title: REV_run56

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

data_processing:
Standard Illumina base calling software was used to base call the 40-42 nucleotide sequence reads. We used SHORE (http://shore.sourceforge.net) as a platform for further analysis. The obtained reads were quality filtered and low quality bases at the 3’ end were pruned as described. GenomeMapper (http://1001genomes.org/software/) was used for mapping to the TAIR9 genome, allowing for up to four mismatching nucleotides and no gaps. To proceed, the mapped data were subjected to a heuristic for removal of duplicate sequence reads which were assumed to be uninformative for the detection of enriched loci. A threshold was applied limiting the number of 5’ ends mapping to the same position on the same strand. To retain the power to discriminate between multiple strongly enriched regions, the threshold for any particular position was varied depending on the coverage in close vicinity, such that the variance of the number of reads per position would roughly equal its mean in a 30 bp sliding window. We further applied a two-step procedure to identify regions significantly enriched in the positive sample when compared to the control. First, potentially enriched regions were identified based on the positive samples only. These sites were then directly compared to the corresponding control sample regions to assess statistical significance. For estimation of the depth of coverage for each position in the genome, all positive sample reads mapping to unique positions were extended in 3’ direction to 130 bp, corresponding to half the experimentally observed approximate DNA fragment size, while discarding all other reads. To detect possible peak sites, a 2 kb wide sliding window was applied to the coverage graph in single base steps. In each step a p-value was assigned to the coverage value at the central base using a one-sided Poisson test, with the distribution parameter set to the average coverage within the sliding window. Only positions with coverage greater than zero were included in the calculation of the average, assuming all other positions to be inaccessible to the experiment. Finally, any consecutive stretch of positions with p-value <0.05 and length >130 bp was retained as a potentially enriched site. To further reduce the number of regions to be considered, each was checked for unwarranted high average coverage in the control sample. A potential peak in the positive sample was discarded if the coverage mean in the control sample in the corresponding region was larger than the median average control coverage plus a tolerance of three standard deviations in all peak regions. For assignment of final p-values to each candidate region, in each replicate a one-sided binomial test was applied to the number of reads mapping to the region in the positive sample, with the distribution parameter N set to the joint read count for the site for the positive and the corresponding control sample. To estimate the probability parameter for the test, from now on called r, we computed a scaling factor s for the control sample and the chromosome containing the considered region. The complete chromosome sequence was subdivided into 400 base pair bins, and for each bin the positive sample as well as the control sample read counts were recorded. Then s was chosen such that the median ChIP sample read count for all bins equaled the median control sample read count multiplied by s. From this the binomial test parameter r was calculated as r=s/(s+1). Finally, false discovery rates were obtained through the Benjamini-Hochberg correction method. To establish a ranking of peak regions across replicates, the rank product over the per-replicate fdr ranks was used. To define the bound DNA set, we used all peaks with fdr > 0.1 in both ChIP experiments, resulting in a set of 1564 peaks.
Genome_build: TAIR9
Supplementary_files_format_and_content: text file with peak positions and signal intensity for both rev and control samples.

source_name: 10 day old seedling

growth_protocol: liquid culture

extract_protocol:
Chromatin‐immunoprecipitation experiments were carried out as described by Kwon et al. (Kwon et al, 2005), except that anti‐FLAG M2 magnetic beads (Sigma) were used and immunoprecipitations were only performed for two hours.
The ChIP‐seq libraries and the Illumina was performed as described by Yant et al. (Yant et al, 2010).

tag: strain

value: seedling

value: F3165 Sigma Monoclonal ANTI-FLAG M2


title: urt1_rep1

status: Public on Mar 11 2016

type: SRA

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description: Small RNA

library_source: transcriptomic

data_processing:
Base calling by Illumina CASAVA-1.8.2.
Trimmed reads of 14nt to 30nt in length were selected to be mapped to TAIR10 genome using Bowtie (Langmead et al., 2009) by permitting up to 1 mismatch in the first 14 read nucleotides and no limit beyond. Reads that could map to more than 50 loci were discarded and only the best alignment(s) of each small RNA sequence was kept.
The resulting alignment was annotated using the intersectBed tool from the BEDTools suite (v2.17.5) (Quinlan and Hall, 2010), and either the Arabidopsis annotation file ath.gff with 427 mature miRNA sequences (http://www.mirbase.org/) or a custom annotation file with genome coordinates for 8 siRNA loci (siR-1: CACGGTCTTGGCTCAACCCGCC, siR-2: GAACGCTATGTTGGACTTAGGATG, siR-3: ATTATCCCCCGTGTTTTGTCC, siR-4: TGCCCGGACCCTGTCGCAC, siR-5: TTAGATTCACGCACAAACTCT, siR-6: CCTTTGCAGACGACTTAAATAC, siR-7: TCCGCTGTAGCACACAGGC, siR-8: CCTTTGTCGCTAAGATTCGA).
Tailing and trimming at the 3' end of small RNA was identified using a homemade python script. Canonical variants were first isolated by looking for reads with perfect match for miRNA and siRNA sequences. Then, miRNA and siRNA sequences were successively trimmed from 1 nt to 7 nt in order to identify trimmed variants. At each matching step, 3' tails were extracted, i.e., untemplated nucleotides at the 3’ end of sRNA reads. To minimize bias due to reads with sequencing errors, that would be considered as having 3' untemplated nucleotide, if the nucleotide after the first mismatch matched to the miRNA/siRNA sequence, the read was removed from the analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, two processed data files are provided with either miRNA or siRNA data. Data were generated using homemade python and R scripts. For each miR loci, we indicate : 1) the name of the miRNA, 2) the canonical sequence, 3) the read sequence, 4) the number of trimmed nucleotides at the 3’ end of the miRNA, 5) the number of added nucleotides at the 3’ end of the miRNA , 6) the composition of the tail , 7) the normalized number of reads (multi-mapped reads were weighted by a factor 1/n, n being the number of identical loci where reads mapped), and 8) the tail category. For each siR loci, we indicate : 1) the name of the siRNA loci, 2) the genomic-encoded sequence, 3) the read sequence, 4) the number of added nucleotides at the 3’ end of the siRNA, 5) the composition of the tail , 6) the normalized number of reads (multi-mapped reads were weighted by a factor 1/n, n being the number of identical loci where reads mapped), and 7) the tail category.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings, urt1 mutant

growth_protocol: Arabidopsis thaliana plants were grown in vitro on MS with 16h light/8h darkness cycles.

extract_protocol:
RNAs were extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
Small RNA libraries were generated from 3µg of total RNA using the Illumina Small RNA TruSeq protocol.

tag: genotype/variation

value: urt1 mutant (Salk_087647C)

tag: tissue

value: seedlings

tag: age

value: two weeks


title: control_run56

status: Public on Mar 12 2016

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: 46c_H3K122ac_rep2

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

description:
processed data file:
46C_H3K122acmerged.10bpres.bed, 46C_H3K122acmerged.10bpres.bedGraph.gz

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.8 (options bowtie -e 40 -m 1 -v 2)
Bedgraph tracks were generated from the aligned reads by the program makeUCSC file from HOMER software suite (version 4.3) at a resolution of 10bp and the total number of tags is normalized to 10 million.
bed peak files were generated using SICER (v1.1) (Zang et al, 2009), using GSM1156619 UD46c input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01
column headers for islands-summary-FDR0.01.bed files;
chrom,start,end,ChIP_island_read_count,CONTROL_island_read_count,p_value,fold_change,FDR_threshold
Genome_build: 46c data: NCBI37/mm9; K562 data: GRCh37/hg19

organism: Mus musculus

growth_protocol: 46c (Sox1-GFP) ESCs (Ying et al. Nature biotechnology 2003) were cultivated without feeders in GMEM media containing With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, Sodium Pyruvate, Lif,  beta-Mercaptoethanol, Nonessential aminoacids, penicillin and streptomycin.  Human erythro-myeloblastoid leukemia cells (K562) were cultured in RPMI 1640 With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, penicillin and streptomycin.

extract_protocol:
Chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Undifferentiated ESCs and K562 cells

tag: cell line

value: 46c (sox1-GFP)

tag: cell type

value: mouse embryonic stem cells

tag: passages

value: anti-H3K122ac (Tropberger et al 2013, PMID:23415232)


title: GFP dsRNA-6days

city: Beijing

first: Gong

last: Cheng

address: 4305 Biotechnology Building, Tsinghua University

country: China

institute: Tsinghua University

description: blood feeding

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: Aaegl3.3
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample

organism: Aedes aegypti

source_name: Midguts

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
Midguts were dissected from mosquitoes, and total RNA was extracted by 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: 7 days old mosquitos were microinjected GFP dsRNA or AaMesh dsRNA;  7 days old mosquitos were feed pre-immune or AaMesh antibody

value: Liverpool strain

tag: Sex

value: female

value: 7 days

value: midguts

tag: microinjected with

value: GFP dsRNA

tag: time point

value: 6 days


title: AaMesh antibody-18h

description: blood feeding

tag: fed with

value: AaMesh antibody


title: AaMesh dsRNA-6days

description: blood feeding

value: AaMesh dsRNA


title: urt1_rep2

description: Small RNA


title: AaMesh dsRNA-3days

description: blood feeding

value: 3 days


title: CCA1-ChIP_IonPGM

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

country: Japan

institute: Nagoya University

data_processing:
For IonPGM. Basecalls was performed by IonPGM pipeline.
For IonPGM. Sequence reads were mapped against to a Arabidopsis reference genome (TAIR10) by IonPGM pipeline, generating Binary Alignment/Map (BAM) format file.
For Illumina GAII. Basecalls was performed by Illumina GAII pipeline.
For Illumina GAII. Sequence reads were mapped against to a Arabidopsis reference genome (TAIR10) by Bowtie 0.12.7 (Langmead et al., Genome Biol., 2009), generating Sequence Alignment/Map (SAM) file.
For Illumina GAII. SAM file was converted into Binary Alignment/Map (BAM) format file by Samtools 0.1.18 (Li et al., Bioinformatics 2009).
For IonPGM and Illumina GAII. Peak-calling of Bam files were performed by MACS2 (Zhang et al., Genome Biol., 2008), generating a Bed files (CCA1-peaks_PGM.bed, CCA1-peaks_Illumina.bed).
Genome_build: TAIR10

source_name: CCA1pro:CCA1-FLAG cca1 lhy

growth_protocol: Seedlings were grown on MS  plate medium with 2% sucrose under 12 h light 12 h dark at 22 Celcius degree. Plants were fixed in the morning (1 hr after light on).

extract_protocol:
Nuclei isolated from fixed plants, were sonicated and immunoprecipitated with anti-FLAG antibody (F3165, SIGMA), according to the method (Nakamichi et al., PNAS,109:17123-17128, 2012).
Libraries were prepared according to suppliers' instructions, Ion Plus Fragment library Kit (4471252, Life Technologies) for IonPGM, and ChIP-Seq Sample Prep Kit (Part# IP-102-1001, Illumina) for Illumina GAII.

tag: accession

value: expressing CCA1-FLAG

value: 14 days

value: Whole seedlings

value: anti-FLAG antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #


title: Pre-immune-18h

description: blood feeding

value: pre-immune


title: isw2_Chd1D513N_MNase

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

country: USA

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Tophat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Between-strain comparisons were done using best-matched MNase digests. For isw2-related parent strains, wild-type 2 is best-matched. For ume6-related strains, wild-type 1 is best-matched. For WT +Chd1Ume6, wild-type 1 is best-matched.
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: coverage file with tab-delimited chromosome/position/normalized dyad counts

organism: Saccharomyces cerevisiae

growth_protocol: log cells were grown to OD600 0.4 to 0.6

extract_protocol:
DNA was purified by phenol/chloroform and mononucleosome size fragments were purified from an agarose gel for library construction
TruSeq protocol (Illumina) was followed

treatment_protocol: cells were treated with zymolyase and spheroplasts were treated with MNase and ExoIII to produce nucleosome ladders corresponding to roughly 80% mononucleosomes

tag: strain background

value: W303 auxotroph

value: isw2 deletion with catalytically inactive hybrid remodeling protein

tag: matched wild type sample


title: xrn4

description:
TAIL-seq
Processed data file: processed_file.txt

data_processing:
Illumina CASAVA-1.8.2.
In order to identify transcripts, Read 1 sequences were mapped onto the Arabidopsis thaliana reference genome (TAIR 10) using Tophat (v2.0.9) (Langmead et al., 2009; Trapnell et al., 2009; Kim and Salzberg, 2011; Kim et al., 2013) and Bowtie2 (Langmead and Salzberg, 2012). Two mismatches were allowed.
After removing multimapped reads, the resulting alignment was annotated using the intersectBed tool from the BEDTools suite (v2.17.5) (Quinlan and Hall, 2010) and the Arabidopsis annotation file TAIR10_GFF3_genes.gff (http://www.arabidopsis.org). Reads 1 that map onto cytosolic mRNA and their corresponding reads 2 were extracted and used for further analyses.
The sequences having completely identical nucleotides in read 1 (insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3' adapter) were deduplicated. The degenerated sequence in 3' adapter was clipped out from read 2 by searching perfect match of delimiter sequence ('GTCAG' as in the direction of read 2) between 10th and 20th cycles in read 2. Reads 2 missing a delimiter sequence were removed from further analyses. In order to extract poly(A)-free 3' ends, the 40nt next to the 3' adapter of the reads 2 were mapped onto the Arabidopsis genome using Tophat with two allowed mismatches.
A python script was then developed to extract polyA tails (>3nt) and their potential 3' end modification from the remaining read 2. Poly(A) were detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3' end modification of poly(A) tails was limited to the last 29 nucleotides of insert. For poly(A) tails longer than 8nt, up to 3 non-consecutive nucleotides other than A were tolerated in the polyA tail in order to include heteropolymeric poly(A) tails in the analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data are provided for reads with poly(A) tail <31nt in one txt file. For each read ID, we indicate the genotype, the size of the poly(A) tail, the composition and the size of the 3’ end modification, the size of the extension PolyA size, the category (no tail, U tail, G tail or C tail) and the Arabidopsis gene AGI.

source_name: seedlings, xrn4 mutant

growth_protocol: Arabidopsis thaliana plants were grown on soil with 16h light/8h darkness cycles.

extract_protocol:
RNAs were extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
TAIL-seq libraries were prepared according to Chang et al., 2014 (PMID 24582499).

value: xrn4-3 mutant (SALK_014209)

value: seedlings

value: two weeks


title: urt1

value: urt1-1 mutant (Salk_087647C)


title: WT

source_name: seedlings, WT

tag: ecotype

value: WT


title: CCA1-ChIP_Illumina

description: CCA1-ChIP_Illumina GAII

tag: genotype/variation


title: 27_L4_744_2

status: Public on Mar 10 2016

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

description: co-cultured with wild type M. maripaludis

data_processing:
reads were trimmed and filtered by using Trimmomatic. LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36, PE, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10
reads were aligned to reference genome by using STAR. --runThreadN 8 --outSAMattributes All --genomeLoad NoSharedMemory --outFilterType Normal --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNoverLmax 0.03 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 5784458574 --readFilesCommand zcat --outReadsUnmapped Fastx --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4 --quantMode TranscriptomeSAM GeneCounts
reads per transcript were counted by using htseq-count. -t "exon" -r pos -f bam
Genome_build: ASM19575v1
Supplementary_files_format_and_content: Tab-delimited file of read counts per transcript calculated with htseq-count

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: bacteria

growth_protocol: Both mono and co-culture strains were grown at 37°C. Media used in these studies were formulated based on CCMA medium as described previously (Walker et al., 2009). Lactate medium for ST growth contain 40 mM of lactate and no sulfate. Lactate sulfate medium for SR growth contains 40 mM of lactate and 15 mM of sulfate. The headspace for tubes or cultures were filled with 80% N2 and 20% CO2 gas to create an anoxic environment. All media pHs were adjusted to 7.2 with bicarbonate. Growth of co-cultures were followed in replicate Balch tubes with 10 ml of culture volume under anaerobic conditions. Optical density was measured by using a Thermo Scientific Spectronic 200 spectrophotometer at 600nm wavelength.

extract_protocol:
Total RNA extraction was performed with MasterPure Complete DNA and RNA Purification kit (Epicentre Technologies, Madison, WI). Ambion DNA-free kit (Life Technologies, Grand island, NY) was used to ensure DNA-free samples. Illumina RiboZero rRNA removal kit (Illumina, San Diego, CA) was used for rRNA depletion.
Samples were prepared with TrueSeq Stranded mRNA HT library preparation kit (Illumina, San Diego, CA) and sequenced by using NextSeq Sequencing machine in mid output 150 v2 flow cell.

treatment_protocol: For state transition experiments between ST and SR, co-cultures were initially grown in ST medium until early log phase (OD ~ 0.15) and 0.5 ml of inoculum was transferred into 10 ml of fresh SR medium. Cells were grown to early log density (OD600 ~ 0.2) and 0.5 ml was transferred back into fresh ST medium. Samples for RNA-seq were collected at transition points.

tag: condition

value: syntrophy

tag: medium

value: Lactate/No-Sulfate

tag: transition

tag: replicate


title: PL45 IGF2BP3 iCLIP 1

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

state: CA

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

description:
total RNA
iCLIP.txt

data_processing:
iCLIP 1: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP 2: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) each read was searched for the presence of adaptor sequence TGGAATTC and trimmed from that point on. Reads without the adaptor were discarded. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP 3: (samples pl45xx_imp3_jh080c, panc1x_imp3_js004b) internal barcode positions 1-9 were trimmed before mapping
iCLIP 3: (samples pl45_imp3h_jh59) 25bp were trimmed from the 3' end of each read before mapping
iCLIP 4: reads mapping (by bowtie2) to human repeatMasker elements were discarded
iCLIP 5: (samples pl45xx_imp3_jh080c, pl45_imp3h_jh59) reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP 5: (samples panc1x_imp3_js004b ) reads were mapped by STAR to hg19 with an additional set of junctions derived from Gencode V19 basic with 100bp overlap
iCLIP 6: for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP 7: peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for hg19.
hg19
iCLIP.txt; contains information on Cell Line, chromosome start and  stop, strand, IGF2BP3 Location in Nearest Intragenic Anchor,  Exon Coordinates First/Internal/Last, Gene Symbol

organism: Homo sapiens

source_name: PL45 cells

growth_protocol: For iCLIP, RIP-seq, and small RNA-seq protocols, PL45 and/or Panc1 cells were grown in 10 cm2 cell culture plates reaching 70-80% confluency. For RNA-seq protocol, PL45 and Panc1 control and IGF2BP3 KD cell lines were grown to 60-70% confluency in 6-well plates.

extract_protocol:
For iCLIP protocol, cytosolic extracts (detergent lysis) were prepared from PL45 and Panc1 cell lines prior to immunoprecipitation.  For RNA-seq, cytosolic extracts (detergent lysis) were prepared from control and IGF2BP3 shRNA Pl45 and Panc1 cell lines, and RNA isolation from these extracts was performed with TRIreagentLS. For PL45 and Panc1 RIP-seq, cells where lysed in polysomal lysis buffer buffer (10 HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP40, 2 mM dithiothreitol) containing proteinase and RNA inhibitors.
For iCLIP, libraries were constructed as previously described (Huppertz, I., et al. Methods. 2014) with minor changes. 3' Adenylated adapter, AIR ligase, and PCR primers used from NEXTflex™  Illumina Small RNA-Seq Library Prep Kit (Bioo Scientific) and RT primers were adapted for kit reagent use. For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ Kit was used (Bioo Scientific). For small RNA-seq library prepartation, NEXTflex™ Small RNA-Seq Kit v2 was used.
For iCLIP, RNA purification was performed as previously described (Huppertz, I., et al. Methods. 2014). For RNA-seq, PolyA+ selection was performed. For small RNA-seq. For Panc1 RIP-seq samples, RNA was eluted from IP using Proteinase K digestion of protein, followed by isolation using acid Phenol-chloroform extraction. For small RNA-seq, total RNA from TRIreagentLS prep was used.

treatment_protocol: PL45 and Panc1 control and IGF2BP3 shRNA cells were selected with puromycin treatment at 5µg/mL for 3 days and later used for RNA isolation and library construction.

tag: cell type

value: Epithelial

tag: disease

value: Pancreatic ductal adenocarcinoma

tag: knockdown


title: 30_LS4_744_4

value: sulfate respiration

value: Lactate/Sulfate


title: 29_LS4_744_2


title: 28_L4_744_4


title: 26_L4_WT_4

value: Wild type


title: 22_LS3_WT_2


title: 24_LS3_744_2


title: 21_L3_744_4


title: 19_L3_WT_4


title: 23_LS3_WT_4


title: GFP dsRNA-3days

description: blood feeding

tag: strain

value: Liverpool strain

tag: Sex

value: female

tag: age

value: 7 days

tag: tissue

value: midguts

tag: microinjected with

value: GFP dsRNA

value: 3 days


title: 20_L3_744_2


title: 17_LS2_744_4


title: 18_L3_WT_2


title: urt1xrn4

source_name: seedlings, urt1 xrn4 double mutant

value: urt1-1 xrn4-3 double mutant

value: seedlings


title: 15_LS2_WT_4


title: Donor 1: Control sample technical rep2

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

country: Australia

institute: WEHI

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were mapped using TopHat (Trapnell etal. Bioinformatics,2009) with default parameters.
Gene-level counts were obtained using the htseq-count utility (Anders et al. Bioinformatics, 2014) from the HTSeq package using the Entrez Gene annotation.
Data was TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Genome_build: GRCh37p10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID and the number of reads mapping to that gene.
Supplementary_files_format_and_content: il13_genewise_counts.txt: Collapsed matrix of read counts

source_name: Donor 1

growth_protocol: PBMC were grown at 37oC with 5% CO2 in RPMI media supplemented with 10% FBS

extract_protocol:
RNA was extracted with QIAGEN mini Rneasy kits
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMC were either untreated or treated with IL-13R antagonist for 30 min then either stimulated or unstimulated with IL-13 for 24 h

value: Blood (PBMC)

tag: timepoint

value: 24 hours

tag: treatment

value: Untreated

tag: antibodystimulation

value: No


title: Donor 1: Control sample technical rep1


title: Donor 1: Control sample technical rep3


title: 12_L2_744_2

value: syntrophy

value: Lactate/No-Sulfate


title: 25_LS3_744_4

value: sulfate respiration


title: 14_LS2_WT_2

value: Lactate/Sulfate


title: Donor 3: IL-13 Stimulated and antagonist stimulation technical rep3

source_name: Donor 3

value: IL-13R Antagonist


title: Donor 3: IL-13 Stimulated and antagonist stimulation technical rep1


title: Cercis gigantea_dgd

city: ShangHai

first: Liucun

last: Zhu

state: ShangHai

address: Room 402, No. 17, ShangDa Road

institute: Shanghai University

description:
The tree was grown in open-air farmland in Jiangsu Provence in eastern China.
degradome-Seq

data_processing:
Raw sequencing reads were obtained using Illumina’s Sequencing Control Stu-dio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Repetitive sequences, 3’ adapter sequences, sequences with lengths shorter than 17 nt and longer than 27 nt sRNA, and sRNA sequences that included junk reads were removed from raw data to obtain unique clean reads for identification of C. gigantea miRNAs using perl scripts.
To identify the known miRNAs from C. gigantea, unique clean reads were used to query the miRBase v. 20.0 (-r 5, -W 4, E-value < 1) that fulfilled any of the following criteria: (1) perfect match with the miRNA sequence or its reverse complementary sequence; (2) exact match with the miRNA seed sequence, with a identity ≥ 95%, length matching ≥ 90% of the read, and read abundance ≥ 5; (3) not exactly matching the sequence, with a similarity ≥ 95%, length matching ≥ 90% of the read, and read abundance ≥10.
To find the novel C. gigantea miRNAs, the previous transcriptome sequencing data were re-assembled and the length of 70 – 200-bp transcripts were used as the candidates of the pre-miRNAs. The unique clean reads with high abundance (> 5) were first located on the transcripts using BLASTN program (E-value < 1). The RNA secondary structure prediction software (RNAFold) was then employed to determine whether the transcripts with an exact sRNA match had a stem-loop structure. Their minimum free energy (MFE) and adjust minimal folding free energy (AMFE) were also measured. The novel miRNA candidate was determined when the stem-loop structure with miRNA candidate located in the arm was required, AMFE was less than -15 kcal/mol, and mismatches between miRNA and miRNA* were no more than 4. Finally, Rfam online database program was used to remove other types of sRNAs (rRNAs, scRNAs, snoRNAs, snRNAs, and tRNAs) to obtain the pre-miRNA sequence and the novel miRNA of C. gigantea.
The identified C. gigantea miRNAs were mapped to the transcript using NCBI-BLASTN. Then, each miRNA and mRNA match was scored according to the following rules: Mismatch: 1 score deduction; G:U match: 0.5 score deduction; and if the above two conditions happened on the 2nd – 13th positions at 5’ end of the miRNA: double the deduction score. The mRNA was identified as an miRNA target if the abundance of degradome reads at the mRNA cleavage site was no less than 5; the miRNA and its target mRNA sequences were reverse complementary, and the total of the deduction scores was less than 4
Genome_build: SRR957672 ; The transcriptome shotgun assembly has been accessioned at GenBank under ID: GAOK00000000
Supplementary_files_format_and_content: miR txt file includes miRNA name, sequence, length and number of raw reads; dgd_txt file includes predicted target name, alignment score, alignment range, cleavage sites, number of raw reads and putative function

organism: Cercis gigantea (nom. inval.)

source_name: young roots, tender shoots, young leaves and flower buds of adult Cercis gigantea tree

extract_protocol:
Samples were collected from young roots, tender stems, young leaves, and flower buds and frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq small RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Small RNA library was prepared for sequencing using standard Illumina protocols


title: Cercis gigantea_miR

description: The tree was grown in open-air farmland in Jiangsu Provence in eastern China.

value: young roots, tender shoots, young leaves and flower buds


title: 13_L2_744_4


title: Donor 3: IL-13 Stimulated PBMCs technical rep3


title: Donor 3: IL-13 Stimulated PBMCs technical rep1


title: Donor 3: IL-13 Stimulated PBMCs technical rep2


title: Donor 3: Control sample technical rep3


title: Donor 3: Control sample technical rep2


title: 09_L2_WT_2

value: Wild type


title: 16_LS2_744_2


title: Donor 2: IL-13 Stimulated PBMCs technical rep3

source_name: Donor 2


title: Donor 2: IL-13 Stimulated PBMCs technical rep2


title: 08_LS1_744_4


title: IGF2BP3 shRNA RNA-seq 2

description:
polyA RNA
DESeq_Results.txt

data_processing:
RNAseq 1: the 101x101bp pairedEnd reads were trimmed to 80x80 by trimming from each read, 21bp from the 3' endend
RNAseq 2: reads mapping (by bowtie2) to human repeatMasker elements were discarded
RNAseq 3: reads were mapped to hg19 by tophat, aided by a gtf file based on UCSC Knowngenes
RNAseq 4: duplicate read mappings of the same start and end position were discarded
RNAseq 5: bam files were converted to coverage using bedtools
RNAseq 6: for each gene in UCSC KnownGenes, the total coverage was calculated over all the coding positions in all potential exons of the gene.
RNAseq 7: the coverage per gene was divided by 160 to generate an effective count of (80x80bp pairedEnd) reads per gene for input to DESeq
RNAseq 8: DESeq was run to compare the 2 control replicates to the 2 knockdown replicates for all genes with coverage in any sample
hg19
DESeq_Results.txt; contains information regarding  gene symbol, genome id, baseMean, baseMean_panc1ctrl, baseMean_panc1shrn, foldChange, log2FoldChange, p-value, adjusted p-value, and Cell Line

value: Epithelial

value: Pancreatic ductal adenocarcinoma


title: Donor 3: Control sample technical rep1


title: Donor 2: Control sample technical rep3


title: Donor 2: IL-13 Stimulated PBMCs technical rep1


title: 07_LS1_744_2


title: Donor 2: Control sample technical rep2


title: 06_LS1_WT_4


title: Donor 1: IL-13 Stimulated and antagonist stimulation technical rep2


title: 05_LS1_WT_2


title: Donor 3: IL-13 Stimulated and antagonist stimulation technical rep2


title: 10_L2_WT_4


title: Donor 1: IL-13 Stimulated and antagonist stimulation technical rep1


title: 03_L1_744_2


title: Donor 1: IL-13 Stimulated PBMCs technical rep3


title: 04_L1_744_4


title: Donor 1: IL-13 Stimulated PBMCs technical rep2


title: 02_L1_WT_4


title: Donor 1: IL-13 Stimulated PBMCs technical rep1


title: LHCN-M2 6hr doxycycline RNA-Seq, LHCNM2iDUX4HTFDox1

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters: ILLUMINACLIP:TruSeq3-SE.fa (or -PE.fa):2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25.  Trimmed reads were mapped to the hg19 genome with STAR (version STAR_2.4.2a_modified).  Mapped reads were indexed and sorted with samtools (1.0).  Uniquely mapped reads were assigned to genes using the Ensembl version 75 annotation. Differential expression and FPKM values were determined with DESeq2 (1.8.2) using custom R scripts available at https://github.com/micahgearhart/dux4
Genome_build: hg19

source_name: immortalized human myoblast line LHCN-M2

growth_protocol: LHCN-M2-iDUX4 cell were cultured on gelatin coated dishes in Ham’s F10 medium containing 20% FBS, penicillin/Streptomycin, 10 pg/ml human basic FGF, 40 pg/ml Dexamethasone, 0.114 mM beta-mercaptoethanol at 37°C in 5% O2/5% CO2.

extract_protocol: Samples were quantified via Ribogreen (Life Technologies, CA) and ran on the Tapestation 2200 (Agilent, CA) instrument to verify RNA integrity. They then underwent library creation using 1 ug total RNA as input with the TruSeq Stranded mRNA Sample Preparation kit (Illumina, CA) in accordance with the protocol. The libraries were pooled in equimolar fashion and then size-selected to 320 bp +/- 5% with the CaliperXT (Perkin-Elmer, MA). Sequencing was performed in on a HiSeq2500 High-Output 50 paired-end flow cell (Illumina, CA).

tag: treatment dose

value: 250 ng/ml doxycycline

tag: treatment time


title: LHCN-M2 6hr doxycycline RNA-Seq, LHCNM2iDUX4HTFDox3


title: LHCN-M2 6hr doxycycline RNA-Seq, LHCNM2iDUX4HTFDox2


title: LHCN-M2 6hr doxycycline ChIP-Seq Histone H3

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters: ILLUMINACLIP:TruSeq3-SE.fa (or -PE.fa):2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the hg19 genomes with bowtie2 (version 2.2.4).
Mapped reads were indexed and sorted with samtools 1.0
Peaks were called with MACS (version 1.4) with the command line options -s 25 -g hs -p 1e-5  --mfold=4,50
Genome_build: hg19

extract_protocol: Blunt end repair of ChIPed DNA was performed using End-it DNA repair kit (Epicentre, ER0720) and “A” base was added to 3’ ends using Klenow Fragment (3'→5' exo-) (NEB, M0212). NEXTflex™ DNA Barcodes (BIOO Scientific, 514103) were ligated to DNA fragments using LigaFast™ Rapid DNA Ligation System (Promega, M8221) and 200-500 base pair DNA was selected using Agencourt AMPpure XP (Beckman Coulter, A63881). 15 cycles of PCR amplification were performed using Phusion High-Fidelity PCR Master Mix with HF Buffer (ThermoFisher Scientific, F531S).

tag: antibody

value: Histone H3 (abcam, ab1791)


title: LHCN-M2 6hr doxycycline 6hr DUX4 ChIP-Seq H3K27Ac

value: H3K27Ac (abcam, ab4729)


title: LHCN-M2 nodox RNA-Seq, LHCNM2iDUX4HTFCtrl1

value: 0 ng/ml doxycycline


title: LHCN-M2 6hr doxycycline ChIP-Seq H3K4me3

value: H3K4me3 (abcam, ab8580)


title: LHCN-M2 6hr doxycycline ChIP-Seq Input


title: LHCN-M2 6hr doxycycline ChIP-Seq Tagged DUX4

value: Flag (Sigma, F1804)


title: LHCN-M2 nodox RNA-Seq, LHCNM2iDUX4HTFCtrl3


title: Donor 2: Control sample technical rep1

value: Blood (PBMC)

value: 24 hours

value: Untreated


title: 01_L1_WT_2

tag: genotype/variation

tag: condition

value: syntrophy

tag: medium

value: Lactate/No-Sulfate


title: LHCN-M2 nodox ChIP-Seq H3K27Ac


title: LHCN-M2 nodox ChIP-Seq Input


title: LHCN-M2 nodox ChIP-Seq Histone H3


title: Donor 1: IL-13 Stimulated and antagonist stimulation technical rep3


title: LHCN-M2 nodox ChIP-Seq H3K4me3


title: MDAMB231_TotalInput

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description:
Total Input
MDA_TI

data_processing:
Adapters stripped using cutadapt
Reads mapped with Bowtie2 using global alignment. Only uniquely mapped reads used.
Duplicates removed using Picard
bedgraph files from HTSEQ, reads extended 200bp.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files show tag densities for the different treatments (NS and ST) and cell type for ChIP

source_name: MDA-MB-231 cell line

growth_protocol: Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.

extract_protocol:
Briefly, 5 x 106 cells were cross-linked with formaldehyde (1%, 10 min) then quenched with glycine (125mM). Fixed cells were lysed in SDS lysis buffer and chromatin-bound DNA sheared by sonication with a Misonix Sonicator S-4000. ChIP samples were incubated overnight at 4°C with Protein A Magnetic Beads (Millipore) and 5 μg of either H3K4me1 (ab8895; Abcam) or H3K27ac (ab4729; Abcam) antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research).
Libraries were prepared from  ChIP DNA (10ng) using the NEBNext®  ChIP-Seq Library for Illumina (New England Biolabs) and Ampure XP Bead clean-up.

treatment_protocol: Cells were left untreated or stimulated with PMA (1.3ng/ml) for 60h.

tag: cell line

tag: chip antibody


title: MCF7_PMA_TotalInput

description:
Total Input
MCF7_ST_TI

source_name: MCF7 cell line

value: PMA


title: MDAMB231_H3K4me1

description:
ChIP-seq
MDA_K4me1

value: H3K4me1 (Abcam, catalog# ab8895, lot# GR61280-1)


title: MCF7_PMA_H3K4me1

description:
ChIP-seq
MCF7_ST_K4me1


title: MDAMB231_H3K27Ac

description:
ChIP-seq
MDA_K27Ac

value: H3K27ac (Abcam, catalog# ab4729, lot# GR155970-2)


title: MCF7_NS_H3K4me1

description:
ChIP-seq
MCF7_NS_K4me1


title: MCF7_PMA_H3K27Ac

description:
ChIP-seq
MCF7_ST_K27Ac


title: MCF7_NS_H3K27Ac

description:
ChIP-seq
MCF7_NS_K27Ac


title: Total_Input_MCF7

description: Total Input

data_processing:
Adapters stripped using cutadapt
Reads mapped with Bowtie2 using global alignment. Only uniquely mapped reads used.
Duplicates removed using Picard
bedgraph files from HTSEQ, reads extended 200bp.
Peaks called against TI, called with SICER (pvalue < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files show tag densities for the different treatments (NS and ST) for FAIRE and Total Input (TI). Bed files are peaks for FAIRE against TI.

extract_protocol:
5x10^6 cells were cross-linked with 1% formaldehyde for 10 minutes, the reaction is then quenched by adding 2.5M glycine (final concentration of 125mM). Fixed cells were lysed in 500ul SDS lysis buffer and chromatin bound DNA was then sheared by sonication. Nucleosome free DNA (FAIRE DNA) was extracted by using phenol-chloroform and reverse-crosslinked at 65oC. The Zymo-SpinTM I kit (Zymo Research) was then used to purify FAIRE DNA.
FAIRE DNA (20ng), and the corresponding total input, were used to prepare the FAIRE-seq DNA library using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (New England BioLabs)

value: mixed


title: MCF7_PMA_FAIRE_rep2

description: FAIRE-seq


title: LHCN-M2 nodox RNA-Seq, LHCNM2iDUX4HTFCtrl2


title: MCF7_PMA_FAIRE_rep1

description: FAIRE-seq


title: MCF7_NS_FAIRE_rep2

description: FAIRE-seq


title: WT2-Tcon

city: Würzburg

first: Martin

last: Vaeth

address: Versbacher Str. 9

department: Institute of Systems Immunology

country: Germany

institute: Julius-Maximilians University of Würzburg

description:
WT cohort  #2
Feske_Tcon_DKO_vs_WT_norm_counts_DE_expression_all.csv

data_processing:
Reads were aligned to the NCBIM37 (iGenome) mouse genome using Bowtie software (Version 1.0.0) (Langmead and Salzberg, 2012) with 2 mismatches allowed.
Uniquely-mapped reads were further processed by removing PCR duplicates with Picard MarkDuplicates (http://broadinstitute.github.io/picard/) and transcripts were counted using HTSeq (Anders et al., 2015).
Differential gene expression between Stim1Stim2 Cd4cre and WT mice was performed separately for each cell type using DESeq2 (Love et al., 2014) Bioconductor package in the R statistical programming environment; differences in gene expression were considered significant if padj<0.01.
Genome_build: NCBIM37/mm9 (iGenome version)
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized counts

source_name: WT #2 CD4+CXCR5-PD-1- non-Tfh cells

growth_protocol: 4-6 WT and Stim1Stim2 Cd4cre mice (females, 8-12 weeks old) were infected with LCMV-Arm for 10 days.

extract_protocol:
After 10 days of infection, splenic CD4+B220–CD25–CXCR5hiPD-1hi TFH and CD4+B220–CD25–CXCR5–PD-1– non-TFH cells were purified using flow cytometry (for gating strategy see Vaeth et al, Immunity, 2016 Fig. S8B) and total RNA was extracted using the RNeasy Micro RNA Isolation Kit (Qiagen). RNA quality and quantity was analyzed on a Bioanalyzer 2100 (Agilent) using a PICO chip.
RNAseq libraries were prepared using the TruSeq RNA sample prep v2 kit (Illumina), starting from 100 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol with 15 PCR cycles. The amplified libraries were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized in an Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on the HiSeq 2500 Sequencing System (Illumina) and run as single 50 nucleotide reads generating about 30 million reads per sample.

treatment_protocol: I.p. infection with 2x10^5 PFU LCMV-Armstrong for 10 days

value: splenocytes

tag: facs-sort

tag: cell type

value: non-Tfh / Tcon

value: wild type


title: WT2-Tfh

description:
WT cohort  #2
Feske_Tfh_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: WT #2 CD4+CXCR5hiPD-1hi Tfh cells

value: Tfh


title: MCF7_NS_FAIRE_rep1

description: FAIRE-seq


title: WT1-Tfh

description:
WT cohort  #1
Feske_Tfh_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: WT #1 CD4+CXCR5hiPD-1hi Tfh cells


title: WT1-Tcon

description:
WT cohort  #1
Feske_Tcon_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: WT #1 CD4+CXCR5-PD-1- non-Tfh cells


title: DK02-Tcon

description:
Stim1Stim2 Cd4cre cohort #2
Feske_Tcon_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: Stim1Stim2 CD4cre #2 CD4+CXCR5-PD-1- non-Tfh cells


title: DK02-Tfh

description:
Stim1Stim2 Cd4cre cohort #2
Feske_Tfh_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: Stim1Stim2 CD4cre #2 CD4+CXCR5hiPD-1hi Tfh cells


title: MCF7_NS_TotalInput

description:
Total Input
MCF7_NS_TI


title: Bsubtilis_399_2_RNAseq

status: Public on Mar 09 2016

city: San Francisco

first: Jason

middle: Matthew

last: Peters

address: 600 16th Street

department: Microbiology and Immunology

institute: University of California, San Francisco

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were aligned using Bowtie v0.12.7 against the reference genome using parameters -a -v 3 -m 1
Bowtie alignments against the reference genome were converted to wiggle files. The position of each alignment was mapped to the 3' end of the nascent transcript.
Genome_build: B. subtilis: NC000964
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: For each sample, 500 mL liquid LB cultures were grown in 2.8 L flasks with shaking (180 rpm) at 37C from an OD (600 nm) 0.05 to OD 0.45 ± 0.05.

extract_protocol:
Cell culture was rapidly filtered in 250 mL increments at 37C over 0.22 μm nitrocellulose ﬁlters (GE) and frozen in liquid nitrogen to simultaneously halt all transcriptional progress. Frozen cells (100 μg) were pulverized on a Qiagen TissueLyser II mixer mill 6 times at 15 Hz for 3 min in the presence of 500 μL frozen lysis buffer (20 mM Tris pH 8, 0.4% Triton X-100, 0.1% NP-40, 100 mM NH4Cl, 50 U/mL SUPERase•In (Ambion)) and 1X protease inhibitor cocktail (Complete, EDTA-free, Roche), supplemented with 10 mM MnCl2. The lysate was resuspended on ice by pipetting. RQ1 DNase I (110 U total, Promega) was added and incubated for 20 min on ice. The reaction was quenched with EDTA (25 mM final), which releases polysomes from the transcript and reduces contamination from ribosomal RNA and ribosome-associated tRNAs. The lysate was clarified at 4 °C by centrifugation at 20,000 g for 10 min. The lysate was loaded onto a PD MiniTrap G-25 column (GE Healthcare) and eluted with lysis buffer supplemented with 1 mM EDTA. Total RNA was purified from the clarified lysate using the miRNeasy kit (Qiagen). For nascent RNA purification, the clarified lysate was added to 0.5 mL anti-FLAG M2 affinity gel (Sigma Aldrich). The affinity gel was washed twice with lysis buffer supplemented with 1 mM EDTA before incubation with the clarified lysate at 4 °C for 2.5 h with nutation. The immunoprecipitation was washed 4 × 10 mL with lysis buffer supplemented with 300 mM KCl, and bound RNAP was eluted twice with lysis buffer supplemented with 1 mM EDTA and 2 mg/mL 3XFLAG peptide (Sigma Aldrich). Nascent RNA was purified from the eluate using the miRNeasy kit (Qiagen).
The full library construction protocol was described in detail previously (Larson et al., Science 2014). Purified nascent RNA was ligated to a 5' adenylated DNA oligo and fragmented to generate RNA ranging from 30-100 nt. The RNA was reverse transcribed, and the single-stranded DNA circularized and PCR amplified. For RNA-seq, the total RNA was fragmented and dephosphorylated with T4 PNK before continuing onto the reverse transcription, circularization, and PCR steps.

tag: strain

tag: media

value: LB

tag: molecule subtype

value: Total RNA


title: CTC3_S3 Ecad positive cells (i)

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: PyMT breast tumors

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: tissue

value: Ecad positive PyMT bulk tumor cells


title: Bsubtilis_913_2_RNAseq


title: Bsubtilis_913_1_RNAseq


title: CTC1_S1 Ecad positive cells (i)


title: Uhrf1 KO ST1 cells

city: Shanghai

first: Yu

last: Cui

state: Shanghai

address: Yueyang road 320

institute: Chinese Academy of Sciences

data_processing:
base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8);
High-quality, clean reads were generated using the FASTX toolkit pipeline (version 0.0.13);
the resulting high-quality reads were then mapped onto the UCSC using TopHat (version 2.0.9);
The differentially expressed genes were analyzed by using Cufflinks (version 2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: xls

source_name: iNKT cells

growth_protocol: Freshly prepared cells from thymus of the mice

extract_protocol:
Cells were lysed with Trizol reagent and RNA was extracted
Libraries were generated by using the TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: Staining with surface antibodies and sorting target cells with Aria II

tag: strain background

value: thymus

tag: age

value: 5 weeks old

value: Uhrf1 KO

value: stage 1 iNKT cells


title: WT  ST1 cells


title: CTC2_S2 Ecad positive cells (i)


title: Bsubtilis_399_1_RNAseq


title: Bsubtilis_230_RNAseq


title: Bsubtilis_229_RNAseq


title: Bsubtilis_230_NETseq

value: Nascent RNA


title: Bsubtilis_229_NETseq


title: het_U6_shHCV_1m

first: Paul

last: Valdmanis

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

data_processing:
RNAseq reads were aligned to the mm9 genome through a standardized pipeline generated by the Stanford Center for Genomics and Personalized Medicine
FPKM values were calculated by use of Cufflinks v2.2.1 with the following parameters: “--library-norm-method quartile” and removing ribosomal, snoRNA and mitochondrial sequences.
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker-1 clipped and aligned to mouse hairpins from mirBase release 15 using bowtie (version 0.12.7) with 2 mismatches and command -- best
small RNA sequences from 293 cells were aligned to the miR-122 plasmid that was transfected and raw counts for each small RNA that was generated were tabulated
Genome_build: mm9, mirBase release 15
Supplementary_files_format_and_content: File of FPKM values for RNAseq samples,  of reads per million (RPM) mapped microRNA hits for mouse small RNA sequencing samples, and alignment to a transfected plasmid in human cell line samples, all in tab delimited text format

source_name: liver - total RNA

extract_protocol:
Large RNA samples were homogenized and extracted by Trizol; mRNAs were enriched through poly-A purification from a poly-A spin kit (NEB); small RNA samples were extracted using a miRvana microRNA isolation kit (samples 13-50) or total Trizol-extracted RNA (samples 51-93)
RNAseq library samples 1-6 were prepared using an Illumina TruSeq kit.  RNAseq library samples 7-12 were prepared using a ScriptSeq v2 kit (Epicentre).
3ug of miRvana extracted or 5ug of Trizol extracted small RNAs were ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to barcoded adapters. Dual-ligated RNA was reverse transcribed, PCR amplified and size selected on 4% NuSieve (Lonza) agarose.  Small RNA sequencing was performed on the Illumina GAII (samples 13-50) and miSeq (samples 51-93) platforms.

value: liver


title: het_U6_hAAT_7d_rep2


title: het_U6_hAAT_7d_rep1


title: miR122_floxed_Cre_7d


title: miR122_floxed_uninjected


title: DK01-Tfh

description:
Stim1Stim2 Cd4cre cohort #1
Feske_Tfh_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: Stim1Stim2 CD4cre #1 CD4+CXCR5hiPD-1hi Tfh cells


title: DK01-Tcon

description:
Stim1Stim2 Cd4cre cohort #1
Feske_Tcon_DKO_vs_WT_norm_counts_DE_expression_all.csv

source_name: Stim1Stim2 CD4cre #1 CD4+CXCR5-PD-1- non-Tfh cells


title: miR_122KO_no_injection_rep2


title: miR122_floxed_Cre_6w


title: het_U6_hAAT_2mo


title: miR_122KO_H1_hAAT_rep3


title: miR_122KO_GFP_rep3


title: control_liver_rep3_total


title: het_U6_shHCV_7d_rep2


title: het_U6_shHCV_7d_rep1


title: het_uninjected_rep3


title: U6_sh_miR_122_2months_rep2


title: het_uninjected_rep2


title: U6_sh_miR_122_2months_rep1


title: miR122_floxed_Cre_3d


title: het_uninjected_rep1


title: miR_122KO_H1_hAAT_rep1


title: miR122_floxed_Cre_14d


title: miR_122KO_U6_hAAT_rep3


title: U6_sh_miR_122_rep1


title: U6_sh_miR_30_24ntB


title: miR_122KO_H1_hAAT_rep2


title: U6_sh_miR_122_rep3


title: miR_122KO_GFP_rep2


title: U6_sh_miR_122_rep2


title: miR_122KO_HCV_21nt_d7


title: U6_sh_miR_122_2months_rep3


title: miR_122KO_no_injection_rep1


title: miR_122KO_HCV_21nt_d21


title: miR_122KO_GFP_rep1


title: U6_sh_HCV_21nt


title: miR_122KO_U6_hAAT_rep1


title: miR_122KO_U6_hAAT_rep2


title: H1_hAAT_25nt_5x


title: H1_hAAT_25nt_2x


title: Cisplatin+Dichloroacetate_rep3

description: mouse was pre-treated intraperitoneally daily with DCA (250mg/kg) for 5 days then intraperitoneally once with 20mg/kg cisplatin and DCA. sacrificed 24h later

data_processing:
Trimmomatic (HEADCROP:14 LEADING:3 TRAILING:3 MINLEN:70)
and mapped to the mouse genome (GRC38.72) with tophat (--b2 –very sensitive)
Cufflinks and HTSeq (-a –s no)
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated from tophat bam files using bedtools and scaling to reads per 10 million.  genomeCoverageBed -bg -split -scale $sc -ibam. Raw.txt: Counts for ensembl genes were generated in HTSeq. normalised.txt: normalised in DESeq (R) using estimateSizeFactors() and counts(normalized=TRUE)

extract_protocol:
Total RNA was extracted with RNeasy mini kits (Qiagen, Venlo, Netherlands) and treated with Turbo DNAse (Life Technologies, Carlsbad, CA). Libraries were prepared with a Truseq RNA Sample Preparation kit (Illumina, San Diego, CA).
Libraries were prepared with a Truseq RNA Sample Preparation kit (Illumina, San Diego, CA). RNA (1µg/sample) was fragmented and subject to first and second strand synthesis, 3' end adenylation, adaptor ligation and PCR amplification using the TruSeq Rapid SBS Kit

value: BALB/c

value: Kidney

value: 8 weeks old

tag: agent

value: dichloroacetate + cisplatin

tag: Sex

value: male


title: Cisplatin+Dichloroacetate_rep2


title: control_liver_rep2_total


title: Cisplatin+Dichloroacetate_rep1


title: Cisplatin_rep3

description: mouse was pre-treated intraperitoneally daily with saline for 5 days intraperitoneally with 20mg/kg cisplatin once. sacrificed 24h later

value: cisplatin


title: M-20-RC

city: Notre Dame

first: Hilary

middle: April

last: Uyhelji

state: IN

address: 317 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

data_processing:
Demultiplexing and filtering with the Illumina chastity filter
Trimmomatic for trimming adapters and quality filtering (default settings)
mapping reads to An. gambiae PEST genome (AgamP4.2 reference) with Bowtie2 and TopHat2
HTSeq (union option) to count numbers of uniquely mapped reads
TMM normalization, and exclusion of reads with low counts (<1 count per million reads in ≥3 libraries), using the R/bioconductor package edgeR; exclusion of reads mapped to rRNA
Genome_build: An. gambiae PEST genome (AgamP4.2, downloaded from VectorBase; https://www.vectorbase.org/)
Supplementary_files_format_and_content: counts per million reads of TMM-normalized data for each transcript

molecule: polyA RNA

organism: Anopheles merus

source_name: An. merus_20%_6 hrs_whole tissue

growth_protocol: Reared in FW until 18 h post-hatch, at which time experimental exposures (treatment) began

extract_protocol:
Total RNA was extracted and DNAse treated
TruSeq® RNA Sample Preparation kit v2 (Illumina) for construction of RNA libraries (including a polyA-selection step), following manufacturer's protocols

treatment_protocol: Exposure for 6 h to either water of one of the following salinities: 0, 10, 20, 30, 40, or 50 percent the salinity of sea water

tag: water salinity (%)

value: 18 h post-hatch

tag: exposure time

value: 6 hours

value: pool of whole body of 35-50 larvae


title: M-10-RC

source_name: An. merus_10%_6 hrs_whole tissue


title: M-00-RC

source_name: An. merus_0%_6 hrs_whole tissue


title: M-40-RB

source_name: An. merus_40%_6 hrs_whole tissue


title: M-30-RB

source_name: An. merus_30%_6 hrs_whole tissue


title: M-00-RB


title: M-40-RC


title: M-30-RC


title: M-50-RC

source_name: An. merus_50%_6 hrs_whole tissue


title: M-20-RB


title: M-50-RA


title: M-50-RB


title: M-10-RB


title: Cisplatin_rep2


title: Dichloroacetate_rep2

description: mouse was pre-treated intraperitoneally daily with DCA (250mg/kg) for 6 days

value: Dichloroacetate


title: Dichloroacetate_rep3


title: Dichloroacetate_rep1


title: M-30-RA


title: M-20-RA


title: Saline_rep3

description: mouse was pre-treated intraperitoneally daily with saline for 6 days

value: saline


title: M-00-RA


title: Saline_rep2


title: M-10-RA


title: M-40-RA


title: Saline_rep1


title: Cisplatin_rep1


title: liver_control_saline

source_name: liver


title: liver_U6-sh-miR-30-24ntB


title: liver_U6-sh-miR-30-24nt


title: liver_U6-sh-hAAT_25nt_rep2


title: BarcodedLibrary31_M_66h_SW

description: pool of whole body of 35-50 larvae

data_processing:
Demultiplexing with FASTX-toolkit allowing 1 mismatch, after receipt of fastq files that had been filtered with the Illumina chastity filter
Trimmomatic for trimming adapters and quality filtering (default settings)
mapping reads to An. gambiae PEST genome (AgamP3.7 reference) with Bowtie 2 and TopHat2
HTSeq (union option) to count numbers of uniquely mapped reads
TMM normalization, and exclusion of reads with low counts (<1 count per million reads in ≥4 libraries), using the R/bioconductor package edgeR
Genome_build: An. gambiae PEST genome (AgamP3.7, downloaded from VectorBase)
Supplementary_files_format_and_content: excel file with counts per million reads of TMM-normalized data for each transcript

source_name: whole tissue

growth_protocol: Reared in FW until 18 h (or 66 h) post-hatch, at which time experimental exposures (treatment) began

treatment_protocol: Exposure for 6 h to either FW or SW

tag: water type

value: Saltwater

tag: age post-hatch

value: 66 hour


title: liver_U6-sh-HCV-21nt


title: CMV_miR_122_23T_24h_rep3

source_name: 293 cells


title: CMV_miR_122_23T_48h_rep2


title: liver_U6-sh-miR-30-21nt


title: BarcodedLibrary28_M_66h_DI

description: pool of whole body of 35-50 larvae

value: Freshwater


title: CMV_miR_122_23C_48h_rep2


title: BarcodedLibrary26_M_66h_DI

description: pool of whole body of 35-50 larvae


title: liver_U6-sh-HCV-29ntB


title: liver_H1-sh-hAAT_25nt_rep1


title: BarcodedLibrary16_M_18h_SW

description: pool of whole body of 35-50 larvae

value: 18 hour


title: BarcodedLibrary30_M_66h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary32_M_66h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary29_M_66h_SW

description: pool of whole body of 35-50 larvae


title: CMV_miR_122_23C_30h_rep1


title: BarcodedLibrary25_M_66h_DI

description: pool of whole body of 35-50 larvae


title: CMV_miR_122_23T_30h_rep1


title: BarcodedLibrary27_M_66h_DI

description: pool of whole body of 35-50 larvae


title: CMV_miR_122_23C_18h_rep1


title: liver_control_rep2


title: liver_U6-sh-hAAT_25nt_rep1


title: BarcodedLibrary14_M_18h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary15_M_18h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary13_M_18h_SW

description: pool of whole body of 35-50 larvae


title: CMV_miR_122_23T_18h_rep1


title: liver_H1-sh-hAAT_25nt_rep2


title: liver_control_rep1


title: CMV_miR_122_23C_12h_rep1


title: BarcodedLibrary11_M_18h_DI

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary10_M_18h_DI

description: pool of whole body of 35-50 larvae


title: control_liver_rep1_total


title: G-50-RC

organism: Anopheles coluzzii

source_name: An. coluzzii_50%_6 hrs_whole tissue


title: H1_sh_hAAT_25nt_rep1_total


title: G-40-RC

source_name: An. coluzzii_40%_6 hrs_whole tissue


title: H1_sh_hAAT_25nt_rep2_total


title: G-30-RC

source_name: An. coluzzii_30%_6 hrs_whole tissue


title: H1_sh_hAAT_21nt_rep2_total


title: H1_sh_hAAT_21nt_rep3_total


title: CMV_miR_122_23T_24h_rep2


title: CMV_miR_122_23T_24h_rep1


title: CMV_miR_122_23T_48h_rep1


title: CMV_miR_122_23C_24h_rep2


title: CMV_miR_122_23T_12h_rep1


title: G-20-RC

source_name: An. coluzzii_20%_6 hrs_whole tissue


title: G-10-RC

source_name: An. coluzzii_10%_6 hrs_whole tissue


title: CMV_miR_122_23C_72h_rep1


title: H1_sh_hAAT_19nt_rep2_total

source_name: liver - total RNA


title: CMV_miR_122_23C_24h_rep1


title: CMV_miR_122_23T_72h_rep2


title: G-00-RD

source_name: An. coluzzii_0%_6 hrs_whole tissue


title: H1_sh_hAAT_19nt_rep1_total


title: H1_sh_hAAT_19nt_rep3_total


title: BarcodedLibrary12_M_18h_DI

description: pool of whole body of 35-50 larvae


title: H1_sh_hAAT_25nt_rep3_total


title: BarcodedLibrary9_M_18h_DI

description: pool of whole body of 35-50 larvae


title: CMV_miR_122_23C_72h_rep2


title: H1_sh_hAAT_21nt_rep1_total


title: G-40-RB


title: U6_sh_hAAT_25nt_rep3_total


title: U6_sh_hAAT_25nt_rep2_total


title: CMV_miR_122_23C_48h_rep1


title: G-30-RB


title: U6_sh_hAAT_21nt_rep2_total


title: G-10-RB


title: G-00-RB


title: U6_sh_hAAT_21nt_rep3_total


title: G-20-RB


title: U6_sh_hAAT_21nt_rep1_total


title: G-50-RA


title: U6_sh_hAAT_19nt_rep3_total


title: U6_sh_hAAT_25nt_rep1_total


title: U6_sh_hAAT_19nt_rep1_total


title: G-30-RA


title: U6_sh_hAAT_19nt_rep2_total


title: G-20-RA


title: control_liver_rep1_Ago2IP

source_name: liver - Ago2 IP


title: BarcodedLibrary24_G_66h_SW

description: pool of whole body of 35-50 larvae


title: G-00-RA


title: H1_sh_hAAT_25nt_rep1_Ago2IP


title: H1_sh_hAAT_25nt_rep3_Ago2IP


title: G-10-RA


title: G-50-RB


title: H1_sh_hAAT_21nt_rep2_Ago2IP


title: BarcodedLibrary23_G_66h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary22_G_66h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary21_G_66h_SW

description: pool of whole body of 35-50 larvae


title: H1_sh_hAAT_21nt_rep3_Ago2IP


title: Male mTEC pool2

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Low quality reads were filtered using Trimmomatic
Alignment to the mm9 genome was performed using Tophat2
Reads were counted at mm9 genes using HTseq-count
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file contains read counts per gene for each replicate

source_name: Male mTEC cells

extract_protocol:
Sorted mTECs (PI- CD45- MHCII+ Ly51low) were pooled from 10 mice per replicate. mTECs were pelleted, lysed in RLT lysis buffer (Qiagen), and total RNA was recovered using the RNeasy Micro Kit (Qiagen). RNA quality and concentration were assessed by Experion high sensitivity RNA analysis kit (Biorad)
cDNA libraries were prepared using the SMARTer Ultra Low kit v3 (Clontech)

value: 6-8 weeks

tag: genotype

value: wild-type


title: H1_sh_hAAT_21nt_rep1_Ago2IP

value: liver


title: Male mTEC pool1


title: H1_sh_hAAT_19nt_rep2_Ago2IP


title: G-40-RD


title: BarcodedLibrary18_G_66h_DI

description: pool of whole body of 35-50 larvae


title: H1_sh_hAAT_19nt_rep1_Ago2IP


title: H1_sh_hAAT_19nt_rep3_Ago2IP


title: BarcodedLibrary19_G_66h_DI

description: pool of whole body of 35-50 larvae


title: Female mTEC pool2

source_name: Female mTEC cells


title: Female mTEC pool1


title: BarcodedLibrary17_G_66h_DI

description: pool of whole body of 35-50 larvae


title: Input DNA

city: Houston

first: Ramakrishna

last: kommagani

state: TX - Texas

address: M732, One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
50-nt sequence reads identified by the Sequencing Service (using Ilumina's Hi-seq)
reads mapped to the genome using the BWA algorithm with default settings
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
density of fragments, in 32-nt bins divided genome, defined in BAM files
Peak calling was performed by applying a threshold of 18 (5 consecutive bins containing 0.18 aligns) before the resultant-called peaks were stored as BED files
Genome_build: GRCh37.p2-Primary Assembly
Supplementary_files_format_and_content: Bed files and feature tracks

source_name: hESCs

growth_protocol: DMEM F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3

extract_protocol: Lysates were clarified from sonicated nuclei and PLZF bound DNA was isolated with antibody.

treatment_protocol: 10nM 17β-estradiol, 100nM medroxyprogesterone acetate, and 1mM cAMP OPTI-MEM I reduced serum media supplemented with 2% stripped fetal bovine serum and antibiotic and antimycotics

value: Primary stromal cells

tag: passage

value: 2 to 4

tag: antibody


title: BarcodedLibrary8_G_18h_SW

description: pool of whole body of 35-50 larvae


title: U6_sh_hAAT_25nt_rep3_Ago2IP


title: U6_sh_hAAT_25nt_rep2_Ago2IP


title: H1_sh_hAAT_25nt_rep2_Ago2IP


title: PLZF_Chipseq

source_name: PLZF ChIP DNA from hESCs

value: Goat polyclonal anti-human PLZF antibody (sc-11146; Santa Cruz Biotechnology, Inc.)


title: U6_sh_hAAT_25nt_rep1_Ago2IP


title: BarcodedLibrary7_G_18h_SW

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary6_G_18h_SW

description: pool of whole body of 35-50 larvae


title: U6_sh_hAAT_21nt_rep3_Ago2IP


title: BarcodedLibrary20_G_66h_DI

description: pool of whole body of 35-50 larvae


title: BarcodedLibrary5_G_18h_SW

description: pool of whole body of 35-50 larvae


title: U6_sh_hAAT_21nt_rep2_Ago2IP


title: U6_sh_hAAT_21nt_rep1_Ago2IP


title: BarcodedLibrary4_G_18h_DI

description: pool of whole body of 35-50 larvae


title: duck 2-FBS

first: LIANG

last: YAN

address: NO 131, Dongan Road

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  whole genome (PRJNA46621) using TopHat v2.0.12.
Cufflinks v2.2.1 software (http://cufflinks.cbcb.umd.edu/) was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression.
Genome_build: PRJNA46621
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Anas platyrhynchos

source_name: primary duck hepatocytes_FBS

growth_protocol: Primary duck hepatocytes were cultured in Leibovitz’s L-15 medium supplemented with 100 units/ml penicillin-streptomycin, 1 mg/L insulin, and 10−5 M hydrocortisone-hemisuccinate. In addition, 5% FBS or 1.5% DMSO was added and PDH were cultured for 8 days.

extract_protocol:
Primary duck hepatocytes under different culture conditions were cultured for 8 days, and 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

value: 1-day-old duckling

value: wild type


title: U6_sh_hAAT_19nt_rep3_Ago2IP


title: duck 3-DMSO

source_name: primary duck hepatocytes_DMSO


title: BarcodedLibrary3_G_18h_DI

description: pool of whole body of 35-50 larvae


title: duck 2-DMSO


title: duck 3-FBS


title: duck 1-FBS


title: BarcodedLibrary1_G_18h_DI

description: pool of whole body of 35-50 larvae


title: U6_sh_hAAT_19nt_rep1_Ago2IP


title: U6_sh_hAAT_19nt_rep2_Ago2IP


title: R4000 H3K27me3 ChIPSeq

status: Public on Mar 08 2016

city: Los Angeles

first: Larry

last: Lam

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

data_processing:
The RRBS reads were aligned using the bisulfite aligner, BS Seeker2, to determine which fragment they uniquely mapped to allowing for 3 mismatches to the reference genome (mouse mm9).
The methylation call script from BS Seeker2 was used to generate CGmap.gz files
The ChIP reads were aligned using bowtie to the mm9 reference genome.
Peak calling was performed on uniquely aligned reads.  The reference genome was tiled into 100-bp windows. Each read was extended by 150 bases and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other. The average value for all windows was assigned to windows with zero counts. A Poisson distribution to estimate the probability of observing the ChIP counts within a window given the expected counts in the input sample window. All windows with P-values less than 1.0 × 10−3 to have significant peaks. A P-value < 1.0 × 10−3 was chosen to give a False Discovery Rate (FDR) of <5%.
Genome_build: mm9
Supplementary_files_format_and_content: CGmap files are tab delimeted text files containing the cytosine methylation level. bed files contain the ChIP peaks.

source_name: B cell

extract_protocol:
The ChIP-Seq sample 100 μl of the lysate (5 × 106139 cells) were used for each immunoprecipitation with anti-H3K27me3 (Active Motif cat # 39155).
DNA was recovered by electroelution, phenol extraction and ethanol precipitation.

value: E{mu}-Myc

tag: chip antibody

value: H3K27me3 (Active Motif cat # 39155)


title: R500 RRBS

extract_protocol:
The RRBS genome samples were digested with the methylation-insensitive restriction enzyme MspI, and fragments from 100 to 300 bases were selected. The fragments were ligated with Illumina adaptors, denatured and treated with sodium bisulfite.
DNA was recovered by electroelution, phenol extraction and ethanol precipitation.

tag: rrbs enzyme digestion

value: MspI


title: R100 H3K27me3 ChIPSeq

tag: strain


title: Parental H3K27me3 ChIPSeq


title: R1000 RRBS


title: R4000 RRBS


title: Pdxcre;Gata4fl/fl;Gata6fl/fl

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: xcl-file includes DeSeq analysis for all samples, 251 genes with significant p-value are listed

source_name: e12.5 pancreas

extract_protocol:
Whole pancreas were dissected and total RNA was isolated using QIAGEN RNeasy Micro kits. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rna-seq id

tag: developmental stage

value: pancreas

tag: genotype/variation

tag: sample type

value: pooled from 12 pancreata


title: Control

tag: tissue

value: control

value: pooled from 6 pancreata


title: R100 RRBS


title: Wildtype zone 6

city: Portland

first: Bret

middle: J

last: Pearson

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Basecalls and demultiplexing were done with Illumina bcl2fastq version 1.8.3.
Untrimmed reads were aligned to the transcriptome associated with BioProject PRJNA215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Specific zones in which transcripts were highly expressed were determined by the edgeR exact test using RNAseq raw counts of the zones 1-6.  The procedure includes data filtering, normalization, differential expression tests, and scoring.  There were total 82827 transcripts detected for the zones 1-6.  Transcripts that had less than 0.5 count per million (CPM) in each zone were filtered out.  The CPM cutoff was chosen such that the quantile normalized CPMs have an identical distribution for each zone after filtering the transcripts of extremely low CPM.  The filtered transcripts, which had extremely low CPM, could not be found to be specific to any zone.  Finally 24578 transcripts were kept.  The RNAseq raw counts of the zones 1-6 were normalized using the edgeR Trimmed Mean of M-values (TMM) method.  The normalization factors are calculated using the TMM method as follows:
effective library size = library size * normalization factor
normalized CPM = 1e6 * counts / effective library size
Box-plot, smoothing density-plot, hierarchical clustering, and multidimensional scaling (MDS) were used to show the zone relations after normalizing.  Using the edgeR exact test, we compared one zone to the average over other five zones to determine if a transcript was specific to a zone.  If the differential expression test for a transcript was significant and the log-fold-change (logFC) > 0, the transcript was considered to be specific to that zone.  A transcript may be specific to more than one zone, in which case, the zones will be ordered by scores of the zones, and the zone of higher expression listed first.  For example, a transcript with the score “2.1” would mean that it has significant specificity to both zones 1 and 2, with higher expression in zone 2.  Zone membership and normalized CPM for all transcripts are in Currie_NCBI_processeddata.txt.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Currie_NCBI_processeddata.txt.  CPM values for each sample for each transcript are listed following edgeR row normalization.  Only transcripts showing zone specific expression are listed.

organism: Schmidtea mediterranea

source_name: Wildtype animals

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol:
All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: 5 animals were immobilized on peltier coolers and carefully amputated into 6 Anterior-Posterior zones, as illustrated in Figure 2 of the manuscript.  RNA was extracted from each zone, and deep sequenced to a depth >52 million reads.

value: Asexual CIW4

tag: plane of amputation

value: last remaining piece of tail tip

tag: treatment

value: Amputation fragment

tag: zone


title: Wildtype zone 4

value: posterior extent of the pharynx


title: Wildtype zone 3

value: anterior extent of the pharynx


title: Wildtype zone 5

value: midpoint between posterior pharynx and tail tip


title: Wildtype zone 2

value: posterior extent of the brain


title: Wildtype zone 1

value: posterior extent of the photoreceptors


title: duck 1-DMSO

value: liver

tag: age

value: 1-day-old duckling


title: BMP-2 (−), IL-17A(+)

city: Tokyo

first: Takehito

last: Ono

address: Yushima, 1-5-45

department: Department of Cell Signaling

institute: Tokyo Medical and Dental University

data_processing:
Data were acquired on an Ion Proton (Thermo Fisher)
The software used for the analysis was CLC Genomics Workbench ver. 8 (CLC).
The reads acquired were aligned to the Mm10 genome assembly.
Filtering parameters were as follows; Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8 and Similarity fraction, 0.8.
RPKM value was calculated and regarded as gene expression.
Genome_build: Mm10
Supplementary_files_format_and_content: Xls files include RPKM values for each Sample.

source_name: PαS cells

growth_protocol: PαS cells were sorted out by using FACS Aria III (BD Biosciences). 3.0× 10^3 cells per well in an osteogenic medium supplemented with BMP-2 and IL-17A were seeded in 48 well plates, at a final concentration of 500 ng ml−1 and 10 ng ml−1, respectively. Cells were cultured for 7 days.

extract_protocol:
Total RNA of cultured PαS cells was extracted using Maxwell 16 LEV simplyRNA Cells and Tissue Kit (Promega).
cDNA was synthesized and amplified using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories).

value: wild type

value: Injury tissues within and around the femur

tag: cell type

value: P-alpha-S cells

tag: cell surface markers

tag: cytokines


title: R500 H3K27me3 ChIPSeq

tag: genotype

value: E{mu}-Myc

value: H3K27me3 (Active Motif cat # 39155)


title: BMP-2 (+), IL-17A(+)


title: BMP-2 (−), IL-17A(−)


title: R1000 H3K27me3 ChIPSeq


title: trp1-1::pGAL-H3:TRP1 Rad5+  t2 batch 3

city: Seattle

first: Sue

last: Biggins

address: 1100 Fairview Ave N MS A2-168

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Sample 36

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered prior to alignment to the reference genome (UCSC hg19 assembly) using TopHat v2.1.0
Counts were generated from TopHat alignments for each gene using the Python package HTSeq v0.6.1
Genes with low counts across all samples were removed, prior to identification of differentially expressed genes using the Bioconductor package edgeR v3.12.0 A false discovery rate (FDR) method was employed to correct for multiple testing.  Differential expression was defined as |log2 (ratio) | ≥ 0.585 (± 1.5-fold) with the FDR set to 5%.
Genome_build: UCSC SacCer3
Supplementary_files_format_and_content: txt files contain edgeR results. Replicates of the corresponding genotypes in each batch were pooled for the differential expression analysis. A key to the sample names in the EdgeR output can be found on the series record in the file SampleName_to_edgeRName.xlsx.

source_name: asynchronous cells

growth_protocol: Yeast cells were grown in YEP + Lactic Acid media to log phase at 23 degrees C. t=0 hours timepoint was taken at approx OD 0.55, galactose was added to 2%, and cells were grown for 2 hours at 23 degrees C, at which point the t=2 hour timepoint was taken.

extract_protocol:
RNA was extracted using the Acid-Phenol RNA extraction methods, followed by DNAseI treatment (Invitrogen, Amplification Grade) and phenol:chloroform extraction following by ethanol precipitation.
Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).  RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization were performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  RNA-seq libraries were pooled (18-plex) and clustered onto a flow cell lane.

tag: strain number

tag: timepoint

value: 2 hours

tag: batch

tag: medium

value: YEP + Lactic Acid + 2% Galactose


title: leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t0 batch 3

description: Sample 27

value: 0 hours

value: YEP + Lactic Acid


title: Parental RRBS

tag: strain

tag: rrbs enzyme digestion

value: MspI


title: psh1∆KAN Rad5+  t0 batch 3

description: Sample 26


title: psh1∆KAN Rad5+  t2 batch 3

description: Sample 32


title: trp1-1::pGAL-H3:TRP1 Rad5+  t0 batch 3

description: Sample 30


title: htz1∆HYG Rad5+  t2 batch 3

description: Sample 35


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t2 batch 3

description: Sample 34

value: psh1_delta  pGAL-3Flag-CSE4


title: htz1∆HYG Rad5+  t0 batch 3

description: Sample 29


title: leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t2 batch 3

description: Sample 33


title: trp1-1::pGAL-H3:TRP1 Rad5+ t2 batch 2

description: Sample 24


title: WT Rad5+ t0 batch 3

description: Sample 25

value: WT


title: htz1∆HYG Rad5+ t2 batch 2

description: Sample 23


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+ t2 batch 2

description: Sample 22


title: BMP-2 (+), IL-17A(−)

tag: genotype/variation


title: leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+ t2 batch 2

description: Sample 21


title: WT Rad5+ t2 batch 3

description: Sample 31


title: psh1∆KAN Rad5+ t2 batch 2

description: Sample 20


title: WT Rad5+ t2 batch 2

description: Sample 19


title: PIWIL4_SH3_smallRNA

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

description: total small RNAs

data_processing:
The small RNA sequences were generated with Illumina HiSeq 2500, and trimmed off linkers with FASTX-Toolkit.
We selected sequences with size ranging from 12 nucleotides to 43 nucleotides for analysis. The reference genome was human genome hg38.
The gene annotation information was based on Ensembl annotation. The miRNA annotation was based
on version 21 from miRBase. Repeats and transposon annotation was based on RepeatMasker.
Complete rRNA references were from NCBI. One mismatch was allowed for mapping sequences against rRNA, tRNA, snoRNA, snRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: text file containing sequences with their read information

source_name: PIWIL4 knock-down MDA-MB-231 cell

growth_protocol: MDA-MB-231 cells were cultured by L-15  Medium (Leibovitz, Sigma, L1518-500ML) supplemented with 10 % fetal calf serum, and  incubate at 37°C without CO 2 .

extract_protocol: total small RNAs were isolated and libraries were prepared according to Illumina TrueSeq SmallRNA SamplePrep kit

value: breast cancer

tag: cell line

value: Breast cancer-derived MDA-MB-231 cell line

value: PIWIL4 knock-down


title: D1_CDI alone_50percent MMP

city: Madison

first: Hamisha

last: Ardalani

state: WI

address: 330 N. Orchard St.

institute: UW-Madison

description: Day 1 (column D in Suppl Table 1))

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing TPM expression estimates calculated by RSEM

source_name: Day 1

growth_protocol: passage 3 IPSC-ECs were thawed and plated at 10000-15000 iPSC-ECs/cm2 onto tissue culture plates treated with 3ug/cm2  fibronectin. CDI recommendend medium was used for culturing the iPS endothelial cells both in 2D and 3D culture of cells. For 3D culture in MMP degradable hydrogel cells pellets were re-suspended in a 2X photoinitiator solution (0.1 % wt./wt. Irgacure 2959) and mixed 1:1 with a 2X PEG monomer solution. For experiments using standard plates, 5 μL of the cell/monomer solution was pipetted onto tissue culture treated surfaces and polymerized for 2 min using ~5-10 mW/cm2 UV light centered at ~365 nm (multiwell plates were placed on the top shelf of the exposure stand for a UVP XX-15L series UV lamp, Fisher).

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen) and included lysing in 350 μL RLT lysis buffer and the optional DNase treatment.
cDNA libraries were prepared from 50 nanograms of total RNA and indexed with Illumina’s TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 and RS-122-2002).  Final indexed cDNA libraries were pooled with 12 uniquely indexed TruSeq cDNA libraries for a total of 6 samples per lane.  Multiplexed samples were sequenced on an Illumina HiSeq 2500 with a single 51 bp read and a 7 bp index read. Base-calling and demultiplexing were performed using Casava (v1.8.2). Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts. The remaining reads were aligned to 19084 Refseq genes extracted from the Illumina iGenomes reference, selecting only those with ‘NM_’ annotations.  Bowtie (v 0.12.9) was used for alignment, allowing two mismatches in a 28 bp seed [64]. Reads with more than 200 alignments were excluded from further analysis. RSEM (v1.2.3) was used to estimate isoform and relative gene expression levels (transcripts per million or “TPM”)

value: iPS derived endothelial cells from CDI

tag: condition

value: 3D culture of endothelial cells in 50% MMP degradable PEG-NB hydrogel, day1

tag: passage


title: PURO_smallRNA

description: total small RNAs

source_name: MDA-MB-231 cell

tag: tissue

value: control


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t0 batch 3

description: Sample 28


title: trp1-1::pGAL-H3:TRP1 Rad5+ t0 batch 2

description: Sample 18


title: pifq dark  Linc rep2

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

description: 3'-end polyA RNA

data_processing:
Single-end 50-nt reads
Reads passed quality filtering were aligned to the TAIR10 transcriptome assembly using Bowtie-0.12.7 with the following settings: -v 1 --norc -a.
Only reads mapped uniquely to the 3'-end 500-bp region of the single locus were counted for gene expression.
Differential expression between two genotypes was determined using EdgeR (Bioconductor)
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files containing raw reads counts of every locus in each biological triplicate sample.

source_name: whole etiolated seedlings

growth_protocol: Stratified seeds were irradiated with WL at 21 ºC for 3 h to induce germination and grown in darkness at 21 ºC for 3 days before harvest.

extract_protocol:
Rneasy Plus mini kit was used to prepare total RNA from ~100 mg ttissue (fw).  20 ug total RNA was used for construction of each library. There are technical duplicate runs for each biological triplicate sample. The sequencing library construction was adapted from Illumina's directional mRNA-seq sample preparation protocol. The mRNA was fractionated from 20 µg of total RNA using Dynabeads Oligo (dT)25 (Invitrogen), and fragmented using Fragmentation Reagents (Ambion) at 70°C for 2.5 min in 20 µl of reaction. The polyA-tailed 3'-end fragments were captured by another run of mRNA purification as described above, and then treated by Antarctic Phosphatase and T4 Polynucleotide Kinase (NEB) at 37°C for 1 h and 2 h, respectively. The sample was purified using RNeasy MinElute Cleanup Kit (Qiagen) according to Illumina's protocol. The eluted mRNA fragments were ligated with 2.5 µM of Illumina's SRA 5' adaptor by T4 RNA Ligase 1 (NEB) at 20 °C for 4 h. The 3' cDNA adapter derived from Illumina's v1.5 sRNA 3' adapter was conjugated with the anchored oligo (dT)20 primer, and introduced through reverse transcription using the SuperScript III First-Strand Synthesis System (Invitrogen). The first-strand cDNA was purified using the Agencourt AMPure XP system (Beckman Coulter Genomics), and then amplified by PCR reaction using Phusion High-Fidelity DNA Polymerase (NEB) with Illumina's sRNA PCR primer set. The size of purified library DNA was validated by Bioanalyzer 2000 (Agilent).
Construction strategy is  directional - mRNA's are sequenced only 5' to 3' to avoid ambiguities in overlapping ORFS.

treatment_protocol: For samples growing with lincomycin medium was supplemented with 0.5 mM lincomycin

tag: developmental stage

tag: growth conditions

value: darkness and Lincomycin

tag: genetic background

value: Columbia


title: pifq dark  Linc rep3

description: 3'-end polyA RNA


title: htz1∆HYG Rad5+ t0 batch 2

description: Sample 17


title: pifq dark rep3

description: 3'-end polyA RNA

value: darkness


title: pifq dark rep2

description: 3'-end polyA RNA


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t0 batch 2

description: Sample 16


title: leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+  t0 batch 2

description: Sample 15


title: pifq dark rep1

description: 3'-end polyA RNA


title: WT dark  Linc rep1

description: 3'-end polyA RNA


title: pifq dark  Linc rep1

description: 3'-end polyA RNA


title: psh1∆KAN Rad5+  t0 batch 2

description: Sample 14


title: p30_DF5S_D0

description: iPS control (Column B in Suppl Table 1)

source_name: iPS control

tag: cell type

value: undifferntiated iPS cells

value: non-cultured iPSC-Ecs, fresh after thawing


title: D3_CDI alone_50percent MMP

description: Day 3 (column F in Suppl Table 1)

source_name: Day 3

value: iPS derived endothelial cells from CD

value: 3D culture of endothelial cells in 50% MMP degradable PEG-NB hydrogel, day3


title: D0_CDI

description: 2D (TCP) (Column C in Suppl Table 1))

source_name: 2D (TCP)

value: 2D culture on tissue culture polystyrene, day0


title: D5_CDI alone_50percent MMP

description: Day 5 (column G in Suppl Table 1)

source_name: Day 5

value: 3D culture of endothelial cells in 50% MMP degradable PEG-NB hydrogel, day5


title: D2_CDI alone_50percent MMP

description: Day 2 (column E in Suppl Table 1)

source_name: Day 2

value: 3D culture of endothelial cells in 50% MMP degradable PEG-NB hydrogel, day2


title: BarcodedLibrary2_G_18h_DI

description: pool of whole body of 35-50 larvae

source_name: whole tissue

tag: water type

value: Freshwater

tag: age post-hatch

value: 18 hour

tag: exposure time

value: 6 hours


title: WT dark  Linc rep2

description: 3'-end polyA RNA

tag: genotype

value: WT


title: WT Rad5+ t0 batch 2

description: Sample 13

tag: strain number

tag: timepoint

value: 0 hours

tag: batch

value: YEP + Lactic Acid


title: trp1-1::pGAL-H3:TRP1 Rad5+ t2 batch 1

description: Sample 12

value: 2 hours

tag: medium

value: YEP + Lactic Acid + 2% Galactose


title: WT dark rep2

description: 3'-end polyA RNA

value: Columbia


title: htz1∆HYG Rad5+ t2 batch 1

description: Sample 11


title: WT dark rep1

description: 3'-end polyA RNA

value: darkness


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+ t2 batch 1

description: Sample 10

value: psh1_delta  pGAL-3Flag-CSE4


title: miP1b_2

city: Frederiksberg C

first: Daniel

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

institute: University of Copenhagen

data_processing:
Basecalls performed using HiSeq Control Software v2.0.12.0
First 10 bases were clipped using Trimmomatic v0.32 (Lohse et al. 2012) with the arguments “HEADCROP:11 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50”, in each sample more than 98% of reads passed the trimming.
63-65% of clipped reads were successfully mapped to A. thaliana TAIR10 genome sequence and annotation (TAIR) using RobiNA’s v1.2.4_build656 Bowtie (Langmead et al. 2009).
normalization and statistical evaluation of differential gene expression has been performed using edgeR v2.6.12 using the Benjamini-Hochberg (1995) method for multiple testing.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include ID, LogFC, logCPM, LR, Pvalue and FDR (BH corrected) values for each Sample

source_name: leaf, 4 week old plants

growth_protocol: long-day; 16h light, 8h dark, 20°C

extract_protocol:
RNA was extracted from leaves using Roboklon total RNA purification kit
Illumina TruSeq RNA Sample Prep protocol

treatment_protocol: no treatments

tag: ecotype

value: leaf


title: miP1a_1


title: WT dark  Linc rep3

description: 3'-end polyA RNA

value: darkness and Lincomycin


title: co-sail_2

value: co-SAIL


title: miP1a_2


title: miP1b_1


title: psh1∆KAN Rad5+ t2 batch 1

description: Sample 8


title: WT dark rep3

description: 3'-end polyA RNA


title: WT Rad5+ t2 batch 1

description: Sample 7


title: C4-2B_Veh

city: Sacramento

first: Junjian

last: Wang

state: california

department: Biochemistry and molecular medicine

institute: UC Davis

description: Illumina next-generation sequencing (2x100bp, paired-end)

data_processing:
sequence reads were mapped to the reference human genome assembly (Feb. 2009,GRCh37/hg19) with BWA and Bowtie software.
the Cufflinks package  was applied for transcript assembly, quantification of normalized gene and isoform expression in FPKM (Fragments per kilobase of exon per million fragments mapped), and testing for differential expression (Cuffdiff).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene symbol and FPKM values for each gene and were prepared from the Cufflinks output files (tracking).

source_name: C4-2B cells cultured in medium with vehicle control.

growth_protocol: C4-2B cells were cultured in RPMI supplemented with 10% FBS for maintenance or 9% cds-FBS and 1% regular FBS (to mimic the CRPC condition) for experiments. Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2B cells treated with Vehicle or SR2211  for 48 hours.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, poly-adenylated mRNA was purified from total RNA and rRNA removed by two rounds of binding to magnetic poly-T beads.  This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94ºC for 5 minutes.  Double-stranded cDNA was generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I.  The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove 3′-overhangs and fill in 5′-overhangs, phosphorylated with T4 PNK, and then 3′-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP.  Illumina paired-end (PE) adapters were ligated, followed by purification wit AMPure XP beads.  The library was enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.

treatment_protocol: C4-2B cells were seeded into 6 well plate and cultured in CRPC medium (RPMI 1640, 9%cds-FBS and 1% regular FBS, L-Glutamine, Pen-Strep), next day, cell were then treated with vehicle or ENZ (20µM)  for another 48 hours.

tag: cell line

value: C4-2B human prostate cancer cell line

value: Bone metastatic LNCaP-derivative