title: M5 rep1


title: wt_1H_C

status: Public on Jul 01 2017

type: SRA

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic

data_processing:
mRNA-seq reads were aligned to the ce6 genome by STAR (Dobin et al., 2013) and differentially expressed genes were identified by HOMER (Heinz et al., 2010) and EdgeR (Robinson et al., 2010)
Genome_build: ce6
Supplementary_files_format_and_content: bedGraph

molecule: total RNA

organism: Caenorhabditis elegans

source_name: wild type

growth_protocol: Nematodes were grown at 20C on NGM plates seeded with OP50 bacteria when not starved.

extract_protocol:
Nematodes were harvested, flash frozen with liquid nitrogen, and RNA was harvested using Isol-RNA Lysis Reagent (Ref #2302700 5 PRIME), RNA was further cleaned using Qiagen RNeasy Protect Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA-seq: Libraries were prepared from purified RNA (TruSeq Illumina mRNA prep kit) and sequenced according to the manufacturer’s instructions (HiSeq v4 Illumina SR sequencing kit).

treatment_protocol: Nematodes were starved for 0, 1, 2, 3, 4, 6, or 16 hours by transfering them to empty NMG plates.

tag: genotype/variation

value: wild type

tag: starvation timepoint


title: wt_16H_C


title: S. viridis A10.1 LDHH-F ZT40 REP1

city: St. Louis

first: Malia

last: Gehan

state: Missouri

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

data_processing:
BBTools (v36.20)   using parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo ktrim=l k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=20 minlen=20 (Bushnell, 2016). Any parameters not specified were run as default.
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to index the transcripts with the default parameters and the Setaria viridis transcripts fasta file (Sviridis_311_v1.1) from Phytozome (Goodstein et al., 2012).
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to quantify reads with parameters:-t 40 -b 100. Any parameters not specified were run as default.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Setaria viridis

source_name: Leaf Tissue

growth_protocol: Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.

extract_protocol: Wang et al. 2012; http://dx.doi.org/10.1371/journal.pone.0026426

tag: tissue

value: Leaf

tag: accession

tag: sample age

value: 10  Days  After Planting

tag: treatment


title: wt_16H_B


title: S. viridis A10.1 LDHH-F ZT42 REP1

value: 12 hour photocycles (12h light/12h dark)


title: wt_16H_A


title: Spom.hsr1.BMW.T0_A

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

institute: Wisconsin Institute for Discovery

data_processing:
Reads were aligned to the reference genomes using TopHat with default setttings.
Gene expression levels were quantified using Cuffquant (Cufflinks 2.2.1 suite) with default settings.
Gene expression levels were normalized across all samples using Cuffnorm (Cufflinks2.2.1 suite) with default settings.
Genome_build: C. albicans was downloaded from the Candida Genome Database (accession number AACQ00000000); S. pombe was downloaded from PombeDB (accession numbers CU329670–CU329672); S. cerevisiae was downloaded July 2005 from the Saccharomyces Genome Database
Supplementary_files_format_and_content: Tab-delimited text files with normalized gene expression levels

organism: Schizosaccharomyces pombe

source_name: S. pombe hsr1 knockout with normal media at T=0, replicate A

growth_protocol: For each strain, cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and re-suspended into 3.5 mL BMW culture (with or without drug depending if WT or hog1Δ) and placed in a New Brunswick Scientific Edison model TC-7 roller drum on the fastest rotation until saturated (1-2 days). For each species, saturated cultures were diluted to OD600 ~ 0.001 – 0.008, where for each species care was taken to ensure that the OD600 of the WT and hog1Δ strains were the same. These starting cultures were further diluted serially at 1:4 in at least 6 rows of a 96 well plate with 2 biological replicates per strain. Growth curves were measured using the Biotek Synergy H1 Hybrid Reader with OD600 measurements every 15 minutes, operating at continuous low shaking at 30°C for each species.

extract_protocol:
Qiagen Yeast RNA extraction
Refer to Trombetta et al, 2014

treatment_protocol: Osmotic Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with BMW (Ctrl) or KCl to a final concentration of 0.4M. Samples were harvested at 0, 10, or 20 minutes following treatment.  After growth, 150ml of each culture was transferred to each of 100ml BMW (CTRL - defined in the Growth protocol) and 100ml BMW+KCl (EXP).  Both CTRL and EXP media were pre-warmed for 40-60 minutes in the shaker prior to the experiment. EXP media was either BMW + 0.5M KCl or 1M KCl yielding a final concentration of 0.2M KCl or 0.4M KCl, respectively, upon addition of the culture. In each case, CTRL media was added first, followed by the EXP media, whereupon the shaker was immediately activated to 180 rpm and the timer started simultaneously. Samples (20ml) were collected from the CTRL media + culture immediately upon activation of the shaker (T=0), then at T=10, 20, 40, and 80 minutes from the EXP media + culture.

tag: genotype

value: hsr1 knockout


title: Spom.hsr1.BMW.T0_B

source_name: S. pombe hsr1 knockout with normal media at T=0, replicate B


title: S. viridis A10.1 LDHH-F ZT42 REP2


title: S. viridis A10.1 LDHH-F ZT40 REP2


title: H_fed_C

source_name: hlh-30 mutant

value: hlh-30 mutant


title: S. viridis A10.1 LDHH-F ZT38 REP2


title: S. viridis A10.1 LDHH-F ZT38 REP1


title: Spom.WT.BMW.T0_B

source_name: Wildtype S. pombe with normal media at T=0, replicate B

value: Wildtype


title: Spom.WT.KCl.T20_B

source_name: Wildtype S. pombe with KCl stress at T=20, replicate B


title: Spom.WT.KCl.T20_A

source_name: Wildtype S. pombe with KCl stress at T=20, replicate A


title: H_fed_B


title: H_fed_A


title: S. viridis A10.1 LDHH-F ZT36 REP2


title: Spom.WT.BMW.T0_A

source_name: Wildtype S. pombe with normal media at T=0, replicate A


title: H_6H_C


title: Spom.hsr1.KCl.T20_A

source_name: S. pombe hsr1 knockout with KCl stress at T=20, replicate A


title: S. viridis A10.1 LDHH-F ZT44 REP1


title: H_6H_B


title: S. viridis A10.1 LDHH-F ZT36 REP1


title: H_6H_A


title: H_4H_C


title: S. viridis A10.1 LDHH-F ZT32 REP1


title: H_4H_B


title: H_4H_A


title: H_3H_C


title: S. viridis A10.1 LDHH-F ZT30 REP2


title: H_3H_B


title: S. viridis A10.1 LDHH-F ZT32 REP2


title: H_3H_A


title: S. viridis A10.1 LDHH-F ZT34 REP2


title: S. viridis A10.1 LDHH-F ZT34 REP1


title: S. viridis A10.1 LDHH-F ZT28 REP2


title: S. viridis A10.1 LDHH-F ZT28 REP1


title: S. viridis A10.1 LDHH-F ZT26 REP1


title: H_2H_B


title: S. viridis A10.1 LDHH-F ZT26 REP2


title: S. viridis A10.1 LDHH-F ZT30 REP1


title: H_2H_A


title: S. viridis A10.1 LDHH-F ZT24 REP1


title: S. viridis A10.1 LDHH-F ZT24 REP2


title: H_1H_C


title: H_1H_B


title: S. viridis A10.1 LDHH-F ZT22 REP1


title: H_2H_C


title: H_1H_A


title: Scer.msn2/4.BMW.T0_A

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae msn2/4 knockout with normal media at T=0, replicate A

value: msn2/4 knockout


title: Scer.msn2/4.BMW.T0_B

source_name: S. cerevisiae msn2/4 knockout with normal media at T=0, replicate B


title: H_16H_C


title: Scer.sko1.KCl.T20_A

source_name: S. cerevisiae sko1 knockout with KCl stress at T=20, replicate A

value: sko1 knockout


title: H_16H_B


title: S. viridis A10.1 LDHH-F ZT20 REP2


title: S. viridis A10.1 LDHH-F ZT20 REP1


title: Scer.sko1.BMW.T0_A

source_name: S. cerevisiae sko1 knockout with normal media at T=0, replicate A


title: S. viridis A10.1 LDHH-F ZT18 REP2


title: Scer.WT.KCl.T20_B

source_name: Wildtype S. cerevisiae with KCl stress at T=20, replicate B


title: H_16H_A


title: Scer.msn2/4.KCl.T20_B

source_name: S. cerevisiae msn2/4 knockout with KCl stress at T=20, replicate B


title: S. viridis A10.1 LDHH-F ZT16 REP1


title: cx_exo_5ppp_2

city: Philadelphia

first: Yu

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

description: exosome RNA

data_processing:
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -q 10 -m 30 -O 4)
Trimmed reads were mapped to consensus rRNA sequences and RN7SL1 using bowtie2 v2.2.4 to remove rRNA reads and get more accurate count of 7SL RNA (parameter --fr --no-mixed --no-discordant)
Reads were then aligned with STAR v2.4.0k to GRCm38/mm10 reference genome (parameter --outFilterMultimapNmax 100 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06)
Non primary alignment and QC failed reads were removed with samtools (parameter -F 772)
Aligned and filtered reads were shrinked to 5' end, then counted against transcript start sites of GENCODE annotation v21  and RepeatMasker features (UCSC genome browser) using Subread v1.4.6
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited txt file including raw read count with matching 5' end of GENCODE gene features and repeatmasker features.

organism: Homo sapiens

source_name: exosome isolated from MRC5/1833 co-culture

growth_protocol: All human breast cancer and/or stromal cell lines were cultured at 37oC in DMEM supplemented with 10% exosome depleted FBS, 100U/ml penicillin and 100µg/ml streptomycin.  For co-culutre experiment, stroma cells and breast cancer cells were mixed at 1:1.

extract_protocol:
Exosomes were isolated from conditioned media collected at 48-72 hours by serial high speed ultracentrifugation, or using 10% final concentration of polyethylene-glycol and low speed centrifugation. Exosome RNA was extracted with TRIzol.
0.1-2 µg of exosomal RNA was prepared by first degrading 5’monophosphate RNA with Terminator 5´-Phosphate-Dependent Exonuclease (Epicentre), then converting 5’triphosphate to 5’p with RNA 5’ Polyphosphatase (Epicentre), to allow for specific ligation of RNA adaptor P5_RNA to RNAs that originally have 5’ triphosphate. Then, cDNAs were synthesized by using a primer with 5’ random 9mer (P7_N9), and amplified with NEBNext PCR reagents (NEB).

tag: cell line

value: MRC5 and 1833

tag: culture

value: co-culture


title: Scer.WT.KCl.T20_A

source_name: Wildtype S. cerevisiae with KCl stress at T=20, replicate A


title: Scer.WT.BMW.T0_B

source_name: Wildtype S. cerevisiae with normal media at T=0, replicate B


title: BC077

city: Worcester

last: Liu

state: MA

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

data_processing:
The fastq files were obtained using Illumina CASAVA v1.8
The quality of fastq reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The fastq read were mapped on human geneome (hg19) using Tophat 1.4.1
The read counts were calculated using customed R scripts to calculate transcript union reads per million reads (truRPMs)
Genome_build: hg19
Supplementary_files_format_and_content: all_truRPMs.txt: coding gene expression of all the samples in the cohort

source_name: FFPE bladder tumor block

extract_protocol:
The viable tumor regions were first marked by a pathologist and the total RNAs were then extracted from the tumor regions
The sequencing libraries were constructed using RiboZero and Illumina TruSeq RNA preparation kit following the kit instructions. For FFPE samples, the RNA fragmentation step was removed because FFPE RNAs are fragments.

value: Bladder

tag: tumor grade (2004 who)

value: unknown

tag: tumor stage


title: BC076

source_name: Fresh frozen bladder tumor


title: S. viridis A10.1 LDHH-F ZT14 REP2

source_name: Leaf Tissue


title: BC075


title: S. viridis A10.1 LDHH-F ZT22 REP2


title: BC074


title: Scer.sko1.KCl.T20_B

source_name: S. cerevisiae sko1 knockout with KCl stress at T=20, replicate B


title: S. viridis A10.1 LDHH-F ZT12 REP2


title: BC073


title: Scer.sko1.BMW.T0_B

source_name: S. cerevisiae sko1 knockout with normal media at T=0, replicate B


title: S. viridis A10.1 LDHH-F ZT12 REP1


title: BC072


title: S. viridis A10.1 LDHH-F ZT10 REP2


title: BC071


title: S. viridis A10.1 LDHH-F ZT8 REP2


title: S. viridis A10.1 LDHH-F ZT16 REP2


title: S. viridis A10.1 LDHH-F ZT6 REP2


title: S. viridis A10.1 LDHH-F ZT6 REP1


title: S. viridis A10.1 LDHH-F ZT4 REP1


title: S. viridis A10.1 LDHH-F ZT2 REP2


title: S. viridis A10.1 LDHH-F ZT2 REP1


title: S. viridis A10.1 LDHH-F ZT18 REP1


title: S. viridis A10.1 LDHH-F ZT14 REP1


title: cx_exo_5ppp_1

description: exosome RNA


title: E11_phyB

city: Jinan

first: Xiao Hui

last: Xu

address: No. 202, Gongyebei Road

country: China

institute: Shandong Academy of Agricultural Sciences

description: phyB mutant

data_processing:
Raw reads containing adaptor sequences, with low quality and unknown nucleotides N were filtered to obtain clean reads. Then the clean reads were conducted for quality assessments, which include classification of total and distinct reads and count their percentage in the library, analysis the saturation of the library and correlation analysis of biological replicates. All clean reads were mapped to the rice genome (http://phytozome.jgi.doe.gov/pz/portal.html) by Bowtie (version 1.0.0), with only one base pair mismatch was allowed. The number of perfect clean reads corresponding to each gene was calculated and normalized to the number of Reas per Kilobase of exon model per Million mapped reads (RPKM) (Mortazavi et al., 2008).
Transcripts with fold change ≥ 2, FDR value ≤ 0.01 and reads number ≥ 20 in at least one of the two comparison sample were considered to be differentially expressed. Based on the Mapman and GO annotation, all these differentially expressed genes were classified into 18 categories. Gene Ontology (GO) analysis were performed by using AgriGO (Du et al., 2010).
Genome_build: http://phytozome.jgi.doe.gov/pz/portal.html
Supplementary_files_format_and_content: RPKM

organism: Oryza sativa

source_name: Anther

extract_protocol: Total RNA was extracted from rice anthers using the modified CTAB method as described in Xu et al., (2012)(Xu et al., 2012). The quantity and purity of total RNA were analyzed by a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). RNAs with integrity number (RIN) >7.0 were left for libraries construction. Approximately 10 μg total RNA was used for generating complementary DNA (cDNA) according to the manufacturer’s instructions (Illumina, Aan Diego, CA). The products were single end sequenced on an Illumina Hiseq 2500 at LC Sciences (Hangzhou, China) following the vendor’s recommended protocol. The processing of fluorescent images into sequences, base-calling and quality value calculations were finished using the Illumina data processing pipeline (version 1.8).

treatment_protocol: Seeds were surface sterilized in 70% (v/v) ethanol for 30 s, then they were transferred into 5% NaClO (v/v) for 20 min. After six times rinsed in sterile double-distilled water, seeds were incubated in the dark at 28°C for 3 days to induce germination. During July to August, seedlings were transferred to the soil in the farm of Shandong Academy of Agricultrual Sciences in Jinan, Shandong, China (latitude 36°40’N; longitude 117°00’E). Anthers from the four plant materials were collected before anthesis, they were stored firstly in liquid nitrogen, and then transferred to -80°C refrigerator until RNA extraction.

tag: development

value: anthesis

value: anthers from 4 plants

value: phyb


title: E10_phyA

description: phyA mutant

value: phya


title: E12_phyB

description: phyB mutant


title: E9_phyA

description: phyA mutant


title: E3_phyA

description: phyA mutant


title: E7_phyAphyB

description: phyA phyB mutant

value: phya phyb


title: E2_phyAphyB

description: phyA phyB mutant


title: S. viridis A10.1 LDHH-F ZT10 REP1

value: Leaf


title: BC070


title: E6_WT

description: Oryza sativa L. cv. Nipponbare

value: wt


title: E1_WT

description: Oryza sativa L. cv. Nipponbare


title: E5_WT

description: Oryza sativa L. cv. Nipponbare


title: ID-seq spike-in DNA-tags

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description:
Antibody specific DNA-tag.
Template DNA-tags were diluted and prepared for sequencing. No immuno-staining was performed before sample-preparation.

library_source: genomic

data_processing:
Library strategy: ID-seq
bcl2fastq conversion v2.16.0.10.
Split reads from fastq files using R-package immunoSeq version 1.0.0.
Remove duplicate reads and count unique barcodes.
Match barcode sequences to antibody and sample.
Supplementary_files_format_and_content: The txt files are the index files used to match DNA-barcode sequences to antibody and samples for that specific experiment.
Supplementary_files_format_and_content: The .tsv files contain the barcode counts with matched antibody and sample specific information.

molecule: other

organism: synthetic construct

source_name: synthetic ID-seq DNA-tags

extract_protocol:
DNA-tags were released from immuno-stained cell populations using 1.5 hour DTT treatment.
Released DNA-tags were used in an overhang PCR reaction that adds sample-specific barcode sequence. Then a pool of these barcoded DNA-tags was used for a second PCR to add Illumina adaptor and index sequence to the DNA fragments.

tag: sample type

value: template DNA-tags


title: S. viridis A10.1 LDHH-F ZT4 REP2

value: 10  Days  After Planting

value: 12 hour photocycles (12h light/12h dark)


title: N44

city: Guangzhou

first: Jian-Rong

last: Yang

address: No. 74, Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
All raw read sequences generated by RNA-seq were first processed by cutadapt to trim any remaining adaptor sequences
The trimmed reads were then aligned to the genome of the corresponding strains by tophat under the default parameter set except that a maximal intron size of 10 kb was allowed because the largest annotated intron in S. cerevisiae is 9349 bp
Alignment results were fed to cufflinks for quantification of known transcripts in S. cerevisiae, S. paradoxus, and S. mikatae.
Some ORFs are further filtered when they have no reliable one-to-one orthologs between the three species, giving rise to a final list of expression level for 4325 ORFs in the 9 species
Genome_build: S.cerevisiae (SGD R64.1.1), S. paradoxus and S.mikatae from [Scannell DR, et al. (2011) The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1:11-25.]
Supplementary_files_format_and_content: Tab-delimited text files. Containing ORF names (represented by the S.cerevisiae ORF ID) and expression level (RPKM) in each strain.

molecule: polyA RNA

organism: Saccharomyces paradoxus

growth_protocol: Each of the nine yeast strains was streaked to form single colonies from frozen glycerol stocks held at -80°C onto YPD plates (1% yeast extract, 2% peptone, 2% glucose, 2% agar).  After 48 hours of growth at 30°C, a single colony was picked and inoculated into 5 ml of the synthetic oak exudate medium (1% sucrose, 0.5% fructose, 0.5% glucose, 0.1% yeast extract, and 0.15% peptone).  Strains were grown for 24 hours at 30°C before dilution into fresh synthetic oak exudate medium to an OD660 of 0.1.  Cultures were grown at 30°C until OD660 = 0.5 (mid-log phase), at which point cells were harvested by centrifugation.

extract_protocol:
Extraction of mRNA was carried out using MicroPoly(A)Purist Kit (Ambion) and 200 ng of the resulting mRNA sample was fragmented (Fragmentation Buffer, NEB) before ethanol precipitation.
First strand cDNA synthesis was performed using random hexamer priming (Superscript II, Invitrogen), followed by second strand cDNA synthesis (Invitrogen) as recommended by the manufacturer.  End repair, A-tailing, and ligation of the Illumina adapters necessary for sequencing were then carried out using the NEBnext mRNA sample preparation kit (NEB).  Libraries were then size-selected by agarose gel electrophoresis followed by gel extraction such that libraries consisted of fragments containing inserts of approximately 250 bp in length.  Polymerase-chain-reaction amplification was performed for 15 cycles using NEBnext mRNA sample preparation kit

tag: location isolated

value: Ternei, Russia

tag: source

value: Oak tree

tag: ecological environment

value: Wild


title: N17

value: Tartastan, Russia


title: S. viridis A10.1 LDHH-F ZT8 REP1


title: E4_phyB

description: phyB mutant


title: E8_phyAphyB

description: phyA phyB mutant


title: DR_685

city: Mainz

first: Austin

last: Alleman

address: Joh.-v.-Müller-Weg 6

department: Evolutionary Biology

country: Germany

institute: Feldmeyer-Foitzik Group

description: Barcode: ACTTGA

data_processing:
FastQC
Trimmomatic
CLC Genomics Workbench 7.0.3: bubble size auto, word size 35, otherwise default parameters
MIRA 3.4.0:  mira --project=PROJECTNAME --job=denovo,genome,draft,sanger –noclipping --notraceinfo --fasta=INPUTFASTA SANGER_SETTINGS -LR:wqf=no COMMON_SETTINGS -MI:sonfs=no -MI:somrnl=0 -GE:not=1 -SK:mmhr=100 -AS:base_default_quality=30 -AS:epoq=no -AS:mrpc=1 -OUT:sssip=yes
CD-Hit-Est 4.6.1
TopHat 2.0.13
Bowtie-build
Qualimap 2.1
Blastx 2.2.30+
OrthoMCL 2.0.9
Genome_build: de novo transcriptome assembly
Supplementary_files_format_and_content:
SuppTable_S4_AllDiffExpressedGenes.xlsx contains normalized read count information and differential expression data for each significantly-differentially-expressed contig produced from the assembly of RAW read files.
ExpressionTable+Contigs_AllReplicates_*.xlsx files contain count data for all contigs within their respective transcriptomes
2017July_TemnoClusters.fas-gb.tar.gz: OrthoMCL homologous sequence clusters, containing all previously-identified contigs that are present within all six Temnothorax species herein examined; 5,197 OrthoMCL homologous cluster files (.fas-gb)

organism: Temnothorax pilagens

source_name: whole body

extract_protocol:
life ants were directly put in Trizol, ground and then used for RNA extraction following the Qiagen extraction protocol
Libraries were constructed by GENterprise Genomics (Mainz) immediately prior to sequencing

tag: behavior

value: Slavemaker - During raid

value: whole body


title: BR_683

description: Barcode: GCCAAT

value: Slavemaker - Before raid


title: BR_681

description: Barcode: TGACCA


title: DR_686

description: Barcode: GATCAG


title: DR_684

description: Barcode: CAGATC


title: IFO1815

organism: Saccharomyces mikatae

value: Japan

value: Soil and decayed leaf


title: BR_426

description: Barcode: ACTTGA

organism: Temnothorax longispinosus

value: Host - Before raid


title: BR_427

description: Barcode: GATCAG


title: BR_428

description: Barcode: TAGCTT


title: DR_431

description: Barcode: AGTCAA

value: Host - During raid


title: DR_429

description: Barcode: GGCTAC


title: Fibroblasts infected Human and Candida with T cells BR2

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_30_br2

data_processing:
Basecalls were performed using standard software supplied by Illumina for HiSeq2500 sequencing.
Reads generated with HiSeq2000 were mapped with NextGenMap (version 0.4.12) using default settings and producing bam-files.
Genome_build: GRCh38.p2 and SC5314 assembly 21 where applicable
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. RPKM was calculated according to Mortazavi et al.

organism:
Homo sapiens
Candida albicans SC5314

source_name: CD4+ T cell-supplemented human skin model infected with C. albicans

growth_protocol: 3D skin models were grown in KGM-2 medium in 24 well plate transwell inserts with a pore size of 8 µm.

extract_protocol:
Tissue cell layers were separated, quickly washed in PBS and immediately frozen down in liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT (QIAGEN, Hilden, Germany) supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Protocol for the isolation of total RNA using the RNeasy Plus Mini Kit. Concentration and integrity of total RNA was analyzed using the Agilent 2100 Bioanalyzer using the RNA Nano kit.
TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Skin models were infection with 100 colony forming units of an overnight culture of C. albicans strain SC5314 in 5 µl PBS. Uninfected models were treated with mock PBS. Infected skin models were kept at 37°C in a humidified 5 % CO2-containing atmosphere for 24h

value: S1F fibroblasts / C. albicans SC5314

tag: model type

value: Fibroblasts + Keratinocytes + T cells + C. albicans


title: DR_432

description: Barcode: AGTTCC


title: Fibroblasts infected Human and Candida no T cells BR3

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_29_br4

source_name: human skin model infected with C. albicans

value: Fibroblasts + Keratinocytes + C. albicans


title: DR_430

description: Barcode: CTTGTA


title: DR_423

description: Barcode: GTTTCG

organism: Temnothorax duloticus


title: DR_424

description: Barcode: CGTACG


title: BR_425

description: Barcode: TTAGGC


title: BR_680

description: Barcode: CGATGT


title: DR_687

description: Barcode: GGCTAC


title: DR_422

description: Barcode: GTGGCC


title: Keratinocytes infected Human and Candida BR3

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_14_br3

value: Ker-CT keratinocytes / C. albicans SC5314


title: Keratinocytes infected Human and Candida BR2

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_14_br2


title: DR_421

description: Barcode: GTGAAA


title: Fibroblasts infected Human and Candida with T cells BR3

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_30_br3


title: Keratinocytes infected Human and Candida BR1

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_14_br1


title: Fibroblasts infected Human and Candida with T cells BR1

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_30_br1


title: Fibroblasts infected Human and Candida BR1

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_9_br1


title: Fibroblasts infected Human and Candida BR2

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_9_br2


title: BR_417

description: Barcode: AGTTCC


title: BR_418

description: Barcode: ATGTCA


title: Fibroblasts infected Human and Candida no T cells BR1

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_29_br1


title: NA20764

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

institute: The Chinese University of Hong Kong

data_processing:
Base calling was done via Zebra Call from BGIseq-500
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5) with parameters as: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
FPKM values of each gene for each sample was measured via RSEM (version v1.2.12) with parameters as: --paired-end -p 8
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in each sample

source_name: EB virus transformation cell line

growth_protocol: Recover cell lines from the liquid nitrogen by thawing a vial rapidly in a 37 degree centigrade water bath. Re-suspend the entire contents of the vial in fresh culture medium. Cell culture in the T25 tissue culture flask with 10 ml medium (85%RPMI 1640+15% fetal bovine serum) in the 37 degree centigrade incubator (5% CO2) for 4 to 5 days

extract_protocol:
Total RNA was extracted from each cell with TRIzol Reagent (Invitrogen, Life Technologies, USA), then was treated with DNase I (Invitrogen, Life Technologies, Waltham, MA)
mRNA enrichment with Oligo(dT)25 Dynabeads twice and purified with Dynabeads® mRNA Purification Kit (Invitrogen, No. 61006). The eluted mRNA was fragmented with Fragmentation Buffer Mix at 94 degree centigrade for 10min. Reverse transcription was performed with RT Buffer Mix and RT Enzyme Mix and followed by the double strand cDNA (dscDNA) synthesis with Second Strand Buffer Mix and Second Strand Enzyme Mix. End repairing, adaptor (with barcode) ligation and PCR amplification were performed after dscDNA purification. Then the purified double stranded PCR products were heat denatured to single strand and circularized with Splint Oligo Mix and Ligation Enzyme. The single strand circle DNA (ssCirc DNA) library was rolling circle amplified to make DNA nanoball (DNB) and load into the patterned nanoarray

tag: cell type

value: Lymphocyte


title: Fibroblasts infected Human and Candida BR3

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_9_br3

tag: tissue


title: NA18612


title: HG02260


title: DR_415

description: Barcode: CTTGTA

organism: Temnothorax curvispinosus


title: BR_420

description: Barcode: GTCCGC


title: HG03729


title: Calb.mnl1.KCl.T20_B

organism: Candida albicans

source_name: C. albicans mnl1 knockout with KCl stress at T=20, replicate B

value: mnl1 knockout


title: DR_414

description: Barcode: GGCTAC


title: BR_419

description: Barcode: CCGTCC


title: BR_412

description: Barcode: GATCAG


title: Calb.sko1.BMW.T0_A

source_name: C. albicans sko1 knockout with normal media at T=0, replicate A

value: sko1 knockout


title: DR_416

description: Barcode: AGTCAA


title: Calb.sko1.BMW.T0_B

source_name: C. albicans sko1 knockout with normal media at T=0, replicate B


title: Calb.mnl1.KCl.T20_A

source_name: C. albicans mnl1 knockout with KCl stress at T=20, replicate A


title: Calb.mnl1.BMW.T0_B

source_name: C. albicans mnl1 knockout with normal media at T=0, replicate B


title: Calb.sko1.KCl.T20_B

source_name: C. albicans sko1 knockout with KCl stress at T=20, replicate B


title: DR_413

description: Barcode: TAGCTT


title: BR_410

description: Barcode: CAGATC


title: BR_411

description: Barcode: ACTTGA


title: Calb.mnl1.BMW.T0_A

source_name: C. albicans mnl1 knockout with normal media at T=0, replicate A


title: BR_409

description: Barcode: TGACCA


title: Calb.WT.KCl.T20_A

source_name: Wildtype C. albicans with KCl stress at T=20, replicate A

value: Wildtype


title: Calb.WT.KCl.T20_B

source_name: Wildtype C. albicans with KCl stress at T=20, replicate B


title: Calb.sko1.KCl.T20_A

source_name: C. albicans sko1 knockout with KCl stress at T=20, replicate A


title: DR_438

description: Barcode: GTTTCG

organism: Temnothorax americanus


title: DR_440

description: Barcode: GAGTGG


title: DR_439

description: Barcode: CGTACG


title: DR_437

description: Barcode: GTGGCC


title: DR_695

description: Barcode: GTGGCC

organism: Temnothorax ambiguus


title: DR_694

description: Barcode: GTGAAA


title: Calb.WT.BMW.T0_B

source_name: Wildtype C. albicans with normal media at T=0, replicate B


title: BR_435

description: Barcode: GTCCGC


title: DR_693

description: Barcode: GTCCGC


title: BR_434

description: Barcode: CCGTCC


title: DR_692

description: Barcode: CCGTCC


title: BR_433

description: Barcode: ATGTCA


title: BR_682

description: Barcode: ACAGTG


title: BR_690

description: Barcode: AGTTCC


title: N. stephensi replicate 3

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description:
Sample 714
PolyA RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were quality filtered and trimmed using Trimmomatic (Bolger et al. 2014).
The subsequent overlapping paired-end reads were merged using FLASH (Mago_ and Salzberg 2011).
The coding transcripts from the M7 release of the GENCODE mouse genome annotation (gencode.vM7.pc_transcripts.fa) were formatted as a nucleotide database and Illumina reads were aligned using a fast version of the Smith-Waterman algorithm implemented in cross_match (Gordon et al. 1998) with a -minscore parameter of 50 and a -masklevel parameter of 101 to allow reads to align to multiple transcripts.
Total read counts were generated from read alignments per CDS region using custom Perl scripts that collapsed transcript level alignments (ENSMUST identifiers) to gene level alignments (ENSMUSG identifiers).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw read counts for each Sample.

organism: Neotoma stephensi

source_name: foregut tissue

extract_protocol:
We collected a small section of the fornix ventricularis of the stomach (or the fundus of the stomach), which was immediately rinsed in ice-cold physiological saline buffer and placed in RNAlater solution. After 24 hours, the RNAlater solution was removed and tissues were frozen at -80°C. Total RNA from each animal was isolated from frozen tissue samples using Qiagen RNeasy kit according to manufacturer instructions (Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: fornix ventricularis of the stomach

tag: sex type

value: virgin female


title: BR_691

description: Barcode: ATGTCA


title: N. stephensi replicate 2

description:
Sample 711
PolyA RNA


title: N. stephensi replicate 1

description:
Sample 705
PolyA RNA


title: BR_688

description: Barcode: CTTGTA


title: PD-1 blockade-treated Chronic WT

status: Public on Jun 30 2017

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

description:
740253_BAYWTR0061
PD-1 blockade-treated Chronic_WT antigen-specific CD8 T cells
Whole genome bisulfite sequencing.

data_processing:
Basecalling was performed using Illumina Casava 1.7.
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by BSMAP.
CpGs were extracted by the methratio.py in the BSMAP package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bed: Bed-formatted files contain methylation ratio for each CpG.

molecule: genomic DNA

organism: Mus musculus

source_name: PD-1 blockade-treated Chronic WT CD8 cells

extract_protocol:
DNA was extracted followed by bisulfite treatment for library preparation.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer. The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: strain/background

tag: genotype/variation

value: WT

tag: infection

value: Chronic LCMV

tag: time point (post-infection)

value: Day 35

value: PD-L1 blockade

value: Antigen-specific CD8 T cells


title: Untreated Chronic WT

description:
740252_BAYWUN0061
Untreated Chronic_WT antigen-specific CD8 T cells
Whole genome bisulfite sequencing.

source_name: Untreated Chronic WT CD8 cells

tag: treatment

value: Mock


title: Acute Memory WT

description:
Arm_FM_bismarked
Day 35_Acute_WT antigen-specific CD8 T cells
Whole genome bisulfite sequencing.

source_name: Acute Memory WT CD8 cells

value: Acute LCMV


title: Calb.WT.BMW.T0_A

source_name: Wildtype C. albicans with normal media at T=0, replicate A

tag: genotype


title: Chronic Dnmt3a cKO#2

description:
D3acKO_GK_bismarked
Day 35_Chronic_cKO antigen-specific CD8 T cells#2
Whole genome bisulfite sequencing.

source_name: Chronic Dnmt3a cKO CD8 cells

value: Dnmt3a cKO


title: Chronic Dnmt3a cKO#1

description:
D3acKO_Tetramer_GK_D35
Day 35_Chronic_cKO antigen-specific CD8 T cells#1
Whole genome bisulfite sequencing.


title: Scer.WT.BMW.T0_A

source_name: Wildtype S. cerevisiae with normal media at T=0, replicate A


title: Scer.msn2/4.KCl.T20_A

source_name: S. cerevisiae msn2/4 knockout with KCl stress at T=20, replicate A

value: msn2/4 knockout


title: Chronic WT#2

description:
WT_GK_bismarked
Day 35_Chronic_WT antigen-specific CD8 T cells#2
Whole genome bisulfite sequencing.

source_name: Chronic WT CD8 cells


title: Chronic WT#1

description:
WT_Tetramer_GK_D35
Day 35_Chronic_WT antigen-specific CD8 T cells#1
Whole genome bisulfite sequencing.


title: Effector Dnmt3a ckO

description:
D8_D3acKO_GK_CL13
Day 8_Chronic_cKO antigen-specific CD8 T cells
Whole genome bisulfite sequencing.

source_name: Effector Dnmt3a ckO CD8 cells

value: Day 8


title: BR_436

description: Barcode: GTGAAA

source_name: whole body

value: Slavemaker - Before raid

value: whole body


title: Effector WT

description:
D8_WT_GK_CL13
Day 8_Chronic_WT antigen-specific CD8 T cells
Whole genome bisulfite sequencing.

source_name: Effector WT CD8 cells


title: Naïve WT

description:
WT_Naive_D35
Naïve WT CD8 T cells
Whole genome bisulfite sequencing.

source_name: Naïve WT CD8 cells

value: Naive CD8 T cells


title: s-958

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

description: uterus single cell RNA-Seq counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented by TPM (tags per million)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of each gene from each sample

source_name: uterus

extract_protocol:
Single cells were lysated, preamplified and library prepared accoring to the CEL-seq protocol (Science. 2014 Feb 14;343(6172):776-9.)
Single cells were lysated, preamplified and library prepared accoring to the CEL-seq protocol (Science. 2014 Feb 14;343(6172):776-9.)

treatment_protocol: 714 single CD326+ mice uterine epithelia from 5 developmental stages (post natal day 0, 7, 14, 28, 56)

tag: strain

value: ICR

value: uterus

tag: ages


title: s-960

description: uterus single cell RNA-Seq counts.txt


title: Naïve Dnmt3a cKO

description:
D3acKO_Naive_D35
Naïve cKO CD8 T cells
Whole genome bisulfite sequencing.

source_name: Naïve Dnmt3a cKO CD8 cells


title: s-959

description: uterus single cell RNA-Seq counts.txt


title: s-957

description: uterus single cell RNA-Seq counts.txt


title: s-956

description: uterus single cell RNA-Seq counts.txt


title: s-954

description: uterus single cell RNA-Seq counts.txt


title: BR_689

description: Barcode: AGTCAA

value: Host - Before raid


title: s-955

description: uterus single cell RNA-Seq counts.txt


title: s-953

description: uterus single cell RNA-Seq counts.txt


title: s-952

description: uterus single cell RNA-Seq counts.txt


title: s-951

description: uterus single cell RNA-Seq counts.txt


title: s-949

description: uterus single cell RNA-Seq counts.txt


title: s-950

description: uterus single cell RNA-Seq counts.txt


title: s-945

description: uterus single cell RNA-Seq counts.txt


title: s-943

description: uterus single cell RNA-Seq counts.txt


title: s-944

description: uterus single cell RNA-Seq counts.txt


title: s-942

description: uterus single cell RNA-Seq counts.txt


title: s-941

description: uterus single cell RNA-Seq counts.txt


title: s-946

description: uterus single cell RNA-Seq counts.txt


title: s-939

description: uterus single cell RNA-Seq counts.txt


title: s-938

description: uterus single cell RNA-Seq counts.txt


title: s-937

description: uterus single cell RNA-Seq counts.txt


title: s-934

description: uterus single cell RNA-Seq counts.txt


title: s-928

description: uterus single cell RNA-Seq counts.txt


title: s-933

description: uterus single cell RNA-Seq counts.txt


title: s-930

description: uterus single cell RNA-Seq counts.txt


title: s-936

description: uterus single cell RNA-Seq counts.txt


title: s-947

description: uterus single cell RNA-Seq counts.txt


title: s-926

description: uterus single cell RNA-Seq counts.txt


title: s-923

description: uterus single cell RNA-Seq counts.txt


title: s-925

description: uterus single cell RNA-Seq counts.txt


title: s-921

description: uterus single cell RNA-Seq counts.txt


title: s-920

description: uterus single cell RNA-Seq counts.txt


title: s-948

description: uterus single cell RNA-Seq counts.txt


title: Fibroblasts infected Human and Candida no T cells BR2

description:
3D skin models were infected with C. albicans for 24 h, then cell layers were separated mechanically and frozen down in liquid nitrogen.
akue_29_br3

source_name: human skin model infected with C. albicans

value: S1F fibroblasts / C. albicans SC5314

value: Fibroblasts + Keratinocytes + C. albicans


title: s-922

description: uterus single cell RNA-Seq counts.txt


title: s-927

description: uterus single cell RNA-Seq counts.txt


title: s-919

description: uterus single cell RNA-Seq counts.txt


title: s-918

description: uterus single cell RNA-Seq counts.txt


title: s-917

description: uterus single cell RNA-Seq counts.txt


title: s-916

description: uterus single cell RNA-Seq counts.txt


title: s-929

description: uterus single cell RNA-Seq counts.txt


title: s-913

description: uterus single cell RNA-Seq counts.txt


title: s-912

description: uterus single cell RNA-Seq counts.txt


title: s-911

description: uterus single cell RNA-Seq counts.txt


title: s-914

description: uterus single cell RNA-Seq counts.txt


title: s-940

description: uterus single cell RNA-Seq counts.txt


title: s-935

description: uterus single cell RNA-Seq counts.txt


title: s-910

description: uterus single cell RNA-Seq counts.txt


title: s-909

description: uterus single cell RNA-Seq counts.txt


title: s-932

description: uterus single cell RNA-Seq counts.txt


title: s-905

description: uterus single cell RNA-Seq counts.txt


title: s-906

description: uterus single cell RNA-Seq counts.txt


title: s-904

description: uterus single cell RNA-Seq counts.txt


title: s-903

description: uterus single cell RNA-Seq counts.txt


title: s-908

description: uterus single cell RNA-Seq counts.txt


title: s-899

description: uterus single cell RNA-Seq counts.txt


title: s-900

description: uterus single cell RNA-Seq counts.txt


title: s-902

description: uterus single cell RNA-Seq counts.txt


title: s-901

description: uterus single cell RNA-Seq counts.txt


title: s-895

description: uterus single cell RNA-Seq counts.txt


title: s-897

description: uterus single cell RNA-Seq counts.txt


title: s-893

description: uterus single cell RNA-Seq counts.txt


title: s-891

description: uterus single cell RNA-Seq counts.txt


title: s-890

description: uterus single cell RNA-Seq counts.txt


title: s-889

description: uterus single cell RNA-Seq counts.txt


title: s-887

description: uterus single cell RNA-Seq counts.txt


title: s-892

description: uterus single cell RNA-Seq counts.txt


title: s-886

description: uterus single cell RNA-Seq counts.txt


title: s-888

description: uterus single cell RNA-Seq counts.txt


title: s-884

description: uterus single cell RNA-Seq counts.txt


title: s-894

description: uterus single cell RNA-Seq counts.txt


title: s-885

description: uterus single cell RNA-Seq counts.txt


title: s-882

description: uterus single cell RNA-Seq counts.txt


title: s-880

description: uterus single cell RNA-Seq counts.txt


title: s-907

description: uterus single cell RNA-Seq counts.txt


title: s-879

description: uterus single cell RNA-Seq counts.txt


title: s-883

description: uterus single cell RNA-Seq counts.txt


title: s-877

description: uterus single cell RNA-Seq counts.txt


title: s-876

description: uterus single cell RNA-Seq counts.txt


title: s-875

description: uterus single cell RNA-Seq counts.txt


title: s-874

description: uterus single cell RNA-Seq counts.txt


title: s-873

description: uterus single cell RNA-Seq counts.txt


title: s-872

description: uterus single cell RNA-Seq counts.txt


title: s-878

description: uterus single cell RNA-Seq counts.txt


title: s-898

description: uterus single cell RNA-Seq counts.txt


title: s-896

description: uterus single cell RNA-Seq counts.txt


title: s-868

description: uterus single cell RNA-Seq counts.txt


title: s-867

description: uterus single cell RNA-Seq counts.txt


title: s-866

description: uterus single cell RNA-Seq counts.txt


title: s-865

description: uterus single cell RNA-Seq counts.txt


title: s-860

description: uterus single cell RNA-Seq counts.txt


title: s-858

description: uterus single cell RNA-Seq counts.txt


title: s-863

description: uterus single cell RNA-Seq counts.txt


title: s-857

description: uterus single cell RNA-Seq counts.txt


title: s-856

description: uterus single cell RNA-Seq counts.txt


title: s-861

description: uterus single cell RNA-Seq counts.txt


title: s-852

description: uterus single cell RNA-Seq counts.txt


title: s-841

description: uterus single cell RNA-Seq counts.txt


title: s-844

description: uterus single cell RNA-Seq counts.txt


title: s-840

description: uterus single cell RNA-Seq counts.txt


title: s-853

description: uterus single cell RNA-Seq counts.txt


title: s-847

description: uterus single cell RNA-Seq counts.txt


title: s-838

description: uterus single cell RNA-Seq counts.txt


title: s-843

description: uterus single cell RNA-Seq counts.txt


title: s-830

description: uterus single cell RNA-Seq counts.txt


title: s-870

description: uterus single cell RNA-Seq counts.txt


title: s-850

description: uterus single cell RNA-Seq counts.txt


title: s-871

description: uterus single cell RNA-Seq counts.txt


title: s-834

description: uterus single cell RNA-Seq counts.txt


title: s-869

description: uterus single cell RNA-Seq counts.txt


title: s-828

description: uterus single cell RNA-Seq counts.txt


title: s-829

description: uterus single cell RNA-Seq counts.txt


title: s-827

description: uterus single cell RNA-Seq counts.txt


title: s-825

description: uterus single cell RNA-Seq counts.txt


title: s-824

description: uterus single cell RNA-Seq counts.txt


title: s-826

description: uterus single cell RNA-Seq counts.txt


title: s-821

description: uterus single cell RNA-Seq counts.txt


title: s-820

description: uterus single cell RNA-Seq counts.txt


title: s-819

description: uterus single cell RNA-Seq counts.txt


title: s-810

description: uterus single cell RNA-Seq counts.txt


title: s-811

description: uterus single cell RNA-Seq counts.txt


title: s-818

description: uterus single cell RNA-Seq counts.txt


title: s-816

description: uterus single cell RNA-Seq counts.txt


title: s-812

description: uterus single cell RNA-Seq counts.txt


title: s-807

description: uterus single cell RNA-Seq counts.txt


title: s-804

description: uterus single cell RNA-Seq counts.txt


title: s-800

description: uterus single cell RNA-Seq counts.txt


title: s-801

description: uterus single cell RNA-Seq counts.txt


title: s-806

description: uterus single cell RNA-Seq counts.txt


title: s-805

description: uterus single cell RNA-Seq counts.txt


title: s-803

description: uterus single cell RNA-Seq counts.txt


title: s-799

description: uterus single cell RNA-Seq counts.txt


title: s-797

description: uterus single cell RNA-Seq counts.txt


title: s-798

description: uterus single cell RNA-Seq counts.txt


title: s-796

description: uterus single cell RNA-Seq counts.txt


title: s-794

description: uterus single cell RNA-Seq counts.txt


title: s-795

description: uterus single cell RNA-Seq counts.txt


title: s-787

description: uterus single cell RNA-Seq counts.txt


title: s-773

description: uterus single cell RNA-Seq counts.txt


title: s-784

description: uterus single cell RNA-Seq counts.txt


title: s-781

description: uterus single cell RNA-Seq counts.txt


title: s-775

description: uterus single cell RNA-Seq counts.txt


title: s-779

description: uterus single cell RNA-Seq counts.txt


title: s-789

description: uterus single cell RNA-Seq counts.txt


title: s-792

description: uterus single cell RNA-Seq counts.txt


title: s-771

description: uterus single cell RNA-Seq counts.txt


title: s-777

description: uterus single cell RNA-Seq counts.txt


title: s-768

description: uterus single cell RNA-Seq counts.txt


title: s-767

description: uterus single cell RNA-Seq counts.txt


title: s-758

description: uterus single cell RNA-Seq counts.txt


title: s-759

description: uterus single cell RNA-Seq counts.txt


title: s-772

description: uterus single cell RNA-Seq counts.txt


title: s-752

description: uterus single cell RNA-Seq counts.txt


title: s-757

description: uterus single cell RNA-Seq counts.txt


title: s-837

description: uterus single cell RNA-Seq counts.txt


title: s-743

description: uterus single cell RNA-Seq counts.txt


title: s-747

description: uterus single cell RNA-Seq counts.txt


title: s-744

description: uterus single cell RNA-Seq counts.txt


title: s-745

description: uterus single cell RNA-Seq counts.txt


title: s-751

description: uterus single cell RNA-Seq counts.txt


title: s-741

description: uterus single cell RNA-Seq counts.txt


title: s-742

description: uterus single cell RNA-Seq counts.txt


title: s-739

description: uterus single cell RNA-Seq counts.txt


title: s-736

description: uterus single cell RNA-Seq counts.txt


title: s-727

description: uterus single cell RNA-Seq counts.txt


title: s-735

description: uterus single cell RNA-Seq counts.txt


title: s-721

description: uterus single cell RNA-Seq counts.txt


title: s-722

description: uterus single cell RNA-Seq counts.txt


title: s-714

description: uterus single cell RNA-Seq counts.txt


title: s-733

description: uterus single cell RNA-Seq counts.txt


title: s-713

description: uterus single cell RNA-Seq counts.txt


title: s-720

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title: s-142

description: uterus single cell RNA-Seq counts.txt


title: s-139

description: uterus single cell RNA-Seq counts.txt


title: s-140

description: uterus single cell RNA-Seq counts.txt


title: s-165

description: uterus single cell RNA-Seq counts.txt


title: s-163

description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


title: s-130

description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


title: s-125

description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


title: s-136

description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


title: s-105

description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


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description: uterus single cell RNA-Seq counts.txt


title: s-107

description: uterus single cell RNA-Seq counts.txt


title: s-102

description: uterus single cell RNA-Seq counts.txt


title: s-97

description: uterus single cell RNA-Seq counts.txt


title: s-99

description: uterus single cell RNA-Seq counts.txt


title: s-94

description: uterus single cell RNA-Seq counts.txt


title: s-91

description: uterus single cell RNA-Seq counts.txt


title: s-95

description: uterus single cell RNA-Seq counts.txt


title: s-92

description: uterus single cell RNA-Seq counts.txt


title: s-121

description: uterus single cell RNA-Seq counts.txt


title: s-88

description: uterus single cell RNA-Seq counts.txt


title: s-85

description: uterus single cell RNA-Seq counts.txt


title: s-84

description: uterus single cell RNA-Seq counts.txt


title: s-83

description: uterus single cell RNA-Seq counts.txt


title: s-87

description: uterus single cell RNA-Seq counts.txt


title: s-82

description: uterus single cell RNA-Seq counts.txt


title: s-86

description: uterus single cell RNA-Seq counts.txt


title: s-81

description: uterus single cell RNA-Seq counts.txt


title: s-103

description: uterus single cell RNA-Seq counts.txt


title: s-77

description: uterus single cell RNA-Seq counts.txt


title: s-80

description: uterus single cell RNA-Seq counts.txt


title: s-76

description: uterus single cell RNA-Seq counts.txt


title: s-78

description: uterus single cell RNA-Seq counts.txt


title: s-75

description: uterus single cell RNA-Seq counts.txt


title: s-93

description: uterus single cell RNA-Seq counts.txt


title: s-74

description: uterus single cell RNA-Seq counts.txt


title: s-73

description: uterus single cell RNA-Seq counts.txt


title: s-72

description: uterus single cell RNA-Seq counts.txt


title: Hop GLKD Total Small RNA

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

data_processing:
Raw small RNA sequencing reads were processed by cutadapt to remove the 3’ sequencing adapter (TGGAATTCTCGGGTGCCAAGG). All processed reads smaller than 18nt and also the reads without sequencing adapter were discarded. Reads were then depleted of rRNA reads and then aligned to dm3 genome using Bowtie. rRNA read mapping allowed 2 mismatches and genomic alignment allowed no mismatches. Only reads that matched 100% to the genome were collected and further analyzed. Processed reads were then collapsed using perl script TBr2_collapse.pl available as a part of NGS Toolbox. Normalization factor was calculated based on the number of uniquely mapping genomic reads. Reads were then mapped to transposon consensus sequences using sRNAmapper using default parameters. Under default parameters, sRNAmapper does not allow any mismatch in the first 18nt from 5’end of piRNAs and at most allows 1 mismatch in the rest of the sequence. Size distribution, orientation and nucleotide composition of such aligned reads were analyzed using perl script checkmap. Output from checkmap was then exported to Apple Numbers and plotted.  Ping Pong signature was analyzed using perl script TBr2_pingpong.pl. TBr2_pingpong.pl performs Ping Pong signature analysis and Z-score calculation in the same way as described in Zhang Z et al (Mol Cell 44, 572-584). Output of TBr2_pingpong.pl was exported to Apple Numbers and plotted.
Genome_build: dm3
Supplementary_files_format_and_content: Tab delimited text files contianing featurecount. Note that 3' adapter is already trimmed.

organism: Drosophila melanogaster

source_name: Ovary

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

tag: developmental stage

value: Adult


title: s-90

description: uterus single cell RNA-Seq counts.txt


title: nos.Luc Total Small RNA


title: Hop GLKD Total mRNA Biological Repeat 2

data_processing:
RNA fragments were aligned to dm3 transcriptome and transposon consensus sequences using Bowtie 2 and quantified using RSEM.
Differential expression analysis was conducted using EBSeq
Genome_build: dm3
Supplementary_files_format_and_content: excel files with results from RSEM. Includes FPKM values.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Ambion) from 10 pairs of manually dissected ovaries and stored at -80°C until use. Two biological repeats of nos.Luc (Control) and Hop GLKD were used. RNA integrity was verified on an Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA). 100-200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA). Please note that polyA containing RNA was first purfied prior to the library preparation step. Single end sequencing (1X50 cycles) was performed on an Illumina HiSeq2500. Sequencing was performed at Hollings Cancer Center Genomics Core Lab at MUSC.
RNA libraries were prepared using TruSeq RNA Sample Prep Kit after selecting for polyA RNA

value: ovary

value: Hop germline knockdown


title: s-69

description: uterus single cell RNA-Seq counts.txt


title: Hop GLKD Total mRNA Biological Repeat 1


title: s-89

description: uterus single cell RNA-Seq counts.txt


title: s-71

description: uterus single cell RNA-Seq counts.txt


title: s-68

description: uterus single cell RNA-Seq counts.txt


title: nos.Luc Total mRNA Biological Repeat 2

value: control


title: s-65

description: uterus single cell RNA-Seq counts.txt


title: s-64

description: uterus single cell RNA-Seq counts.txt


title: s-66

description: uterus single cell RNA-Seq counts.txt


title: s-62

description: uterus single cell RNA-Seq counts.txt


title: nos.Luc Total mRNA Biological Repeat 1


title: s-59

description: uterus single cell RNA-Seq counts.txt


title: s-61

description: uterus single cell RNA-Seq counts.txt


title: s-57

description: uterus single cell RNA-Seq counts.txt


title: s-98

description: uterus single cell RNA-Seq counts.txt


title: s-56

description: uterus single cell RNA-Seq counts.txt


title: s-60

description: uterus single cell RNA-Seq counts.txt


title: s-54

description: uterus single cell RNA-Seq counts.txt


title: s-53

description: uterus single cell RNA-Seq counts.txt


title: s-55

description: uterus single cell RNA-Seq counts.txt


title: s-67

description: uterus single cell RNA-Seq counts.txt


title: s-70

description: uterus single cell RNA-Seq counts.txt


title: s-48

description: uterus single cell RNA-Seq counts.txt


title: s-50

description: uterus single cell RNA-Seq counts.txt


title: s-47

description: uterus single cell RNA-Seq counts.txt


title: s-58

description: uterus single cell RNA-Seq counts.txt


title: s-51

description: uterus single cell RNA-Seq counts.txt


title: s-45

description: uterus single cell RNA-Seq counts.txt


title: s-44

description: uterus single cell RNA-Seq counts.txt


title: s-42

description: uterus single cell RNA-Seq counts.txt


title: s-43

description: uterus single cell RNA-Seq counts.txt


title: s-41

description: uterus single cell RNA-Seq counts.txt


title: s-40

description: uterus single cell RNA-Seq counts.txt


title: s-36

description: uterus single cell RNA-Seq counts.txt


title: s-63

description: uterus single cell RNA-Seq counts.txt


title: s-35

description: uterus single cell RNA-Seq counts.txt


title: s-34

description: uterus single cell RNA-Seq counts.txt


title: s-38

description: uterus single cell RNA-Seq counts.txt


title: s-29

description: uterus single cell RNA-Seq counts.txt


title: s-52

description: uterus single cell RNA-Seq counts.txt


title: s-31

description: uterus single cell RNA-Seq counts.txt


title: s-30

description: uterus single cell RNA-Seq counts.txt


title: s-32

description: uterus single cell RNA-Seq counts.txt


title: s-33

description: uterus single cell RNA-Seq counts.txt


title: s-24

description: uterus single cell RNA-Seq counts.txt


title: s-25

description: uterus single cell RNA-Seq counts.txt


title: s-161

description: uterus single cell RNA-Seq counts.txt


title: s-49

description: uterus single cell RNA-Seq counts.txt


title: s-23

description: uterus single cell RNA-Seq counts.txt


title: s-21

description: uterus single cell RNA-Seq counts.txt


title: s-26

description: uterus single cell RNA-Seq counts.txt


title: s-22

description: uterus single cell RNA-Seq counts.txt


title: s-20

description: uterus single cell RNA-Seq counts.txt


title: s-19

description: uterus single cell RNA-Seq counts.txt


title: s-18

description: uterus single cell RNA-Seq counts.txt


title: s-15

description: uterus single cell RNA-Seq counts.txt


title: s-16

description: uterus single cell RNA-Seq counts.txt


title: s-14

description: uterus single cell RNA-Seq counts.txt


title: s-12

description: uterus single cell RNA-Seq counts.txt


title: s-13

description: uterus single cell RNA-Seq counts.txt


title: s-9

description: uterus single cell RNA-Seq counts.txt


title: s-8

description: uterus single cell RNA-Seq counts.txt


title: s-10

description: uterus single cell RNA-Seq counts.txt


title: s-6

description: uterus single cell RNA-Seq counts.txt


title: s-28

description: uterus single cell RNA-Seq counts.txt


title: s-5

description: uterus single cell RNA-Seq counts.txt


title: s-7

description: uterus single cell RNA-Seq counts.txt


title: s-3

description: uterus single cell RNA-Seq counts.txt


title: s-27

description: uterus single cell RNA-Seq counts.txt


title: Developing_Root_Cortex

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description:
Gene expression in Developing Root Cortex
DRC

data_processing:
We assembled the transcriptome for P. pinaster from the 454 sequencing reads by using Newbler (v2.8.1). Before feeding reads to Newbler, we removed reads with adapter sequences and reads shorter than 75bp through seqclean. Newbler then assembled the remaining rest reads in six rounds for P. pinaster, until all of the over-represented sequences were removed. CD-HIT-EST (Weizhong Li & Godzik 2006) then clustered the Newbler assemblies in each isogroup, which stands for unique transcriptional locus in Newbler assembly result, and selected the longest transcript, which had to be ≥ 150 bp, to represent each isogroup.
For the read mapping the raw data was first checked for quality using the fastqc software.
Based on examination of the output quality plots it was decided to clip off the first 35bp of each read. To that end, we used the FastX toolkit (fastx_trimmer).
Next the reads where filtered for overall quality using fastq_quality_filter with a minimum Q-score of 30 and minimum remaining length of 60%.
The remaining reads where subsequently used for read mapping with the BWA software (default parameter settings) against the reference transcriptome composed by  206,574 contigs.
Contigs with at least 25 reads in a sample were conserved, the rest of contigs were filterd. Filtering and normalization were done using edgeR package for R.
Gene co-expression analyses were made using the WGCNA package for R.
Genome_build: Reference transcriptome composed by 206,574 contigs from PROCOGEN and SUSTAINPINE pojects and Genbank (http://www.bmbq.uma.es/fmp/Datos/ALL_Procogen.fasta)
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample (AM, EN, YNM, YNV, CM, CV, HC, HV, HP, RC, RV, DRC, DRV and RM).The column ID_REF is the sequence identifier.

organism: Pinus pinaster

source_name: Developing Root Cortex

growth_protocol: Maritime pine seeds (Pinus pinaster Ait.) from the Oria provenance were provided by Centro de Recursos Genéticos Forestales “El Serranillo” (Ministerio de Medio Ambiente y Medio Rural y Marino, Spain). Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were cultivated in a growth room at 25˚C and 50/70% relative humidity with a 16/8-h photoperiod and watered twice a week with distilled water. Fourteen days after imbibitions, seedlings were individually transferred to a 0.2-L pot with soil and watered twice a week with distilled water. The seedlings were harvested 1 month after the emergence of the shoots over the vermiculite.

extract_protocol:
The Laser Capture Microdissection (LCM) procedure was carried out as previously described in Cañas et al. (Tree Physiol. 34:1278-1288). The microdissection samples were placed into the caps of 0.5 mL tubes containing 10 L lysis buffer from the RNAqueous-Micro RNA Isolation Kit (Ambion, USA). Before RNA extraction all the samples were placed at -80ºC. All the RNA extractions from the microdissection of the samples were made using the standard-volume protocol (non-LCM) for the RNAqueous-Micro RNA Isolation Kit (Ambion, USA). RNA quality and first quantification was assessed using the RNA Pico Assay for the 2100 Bioanalyzer (Agilent, USA). The RNA samples with a RNA integrity number (RIN) higher than 7 were used for the subsequent mRNA amplification and 454 pyrosequencing.
As the amounts of RNA isolated form LCM samples were not enough for 454 pyrosequencing, a previous cDNA synthesis and amplification was made using the Conifer RNA Amplification (CRA+) protocol described in  Cañas et al. (Tree Physiol. 34:1278-1288). Transcriptome sequencing was performed at the Universidad de Málaga ultrasequencing facility using the GS-FLX+ platform with a GS FLX Titanium kit, Roche Applied Sciences (Indianapolis, IN, USA). Each sample was run in one half of a 454 PicoTiterPlate following the manufacturer’s sequencing protocol. The quantity of the cDNA libraries was determined using the Quant-iT™ PicoGreen® dsDNA Kit (Invitrogen, Paisley, UK). The quality of the cDNA libraries was determined using the Agilent High Sensitivity DNA Kit in the 2100 Bioanalyzer (Agilent, CA, USA). The runs were analysed using the Roche GS-FLX+ software.

treatment_protocol: The seedlings were cut and tissue sections of 5 mm were mounted in a specimen holder with optimal cutting temperature (OCT) embedding medium (Tissue-Tek, USA) and snap-frozen in liquid nitrogen for cryostat sectioning. The frozen samples were stored at -80ºC until use.

value: Developing Root Cortex

tag: provenance

value: Oria

value: 1 month-old seedling

tag: culture

value: In soil

tag: culture place

value: Culture chamber at Universidad de Malaga (Malaga, Spain)


title: Developing_Root_Vascular

description:
Gene expression in Developing Root Vascular
DRV

source_name: Developing Root Vascular

value: Developing Root Vascular


title: Root_Meristem

description:
Gene expression in Root Meristem
RM

source_name: Root Meristem

value: Root Meristem