title: DF78_11dpi-BR2

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Barcode adaptors from the RNA sequence reads were clipped and low quality reads were removed (read quality < 30) using the Trimmomatic software (Bolger et al., 2014).
RNA sequence reads passing quality filter were aligned to the B. napus genome (v4.1, Chalhoub et al. 2014) using Tophat2 of the Trapnell cufflinks package (Trapnell et al., 2012). Tophat2 alignment was performed in high-sensitivity mode and used B. napus reference annotation v5.0 as a guide (Chalhoub et al., 2014).
Identification of novel transcripts was performed using cufflinks v2.2.1 (Trapnell et al., 2012) and transcript sequences were extracted from this annotation using BedTools.
Cuffquant, CuffNorm and Cuffdiff were used to generate normalized counts in FPKM and to identify differentially expressed genes (pooled dispersion method). Genes were considered significantly differentially expressed with a corrected p-value of < 0.05 (false discovery rate = 0.05).
Genome_build: B. napus v. 4.1
Supplementary_files_format_and_content: excel file with FPKM.

organism:
Brassica napus
Plenodomus lingam

source_name: Cotyledon

growth_protocol: Universally susceptible B. napus cv. Westar and advanced B. napus breeding line DF78 (Rlm3, LepR1) were inoculated with L. maculans isolate D3 (AvrLm5, AvrLepR1; Dr. A. Van de Wouw, University of Melbourne). Canola seedlings were grown in controlled environments with a 16-h photoperiod (16ºC dark, 21 ºC light). Plants were grown in Sunshine mix #4 (SunGro Horticulture, www.sungro.com). Fungal inocu

extract_protocol:
RNA was collected from three biological replicates of infected and mock inoculated B. napus cotyledons at 0, 3, 7, and 11 dpi. Total RNA was isolated by using PureLink® Plant RNA Reagent (Ambion) and treated with TURBO DNA-free™ Kit (Ambion) according to the manufacturer’s instructions. RNA quality and integrity was measured using the 2100 Bioanalyzer (Agilent Technologies) with the Agilent 2100 PicoChip.
RNA-sequencing libraries were prepared according to alternative HTR protocol (C2) established by R. Kumar et al. (2012) with the exception of library PCR enrichment that was carried out using 11 PCR cycles. RNA sequencing libraries were validated using the Agilent Bioanalyzer DNA chips (Agilent Technologies) and quantified using the Quant-iT dsDNA Assay kit (ThermoFisher Scientific).

treatment_protocol: Fungal inoculum was prepared according to Zhang et al. (2015). Seven day old seedlings of cv. Westar and line DF78 were point-inoculated with 10 µL of D3 pycnidiospore suspension (2 ×107 pycnidiospores mL-1) or sterilized distilled water (mock).

value: DF78 (LepR1)

tag: inoculation status

value: 11 days post inoculation

tag: pathogen

value: Leptosphaeria maculans

value: Cotyledon


title: DF78_11dpi-BR1

status: Public on Apr 01 2016

type: SRA

library_source: transcriptomic

molecule: polyA RNA

tag: genotype

tag: tissue


title: Vehicle (Nseqveh83)

city: Chapel Hill

first: Mark

last: Zylka

state: NC

address: 5109D Neuroscience Research Building

country: USA

institute: University of North Carolina - Chapel Hill

data_processing:
RNA-seq reads were filtered using TagDust
Reads were aligned to the reference mouse genome (mm9) with TopHat using default parameters
Reads aligning to rRNA genes were removed
Transcript abundance was estimated by computing RPKM using RefSeq gene models aggregated by gene symbol
Genome_build: mm9
Supplementary_files_format_and_content: RPKM for all RefSeq genes and all samples were filtered such that a given gene had >90% of samples with RPKM >0 and gene length exceeded 500 bp.  RPKMs were then log10 transformed, quantile-normalized, median-centered, and subtle batch effects were removed using a mixed model ANOVA

organism: Mus musculus

source_name: cultured cortical neurons

growth_protocol: Primary mouse cortical neuron cultures were prepared as previously described from embryonic day 15 (E15) pregnant C57BL/6J (Cat. #000664, Jackson) dams crossed to CAST/EiJ (Cat. #000928, Jackson) males{King, 2013 #1414}.  Hybrid cultures are thought to better model genetic variation associated with human populations{French, 2015 #1509}.  Dissociated cells were placed in multiwell plates coated with poly-D-lysine (0.1 mg ml−1) in Neurobasal medium (Life Technologies) containing 5% FBS (Gibco), B27 (17504-044, Invitrogen), Antibiotic-Antimycotic (15240-062, Invitrogen), and GlutaMAX (35050-061, Invitrogen).  At days in vitro (DIV) 3 a half medium change was performed with feeding medium identical to the plating medium except that we omitted FBS and included 4.84 μg ml−1 uridine 5'-triphosphate (U6625, Sigma-Aldrich) and 2.46 μg ml−1 5-fluoro-2′-deoxyuridine (F0503, Sigma-Aldrich) to inhibit mitosis in dividing cells.

extract_protocol:
RNA was isolated with RNeasy plus mini kit (Cat. #74134, Qiagen).  RNA yield and quality was determined with a Nanodrop 1000 Spectrophotometer (Thermo Scientific).  Samples were further assessed for quality using either an Agilent Bioanalyzer 2100 or TapeStation 2200 to obtain a RNA integrity number (RIN).  RIN values exceeding 7 were used for sequencing.
RNA samples were used to generate and barcode cDNA libraries using the TruSeq RNA Library Preparation Kit at the UNC High Throughput Sequencing Facility.

treatment_protocol: Cultures were treated with the non-cytotoxic dose of each chemical on DIV 7 for 24 hours in 12-well plates at a density of 5 x 10^5 cells per well.

tag: cell type

value: cortical neurons

tag: developmental stage

value: embryonic day E15

tag: strain

value: CAST x C57BL6


title: DF78_7dpi-BR3

value: 7 days post inoculation


title: DF78_7dpi-BR2


title: Vehicle (Nseqveh82)


title: Sulforaphane 10uM + Fenamidone 10uM Rep3

description: processed data file: SULF10-FENAM-VS-VEH-FENAM_rawCounts_matrix.txt

source_name: Cortical neurons

treatment_protocol: Cultures were treated with the non-cytotoxic dose of each chemical on DIV 7 for 24 hours in 12-well plates at a density of 5 x 105 cells per well.


title: Zoxamide 1uM (Nseq524)


title: Vinclozolin 10uM (Nseq523)


title: Vehicle (Nseqveh81)


title: Vehicle (Nseqveh71)


title: DF78_11dpi-BR3


title: Vehicle (Nseqveh64)


title: DF78_7dpi-BR1


title: Vehicle (Nseqveh85)


title: Vehicle (Nseqveh62)


title: Vehicle (Nseqveh63)


title: Vehicle (Nseqveh84)


title: DF78_3dpi-BR2

value: 3 days post inoculation


title: DF78_3dpi-BR1


title: DF78_3dpi-BR3


title: Westar_11dpi-BR3

value: Westar


title: Vehicle (Nseqveh6)


title: Vehicle (Nseqveh54)


title: Vehicle (Nseqveh55)


title: Westar_11dpi-BR1


title: Westar_11dpi-BR2


title: Vehicle (Nseqveh5)


title: Vehicle (Nseqveh44)


title: Vehicle (Nseqveh42)


title: Vehicle (Nseqveh4)


title: Westar_3dpi-BR1


title: Vehicle (Nseqveh41)


title: Vehicle (Nseqveh40)


title: Westar_3dpi-BR2


title: Vehicle (Nseqveh43)


title: Westar_3dpi-BR3


title: Vehicle (Nseqveh29)


title: Vehicle (Nseqveh39)


title: Vehicle (Nseqveh38)


title: Vehicle (Nseqveh3)


title: Vehicle (Nseqveh28)


title: Westar_7dpi-BR3


title: Westar_7dpi-BR2


title: Vehicle (Nseqveh124)


title: Vehicle (Nseqveh123)


title: Vehicle (Nseqveh110)


title: Vehicle (Nseqveh112)


title: Vehicle (Nseqveh27)


title: Westar_7dpi-BR1


title: Vehicle (Nseqveh109)


title: Vehicle (Nseqveh122)


title: Vehicle (Nseqveh114)


title: Vehicle (Nseqveh121)


title: Vehicle (Nseqveh117)


title: Vehicle (Nseqveh116)


title: Vehicle (Nseqveh118)


title: Vehicle (Nseqveh113)


title: Vehicle (Nseqveh107)


title: Vehicle (Nseqveh106)


title: Vehicle (Nseqveh108)


title: Vehicle (Nseqveh102)


title: Vehicle (Nseq641)


title: NCYC3290 YPD REP2

city: Madison

first: Maria

middle: Isabel

last: Sardi

state: Wisconsin

address: 425 Henry Mall

department: Microbiology

institute: University of Wisconsin-Madison

data_processing:
Sequencing reads were processed with Trimmomatic version 0.30
Trimmed sequencing reads were mapped to the S288c reference V64-1-1, using Bowtie2
HTseq version 0.6.0 was used to sum read counts per gene
Sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM) method.
Normalized data was transformed to log 2 values
Supplementary_files_format_and_content: Tab-delimited text file includes normalized log 2 values for each gene in each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: Strains were grown in the specified media (YPD, SynH and SynH -HT) for 3 generations to OD600 ~0.5

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with TruSeq Stranded Total RNA (Human/Mouse/Rat) kit (Illumina)
Library was contructed with TruSeq Stranded Total RNA (Human/Mouse/Rat) kit

tag: lab or wild strain

value: wild

tag: media (ypd, synh -hts, synh)

value: YPD

tag: resistance to synh

value: medium resistance


title: NCYC3290 SynH REP1

value: SynH


title: NCYC3290 SynH -HT REP2

value: SynH -HTs


title: Vehicle (Nseqveh104)


title: Vehicle (Nseqveh105)


title: Triticonazole 10uM (Nseq504)


title: Trifluralin 10uM (Nseq637)


title: NCYC3290 SynH -HT REP1


title: NCYC3290 SynH REP2


title: NCYC3290 YPD REP1


title: Triflusulfuron 10uM (Nseq44)


title: Triflumizole 10uM (Nseq649)


title: Trifloxysulfuron-sodium 10uM (Nseq503)


title: YPS128 SynH REP1

value: resistant


title: Trifloxystrobin 10uM (Nseq435)


title: YPS128 SynH -HT REP2


title: Triclosan 10uM (Nseq276)


title: Triclopyr 10uM (Nseq502)


title: YPS128 SynH -HT REP1


title: YPS128 YPD REP2


title: Trichlorfon 10uM (Nseq501)


title: K11 SynH REP2

value: sensitive


title: Tribenuron 10uM (Nseq30)


title: K11 SynH REP1


title: Triadimenol 10uM (Nseq647)


title: K11 SynH -HT REP2


title: K11 YPD REP2


title: Triadimefon 10uM (Nseq499)


title: Topotecan 0.3uM (Nseq678)


title: K11 YPD REP1


title: Tralkoxydim 10uM (Nseq498)


title: Topotecan 0.3uM (Nseq661)


title: K11 SynH -HT REP1


title: Topotecan 0.3uM (Nseq638)


title: YPS128 SynH REP2


title: Y7568 SynH REP2


title: Topotecan 0.3uM (Nseq628)


title: Y7568 SynH REP1


title: YPS128 YPD REP1


title: Y7568 SynH -HT REP1


title: Tribufos 10uM (Nseq648)


title: UWO.S05.22-7 SynH REP2


title: Y7568 YPD REP1


title: Y7568 YPD REP2


title: UWO.S05.22-7 SynH REP1


title: Tri-allate 10uM (Nseq500)


title: UWO.S05.22-7 SynH -HT REP2


title: Topotecan 0.3uM (Nseq597)


title: UWO.S05.22-7 SynH -HT REP1


title: Topotecan 0.3uM (Nseq558)


title: Topotecan 0.3uM (Nseq64)


title: Topotecan 0.3uM (Nseq541)


title: UWO.S05.22-7 YPD REP2


title: NCYC361 SynHv REP1


title: NCYC361 SynHv REP2


title: UWO.S05.22-7 YPD REP1


title: Topotecan 0.3uM (Nseq526)


title: NCYC361 SynH -HTs REP2


title: Topotecan 0.3uM (Nseq505)


title: Topotecan 0.3uM (Nseq522)


title: NCYC361 YPD REP2


title: Topotecan 0.3uM (Nseq484)


title: Topotecan 0.3uM (Nseq607)


title: Topotecan 0.3uM (Nseq494)


title: Topotecan 0.3uM (Nseq426)


title: Topotecan 0.3uM (Nseq42)


title: Topotecan 0.3uM (Nseq584)


title: Topotecan 0.3uM (Nseq381)


title: Topotecan 0.3uM (Nseq365)


title: Topotecan 0.3uM (Nseq31)


title: Topotecan 0.3uM (Nseq372)


title: Topotecan 0.3uM (Nseq306)


title: Topotecan 0.3uM (Nseq295)


title: Topotecan 0.3uM (Nseq275)


title: Topotecan 0.3uM (Nseq285)


title: Topotecan 0.3uM (Nseq266)


title: Topotecan 0.3uM (Nseq517)


title: Topotecan 0.3uM (Nseq166)


title: Thiram 10uM (Nseq274)


title: Topotecan 0.3uM (Nseq177)


title: Topotecan 0.3uM (Nseq618)


title: Thiophanate 10uM (Nseq497)


title: Thiodicarb 1uM (Nseq496)


title: Thidiazuron 1uM (Nseq646)


title: Thiobencarb 10uM (Nseq495)


title: NCYC361 SynH -HTs REP1


title: NCYC361 YPD REP1


title: Thiamethoxam 10uM (Nseq492)


title: Thiazopyr 10uM (Nseq493)


title: Tetramethrin 10uM (Nseq490)


title: Thiacloprid 10uM (Nseq491)


title: Thiabendazole 10uM (Nseq434)


title: Topotecan 0.3uM (Nseq317)


title: Tetraconazole 10uM (Nseq645)


title: Terbacil 10uM (Nseq489)


title: Tepraloxydim 10uM (Nseq488)


title: Topotecan 0.3uM (Nseq262)


title: Thiram 10uM (Nseq22)


title: Tebufenpyrad 0.01uM (Nseq485)


title: Tebupirimfos 10uM (Nseq608)


title: Tebufenozide 10uM (Nseq36)


title: TCMTB [2-(Thiocyanomethylthio)benzothiazole] 10uM (Nseq63)


title: 908 TGFb

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against themm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

source_name: ESdM

growth_protocol: ESdM, generated from C57BL/6-ATCC ES cells, were grown in sterile-filtered N2-medium (DMEM/F12, supplemented with 5 ml N2 supplement, 0.48 mM L-glutamine, and 100 μg/ml penicillin/streptomycin) at 37°C and 5 % CO2

extract_protocol:
Cultured ESdM were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: ESdM were either left untreated or stimulated with a combination of LPS+IFNg (500+20 ng/ml), IL4 (100U/ml), or TGFb (50ng/ml) for 24h to polarize ESdM into different activation states

value: ESdM

tag: stimulation

value: TGFb


title: Symclosene 10uM (Nseq433)


title: 907 IL4


title: 909 TGFb


title: 910 TGFb


title: 906 IL4


title: 905 IL4


title: Sulfentrazone 10uM (Nseq41)


title: Spiroxamine 10uM (Nseq603)


title: 902 LPS+IFNg

value: LPS+IFNg


title: Spirodiclofen 10uM (Nseq660)


title: 898 untreated

value: unstimulated


title: 903 LPS+IFNg


title: Sethoxydim 10uM (Nseq644)

value: cortical neurons


title: 904 LPS+IFNg


title: Tefluthrin 0.1uM (Nseq487)

value: embryonic day E15


title: 897 untreated


title: Tebuthiuron 10uM (Nseq486)

value: CAST x C57BL6


title: Rotenone 0.01uM (Nseq21)


title: Rotenone 0.01uM (Nseq272)


title: S-Bioallethrin 10uM (Nseq265)


title: Resmethrin 10uM (Nseq326)


title: 895 untreated


title: 894 untreated


title: 896 untreated


title: Quizalofop-ethyl 10uM (Nseq431)


title: Quintozene 10uM (Nseq430)


title: Utp24#1

city: Newcastle upon Tyne

first: Claudia

last: Schneider

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description:
5' barcode: ATTAGC
total cross-linked RNA

data_processing:
Library strategy: CRAC
Basecalls performed using Illumina CASAVA version 1.8
CRAC reads were mapped to the sacCer2 genome with Novoalign, using the following settings:-F STDFQ -aTGGAATTCTCGGGTGCCAAGG -f XXX_clipped_qf.fastq -r Random -h 150 -s > XXX.novo
Genome_build: SacCer2 (SGD)
Supplementary_files_format_and_content: Mapped coordinates were converted to wig format using custom perl scripts

source_name: cells grown in SD (-URA/-TRP) medium

growth_protocol: Yeast cell cultures were grown in SD medium (OD600 ~0.5).

extract_protocol: Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).

treatment_protocol: To generate RNA-protein crosslinks, actively growing yeast cell cultures in SD medium were UV-irradiated in a 1.2 m metal tube for 100 sec at 254 nm (according to Granneman et al., EMBO J., 2011).

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; met15-delta-0; ura3-delta-0)

tag: tagged protein

value: Utp24-HTP (genomic)


title: Quinclorac 10uM (Nseq611)


title: Pyrithiobac Sodium 10uM (Nseq695)


title: Pyrimethanil 10uM (Nseq429)


title: Pyriproxyfen 10uM (Nseq324)


title: Quinoxyfen 1uM (Nseq325)


title: Pyridaben 0.1uM (Nseq659)


title: Pymetrozine 10uM (Nseq43)


title: Pyraflufen-ethyl 10uM (Nseq46)


title: Pyraclostrobin 0.1uM (Nseq428)


title: Propyzamide 10uM (Nseq677)


title: Propoxycarbazone-Na 10uM (Nseq58)


title: Propiconazole 10uM (Nseq602)


title: Propoxur 10uM (Nseq696)


title: Propetamphos 10uM (Nseq636)


title: Propargite 1uM (Nseq683)


title: Propazine 10uM (Nseq51)


title: Propamocarb hydrochloride 10uM (Nseq323)


title: Prometryn 10uM (Nseq657)


title: Propanil 10uM (Nseq530)


title: 893 untreated


title: Prometon 10uM (Nseq55)


title: Profenofos 10uM (Nseq322)


title: Prodiamine 10uM (Nseq600)


title: 48h_85

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

data_processing:
Reads were aligned to the Arabidopsis genome TAIR10 using Bowtie2
Gene calls were calculated by summing the number of reads hitting a gene, calculated with ngsutils.
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2 normalized expression calls for genes (Excell File)

organism: Arabidopsis thaliana

source_name: Root Stele cells

growth_protocol: Plants were grown on plates (1xMS, 0.5% Sucrose, 0.8% Agar) for 6 DAS

extract_protocol:
Roots were treated with cell-wall digestion solution as in (Birnbaum et al., Nature Methods, 2005). And Individual flourescent cells were isolated using Flourescent Activated Cell Sorting into individual wells of 96-well plates containing extraction buffer
mRNA was converted to cDNA,amplified and library constructed according to Trombetta et al., 2014, Current Protocol in molecular biology, pp 4.22.1-4.22.17

tag: age

value: 7 DAS

value: Root Stele cells

tag: timepoint

value: 48h post root tip decapitation


title: Prochloraz 10uM (Nseq557)


title: Pirimiphos-methyl 10uM (Nseq321)


title: Prallethrin 10uM (Nseq635)


title: 48h_82


title: 48h_83


title: Piperonyl butoxide 10uM (Nseq319)


title: 48h_84


title: 48h_81


title: Picloram 10uM (Nseq580)


title: Picloram 10uM (Nseq528)


title: 48h_80


title: Phthalic acid, mono-2-ethylhexyl ester [MEHP] 10uM (Nseq518)


title: 48h_79


title: 48h_78


title: Phosalone 10uM (Nseq318)


title: Permethrin 10uM (Nseq655)


title: Prochloraz 10uM (Nseq529)


title: 16h_34

value: 16h post root tip decapitation


title: 48h_86


title: 16h_31


title: Perfluorooctanoic acid 10uM (Nseq654)


title: Perfluorooctane sulfonic acid 10uM (Nseq395)


title: 16h_32


title: 16h_30


title: Pendimethalin 10uM (Nseq394)


title: Pirimicarb 10uM (Nseq320)


title: 16h_29


title: Penoxsulam 10uM (Nseq598)


title: Parathion-methyl 10uM (Nseq593)


title: 16h_28


title: 3h_63

value: 3h post root tip decapitation


title: 3h_64


title: Parathion 10uM (Nseq393)


title: Paclobutrazol 10uM (Nseq579)


title: Oxytetracycline dihydrate 1uM (Nseq316)


title: 16h_33


title: Oxyfluorfen 10uM (Nseq315)


title: 3h_62


title: Novaluron 10uM (Nseq37)


title: Oryzalin 10uM (Nseq314)


title: 3h_61


title: 3h_60


title: Oxamyl 10uM (Nseq556)


title: 3h_58


title: 3h_57


title: Norflurazon 10uM (Nseq592)


title: Y7568 SynH -HT REP2

value: wild

value: SynH -HTs


title: 3h_55


title: 3h_54


title: time point 40 experiment 2 arrested cells

city: Gothenburg

first: Zsolt

last: Szilagyi

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

description: 40A exp2

data_processing:
Mapping with Tophat to S.pombe reference genome, with default parameters, tophat/2.0.8b
Counts generated with htseq, htseq/0.5.3p3
Differential expression analysis performed with DESeq2
Genome_build: EF2 (ASM294v2)
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample

organism: Schizosaccharomyces pombe

source_name: time point 40 arrested cells

extract_protocol:
Hot phenol RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: arrested

tag: time

value: 40 min


title: 3h_53


title: time point 40 experiment 1 arrested cells

description: 40A exp1


title: 3h_51


title: time point 20 experiment 2 arrested cells

description: 20A exp2

source_name: time point 20 arrested cells

value: 20 min


title: 3h_59


title: time point 20 experiment 1 arrested cells

description: 20A exp1


title: 3h_50


title: 3h_56


title: 3h_49


title: time point 40 experiment 2 released cells

description: 40R exp2

source_name: time point 40 released cells

value: released


title: time point 40 experiment 1 released cells

description: 40R exp1


title: time point 20 experiment 2 released cells

description: 20R exp2

source_name: time point 20 released cells


title: 3h_48


title: 3h_47


title: Monobutyl phthalate [Mono-n-butyl phlalate] 10uM (Nseq308)


title: Niclosamide 1uM (Nseq312)


title: MGK 10uM (Nseq305)


title: Milbemectin 1uM (Nseq653)


title: Myclobutanil 10uM (Nseq634)


title: Naled 10uM (Nseq310)


title: Molinate 10uM (Nseq307)


title: Nitrapyrin 10uM (Nseq313)


title: 3h_46


title: 3h_52


title: Mevinphos 10uM (Nseq553)


title: Napropamide 10uM (Nseq311)


title: Monocrotophos 10uM (Nseq309)


title: Mevinphos 10uM (Nseq531)


title: 3h_45


title: time point 0 experiment 2

description: 0 exp2

source_name: time point 0

value: control

value: 0 min


title: 3h_43


title: Metsulfuron 10uM (Nseq304)

value: cortical neurons

value: embryonic day E15


title: time point 0 experiment 1

description: 0 exp1


title: Metribuzin 10uM (Nseq617)

value: CAST x C57BL6


title: Metolachlor 10uM (Nseq303)


title: 3h_42


title: 3h_41


title: Metiram-zinc 10uM (Nseq552)


title: 3h_40


title: Methyl isothiocyanate 10uM (Nseq301)


title: Methyl hydrogen phthalate 10uM (Nseq591)


title: 3h_36


title: Methylene bis(thiocyanate) 1uM (Nseq302)


title: Methomyl 10uM (Nseq640)


title: Methoxyfenozide 10uM (Nseq616)


title: 3h_35


title: 3h_39


title: 3h_38


title: time point 20 experiment 1 released cells

description: 20R exp1


title: Methyl cellosolve 10uM (Nseq551)


title: Methidathion 10uM (Nseq550)


title: 3h_34


title: 3h_33


title: 3h_44


title: 3h_31


title: 3h_30


title: Metam-sodium hydrate 10uM (Nseq549)


title: 3h_29


title: Mesosulfuron-methyl 10uM (Nseq525)


title: Mesotrione 10uM (Nseq34)


title: 3h_37


title: Methanone 10uM (Nseq436)


title: Mepiquat chloride 1uM (Nseq299)


title: 3h_27


title: Methoxychlor 10uM (Nseq300)


title: 3h_32


title: 3h_26


title: Methamidophos 10uM (Nseq33)


title: Mancozeb 10uM (Nseq697)


title: Mancozeb 10uM (Nseq27)


title: Maneb 10uM (Nseq298)


title: MCPA 10uM (Nseq547)


title: 46h_76

data_processing:
Reads were aligned to the Arabidopsis genome TAIR10 using Bowtie2
Gene calls were calculated by summing the number of reads hitting a gene, calculated with ngsutils.
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2 normalized expression calls for genes in csv file

value: root

value: Stele

tag: hours post root tip decapitation


title: Malathion 10uM (Nseq26)


title: 46h_75

value: 7 DAS


title: Metalaxyl 10uM (Nseq548)


title: 46h_73


title: 46h_74


title: 3h_28

value: Root Stele cells


title: Malaoxon 10uM (Nseq296)


title: Linuron 10uM (Nseq546)


title: 46h_71


title: 46h_70


title: Lindane 10uM (Nseq294)


title: 46h_69


title: Isoxaben 10uM (Nseq609)


title: Isazofos 10uM (Nseq292)


title: Maleic hydrazide 10uM (Nseq297)


title: 46h_66


title: 46h_67


title: 46h_65


title: Isoxaflutole 10uM (Nseq545)


title: Iprodione 10uM (Nseq291)


title: Irinotecan 10uM (Nseq692)


title: 46h_68


title: Lactofen 10uM (Nseq293)


title: 46h_63


title: 46h_72


title: 46h_62


title: Iodosulfuron-methyl-sodium 10uM (Nseq544)


title: 46h_61


title: 46h_64


title: Imazaquin 10uM (Nseq543)


title: Imazethapyr 10uM (Nseq289)


title: Imidacloprid 10uM (Nseq290)


title: 46h_59


title: 46h_60


title: 46h_58


title: Imazaquin 10uM (Nseq532)


title: Imazapyr 10uM (Nseq542)


title: 46h_77


title: 46h_56


title: 46h_54


title: Imazamox 10uM (Nseq288)


title: 46h_55


title: Imazalil 10uM (Nseq633)


title: 46h_53


title: Indoxacarb 10uM (Nseq615)


title: 46h_52


title: Icaridin 10uM (Nseq590)


title: 46h_51


title: Hexazinone 10uM (Nseq286)


title: Hexaconazole 10uM (Nseq521)


title: 46h_50


title: Hexythiazox 10uM (Nseq287)


title: 46h_49


title: 46h_48


title: 46h_47


title: 46h_46


title: 46h_45


title: Folpet 10uM (Nseq49)


title: Formetanate hydrochloride 10uM (Nseq285-formetanate)


title: Flutolanil 10uM (Nseq283)


title: Forchlorfenuron 10uM (Nseq284)


title: 46h_57


title: Fluthiacet-methyl 10uM (Nseq606)


title: Flusilazole 10uM (Nseq282)


title: 46h_43


title: Imazapic 10uM (Nseq643)


title: Fluroxypyr-meptyl 10uM (Nseq612)


title: 46h_42


title: 46h_40


title: 46h_39


title: Flumioxazin 10uM (Nseq280)


title: 46h_38


title: Fluometuron 10uM (Nseq632)


title: Fluoxastrobin 1uM (Nseq651)


title: Fluroxypyr 10uM (Nseq281)


title: 46h_37


title: Fosthiazate 10uM (Nseq610)


title: Flumetsulam 10uM (Nseq589)


title: 46h_36


title: Flumiclorac-pentyl 10uM (Nseq631)


title: 46h_34


title: Flumetralin 10uM (Nseq588)


title: Flufenacet 1uM (Nseq587)


title: Flufenpyr-ethyl 10uM (Nseq60)


title: 46h_32


title: Fludioxonil 10uM (Nseq279)


title: 46h_31


title: 46h_44


title: Fluazinam 0.1uM (Nseq586)


title: 46h_41


title: Fluazifop-P-butyl 10uM (Nseq520)


title: 46h_29


title: Fluazifop-butyl 0.1uM (Nseq630)


title: Fipronil 1uM (Nseq391)


title: 46h_28


title: 46h_27


title: 46h_35


title: 46h_25


title: wrky25 wrky33 ozone rep2

status: Public on Apr 03 2016

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

country: Finland

institute: University of Helsinki

data_processing:
RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 13 reads were trimmed PRINSEQ package, then mapped to wild type Col-0 whole genome using TopHat2 with following settings:Do not ignore novel junctions, hits allowed=2, allowing 2 nucleotide mismatches, minimum anchor length=8, Maximum number of mismatches allowed in the anchor=0, minimum intron length=20, Maximum intron length=2000
Generated BAM files were sorted and indexed with SAMtools package
Number of reads per gene was counted and calculated with HTSeq package (only unique alignments included)
Genome_build: Col-0 TAIR10.23
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromosome, start, end, length, strand and read count per gene

source_name: whole rosette

growth_protocol: Before the treatment, plants were grown until the age of 3 weeks in the following conditions: Seeds were sown on 1:1 peat: vermiculite, stratified for three days, and then grown at 22° C/19° C for seven days. The geminated seedlings were transplanted into new 1:1 peat: vermiculite mixture. Plants were at 22°C/19°C, relative humidity of 70%/90% under a light cycle of 12 h/12 h.

extract_protocol:
Five rosettes per genotype (Col-0, wrky25 wrky33, wrky75 ) from control and ozone treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: Plants were exposed with 350 nL L-1 ozone for two hours.

value: wrky25 wrky33

value: whole rosette

value: 3 weeks old plants

tag: treatment

value: 350 ppb ozone exposure for 2hr


title: Fenthion 10uM (Nseq390)


title: Fentin 0.01uM (Nseq629)


title: 46h_33


title: 46h_24


title: Fenpropathrin 10uM (Nseq388)


title: Fenitrothion 10uM (Nseq40)


title: 46h_23


title: Fenpyroximate 0.1uM (Nseq389)


title: 46h_22


title: Fenoxaprop-ethyl 10uM (Nseq387)


title: Fenoxycarb 1uM (Nseq585)


title: Fenarimol 10uM (Nseq519)


title: 46h_21


title: 46h_30


title: Fenhexamid 10uM (Nseq45)


title: 46h_18


title: Fenamiphos 10uM (Nseq386)


title: 46h_19


title: Fenamidone 10uM (Nseq56)


title: 46h_16


title: Fenamidone 10uM (Nseq347)


title: Famoxadone 10uM (Nseq385)


title: 46h_15


title: 46h_17


title: 46h_26


title: 46h_20


title: Famoxadone 10uM (Nseq348)


title: 46h_14


title: 46h_13


title: 46h_11


title: Etridiazole 10uM (Nseq685)


title: 46h_10


title: Ethylenethiourea 10uM (Nseq443)


title: 46h_9


title: Ethoprop 10uM (Nseq383)


title: 46h_8


title: Ethofumesate 10uM (Nseq382)


title: 46h_7


title: Ethephon 10uM (Nseq604)


title: 46h_4


title: 46h_5


title: 46h_6


title: Ethalfluralin 10uM (Nseq380)


title: Esfenvalerate 10uM (Nseq379)


title: Emamectin benzoate 1uM (Nseq378)


title: EPTC 10uM (Nseq583)


title: Diuron 10uM (Nseq377)


title: 46h_1


title: Endosulfan 10uM (Nseq271)


title: 16h_27


title: 46h_2


title: Ethylenethiourea 10uM (Nseq25)


title: Dithiopyr 0.1uM (Nseq626)


title: Disulfoton 10uM (Nseq540)


title: Diquat dibromide 1uM (Nseq652)


title: 46h_12


title: Etoxazole 10uM (Nseq627)


title: 16h_26


title: 16h_25


title: 16h_23


title: 16h_24


title: Diphenylamine 10uM (Nseq676)


title: 16h_22


title: Dimethyl phthalate 10uM (Nseq376)


title: 16h_21


title: Diniconazole 10uM (Nseq270)


title: Dimethomorph 10uM (Nseq35)


title: 16h_20


title: 16h_18


title: 16h_19


title: 46h_3


title: Dimethenamid 10uM (Nseq625)


title: Difenzoquat metilsulfate 1uM (Nseq686)


title: Diethyltoluamide 10uM (Nseq50)


title: Diethyltoluamide 10uM (Nseq441)


title: 16h_17


title: Difenoconazole 10uM (Nseq38)


title: Dimethoate 10uM (Nseq539)


title: 16h_15


title: 16h_14


title: Diethyltoluamide 10uM (Nseq392)


title: 16h_12


title: Diethyltoluamide 10uM (Nseq432)


title: 16h_13


title: Dicrotophos 10uM (Nseq605)


title: Diethylhexyl pthalate 10uM (Nseq269)


title: Dicofol 10uM (Nseq268)


title: Diclosulam 0.1uM (Nseq516)


title: Diclofop-methyl 10uM (Nseq537)


title: 16h_9


title: 16h_10


title: 16h_16


title: 16h_8


title: Dichlorvos 10uM (Nseq601)


title: 16h_6


title: Dichlorprop [alpha-(2,4-Dichlorophenoxy) propionic acid] 10uM (Nseq375)


title: Dichloran 10uM (Nseq515)


title: 16h_5


title: 16h_3


title: 16h_4


title: 16h_2


title: Dichlobenil 10uM (Nseq374)


title: Dicamba 1uM (Nseq373)


title: Dibutyl phthalate 10uM (Nseq24)


title: 16h_11


title: Utp24#4

value: BY4741 (MATa; his3-delta-1; leu2-delta-0; met15-delta-0; ura3-delta-0)

value: Utp24-HTP (genomic)


title: 16h_1


title: Diazinon 10uM (Nseq267)


title: Diazoxon 10uM (Nseq624)


title: 3h_25


title: 3h_24


title: Dazomet 1uM (Nseq370)


title: Daminozide 10uM (Nseq52)


title: 3h_22


title: 3h_23


title: d-cis,trans-Allethrin 1uM (Nseq371)


title: 3h_19


title: 16h_7


title: Cyproconazole 1uM (Nseq582)


title: 3h_20


title: 3h_18


title: Cyromazine 10uM (Nseq369)


title: 3h_16


title: 3h_21


title: Cyhalofop-butyl 10uM (Nseq623)


title: 3h_15


title: Cymoxanil 10uM (Nseq514)


title: Cycloate 10uM (Nseq581)


title: Cyfluthrin 10uM (Nseq513)


title: 3h_14


title: 3h_11


title: 3h_12


title: Cyclanilide 10uM (Nseq366)


title: 3h_10


title: 3h_9


title: 3h_13


title: Cyanamide 10uM (Nseq565)


title: Cyanazine 10uM (Nseq191)


title: Clothiandin 10uM (Nseq62)


title: Coumaphos 10uM (Nseq190)


title: Cypermethrin 10uM (Nseq367)


title: 3h_17


title: 3h_6


title: 3h_7


title: 3h_5


title: Clorophene 10uM (Nseq614)


title: Clopyralid 10uM (Nseq57)


title: 3h_4


title: Clopyralid 10uM (Nseq554)


title: Clopyralid-olamine 10uM (Nseq622)


title: Cyprodinil 10uM (Nseq368)


title: Cloprop 10uM (Nseq642)


title: 3h_2


title: 3h_8


title: Clomazone 10uM (Nseq512)


title: 3h_1


title: Clofentezine 10uM (Nseq536)


title: Cyazofamid 10uM (Nseq684)


title: Uncut_31

value: uncut


title: Clodinafop-propargyl 10uM (Nseq535)


title: Cinmethylin 10uM (Nseq189)


title: Uncut_29


title: Chlorpyrifos-methyl 10uM (Nseq187)


title: Chlorpyrifos oxon 10uM (Nseq675)


title: Uncut_28


title: Uncut_27


title: Chlorpropham 10uM (Nseq32)


title: Chlorothalonil 1uM (Nseq442)


title: Uncut_26


title: Uncut_24


title: Chlorothalonil 1uM (Nseq186)


title: 3h_3


title: Uncut_23


title: Uncut_21


title: Uncut_25


title: Uncut_22


title: Uncut_20


title: Uncut_19


title: Chloroneb 10uM (Nseq185)


title: Carbaryl [1-naphthyl N-methylcarbamate] 10uM (Nseq181)


title: Carboxin 10uM (Nseq182)


title: Chloridazon 1uM (Nseq564)


title: Captan 10uM (Nseq667)


title: Uncut_17


title: Captafol 1uM (Nseq669)


title: VZ1Plus

city: Houston

first: Katie

last: McCallum

state: TX

address: 6431 Fannin St

institute: UT Health Science Center

data_processing:
The fastq files were mapped to reference genome precessed by Tophat that utilize Bowtie2 for read alignment.
The mapped reads were further precessed by Cufflinks that will assemble the transcripts and calculate the differential expression based on the estimation of transcripts' abundance.
The differentially expressed result was visuallized by the R programming package Venn package.
Genome_build: Caenorhabditis elegans genome (version ce10)
Supplementary_files_format_and_content: The significant gene lists were generated for each of the comparisons and the files were save as four spreadsheets in the 'ProcessedDataFiles_McCallumSubmission.xls' file that make comparisons between the 4 samples. They are as follows: N2plus_N2minus (sheet 1), VzPlus_VzMinus (sheet 2), N2MinusVzMinus (sheet 3), N2Plus_VzPlus (sheet 4).

organism: Caenorhabditis elegans

source_name: stressed animals

growth_protocol: grown on non-pathogenic OP50 until young adult stage

extract_protocol:
Total RNA was extracted using several freeze/thaw cycles in Trizol and RNA precipitated using ethanol
Total RNA from C. elegans nematodes

treatment_protocol: populations were either left unstresed on non-pathogenic OP50 or stressed for 5 hours with 10mM NaAs

tag: growth condition

value: 5 hr 10mM NaAs stress

tag: sample type

value: oxidative stress


title: Uncut_16

tag: tissue


title: Carfentrazone-ethyl 10uM (Nseq183)

tag: cell type


title: Uncut_30


title: N2Minus

source_name: unstressed animals

value: grown on non-pathogenic OP50


title: N2Plus


title: Cacodylic acid 10uM (Nseq511)

value: cortical neurons

tag: developmental stage


title: Uncut_14


title: Butylate 10uM (Nseq563)

value: embryonic day E15

tag: strain


title: Uncut_15


title: Chlorethoxyfos 10uM (Nseq184)

value: CAST x C57BL6


title: Flag-Lef1 plus Dox_3

city: Frederick

middle: W

last: Kennedy

state: MD

address: 1050 Boyles St., Bldg 539, Rm 205

department: Cancer and Developmental Biology

institute: NIH/NCI

data_processing:
Base calling was performed with the RTA 1.9.35.0 software
After adapter removal, low-quality read filtering and trimming, Fastq reads were aligned to mouse mm9 genome using Tophat2 Version 2.0.8, with Bowtie index 2.0.0-beta7 for paired-end splice-aware alignment
Post-alignment QC metrics were generated using Picard and RNA-SeQC tools
Cufflinks Version 2.0.2 was used for transcriptome assembly with the known genes option only
Cuffmerge was used for merging the transcriptome assemblies of all the samples and the merged assemblies were used for differential expression using Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: 3F_Lef1_PlusversusMinusDOX_ProcessedFiles.txt represents a differentially expressed gene-list

source_name: embryonic stem cells, FLef1plusDox

growth_protocol: ES cells were maintained in 15%serum/DMEM supplemented with 1unit per ml culutre medum and grown on primary MEFs (derived from FVB mouse stain). ES colonies were dissociated with TypLE and MEFs were stripped away. ES cells were then plated at 2.5x10^6 per 100mm petri dish for suspension growth and embryoid body formation. Flag-Lef1 expression was initiated on day 2 of embryoid body formation, for a total of 24 hrs.

extract_protocol:
ES cells were havested on day 3 of culture plus/minus 24 treatment of doxycycline. Total RNA was extract using standard trizol-based extaction protocols. Total RNA was then treated with Turbo DNAse (Ambion) to eliminate genomic DNA contamination.
The libraries were prepared according to Illumina’s TruSeq RNA library protocol. We use between 100ng to 1ug of total RNA as the input to an mRNA capture with oligo-dT coated magnetic beads. The mRNA is fragmented, and then a random-primed cDNA synthesis is performed. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that would go to the sequencer.

treatment_protocol: After 2 days of embryoid body formation cells were treated with Doxycycline to induce Flag-Lef1 expression for 24 hrs

tag: cell line

value: A2Lox.cre ES cells

value: plus Dox to induce Flag-Lef1 expression

value: Day 3 differentiation


title: Flag-Lef1 plus Dox_2

description: 3F_Lef1_PlusversusMinusDOX_ProcessedFiles.txt


title: Camptothecin 0.3uM (Nseq671)


title: Butralin 10uM (Nseq180)


title: Uncut_12

value: 7 DAS

value: root

value: Stele


title: Uncut_18


title: Uncut_11


title: Flag-Lef1 minus Dox_4

source_name: embryonic stem cells, FLef1minDox

value: minus Dox


title: VZ1Minus


title: Uncut_10


title: Uncut_13


title: Flag-Lef1 minus Dox_3


title: Flag-Lef1 minus Dox_1


title: Buprofezin 10uM (Nseq510)


title: Bromoxynil 10uM (Nseq23)


title: Uncut_9


title: Boscalid 10uM (Nseq437)


title: Butachlor 10uM (Nseq179)


title: Flag-Sp5 plus Dox_3

data_processing:
Base calling was performed with the RTA 1.9.35.0 software
After adapter removal, low-quality read filtering and trimming, Fastq reads were aligned to mouse mm9 genome using Tophat2 Version 2.0.8, with Bowtie index 2.0.0-beta7 for paired-end splice-aware alignment
Post-alignment QC metrics were generated using Picard and RNA-SeQC tools
Cufflinks Version 2.0.2 was used for transcriptome assembly with the known genes option only
Cuffmerge was used for merging the transcriptome assemblies of all the samples and the merged assemblies were used for differential expression using Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: F_Sp5_PlusversusMinusDOX_ProcessedFiles.txt represents differentially expressed gene-list

source_name: embryonic stem cells, FSp5plusDox

growth_protocol: ES cells were maintained in 15%serum/DMEM supplemented with 1unit per ml culutre medum and grown on primary MEFs (derived from FVB mouse stain). ES colonies were dissacociated with TypLE and MEFs were stripped away. ES cells were then plated at 2.5x10^6 per 100mm petri dish for suspension growth and embryoid body formation. Flag-Sp5 expression was initiated on day 2 of embryoid body formation, for a total of 24 hrs.

treatment_protocol: After 2 days of embryoid body formation cells were treated with Doxycycline to induce Flag-Sp5 expression for 24 hrs

value: plus Dox to induce Flag-Sp5 expression

value: Day 3 embryoid body differentiation


title: Flag-Sp5 plus Dox_1

description: F_Sp5_PlusversusMinusDOX_ProcessedFiles.txt


title: Uncut_6


title: Bisphenol A 10uM (Nseq666)

source_name: cultured cortical neurons


title: Butafenacil 10uM (Nseq534)


title: Flag-Sp5 minus Dox_4

source_name: embryonic stem cells, FSp5minDox


title: Uncut_5


title: Uncut_4


title: Flag-Sp5 minus Dox_3


title: Flag-Sp5 minus Dox_2


title: Uncut_8


title: Bifenthrin 10uM (Nseq178)


title: Uncut_3


title: Benzoic Acid 10uM (Nseq527)


title: Bentazone 10uM (Nseq613)


title: Flag-Sp5 plus Dox_4


title: Uncut_1


title: Uncut_2


title: Bensulide 10uM (Nseq176)


title: Flag-Lef1 plus Dox_1


title: Post ICR 2FL 3

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Small bowel obtained from a male, C57BL/6 mouse 8 weeks post-ileocecal resection with 2'-FL supplementation

data_processing:
Primers and barcodes were removed from all sequences, which were then aligned to the mm10 genome build using reference annotations from UCSC.
Aligned reads were quantified and used to compute reads per kilobase permillion mapped reads.  Raw counts were normalized using the DESeq algorithm.
Each 8-week post-surgery sample was baselined to its own pre-surgery sample.
Data was filtered, requiring at least 3 reads in all samples of at least one fo the four experimental conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files each contain  four columns, including Gene ID, Gene Symbol, Entrez ID, and the sample's expression values (RPKM).

source_name: small bowel, 2'-FL supplementation

growth_protocol: Male C57BL/6 mice aged 8-10 weeks were submitted to ileocecal resection on experimental Day 0.  Seven days postoperative all animals were given liquid diets then transitioned to standard chow with access to water.

extract_protocol:
Small bowels were obtained from all animals at 8 weeks post ileocecal resection.  Libraries were prepared using approximately 1.5ug RNA using the TruSeq RNA Sample Preparation Kit (Illumina, CA).
Standard Illumina protocols using the HiSeq 2000 Sequencing System (Illumina, CA)

treatment_protocol: 2'-FL supplementation began on experimental day 0 in the treatement arm, at a concentration of 2.5 grams/L.

tag: gender

value: male

value: 8 weeks post-ileocecal resection


title: Bifenazate 10uM (Nseq621)


title: Uncut_7

value: uncut


title: Post ICR 2FL 1


title: Post ICR Control 3

description: Small bowel obtained from a male, C57BL/6 mouse 8 weeks post-ileocecal resection with no 2'-FL supplementation

source_name: small bowel, no 2'-FL supplementation


title: Bensulfuron-methyl 10uM (Nseq175)


title: Benomyl 10uM (Nseq665)


title: Benfluralin [Benefin] 10uM (Nseq59)


title: Bendiocarb 10uM (Nseq61)


title: Post ICR 2FL 2


title: Pre ICR 2FL 2

description: Small bowel obtained from a male, C57BL/6 mouse pre-ileocecal resection with 2'-FL supplementation

value: pre-ileocecal resection


title: Azoxystrobin 0.1uM (Nseq264)


title: Azoxystrobin 0.1uM (Nseq168)


title: Pre ICR 2FL 3


title: Pre ICR 2FL 1


title: Atrazine 10uM (Nseq507)


title: Azinphos-methyl 10uM (Nseq533)


title: Pre ICR Control 2

description: Small bowel obtained from a male, C57BL/6 mouse pre-ileocecal resection with no 2'-FL supplementation


title: Pre ICR Control 1


title: Azamethiphos 10uM (Nseq508)


title: Pre ICR Control 3


title: Asulam 10uM (Nseq620)


title: Anilazine 10uM (Nseq29)


title: Msi2-HITS-CLIP, 1:75 Rnase, rep.5

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
3'UTR_msi2-HITS-CLIP_filtered_peaks.bed
All_msi2-HITS-CLIP_filtered_peaks.bed

data_processing:
Reads were trimmed to remove adapters (Cutadapt, default settings), then sequence duplicates were discarded, followed by alignment to the mouse genome (mm10) using Novoalign (autothreshold alignment with -s 1 setting), requiring a minimum of 20 nucleotide alignment length. Alignments with identical start and stop positions were collapsed to a single alignment and continuous alignments were then clustered to identify binding sites. Binding sites were further refined by using PeakSplitter (settings default except -v 0.6). Peaks were then annotated to the genome using Gencode (VM4) and UCSC (mm10) annotations. 3'UTR regions were extended 5Kbp to include non-annotated 3'UTR extensions.
Genome_build: mm10

source_name: keratinocytes

growth_protocol: Keratinocytes isolated from neonatal skin, cultured on mitomycin-C pretreated NIH-3T3 J2 cells for 3 passages to obtain a sponteanously immortalized cell popultation, then transferred to uncoated dishes for continued passage

extract_protocol:
Keratinocytes were lysed in Lysis Buffer (50mM Tris pH 7.4 100mM NaCl 1mM MgCl2 1% NP-40 .5% Na-Deoxycholate .1% SDS). Msi2-RNA crosslinked material was recovered using IP, and purified via Novex PAGE followed by transfer to nitrocellulose and extraction with Phenol-Chloroform
Msi2-Hits-Clip libraries were prepared using methods described in Wang, Zhen, James Tollervey, Michael Briese, Daniel Turner, and Jernej Ule. (2009) CLIP: Construction of cDNA Libraries for High-Throughput Sequencing from RNAs Cross-Linked to Proteins in Vivo. Methods 48, no. 3 (July 2009): 287–93.

treatment_protocol: Cultures were irradiated twice with 200mJ/cm2 UVC prior to harvesting in Lysis Buffer (50mM Tris pH 7.4 100mM NaCl 1mM MgCl2 1% NP-40 .5% Na-Deoxycholate .1% SDS)

value: Spontaneously Immortalized Mouse Keratinocyte Culture

tag: clip-antibody

value: rabbit monoclonal antibody to Msi2. Abcam (ab76148)


title: Amitraz 10uM (Nseq562)

value: cortical neurons

value: embryonic day E15


title: Bromacil 10uM (Nseq509)

value: CAST x C57BL6


title: Msi2-HITS-CLIP, 1:20x RNase Hi MW, rep.3


title: Msi2-HITS-CLIP, 1:50 Rnase, rep.4


title: Aldicarb 10uM (Nseq561)


title: Post ICR Control 2


title: Alachlor 10uM (Nseq54)


title: Msi2-HITS-CLIP, 1:20x RNase Low MW,rep.2


title: Post ICR Control 1


title: Acifluorfen 10uM (Nseq174)


title: Acibenzolar-S-Methyl [1,2,3-Benzothiadiazole-7-carbothioic acid, S-methyl ester] 10uM (Nseq173)


title: RNA-Seq, Scrambled shRNA, rep.3

data_processing:
Reads were aligned via Tophat using default settings with a supplied .gtf annotation file from the illumina iGenomes project. Alignments overlapping uniquely with CDS regions were then counted using HTSeq (--stranded=reverse). Differential gene expression was then calculated with DESeq
Genome_build: mm10

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturers instructions
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Scrambled or Msi2 shRNA lenti-vectors were used to infect the keratinocytes. 2 days following infection, cultures were treated with 2ug/ml puromycin and selected for 2 more days. Cultures were then expanded and harvested


title: RNA-Seq, Scrambled shRNA, rep.1


title: RNA-Seq, Scrambled shRNA, rep.2


title: RNA-Seq, Msi2 shRNA, rep.3


title: Acetochlor 10uM (Nseq560)


title: Acetamiprid 10uM (Nseq172)


title: 2,5-Pyridinedicarboxylic acid, dipropyl ester 10uM (Nseq169)


title: RNA-Seq, Msi2 shRNA, rep.1


title: Ribo-Seq, Msi2 shRNA, rep.2

data_processing:
Reads were aligned via Tophat using default settings with a supplied .gtf annotation file from the illumina iGenomes project. Alignments overlapping uniquely with CDS regions were then counted using HTSeq (--stranded=yes). Differential gene expression was then calculated with DESeq
Genome_build: mm10

extract_protocol: Ribosome protected RNA fragments were isolated as described in the Artseq Ribosome Profiling kit guidelines (EpiCentre)

treatment_protocol: Scrambled or Msi2 shRNA lenti-vectors were used to infect the keratinocytes. 2 days following infection, cultures were treated with 2ug/ml puromycin and selected for 2 more days. Cultures were then expanded and harvested.Cultures were treated with Cycloheximide (50mg/ml) in E-low media for 1 min at 37 degrees C, then washed with PBS containing cycloheximide, then harvested in Mammalian Polysome buffer containing cycloheximide.


title: Ribo-Seq, Msi2 shRNA, rep.3


title: Acephate 10uM (Nseq171)


title: 2,4-DB [4-(2,4-dichlorophenoxy)butyric acid] 10uM (Nseq619)


title: 3-Iodo-2-propynylbutylcarbamate 1uM (Nseq170)


title: Ribo-Seq, Msi2 shRNA, rep.1


title: Ribo-Seq, Scrambled shRNA, rep.3


title: 2,4-D 10uM (Nseq674)


title: Msi2-HITS-CLIP, 1x Rnase, rep.1


title: 2,2-Bis(4-hydroxyphenyl)-1,1,1-trichloroethane 10uM (Nseq599)


title: Ametryn 10uM (Nseq506)


title: Ribo-Seq, Scrambled shRNA, rep.1

extract_protocol:
Ribosome protected RNA fragments were isolated as described in the Artseq Ribosome Profiling kit guidelines (EpiCentre)
Artseq Ribosome Profiling Kit guidelines (EpiCentre)


title: WT48B_H3K9me3

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

library_source: genomic

data_processing:
Mapping was performed using Novoalign (NovoCraft)
reverse transcripts were counted using python script HTSeq (Anders et al., 2014)
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages
mean-variance weighting (voom) and TMM normalisation (Gentleman et al., 2004)
Genome_build: A_nidulans_FGSC_A4_version_s10-m03-r07
Supplementary_files_format_and_content: Transcription: Tab-delim file, log2(CPM) counts per million reads, rows for each gene, columns for samples WT_17,WT_48,d8211_17,d8211_48 (WT samples are published under GSE63672); ChIP-seq: sgr files, columns: chromosome, nucleotide, value

molecule: genomic DNA

organism: Aspergillus nidulans

source_name: WT 48 h H3k9me3 ChIP

growth_protocol: ANM minimal media, complete medium, supplements and growth conditions were as described by Todd et al., 2007.

extract_protocol:
A. nidulans genomic DNA was extracted from frozen mycelia as described by Lee and Taylor (Lee & Taylor, 1990). For small-scale preparations, a dilute spore solution was lysed by brief sonication (Branson Ultrasonics) and purified by phenol/chloroform extraction. Total RNA was isolated from filtered, flash frozen mycelia using a Fastprep bead-beater (MP Biomedicals) and Trizol reagent (Invitrogen) following the manufacturers’ protocol.
Illumina sequencing libraries were made from RNA samples according to TruSeq RNA Sample prep kit v2 (Illumina) following the manufacturers protocol with 1µg total RNA input. ChIP-seq libraries were made from ChIP xperiments using indicated antibodies and prepared according to Illumina Tru-seq ChIP-seq kit (Cat# FC-121-2002). 50 bp single end sequencing was performed using a HiSeq Illumina sequencer. Obtained sequences were de-multiplexed, quality controlled and mapped on the Aspergillus nidulans genome assembly (A_nidulans_FGSC_A4_version_s10-m03-r07).

treatment_protocol: Two different growth periods were applied, 17h and 48h.

value: WT

tag: antibody

tag: library strategy

value: ChIP-seq


title: WT48B_H3K4me3

source_name: WT 48 h H3K4me3 ChIP


title: RNA-Seq, Msi2 shRNA, rep.2


title: Panax_japonicus_secRoot

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
The Trinity program ver 2.0.6 was used for the de novo transcriptome assembly using clean reads from all the samples. De novo assembly resulted in 165 206,610 contigs and 135,235 unigenes, with a N50 value of 957 bps.
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 and RSEM respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were alligned on Panax japonicus de novo transcriptome assembly that were generated using Trinity, and abundace were measured using RSEM. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM, and IsoPct for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: tab-delimited text file includes contig_id, unigene_id, and FPKM values for each tissues. FPKM values were calculated using RSEM program. results files for all tissues were used to extract FPKM values for each tissues, and were combind/alligned against transcript_id and gene_id

organism: Panax japonicus

source_name: A voucher specimen for Panax japonicus (Accession No. 134 E4532-42-0003-3-C4) was deposited in the Herbarium of Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido

growth_protocol: All five tissues, namely flower, leaf, secRoot, rhizome_Y, and rhizome_old were harvested in the month of June, 2014 from a 7-year old P. japonicus plant, growing in the natural environment at the medicinal plant garden, Health Sciences University of Hokkaido, Japan.

extract_protocol:
The frozen samples of P. japonicus were powdered using a Multi Beads Shocker (Yasui Kikai, Japan), were used for subsequent RNA extraction. Total RNA, from thus obtained powdered tissues of P. japonicus, was extracted using the RNeasy Plant Mini Kit (Qiagen, USA), according to manufacturer’s instruction. The extracted RNA was treated with RNase-free DNase (TaKaRa, Japan) and further purified by ethanol precipitation. To create cDNA sequencing library, firstly, mRNA with poly(A) tail were isolated from the total RNA  using beads with oligo(dT). Fragmentation buffer was then added to shear mRNA into short fragments, which then served as templates for the synthesis of first strand of cDNA using random hexamer primers.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications.

treatment_protocol: Not applicable

tag: tissues

value: Secondary Root

tag: age


title: Panax_japonicus_rhizome_Y


title: WT48B_H3Ac

source_name: WT 48 h H3Ac ChIP


title: Ribo-Seq, Scrambled shRNA, rep.2


title: Panax_japonicus_rhizome_old


title: WT48A_H3K9me3


title: Panax_japonicus_Leaf

value: Leaf


title: Panax_japonicus_Flower

value: Flower


title: WT48A_H3K4me3


title: RNA-Seq_homoz

city: Chicago

first: Aparna

last: Vasanthakumar

state: IL

address: 900 E.57th Street, KCBD

department: Medicine

institute: The University of Chicago

description: Sample 3

data_processing:
Sequenced reads were aligned to mm9 using Tophat2 and Bowtie2
Fragments per kilobase per megabase of library size (FPKM) were calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files, which include FPKM values

source_name: Mouse fetal liver LSK cells

extract_protocol:
Lineage-,Sca1+,c-Kit+ cells were isolated from wild-type, hemizygous and homozygous DNMT3B7 transgenic embryos at E14.5.  Cells from four to five embryos of each genotype were pooled.  Total RNA was isolated using the RNeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fetal liver

value: LSK cells

tag: genotype/variation

value: homozygous DNMT3B7


title: WT48A_H3K36me3

source_name: WT 48 h H3K36me3 ChIP

tag: time


title: RNA_Seq_hemiz

description: Sample 2

value: hemizygous DNMT3B7


title: WT48A_H3Ac


title: RNA_Seq_WT

description: Sample 1


title: WT15B_H3K36me3

source_name: WT 17 h H3K36me3 ChIP


title: WT15A_H3K9me3

source_name: WT 17 h H3k9me3 ChIP


title: WT15A_H3K4me3

source_name: WT 17 h H3K4me3 ChIP


title: WT15B_H3Ac

source_name: WT 17 h H3Ac ChIP


title: antiPhry_2

city: North Bethesda

first: sandip

last: de

address: 6 center drive

department: rm 3B-331, bldg 6B

institute: NICHD/NIH

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the Drosophila reference genome (release 5.22/6.02).
.tdf files were generated from .bam files via IGV tools.
Genome_build: Release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format.

organism: Drosophila melanogaster

source_name: 3rd instar brains and imaginal disks, Ph ChIP

growth_protocol: All flies were grown at 25°C. 3rd instar larvae were dissected for brains and imaginal discs.

extract_protocol:
Fixed brains and imaginal discs were dissected from 10 third instar larvae. Sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Pho (custom made), anti-Ph (a kind gift from Donna Arndt-Jovin), and anti-Engrailed (custom made) antibodies, and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies.
Input ChIP DNA (30 ng) was blunt-ended and phosphorylated. A single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products were purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA was purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated before cluster generation.

tag: strain/background

value: ry

value: 3rd instar larvae

value: CNS and imaginal disks

tag: chip antibody

value: anti-Ph


title: antiH3K27ry-1-Input

source_name: 3rd instar brains and imaginal disks, H3K27me3 input


title: antiEnry_1

source_name: 3rd instar brains and imaginal disks, En ChIP

value: anti-En


title: WT48B_H3K36me3


title: antiPhry-1-Input

source_name: 3rd instar brains and imaginal disks, Ph input


title: WT15B_H3K9me3


title: WT15A_H3Ac


title: antiPhory_2

source_name: 3rd instar brains and imaginal disks, Pho ChIP

value: anti-Pho


title: Pho input

source_name: 3rd instar brains and imaginal disks, Pho input


title: WT15A_H3K36me3


title: antiPhry_1


title: antiPhory_1


title: NoAb_control

source_name: NoAb_control ChIP


title: DF78_mock-11dpi-BR2

data_processing:
Barcode adaptors from the RNA sequence reads were clipped and low quality reads were removed (read quality < 30) using the Trimmomatic software (Bolger et al., 2014).
RNA sequence reads passing quality filter were aligned to the B. napus genome (v4.1, Chalhoub et al. 2014) using Tophat2 of the Trapnell cufflinks package (Trapnell et al., 2012). Tophat2 alignment was performed in high-sensitivity mode and used B. napus reference annotation v5.0 as a guide (Chalhoub et al., 2014).
Identification of novel transcripts was performed using cufflinks v2.2.1 (Trapnell et al., 2012) and transcript sequences were extracted from this annotation using BedTools.
Cuffquant, CuffNorm and Cuffdiff were used to generate normalized counts in FPKM and to identify differentially expressed genes (pooled dispersion method). Genes were considered significantly differentially expressed with a corrected p-value of < 0.05 (false discovery rate = 0.05).
Genome_build: B. napus v. 4.1
Supplementary_files_format_and_content: excel file with FPKM.

organism: Brassica napus

source_name: Cotyledon

extract_protocol:
RNA was collected from three biological replicates of infected and mock inoculated B. napus cotyledons at 0, 3, 7, and 11 dpi. Total RNA was isolated by using PureLink® Plant RNA Reagent (Ambion) and treated with TURBO DNA-free™ Kit (Ambion) according to the manufacturer’s instructions. RNA quality and integrity was measured using the 2100 Bioanalyzer (Agilent Technologies) with the Agilent 2100 PicoChip.
RNA-sequencing libraries were prepared according to alternative HTR protocol (C2) established by R. Kumar et al. (2012) with the exception of library PCR enrichment that was carried out using 11 PCR cycles. RNA sequencing libraries were validated using the Agilent Bioanalyzer DNA chips (Agilent Technologies) and quantified using the Quant-iT dsDNA Assay kit (ThermoFisher Scientific).

tag: genotype

value: DF78 (LepR1)

tag: inoculation status

value: 11 days (mock)

tag: pathogen

value: Cotyledon


title: antiEnry_2

tag: tissue


title: d8211_48B_H3K9me3

source_name: KdmB 48 h H3k9me3 ChIP

value: kdmB

value: ChIP-seq


title: DF78_mock-7dpi-BR2

value: 7 days (mock)


title: DF78_mock-11dpi-BR1


title: DF78_mock-7dpi-BR1


title: d8211_48B_H3Ac

source_name: KdmB 48 h H3Ac ChIP


title: WT15B_H3K4me3

value: WT


title: d8211_48B_H3K36me3

source_name: KdmB 48 h H3K36me3 ChIP


title: 2-Phenylphenol 1uM (Nseq559)

data_processing:
RNA-seq reads were filtered using TagDust
Reads were aligned to the reference mouse genome (mm9) with TopHat using default parameters
Reads aligning to rRNA genes were removed
Transcript abundance was estimated by computing RPKM using RefSeq gene models aggregated by gene symbol
Genome_build: mm9
Supplementary_files_format_and_content: RPKM for all RefSeq genes and all samples were filtered such that a given gene had >90% of samples with RPKM >0 and gene length exceeded 500 bp.  RPKMs were then log10 transformed, quantile-normalized, median-centered, and subtle batch effects were removed using a mixed model ANOVA

source_name: cultured cortical neurons

extract_protocol:
RNA was isolated with RNeasy plus mini kit (Cat. #74134, Qiagen).  RNA yield and quality was determined with a Nanodrop 1000 Spectrophotometer (Thermo Scientific).  Samples were further assessed for quality using either an Agilent Bioanalyzer 2100 or TapeStation 2200 to obtain a RNA integrity number (RIN).  RIN values exceeding 7 were used for sequencing.
RNA samples were used to generate and barcode cDNA libraries using the TruSeq RNA Library Preparation Kit at the UNC High Throughput Sequencing Facility.

tag: cell type

value: cortical neurons

tag: developmental stage

value: embryonic day E15

value: CAST x C57BL6


title: d8211_48A_H3K9me3

tag: strain


title: DF78_mock-3dpi-BR2

value: 3 days (mock)


title: d8211_48A_H3K4me3

source_name: KdmB 48 h H3K4me3 ChIP


title: d8211_48A_H3K36me3


title: DF78_mock-3dpi-BR1


title: d8211_48A_H3Ac


title: DF78_mock_0dpi-BR3

value: 0 days post inoculation


title: DF78_mock_0dpi-BR2


title: d8211_15B_H3K4me3

source_name: KdmB 17 h H3K4me3 ChIP


title: d8211_15B_H3K9me3

source_name: KdmB 17 h H3k9me3 ChIP


title: Westar_mock-11dpi-BR2

value: Westar


title: DF78_mock_0dpi-BR1


title: d8211_48B_H3K4me3


title: Westar_mock-11dpi-BR1


title: d8211_15B_H3Ac

source_name: KdmB 17 h H3Ac ChIP


title: Westar_mock-7dpi-BR2


title: d8211_15A_H3K9me3


title: Westar_mock-7dpi-BR1


title: d8211_15A_H3K4me3


title: Westar_mock-3dpi-BR2


title: d8211_15A_H3K36me3

source_name: KdmB 17 h H3K36me3 ChIP


title: Westar_mock-3dpi-BR1


title: d8211_48B

source_name: kdmB 48 h transcript

value: RNA-seq


title: d8211_15A_H3Ac


title: Westar_mock_0dpi-BR2


title: Westar_mock_0dpi-BR1


title: d8211_48A


title: d8211_17B

source_name: kdmB 17 h transcript


title: d8211_17A


title: input

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Genome_build: hg18
Supplementary_files_format_and_content: *peaks.bed files can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)

organism: Homo sapiens

source_name: prostate cancer cells

growth_protocol: LNCaP and VCaP cells were cultured in DMEM or RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free DMEM or RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

treatment_protocol: LNCaP and VCaP cells were treated with vehicle or DHT 10 nM for 24 h.

tag: cell line

value: AR-positive prostate cancer cell line LNCaP

tag: treatment (pre-hormone)

value: vehicle control

tag: hormone treatment

value: DHT 10 nM

value: none (input)


title: lncap_dht10nM_24h-PIpolyamide1_OCT1_hg18_-a_b_st_m1v2_1e-4

value: PI polyamide Oct1-1

value: Oct1 (Abcam, catalog# ab8895, lot# GR114621-3)


title: lncap_dht10nM_24h-PIpolyamide3_OCT1_hg18_-a_b_st_m1v2_1e-4

value: PI polyamide Oct1-3


title: LNCaP_siOCT1_AR

value: AR (Santa Cruz, catalog# H-280, lot# K2912)


title: lncap_dht10nM_24h_control_OCT1_hg18_-a_b_st_m1v2_1e-4


title: d8211_15B_H3K36me3

value: kdmB

tag: antibody

tag: library strategy

value: ChIP-seq


title: LNCaP_Cont_AR

value: siControl


title: LNCaP_input


title: Flag-Sp5_Flag ChIPseq_sample 2

data_processing:
Base calling was performed with the RTA 1.9.35.0 software.
Raw Fastq reads were aligned to the mouse mm9 build using Bowtie aligner with default parameters. Library complexity was measured by uniquely aligned reads using Picard’s markduplicate utility
Peak calling between the replicate samples for Sp5 and the replicate samples for the Input control was carried out using MACS2 algorithm. Peaks were called using the following parameters in MACS2: significance threshold q<0.1, bandwidth=300bp, model fold = [5,50].
HOMER was used to annotate the peaks to the nearest genomic features on the mm9 reference genome. The distance to TSS information and the gene start and end co-ordinates were used to determine if a peak was either upstream of the gene, within the gene-body or downstream of the gene.
Motif analysis was carried out using Genomatix Genome Analysis software, based on Matrix library 8.4, ElDorado database version 08-2011, search mode: TF matrices and both the genomic and promoter background for calculating enrichment statistics.
Genome_build: mm9
Supplementary_files_format_and_content: BED format file containing Chromosome, Start co-ordinate and Stop co-ordinates for the statistically significant peaks between Sp5 and Input

source_name: embryonic stem cells_Day 3 differentiation, Sp5

extract_protocol:
Cells were fixed for 15mins in 1% formaldehyde, quenched with glycine. Cells were lysed to extract nuclei which were then sonicated to obtain sheared genomic DNA ~100-300bp in size for sequencing.
The libraries were prepared according to standard Illumina's TruSeq Chip protocol. The ChIP DNA is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and size-selected. The size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated by qPCR before cluster generation and sequencing.

value: A2Lox.cre ES cells

tag: treatment

value: plus Dox to induce Flag-Sp5 expression

value: Day 3 differentiation

value: M2 (Sigma, catalog#  F3165, lot# SLBF1225). Used 4ug of antibody per ChIP


title: Flag ESC_Input 1

source_name: embryonic stem cells_Day 3 differentiation, Input


title: Flag-Sp5_Flag ChIPseq_sample 1

value: M2 (Sigma, catalog# F3165, lot# SLBF1225). Used 4ug of antibody per ChIP


title: D-37C.CO2.90m-2-11.06.15-11.16.15-620

status: Public on Mar 31 2016

city: Saint Louis

first: Ezekiel

last: Maier

state: MO

address: 4515 McKinley Ave

department: Computer Science

institute: Washington University in Saint Louis

description: P-CNAG_07442:GAT201(CNAG_01551)  in 37°C DMEM + 5% CO2 for 90mins

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using TopHat version 2.0.4 and Bowtie version 0.12.8
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with Cufflinks version 2.0.2. Gene boundaries were defined using the current C. neoformans genome annotation provided by the Broad institute. Gene expression was normalized using the Cufflinks provided option for quartile normalization.
After gene expression quantification, samples not passing the following quality control filters were removed from consideration. The expression of the deleted gene in mutant expression profiles was required to be less than 10% of its expression in WT. The mean and median expression of USV101 in deletion mutants was 0.3% and 0% of WT USV101 levels respectively. The low levels of expression that remained for some samples were likely the result of errors in the sequencing process itself, either due to contamination between samples or a low level of error in matching barcodes for multiplexed samples to reads. In addition, the mean and median expression of USV101 in overexpression mutants was 801% and 844% of WT USV101 levels respectively. Wild-type samples were required to express the resistance marker at less than 10% of its median level in all mutant expression profiles. In addition, to maximize the power to detect differentially expressed genes, a quality control filter was established to ensure that replicate expression profiles were in agreement. Specifically, within a replicate set the median of all gene coefficients of variation (CoV), defined as the standard deviation of gene expression over mean gene expression, was required to be less than or equal to 0.2. Any replicate set which did not pass this CoV filter was not used for differential expression analysis, and the mutant expression profiles were remade. However, replicate sets were rescued if the median CoV could be lowered below 0.2 by removing an outlier expression profile replicate.
Counts of reads mapping to each gene were quantitated using the htseq-count tool in version 0.5.3 of the HTSeq Python package.
Differential expression analysis comparing mutant and wildtype expression profiles sets in the same condition was performed by using LIMMA with the voom transformation applied to read counts.
Genome_build: C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project) – ASM14924v2
Supplementary_files_format_and_content: cuff: Gene expression was quantified processing tophat produced bam alignments with Cufflinks v2.0.2 with the current H99 annotation (v2) provided by the Broad institute's Fungal Genome initiative. Expression was normalized by applying the Cufflinks supplied quartile normalization routine. counts: Counts of reads mapping to each gene were quantitated using the htseq-count tool in version 0.5.3 of the HTSeq Python package (Anders et al. 2014).

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: All strains were constructed in the C. neoformans KN99α background. Cells were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
For RNA isolation, the culture was treated with ice-cold stop solution (5% Tris-saturated phenol in ethanol) to prevent RNA degradation and then collected by centrifugation. The cells were suspended in TRIzol reagent (Life Technologies) and lysed by mechanical bead-beating at 4°C with 0.5-mm silica-zirconia beads (4 cycles of 3 min of beating followed by 2 min on ice). Following lysis, total RNA was extracted according to the manufacturer’s instructions. Residual DNA was removed from the RNA preparation with the TURBO DNA-free kit (Life Technologies).
Poly(A) RNA was selected from the total using the mRNA Catcher Plus Kit (Life Technologies) with an epMotion 5075 automated pipettor (Eppendorf). The poly(A) RNA was subsequently sheared by incubating in TURBO DNA-free buffer at 75°C for 10 minutes and purified with the QIAquick PCR Purification Kit (Qiagen). First strand cDNA synthesis was performed using random hexameric primers and SuperScript III Reverse Transcriptase, followed by treatment with E. coli DNA ligase, DNA polymerase I, and RNase H for second-strand synthesis, all using standard methods. The cDNA libraries were end-repaired with a Quick Blunting kit and A-tailed using Klenow exo- with dATP (New England Biolabs). Illumina adapters were ligated to the cDNA and fragments ranging from 150-250 bp in size were selected using gel electrophoresis. The libraries were enriched and indexed in a 10-cycle PCR using Phusion Hot Start II High-Fidelity DNA (Fermentas), purified, and pooled in equimolar ratios for multiplex sequencing on an Illumina HiSeq 2500 at the Genome Technology Access Center.

treatment_protocol: Cells were transfered to grow for 90 minutes in capsule-inducing (DMEM, 37 °C, 5% CO2) conditions, 24 hours in capsule-inducing conditions,  or 90 minutes in capsule non-inducing (YPD, 30 °C, room air) conditions prior to isolation of total RNA.

tag: condition description

value: capsule-inducing

tag: condition

value: 37°C DMEM + 5% CO2 for 90mins

tag: induction date

tag: library date


title: D-37C.CO2.90m-3-11.06.15-11.16.15-621

tag: genotype


title: Westar_mock_0dpi-BR3

city: Winnipeg

first: Michael

last: Becker

address: 66 Chancellors Circle

institute: University of Manitoba

growth_protocol: Universally susceptible B. napus cv. Westar and advanced B. napus breeding line DF78 (Rlm3, LepR1) were inoculated with L. maculans isolate D3 (AvrLm5, AvrLepR1; Dr. A. Van de Wouw, University of Melbourne). Canola seedlings were grown in controlled environments with a 16-h photoperiod (16ºC dark, 21 ºC light). Plants were grown in Sunshine mix #4 (SunGro Horticulture, www.sungro.com). Fungal inocu

treatment_protocol: Fungal inoculum was prepared according to Zhang et al. (2015). Seven day old seedlings of cv. Westar and line DF78 were point-inoculated with 10 µL of D3 pycnidiospore suspension (2 ×107 pycnidiospores mL-1) or sterilized distilled water (mock).

value: Westar

tag: inoculation status

value: 0 days post inoculation

value: Cotyledon


title: C-37C.CO2.90m-3-11.06.15-11.16.15-618

description: P-CNAG_03437:GAT201(CNAG_01551)  in 37°C DMEM + 5% CO2 for 90mins


title: D-37C.CO2.90m-1-11.06.15-11.16.15-619


title: C-37C.CO2.90m-2-11.06.15-11.16.15-617


title: B-37C.CO2.90m-3-11.06.15-11.16.15-615

description: P-CNAG_00456:GAT201(CNAG_01551) usv101(CNAG_05420)Δ in 37°C DMEM + 5% CO2 for 90mins


title: B-37C.CO2.90m-2-11.06.15-11.16.15-614


title: C-37C.CO2.90m-1-11.06.15-11.16.15-616


title: A-37C.CO2.90m-2-11.06.15-11.16.15-611

description: P-CNAG_02044:GAT201(CNAG_01551) usv101(CNAG_05420)Δ in 37°C DMEM + 5% CO2 for 90mins


title: A-37C.CO2.90m-3-11.06.15-11.16.15-612


title: 05420-37C.CO2.90m-2-11.06.15-11.16.15-608

description: usv101(CNAG_05420)Δ in 37°C DMEM + 5% CO2 for 90mins


title: A-37C.CO2.90m-1-11.06.15-11.16.15-610


title: Flag ESC_Input 2

first: Mark

tag: time

tag: chip antibody


title: 05420-37C.CO2.90m-3-11.06.15-11.16.15-609


title: B-37C.CO2.90m-1-11.06.15-11.16.15-613


title: LNCaP_siOCT1_FOXA1

value: AR-positive prostate cancer cell line LNCaP

value: DHT 10 nM

value: FOXA1 (Abcam, catalog# ab94580)


title: 00156-37C.CO2.90m-2-11.06.15-11.16.15-605

description: sp1(CNAG_00156)Δ in 37°C DMEM + 5% CO2 for 90mins


title: 05420-37C.CO2.90m-1-11.06.15-11.16.15-607


title: 01551_over-37C.CO2.90m-3-11.06.15-11.16.15-603

description: GAT201(CNAG_01551) Overexpression in 37°C DMEM + 5% CO2 for 90mins

value: GAT201(CNAG_01551) Overexpression


title: 00156-37C.CO2.90m-3-11.06.15-11.16.15-606


title: 01551_over-37C.CO2.90m-1-11.06.15-11.16.15-601


title: 00156-37C.CO2.90m-1-11.06.15-11.16.15-604


title: 00000-37C.CO2.90m-2-11.06.15-11.16.15-599

description: wildtype in 37°C DMEM + 5% CO2 for 90mins

value: wildtype


title: 00000-37C.CO2.90m-3-11.06.15-11.16.15-600


title: 01551_over-37C.CO2.90m-2-11.06.15-11.16.15-602


title: 00000-37C.CO2.90m-1-11.06.15-11.16.15-598


title: 05420-37C.CO2.1440m-1-09.17.14-09.24.14-529

description: usv101(CNAG_05420)Δ in 37°C DMEM + 5% CO2 for 1440mins

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using TopHat version 2.0.4 and Bowtie version 0.12.8
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with Cufflinks version 2.0.2. Gene boundaries were defined using the current C. neoformans genome annotation provided by the Broad institute. Gene expression was normalized using the Cufflinks provided option for quartile normalization.
After gene expression quantification, samples not passing the following quality control filters were removed from consideration. The expression of the deleted gene in mutant expression profiles was required to be less than 10% of its expression in WT. The mean and median expression of USV101 in deletion mutants was 0.3% and 0% of WT USV101 levels respectively. The low levels of expression that remained for some samples were likely the result of errors in the sequencing process itself, either due to contamination between samples or a low level of error in matching barcodes for multiplexed samples to reads. In addition, the mean and median expression of USV101 in overexpression mutants was 801% and 844% of WT USV101 levels respectively. Wild-type samples were required to express the resistance marker at less than 10% of its median level in all mutant expression profiles. In addition, to maximize the power to detect differentially expressed genes, a quality control filter was established to ensure that replicate expression profiles were in agreement. Specifically, within a replicate set the median of all gene coefficients of variation (CoV), defined as the standard deviation of gene expression over mean gene expression, was required to be less than or equal to 0.2. Any replicate set which did not pass this CoV filter was not used for differential expression analysis, and the mutant expression profiles were remade. However, replicate sets were rescued if the median CoV could be lowered below 0.2 by removing an outlier expression profile replicate.
Counts of reads mapping to each gene were quantitated using the htseq-count tool in version 0.5.3 of the HTSeq Python package.
Differential expression analysis comparing mutant and wildtype expression profiles sets in the same condition was performed by using LIMMA with the voom transformation applied to read counts.
Genome_build: ASM14924v2, C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: cuff: Gene expression was quantified processing tophat produced bam alignments with Cufflinks v2.0.2 with the current H99 annotation (v2) provided by the Broad institute's Fungal Genome initiative. Expression was normalized by applying the Cufflinks supplied quartile normalization routine.
Supplementary_files_format_and_content: The expression.mtr file is a matrix of fully processed gene expression values (upper-quartile normalized Cufflinks reported FPKM values). The matrix is of size: number of C. neoformans genes (rows) BY number of expression profiles (columns). Each column in the expression.mtr file lists gene FPKM values from the matching .cuff file.

value: 37°C DMEM + CO2 for 1440mins


title: 05420-37C.CO2.1440m-3-09.17.14-09.24.14-531


title: 00000-37C.CO2.1440m-3-09.17.14-09.24.14-513

description: wildtype in 37°C DMEM + 5% CO2 for 1440mins


title: 05420-37C.CO2.1440m-2-09.17.14-09.24.14-530


title: 00000-37C.CO2.1440m-1-09.17.14-09.24.14-511


title: 05420-37C.CO2.1440m-2-06.18.14-07.14.14-447


title: 00000-37C.CO2.1440m-2-06.18.14-07.14.14-438


title: 00000-37C.CO2.1440m-1-06.18.14-07.14.14-437


title: 05420_over-30C.0m-3-09.13.13-10.08.13-434

description: USV101(CNAG_05420) Overexpression in 30°C YPD

value: USV101(CNAG_05420) Overexpression

value: capsule non-inducing

value: 30° YPD


title: 05420_over-30C.0m-2-09.13.13-10.08.13-433


title: 05420_over-30C.0m-1-09.13.13-10.08.13-432


title: 05420-30C.0m-2-09.13.13-10.08.13-430

description: usv101(CNAG_05420)Δ in 30°C YPD


title: 00000-30C.0m-3-09.13.13-10.08.13-428

description: wildtype in 30°C YPD


title: 00000-30C.0m-2-09.13.13-10.08.13-427

description: wildtype in 30°C YPD


title: 05420-30C.0m-1-09.13.13-10.08.13-429

description: usv101(CNAG_05420)Δ in 30°C YPD


title: 05420-30C.0m-3-09.13.13-10.08.13-431

description: usv101(CNAG_05420)Δ in 30°CYPD


title: 00000-30C.0m-1-09.13.13-10.08.13-426

description: wildtype in 30°C YPD


title: 05420_over-37C.CO2.90m-1-09.13.13-10.08.13-423

description: USV101(CNAG_05420) Overexpression in 37°C DMEM + 5% CO2 for 90mins

value: 37°C DMEM + CO2 for 90mins


title: 05420_over-37C.CO2.90m-3-09.13.13-10.08.13-425


title: 05420_over-37C.CO2.90m-2-09.13.13-10.08.13-424


title: BrdtBD1del_Input_Spermatocytes

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Sequence reads of 50+35 bp reads were produced with a SOLiDTM 4 sequencer, according to standard Life Technologies protocols. The sequence reads were analyzed with the BioScope™ software suite (cms_4448431.pdf).
After sequence read mapping to version 9 build 37 of the mouse genome allowing up to 4 mismatches, only reads mapping once to the genome were retained for subsequent analyses, to prevent spurious calls in repetitive regions.
Four BAM files were generated by the Bioscope pipeline, corresponding to the two biological conditions (P, Brdt ChIP-seq from premeiotic spermatocytes and R, Brdt ChIP-seq from postmeiotic, round spermatids), and their respective sonicated DNA inputs.
BAM files were transformed into SAM format (Li et al, 2009; PMID: 19505943).
Genome_build: mm9
Supplementary_files_format_and_content: The aligned reads files were then processed using SICER (Garmire et al, 2011, PMID:21980340; Zang et al, 2009; PMID:19505939) for input subtraction and peaks detection. Island filtered peaks were detected in spermatocytes and round spermatids with the following parameters: Redundancy threshold: 1;  Window size: 200bp; Fragment size: 150bp; Gap size: 600bp; FDR: 0.01.

source_name: Male germ cells

extract_protocol: Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded, paired-end libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf).

treatment_protocol: Spermatogenic cell suspensions were fractionated using a BSA gradient and pooled fraction of spermatocytes and round spermatids were used for ChIP with an anti-Brdt exactly as previously reported in (Tan et al, 2011; PMID: 21925322).

tag: cell type

value: Spermatocytes (meiotic)

value: Brdt BD1del


title: BrdtBD1del_ChipSeq_Spermatocytes

value: anti-Brdt


title: BrdtBD1del_ChipSeq_Round_spermatids

value: Round spermatids (post-meiotic)


title: BrdtBD1del_Input_Round_spermatids


title: 00000-37C.CO2.1440m-2-09.17.14-09.24.14-512

value: capsule-inducing


title: ur89_OP_24h_25c_rep3

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using tophat-2.0.8 with parameters --no-coverage-search  --b2-very-sensitive
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using cufflinks-2.0.2
Genome_build: WS235; GCF_000002985.6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were exposed to PA and BT at the stage L4. The BT strains were diluted in 1:250 (E.coli OP50). PA14 was diluted in 4:1 (E.coli OP50). The experiments with BT were performed at 20°C and with PA14 at 25°C.

tag: strain background

tag: genotype/variation

tag: develpmental stage

tag: exposed to

tag: timepoint

tag: medium

value: PFM

tag: temperature

tag: tissue

value: whole body


title: 05420-37C.CO2.1440m-3-06.18.14-07.14.14-448

tag: strain

tag: condition description


title: gills

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

data_processing:
Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters (> 15 nt) were retrieved for downstream analysis using the miRDeep software (https://www.mdc-berlin.de/8551903/en/).
miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12, the traditional blast output, and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the 3' end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept, and using the remaining alignments as guidelines, the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally, miRDeep predicted miRNAs by discarding non-plausible Dicer products and scoring plausible ones. To assess seed conservation, plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs, selected pre-miRNAs were blasted against Danio rerio stem loop sequences (miRBase) and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation, using miRDeep. To overcome the inherent lack of sensitivity of miRDeep, novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs.
Read numbers were normalized as described by Chen and colleagues (Genes & Development 2005, 19:1288-1293), and a miRNA expression profile, using identical number of reads for each sample, was generated. The number of reads between samples was normalized as indicated below:

Expression Reads = [1000 x (NRmiRNAXY)]/ TNRmiRNAsY

where NRmiRNAXY is the number of reads of miRNAX (X = any miRNA) in sample Y, and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package (http://www.tm4.org/mev.html).
Genome_build: Zv8
Supplementary_files_format_and_content: Tab-delimited text files include the miRNA IDs, sequences and respective raw counts after data processing for each sample.

organism: Danio rerio

source_name: adult gills (1 year old)

growth_protocol: Wild type AB zebrafish strain was maintained at 28ºC on a 14 h-light/10 h-dark cycle.

extract_protocol:
100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15-30 nt were gel-isolated using Gel Filtration cartridges from Edge Biosystems.
For cDNA synthesis, the small RNA molecules previously isolated were first ligated to a 3' adapter (AMP-5'p-5'p/CTGTAGGCACCATCAATdi-deoxyC- 3') in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the 5' adapter ("Nelson's linker" 5'ATCGTrArGrGrCrArCrCrUrGrArArA 3'), for 1 hour at 37°C, followed by phenol extraction. First strand cDNA synthesis was then performed using a specific 3'-primer and Superscript™ III reverse transcriptase (Invitrogen). RNase H treated cDNA was PCR-amplified with adapter-specific primers. Each sample contained a specific TAG constituted by 3 nucleotides, as detailed next. 24hpf - ATC; 72hpf - ACT; 96hpf - CAG; 5dpf - ATG; 45dpf - CCG; entire adult - GTA; brain - CGG; Heart - CTG; Eyes - GCT; fins - GTT; skin - TAC; gills - TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band (100 nt) was eluted from the gel with Probe Elution Buffer from Ambion, at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX (Roche), following established protocols for DNA library sequencing.

tag: strain/background

value: AB

value: wild type

value: gills

tag: developmental stage

value: adult

tag: age

value: 1 year


title: heart

source_name: adult heart (1 year old)

value: heart


title: brain

source_name: adult brain (1 year old)

value: brain


title: ur89_OP_24h_25c_rep2


title: skin

source_name: adult skin (1 year old)

value: skin


title: eyes

source_name: adult eyes (1 year old)

value: eyes


title: ur89_OP_24h_25c_rep1


title: N2_OP_24h_25c_rep3

value: Wide type


title: adult

source_name: entire adult


title: N2_OP_24h_25c_rep2


title: 45dpf

source_name: 45 days post-fertilization embryos

value: embryo


title: 5dpf

source_name: 5 days post-fertilization embryos


title: 96hpf

source_name: 96 hour post-fertilization embryos


title: fins

source_name: adult fins (1 year old)

value: fins


title: N2_OP_24h_25c_rep1


title: ur89_PA14_24h_rep3

value: mNGM


title: antiCgry-2-Input

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the Drosophila reference genome (release 5.22/6.02)
.tdf files were generated from .bam files via IGV tools
Genome_build: release 5.22/6.02
Supplementary_files_format_and_content: igvtools package (count command) generates a binary read count density file in TDF format

source_name: 3rd instar brains and imaginal discs

growth_protocol: All flies were grown at 25°C, 3rd instar larvae were dissected for brains and imaginal discs

extract_protocol:
Fixed brains and imaginal discs were dissected from 10 third instar larvae, and sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Cg [custom made], anti-Ph (a kind gift from Donna Arndt-Jovin) antibodies and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies.
Input ChIP DNA (30 ng) is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated before cluster generation. http://ethanomics.wordpress.com/chip-seq-library-construction-using-the-illumina-truseq-adapters/.

value: ry- wild type

value: 3rd instar larva

value: CNS and imaginal discs


title: 24hpf

source_name: 24 hour post-fertilization embryos

value: whole body


title: antiCgry-1

value: antiCg (custom-made)


title: antiH3K27cg-1-I

value: cgA22 mutant

value: anti-H3K27me3 (Millipore, 17-622)


title: 72hpf

source_name: 72 hour post-fertilization embryos

value: AB

value: wild type


title: ur89_PA14_24h_rep2


title: antiH3K27-cg-2


title: ur89_OP_24h_NGM_rep1

description:
Matched control of npr-1 (ur89) to PA14 at 24h
B1681


title: antiPh-cg-1

value: anti-Ph (a kind gift from Donna Arndt-Jovin)


title: N2_PA14_24h_rep2


title: antiH3K27-cg-1


title: N2_PA14_24h_rep1


title: ur89_OP_24h_rep2

description:
Matched control of npr-1 (ur89) to BT247 at 24h
B1683

value: PFM


title: ur89_OP_24h_rep3

description:
Matched control of npr-1 (ur89) to BT247 at 24h
B1763


title: ur89_OP_24h_NGM_rep2

description:
Matched control of npr-1 (ur89) to PA14 at 24h
B1761


title: N2_OP_24h_NGM_rep1

description:
Matched control of N2 to PA14 at 24h
B1684


title: ur89_OP_24h_rep1

description:
Matched control of npr-1 (ur89) to BT247 at 24h
B1668


title: N2_OP_24h_NGM_rep2

description:
Matched control of N2 to PA14 at 24h
B1764


title: ur89_BT_24h_rep3


title: ur89_BT_24h_rep1


title: antiCgry-2


title: ur89_BT_24h_rep2


title: ur89_PA14_24h_rep1


title: N2_BT_24h_rep3


title: antiPh-cg-2


title: N2_OP_24h_rep2

description:
Matched control of N2 to BT247 at 12h
B1685


title: ur89_OP_12h_25c_rep3


title: N2_OP_24h_rep1

description:
Matched control of N2 to BT247 at 12h
B1659


title: N2_BT_24h_rep2


title: N2_BT_24h_rep1


title: N2_OP_12h_25c_rep1


title: ur89_OP_12h_25c_rep1


title: ur89_OP_12h_25c_rep2


title: N2_OP_24h_rep3

description:
Matched control of N2 to BT247 at 12h
B1765


title: N2_OP_12h_25c_rep3


title: N2_PA14_24h_rep3


title: N2_OP_12h_25c_rep2


title: N2_PA14_12h_rep2


title: ur89_PA14_12h_rep1


title: N2_PA14_12h_rep3


title: ur89_OP_12h_NGM_rep2

description:
Matched control of npr-1 (ur89) to PA14 at 12h
B1718


title: ur89_PA14_12h_rep3


title: ur89_PA14_12h_rep2


title: N2_PA14_12h_rep1


title: ur89_OP_12h_NGM_rep1

description:
Matched control of npr-1 (ur89) to PA14 at 12h
B1670


title: N2_OP_12h_NGM_rep2

description:
Matched control of N2 to PA14 at 12h
B1720


title: ur89_OP_12h_rep2

description:
Matched control of npr-1 (ur89) to BT247 at 12h
B1677


title: ur89_OP_12h_rep3

description:
Matched control of npr-1 (ur89) to BT247 at 12h
B1725


title: N2_OP_12h_NGM_rep1

description:
Matched control of N2 to PA14 at 12h
B1672


title: ur89_BT_12h_rep1


title: ur89_OP_12h_rep1

description:
Matched control of npr-1 (ur89) to BT247 at 12h
B1667


title: N2_OP_12h_rep1

description:
Matched control of N2 to BT247 at 12h
B1665


title: N2_BT_12h_rep2


title: ur89_BT_12h_rep3


title: WT-control (OE)

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat-2.0.9 with parameters --bowtie1 --segment-length 21
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: EML Cell Line

growth_protocol: EML cells were maintained in medium containing stem cell factor (SCF). EML cells were grown in IMDM containing 20% FBS and SCF (200 ng/ml, PeproTech).

extract_protocol:
RNA was extracted from TRIZOL (Invitrogen) or RNeasy RNA isolation kit (Qiagen).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Pusion PCR master mix (Thermo Scientific, Hudson, NH).

tag: cell line

value: EML

tag: treatment

value: overexpression control

value: Bone marrow

value: Basophil


title: KAI1-OE

value: KAI1 overexpression


title: KAI1-KD rep1

value: KAI1 knockdown


title: WT-control (KD) rep2

value: knockdown control


title: WT-control (KD) rep1


title: N2_BT_12h_rep3

value: Wide type


title: N2_BT_12h_rep1


title: NSK_HOD2_20Tags

city: Grenoble

first: sandeep

middle: kumar

last: Nadendla

state: Isere

address: 17 Rue des martyrs

department: iRTSV/Biomics

institute: CEA

description: 20 random DNA barcodes flanked by pGEX adapters

data_processing:
FASTQC initial quality and copy number analysis. This is the only result needed for the validating SRiD: DNA barcode generator and management system. Further alignments are not necessary for our project.
Copy numbers are generated automatically by FASTQC software during the initial quality check-up step.
Here, the term 'copy  number' refers to the final number of individual DNA barcodes/sequences that are significantly represented in a high throughput sequencing run.
Supplementary_files_format_and_content: FASTQC output which includes number of significant sequences and their respective percent representation in our screen.

organism: synthetic construct

source_name: Random DNA sequences

growth_protocol: PC3 cells maintained in RPMI-Glutamax medium

extract_protocol:
genomic DNA extraction from Qiagen
P5 and P7 adapters by blunt end ligation to DNA barcodes eluted from E-gel size select post 10cycle PCR at 60°C

treatment_protocol: Lipofectamine-RNAiMAX transfection with DNA barcodes

tag: molecule type

value: DNA barcodes

tag: host cell line