_22_1
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO2_Liver_ZT18_male

description:
Cry_KO_Exon_ZT_18_2
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO1_Liver_ZT14_male

description:
Cry_KO_Exon_ZT_14_1
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO2_Liver_ZT14_male

description:
Cry_KO_Exon_ZT_14_2
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO2_Liver_ZT10_male

description:
Cry_KO_Exon_ZT_10_2
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO1_Liver_ZT18_male

description:
Cry_KO_Exon_ZT_18_1
Processed data file: raw_exon_CryKO_male.txt


title: 6 days after DEN 3 weeks-old 2

description:
processed data header: D6_3W_2
DESeq2_final-2.xls


title: Cry_KO1_Liver_ZT10_male

description:
Cry_KO_Exon_ZT_10_1
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO2_Liver_ZT06_male

description:
Cry_KO_Exon_ZT_06_2
Processed data file: raw_exon_CryKO_male.txt


title: Q215X/+ rep2

city: Buffalo

first: Jie

state: NY

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Sequence reads were mapped to mm10 genome using software TopHat (v 2.0.9), only one mismatch was allowed at most.
The gene expression (FPKM) was quantifiled using Cufflinks (v 2.2.0) for all the sampels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all Sample

source_name: Sciatic nerve

extract_protocol:
Sciatic nerves were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample preparation kit (Illumina) was used to prepare cDNA libraries from RNA samples. Samples were poly A selected to isolate mRNA, the mRNA was cleaved into fragments, the first strand reverse transcribed to cDNA using SuperScript II reverse Transcriptase (Invitrogen) and random primers, followed by second strand cDNA synthesis using Second Strand Master Mix supplied with the kit. After end repair, the addition of a single ‘A’ base, and ligation with adapters, the products were enriched and purified with PCR to create the final cDNA library as per manufacturer’s protocol. cDNA libraries were quantified using Picogreen Assay (Invitrogen) and Library Quantification kit (Kapa Biosystems). Agilent Bioanalyzer 2100 DNA 7500 chip was used to confirm the quality and size of the cDNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: F1 C57BL/6;FVB/N

value: Sciatic nerve

value: post natal day 30


title: HA-NRG1 type III/+ rep2

value: HA-NRG1 type III/+


title: HA-NRG1 type III/+ rep1


title: Cry_KO1_Liver_ZT06_male

description:
Cry_KO_Exon_ZT_06_1
Processed data file: raw_exon_CryKO_male.txt


title: Q215X/+ rep1


title: WT rep2


title: WT rep1


title: GFM2_Liver_ZT22_female

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i
A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene, all exons of the respective annotated protein-coding transcripts were considered.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of fragments

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium  thiocyanate lysis buffer.  Duodenum, ileum, and epididymal white adipose tissue were disrupted and extracted using the tissue lyser II (Qiagen) and the miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol, repectively.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). 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. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was strictly followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 24 and each pool was clustered at a concentration of 7 pmol on 8 lanes of a v3 paired-end sequencing flow cell (Illumina). Sequencing was performed for 2 x 100 cycles on a HiSeq 2500 strictly following Illumina’s recommendations.

value: 15-16 weeks

value: germ-free

value: Female


title: GFM2_Liver_ZT18_female


title: GFM2_Liver_ZT14_female


title: GFM1_Liver_ZT22_female


title: GFM2_Liver_ZT06_female


title: GFM2_Liver_ZT10_female


title: GFM2_Liver_ZT02_female


title: GFM1_Liver_ZT18_female


title: GFM1_Liver_ZT14_female


title: GFM1_Liver_ZT02_female


title: GFM1_Liver_ZT10_female


title: GFM1_Liver_ZT06_female


title: HA-NRG1 type III/+:Q215X/+ rep2

value: HA-NRG1 type III/+:Q215X/+


title: HA-NRG1 type III/+:Q215X/+ rep1


title: Cry_KO2_Liver_ZT02_male

description:
Cry_KO_Exon_ZT_02_2
Processed data file: raw_exon_CryKO_male.txt


title: Cry_KO1_Liver_ZT02_male

description:
Cry_KO_Exon_ZT_02_1
Processed data file: raw_exon_CryKO_male.txt


title: CTR2_Liver_ZT18_female


title: CTR2_Liver_ZT14_female


title: CTR2_Liver_ZT02_female


title: CTR2_Liver_ZT06_female


title: CTR1_Liver_ZT10_female


title: CTR1_Liver_ZT06_female


title: CTR2_Liver_ZT10_female


title: CTR1_Liver_ZT18_female


title: CTR1_Liver_ZT14_female


title: E117_SPOC1_Rep3

city: Erlangen

first: Soeren

last: Lukassen

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Friedrich-Alexander Universitaet Erlangen Nuernberg

description: SPOC1-ChIP rep3

data_processing:
Sequenced reads were mapped to the mouse genome (build mm10) using bowtie2 2.2.2. Duplicate reads were discarded using samtools. For the final analysis, biological replicates were pooled.
Peaks were called using Homer v4.6.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt file containing annotated peak positions.

source_name: Testis

extract_protocol:
Chromatin was isolated using the Blueprint transcription factor protocol (blueprint-epigenome.org).
Libraries were prepared using the using the TruSeq ChIP kit.

value: testis

value: 5 weeks


title: E117_Input_Rep3

description: Input rep3


title: D821_Input_Rep2

description: Input rep2

value: wild type


title: D821_SPOC1_Rep2

description: SPOC1-ChIP rep2


title: D707_SPOC1_Rep1

description: SPOC1-ChIP rep1


title: D707_Input_Rep1

description: Input rep1


title: Phf13-KO rep2

data_processing:
Sequenced reads were mapped to the mouse genome (build mm10) using STAR 2.4.0 with the additional paramter outFilterMultimapNMax 50. Duplicate reads were discarded using samtools.
Read counts per gene were acquired and normalized using Homer v4.6. Differential expression analysis was performed using EdgeR 3.8.6.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt file containing transcript Ids, genomic positions of transcripts, transcript names, and normalized read counts for each sample.

extract_protocol:
Total RNA from testis was isolated using the Trizol method.
Libraries were prepared using the using the NuGen Ovation RNA-seq FFPE kit.


title: WT rep1


title: Phf13-KO rep3


title: Phf13-KO rep1


title: WT rep3


title: CTR1_Liver_ZT22_female


title: GFM2_WAT_ZT22_male

source_name: WAT Total RNA

value: WAT


title: GFM2_WAT_ZT14_male


title: GFM2_WAT_ZT06_male


title: GFM2_WAT_ZT02_male


title: CTR1_Liver_ZT02_female


title: GFM2_WAT_ZT10_male


title: GFM2_Liver_ZT10_male

source_name: Liver Total RNA


title: GFM2_Liver_ZT14_male


title: GFM2_Liver_ZT06_male


title: GFM2_Ileum_ZT22_male

source_name: Ileum Total RNA

value: Ileum


title: WT rep2


title: GFM2_Liver_ZT02_male

value: male


title: GFM2_Ileum_ZT14_male


title: GFM2_Ileum_ZT06_male


title: GFM2_Ileum_ZT10_male


title: GFM2_Ileum_ZT18_male


title: GFM2_Ileum_ZT02_male


title: GFM2_Duod_ZT22_male

source_name: Duodenum Total RNA

value: Duodenum


title: GFM2_Duod_ZT14_male


title: GFM2_Duod_ZT10_male


title: GFM2_WAT_ZT18_male


title: GFM2_Liver_ZT22_male

value: Liver


title: GFM2_Duod_ZT06_male


title: GFM2_Liver_ZT18_male


title: GFM1_WAT_ZT10_male


title: GFM2_Duod_ZT02_male


title: GFM1_WAT_ZT06_male


title: GFM1_Liver_ZT22_male


title: GFM1_Liver_ZT14_male


title: GFM1_Liver_ZT06_male


title: GFM1_Liver_ZT10_male


title: GFM1_Liver_ZT02_male


title: GFM1_Ileum_ZT22_male


title: GFM1_Ileum_ZT06_male


title: GFM1_Ileum_ZT18_male


title: GFM1_Duod_ZT22_male


title: GFM1_Liver_ZT18_male


title: GFM1_Duod_ZT18_male


title: GFM1_Ileum_ZT10_male


title: GFM1_Duod_ZT10_male


title: GFM1_Ileum_ZT14_male


title: GFM1_Duod_ZT14_male


title: GFM2_Duod_ZT18_male


title: CTR2_WAT_ZT22_male

value: conventional raised


title: GFM1_Duod_ZT02_male


title: GFM1_Duod_ZT06_male


title: GFM1_WAT_ZT22_male


title: CTR2_WAT_ZT14_male


title: CTR2_WAT_ZT18_male


title: CTR2_WAT_ZT06_male


title: CTR2_Liver_ZT22_male


title: CTR2_Liver_ZT10_male


title: CTR2_Liver_ZT18_male


title: CTR2_WAT_ZT10_male


title: CTR2_Liver_ZT02_male


title: CTR2_Liver_ZT06_male


title: CTR2_Ileum_ZT22_male


title: CTR2_Ileum_ZT18_male


title: D2-Q_Q175-Het_D2_cells_dStr_5-6mo_M

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.B37, gene models version Ensembl.R67
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Het(Q175)-HD_Striatum_ dopamine D2 receptor-expressing neurons

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Corpus striatum

value: Het (Q175) knock-in

tag: background strain

value: Medium spiny neurons

tag: cell subtype

value: dopamine D2 receptor-expressing neurons

value: Male


title: D1-C_Q175-WT_D1_cells_dStr_5-6mo_M

source_name: Het(Q175)-WT_Striatum_dopamine D1 receptor-expressing neurons

value: Wild type

value: dopamine D1 receptor-expressing neurons


title: CTR2_Ileum_ZT10_male

value: 15-16 weeks


title: D1-Q_Q175-Het_D1_cells_dStr_5-6mo_M

source_name: Het(Q175)-HD_Striatum_dopamine D1 receptor-expressing neurons


title: D2-C_Q175-WT_D2_cells_dStr_5-6mo_M

source_name: Het(Q175)-WT_Striatum_dopamine D2 receptor-expressing neurons


title: CTR2_Duod_ZT22_male


title: CTR2_Ileum_ZT06_male


title: CTR2_Duod_ZT18_male


title: CTR2_Ileum_ZT14_male


title: CTR2_Duod_ZT02_male


title: CTR1_WAT_ZT22_male


title: CTR1_WAT_ZT18_male


title: CTR2_Duod_ZT10_male


title: CTR2_WAT_ZT02_male


title: CTR1_WAT_ZT10_male


title: CTR2_Liver_ZT14_male


title: CTR1_WAT_ZT06_male


title: CTR1_Liver_ZT22_male


title: CTR1_WAT_ZT02_male


title: CTR1_Liver_ZT14_male


title: CTR1_Liver_ZT10_male


title: CTR2_Duod_ZT14_male


title: CTR1_Liver_ZT02_male


title: CTR1_Ileum_ZT22_male


title: CTR1_Liver_ZT06_male


title: whole L4 stage wildtype C. elegans gDNA

data_processing:
Base modification was detected using SMRT Analysis 2.3.0
The RS_Modification_Detection_and Motif_Analysis.1 protocal was used, only the unambiguously mapped reads with minimum map QV30 were used and reads in the modification detection step
The SMRT-seq data in the study GSE66504 was included to get enough coverage for detecting the modification.
Genome_build: ce10
Supplementary_files_format_and_content: GFF file is the output from the SMRT Analysis pipeline, it contains 4mCs sites information, coverage, IPD ratio, context sequence.

organism: Caenorhabditis elegans

source_name: whole L4 stage wildtype C. elegans gDNA

growth_protocol: worms were grown on standard NGM plates with Ampicillin antibiotics and fed dam-dcm- bacteria

extract_protocol:
gDNA was extracted as per the protocol of Invitrogens PureLink Genomic DNA kit with 6 freeze thaws in liquid nitrogen before the isolation began
Library was constructed and sequenced at Umass Medical School Deep Sequencing core
SMRT-seq

tag: developmental stage


title: CTR1_Ileum_ZT18_male


title: CTR2_Duod_ZT06_male


title: CTR1_Ileum_ZT10_male


title: CTR1_Ileum_ZT14_male


title: CTR1_Ileum_ZT06_male


title: CTR1_WAT_ZT14_male


title: CTR1_Ileum_ZT02_male


title: CTR1_Duod_ZT14_male


title: CTR1_Duod_ZT18_male


title: CTR1_Duod_ZT10_male


title: CTR1_Duod_ZT06_male


title: CTR1_Duod_ZT02_male


title: CTR1_Liver_ZT18_male


title: mek1_2

city: New York

first: Isabel

last: Lam

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 30°C.

extract_protocol:
Based on Pan et al. 2011 Cell, and Zhu and Keeney 2015 Genetics, with modifications. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

value: mek1 null

tag: epitope tag

tag: meiotic time-point

value: 4 hr in meiosis


title: mek1_1

description: Spo11-associated DNA oligonucleotides


title: hop1_1

description: Spo11-associated DNA oligonucleotides

value: hop1 null


title: red1_1

description: Spo11-associated DNA oligonucleotides

value: red1 null


title: red1_2

description: Spo11-associated DNA oligonucleotides


title: hop1_2

description: Spo11-associated DNA oligonucleotides


title: CTR1_Duod_ZT22_male

tag: Sex


title: α7nAChR-/- Nicotine

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

data_processing:
Basecall data was generated by Illumina's system software and then fastq file was generated with demultiplexation using CASAVA Ver.1.8.
RNAseq data  was aligned to genome mm10 using hisat2 with the parameter  '-q --dta-cufflinks'.
The SAM file was converted into BAM format and subsequently fpkm was calculated using cuffdiff and cummerBund.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing fpkm values

source_name: Peritoneal macrophage

growth_protocol: After isolating peritoneal cells, the cells were resuspended in culture medium (RPMI, 10% FBS, 1% glutamine, 1% penicillin-streptomycin) at a concentration of 1 x 10E6 cells/ml and were plated in 24 well cell culture plates. The cells were washed with PBS 1 hour after being plated, and PBS was replaced with the medium. The next day the cells were washed with PBS and used for further experiments.

extract_protocol:
RNA was isolated from the peritoneal macrophages using the RNeasy Micro Kit. Poly(A)-containing mRNA molecules were isolated from total RNA. Illumina TruSeq RNA Sample Prep Kit v2 was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophage were treated with nicotine (10 μM) or vehicle for 15 minutes and then stimulated with LPS (100 ng/ml) or vehicle for 4 hours at 37 °C.

value: Peritoneal macrophage

value: Nicotine


title: WT Ctl

value: wild type

value: Vehicle


title: WT Nicotine


title: WT Nicotine+LPS

value: Nictoine+LPS


title: α7nAChR-/- LPS

value: LPS


title: α7nAChR-/- Nicotine+LPS


title: CTR2_Liver_ZT22_female

value: Liver

value: conventional raised

value: Female


title: PrEC, rep1 [RNA-Seq]

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

institute: Garvan Institute of Medical Research

description:
sample_id: q2_0
Sample name: RNA_SEQ_CSP_TGACCA

data_processing:
Illumina software (version 1.9) was used to generate fastq files.
Sequenced reads were trimmed for adaptor sequence using trimgalore.
Trimmed reads were mapped using tophat with the parameter --library-type "fr-un-stranded" and raw counts for properly paired reads uniquely mapping to exonic regions of gencode genes (version 19) were obtained using ht-seq-count as implemented in the NGSANE framework (version 0.5.0).
Novel transcripts were assmebled using cufflinks and expression of genes and transcripts quantified using cuffquant and cuffnorm  as implemented in the NGSANE framework (version 0.5.0).
Software used to process data (with version in brackets): igvtools(2.3.23), pigz(2.3), picard-tools(1.121), boost (1.53.0), samstat(1.08), java (jdk1.7.0_45), bedtools(2.19.1), python (2.7.3), bowtie (2.2.3), R (3.0.0),    tophat (2.0.13), samtools (1.1), bedtools (2.19.1), pigz (2.3), htseq-count (0.6.1p1), cufflinks (2.2.1) and ImageMagick (6.8.5-8).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited text files include raw counts of uniquely mapped properly paired reads for Gencode 19 genes.
Supplementary_files_format_and_content: Tab-delimited files generated by cuffnorm including for genes, transcripts, TSS groups, and CDS groups as described in the cufflinks manual. Transcripts assembled by cufflinks are provided as a GTF.

source_name: normal prostate epithelial cells (PrEC)

growth_protocol: LNCaP cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum. PrEC cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).

extract_protocol:
Poly A+ Illumina TruSeq
RNA was extracted using Trizol and libraries prepared as per the manufacturers instructions and libraries were constructed at the Next Generation Genome Sequencing Facility (University of Western Sydney, Hawkesbury, NSW, Australia).
Illumina TruSeq (unstranded) with PolyA selection.

treatment_protocol: Untreated.

tag: cell line

value: PrEC

value: Normal


title: WT-Rep2

city: Seoul

first: Hye Shin

last: Lee

department: College of pharmacy

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.2b
Raw counts were calculated using featureCounts from Subread package v1.5.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

source_name: WT, liver

extract_protocol:
liver was removed, snap frozen in liquid nitrogen, RNA was isolated using Trizol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

value: WT

value: liver


title: AKAP12KO-Rep1

source_name: AKAP12KO, liver

value: AKAP12 null


title: LNCaP, rep1 [RNA-Seq]

description:
sample_id: q1_0
Sample name: RNA_SEQ_CSL_TTAGGC

source_name: androgen-sensitive human prostate adenocarcinoma (LNCaP)

value: LNCaP

value: Cancer


title: WT-Rep1


title: Berlin female mated to male lacking a germline (tud/+) 3 days post-mating rep 3

city: Tallahassee

first: Michelle

last: Arbeitman

address: 1115 West Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic ( version 0.32, minlen set to 50, 2 seed mismatches )
Unique reads were aligned to Drosophila Melanogaster genome, release 71 (Ensembl) using Tophat ( version 2.0.8, --read-mismatches and --read-edit-dist set to 6 )
Expression was quantified for genes, to raw counts using easyRNASeq ( from Bioconductor version 3.0.2, geneModels summarization )
edgeR, Fisher's exact test for differential expression ( from Bioconductor version 3.0.2, tagwise dispersion, Benjamini-Hochberg FDR correction )
Cufflinks quantification to Fragments Per Kilobase Per Million Mapped Reads (FPKM) (Cufflinks version 2.1.1, -- no-effective-length-correction )
Genome_build: Ensembl release 71

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
Flies were flash frozen and heads were separated from the bodies. Total RNA was extracted from the heads using Trizol, mRNA was isolated using MicroPoly(A) Purist columns (Ambion).
After adding the spike-in control RNAs, samples were fragmented to ∼250 bp by chemical fragmentation. First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) and a combination of random hexamer and oligo (dT) primers; second-strand cDNA was synthesized using DNA polymerase I in combination with ribonuclease H. Double-stranded cDNA templates were blunt ended using End-It Repair kit (Epicentre), and A-overhangs were added at both ends with Klenow fragment (3′→5′ exo-minus). Illumina GAII sequencing adaptors were then ligated to both ends of the cDNA templates using Fast-Link DNA ligation kit (Epicentre). We then enriched for cDNA templates by performing multiplex incorporating PCR reactions (18 cycles) and isolated 250- to 550-bp fragments by gel purification

tag: age

value: 8 days post-eclosion

tag: mated

value: Mated

tag: days post-mating

tag: female genotype

value: Wildtype

tag: male genotype

value: tud/+ no germline


title: Berlin female mated to male lacking a germline (tud/+) 3 days post-mating rep 2


title: WT-Rep3

tag: strain

tag: genotype

tag: tissue


title: Berlin female mated to male with germline (tud/+) 3 days post-mating rep 3

value: tud/+ germline


title: Berlin female mated to male with germline (tud/+) 3 days post-mating rep 1


title: Berlin female mated to male with germline (tud/+) 3 days post-mating rep 2


title: WT LPS

tag: cell type

value: Peritoneal macrophage

value: wild type

tag: treatment

value: LPS


title: Tud/+ female lacking germline 3 days post-mating rep 3

value: Female


title: α7nAChR-/- Ctl

value: Vehicle


title: Tud/+ female lacking germline 3 days post-mating rep 2


title: Tud/+ female with germline 3 days post-mating rep 2


title: Tud/+ female with germline 3 days post-mating rep 3


title: AKAP12KO-Rep3


title: Tud/+ female with germline 3 days post-mating rep 1


title: Berlin female mated to male lacking a germline (tud/+) 1 day post-mating rep 3


title: Berlin female mated to male lacking a germline (tud/+) 1 day post-mating rep 2


title: Berlin female mated to male with germline (tud/+) 1 day post-mating rep 1


title: Berlin female mated to male with germline (tud/+) 1 day post-mating rep 2


title: Tud/+ female lacking germline 1 day post-mating rep 2


title: Berlin female mated to male lacking a germline (tud/+) 1 day post-mating rep 1


title: Berlin female mated to male with germline (tud/+) 1 day post-mating rep 3


title: Tud/+ female lacking germline 1 day post-mating rep 1


title: Tud/+ female with germline 1 day post-mating rep 3


title: Tud/+ female with germline 1 day post-mating rep 1


title: Tud/+ female with germline 1 day post-mating rep 2


title: Berlin female mated to male lacking a germline (tud/+) 3 days post-mating rep 1


title: Virgin lacking germline (tud/+) rep 1

value: Virgin


title: Virgin with germline (tud/+) rep 3


title: Virgin lacking germline (tud/+) rep 2


title: Virgin with germline (tud/+) rep 1


title: H1N1_6hr [miRNA]

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

data_processing:
Basecalls performed using Illumina pipeline version 1.3.
The small RNA sequencing reads were trimmed with low-quality ends and primer adapters. The trimmed high-quality reads were mapped to the miRBase database (http://www.mirbase.org/) using CLC Genomics Workbench. Due to the imperfect Dicer processing, a 5 bp overhang on the 5’- and 3’-end of mature/mature* miRNAs and 2 mismatches within the mature/mature* miRNAs were allowed. The abundance level of mature/mature* miRNA is measured with RPM (Reads mapped Per Million mappable reads), by normalizing to the total number of mapped reads for each sample. The relative abundance of miRNAs was evaluated by comparing the RPM between H1N1/H5N1 infection and mock infection and the significance was assessed with Z-score using Z-test.
Supplementary_files_format_and_content: Excel file containing the normalized miRNA expression (RPM) and differential expression values (including fold-change and Z-score).

source_name: macrophage cell type

extract_protocol:
The macrophages were infected with H1N1 and H5N1 separately at a MOI of two. The cells were washed with warm culture medium and incubated in macrophage serum free medium (Invitrogen) supplemented with 0.6 mg/l penicillin and 60 mg/l streptomycin. The total RNA was extracted from cells at 1-, 3-, and 6-hr post-infection using the mirVana miRNA Isolation Kit (Ambion, Inc. TX, USA).
Small RNA library was prepared from rRNA-depleted RNA from 1 µg of total RNA. The 3’ adapter (5’-rAppAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG/3ddC/-3’, 3ddC represents a 3’ OH blocking group) that had an adenylated 5’-end and a ddC 3’-end was ligated to the 3’ end of the RNA using T4 RNA Ligase 2 (NEB, Ipswich, MA). The 5’ adapter (5’-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3’) ligation was performed using T4 RNA Ligase 1 (NEB, Ipswich, MA). The ligation product was used as template for cDNA synthesis using SuperScript II Reverse Transcriptase (Invitrogen) and an oligonucleotide with sequence complementary to 3’ adapter as RT primer (5’-CTCGGCATTCCTGCTGAACCGCTC–3’).

treatment_protocol: Primary human macrophage was separated from peripheral-blood leucocytes from healthy blood donors. The macrophages were seeded onto tissue culture plates in RPMI 1640 medium (Sigma-Aldrich) supplemented with 5% heat-inactivated autologous plasma.

tag: sample type

value: Low virulence

tag: time post infection

tag: molecule

value: rRNA-depleted RNA


title: H5N1_3hr [miRNA]

value: Highly pathogenic


title: Virgin Berlin rep 2


title: Virgin Berlin rep 3


title: Tud/+ female lacking germline 1 day post-mating rep 3


title: H5N1_6hr [miRNA]


title: Virgin with germline (tud/+) rep 2


title: H5N1_1hr [miRNA]


title: Virgin Berlin rep 1


title: H1N1_3hr [miRNA]


title: H1N1_1hr [miRNA]


title: 2DD_Met1mM_2

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

data_processing:
TOPHAT/CUFFLINK 2.0 was used with parameters --bowtie1 -p 8 -r 20 --solexa-quals --coverage-search --microexon-search--library-type fr-unstranded
Reads per kilobase per million reads (RPM) were calculated using the Seqmonk tool http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/. 2-fold changes in transcript abudnance are reported.
Genome_build: hg38

source_name: normal foreskin fibroblast

growth_protocol: 10 % FBS DMEM

extract_protocol:
Trizol extraction
polyA purified mRNAs

treatment_protocol: metformin: 5 day treatments in either 0.5mM or 1.0 mM

value: Metformin treated (1.0mM)

tag: passages


title: 2DD_Met1mM_1


title: Virgin lacking germline (tud/+) rep 3


title: 2DD_Met0.5mM_2

value: Metformin treated (0.5mM)


title: Mock_6hr [miRNA]

value: Mock control


title: 2DD_Met0.5mM_1


title: Mock_3hr [miRNA]


title: 2DD_Pro_2

value: proliferative fibroblast


title: Mock_1hr [miRNA]


title: 2DD_Pro_1


title: LNCaP_2_GRCh37_74

description: Genome-wide polyA+ transcript abundance of LNCaP cells.

data_processing:
Illumina software was used to generate fastq files. Before quantification Illumina adaptors were trimmed using  Trim Galore version: 0.4.0 and Cutadapt version: 1.8.1 using the --paired flag.
A kallisto (version 0.42.1) index was created from all transcripts in ensembl GRCh37 build 74 downloaded from ensembl.
Each sample had transcript abundances quantified processed using kallisto quant (version 0.42.1)
Transcript abundances in transcripts per million were subsequently extracted using R (version 3.2.0) for downstream analysis.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Transcripts per million are presented for each sample per ensemble transcript ID in a comma delimited table.

source_name: LNCaP, biological replicate 2

extract_protocol:
RNA was extracted using Trizol. Each sample was processed from cells cultured independently.
Libraries were prepared as per the manufacturers instructions using Illumina TruSeq kits with PolyA+ selection maintinaing strand informations and libraries were constructed at the Kinghorn Center for Clinical Genomics  (The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia).

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma (LNCaP)


title: LNCaP_3_GRCh37_74

source_name: LNCaP, biological replicate 3


title: PrEC_1_GRCh37_74

description: Genome-wide polyA+ transcript abundance of PrEC cells.

source_name: PrEC, biological replicate 1

value: PrEC

value: normal prostate epithelial cells (PrEC)


title: PrEC_2_GRCh37_74

source_name: PrEC,  biological replicate 2


title: PrEC_3_GRCh37_74

source_name: PrEC, biological replicate 3


title: LNCaP_1_GRCh37_74

source_name: LNCaP, biological replicate 1


title: Sample_21_HCD0155_NV

city: Atlanta

first: Scott

last: Jenks

state: Georgia

address: 615 Michael St, Whitehead Research Building Rm 255

department: Department of Medicine

institute: Emory University

data_processing:
Reads were mapped to the human genome (hg19) with TopHat 2.0.13 using default parameters (5),
Aligned reads were transformed with SAMtools (2) to quantify number of reads at the gene level with HTSeq-0.6.1 (3) using default “union” mode.
Raw counts were normalized using TMM normalization with edgeR using the SARTools R pipeline
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts at the gene level for each Sample

source_name: peripheral blood mononuclear cells

extract_protocol:
B cells were sorted directly into RLT lysis buffer and RNA was isolated using the Qiagen AllPrep DNA/RNA Micro kit.
cDNA was generated from RNA using RIBO-SPIA and libraries were prepared for sequencing using standard Illumina protocols

tag: disease status

value: healthy control donor

tag: b cell subset

value: Naïve

tag: cell phenotype

value: IgD+, CD27-

tag: gender

value: Male


title: Sample_24_HCD0155_DN2

value: Double negative 2

value: IgD-, CD27-, CXCR5-

tag: age


title: Sample_22_HCD0155_SWM

value: Switched memory

value: IgD-, CD27+, CXCR5+


title: SL476 heatshock [SHH62_H]

city: West Lafayette

first: Andrea

middle: J

last: Ray

state: IN

address: 745 Agriculture Mall Drive

department: Food Science

institute: Purdue University

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022005_SHH-6-2_CCGTCC

data_processing:
samples quality trimmed by sequencing core to Q20 using Trimmomatics; adaptors and barcodes also removed in this step
SL476 index constructed from NCBI reference sequence (NC_011083.1) using Bowtie 2 (v. 2.1.0)
Trimmed reads were aligned with the SL476 index using Tophat (v.2.1.1)
Tophat Bam files were sorted using sam tools  to obtain name-sorted .sam files necessary for HTSeq proper functioning
Read counts were obtained using HTSeq (v.0.6.1)
Genome_build: SL476 refseq genome NC_011083.1
Supplementary_files_format_and_content: Name-sorted read count files (Tophat 2 output). In tab-delimited text file format which can be opened using Excel or a text editor. Each file contains a column with the gene name and the number of reads associated with that gene

organism: Salmonella enterica subsp. enterica serovar Heidelberg

source_name: SL476 heatshock

growth_protocol: Overnight aerobic cultures in tryptic soy broth (TSB,BD, Franklin Lake, NJ) started from a single colony on tryptic soy agar (TSA; BD, Franklin Lake, NJ) were diluted to 103 CFU/mL into TSB and grown for 12 hours at 37C, 200 rpm to stationary phase (10 log10 CFU/mL) prior to RNA extraction. Growth phase had been previously confirmed by dilution plating onto TSA.

extract_protocol:
RNA was extracted using Trizol (Ambion, Foster City, CA) with an additional phenol:chloroform extraction  in triplicate for each isolate and condition. RiboZero (Illumina, San Diego, CA) was used to remove rRNA; TURBO DNAse (Thermo Fisher, Waltham, MA) was used to remove DNA. DNA removal was assessed using qRT-PCR for rpoD and gyrB (Table 3.2) (25, 34, 61, 80). Primers and probes were purchased from Integrated DNA Technologies (IDT, Coralville, IA); qRT-PCR was performed using IDT’s 2x master mix. If negative control samples (RNA samples with no reverse transcriptase added) did not amplify across the CT threshold prior to cycle 36, the sample was deemed free of DNA contamination.
Illumina's ScriptSeq v. 2 bacterial kit with Ribozero gold; constructed with low-concentration protocol
Enzymatic fragmentation, random-hexamer priming for amplification

treatment_protocol: 2mL stationary-phase samples were heat shocked at 56C for 7.5 minutes, with a time-to-temperature of 2.43 minutes. A 10% ice-cold phenol:ethanol stop-solution was immediately added to each solution upon removal from heat and samples were placed on ice

tag: isolate

tag: antimicrobial resistance

value: Gen Amp Kan Str Tet Aug Cep Smx

tag: pfge pattern

value: Unknown

tag: source type

value: Food isolate; reference strain

tag: culture condition

value: Stationary-phase culture heat shocked at 56C for 7.5 min


title: SL476 control [SHC331_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022013_SHC-3-31_ATCACG

source_name: SL476 control

value: Stationary-phase culture grown at 37C


title: SL476 heatshock [SHH48_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022012_SHH48_ACAGTG


title: Sample_18_HCD0371_SWM

value: Female


title: Sample_19_HCD0371_DN1

value: Double negative 1

value: IgD-, CD27-, CXCR5+


title: SL476 heatshock [SHH531_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022002_SHH-5-31_AGTCAA


title: Sample_20_HCD0371_DN2


title: Sample_17_HCD0371_NAV


title: R1-0007 (FSIS-FY14-10) heatshock [F10H331_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022018_F10H-3-31_CTTGTA

source_name: R1-0007 (FSIS-FY14-10) heatshock

value: Pan-Susceptible

value: Outbreak-associated food isolate


title: SL476 control [SHC24_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022009_2-4SHC_TGACCA


title: R1-0007 (FSIS-FY14-10) heatshock [F10H531_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022004_F10H-5-31_ATGTCA


title: Sample_16_HCD0200_DN2

value: healthy control donor


title: Sample_15_HCD0200_DN1


title: SL476 control [SHC218_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022008_SHC2-18_ACTTGA


title: R1-0007 (FSIS-FY14-10) heatshock [F10H62_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022007_F10H-6-2_GTGGCC


title: Sample_14_HCD0200_SWM


title: Sample_23_HCD0155_DN1


title: CTR2_Ileum_ZT02_male

source_name: Ileum Total RNA

tag: strain

tag: Sex

value: male

tag: tissue

value: Ileum

value: 15-16 weeks

tag: gut microbiome status

value: conventional raised

tag: zeitgeber time


title: R1-0007 (FSIS-FY14-10) control [F10C48_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022019_F10C-4-8_CTTGTA

source_name: R1-0007 (FSIS-FY14-10) control


title: Sample_13_HCD0200_NAV

value: Naïve

value: IgD+, CD27-


title: R1-0007 (FSIS-FY14-10) control [F10C24_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022010_2-4F10C_GCCAAT


title: R1-0007 (FSIS-FY14-10) control [F10C218_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022011_2-18F10C_CAGATC


title: Sample_11_SLE6696_DN1

value: systemic lupus erythematosus


title: R1-0006 (FSIS-FY14-9) heatshock [F9H613_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022003_F9H-6-13_AGTTCC

source_name: R1-0006 (FSIS-FY14-9) heatshock

value: Kan Str Tet


title: R1-0006 (FSIS-FY14-9) heatshock [F9H62_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022006_F9H_6-2_GTGAAA


title: Sample_12_SLE6696_DN2

value: Double negative 2

value: IgD-, CD27-, CXCR5-


title: R1-0006 (FSIS-FY14-9) heatshock [F9H331_H]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022016_F9H-3-31_GATCAG

value: Stationary-phase culture heat shocked at 56C for 7.5 min


title: Sample_08_SLE2581_DN2

value: Female


title: R1-0006 (FSIS-FY14-9) control [F9C48_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022017_F9C-4-8_TAGCTT

source_name: R1-0006 (FSIS-FY14-9) control

value: Stationary-phase culture grown at 37C


title: R1-0006 (FSIS-FY14-9) control [F9C29_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022014_F9C-2-9_CGATGT


title: R1-0006 (FSIS-FY14-9) control [F9C331_C]

description:
File names with C indicate control samples, samples with H indicate heat shock samples
022015_F9C-3-31_TTAGGC


title: Sample_09_SLE6696_NAV


title: Sample_04_SLE4079_DN2


title: Sample_06_SLE2581_SWM

value: Switched memory

value: IgD-, CD27+, CXCR5+


title: Sample_05_SLE2581_NAV


title: Sample_07_SLE2581_DN1

value: Double negative 1

value: IgD-, CD27-, CXCR5+


title: Sample_03_SLE4079_DN1


title: C58 wt minimal medium + opines_rep3

city: Gif-sur-Yvette

first: Almudena

last: González Mula

state: Ile-de France

address: 1 Avenue de la Terrasse

country: France

institute: CNRS

data_processing:
The generated data were demultiplexed using CASAVA software suite (CASAVA-1.8.2; Illumina, San Diego, USA)
The quality of the data was checked with the software FastQC 0.10.1 from Babraham Bioinformatics, Cambridge, UK). The Illumina 3′-adapter was trimmed using Cutadapt-1.2.1 (Python community), and only reads with a minimal length of 15 nucleotides were kept.
After the trimming step, the data were mapped using BWA-0.7.5a (Li and Durbin, 2010) with a seed length of 8 (default value) to the appropriate reference genome of A. tumefaciens C58. Only unique reads were analyzed. Bam output files were sorted with Samtools (http://www.htslib.org/).
HTSeq-count (EMBL, Heidelberg, Germany) was used to evaluate the number of reads by gene or by CDS.
The DESEQ package (Anders and Huber, 2010) was used to analyze the differential expression of genes between the control and the opine induced cultures. When the opine and opine-free conditions were compared, only genes with an absolute fold change ≥ 5 (i.e. log2 ≥ 2.3) and with a p-value < 0.05 were discussed.
Genome_build: NC_003062.2; NC_003063.2; NC_003064.2; NC_003065.3
Supplementary_files_format_and_content: tab-delimited text files include number of reads for each sample

organism: Agrobacterium tumefaciens

source_name: bacterial cells

growth_protocol: An overnight culture of A. tumefaciens C58 was grown in AB medium supplemented with mannitol and ammonium chloride.

extract_protocol:
Exponential phase cultures were centrifuged and total RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel Ltd., Oensingen, Switzerland).  RNA was further treated using RNase-free DNAse Ambion (Austin, TX, USA) according to manufacturer’s instructions to ensure the absence of any contaminating DNA.
Libraries were prepared using the 50-cycles TruSeq SBS Kit v3 (FC-401-3002, Illumina) and pooled in equimolar proportions and diluted to a final concentration of 12 pM, according to Illumina recommendations.

treatment_protocol: This culture was washed twice with NaCl 0.8% and served to inoculate three replicates of AB medium with low phosphate concentration supplemented, or not, with the two opines nopaline and agrocinopine A.

tag: growth phase

value: exponential phase culture

tag: genotype

value: wild type


title: Sample_02_SLE4079_SWM

tag: disease status


title: C58 wt minimal medium_rep3


title: C58 wt minimal medium + opines_rep2


title: C58 wt minimal medium_rep2


title: C58 wt minimal medium_rep1


title: Sample_10_SLE6696_SWM

tag: b cell subset


title: dcp5-1 inflorensences replicate 2

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

data_processing:
FastaQ files of each sample were aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) of each TU were calculated using cuffdiff.
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks.

source_name: dcp5-1 inflorensences

growth_protocol: Arabidopsis plant (Col-0 and dcp5-1) materials were grown under long day conditions at 22℃. Aerial samples (shoots) and roots were collected from two-week old plants that grew on MS plate. Inflorensences and siliques were collected from five-week old plants that grew in soil.

extract_protocol:
All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq strand-specific RNA sample Prep kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.
101-nt Single-end strand-specific RNA-seq by Illumina HiSeq 2000

tag: ecotype background

tag: genotype/variation

value: dcp5-1 mutant; DCP5 knockout

value: five weeks

value: inflorensences


title: dcp5-1 inflorensences replicate 3

tag: age


title: dcp5-1 inflorensences replicate 1


title: dcp5-1 shoots replicate 2

source_name: dcp5-1 shoots

value: two weeks

value: shoots


title: Wild type inflorensences replicate 3

source_name: WT inflorensences


title: Sample_01_SLE4079_NAV

value: systemic lupus erythematosus

value: Naïve

tag: cell phenotype

value: IgD+, CD27-

tag: gender


title: C58 wt minimal medium + opines_rep1


title: dcp5-1 roots replicate 3

source_name: dcp5-1 roots

value: roots


title: dcp5-1 shoots replicate 1


title: dcp5-1 roots replicate 2


title: Wild type inflorensences replicate 2


title: dcp5-1 roots replicate 1


title: Wild type shoots replicate 3

source_name: WT shoots


title: Wild type inflorensences replicate 1


title: Wild type roots replicate 3

source_name: WT roots


title: Wild type roots replicate 1


title: Wild type roots replicate 2


title: Pcb1692ΔexpI_E24-1

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

data_processing:
Base-calling and adapter sequence removal were done at BGI-Shenzhen
Clean reads were quality checked using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and mapped to the Pectobacterium carotovorum subsp. brasiliense draft genome using Bowtie2
Mapped reads with a MAPQ > 10 were counted using HTSeq-count
Differential expression analysis was performed using DESeq2 and genes with a q-value < 0.01 and absolute log2 fold change > 1 were considered
Genome_build: https://www.ncbi.nlm.nih.gov/genome/1799?genome_assembly_id=171682
Supplementary_files_format_and_content: counts

organism: Pectobacterium brasiliense PBR1692

source_name: Pcb1692ΔexpI_in planta at 24

growth_protocol: WildtypePcb1692 and the Pcb1692ΔexpI the mutant strains were grown on nutrient agar (supplemented with 50ug/ml kanamycin for the mutant strain) plate at 37°C for 24 hours. Overnight cultures were prepared by inoculating a single colony into10 ml Luria-Bertani (LB) broth (supplemented with 50ug/ml kanamycin for mutant strains) at 37 °C for 16 hours with constant shaking at 200 rpm

extract_protocol:
Total RNA extraction. Potato-inoculated and in vitro cultured bacterial cells were stabilized using the RNAprotect® reagent (Qiagen, USA) according to manufactures’ instructions. Total RNA from in vitro grown and potato-inoculated bacteria was extracted as previously described using the RNeasy mini kit (Qiagen, Hilden, Germany) with slight modifications.  The concentration and purity of each extracted total RNA sample was evaluated using spectrophotometric analysis (NanoDrop® ND-1000; NanoDrop® technologies, Wilmington, DE) at a ratio of 230/260 nm. Using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.), total RNA samples’ concentration, RIN and 28S/18S ratio were determined.
cDNA library construction and sequencing. The Illumina sequencing service was provided by the BGI Co., Ltd (China). TruSeq RNA Sample Prep Kit v2 (Illumina, USA) was used to construct the cDNA libraries following the manufacturer’s protocol. In summary, the mRNA was cleaved into small fragments, followed by the synthesis of first-strand cDNA with random hexamer-primed reverse transcription. RNase H and DNA polymerase I were used to synthesize second-strand cDNA. The double-stranded cDNA was subjected to terminal modification, by addition of adenosine and ligated with adapters. Adaptor-ligated fragments with suitable sizes were selected and enriched by PCR using the PureLinkTM PCR Purification Kit (Invitrogen, USA) to create the cDNA libraries for sequencing. The paired-end sequencing (PE91) was performed on the Illumina HiSeq 2000 sequencing platform.

treatment_protocol: To obtain in vitro cultured Pcb1692 or Pcb1692ΔexpI cells, overnight cultures were prepared as previously outlined. To obtain potato inoculated Pcb1692 cells, healthy potato tubers (Solanum tuberosum cv. Mondial) were inoculated with either Pcb1692 wild type or Pcb1692ΔexpI mutant strain as previously described7. The experiments were performed using three biological replicates, with three tubers per replicate. Macerated potato tissue was scooped out at 6, 24, and 72 hours post inoculation (hpi). Macerated potato tissue was then homogenized in double distilled water. Bacterial cells were recovered by grinding the scooped macerated potato tissues using autoclaved pestle and mortar with 20 ml of double distilled water. Starch material was removed by centrifuging the ground tissue at 10000 rpm for 1 minute.

tag: strain background

value: ExpI mutant

tag: sample source

value: Potato tuber

tag: sample type

value: in planta at 24


title: Pcb 1692_W72-1

source_name: WT_in planta at 72

value: Wild type

value: In planta at 72


title: Pcb1692ΔexpI_CE-1

source_name: Pcb1692ΔexpI_in Vitro

value: In Vitro


title: Pcb1692ΔexpI_CE-2


title: Pcb1692ΔexpI_CE-3


title: dcp5-1 shoots replicate 3


title: Pcb 1692_W24-3

source_name: WT_in planta at 24


title: Pcb 1692_CW-2

source_name: WT_In Vitro


title: Pcb 1692_W24-1


title: Pcb 1692_CW-1


title: Pcb 1692_W24-2


title: Wild type shoots replicate 2


title: Pcb1692ΔexpI_E24-2


title: Wild type shoots replicate 1


title: High salinity and temperature 45A

status: Public on Aug 31 2018

city: Seville

first: Carmen

last: Vargas

state: Seville

address: C/profesor García Gonzalez n2

country: Spain

institute: University of Seville

description: High salinity and temperature

data_processing:
Basecalls performed using SOLiD™ Instrument Control Software
Sequenced reads were trimmed for adaptor sequence. BioScope (version 1.3, Applied Biosystems, CA) was used to map the color sequences of each bead to the annotated NC_007963 reference genome obtained from the National Center for Biotechnology Information (NCBI).
Low quality mapped reads were evaluated and eliminated by using Picard Tools.
Assembling, identification, and quantification was performed by Bayesian inference by using the cufflinks v2.02 software
To assess the genes differentially expressed in the different stress conditions, the HTSeq software (http://www-huber.embl.de/users/anders/HTSeq) was used to determine the number of reads per gene.
The EDAseq software from the Bioconductor package was used to perform the different normalization procedures. For the differential expression analysis, a negative binomial distribution was assumed using DESeq.
Genome_build: NC_007963.1
Supplementary_files_format_and_content: Excel file includes a matrix table with raw counts of sequencing reads and normalized abundance measurements

organism: Chromohalobacter israelensis DSM 3043

growth_protocol: Cells were grown in M63 minimal medium with 20 mM glucose as the sole carbon source. Cultures were incubated in an orbital shaker at 200 rpm. Three different growth conditions were used: low salinity (0.6 M NaCl, 37 ºC), high salinity (2.5 M NaCl, 37 ºC) and high salinity plus high temperature (2.5 M, 45 ºC). Three replicate cultures were grown for each condition.

extract_protocol:
Cell total RNA was extracted using the High Pure RNA isolation kit (Roche). Depletion of 23S and 16S rRNA was performed using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) followed by Ribo-Zero rRNA.Removal kit for Gram-negative bacteria (Epicentre)
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: strain

tag: growth medium

value: Glucose 20 mM M63 minimal medium suplemented with 2.5 M of NaCl

tag: growth temperature

value: 45 ºC


title: Low salinity 06B

description: Low salinity

value: Glucose 20 mM M63 minimal medium suplemented with 0.6 M of NaCl

value: 37 ºC


title: High salinity and temperature 45C

description: High salinity and temperature


title: High salinity 25A

description: High salinity


title: Low salinity 06C

description: Low salinity


title: Low salinity 06A

description: Low salinity


title: High salinity and temperature 45B

description: High salinity and temperature


title: Pcb 1692_W72-2