title: CAGE_dcp2_2

description:
Barcode = TAG
CAGE-Seq
processed data file: peaks_dcp2.gff
Barcode = GCC
CAGE-Seq
processed data file: peaks_dcp2.gff

data_processing:
After demultiplexing using in-house script, reads were filtered to retain only those containing the EcoP15I restriction site and with a G as a first base of the insert.
Adapter sequences were removed using version 1.2.1 of Cutadapt.
Reads with 25-27 nt insert were selected and mapped using version 0.12.7 of Bowtie (3 mismatches tolerance).
Briefly, the CAGE-Seq signal was scanned within a +/- 200 nt window around the n nucleotide of the genome, and two parameters were used to define peaks within the window: for each position of the window, the minimum number a uniquely mapped reads starting at the considered position, in each of the two biological replicates (1, 2, 5, 10, 15 or 20), and the minimum ratio between the signal at this position and the total signal within the window (0,05, 0.1, 0,15 or 0,2).
The window was then slided 10, 25 or 50 nt downstream (therefore centred on nucleotide n+10, n+25 or n+50, respectively), so that each position of the genome was encompassed in several sliding windows.
In total, 72 combinations of parameters were tested for the wild-type and for the dcp2-7 conditions.
Parameters selected for the two conditions were: interval between two sliding windows = 10 nt, minimum of reads/replicate = 5, minimum ratio of signal/total = 0.15
Finally, a position was defined as a genuine CAGE peak when it passed the criteria mentioned above in ≥ 90% of the windows encompassing it.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: For each of the two strains analyzed, a gff file including position of the CAGE peaks identified by the peak-calling procedure.

source_name: YAM2283 dcp2-7 strain (37°C)

growth_protocol: Biological replicates of YAM1 (wild-type) and YAM2283 (dcp2-7) were grown to mid-log phase in YPD medium, then shifted for 2 hours at 37°C.

extract_protocol:
Total RNA was extracted using standard hot phenol procedure.
CAGE-Seq libraries were constructed starting from 5 µg of total RNA.

value: YAM2283 dcp2-7 strain


title: TCR-NK1.1+_2

status: Public on Jan 21 2016

type: SRA

city: New York

first: Saida

last: Dadi

state: NY

address: 1275 York Ave

department: Immunology

country: USA

institute: MSKCC

library_source: transcriptomic

data_processing:
The raw output BAM files were converted to FASTQ using PICARD Sam2Fastq. Reads were then trimmed using fastq_quality_trimmer with default settings.
The trimmed reads were first mapped to the mouse genome using rnaStar (version 2.3.0e).
The genome assembly mm9 was used with junctions from ENSEMBL (Mus_musculus.NCBIM37.67) and a read overhang of 49.  Then any unmapped reads were mapped to mm9 using BWA MEM (version 0.7.5a).  The two resulting BAM files were merged and gene level counts were computed using htseq-count (options -s y -m intersection-strict) and the same gene models (Mus_musculus.NCBIM37.67).
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file where 1st column contains Ensembl gene ids. Each column after the first one contains the counts for a sample

molecule: total RNA

organism: Mus musculus

source_name: Mammary tumors of 20- to 24-week-old PyMT C57BL/6 mice

extract_protocol:
Cells were isolated from pooled tumors of 20- to 24-week-old PyMT mice. Tumors were prepared by mechanical disruption using a razor blade followed by treatment with 280 U/ml Collagenase Type 3 (Worthington Biochemical) and 4 μg/ml DNase I (Sigma) at 37°C for 1 h with periodic short vortexing. Digested tissues were mashed through 70-μm filters, and collected by centrifugation. Cell pellet was resuspended in 44% Percoll, layered on top of 66% Percoll (Sigma), and centrifuged at 1,900 g for 30 min without brake. Cells at the Percoll interface were collected, stained with antibodies and analyzed by flow cytometry. Cells were sorted using FACS Aria-II machines directly in Tri-Reagent (Sigma).
RNA was prepared and complementary DNA (cDNA) libraries were amplified using the SMARTer RACE Amplification Kit (Clontech)

tag: strain

tag: gender

value: female

tag: age

value: 20- to 24-week-old

tag: tissue

value: mammary tumor

tag: cell population


title: RNAseq_Atoh1_restoration_rep1

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
For ChIP-Seq, reads were aligned to the murine genome (mm9) with BOWTIE v0.12.8 using either the -m 1, -v 0 options (ChIPs from sorted tumor cells) or standard-options (ChIPs from tumorspheres). For RNA-Seq data, we sequential map reads using an in-house script implementing BWA with default settings, STAR (extra settings: "--outSAMunmapped Within --outSAMstrandField intronMotif") and SIM4 with default settings, followed by a re-implementation of Picard's CleanSam in which we enable trimming for alignments that run off the end of the reference, and in which we also enable extending alignments by identifying soft-clipping that could align in-place.
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R, Excel and Seqminer or with bedtools. For RNA-Seq, reads for each ensembl gene were counted using the summarizeOverlaps {GenomicAlignments} function in R. Weakly expressed genes were removed (read sum of all samples per gene > 18) and differentially expressed genes were called using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: MACS-output files in wig-format or bed-format are provided. For RNA-Seq, matrix file contains read count and edgeR output contains gene name, ensembl ID, Log2 fold change, log2 CPM, p-value and Benjamini-Höchberg-adjusted p-value (FDR).

growth_protocol: The Group3 (G3) medulloblastoma (MB) model relies on enforced expression of c-Myc (Myc) in primary granule neuron progenitors (GNPs) isolated from the cerebella of 7 day-old Trp53-/-;Cdkn2c-/- mice followed by orthotopic transplantation of the transduced cells into the cortices or cerebella of naïve immunocompromised CD-1 nu/nu recipient animals (Kawauchi et al., 2012).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies).
Libraries forRNA-seq samples were contructed following manufactor's intructions using the TruSeq Stranded Total RNA Kit (Illumina).

treatment_protocol: Three G3 MB tumorsphere lines (#19251, 19554, and 19568) infected with retroviruses encoding Atoh1 followed by cranial implants into the cortices of recipient animals. Tumor cells were dissociated and purified by percoll-gradient.

tag: generation of cells

value: spheres from tumor cells


title: CAGE_dcp2_1

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Barcode = TAG

organism: Saccharomyces cerevisiae

tag: genotype/variation

tag: background strain

tag: replicate


title: TCRb+CD8a+PD1-NK1.1-_1


title: CAGE_WT_2

description:
Barcode = CTT
CAGE-Seq
processed data file: peaks_WT.gff

source_name: YAM1 wild-type strain (37°C)

value: YAM1 wild-type strain


title: TCRb+CD8a+PD1+_1


title: CAGE_WT_1

description:
Barcode = AGA
CAGE-Seq
processed data file: peaks_WT.gff


title: RNAseq_control_rep6


title: RNAseq_control_rep5


title: TCRb+CD8a-NK1.1+_1


title: TCRb+CD8a+NK1.1+_1


title: FH-1

city: Charlotte

first: Adam

middle: Michael

last: Whaley

state: NC

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: UNCC

data_processing:
Published Cufflinks analysis pipeline (tophat v.2.0.9, cufflinks v.2.1.1).
Sequences aligned to Glycine max reference genome version 2.75 (available at JGI-phytozome).
Mapping step done with suggested non-mammalian parameters (-I 5000), reference GTF file used (also available at phytozome).
Genome_build: V2.75

organism: Glycine max

source_name: G. Max 5th trifiolate leaf

extract_protocol:
Whole leaf tissue from each of the three leaflets from the  5th trifoliate leafs was extracted using the Qiagen Plant RNAEasy extraction kit (Qiagen, CA) followed by Ambion DNA-free treatment (Life Technologies, NY).
RNA-seq libraries were subsequently created using Illumina TruSeq RNA-seq kit (Illumina, CA).  Each library was quantified on the Bioanalyzer using RNA nano chips (Agilent, CA)

treatment_protocol: High Ozone treatments exposed to 75 ppb ozone atmospheric conditions in CSTR

tag: ozone level

tag: time point


title: RNAseq_control_rep4


title: TCR-NK1.1+_1


title: RNAseq_control_rep1


title: R-Het rep1

city: Shanghai

first: Gang

last: Wang

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.8 with parameters -aS --chumkmbs 128 -v 3 -p 30 --best --strata
Fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) were generated using eXpress V1.5.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Calvaria

extract_protocol:
Calvaria were removed from newborn mice, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: Newborn

tag: genotype

value: calvaria


title: R-Het rep3


title: R-WT rep3

value: WT


title: R-WT rep2


title: NMyc_G3-tumorspheres

description: fixed chromatin

library_source: genomic

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the murine genome (mm9) with BOWTIE v0.12.8 using either the -m 1, -v 0 options (ChIPs from sorted tumor cells) or standard-options (ChIPs from tumorspheres).
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R, Excel and Seqminer or with bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: MACS-output files in wig-format or bed-format are provided.

molecule: genomic DNA

extract_protocol:
Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (Miz1, c-Myc, NMyc) was precipitated by incubation with Protein A- and Protein G-dynabeads beads for 6 hrs or overnight. After several washings chromatin was eluted with 1 % SDS and  crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR.
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired,  A-tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.

tag: antibody


title: R-WT rep1


title: Miz1_SHH-tumorspheres

description: fixed chromatin

source_name: SHH-medulloblastoma


title: RNAseq_control_rep7


title: NMyc_SHH-tumorspheres

description: fixed chromatin


title: input_SHH-tumorspheres

description: fixed chromatin

value: none (input)


title: P-KO rep3

value: Med23-/- (Mensenchymal stem cells specific deletion)


title: RNAseq_control_rep3


title: Miz1_G3-tumorspheres

description: fixed chromatin


title: input_G3-tumorspheres

description: fixed chromatin


title: Myc_G3-medulloblastoma

description: fixed chromatin

value: sorted primary tumor cells


title: P-Ctrl rep3


title: P-KO rep1


title: RNAseq_control_rep2


title: young-chm 5

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: Males (From mix males/female population)

data_processing:
Illumina RTA 1.18.64
Alignment was performed using Tophat2 v2.0.5 (Kim et al., 2013) against the reference genome (BDGP5.74) with an average alignment rate of 92%.
Reads were counted at genomic features (i.e. exons) using the summarizeOverlaps function in the GenomicAlignments R/Bioconductor package.
Normalization and differential expression tests were performed using the EdgeR package and significant differences were called with an FDR cutoff 0.05
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Normalized counts (pseudo counts generated by EdgeR) in table format (csv file)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: adult head

extract_protocol:
Total RNA was prepared from 25-30 fly heads using 0.5 ml Qiazol (Qiagen) according to manufacturer’s instructions.
2.5 µg of RNA were used for polyA selection and subsequent RNA purification was achieved with RNeasy mini columns (Qiagen). Libraries were prepared using New England Biolabs reagents according to protocols (E7490, E6150, E7525, E6111, E7442, E7335). The ligation was done at 16°C overnight with regular ligase (M0202) and High Fidelity PCR mix (M0541) was used for amplification. Quantifications and quality controls were done with Qubit RNA HS detection kit (Life Technologies) and the RNA 6000 pico kit and DNA 2000 kits (Agilent). 50 bp single reads were obtained on an Illumina Hiseq sequencer.

value: young 7 days

value: chm/+

value: male


title: Miz1_G3-medulloblastoma

description: fixed chromatin


title: input_G3-medulloblastoma

description: fixed chromatin


title: R-Het rep2


title: young-chm 4


title: H2AZ_K3R3 ChIP-Seq

city: Cambridge

first: Laurie

middle: A

last: Boyer

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Sequences were extended +200 bp for histone marks and allocated in 25-bp bins.
A Poissonian model was used to determine statistically enriched bins with a P-value threshold set at 1x10-9 as described previously (Marson et al., 2008).  Additionally, we required that genomic bins were at least 5 fold over input to be considered enriched peaks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstadt et al. Cell 2012).

source_name: ES cells

growth_protocol: V6.5 (129SvJae and C57BL/6; male) ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 10% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). ESCs used for the majority experiments, including ChIP-Seq, RNA-Seq and RT-qPCR, were plated without irradiated MEFs for the final passage.

extract_protocol: The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification. Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on, 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Antibodies used for ChIP include:  ~200 ng of DNA was submitted to SPRI-works Fragment Library System I (Beckman Coulter) for each library prepared. Briefly, the DNA is subjected to size selection (200-400bp) with magnetic beads, end repaired, then a single adenine nucleotide is added to allow for directional ligation of adaptors. For this study, a 1:100 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was then amplified for 19 cycles, using the Illumina protocol, adding additional bases from the PCR primers that aid sequences to anneal to the Illumina Genome Analyzer flow cell. The samples were then purified on a Qiagen MinElute column, and libraries were quantified by Quant-it DNA Assay (Invitrogen, Q-33120), and examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

treatment_protocol: H2AZ-YFP, and H2A.Z.K3R3-YFP constructs were modified from vectors generated in Sarcinella et al., 2007. The H2AZ.K3R3 mutant is a triple point mutant in the C-terminus of H2AZ with replacement of K119,K120, K123 with arginines, with the GFP in this vector being replaced by YFP, such that it is in frame C-terminal to the cDNA. EcoRI and XbaI digestion was performed to place H2AZ, AP3 and H2A cDNA in frame. This vector contains a CMV-promoter driven by an rtTA drug inducible system. The resulting lentiviral constructs were transfected into 293 cells using the protocol outlined by the RNAi consortium (BROAD Institute, http://www.broadinstitute.org/rnai/public/). The viral supernatant generated 48hrs after transfection was used to infect KH2 ESCs (Beard, 2006) to generate wildtype and mutant H2AZ transgenic ESC lines. The YFP transgenic ESCs were induced with 1µg/ml of doxycycline and FACS sorted for YFP positive cells. In order to study the selective impact of the H2AZ mutants, lentiviral constructs expressing short hairpins specifically directed at the 3’ UTR of endogenous H2AZ were introduced into the wild-type and mutant H2AZ transgenic KH2 ESC lines using RNA. Sequences of the different H2AZ 3’UTR-directed hairpin oligos are as follows: sh#2 5’- AACAGCTGTCCAGTGTTGGTG-3’; sh#5 5’- AATTAGCCTTCCAACCAACCA-3’. Hairpin oligos were annealed and cloned into pLKO.1 vector (Sigma) as detailed by the RNAi consortium, BROAD (http://www.broadinstitute.org/rnai/trc/lib). Blasticidin was used as a selection marker for the generation of endogenous H2AZ-depleted transgenic KH2 ESCs. The puromycin marker in the pLKO.1 vector was removed by digestion with BamHI and KpnI and replaced with blasticidin. The blasticidin cDNA was PCR amplified from pLenti6.2/V5-DEST Gateway® Vector (Invitrogen). V6.5 (129SvJae and C57BL/6) and the YFP transgenic ESCs were cultured as previously described (Boyer et al., 2006). The endogenous H2AZ-depleted transgenic KH2 ESCs were similarly cultured with the addition of blasticidin (5µg/ml) on blasticidin-resistant feeder cells (Iuchi, 2006).

tag: cell type

value: Embryonic stem cells

tag: chip antibody


title: lsm1a lsm1b-NaCl

city: Madrid

first: Carlos

last: Perea-Resa

address: Ramiro de Maeztu,9

country: Spain

institute: CIB-CSIC

data_processing:
RNAseq reads were aligned to the TAIR10 Col-0 reference genome using TopHat2 (Kim et al, 2013) with default parameters
Uniquely mapped reads were counted per representative gene model (excluding introns) according to the TAIR10 annotation using custom R scripts
Differential expression between WT and mutant in each condition was calculated using DEseq2 (Love et al. 2014) following its manual
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files include raw counts for each sample

organism: Arabidopsis thaliana

source_name: leaves from two-week-old plants_salt

growth_protocol: Plants were grown under long-day photoperiod (photon flux of 90µmol m-2 s-1). For cold treatments, plants were grown on soil. For drought and high salt treatments, plants were grown on GM medium plates

extract_protocol:
Stressed plants were colected, inmediately frozen on liquid nitrogen and homogenized. Total RNA was extracted using TRIzol® Reagent (Life Technologies) and cleaned with RNeasy Plant Mini Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiod (photon flux of 40µmol m-2 s-1). For drought and high salt treatments, plants were transferred from GM medium to PEG (55%)- or NaCl (150mM)-containning plates for 10h, respectively

value: lsm1a lsm1b

tag: developmental stage

value: two-week-old

value: leaves


title: midlife-chm 5

value: midlife 22-23 days


title: K3R3 Brd4 ChIP-seq Rep 2

data_processing:
Illumina Offline BaseCaller1.9.3 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.0.1, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S
Enriched regions were defined using Macs 1.4.2 with the following parameters -p 1e-9 -w -S --space=50, peaks regions were called based on merging the biological replicates
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files were generated using MACS 1.4.2, with reads extended 150bp and allocated into 25bp bin. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.  Bed file represent peak call genomic coordinates, fifth column is -10*log10(pvalue) for the peak calls.

source_name: K3R3 Brd4 ChIP-seq

growth_protocol: V6.5 (129SvJae and C57BL/6; male) and KH2 ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates. Briefly, cells were grown in Knockout DMEM supplemented with 10% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006)

extract_protocol:
The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification. Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on, 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water.
~200 ng of DNA was submitted to SPRI-works Fragment Library System I (Beckman Coulter) for each library prepared. Briefly, the DNA is subjected to size selection (200-400bp) with magnetic beads, end repaired, then a single adenine nucleotide is added to allow for directional ligation of adaptors. For this study, a 1:100 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was then amplified for 19 cycles, using the Illumina protocol, adding additional bases from the PCR primers that aid sequences to anneal to the Illumina Genome Analyzer flow cell.  Specific primers were used for 3’ barcoding, adding 6 nt barcodes to uniquely identify each sample (V6.5 Brd2 Rep 1: TACCGC, Rep 2: GTCCAG, WT Brd2 Rep 1: TTCAGA, WT Brd2 Rep 2: TGCTGT, WT Brd4 Rep 1: ACGGTG, WT Brd4 Rep 2: CATCAC, K3R3 Brd2 Rep 1: GTAACA, K3R3 Brd2 Rep 2: GGATCT, K3R3 Brd4 Rep 1: TCCGGG, K3R3 Brd4 Rep 2: AAGCTC). The samples were then purified on a Qiagen MinElute column, and libraries were quantified by Quant-it DNA Assay (Invitrogen, Q-33120), and examined for proper size and structure by Bioanalyzer (Agilent) and qPCR

treatment_protocol: For transgenic lines, H2A.Z-YFP,and H2A.Z ubiquitin mutant (K3R3)-YFP constructs were generated as described (Surface, 2015). This vector contains a CMV-promoter driven by an rtTA drug inducible system. The resulting lentiviral constructs were transfected into 293 cells using the protocol outlined by the RNAi consortium (BROAD Institute, http://www.broadinstitute.org/rnai/public/). The viral supernatant generated 48hrs after transfection was used to infect KH2 ESCs (Beard, 2006) to generate wildtype and mutant H2A.Z transgenic ESC lines. The YFP transgenic ESCs were induced with 1µg/ml of doxycycline and FACS sorted for YFP positive cells. In order to study the selective impact of the H2A.Z mutants, lentiviral constructs expressing short hairpins specifically directed at the 3’ UTR of endogenous H2AZ were introduced into the wild-type and mutant H2A.Z transgenic KH2 ESC lines. Sequences of the H2A.Z 3’UTR-directed hairpin oligo is as follows: shRNA 5’- AACAGCTGTCCAGTGTTGGTG-3’; Hairpin oligos were annealed and cloned into pLKO.1 vector (Sigma) as detailed by the RNAi consortium, BROAD (http://www.broadinstitute.org/rnai/trc/lib). Blasticidin was used as a selection marker for the generation of endogenous H2A.Z-depleted transgenic KH2 ESCs (Subramanian, 2013). The endogenous H2A.Z-depleted transgenic KH2 ESCs were cultured with the addition of blasticidin (5µg/ml) on blasticidin-resistant feeder cells (Iuchi, 2006).

tag: strain background

value: Embryonic stem cells (ESCs)

tag: transfected with

value: expressing a ubiquitin mutant version of H2A.Z

value: Brd4 (Bethyl A301-985A50, lot 3)


title: midlife-chm 4

tag: gender


title: K3R3 Brd4 ChIP-seq Rep 1


title: Col-0-NaCl


title: Col-0-PEG

source_name: leaves from two-week-old plants_drought


title: midlife-chm 3

tag: age


title: K3R3 Brd2 ChIP-seq Rep 2

source_name: K3R3 Brd2 ChIP-seq

value: Brd2 (Bethyl A302-583A, lot 1)


title: WT Brd4 ChIP-seq Rep 2

source_name: WT Brd4 ChIP-seq

value: expressing wild type H2A.Z


title: OE_1

city: Hong Kong

first: Anna

last: Liu

state: Hong Kong

address: Pokfulam Road

department: CS

country: Hong Kong

institute: HKU

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC).After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences (TAIR 10 version) with SOAPaligner/SOAP2(parameters: -m 0 -x 10000 -s 40 -l 32 -v 5 -r 2 -p 6) (Li et al., 2009).
The transcript abundance were estimated by RPKM (Reads per kilobase transcript per million reads) calculation for each gene in each compartment (Mortazavi et al., 2008). RPKM = 109*C/N*L (C is the number of mappable reads that fell onto the genes; N is the total number of mappable reads in the experiment; L is the sum of the genes in base pairs).
Genome_build: TAIR 10 version
Supplementary_files_format_and_content: RPKM

source_name: leaf

growth_protocol: Arabidopsis thaliana ecotypes Columbia (Col-0) (Overexpression line) was used in this study. After sterilization, the seeds were placed on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22°C) / 8 hours dark (18°C) period in growth chamber at a light intensity of 120–150 µmol m-2 s-1. 20-day-old Arabidopsis leaves without bolting were immediately frozen in liquid nitrogen for RNA and protein and metabolites extraction. Leaves were harvested at three different time points: t = 0 hr (end of night), t = 1 hr (one hour after light turn on) and t = 8 hr (eight hours after light turn on), respectively.

extract_protocol:
Total RNA was extracted from leaves at all three time points and DNA contamination was removed by DNase I (RNeasy Plant Mini Kit, Qiagen, Hong Kong).
Ribosomal RNAs were removed from the total RNA by the Ribo-Zero rRNA removal kit for plant leaf (Epicentre, USA) before cDNA library construction. The libraries were sequenced using Illumina HiSeqTM2000. After removal of low quality reads, clean reads from three different RNA-seq samples (WT 3 times points, t = 0, 1, 8) were aligned to Arabidopsis genome.

tag: ecotype

value: Overexpression line

tag: time point (hr)


title: OE_8


title: midlife-wt 4

value: wt


title: WT Brd4 ChIP-seq Rep 1


title: P-Ctrl rep1

tag: strain

value: Newborn

value: WT

tag: tissue

value: calvaria


title: P-KO rep2

value: Med23-/- (Mensenchymal stem cells specific deletion)


title: OE_0

tag: genotype/variation


title: midlife-wt 3

value: male


title: WT Brd2 ChIP-seq Rep 1

source_name: WT Brd2 ChIP-seq


title: P-Ctrl rep2


title: young-chm 3

value: young 7 days

value: chm/+


title: WT Brd2 ChIP-seq Rep 2


title: young-chm 2


title: Brd2 ChIP-seq Rep 2

source_name: Brd2 ChIP-seq

value: wild type (control)


title: lsm1a lsm1b-PEG

value: lsm1a lsm1b

value: two-week-old

value: leaves


title: H2AZ_WT ChIP-Seq

value: Embryonic stem cells


title: young-chm 1


title: young-wt 5


title: K3R3 Brd2 ChIP-seq Rep 1

value: Embryonic stem cells (ESCs)

value: expressing a ubiquitin mutant version of H2A.Z


title: young-wt 4


title: H2AZ_K3R3_ESC

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
The reads were mapped to mm9 genome using OLego (Wu et al.,2013) (1.1.2). Known junctions extracted from igenome (Illumina) were provided to OLego to maximize the sensitivity. Default options were used for OLego. Afterwards, HTSeq-count (0.5.4p1) was used to summarize the read counts mapped to each transcript (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
The RPKM values were computed by normalizing the raw read counts with the transcript lengths and total numbers of reads for each sample.  Raw read counts were used to detect differentially expressed genes using DEseq (1.10.1) with default parameters (Anders et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file that includes RPKM values for each Sample, and log2(fold-changes) among samples at each time-point.

extract_protocol: RNA was extracted using TRIzol. Strand specific libraries were prepared with the purified RNA subjected to oligo (dT) selection, fragmentation and first and double strand synthesis with the Illumina Tru-Seq kit using manufacturer’s instructions. DNA fragments above 30bp was purified using SPRI-TE beads according to manufacturer’s instructions. The purified DNA was end repaired and single A bases were added for adaptor ligations. The adaptor-ligated DNA was then subjected to  Pippin purification to select for 300bp DNA fragments. These fragments were enriched and barcoded by PCR for multiplexing. A final Pippin purification was performed to clean up the barcoded RNA-Seq libraries.


title: midlife-chm 1

value: midlife 22-23 days


title: YH-A-2

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

description: processed_data_file: YH.txt

data_processing:
RNA-seq: the cDNA library with a fragment length range of 200-500 bp was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500).
Filtering: the trimming adapter sequences were removed and low-quality reads  were filtered with the software
Assembly:the clean reads were used to de novo assemble the radish transcriptome using Trinity
Gene annotation: for annotation of unigenes using various bioinformatics approaches, the unigenes were firstly searched against the Nr, KOG, KO, GO and Swiss-Prot protein database using local BLASTx with E value cutoff of 10-5.
Gene Expression Analysis: Gene expression levels were measured in the RNA-Seq analysis as reads per kilobase of exon model per million mapped reads (RPKM). The DEseq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR < 0.001).
Genome_build: de novo assembly; fasta file is available on the series record.
Supplementary_files_format_and_content: the text file contains the gene name, gene length,gene annotation, RPKM value, the number of total reads of two replicates, Q value, P value, and  value of log2(Fold_change)

organism: Raphanus sativus

growth_protocol: The CMS lines of two varieties HYBP-A and YH-A and their corresponding maintainer lines HYBP-B and YH-B were grown in the experimental field under natural conditions and normal field management.

extract_protocol:
The dual-core period anthers of microspore mother cells of two CMS lines and two maintainer lines were corrected. Anthers collected from five individuals for each line were mixed as a sample. Total RNA of each sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, USA) according to the manufacturer’s protocol.
RNA of four samples were separately used to construct the cDNA library with a fragment length ranging from 200 to 500 bp. Then, the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2500) according to the manufacturer’s instructions (Illumina, San Diego, CA).

value: anther

value: dual-core period of microspore mother cells

tag: cultivar

value: YuanHong

tag: cms status

value: CMS (line A)


title: YH-B-2

description: processed_data_file: YH.txt

value: Non-CMS (maintainer line B)


title: YH-B-1

description: processed_data_file: YH.txt


title: H2AZ_WT_ESC_Rep2


title: young-wt 3

value: wt


title: H2AZ_WT_ESC_Rep1


title: young-wt 2

value: male


title: young-wt 1

value: young 7 days


title: HYBP-B-1

description: processed_data_file: HYBP.txt

value: HuaYeBaiPi


title: midlife-chm 2

value: chm/+


title: YH-A-1

description: processed_data_file: YH.txt


title: HYBP-B-2

description: processed_data_file: HYBP.txt


title: midlife-wt 2


title: midlife-wt 1


title: HYBP-A-2

description: processed_data_file: HYBP.txt


title: HYBP-A-1

description: processed_data_file: HYBP.txt


title: Brd2 ChIP-seq Rep 1

value: wild type (control)

value: Brd2 (Bethyl A302-583A, lot 1)


title: Input

status: Public on Jan 20 2016

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated

organism: Homo sapiens

source_name: DNA from BT549_TNFalpha

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium  supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol:
Standard Illumina DNA library construction
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested

tag: cell line

value: Triple negative breast cancer cells

tag: treated with

value: TNFα for 6 h


title: Jun_TNF

description:
39TNFJun_35IgG_peaks.bed
TNFJun39_Input38_peaks.bed

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated
39TNFJun_35IgG_peaks.bed: During Peak calling Jun_TNF was treated as Chip and IgG as control.
TNFJun39_Input38_peaks.bed: During Peak calling Jun_TNF was treated as Chip and Input as control.

source_name: BT549_TNFalpha_c-Jun antibody

value: c-Jun (H-79, Santa Cruz)


title: Jun_no_TNF

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated
36noTNFJun_35IgG_peaks.bed: During Peak calling Jun_no_TNF was treated as Chip and IgG as control.
noTNFJun36_Input38_peaks.bed: During Peak calling Jun_no_TNF was treated as Chip and Input as control.

source_name: BT549_without TNFalpha_c-Jun antibody


title: mes-1 sterile adults #2

city: Santa Cruz

first: Andrew

middle: Kekupa'a

last: Knutson

state: CA

address: 1156 High St

department: MCD Biology

institute: University of California, Santa Cruz

data_processing:
Raw sequences were mapped to transcriptome version WS220 using Tophat2.  Only reads with one unique mapping were allowed; otherwise default options were used.  Reads mapping to ribosomal RNAs were removed from further analysis.
The Bioconductor package DESeq2 was used for differential expression analysis. A Benjamini-Hochberg multiple hypothesis corrected p-value cutoff of 0.05 was used as a significance cutoff.
Transcript length and sequencing depth normalized read counts per transcript (RPKM) were obtained using the program Cuffdiff2.
Genome_build: WS220
Supplementary_files_format_and_content: WS220 Gene names, chr, start, end, Mean expression (DESeq2), log2 FoldChange mes-1;daf-2/mes-1 (DESeq2); adjusted p-value (Benjamini-Hochberg, DESeq2), RPKM mes-1 (Cuffdiff2), RPKM mes-1;daf2 (Cuffdiff2)

organism: Caenorhabditis elegans

source_name: sterile whole adults

growth_protocol: mes-1 single and daf-2; mes-1 double mutant adults were allowed to lay embryos overnight at 24°C.  The next day (Day 1), embryos were downshifted to 15°C to prevent formation of dauer larvae.  On Day 5, the adult worms were upshifted back to 24°C.  Our reasoning for upshifting adults back to 24°C was because ectopic expression of germline genes has been shown to be stronger at higher temperatures.  On Day 6, 100 sterile, germlineless adult worms (that visually lacked embryos) were manually picked into Trizol and total RNA was extracted.

extract_protocol:
Total RNA was extracted using Trizol reagent and ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (Cat. #E6310).
Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina sequencing (Cat. #E7530). Libraries were sequenced at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley using the Illumina HiSeq 2000 platform.

tag: genotype

value: mes-1(bn84ts) X

tag: temperature


title: mes-1 sterile adults #1


title: IgG

tag: cell type

tag: chip antibody

value: normal rabbit IgG (sc-2027, Santa Cruz)


title: daf-2; mes-1 sterile adults #3

value: daf-2(e1370) III; mes-1(bn84ts) X


title: daf-2; mes-1 sterile adults #1


title: mes-1 sterile adults #3


title: L1-Starved-AvaII

city: Stanford

first: Idan

last: Gabdank

state: California

address: 3165 Porter Drive

department: Genetics

institute: Stanford

description:
Raw data files for this sample were generated from Illumina MiSeq and Illumina HiSeq 2000 instruments.
animals starved for 24 hours after bleaching

data_processing:
Library strategy: Tethered Chromosome Conformation Capture
Basecalls performed using Illumina Casava software
Read pairs obtained by massive parallel sequencing were aligned to the C. elegans reference genome (ce10) using an iterative mapping approach utilizing ICE software, utilizing Bowtie2 v2.2.5
Uniquely mapped pairs were filtered from duplicates and pairs that map concordantly (distance<500 and correct orientation)
Exact locations of contact junctions were calculated using specific alignments to the reference genome (ce10)
Genome_build: ce10
Supplementary_files_format_and_content: TSV files containing detected contact of chromatin architecture, the files contain the following fields: readname, mapped chr read1, mapped position read1, boolean of sense strand of read1, aligned sequence of read1, mapped chr read2, mapped position read2, boolean of sense strand of read2, aligned sequence of read2, reference sequenced read1 was aligned to, reference sequence read2 was aligned to, read1 sequence, read2 sequence, contact read1 chr, contact read1 pos, contact read2 chr, contact read2 pos.           In case of single ended sequencing run, alignment is performed using two sides of a single read.

extract_protocol:
Animals were harvested by chilling on ice, centrifugation at 950g for two minutes and washing several times with cold M9. Pellets consisting each of approximately 100µl of closely packed worms were flash frozen in liquid nitrogen and stored in -80°C.  The flash frozen worm pellets were ground to fine powder in liquid nitrogen. The grinding was performed either using mortar and pestle or using an electric drill with “Cellcrusher” drill-bit and “Cellcrusher” base held at liquid nitrogen temperatures. The grinding was done for several minutes, until reaching a fine powder. The powder was stored at -80°C. To get the DNA used for libraries construction, freeze-ground tissue was processed using procedures from (Kalhor, et al, 2012) with some modifications.
Libraries were prepared according to Illumina's instructions in Nextera DNA Sample Preparation Guide (Part# 15027987Rev. B) with some modifications. Briefly, DNA was tagmented using Tagmentase (TDE1), then cleaned-up using Zymo DNA Clean & Concentrator™-5 kit. The biotinylated purified DNA was selected using MyOne Streptavidin C1 magnetic beads (Invitrogen), fragments ion the beads were PCR amplified with Illumina primers for 12 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from 1% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

value: whole organism

value: wild-type

tag: developmental stage


title: GFP3

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

description: GFP-expressing beta-cells

data_processing:
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed  by quality, reads were filtered by quality and mapped to mm9 using the Tophat2 software
Quantification and normalization were done using Cuffnorm/Cuffdiff to produce gene-level normalized expression values (FPKMs)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include average expression (FPKM) for each group, Log2(fold change) (differential expression between GAP and P16), p- and q-values  (from Cuffdiff)

source_name: pancreatic beta-cells

growth_protocol: Ins-rtTA/tet-GFP/tet-p16ink4a mice and control Ins-rtTA/tet-GFP mice were treated with tetracyclin for 10 days.

extract_protocol:
Qiagen RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pancreatic islets were dissected and dissociated, and GFP-positive cells were isolated by FACS.

tag: transgene expressed

value: GFP

value: beta-cells from dissociated pancreatic islets

tag: transgene induction time

value: 10 days Tet induction


title: GFP2

description: GFP-expressing beta-cells

data_processing: Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed  by quality, reads were filtered by quality and mapped to mm9 using the Tophat2 software. Quantification and normalization were done using Cuffnorm/Cuffdiff to produce gene-level normalized expression values (FPKMs). Genome_build: mm9. Supplementary_files_format_and_content: tab-delimited text files include average expression (FPKM) for each group, Log2(fold change) (differential expression between GAP and P16), p- and q-values  (from Cuffdiff).


title: p16_3

description: p16INK4a, GFP-expressing beta-cells

value: GFP and p16INK4a


title: p16_2

description: p16INK4a, GFP-expressing beta-cells


title: Renal tissue, 7 days after UUO, C57Bl/6, biological replicate 3

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

institute: Klinikum der Universität München, Klinische Biochemie

description: Gene expression data from kidney of C57Bl/6 mouse 7 days after UUO

data_processing:
Read counts were TMM normalized and tested for differentially expression between groups using the negative binomial regression model implemented in the Bioconductor package edgeR
Benjamini-Hochberg (BH) correction of p-values was applied to control false discovery rate. Genes with adjusted p-values below 0.05 were considered statistically significant.
Differentially expressed genes were tested for over-representation of gene ontology (GO) terms using one-sided hypergeometric tests. P-values for GO terms were adjusted for multiple testing using BH correction
Read counts were transformed to log2 counts-per-millions (cpm) and scaled for visualization in heatmaps.
All analyses were performed with R 3.2.
Genome_build: Genome Build 38, or mm10 in UCSC terms
Supplementary_files_format_and_content: Excel Sheet of differentially expressed genes, based on analysis detailed above

source_name: Whole kidney, 7 days after UUO, C57Bl/6 mouse

growth_protocol: Kidneys 7 for RNA-seq analysis were freshly isolated from Dkk3-/- and C57Bl/6 mice 7 days after UUO and directly subjected to RNA isolation.

extract_protocol:
Total RNA was extracted from kidneys and cells using the Chomczynski and Sacchi´s protocol. 10 μg of total RNA was digested with DNase I according to the standard protocol. Total amount of 1 μg RNA was taken for each sample.
Samples were prepared as a 10-plex, which was sequenced on three lanes. HiSeq 2000 50bp SR run was used. Total amount of 1 μg RNA was taken for each sample.

tag: background strain

tag: mouseid

value: kidney

tag: condition

value: 7 days after UUO

value: Dkk3 wildtype


title: Renal tissue, 7 days after UUO, C57Bl/6, biological replicate 1

tag: strain


title: Renal tissue, 7 days after UUO, Dkk3-/-, biological replicate 1

description: Gene expression data from kidney of Dkk3-/- mouse 7 days after UUO

source_name: Whole kidney, 7 days after UUO, Dkk3-/- mouse

tag: tissue

value: Dkk3 knockout


title: p16_1

description: p16INK4a, GFP-expressing beta-cells


title: NEG - untreated and extracted

city: Milan

first: Heiko

last: Muller

address: Via Adamello 16

country: Italy

institute: Italian Institute of Technology

description:
4SU labeled miRNA
small RNA sequencing Illumina

data_processing:
base calling: Illumina RTA 1.17.20
demultiplexing: CASAVA-1.8.0, mismatches=1
adapter removal: Flexible Adapter Remover, version 2.15,  -end any -th 10 -l CHANGED -n FAR; adapter: TrueSeq_RNA_Primer_3_index_common_RPI: GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
isoform quantitation: Isomirage
Genome_build: mirBase version 21
Supplementary_files_format_and_content: text file with raw read counts for miRNA isoforms

source_name: 3T9 FIBROBLAST_NEG - untreated and extracted

growth_protocol: cells were grown in DMEM 10% serum

extract_protocol:
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen). 4SU RNA was prepared starting from 40 μg of total RNA diluted in 100 µl of RNase-free water. 100µl of biotinylation buffer (2.5× stock: 25mM Tris pH:7.4, 2.5mM EDTA) and 50 µl of EZ-link biotin-HPDP (1 mg ml−1 in DMF; Pierce/Thermo Scientific 21341) were added and incubated for 3h at RT. Unbound biotin-HPDP was removed by adding chloroform/isoamylalcohol (24:1) and purifying the mix using MaXtract high-density tubes (Qiagen). RNA was precipitated by adding NaCl (5M???) at 1/10 volume and isopropanol at equal volume. Biotinylated RNA was resuspended in water, quantified with a Nanodrop 1000 spectrophotometer (to keep track of the yield after the first phase of the procedure) and, then, purified using 50µl of Dynabeads MyOne Streptavidin T1 (Invitrogen). Before mixing with RNA, beads were washed twice in Wash Buffer A (100mM NaOH, 50mM NaCl) and once in Wash Buffer B (100mM NaCl), then resuspended in 100 µl of Buffer C (2M NaCl, 10mM Tris-pH:7.5, 1mM EDTA, 0.1% Tween-20) to a final concentration of 5μg/μl. RNA was added in an equal volume and rotated at RT for 15min. Beads were washed 3 times with Wash buffer D (1M NaCl, 5mM Tris pH7.5, 0.5mM EDTA, 0.05% Tween-20). RNA was eluted from the beads in 100µl of 10 M EDTA in 95% formamide (65°C, 10 min). Eluted fraction was diluted in TRIzol® LS Reagent (Life Technologies; cat.no. 10296-028) and RNA extracted with miRNeasy Micro Kit (Qiagen; cat.no. 217084) and finally eluted in 14 μl of RNAse free water. 4SU-RNA quantification was conducted with Qubit® (Life Technologies).
300 nanograms of total RNA or 4SU RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: 4SU 300 uM for 3hrs followed by 1mM uridine

value: fibroblast


title: Renal tissue, 7 days after UUO, Dkk3-/-, biological replicate 3


title: 4SU - treated not extracted

description:
total miRNA
small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_4SU - treated not extracted


title: Renal tissue, 7 days after UUO, Dkk3-/-, biological replicate 2


title: UNT - untreated not extracted

source_name: 3T9 FIBROBLAST_UNT - untreated not extracted


title: 4SU - 12hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 12hrs - EXP3


title: daf-2; mes-1 sterile adults #2


title: 4SU - 8hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 8hrs - EXP3


title: 4SU - 6hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 6hrs - EXP3


title: 4SU - 4hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 4hrs - EXP3


title: 4SU - 10hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 10hrs - EXP3


title: 4SU - 0hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 0hrs - EXP3


title: 4SU - 8hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 8hrs - EXP2


title: 4SU - 10hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 10hrs - EXP2


title: 4SU - 12hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 12hrs - EXP2


title: 4SU - 4hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 4hrs - EXP2


title: 4SU - 2hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 2hrs - EXP2


title: Renal tissue, 7 days after UUO, C57Bl/6, biological replicate 2


title: 4SU - 0hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 0hrs - EXP2


title: 4SU - 12hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 12hrs - EXP1


title: 4SU - 10hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 10hrs - EXP1


title: 4SU - 6hrs - EXP2

source_name: 3T9 FIBROBLAST_4SU - 6hrs - EXP2


title: 4SU - 4hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 4hrs - EXP1


title: 4SU - 2hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 2hrs - EXP1


title: 4SU - 0hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 0hrs - EXP1


title: 12hrs_2

description: small RNA sequencing Illumina

data_processing:
base calling: Illumina RTA 1.17.20
demultiplexing: CASAVA-1.8.0, mismatches=1
adapter removal: Flexible Adapter Remover, version 2.15, -end any -th 10 -l CHANGED -n FAR; adapter: TrueSeq_RNA_Primer_3_index_common_RPI: GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
isoform quantitation: Isomirage
Genome_build: miRBase version 21
Supplementary_files_format_and_content: text file with raw counts of miRNA isoforms

source_name: 3T9 FIBROBLAST_12hrs_serum_stimulation

growth_protocol: cells were driven in quiescence by serum-deprivation for 72hrs. Subsequently, cells were stimulated with complete medium (10% FBS)

extract_protocol:
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions


title: 6hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_6hrs_serum_stimulation


title: 10hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_10hrs_serum_stimulation


title: 4SU - 8hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 8hrs - EXP1


title: 4hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_4hrs_serum_stimulation


title: 1hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_1hr_serum_stimulation


title: 4SU - 2hrs - EXP3

source_name: 3T9 FIBROBLAST_4SU - 2hrs - EXP3


title: 0hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_0hrs_serum stimulation


title: 2hrs_2

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_2hrs_serum_stimulation


title: 8hrs_1

description: small RNA sequencing Illumina

source_name: 3T9 FIBROBLAST_8hrs_serum_stimulation


title: 6hrs_1

description: small RNA sequencing Illumina


title: 1hrs_1

description: small RNA sequencing Illumina


title: 2hrs_1

description: small RNA sequencing Illumina


title: 4SU - 6hrs - EXP1

source_name: 3T9 FIBROBLAST_4SU - 6hrs - EXP1


title: 0hrs_1

description: small RNA sequencing Illumina


title: 8hrs_2

description: small RNA sequencing Illumina


title: SET1A_ChIPSeq

first: Jiemin

last: Wong

address: 500 Dongchuan Road

institute: Institute of Biomedical Sciences and School of Life Sciences, East China Normal University

data_processing:
Basecalls performed using Off-Line Basecaller 1.9.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.0.10 with the following setting: shift-size (73), p-value (0.001)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.

source_name: CGR8 ESC

growth_protocol: The stable CGR8 cells were cultured feeder-free in GMEM containing 15% FBS, 2mM L-glutamine, 0.1mM β-mercaptoethanol, LIF and penicillin/streptomycin at 37℃, 5% CO2. The culture surface was pre-coated with 0.2% (w/v) gelatin.

extract_protocol:
Lysates were clarified from sonicated nuclei and SET1A-DNA complexes were isolated with M2 beads (Sigma).
For ChIP-seq libraries, 10 ng of input chromatin DNA or ChIP DNA were processed using the ThrePLEXTM-FD Prep kit (Rubcicon, 40048). Gel-purified ChIP-seq library DNA was further purified by phenol-chloroform extraction and ethanol precipitation, and processed for cluster generation, 15-cycle sequencing, and sequence analysis using Illumina Hiseq performed at the Beijing Genomics Institute (BGI)

treatment_protocol: To maintain the expression of Flag-Set1a, cells were treated with 1μg/ml puromycin in culture medium.

value: stable Flag-Set1a CGR8 cell

value: M2 beads (Sigma:M8823)


title: LLC-R_H3K27me3_ChIPSeq

first: Jiejun

last: Shi

address: No.1239, Siping Road

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were mapped to mm9 assembly of Mus musculus reference genome using Bowtie (v 0.12.7) with up to two mismatches.
The aligned ChIP-seq reads were applied for peak calling using GeneTrack software (Penn State Genome Cartograph program, http://atlas.bx.psu.edu/index.html#).
Genome_build: mm9
Supplementary_files_format_and_content: The coordinates of nucleosomes with histone modifications are listed in bed files.

source_name: drug resistance Lewis lung carcinoma isograft

extract_protocol:
Tissue homogenate were harvested for extraction of nuclei and digested with micrococcal nuclease. Then histone modification antibodies (i.e. H3K4me3,H3K27me3,H3K36me3,H3K9ac) were used to immunoprecipitate the chromatin.
Libraries were prepared for sequencing using standard Illumina HiSeq protocols.

value: LLC-R

tag: phenotype

value: drug resistance

value: lung


title: LLC-NR_H3K27me3_ChIPSeq

source_name: drug sensitive Lewis lung carcinoma isograft

value: LLC-NR

value: drug sensitive


title: LLC-NR_H3K9ac_ChIPSeq

value: H3K9ac (Abcam, #ab10812)


title: LLC-NR_H3K36me3_ChIPSeq


title: LLC-NR_H3K4me3_ChIPSeq

value: H3K4me3 (Abcam, #ab8580)


title: LLC-R_H3K36me3_ChIPSeq


title: 12hrs_1

description: small RNA sequencing Illumina


title: 10hrs_1

description: small RNA sequencing Illumina


title: 4hrs_1

description: small RNA sequencing Illumina


title: Thiobacillus_denitrificans_ATCC25259_native

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

data_processing:
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 2.0.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Modified sites were grouped into motifs using MotifFinder (v1)2.
Genome_build: As indicated by IMG genome ID in the individual samples section (http://img.jgi.doe.gov/home.html)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage.  (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: motif_summary.csv files contain the genome-wide summary of the methyltransferase recognition motifs discovered in this sample.  (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).
Supplementary_files_format_and_content: motifs.gff files are similar to the modifications.gff files. These files contain information about all sites detected as modified, all locations of a discovered motif (including those which are apparently unmodified), and also the overlap between the modifications and motifs. (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).

organism: Thiobacillus denitrificans ATCC 25259

source_name: Bacterial gDNA

extract_protocol:
gDNA was randomly sheared, end repaired, and ligated to blunt end hairpin adapters to form standard SMRTbell templates
SMRT-sequencing

tag: dna treatment

tag: pacbio sequencing chemistry

tag: genome build (img genome id)


title: Thermosipho_melanesiensis_BI429_native

organism: Thermosipho melanesiensis BI429

value: XL / C2


title: Thioalkalivibrio_sp_ARh3_native

organism: Thioalkalivibrio sp. ARh3


title: Thermoplasma_volcanium_GSS1_native

organism: Thermoplasma volcanium GSS1


title: Sulfolobus_acidocaldarius_DSM639_Tet

organism: Sulfolobus acidocaldarius DSM 639

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: Zymomonas_mobilis_pomaceae_Barker_1_ATCC29192_native

organism: Zymomonas mobilis subsp. pomaceae ATCC 29192

value: Barker 1, ATCC 29192


title: Streptococcus_bovis_AG46_native

organism: Streptococcus equinus


title: Streptomyces_sp_WmmB714_native

organism: Streptomyces sp. WMMB 714

value: WMMB 714


title: Selenomonas_ruminantium_AC2024_native

organism: Selenomonas ruminantium AC2024


title: Shewanella_woodyi_MS32_ATCC51908_native

organism: Shewanella woodyi ATCC 51908


title: Streptosporangium_roseum_NI_9100_DSM43021_native

organism: Streptosporangium roseum DSM 43021


title: LLC-R_H3K4me3_ChIPSeq

organism: Mus musculus


title: Selenomonas_ruminantium_AB3002_native

organism: Selenomonas sp. AB3002


title: Sediminibacterium_sp_OR53_native

organism: Asinibacterium sp. OR53


title: Input DNA

tag: cell line


title: Rikenella_microfusus_Q_1_DSM15922_native

organism: Rikenella microfusus DSM 15922


title: Robinsoniella_sp_KNHs210_native

organism: Robinsoniella sp. KNHs210


title: Rhodopseudomona_palustris_CGA009_Tet

organism: Rhodopseudomonas palustris CGA009


title: Rhizobium_etli_CIAT_652_native

organism: Rhizobium etli CIAT 652

value: CIAT 652


title: Peptostreptococcaceae_bacterium_VA2_native

organism: Peptostreptococcaceae bacterium VA2


title: Persephonella_lauensis_IFO5_L8_native

organism: Persephonella


title: Persephonella_lauensis_KM09_Lau8_native


title: Pelobacter_seleniigenes_DSM_18267_native

organism: Pelobacter seleniigenes DSM 18267


title: young-chm 6

data_processing:
Illumina RTA 1.18.64
Alignment was performed using Tophat2 v2.0.5 (Kim et al., 2013) against the reference genome (BDGP5.74) with an average alignment rate of 92%.
Reads were counted at genomic features (i.e. exons) using the summarizeOverlaps function in the GenomicAlignments R/Bioconductor package.
Normalization and differential expression tests were performed using the EdgeR package and significant differences were called with an FDR cutoff 0.05
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Normalized counts (pseudo counts generated by EdgeR) in table format (csv file)

organism: Drosophila melanogaster

source_name: adult head

extract_protocol:
Total RNA was prepared from 25-30 fly heads using 0.5 ml Qiazol (Qiagen) according to manufacturer’s instructions.
2.5 µg of RNA were used for polyA selection and subsequent RNA purification was achieved with RNeasy mini columns (Qiagen). Libraries were prepared using New England Biolabs reagents according to protocols (E7490, E6150, E7525, E6111, E7442, E7335). The ligation was done at 16°C overnight with regular ligase (M0202) and High Fidelity PCR mix (M0541) was used for amplification. Quantifications and quality controls were done with Qubit RNA HS detection kit (Life Technologies) and the RNA 6000 pico kit and DNA 2000 kits (Agilent). 50 bp single reads were obtained on an Illumina Hiseq sequencer.

tag: age

value: young 7 days

tag: genotype

value: chm/+

tag: gender

value: male


title: Neisseria_meningitidis_FAM18_reduced_CG_homopolymers_Tet

organism: Neisseria meningitidis FAM18


title: Neisseria_gonorrhoeae_FA1090_native

organism: Neisseria gonorrhoeae FA 1090


title: Pedobacter_heparinus_HIM_762_3_DSM2366_native

organism: Pedobacter heparinus DSM 2366


title: Microbacterium_sp_KROCY2_native

organism: Microbacterium sp. KROCY2


title: LLC-R_H3K9ac_ChIPSeq

tag: cell type

tag: chip antibody


title: Neisseria_meningitidis_FAM18_native


title: Methanocorpusculum_labreanum_Z_native

organism: Methanocorpusculum labreanum Z

value: Z


title: Methanohalophilus_mahii_SLP_DSM5219_native

organism: Methanohalophilus mahii DSM 5219

value: SLP, DSM 5219


title: Methanocaldococcus_jannaschii_DSM2661_native

organism: Methanocaldococcus jannaschii DSM 2661


title: Methanospirillum_hungatei_JF_1_native

organism: Methanospirillum hungatei JF-1


title: Lachnospiraceae_bacterium_AC2012_native

organism: Lachnospiraceae bacterium AC2012


title: Klebsiella_sp_BRL6_2_native

organism: Klebsiella oxytoca BRL6-2


title: Lachnobacterium_bovis_AE2004_native

organism: Lachnobacterium bovis


title: Methanocorpusculum_labreanum_Z_Tet


title: Lachnospiraceae_bacterium_AC2029_native

organism: Lachnospiraceae bacterium AC2029


title: TCRb+CD8a-NK1.1+_2

city: New York

first: Saida

last: Dadi

address: 1275 York Ave

institute: MSKCC

data_processing:
The raw output BAM files were converted to FASTQ using PICARD Sam2Fastq. Reads were then trimmed using fastq_quality_trimmer with default settings.
The trimmed reads were first mapped to the mouse genome using rnaStar (version 2.3.0e).
The genome assembly mm9 was used with junctions from ENSEMBL (Mus_musculus.NCBIM37.67) and a read overhang of 49.  Then any unmapped reads were mapped to mm9 using BWA MEM (version 0.7.5a).  The two resulting BAM files were merged and gene level counts were computed using htseq-count (options -s y -m intersection-strict) and the same gene models (Mus_musculus.NCBIM37.67).
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file where 1st column contains Ensembl gene ids. Each column after the first one contains the counts for a sample

organism: Mus musculus

source_name: Mammary tumors of 20- to 24-week-old PyMT C57BL/6 mice

extract_protocol:
Cells were isolated from pooled tumors of 20- to 24-week-old PyMT mice. Tumors were prepared by mechanical disruption using a razor blade followed by treatment with 280 U/ml Collagenase Type 3 (Worthington Biochemical) and 4 μg/ml DNase I (Sigma) at 37°C for 1 h with periodic short vortexing. Digested tissues were mashed through 70-μm filters, and collected by centrifugation. Cell pellet was resuspended in 44% Percoll, layered on top of 66% Percoll (Sigma), and centrifuged at 1,900 g for 30 min without brake. Cells at the Percoll interface were collected, stained with antibodies and analyzed by flow cytometry. Cells were sorted using FACS Aria-II machines directly in Tri-Reagent (Sigma).
RNA was prepared and complementary DNA (cDNA) libraries were amplified using the SMARTer RACE Amplification Kit (Clontech)

value: female

value: 20- to 24-week-old

value: mammary tumor

tag: cell population


title: Geopsychrobacter_electrodiphilus_DSM16401_native

organism: Geopsychrobacter electrodiphilus DSM 16401


title: Geovibrio_thiophilus_L21_Ace_BES_native

organism: Limisalsivibrio acetivorans


title: Phaeobacter_gallaeciensis_DSM_17395_native

organism: Phaeobacter inhibens DSM 17395


title: Frankia_sp_DC12_native

organism: Pseudofrankia sp. DC12


title: Rhodopseudomona_palustris_CGA009_native

organism: Rhodopseudomonas palustris CGA009


title: Flexistipes_sinusarabici_MAS10_DSM4947_native

organism: Flexistipes sinusarabici DSM 4947


title: Dyadobacter_fermentans_NS114_DSM18053_native

organism: Dyadobacter fermentans DSM 18053


title: Clostridium_sp_KNHs205_native

organism: Clostridium sp. KNHs205


title: Enterobacter_aerogenes_FGI35_native

organism: Klebsiella aerogenes FGI35


title: Dinoroseobacter_shibae_DFL_12_DSM16493_native

organism: Dinoroseobacter shibae DFL 12 = DSM 16493


title: Echinicola_vietnamensis_KMM_6221_DSM17526_native

organism: Echinicola vietnamensis DSM 17526


title: Mycoplasma_bovis_PG45_native

organism: Mycoplasmopsis bovis PG45

value: Donetta PG45


title: glp-1-Adults-DpnII

description:
Raw data files for this sample were generated from Illumina NextSeq 500 and Illumina MiSeq instruments.
Young adult animals grown in restrictive temperature, germline depleted

organism: Caenorhabditis elegans

value: whole organism

tag: developmental stage

value: adult


title: Clostridium_sp_isolate_12A_native

organism: Clostridium sp. 12(A)


title: glp-1-Adults-AvaII


title: N2-Adults-AvaII

description:
Raw data files for this sample were generated from Illumina NextSeq 500 and Illumina MiSeq instruments.
Young adult animals grown in non restrictive conditions

value: wild-type


title: N2-Adults-DpnII


title: Clostridium_phytofermentans_KNHs2132_native


title: Clostridium_sp_ASBs410_6661_native

organism: Clostridium sp. ASBs410

value: XL / C2


title: Cellulomonas_sp_KRMCY2_native

organism: Cellulomonas sp. KRMCY2


title: Caldithrix_abyssi_LF13_DSM13497_native

organism: Caldithrix abyssi DSM 13497


title: Capnocytophaga_ochracea_DSM7271_native

organism: Capnocytophaga ochracea DSM 7271


title: Butyrivibrio_sp_FCS014_native

organism: Butyrivibrio sp. FCS014


title: Verrucomicrobia_bacterium_LP2A_native

organism: Verrucomicrobia bacterium LP2A


title: Alteromonadaceae_bacterium_Bs12_native

organism: Teredinibacter purpureus


title: Thiomonas_sp_FB_6_DSM25805_native

organism: Thiomonas sp. FB-6


title: Alicyclobacillus_macrosporangiidus_CPP55_native


title: Caldicoprobacter_oshimai_DSM21659_native

organism: Caldicoprobacter oshimai DSM 21659


title: Altermomonas_sp_Alt_199_native

organism: Alteromonas sp. ALT199


title: Aminiphilus_circumscriptus_DSM16581_native

organism: Aminiphilus circumscriptus DSM 16581


title: Treponema_succinifaciens_DSM2489_native

organism: Treponema succinifaciens DSM 2489


title: Veillonella_parvula_Te3_DSM2008_native

organism: Veillonella parvula DSM 2008


title: Treponema_denticola_ATCC35405_native

organism: Treponema denticola ATCC 35405


title: Thiomicrospira_pelophila_1534_native

organism: Thiomicrospira pelophila DSM 1534


title: Xenorhabdus_nematophila_ATCC19061_native

organism: Xenorhabdus nematophila ATCC 19061


title: Thiomicrospira_crunogena_XCL_2_native

organism: Hydrogenovibrio crunogenus XCL-2


title: Thermacetogenium_phaeum_DSM12270_native

organism: Thermacetogenium phaeum DSM 12270


title: Tolumonas_sp_BRL6_1_native

organism: Tolumonas lignilytica


title: Thermanaerovibrio_acidaminovorans_DSM6589_native

organism: Thermanaerovibrio acidaminovorans DSM 6589


title: Thermoplasma_acidophilum_DSM1728_native

organism: Thermoplasma acidophilum DSM 1728


title: Syntrophobotulus_glycolicus_FlGlyR_DSM8271_native

organism: Syntrophobotulus glycolicus DSM 8271

value: FlGlyR, DSM 8271


title: Teredinibacter_sp_strain_991HS0a06_native

organism: Teredinibacter turnerae


title: Spirochaeta_thermophila_Z_1203_DSM6578_native

organism: Winmispira thermophila DSM 6578


title: Streptobacillus_moniliformis_9901_DSM12112_native

organism: Streptobacillus moniliformis DSM 12112


title: Teredinibacter_sp_strain_1162TS0a05_native


title: Sporocytophaga_myxococcoides_DSM11118_native

organism: Sporocytophaga myxococcoides DSM 11118


title: Spirochaeta_smaragdinae_SEBR_4228_DSM11293_native

organism: Sediminispirochaeta smaragdinae DSM 11293


title: Sphingomonas_melonis_C3_native

organism: Sphingomonas melonis C3


title: Sulfurimonas_denitrificans_DSM1251_native

organism: Sulfurimonas denitrificans DSM 1251


title: Spirochaeta_caldaria_H1_DSM7334_native

organism: Gracilinema caldarium DSM 7334


title: Staphylococcus_epidermidis_AG42_native

organism: Staphylococcus epidermidis AG42


title: Spirochaeta_africana_Z_7692_DSM8902_native

organism: Spirochaeta africana DSM 8902


title: Salmonella_enterica_arizonae_sv_62_z4z23_RSK2980_native

organism: Salmonella enterica subsp. arizonae serovar 62:z4,z23:-


title: Butyrivibrio_sp_AE3004_native

organism: Butyrivibrio sp. AE3004


title: Ruminococcus_sp_HUN007_native

organism: Ruminococcus sp. HUN007


title: Salmonella_bongori_NCTC_12419_native

organism: Salmonella bongori NCTC 12419


title: Sebaldella_termitidis_ATCC33386_native

organism: Sebaldella termitidis ATCC 33386


title: Ruminococcus_flavefaciens_AE3010_native

organism: Ruminococcus flavefaciens AE3010


title: Salmonella_enterica_enterica_sv_Paratyphi_A_ATCC9150_native

organism: Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150

value: ATCC 9150


title: Solitalea_canadensis_USAM_9D_DSM3403_native

organism: Solitalea canadensis DSM 3403

value: USAM 9D, DSM 3403


title: Saccharomonospora_viridis_P101_DSM43017_native

organism: Saccharomonospora viridis DSM 43017


title: 22B p53KD mammary tumor

city: Houston

first: Emily

last: Powell

state: TX

address: 1901 East Road

institute: MD Anderson

description: patient derived xenograft tumor

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the Genome Technology Access Center (Washington University, St. Louis, MO). The RNA-Seq reads were first mapped to the mouse (NCBI Build 37.2) (GRCm37UCSC mm9) reference genome using Tophat2, allowing a maximum of two mismatches per 75 bp read end. The unmapped reads were then aligned to the human genome (NCBI Build 37.2) (GRCh37/UCSC hg19) using the same tool and parameters. Partek Genomics Suite v6.6 and its genomic feature database (RefSeq Transcripts - 2014-01-03) were used to quantify the gene-level read counts.
Genome_build: GRCh37/UCSC hg19
Supplementary_files_format_and_content: Gene-Level Read Count files

organism: Homo sapiens

source_name: breast tumor

growth_protocol: human tumor cells grown in mouse

extract_protocol:
RNA was extracted using trizol and chloroform, then purified using RNEASY columns
poly A capture

treatment_protocol: tumors were grown to 0.5 cm

tag: genotype/variation

value: knock down

value: triple negative breast cancer


title: Thermobacillus_composti_KWC4_DSM18247_native

organism: Thermobacillus composti KWC4


title: Ruminococcus_sp_NK3A76_native

organism: Ruminococcus sp. NK3A76


title: Pyrococcus_horikoshii_OT3_native

organism: Pyrococcus horikoshii OT3


title: Ruminococcaceae_bacterium_AE2021_native

organism: Ruminococcaceae bacterium AE2021


title: 22A p53KD mammary tumor

description: patient derived xenograft tumor


title: Polaromonas_sp_EUR3_1_2_1_native

organism: Polaromonas sp. EUR3 1.2.1


title: 4E p53WT mammary tumor

description: patient derived xenograft tumor

value: wild type


title: Planctomyces_limnophilus_Mu_290_DSM3776_native

organism: Planctopirus limnophila DSM 3776


title: 5A p53KD mammary tumor

description: patient derived xenograft tumor


title: Pseudobutyrivibrio_ruminis_HUN009_native

organism: Pseudobutyrivibrio ruminis HUN009


title: Oxalobacteraceae_bacterium_AB_14_native

organism: Oxalobacteraceae bacterium AB_14


title: Butyrivibrio_sp_AE3003_native

organism: Butyrivibrio sp. AE3003


title: Prevotella_sp_isolate_10H_native

organism: Prevotella sp. 10(H)


title: 4B p53WT mammary tumor

description: patient derived xenograft tumor


title: 4D p53WT mammary tumor

description: patient derived xenograft tumor


title: Pontibacter_actiniarum_KMM_6156_DSM19842_native

organism: Pontibacter actiniarum DSM 19842


title: Orenia_marismortui_DSM5156_native

organism: Orenia marismortui DSM 5156


title: Pseudomonas_stutzeri_RCH2_native

organism: Stutzerimonas stutzeri RCH2


title: Nocardia_sp_BMG51109_native

organism: Nocardia sp. BMG51109


title: TS1471L_RNA-seq_MDBK_BVDVncp-p3,4 + miR-17p3,4

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description:
Table S6.txt
F.BVDVncp-m17p3,4_miR-17p3,4_2

data_processing:
AGO-CLIP data was processed as described (Moore et al. 2014 Nature Protocols). The deposited CLIP sequences are composed of (i) the index (3 OR 4 nts, see individual samples), (ii) the RL5 sequence (AGGGAGGACGAUGCGG), (iii) a 5N degenerate linker, (iv) the actual read sequence and, depending on read length (iv) a complete or partial RL3 sequence (GTGTCAGTCACTTCCAGCGGATCTCGTATGCCGTCTTCTGCTTG).
Processed reads were aligned to human (hg18) or bovine (BosTau7) host genomes as well as to viral genomes corresponding to the infecting agent using Bowtie or Novoalign (Novocraft). After all mapping, reads were collapsed on coordinates such that only those with sufficiently different degenerate linkers were kept; this distinguished unique binding events from PCR duplicates. For AGO-CLIP data, clustering of AGO-bound regions, annotation and calculations of log2 fold changes was done essentially as described (Luna et al. 2015 Cell). For annotation on cow, BosTau7 GTF annotation were downloaded from the USCS genome table browser and intersected with CLIP-derived clusters. CLIP data was based on 4 replicates per condition.
Quality filtered RNA-seq data were mapped to the cow (bosTau7) genome using Bowtie or Tophat2. The number of reads overlapping each gene (USCS Table Browser and Ensembl annotation) was counted with htseq-count. Expression data was processed essentially as described (Luna et al. 2015 Cell) using the edgeR and limma packages in R with general linear models. For MDBK cells, RNA-seq derived gene expression data was merged on gene name with AGO-CLIP data to allow CLIP-guided representation of changes to gene expression.
Changes to miRNA expression in quadruplicate libraries were calculated using edgeR for miRNAs represented in >=4 libraries, and adjusted p-values (FDRs) were presented.
Genome_build: hg18 or BosTau7
Supplementary_files_format_and_content: Table S1: Virus-aligned AGO-CLIP reads. A concatemerized list of all AGO-CLIP reads aligning to viral positive-strand RNA is given as a BED file. Two additional columns give experiment ID and notes for time course and cell type experiments.
Supplementary_files_format_and_content: Table S3: Abundance of AGO-loaded miRNAs in MDBK cells. The abundance of AGO-loaded miRNAs in MDBK cells is given by seed family. In addition, fraction of total for individual miRNAs is given for four replicates each of MDBK (mock) and MDBK (BVDV infected).
Supplementary_files_format_and_content: Table S4: Summarized AGO-CLIP analysis and related mRNA expression for BVDV and mock infected MDBK cells. The table summarizes AGO-CLIP clusters from analysis of BVDVcp vs. mock infected MDBK cells (four replicates each). For clusters in genic regions with a minimum total biologic complexity (BC) of 4, the peak height (PH) and BC for mock, BVDVcp and total are given. The normalized CLIP PH was calculated by addition of a pseudocount of 1 per condition and dividing by the total library size. The log2 fold change in AGO-CLIP binding was calculated directly from the normalized PH. Gene expression values corresponding to CLIP-defined clusters were calculated from mRNA-seq data in edgeR and logCPM (counts per million), log2 fold change and adjusted p-values (FDR) are given. Additional data include the genic region (CDS, UTR, intron) covering the largest fraction of each cluster, the cluster sequence, and the presence or absence of seed sites (6mer, 7merA1, 7merM8, 8mer) of the 50 most abundant miRNAs in MDBK cells.
Supplementary_files_format_and_content: Table S5: Summarized AGO-CLIP analysis for tinyLNA-17 and mock treated MDBK cells. The table summarizes AGO-CLIP clusters from analysis of tinyLNA-17 vs. mock treated MDBK cells (four replicates each). For clusters in genic regions with a minimum total biologic complexity (BC) of 4, the peak height (PH) and BC for mock, tinyLNA-17 and total are given. The normalized CLIP PH was calculated by addition of a pseudocount of 1 per condition and dividing by the total library size. The log2 fold change in AGO-CLIP binding was calculated directly from the normalized PH. Additional data include the cluster fraction mapping to each genic region (CDS, UTR, intron), the cluster sequence, and the presence or absence of seed sites (6mer, 7merA1, 7merM8, 8mer) of the 50 most abundant miRNAs in MDBK cells.
Supplementary_files_format_and_content: Table S6: Summarized mRNA expression analysis for BVDV and mock infected MDBK cells. The table summarizes RNA expression levels measured by mRNA-seq for mock, BVDVcp or BVDVncp infected MDBK cells, and for miR-17p3,4 transfected MDBK cells infected or not with BVDVcp-m17p3,4 or BVDVncp-m17p3,4. Gene expression values were calculated using general linear models in edgeR and logCPM (counts per million), log2 fold change and adjusted p-values (FDR) are given for pairwise comparisons.

organism: Bos taurus

source_name: MDBK

extract_protocol:
Total RNA was isolated via Trizol extraction and DNAse treated.
RNA libraries were prepared for sequencing using standard Illumina protocols with polyA selection.

tag: sample subseries

value: RNA-seq:BVDV vs. Mock

tag: virus

tag: small rna

tag: time point

tag: index

value: GATCAG


title: Nocardia_sp_BMG111209_native

organism: Nocardia sp. BMG111209

tag: strain

tag: dna treatment


title: TS1471K_RNA-seq_MDBK_BVDVncp-p3,4 + miR-17p3,4

description:
Table S6.txt
F.BVDVncp-m17p3,4_miR-17p3,4_1

value: TGACCA


title: 21C p53WT mammary tumor

description: patient derived xenograft tumor

organism: Homo sapiens

tag: tissue


title: Palaeococcus_ferrophilus_DMJ_DSM13482_native

organism: Palaeococcus ferrophilus DSM 13482

tag: pacbio sequencing chemistry

tag: genome build (img genome id)


title: TS1471J_RNA-seq_MDBK_BVDVcp-p3,4 + miR-17p3,4

description:
Table S6.txt
E.BVDVcp-m17p3,4_miR-17p3,4_2

value: TTAGGC


title: Methylophilaceae_bacterium_11_native

organism: Methylophilaceae bacterium 11


title: Nitratifractor_salsuginis_E9I37_1_DSM16511_native

organism: Nitratifractor salsuginis DSM 16511


title: Methylophilus_sp_1_native

organism: Methylophilus sp. 1


title: Oceanicola_sp_HL_35_native

organism: Oceanicola sp. HL-35


title: Methylotenera_sp_73s_native

organism: Methylotenera sp. 73s


title: Prevotella_sp_HUN102_native

organism: Prevotella sp. HUN102


title: Methylophilus_sp_42_native

organism: Methylophilus sp. 42


title: Methylobacterium_extorquens_AM1_native

organism: Methylorubrum extorquens AM1


title: Methylohalobius_crimeensis_strain_10Ki_native

organism: Methylohalobius crimeensis 10Ki


title: Methylocystis_sp_LW5_native

organism: Methylocystis sp. LW5


title: Methanothermus_fervidus_V24S_DSM2088_native

organism: Methanothermus fervidus DSM 2088


title: Patulibacter_minatonensis_KV_614_DSM18081_native

organism: Patulibacter minatonensis DSM 18081


title: Methylobacterium_sp_EUR3_AL_11_native

organism: Methylobacterium sp. EUR3 AL-11

value: EUR3 AL-11


title: TS1471E_RNA-seq_MDBK_BVDVncp

description:
Table S6.txt
C.BVDVncp1

organism: Bos taurus

value: BVDVncp

value: Mock

value: CTTGTA


title: Meiothermus_silvanus_VI_R2_DSM9946_native

organism: Allomeiothermus silvanus DSM 9946


title: Meiothermus_chliarophilus_ALT_8_DSM9957_native

organism: Calidithermus chliarophilus DSM 9957


title: Marinithermus_hydrothermalis_T1_DSM14884_native

organism: Marinithermus hydrothermalis DSM 14884


title: TS1471D_RNA-seq_MDBK_BVDVcp

description:
Table S6.txt
B.BVDVcp2

value: BVDVcp

value: ACTTGA


title: Maribacter_sp_Hel_I_7_native

organism: Maribacter sp. Hel_I_7


title: TS1471I_RNA-seq_MDBK_BVDVcp-p3,4 + miR-17p3,4

description:
Table S6.txt
E.BVDVcp-m17p3,4_miR-17p3,4_1

value: CGATGT


title: Lactococcus_lactis_subsp_lactis_511_native

organism: Lactococcus lactis subsp. lactis

value: XL / C2


title: TS1471C_RNA-seq_MDBK_BVDVcp

description:
Table S6.txt
B.BVDVcp1

value: GCCAAT


title: Leptolyngbya_sp_PCC_6406_native

organism: Leptolyngbya sp. PCC 6406


title: TS1471B_RNA-seq_MDBK_Mock

description:
Table S6.txt
A.Mock2

value: ATCACG


title: Lactobacillus_brevis_AG48_native

organism: Levilactobacillus brevis AG48


title: TS1471A_RNA-seq_MDBK_Mock

description:
Table S6.txt
A.Mock1

value: ACAGTG


title: Joostella_marina_En5_DSM19592_native

organism: Galbibacter orientalis


title: Holophaga_foetida_TMBS4_DSM6591_native

organism: Holophaga foetida DSM 6591

value: TMBS4, DSM 6591


title: Hongiella_marincola_HL_49_native

organism: Algoriphagus marincola HL-49


title: TS1524H_CLIP-seq_MDBK_tinyLNA-17

description: Table S5.txt

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseA digested, clarified by centrifugation, and Argonaute-RNA complexes isolated with pan-Ago 2A8 antibody.
Libraries were prepared as in Moore et al. 2014 Nature Protocols, but with the following modifications: The 2nd PCR step was used to introduce library specific indices that were additionally compatible with MiSeq sequencers using version2 chemistry.

value: AGO-CLIP:tinyLNA-17 vs. Mock

value: TGCA


title: Hirschia_baltica_ATCC49814_native

organism: Hirschia baltica ATCC 49814


title: TS1471F_RNA-seq_MDBK_BVDVncp

description:
Table S6.txt
C.BVDVncp2

value: RNA-seq:BVDV vs. Mock

value: TAGCTT


title: Leisingera_nanhaiensis_NH52F_DSM24252_native

organism: Sedimentitalea nanhaiensis DSM 24252


title: TS1524G_CLIP-seq_MDBK_tinyLNA-17

description: Table S5.txt

value: CATG


title: TS1471G_RNA-seq_MDBK_Mock + miR-17p3,4

description:
Table S6.txt
D.Mock_miR-17p3,4_1

value: GTGAAA


title: Hippea_medeae_KM1_native

organism: Hippea sp. KM1


title: TS1471H_RNA-seq_MDBK_Mock + miR-17p3,4

description:
Table S6.txt
D.Mock_miR-17p3,4_2

value: GGCTAC


title: Gillisia_sp_JM1_native

organism: Gillisia sp. JM1


title: Hippea_alviniae_EP5_r_DSM24586_native

organism: Hippea alviniae EP5-r


title: TS1524F_CLIP-seq_MDBK_tinyLNA-17

description: Table S5.txt

value: Mock

value: ACCG


title: Flavobacterium_psychrophilum_JIP02_86_native

organism: Flavobacterium psychrophilum JIP02/86


title: Haloterrigena_turkmenica_VKM_B_1734_DSM5511_native

organism: Haloterrigena turkmenica DSM 5511


title: TS1524E_CLIP-seq_MDBK_tinyLNA-17

description: Table S5.txt

organism: Bos taurus

value: GTGC


title: Exiguobacterium_sp_GIC31_native

organism: Exiguobacterium chiriqhucha


title: Exiguobacterium_aurantiacum_DSM_6208_native

organism: Exiguobacterium aurantiacum DSM 6208


title: TS1524D_CLIP-seq_MDBK_Mock

description: Table S5.txt

value: GCAT


title: Exiguobacterium_antarcticum_DSM_14480_native

organism: Exiguobacterium antarcticum DSM 14480


title: Escherichia_coli_K12_MG1655_Tet

organism: Escherichia coli str. K-12 substr. MG1655

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: TS1524C_CLIP-seq_MDBK_Mock

description: Table S5.txt

value: CGTA


title: Escherichia_coli_K12_MG1655_native


title: TS1524B_CLIP-seq_MDBK_Mock

description: Table S5.txt

value: GATC


title: Enterococcus_faecalis_68A_native

organism: Enterococcus faecalis 68A

value: XL / C2


title: TS1524A_CLIP-seq_MDBK_Mock

description: Table S5.txt

value: CTAG


title: Exiguobacterium_acetylicum_DSM_20416_native

organism: Exiguobacterium acetylicum DSM 20416


title: Desulfurobacterium_lauensis_TC5_1_native

organism: Desulfurobacterium sp. TC5-1


title: TS1524T_CLIP-seq_MDBK_BVCVpol(-), 24hr

description: Table S1.txt

value: Virus AGO-CLIP

value: BVCVpol(-), 24hr


title: Desulforegula_conservatri_Mb1Pa_DSM13527_native

organism: Desulforegula conservatrix Mb1Pa


title: TS1524S_CLIP-seq_MDBK_BVCVpol(-), 24hr

description: Table S1.txt


title: Desulfobacca_acetoxidans_DSM11109_native

organism: Desulfobacca acetoxidans DSM 11109

value: ASRB2, DSM 11109


title: Cronobacter_sp_FGI57_native

organism: Cronobacter

value: FGI 57


title: Coraliomargarita_akajimensis_DSM45221_native

organism: Coraliomargarita akajimensis DSM 45221


title: TS1524R_CLIP-seq_MDBK_BVCVcp, 24hr

description: Table S1.txt

value: BVCVcp, 24hr


title: Desulfovibrio_alkalitolerans_L21_Syr_AB_native

organism: Desulfohalovibrio reitneri


title: Clostridium_josui_JCM17888_native

organism: Ruminiclostridium josui JCM 17888


title: TS1524Q_CLIP-seq_MDBK_BVCVcp, 24hr

description: Table S1.txt


title: TS1524P_CLIP-seq_MDBK_BVCVpol(-), 12hr

description: Table S1.txt

value: BVCVpol(-), 12hr

value: GAGG


title: Clostridium_indolis_DSM755_native

organism: Lacrimispora indolis DSM 755

value: DSM 755


title: Clostridium_mangenotii_LM2_native

organism: Clostridioides mangenotii LM2


title: Clostridium_perfringens_ATCC13124_native

organism: Clostridium perfringens ATCC 13124


title: TS1524O_CLIP-seq_MDBK_BVCVpol(-), 12hr

description: Table S1.txt

organism: Bos taurus

value: Mock

value: GGCT


title: TS1524N_CLIP-seq_MDBK_BVCVcp, 12hr

description: Table S1.txt

value: BVCVcp, 12hr

value: CTCC


title: Clostridium_algidicarnis_B3_native

organism: Clostridium algidicarnis


title: Eubacterium_sp_AB3007_native

organism: Eubacterium sp. AB3007


title: TS1524M_CLIP-seq_MDBK_BVCVcp, 12hr

description: Table S1.txt

value: CCGA


title: Clostridium_difficile_630_native

organism: Clostridioides difficile 630

value: 630 (epidemic type X)


title: Cellulophaga_lytica_LIM_21_DSM7489_native

organism: Cellulophaga lytica DSM 7489


title: Desulfospira_joergensenii_DSM10085_native

organism: Desulfospira joergensenii DSM 10085


title: Clostridium_difficile_630_Tet

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: Clostridium_clariflavum_10114_native

organism: Acetivibrio clariflavus 4-2a


title: Arthrobacter_chlorophenolicus_A6_native

organism: Pseudarthrobacter chlorophenolicus A6


title: TS1524L_CLIP-seq_MDBK_BVCVpol(-), 6hr

description: Table S1.txt

value: BVCVpol(-), 6hr

value: ATGC


title: Bacteroides_sp_isolate_14A_native

organism: Bacteroides sp. 14(A)

value: XL / C2


title: TS1524K_CLIP-seq_MDBK_BVCVpol(-), 6hr

description: Table S1.txt

value: Virus AGO-CLIP

value: TACG


title: Bacteroides_salanitronis_DSM18170_native

organism: Phocaeicola salanitronis DSM 18170


title: Aminobacterium_colombiense_DSM12261_native

organism: Aminobacterium colombiense DSM 12261


title: TS1524J_CLIP-seq_MDBK_BVCVcp, 6hr

description: Table S1.txt

value: BVCVcp, 6hr

value: AGTG


title: TS1524I_CLIP-seq_MDBK_BVCVcp, 6hr

description: Table S1.txt

value: TCAC


title: Clostridium_thermocellum_LQ8_DSM1313_native

organism: Acetivibrio thermocellus DSM 1313


title: Akkermansia_muciniphila_ATCCBAA_835_native

organism: Akkermansia muciniphila ATCC BAA-835

value: ATCC BAA-835


title: Actinosynnema_mirum_DSM43827_native

organism: Actinosynnema mirum DSM 43827


title: Bacterium_JKG1_native

organism: Kallotenue papyrolyticum


title: Bacillus_subtilis_strW23_native

organism: Bacillus spizizenii str. W23


title: TS1383H_CLIP-seq_MDBK_BVDVcp

description:
Table S1.txt
Table S3.xls
BVDV4
Table S4.txt

value: Virus AGO-CLIP:BVDV vs. Mock

value: BVDVcp


title: TS1383F_CLIP-seq_MDBK_BVDVcp

description:
Table S1.txt
Table S3.xls
BVDV2
Table S4.txt

value: Mock

value: TGCA


title: Acidovorax_sp_JHL_3_native

organism: Acidovorax sp. JHL-3


title: Acidobacterium_sp_PMMR2_native

organism: Pseudacidobacterium ailaaui


title: Acidobacteriaceae_sp_KBS_146_native

organism: Acidobacteriaceae bacterium KBS 146

value: KBS 146


title: Bradyrhizobium_elkanii_USDA_76_native

organism: Bradyrhizobium elkanii USDA 76

value: USDA 76


title: TS1383E_CLIP-seq_MDBK_BVDVcp

description:
Table S1.txt
Table S3.xls
BVDV1
Table S4.txt

organism: Bos taurus

value: CATG


title: TS1383D_CLIP-seq_MDBK_Mock

description:
Table S3.xls
Mock4
Table S4.txt

value: ACCG


title: Acetobacterium_woodii_DSM1030_native

organism: Acetobacterium woodii DSM 1030


title: TS1383C_CLIP-seq_MDBK_Mock

description:
Table S3.xls
Mock3
Table S4.txt

value: GTGC


title: WT_8

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC).After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences (TAIR 10 version) with SOAPaligner/SOAP2(parameters: -m 0 -x 10000 -s 40 -l 32 -v 5 -r 2 -p 6) (Li et al., 2009).
The transcript abundance were estimated by RPKM (Reads per kilobase transcript per million reads) calculation for each gene in each compartment (Mortazavi et al., 2008). RPKM = 109*C/N*L (C is the number of mappable reads that fell onto the genes; N is the total number of mappable reads in the experiment; L is the sum of the genes in base pairs).
Genome_build: TAIR 10 version
Supplementary_files_format_and_content: RPKM

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis thaliana ecotypes Columbia (Col-0) (wild type: WT) was used in this study. After sterilization, the seeds were placed on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22°C) / 8 hours dark (18°C) period in growth chamber at a light intensity of 120–150 µmol m-2 s-1. 20-day-old Arabidopsis leaves without bolting were immediately frozen in liquid nitrogen for RNA and protein and metabolites extraction. Leaves were harvested at three different time points: t = 0 hr (end of night), t = 1 hr (one hour after light turn on) and t = 8 hr (eight hours after light turn on), respectively.

extract_protocol:
Total RNA was extracted from leaves at all three time points and DNA contamination was removed by DNase I (RNeasy Plant Mini Kit, Qiagen, Hong Kong).
Ribosomal RNAs were removed from the total RNA by the Ribo-Zero rRNA removal kit for plant leaf (Epicentre, USA) before cDNA library construction. The libraries were sequenced using Illumina HiSeqTM2000. After removal of low quality reads, clean reads from three different RNA-seq samples (WT 3 times points, t = 0, 1, 8) were aligned to Arabidopsis genome.

tag: ecotype

tag: age

value: Wild type

tag: time point (hr)


title: WT_0


title: TS1330J_CLIP-seq_MDBK_BVDVncp

description: Table S1.txt

value: BVDVncp

value: CTCC


title: TS1383A_CLIP-seq_MDBK_Mock

description:
Table S3.xls
Mock1
Table S4.txt

value: CGTA


title: Acidobacteriaceae_sp_DSM24188_native

organism: Acidobacteriaceae bacterium TAA 166

value: TAA 166

value: XL / C2


title: Sample E

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end sequencing reads were mapped to rn5 whole genome using Tophat2 (v2.0.13). Except for "--read-edit-dist 5" and "-N 5", all parameters were used as default.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks (v1.3.0). Option "-u" was used for multi-reads correction.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of all coding genes in each sample

organism: Rattus norvegicus

source_name: normal liver

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen). Reverse transcription was performed on 500ng of total RNA in 10uL reaction system for each sample using PrimeScript RT Master Mix Perfect Real Time Kit (TAKARA, Code: DRR036A).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver


title: Bacillus_subtilis_strW23_Tet

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: TS1330H_CLIP-seq_MDBK_BVDVncp

description: Table S1.txt

value: Virus AGO-CLIP

value: ATGC


title: Sample N

source_name: AFB1 resistant liver


title: L1-Fed-DpnII

description:
Raw data files for this sample were generated from Illumina MiSeq and Illumina HiSeq 2000 instruments.
animals fed for 3 hours after 24 hours of starving post bleaching

organism: Caenorhabditis elegans

value: whole organism

tag: genotype

value: wild-type


title: TS1383G_CLIP-seq_MDBK_BVDVcp

description:
Table S1.txt
Table S3.xls
BVDV3
Table S4.txt

value: Virus AGO-CLIP:BVDV vs. Mock

value: BVDVcp

value: Mock

value: TCAC


title: L1-Fed-AvaII


title: TS1383B_CLIP-seq_MDBK_Mock

description:
Table S3.xls
Mock2
Table S4.txt

value: GCAT


title: Sample T

source_name: AFB1 induced HCC


title: L1-Starved-DpnII


title: Xylella_fastidiosa_Temecula1_native

organism: Xylella fastidiosa Temecula1


title: TS1330I_CLIP-seq_MDBK_BVDVncp

description: Table S1.txt

value: CCGA


title: Xanthobacter_sp91_native

organism: Xanthobacter sp. 91


title: TS1300H_CLIP-seq_A549_RSV-GFP

description: Table S1.txt

organism: Homo sapiens

value: RSV-GFP


title: TS1383I_CLIP-seq_A549_Flu A/WSV/33

description: Table S1.txt

value: Flu A/WSV/33

value: TACG


title: TS1300G_CLIP-seq_A549_hMPV-GFP

description: Table S1.txt

value: hMPV-GFP


title: Thiomicrospira_sp_MA2_6_native

organism: Hydrogenovibrio sp. MA2-6


title: TS1300I_CLIP-seq_A549_VSV-GFP

description: Table S1.txt

value: VSV-GFP

value: CTCC


title: WT_1

value: Wild type


title: Thermogemmatispora_sp_PM5_native

organism: Thermogemmatispora carboxidivorans


title: TS1383J_CLIP-seq_Huh-7.S10.3 _HEV

description: Table S1.txt

value: Virus AGO-CLIP

value: HEV


title: TS1300L_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

value: HAV

value: AACC


title: TS1300K_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

value: GAGG


title: Sulfurospirillum_barnesii_SES_3_native

organism: Sulfurospirillum barnesii SES-3

value: XL / C2


title: Syntrophothermus_lipocalidus_DSM12680_native

organism: Syntrophothermus lipocalidus DSM 12680


title: TS1180N_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

value: Mock

value: CTT


title: TS1300J_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

value: GGCT


title: Staphylothermus_marinus_F1_DSM3639_native

organism: Staphylothermus marinus F1


title: wt M D T0 R2

city: State College

first: Michael

middle: J

last: Axtell

state: PA

address: University Park

department: Department of Biology

institute: Penn State University

data_processing:
3' and 5' adapters were removed with cutadapt ("-m 15 --discard-untrimmed" Martin, 2011).
Low complexity sequences, containing only two different nucleobases, were removed through a customized Perl script.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to verify that in each library the Q score of the 90th percentile of reads was >= 28 across all bases.
The abundance of the unique sequences was obtained with a customized Perl script.
Genome_build: RefGen ZmB73 Assembly AGPv3
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: the first column is the sequence of the unique, non-redundant sRNA read, and the second column is its total raw abundance.

organism: Zea mays

source_name: shoot apical meristematic area

extract_protocol:
Leaf and shoot apical meristematic area samples of four-five plants for each combination of genotype-treatment-sampling time point were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), using "Protocol A" with 750µL of Binding Solution, to recover more of the small-sized RNA, and subjected to On-Column DNase Digestion (SIGMA).
The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina Hiseq2000 platform by the Istituto di Genomica Applicata (Udine, Italy).

value: shoot apical meristematic area

tag: background strain

value: wt

tag: treatment

value: drought

tag: sampling time point

value: V5/V6 plants after 10 days of treatment

tag: biological replicate


title: Staphylococcus_aureus_USA300_TCH1516_native

organism: Staphylococcus aureus subsp. aureus USA300_TCH1516


title: TS1180M_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

tag: sample subseries

tag: virus

value: AAG


title: wt M D T0 R1