title: BSseq-suvh92.qseq.gz

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description: genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
ChIP-seq -- Reads were filtered for full-length (50bp) reads.  Reads containing adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Samples 1..3, 4..5, 6..7, 8..9 are each technical sequencing replicates for each respective genotype to increase coverage. Sample 1..3 and 14, 8..9 and 15, are biological replicates, as are samples 10 and 19, 13 and 20.
Supplementary_files_format_and_content: ChIP-seq: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)
RNA-seq (size fractionation) - Reads were demultiplexed (perfect matches to each index were required).  Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained.  Reads with no identifiable adapter were discarded.  Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch. Both unique and non-uniquely mapping reads were retained for normalization purposes but only uniquely mapping reads were used for downstream analysis. For downstream analyses up to 100 identical mapping reads were allowed to be counted at any given region, locations with more than 100 siblings were flattened to 100 mapping reads.
Supplementary_files_format_and_content: RNA-seq (size fractionation): Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome for 24nt class of small RNAs with each bin given a value corresponding to the relative 24 nt read density at that location (24nt reads in 25bp bins / total mapping small RNA reads of all size classes - unique and non-uniquely mapping)
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. The suvh2 and suvh9 single mutant libraries used in this study were previously published (GSE39901), as were the 4 other Col replicates used (GSE39901 - WT replicate 2 ; GSE38286 ; GSE36129 ; GSE49090).
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

organism: Arabidopsis thaliana

source_name: 3 week leaf tissue

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013
Samples 1..8 / 9..12 / 13..18 / were extracted by ChIP followed by phenol-chloroform exctract as describen / Trizol extraction followed by PEG and then urea-PAGE fractionation / phenol-chloroform extraction followed by bisulfite treatment
Samples 1..8 / 9..12 / 13..18 /  NuGen Ovation Ultralow DR sample prep kit / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013 /

tag: genotype

value: suvh2 suvh9

tag: ecotype

value: Columbia


title: T. circumcincta Suffolk Day 7 ALNL21

status: Public on Jan 01 2014

type: SRA

city: Dublin

first: Albin

middle: Mostaque

last: Ahmed

address: Veterinary Science Centre, UCD, Belfield

department: Veterinary Medicines

country: Ireland

institute: University College Dublin

description: Sample 21 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag ACAGTG

library_source: transcriptomic

data_processing:
Alignment with Bos Taurus genome (UMD 3.1) using Bowtie
conversion from BAM to SAM, sorting, removal of PCR duplicates using SAMTools
SAM to BAM and sorting using SAMtools
Raw counts per gene using HT-seq
Differential gene expression using edgeR
Genome_build: UMD 3.1
Supplementary_files_format_and_content: frequency counts

molecule: total RNA

organism: Ovis aries

source_name: Abomasal lymph nodes

growth_protocol: Lambs were born indoors and then moved to pasture for a 6-week period.  Lambs were weaned at 6 weeks of age and moved indoors.  Animals were maintained on a concentrate-based diet with free access to water for the remained of the experiment.  Upon housing faecal sampling per rectum was attempted on all lambs, but sufficient material was obtained from only 33 individuals (13 Texel and 20 Suffolk).  All lambs were then treated with Ivermectin (Oramec, Merial Animal Health Limited) according to the manufacturer’s instructions. Mean (±s.e.) Nematodirus sp. faecal egg counts (FECNEM) for Texel and Suffolk were 391 (±154.4) and 508 (±123.1), respectively. Mean values for other trichostrongyle FEC (FECOT) (excluding Strongyloides papillosus) were 11 (±4.6) and 106 (±37.0), respectively.  Animals were quarantined in a slatted pen for a period of 48 h prior to being penned as one group on straw. Five weeks post-housing and anthelmintic treatment, faecal samples were collected on 3 consecutive days to determine GIN infection status.  Lambs with a positive FEC (n = 7) for other trichostrongyles (FECOT) or Strongyloides papillosus  (FECSPAP) on any of these days were treated with Ivermectin (Noromectin Drench, Norbrook Laboratories Limited) according to the manufacturer’s instructions and re-sampled to establish the GIN infection status. All lambs were subsequently observed to be GIN negative. Approximately 1 week prior to administration of the challenge bolus, lambs were weighed, and faecal sampled to confirm the trichostrongyle infection-free status.

extract_protocol:
RNA was extracted uning TRIzol method
The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used. Library was prepared from all the samples except 2 from day 21 post infection due to available resources. Two library on day 7 post infection (23 and 24) did not work and excluded from the study.

treatment_protocol: At approximately 20 weeks of age the lambs were randomly assigned, within breed, to one of 5 slaughter time points (0, 3, 7, 14 or 21  days post-infection). The slaughter days were chosen based on the expected developmental stages of T. circumcincta in the sheep abomasum; day 3 and day 7 (L4), day 14 (immature adult), days 21  (mature adult). Animals assigned to the day 0 time point (6 Texel and 4 Suffolk) did not receive an experimental challenge, while all other lambs (5 per breed per time point) received a single oral dose of 3×104 infective T. circumcincta larvae (L3).

tag: tissue

value: Lymph nodes

tag: breed

value: Suffolk

tag: time point

value: Day 7

tag: infection

value: T. circumcincta

tag: animal id


title: T. circumcincta Suffolk Day 3 ALNL18

description: Sample 18 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CTTGTA

value: Day 3


title: BSseq-ZF-SUVH2_T3.qseq.gz

country: USA

library_source: genomic

molecule: genomic DNA

value: Wild type w/ ZincFinger-SUVH2 transgene (BASTA resistant T3 generation)


title: T. circumcincta Texel Day 3 ALNL19

description: Sample 19 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT

value: Texel


title: BSseq-ZF-SUVH2_T2.qseq.gz

value: Wild type w/ ZincFinger-SUVH2 transgene (BASTA resistant T2 generation)


title: T. circumcincta Texel Day 3 ALNL14

description: Sample 14 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag TGACCA


title: BSseq-ZF-SUVH2_sensitive_4.qseq.gz

value: Wild type w/ ZincFinger-SUVH2 transgene (BASTA sensitive segregant)


title: BSseq-ZF-SUVH2_sensitive_3.qseq.gz


title: 130904_LJ_sRNAseq_index_28_rawreads_50bp.qseq.gz

description: 18-28nt isolated small RNAs from total RNA Trizol preparation; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

source_name: floral tissue

extract_protocol:
Trizol extraction followed by PEG and then urea-PAGE fractionation
Illumina TruSeq small RNA
Samples 1..8 / 9..12 / 13..18 / were extracted by ChIP followed by phenol-chloroform exctract as describen / Trizol extraction followed by PEG and then urea-PAGE fractionation / phenol-chloroform extraction followed by bisulfite treatment
Samples 1..8 / 9..12 / 13..18 /  NuGen Ovation Ultralow DR sample prep kit / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013 /


title: 130904_LJ_sRNAseq_index_26_rawreads_50bp.qseq.gz


title: BSseq-FLAG-ZF-KYP_kypC.qseq.gz

value: Wild type w/ Flag-ZincFinger-KRYPTONITE transgene


title: 130904_LJ_sRNAseq_index_27_rawreads_50bp.qseq.gz


title: 130513_LJ_ChIP_index_2_rawreads_50bp.qseq.gz

description: immunoprecipitated formaldehyde-crosslinked flower tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/3 lane

extract_protocol:
extracted by ChIP followed by phenol-chloroform exctract as described
Illumina TruSeq DNA Prep Kit
Samples 1..8 / 9..12 / 13..18 / were extracted by ChIP followed by phenol-chloroform exctract as describen / Trizol extraction followed by PEG and then urea-PAGE fractionation / phenol-chloroform extraction followed by bisulfite treatment
Samples 1..8 / 9..12 / 13..18 /  NuGen Ovation Ultralow DR sample prep kit / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013 /

value: Wild type

tag: antibody

value: anti-NRPE1 antibody (Wierzbicki et al 2012)


title: control Suffolk Day 0 ALNL5

description: Sample 5 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag GCCAAT

value: Day 0

value: control


title: 121119_LJ_ChIPseq_index_14_rawreads_50bp.qseq.gz

description: immunoprecipitated formaldehyde-crosslinked flower tissue; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/8 lane

value: Columbia w/ NRPE1-Flag transgene

value: anti-FLAG antibody (Sigma M8823)


title: control Texel Day 0 ALNL1

description: Sample 1 was run in three different Flowcell. The process file was a combined file of data from Flowcel 1, 2 and 3 with the tag CGATGT


title: 121119_LJ_ChIPseq_index_13_rawreads_50bp.qseq.gz


title: 121119_LJ_ChIPseq_index_11_rawreads_50bp.qseq.gz

value: suvh2 suvh9


title: 121119_LJ_ChIPseq_index_12_rawreads_50bp.qseq.gz

value: Columbia


title: ATH1_WS_S1_rep2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Replicate 2 of 2

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were aligned to the Arabidopsis thaliana genome assembly (TAIR10) using tophat version 0.12.8 with default parameters.
Digital gene expression files were generated using cuffdiff version v2.0.2 (3522) with default parameters, and results were further annotated and summarised via in-house perl scripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited file containing FPKM gene-level values (abundance counts) for each sample, as well as a cuffdiff generated, merged, and further annotated tab-delimited file containing fold-changes and q-values of S1 versus water and S3 versus S1 (see GeneExpression.txt, linked as a supplementary file on the Series record).

source_name: rosette leaves

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown in potting soil in growth rooms at 22 °C with a 12-h light photoperiod and light intensity of 180 μmol m− 2 s−1.

extract_protocol:
Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were prepared from 4ug total RNA using the Illumina TruSeq RNA Sample Prep Kit-V2 set A (RS-122-2002 ) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and Nanodrop 1000 Spectrophotometer to a concentration of 10nM each.

treatment_protocol: Repeated dehydration stresses were performed by air-drying for 2 h followed by a 22 h period of full re-hydration recovery. S1 sample taken at first dehydration, S3 at third dehydration.

value: rosette leaves

value: WS

tag: stress

value: First drought stress


title: DRag Total RNA-seq paired-end

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

description: total RNA (ribosomal depleted)

data_processing:
High quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1.
Sequencing read were trimmed using csfasta_quality_filter (-m 8 -l  25 -s 14 -n 2). Selected reads were then aligned to mm9 genome using TopHat (version 2.0.4) and multireads were discarded.
Gene annotations (gtf files) and index files were obtained from TopHat website (Illumina iGenome). Cufflinks was subsequently used to discover new isoforms and transcripts (using known transcript list as guide) and perform assembly.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig files (bw) using BEDTtools (bedGraphToBigWig v.4 )

organism: Mus musculus

source_name: DRag2 thymocytes

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, USA) and DNA was digested. For total RNA samples, ribosomal RNA from 8 µg of total RNA was depleted using the eukaryotic Ribominus kit (Invitrogen, USA) according to manufacturer's instructions. Ribosomal RNA depletion was verified using RNA Pico chips on a 2100 Bioanalyzer.  200ng of ribodepleted RNA were used for RNA-seq library preparation according to SOLiD Total RNA-Seq Kit (Life Technologies, Carlsbad, CA).

value: Thymus

tag: strain

tag: cell type

value: CD4-, CD8- double negative (DN) Thymocytes


title: ATH1_WS_S3_rep2

description: Replicate 2 of 2

value: Third drought stress


title: 121119_LJ_ChIPseq_index_9_rawreads_50bp.qseq.gz


title: ATH1_WS_S3_rep1

description: Replicate 1 of 2


title: ATH1_WS_water_rep2

description: Replicate 2 of 2

value: Watered condition (control)


title: ATH1_WS_water_rep1

description: Replicate 1 of 2


title: msh1 mutant, biological rep 1

first: Ying-Zhi

last: Xu

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

description: enriched nuclear DNA

data_processing:
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/).  One mismatch was allowed in the first 50 nucleotides.  Only reads that map to a unique genomic locus were retained.  The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: cytosine methylation status

source_name: msh1 mutant_arieal part

growth_protocol: Plants were grown under 12h light.

extract_protocol: About 15 ug of gemonic DNA was sonicated to a peak range from 200bp to 600bp, then Phenol/ Chloroform purified and ethanol precipitated. About 12ug of sonicated DNA was treated with Mung Bean Nuclease, then Phenol/Chloroform purified and ethanol precipitated. About 3ug of Mung Bean Nuclease treated genomic DNA was End repaired , 3’ Ends adenylated  by using illumine Genomic DNA Samples Prep Kit. The adenylated DNA fragment was then ligated to methylation adapters. Methylation adapted DNA was column purified and ran agarose gel. A fraction of 280bp to 400bp was gel purified by using QIAquick Gel Purification kit. Another 3ug of Mung Nean Nuclease treated genomic DNA was used to repeat the whole process to collect second fraction of 280bp to 400bp methylation adapted DNA. Two methylation adapted fractions were pooled together and subjected to bisulfite treatment MethylEasy Xceed kit according to manufacturer’s instructions (Human Genetics Signature). Three independent library PCR enrichment was done by using 10ul from a total of 30ul bisulfate treated DNA as input template. The PCR reaction mixture were: 10ul DNA, 5ul of 10x pfuTurbo Cx buffer, 0.7ul of PE1.0 primer, 0.7ul PE2.0 primer, 0.5ul of dNTP(25mM), 1ul of PfuTurbo Cx Hotstart DNA Polymerase, and add water to a total volume of 50ul. The PCR parameters were: 95C for 2min, proceeded  by 12 cycles of 95C for30’’, 65C for 30’’ and 72C for 1 min, then followed by 720C for 5min. PCR product was column purified respectively and an equal amount of volume  from each PCR reaction was pooled together to a final concentration of 10nM. Libraries were then sequenced on the Illumina Genome Analyzer II using three 36-cycle TrueSeq sequencing kits v5 to read 116 nucleotides of sequence from a single end of each insert, by V8 protocols.

tag: ecotype background

tag: genotype/variation

value: msh1 mutant

value: above ground part - leaves and flower

tag: development stage

value: Mixed stage


title: Runx1_input

data_processing:
For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. For SOLiD 5500xl, basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2.
ChIP-seq reads were aligned to the Mus musculus genome (assembly NCBI 37/mm9) with BFast 0.7.0, and only reads with a unique best scoring alignment are retained.
Clonal artifacts were filtered out retaining the longer reads.
Peak calling was performed by using the Hypergeometric Optimization of Motif EnRichment (HOMER) tool (v4.1) with default settings (FDR: 0.001; local and input fold enrichment: 4.0).
Genome_build: MGSCv37
Supplementary_files_format_and_content: wig files were generated after reads elongation and normalization of the signal for 10 million reads; bed files contain HOMER scores.

source_name: DP thymocytes, input

growth_protocol: DP cells are directly sorted from mice thymus with Automacs (Miltenyi).

extract_protocol:
Following standard ChIP-seq protocols. Chromatin from 1 x 10^7 cells was used for the ChIP-seq experiment. Antibodies against Runx1 (Abcam, ab23980, lot #GR66230-1) were used at 10µg/1x10^7 cells. After reverse cross-linking and purification with the Qiagen PCR purification kit.
The ChIP-seq libraries have been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066), using 15 PCR cycles. The quality of the libraries has been checked with the Bioanalyser DNA High sensitivity and by Q-PCR. The sequencing was performed with the AB SOLiD 4 System and SOLiD 5500xl sequencer.

value: thymus

value: CD4+ CD8+ double-positive thymocytes

tag: chip antibody


title: 130904_LJ_sRNAseq_index_25_rawreads_50bp.qseq.gz

value: Wild type


title: Col-0

city: Copenhagen

first: Michael

middle: Krogh

last: Jensen

state: N

address: Ole Maaloesvej 5

department: Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Primary base-calling and quality analyses of the Illumina Genome Analyzer II output was performed by the manufacturer’s ELAND program.
QC-based (Illumina default settings) sequencing reads of 36 bases were mapped uniquely to the Arabidopsis reference genome (TAIR9 accession) with no more than 2 mismatches allowed
For detecting peaks, a null distribution of background sequencing signals was calculated. This was used to identify candidate peaks, using a lower window size cut-off of 200 bases, with a higher read count than expected from the null distribution. Using a 5% FDR cut-off (estimated as described in Ji et al., (2008), overlapping candidate peaks were subsequently merged and peaks refined based on the count and the spatial distribution of forward and reverse orientation of reads within the peaks ((No. forward reads – No. reverse reads)/(No. forward reads + No. reverse reads) < 0.5). The latter was applied to ensure that peaks were only called if there was a balanced number of forward and reverse reads within the detected peaks.

source_name: rosette stage (five weeks, short day)

growth_protocol: Transgenic and wild-type plants were grown on soil in controlled environment chambers under an 8 h light regime (150–170 µE/m2s) at 21°C and 65% relative humidity for five weeks.

extract_protocol:
The ChIP procedure was performed according to Reimer and Turck (2010)
Anti-HA antibody-enriched and ethanol precipitated fragmented DNA (10 ng) from wild-type Col-0 and 35S:ATAF1-HA over-expressing plants were adaptor-ligated and size-fractionated according to the single-read library preparation manual (Illumina, CA, USA)

value: wild-type

value: anti-HA antibodies (H6908, Sigma-Aldrich)


title: wild type, biological rep 2

description: enriched nuclear DNA

data_processing:
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/).  One mismatch was allowed in the first 50 nucleotides.  Only reads that map to a unique genomic locus were retained.  The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome Build:
Col0_2_bismarkMap.txt: TAIR10

source_name: arieal part, wild type

extract_protocol: About 15 ug of gemonic DNA was sonicated to a peak range from 200bp to 600bp, then Phenol/ Chloroform purified and ethanol precipitated. About 12ug of sonicated DNA was treated with Mung Bean Nuclease, then Phenol/Chloroform purified and ethanol precipitated. About 3ug of Mung Bean Nuclease treated genomic DNA was End repaired, 3’ Ends adenylated  by using illumine Genomic DNA Samples Prep Kit. The adenylated DNA fragment was then ligated to methylation adapters. Methylation adapted DNA was column purified and ran agarose gel. A fraction of 280bp to 400bp was gel purified by using QIAquick Gel Purification kit. Another 3ug of Mung Nean Nuclease treated genomic DNA was used to repeat the whole process to collect second fraction of 280bp to 400bp methylation adapted DNA. Two methylation adapted fractions were pooled together and subjected to bisulfite treatment MethylEasy Xceed kit according to manufacturer’s instructions (Human Genetics Signature). Three independent library PCR enrichment was done by using 10ul from a total of 30ul bisulfate treated DNA as input template. The PCR reaction mixture were: 10ul DNA, 5ul of 10x pfuTurbo Cx buffer, 0.7ul of PE1.0 primer, 0.7ul PE2.0 primer, 0.5ul of dNTP(25mM), 1ul of PfuTurbo Cx Hotstart DNA Polymerase, and add water to a total volume of 50ul. The PCR parameters were: 95C for 2min, proceeded  by 12 cycles of 95C for 30sec, 65C for 30sec and 72C for 1 min, then followed by 72C for 5min. PCR product was column purified respectively and an equal amount of volume  from each PCR reaction was pooled together to a final concentration of 10nM. Libraries were then sequenced on the Illumina Genome Analyzer II using three 36-cycle TrueSeq sequencing kits v5 to read 116 nucleotides of sequence from a single end of each insert, by V8 protocols.

value: wild type


title: MSH1-epiF3, biological rep 2

description: enriched nuclear DNA

data_processing:
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/).  One mismatch was allowed in the first 50 nucleotides.  Only reads that map to a unique genomic locus were retained.  The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome Build:
F3_2_bismarkMap.txt: TAIR10

source_name: arieal part, MSH-epiF3


title: MSH1-epiF3, biological rep 1

description: enriched nuclear DNA

data_processing:
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/).  One mismatch was allowed in the first 50 nucleotides.  Only reads that map to a unique genomic locus were retained.  The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome Build:
F3_1_bismarkMap.txt: TAIR10


title: PSF_R1881_Input

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using Illumina
Signal scores were calculated using in-house program described at Mol Cell Biol. 2009 Jul;29(13):3544-55. Shortly , rates of ChIP counts / control counts in 300bps window were used.
Genome_build: hg18
Supplementary_files_format_and_content: Bar files can be visualized by integrative genome browser (IGB) downloaded from Affymetrix.

organism: Homo sapiens

source_name: prostate cancer cells

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

extract_protocol:
Lysates were clarified from sonicated nuclei and PSF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: LNCaP cells were treated with vehicle or R1881 10 nM for 24 h.

tag: cell line

value: LNCaP

tag: treatment

value: R1881 10 nM treatment

value: input


title: PSF_Vehicle_Input

value: ethanol (Vehicle) treatment


title: PSF_R1881_ChIP

value: PSF


title: Adult_rat_kidney_cortex_input

city: La Jolla

first: Gleb

last: Martovetsky

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Default settings for the eland_extended algorithm in the Illumina Casava1.8 software were utilized for mapping.
All further analysis on aligned reds was performed using HOMERv3.13 software with default settings. Only one tag per base pair position was considered to remove clonal reads.
Genome_build: rn4
Supplementary_files_format_and_content: Peak files are in the default format generated by HOMERv3.13. Comments in the beginning of peak file contain various parameters of the analysis and column headers. First six columns contain a unique id, chromosome, start location, end location, strand and normalized tag count. Additional statistics are available in columns 7-15.

organism: Rattus norvegicus

source_name: kidney cortex

extract_protocol:
Freshly-isolated kidneys were immediately frozen in liquid nitrogen. To isolate the kidney cortex, a whole adult kidney was kept frozen within a ceramic mortar surrounded by dry ice while the outer ~1mm was shaved off with a razor. Whole kidneys or isolated cortex were thawed and minced in 1% formaldehyde in PBS on ice, followed by rotation for 15 minutes at room temperature. Fixation was quenched with glycine for 5 minutes. Fixed samples were then homogenized with a tissue grinder, washed twice with cold 0.5% IGEPAL CA-630 in PBS, and further disrupted using a type A glass dounce homogenizer. Nuclei were pelleted and sonicated on ice (three 5 minute cycles of 30 seconds on/30 seconds off). A mix of pre-blocked protein A/G beads was used to recover antibody-bound complexes, which were subsequently washed and eluted with SDS-containing buffer. The DNA was purified from the enriched and non-enriched samples by treatment with first RNAse and then Proteinase K, further de-crosslinking overnight at 65C, phenol extraction and ethanol precipitation.
The  protocol provided with the ChIP-Seq DNA Sample Prep Kit (Illumina, IP-102-1001) was followed. 200-400bp fragments were selected for sequencing.

value: kidney cortex

value: Sprague Dawley

tag: age

value: Adult (8 weeks old)

tag: Sex

value: male


title: PSF_Vehicle_ChIP


title: Adult_rat_kidney_input

source_name: whole kidney

tag: tissue

value: whole kidney


title: Adult_rat_kidney_cortex_p300_ChIP

value: p300 (Santa Cruz, sc-585)


title: Adult_rat_kidney_Hnf4a_ChIP

value: Hnf4a (Santa Cruz, sc-8987)


title: P13_rat_kidney_Hnf4a_ChIP

value: Postnatal day 13 (P13)

value: unsexed


title: P13_rat_kidney_input


title: ATAF1-HA

tag: ecotype

tag: genotype


title: 130513_LJ_ChIP_index_4_rawreads_50bp.qseq.gz

value: Columbia

value: anti-NRPE1 antibody (Wierzbicki et al 2012)


title: Drosophila_3d_whole fly_Ago2-IP

city: Philadelphia

first: Ammar

middle: S

last: Naqvi

state: Pennsylvania

address: 2716 South Street

department: Center for Data-Driven Discovery in Biomedicine

institute: Childrens Hospital of Philadelphia

description:
3d Ago2-IP small RNAs from FLAG-HA-Ago2 flies
MA12/Ago2-IP 3d

data_processing:
For base-calling Illumina Casava version 1.8.2 was used
Sequenced reads were trimmed for adapter sequence, then mapped to dm3 genome assembly for drosophila melanogaster using the RUM v1.11 pipeline by setting Bowtie to allow 0 mismatches and Blat to require 100% sequence identity
The uniquely mapping sequences with length between 16-35 nt were checked for overlap with the miRNAs
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files containing the read counts corresponding to each uniquely mapping sequence with length between 16-35 nt

organism: Drosophila melanogaster

source_name: 3d FLAG-HA-Ago2 male flies

growth_protocol: Flies were raised at 25˚C.

extract_protocol:
Immunoprecipitation was performed with anti-Ago1 (ab5070) or anti-FLAG M2 beads (Sigma A2220), followed by purification of small RNA fraction.
Libraries were prepared according to Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA).

treatment_protocol: Whole male flies were collected and aged to 3d and 30d.

tag: gender

value: whole fly

tag: rip antibody

value: anti-FLAG M2 beads (Sigma, A2220)


title: Drosophila_30d_whole fly_Ago2-IP

description:
30d Ago2-IP small RNAs from FLAG-HA-Ago2 flies
MA13/Ago2-IP 30d

source_name: 30d FLAG-HA-Ago2 male flies


title: E20_rat_kidney_Hnf4a_ChIP

value: 20 days post coitum (E20)


title: E20_rat_kidney_input


title: msh1 mutant, biological rep 2

description: enriched nuclear DNA

value: msh1 mutant

value: above ground part - leaves and flower

value: Mixed stage


title: Drosophila_30d_whole fly_Ago1-IP

description:
30d Ago1-IP small RNAs from FLAG-HA-Ago2 flies
MA11/Ago1-IP 30d

value: anti-Ago1 (Abcam, ab5070)


title: Drosophila_3d_whole fly_Ago1-IP

description:
3d Ago1-IP small RNAs from FLAG-HA-Ago2 flies
MA10/Ago1-IP 3d


title: Drosophila_wild-type 30d_head_no-oxidation

description:
30d wild-type small RNAs without oxidation/β-elimination
MA8/5905 30d head no-oxidation

source_name: wild-type male flies

extract_protocol:
Heads were collected on dry ice, followed by RNA preparation and  oxidation/β-elimination.
Libraries were prepared according to Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA).

value: head

tag: treatment of total rna prep

value: without oxidation/β-elimination


title: Drosophila_wild-type 30d_head_oxidation

description:
30d wild-type small RNAs with oxidation/β-elimination
MA9/5905 30d head oxidation

value: male

value: with oxidation/β-elimination


title: Drosophila_wild-type 3d_head_no-oxidation

description:
3d wild-type small RNAs without oxidation/β-elimination
MA6/5905 3d head no-oxidation


title: 121119_LJ_ChIPseq_index_10_rawreads_50bp.qseq.gz

value: Wild type

value: Columbia w/ NRPE1-Flag transgene

tag: antibody

value: anti-FLAG antibody (Sigma M8823)


title: wild type, biological rep 1

description: enriched nuclear DNA

data_processing:
Sequence reads were mapped to the Arabidopsis TAIR10 genome (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) with the program Bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/).  One mismatch was allowed in the first 50 nucleotides.  Only reads that map to a unique genomic locus were retained.  The methylation status of each cytosine in mapped reads were determined by comparing reads to the reference sequence and the context of each cytosine (CpG, CHG, or CHH) was also determined.
Genome Build:
Col0_1_bismarkMap.txt: TAIR10

value: wild type


title: Drosophila_wild-type 3d_head_oxidation

description:
3d wild-type small RNAs with oxidation/β-elimination
MA75905 3d head oxidation


title: IR6-Illumina

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

institute: INRA

description: Sample 4

data_processing:
Adapters were first removed using S-MART tools.
Sample 2 was mapped with Blat, the other samples were mapped with Bowtie. In all samples, only unique, without errors, hits were kept.
We counted the number of hits per gene and transposable elements using the S-MART tools.
FlyBase (release 06/29/11) has been used for the gene annotation. Transposable elements were annotated by the REPET pipe-line (see article).
Genome_build: dmel5
Supplementary_files_format_and_content: For each sample, a 2-column .tab flat file gives the number of hit per transcript, and a GFF3 file gives the number hit per transposable element copy.

molecule: polyA RNA

source_name: whole body

extract_protocol:
For samples 1 & 2, total RNA were extracted from 20 ovaries following provider procedure for the RNAqueous kit (Ambion) and 5 µgr were treated by GATC  to obtain PolyA+ RNA devoided of tRNA and rRNA. For samples 3 to 5,  we extracted polyA+ each from full bodies from 10 adult males (<24 hour) and 10 adult females (0-3 days), and sequenced using Illumina HiSeq technology after random primed retrotranscription.
Libraries were constructed using standard454 and Illumina instructions.

tag: line

tag: cage

value: no

tag: normalization

tag: strandedness


title: Iso1a-Illumina

description: Sample 5

value: yes


title: Rev-Illumina

description: Sample 3

value: Rev


title: WT_RNAseq

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

description: RNA-seq for half of the files below (file name contains "mrna"), and ribosome-footprint sequencing for the other half (file name contains "fp" for footprints)

data_processing: Reads from the fastq files were algined to the Feb 6, 2010 version of the S288C genome from SGD using bowite (http://bowtie-bio.sourceforge.net/index.shtml).  Using custom software, the number of uniquely mapping reads were assigned to corresponding positions in the genome in a strand-specific manner.  For degenerate reads that map to more than one position, each read was split among its mapped locations in proportion to the density of uniquely mapping reads at each location (e.g., a read mapping to two positions, where one is in a gene with 500 unique reads and the other two a gene with 250 unique reads), we incremented the number of counts at the first position by 2/3 (i.e., 500/(250+500)) and at the second position by 1/3 (i.e., 250/(250+500))). For degenerate locations outside of genes, we considered the density in a 56-nt window centered on the location.

organism: Saccharomyces cerevisiae

source_name: Wild-type cells (BY4741)

growth_protocol: Cells were grown to OD600 = 0.6 in 750ml YPD shaking at 30C.

extract_protocol: Methods are as described in Ingolia et al., 2009, except for the use of rRNA substraction for "fp" samples and linker ligation for all samples, which are described in Ingolia et al., 2011.  In fastq files below, trim the 3' linker sequence "CTGTAGGCACCATCAAT" and all bases further toward the 3' end of the read.

treatment_protocol: Cycloheximide was spiked into the cultures at a concentration of 100ug/ml 1 minute prior to harvesting by filtration and freezing in liquid nitrogen.

value: Whole-cell total RNA prep


title: ATH1_WS_S1_rep1

description: Replicate 1 of 2

value: rosette leaves

value: WS

tag: stress

value: First drought stress


title: WT_riboProfiling

value: Isolation of ribosome footprint RNAs


title: loc1_riboProfiling

source_name: loc1- cells (BY4741 loc1::KAN)

value: BY4741 loc1::KAN


title: loc1_RNAseq


title: PsyB728a(pBAD::hrpL)_1

city: Chapel Hill

first: Emma

last: Johnson

state: North Carolina

address: 250 Bell Tower Dr

institute: University of North Carolina - Chapel Hill

description: Biological replicate #1

data_processing:
The PtoDC3000, Pph1448A, Por1_6, Pjap, and Pla107 reads produced using a Illumina GA II.  The PsyB728A reads produced using a Illumina HiSeq system.
A GFF file was created for each genome by BLASTing transcripts to the genomic sequences and recoding gene coordinates for optimal hits.  This was done using an in-house script.  All genomes can be accessed and downloaded from NCBI.  Transcriptomes were constructed by NCBI’s gene prediction pipeline for PtoDC3000, PsyB728A, and Pph1448A.  Por1_6, Pla107, Pjap transcriptomes were constructed by JGI’s Integrated Microbial Genomes – Expert Review gene prediction pipeline.
GENEcounter was used to map RNA-seq reads from each strain to the matching genomic sequence.  Used GENEcounter default parameters.
GENEcounter was used to count the number of reads mapped to each gene for each genome and detect differential expression between HrpL and EV samples within each strain.
A slight modification in GENEcounter allowing for random seeding allowed us to bootstrap the normalization.  Bootstrap values were calculated for 100 random normalizations and differential expression analyses.  Median count values and bootstrapped differential expression occurrences are recorded in the final processed data txt files.
Genome_build: The genomes can be accessed using the following NCBI BIoProject IDs.  PtoDC3000 - PRJNA57967; PtoDC3000_draft - in-house; Pph1448A - PRJNA58099; PsyB728A - PRJNA57931; Por1_6 - PRJNA55447; Pjap - PRJNA33209; Pla107 - PRJNA33205.
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each gene in each sample

organism: Pseudomonas syringae

source_name: bacterial culture

growth_protocol: Pseudomonas strains were grown overnight at 28 ˚C, in KB media supplemented with appropriate antibiotics, then sub-cultured in fresh media at OD600= 0.2, and grown until OD600= 0.4-0.5. Bacteria were washed twice with 10 mM MgCl2 and resuspended in minimal medium (Huynh et al., 1989) supplemented 0.1% peptone. Bactria were then inoculated in supplemented minimal media at OD600= 0.2, and incubated shaking for 1 hour at 28 ˚C.  Expression of hrpL was induced by addition of 200 mM L-arabinose.  Aliquots of cell culture were taken 1, 3, 5 hours post-induction and treated with RNAprotect reagent (Qiagen).

extract_protocol:
RNA isolation was performed by using the RNeasy minikit (Qiagen). Isolated total RNA was treated with TURBO DNase (Ambion). Total RNA of each time point was pooled at 1/3 ratio. 10 μg of pooled RNA was depleted of 16S and 23S ribosomal RNA using RiboMinusTM (Invitrogen). Double stranded cDNA were prepared from ~ 1 μg ribosomal depleted RNA, using random primers (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pathovar

value: syringae

tag: strain

tag: plasmid


title: PsyB728a(pBAD::hrpL)_2

description: Biological replicate #2


title: PsyB728a(pBAD::EV)_2

description: Biological replicate #2


title: PsyB728a(pBAD::EV)_1

description: Biological replicate #1


title: C1_0270 Pool of 10 breast tumors

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
mapping software: LifeScope (version 1)
genome build: hg19
VarScan version: version 2.2

CSFASTA files were mapped to human genome
Samtools mpileup was used to generate pileups from the mapped BAM files.
VarScan was used to call mutations
Events were annotated using a custom script and database built from RefSeq.
Supplementary_files_format_and_content: tab-delimited files containing events and annotations

source_name: breast tumor

extract_protocol:
Genomic DNA was extracted using Formapure kit (Beckman Coulter Genomics).
Amplicons spanning RND1 exons were pooled for 10 samples after amplification by PCR. 1ug of pooled amplicons was concatenated, sheared for 5 minutes (covaris), end repaired, and ligated with barcoded SOLiD sequencing adaptors. 8 cycles of PCR were performed and 2ng of the final 10 libraries were then pooled for one full size emulsion PCR using the EZbead system. The enriched beads were sequenced in an octet of a SOLiD sequencing system for 50bp run with the Exact Call Chemistry module (ECC). An average of 6.2 million reads were generated per pool, the mapping rates ranged from 86.9% and 89.1%.

value: breast tumor


title: B2_0270 Pool of 6 breast tumors


title: C2_0270 Pool of 8 normal tissues

source_name: normal mammary tissue

value: normal mammary tissue


title: A2_0270 Pool of 10 breast tumors


title: G1_0270 Pool of 10 breast tumors


title: E1_0270 Pool of 10 breast tumors


title: D1_0270 Pool of 10 breast tumors


title: F1_0270 Pool of 10 breast tumors


title: H1_0270 Pool of 10 breast tumors


title: AT-06

city: Seoul

first: In-Geol

last: Choi

address: Anam-dong Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: sacCer2
Supplementary_files_format_and_content: comma separated value (CSV) format files including normalized counts & RPKM values for each Sample

growth_protocol: YPD media, 30C

extract_protocol:
Total RNA was extractred by Qiagen RNA extraction kit
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: with or without 0.6 % acetic acid

tag: phenotype

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

tag: treatment

value: acetic acid 0.6%


title: B1_0270 Pool of 10 breast tumors

tag: tissue


title: AC-06


title: AC-00

value: acetic acid 0%


title: AT-00


title: Runx1_ChIP

source_name: DP thymocytes, Runx1 ChIP

value: thymus

tag: cell type

value: CD4+ CD8+ double-positive thymocytes

tag: chip antibody


title: fl_1_e14_5

city: Edinburgh

first: Pedro

last: Coutinho

address: western general hospital, crewe rd

department: MRC IGMM

country: United Kingdom

institute: University of Edinburgh

data_processing:
Library strategy: DGE-SAGE
base calls performed using Illumina 1.5 pipeline
The fastq data was parsed to select sequences for which the probability of a nucleotide mistake at any position is less than 0.001
These were then trimmed to remove adapters and the remaining tags were mapped against the NCBI SAGE mouse repository file Mm_long.best_gene
The tags that did not match were processed using Bowtie, with parameters -S -a -v 1 -m 1 --best –strata
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: tab-delimited files containing the counts per sample and tag

source_name: embryonic forelimb

extract_protocol: The limbs from E14.5 mice embryos were dissected and preserved in RNAlater (Qiagen - 76104), at -20oc.  Two biological replicas were generated for each type of appendage.  The limbs were then processed using RNEasy (Qiagen – 74104) to extract and purify total RNA. The quality of the RNA was checked using a nanodrop machine and using a 2100 bioanalizer (Agilent).  After quality control, 10 ug of total RNA for each sample was processed by the GenePool service (http://genepool.bio.ed.ac.uk/) in order to generate and sequence the respective DGE-SAGE libraries. This was performed according to the standard protocol to prepare samples for digital gene expression, using tag profiling with NlaIII, from illumina.

value: forelimb

tag: developmental stage


title: H1_0136 Pool of 10 breast tumors

data_processing:
mapping software: BioScope (version 1.3)
genome build: hg18
VarScan version: version 1

CSFASTA files were mapped to human genome
Samtools mpileup was used to generate pileups from the mapped BAM files.
VarScan was used to call mutations
Events were annotated using a custom script and database built from RefSeq.
Supplementary_files_format_and_content: tab-delimited files containing events and annotations


title: fl_2_e14_5


title: hl_2_e14_5

source_name: embryonic hindlimb

value: hindlimb


title: D1_0136 Pool of 10 breast tumors


title: E1_0136 Pool of 10 breast tumors


title: hl_1_e14_5


title: F1_0136 Pool of 10 breast tumors


title: C1_0136 Pool of 10 breast tumors


title: A1_0270 Pool of 10 breast tumors


title: B2_0136 Pool of 6 breast tumors


title: B1_0136 Pool of 10 breast tumors


title: A2_0136 Pool of 10 breast tumors


title: A1_0136 Pool of 10 breast tumors


title: ZFP3ox/ABA

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

data_processing:
Basecalls performed using Abi Solid 4+ ICS (Instrument Controller version 2010.04)
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to the NC_003070/NC_003070/NC_003070/NC_003070/NC_003076/NC_003076/Y08501_MT genome assembly using CLC Genomics Workbench version 5.5.1 with the following configurations…*
Calculate expression levels and discover novel exons using CLC Genomics Workbench version 5.5.1
Annotation using CLC Genomics Workbench version  5.5.1 (Data from www.geneontology.org)
Genome_build: NC_003070/NC_003070/NC_003070/NC_003070/NC_003076/NC_003076/Y08501_MT
Supplementary_files_format_and_content: Text file with expression values (Read Per Kilobase of exon Model value)

source_name: ABA-treated seedlings, 84 hours

growth_protocol: ZFP3 overexpressing and Col-0 wild type seeds were germinated on media supplemented with 5µM estradiol or 5µM estradiol and 2.5µM ABA. Seedlings on estradiol containing media were harvested after 36 hours and seedlings germinated in the presence of ABA and estradiol were harvested after 84 hours to obtain seedlings in physiologically identical radical stage for both conditions.

extract_protocol:
Total RNA was isolated with Qiagen Plant RNeasy Kit, followed by DNaseI treatment using Ambion's TURBO DNA-free™ kit. RNA quality and quantity measurements were performed on Bioanalyzer (Agilent Technologies).
Libraries were processed according to the SOLID transcriptome sequencing protocol (Publication Part Number 4452437). Briefly, total RNA was DNaseI treated and rRNA-depleted using RiboMinus Plant Kit. After the fragmentation of RNA, the 50-200nt fraction was cleaned and was the subject of adaptor hybridization and reverse transcription. The cDNA library was cleaned with Qiagen MinElute PCR purification Kit and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel.  The 150-250nt cDNA fraction was amplified to generate sufficient template for SOLID sequencing. To determine the accurate concentration of each library, a SOLID Library TaqMan Quantitation Kit was used according to the manufacturer's instructions. After, each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR (ePCR). ePCR beads were enriched for template-positive beads by hybridization with capture beads. Template-enriched beads were extended at the 3' end in the presence of terminal transferase and 3' bead linker. Approximately 60 million beads per sample with clonally amplified DNA were deposited onto one lane of the 5500 SOLID sequencing flowchip . The flowchip was then loaded onto a SOLID 5500xl Instrument and the 50-base sequences were obtained according to manufacturer's protocol.

value: seedling

tag: genotype/variation

value: ZFP3 overexpressing


title: ZFP3ox/control

source_name: control seedlings, 36 hours


title: Col-0/control

value: Col-0 wild type


title: Col-0/ABA


title: Long Day - rep 9

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

data_processing:
The libraries were quantitated by qPCR, pooled all together and sequenced on three lanes for 101 cycles on a HiSeq 2000 using a TruSeq SBS sequencing kit version 3
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2. Reads from the same sample across multiple lanes were combined into one .fastq.gz file using an in-house pipeline.
Reads were trimmed for quality using seqtk (downloaded 12/2012 from github.com/lh3/seqtk) with parameters trimfq -q 20 -l 25 .
Alignments to the cat genome (Felis_catus_6.2) and cat transcriptome (Ensembl 70) were done using Tophat2 2.0.8 with parameters --b2-very-sensitive --no-sort-bam --transcriptome-index transcriptome/known. Sorting of the BAM files was done with novosort (novocraft 2.08.02) with parameters -f -c.
Read counts for each gene were generated using htseq-count (samtools 0.1.18) with parameters --stranded=no -m intersection-nonempty and combined into one tab-delimited text file for all 20 samples
Genome_build: Felis_catus_6.2
Supplementary_files_format_and_content: a single tab-delimited text file of raw read counts were used directly in edgeR 3.0.8 for statistical analysis and thus are the "normalized" data.

organism: Felis catus

source_name: Subcutaneous adipose

extract_protocol:
Subcutaneous adipose samples were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. Indices (barcodes) were included to be able to differentiate the sequences from each sample.

treatment_protocol: During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing.

value: Long Day

value: Subcutaneous adipose

tag: individual

value: Slim

tag: day length

value: Long

tag: presentation order


title: Long Day - rep 10

value: Tiger


title: Short Day - rep 10

value: Short Day

value: Short


title: Long Day - rep 6

value: Michael


title: Input_hns-F_bcm+#2

city: Bangalore

first: Deepti

last: Chandraprakash

state: Karnataka

address: GKVK, bellary road

country: India

institute: National Centre for Biological Sciences

description: Escherichia coli K12 MG1655 CGSC6300

data_processing:
reads aligned to the reference genome of E. coli K-12 Mg1655 using BWA, with quality threshold of 20
Reads mapped to more than one locus were discarded. The mapped position obtained from the SAM output file from BWA lists was taken and the position was extended to 280 bp which is the average length of DNA fragments submitted for sequencing.
For each co-ordinate coverage was calculated as the number of reads which was aligned againist the position. The coverage was normalized and converted into a z score. Z score threshold of 12 was selected to identify H-NS binding regions.
The binding regions were considered by taking into account base position with z-score greater than threshold and merging adjacent binding regions seperated by a distance of less than 200bo into the single binding regions
consensus binding regions were obtained as the portion which was covered by replicate samples
genome build: ASM584v1
Supplementary_files_format_and_content: format:bed format
Supplementary_files_format_and_content: contents : reference seq,co-ordinate start position,co-ordinate end position,counts for the position, mapping quality, strand position

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

source_name: H-NS flag tagged cells with bcm treatment

growth_protocol: MG1655 hns-FLAG cells were grown in liquid LB medium with and without bicyclomycin (BCM) at 37 degree with shaking at 200rpm

extract_protocol: Standard illumina library construction protocol for ChIP

treatment_protocol: Two biological replicates were performed for samples with and without treatment with bicyclomycin. For samples without BCM treatment, cells were grown OD600 ≈ 0.8 at 370 with shaking at 200 rpm.  For samples with BCM treatment, cells were grown to early log phase (O.D. 600=0.1) ≈ 1h at 370 with shaking at 200 rpm. BCM was added to a final concentration of 25ug mL-1


title: Long Day - rep 7

value: Monster


title: Short Day - rep 8

value: Nickel


title: Short Day - rep 7


title: Short Day - rep 9


title: Long Day - rep 8


title: Input_hns-F_bcm+#1

description: Escherichia coli K12 MG1655 CGSC6300


title: Short Day - rep 5

value: MB


title: Input_hns-F_bcm-#2

description: Escherichia coli K12 MG1655 CGSC6300

source_name: H-NS flag tagged cells without bcm treatment


title: G1_0136 Pool of 10 breast tumors

value: breast tumor


title: Input_hns-F_bcm-#1

description: Escherichia coli K12 MG1655 CGSC6300


title: Long Day - rep 5


title: Short Day - rep 6


title: ChIP_hns-F_bcm+#1

description: Escherichia coli K12 MG1655 CGSC6300

value: anti-FLAG antibody (Sigma Cat #:F3165-1MG)


title: Short Day - rep 4

value: Julio


title: ChIP_hns-F_bcm+#2

description: Escherichia coli K12 MG1655 CGSC6300


title: ChIP_hns-F_bcm-#1

description: Escherichia coli K12 MG1655 CGSC6300


title: Long Day - rep 4


title: ChIP_hns-F_bcm-#2

description: Escherichia coli K12 MG1655 CGSC6300


title: Short Day - rep 3

value: Bugsy


title: Long Day - rep 3


title: Long Day - rep 2

value: Belly


title: Long Day - rep 1

value: Ash


title: Short Day - rep 1


title: Por(pBAD::hrpL)_2

description: Biological replicate #2

value: oryzae


title: Por(pBAD::EV)_2

description: Biological replicate #2


title: Por(pBAD::EV)_1

description: Biological replicate #1


title: Por(pBAD::hrpL)_1

description: Biological replicate #1


title: Pjap(pBAD::hrpL)_2

description: Biological replicate #2

value: japonica

value: MAFF301072 PT


title: Pjap(pBAD::EV)_1

description: Biological replicate #1


title: Pla107(pBAD::hrpL)_1

description: Biological replicate #1

value: lachrymans


title: Pla107(pBAD::hrpL)_2

description: Biological replicate #2


title: Pjap(pBAD::hrpL)_1

description: Biological replicate #1


title: Pla107(pBAD::EV)_2

description: Biological replicate #2


title: Pjap(pBAD::EV)_2

description: Biological replicate #2


title: Pla107(pBAD::EV)_1

description: Biological replicate #1


title: Pph1448A(pBAD::hrpL)_2

description: Biological replicate #2

value: phaseolicala


title: PtoDC3000(pBAD::EV)_1

description: Biological replicate #1

value: tomato


title: PtoDC3000(pBAD::hrpL)_1

description: Biological replicate #1


title: Pph1448A(pBAD::hrpL)_1

description: Biological replicate #1


title: PtoDC3000(pBAD::EV)_2

description: Biological replicate #2


title: Pph1448A(pBAD::EV)_1

description: Biological replicate #1


title: Pph1448A(pBAD::EV)_2

description: Biological replicate #2


title: Short Day - rep 2

value: Short Day

value: Subcutaneous adipose

value: Short


title: Input-A (ChIP-Seq)

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg19
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

source_name: Human primary adult proerythroblasts (ProEs)

growth_protocol: Primary maturing adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For ChIP-seq analysis using the Illumin HiSeq2000, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg19) were retained for downstream data analysis.

value: CD34+ HSPC-derived proerythroblasts

value: bone marrow

value: adult


title: GFI1B-A (ChIP-Seq)

value: GFI1B - Abcam ab26132


title: H3K27me3-A (ChIP-Seq)

value: H3K27me3 - Millipore 07-449


title: GATA1-A (ChIP-Seq)

value: GATA1 - Abcam ab11852


title: TAL1-A (ChIP-Seq)

value: TAL1 - Santa Cruz Biotechnology sc-12984


title: N061011_Alb_Dex

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed by 12bp then mapped to hg19 whole genome using tophat v.2.0.4 with parameters -G [hg19_ERCC_gtf] --no-novel-juncs --transcriptome-only
For each sample, Cufflinks (v.2.0.2) was used to quantify External RNA Controls Consortium (ERCC) Spike-In and hg19 transcripts based on reads that mapped to the provided hg19 and ERCC reference files.
Differential expression of genes and transcripts in samples treated with Dex vs. Untreated samples was obtained using Cuffdiff (v.2.0.2) with the quantified transcripts computed by Cufflinks (v.2.0.2), while applying bias correction. Options: -p 12 --min-outlier-p 0.05 -b [hg19_reference_index] -u [hg19_gtf] -L Dex,Control  [List of accepted_hits.bam for each sample sorted by condition (i.e. Dex,Control)]
CummeRbund R package (v.0.1.3) was used to create FPKM matrix of all samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files on Series record include FPKM values for each sample (ALL_Sample_FPKM_Matrix.txt) and gene-based differential expression results for Dex vs. Untreated condition (Dex_vs_Untreated_gene_exp.diff)

source_name: airway smooth muscle cells

growth_protocol: Primary ASM cells were isolated from four white aborted lung transplant donors with no chronic illness. Passages 4 to 7 ASM cells maintained in Ham's F12 medium supplemented with 10% FBS were used in all experiments.

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA).

treatment_protocol: Cells from each donor were treated with 1 μM dexamethasone,  1 μM albuterol, both dexamethasone and albuterol, or control vehicle for 18 h.

value: human airway smooth muscle cells

tag: cell line

value: airway smooth muscle cells


title: N061011_Dex

value: Dexamethasone


title: N061011_Alb

value: Albuterol


title: N080611_Alb


title: N080611_Alb_Dex


title: N061011_untreated

value: Untreated


title: N080611_untreated


title: N052611_Alb_Dex


title: N080611_Dex


title: H3K27ac-A (ChIP-Seq)

value: H3K27ac - Abcam ab4729


title: N61311_Alb_Dex


title: N61311_Dex


title: N052611_Dex


title: N61311_Alb


title: N052611_Alb


title: N61311_untreated


title: N052611_untreated


title: PR+LPS+P_8h

city: Los Angeles

first: Lauren

last: Goddard

address: 621 Charles E. Young Dr. S.

department: Molecular, Cell, and Developmental Biology

institute: University of California-Los Angeles

description: Sample 6

data_processing:
Debarcoding of the multiplex runs was performed using in house shell script
Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.
The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes

source_name: primary HUVECs

growth_protocol: HUVECs (VEC Technologies, Rensselaer, NY), passages 4-6, were cultured in MCDB-131 (VEC Technologies, Rensselaer, NY) with the addition of 10% fetal bovine serum (Omega Scientific, Tarzana, CA) that was stripped using 0.25% dextran coated charcoal (Sigma, St. Louis, MO).

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.
The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: Primary HUVECS were  infected at passage 4 with a lentivirus containing human PR, then split onto 10cm dishes and grown to confluence. Three days after they reached confluence they were treated with LPS (1μM) and/or progesterone (100nM) for 4 or 8 hours, then harvested for the experiment.

value: primary human umbilical vein endothelial cells

tag: passage

tag: infected with

value: a lentivirus containing human PR

tag: treated with

value: LPS (1μM) + progesterone (100nM) for 8 hrs


title: 2nd_NPC_rna_seq

city: Bronx

first: Herb

last: Lachman

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version  1.3.2 )
The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts
the program Cuffdiff was used to define differential expression
Genome_build: hg19
Supplementary_files_format_and_content: excel files include FPKM for each sample and some statistics

source_name: NPC

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol.  An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2. Briefly, total RNA was converted to cDNA, which was then used for Illumina sequencing library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NPC


title: 2nd_neuron_rna_seq

source_name: neuron

value: neuron


title: PR+LPS_4h

description: Sample 3

value: LPS (1μM) for 4 hrs


title: PR+LPS+P_4h

description: Sample 5

value: LPS (1μM) + progesterone (100nM) for 4 hrs


title: PR

description: Sample 1


title: INPUT_IgG_PR_infected

description: INPUT

data_processing:
Debarcoding of the multiplex runs was performed using Fastx toolkit
Tags were mapped to the human genome (hg19) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
Peaks for PR and PR+P conditions were called using either input, negative control or IgG control as a reference and only peaks that were present in all three analyses (minus IgG peaks) were included in the final list of PR binding sites
PR peaks were mapped to nearby genes within 50kb range from TSS using Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010). Peak intersections and overlaps with differentially expressed genes were performed using Galaxy (Blankenberg et al., 2010) and in house shell scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks

growth_protocol: Human umbilical vein endothelial cells, passages 4-6, were cultured in MCDB-131 (VEC Technologies, Rensselaer, NY) with the addition of 10% fetal bovine serum (Omega Scientific, Tarzana, CA) that was stripped using 0.25% dextran coated charcoal (Sigma, St. Louis, MO).

extract_protocol:
Cells were trypsinized, washed with PBS and crosslinked with 1% formaldehyde in PBS for 10 min at RT. After PBS washing, cells were resuspended in 400 μl of lysis buffer (1% SDS, 20 mM EDTA and 50 mM Tris-HCl (pH 8.0)) containing protease inhibitors (Roche, Indianapolis, IN), incubated for 10 min on ice and sonicated using Misonix cup-horn sonicator to achieve, on average, 200bp fragments for ChIP-seq and 500bp fragments for ChIP-PCR. The lysate was diluted 10 times with ChIP dilution buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 16.7 mM Tris-HCl (pH 8.1) and immunoprecipitatied with 3 ug of anti-PR or IgG antibody overnight at 4 degrees. 20 μl of the lysates were used as input. The complexes were captured using protein A Dynabeads (Invitrogen, Grand Island, NY) and washed twice with the following buffers: low-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1); high-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl); LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE (10 mM Tris-HCl and 1 mM EDTA (pH 8.0)). After elution with 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 1% SDS, crosslinks were reversed by overnight incubation at 65°C. Samples were then treated with RNase A for 30 min at 37°C and proteinase K for 2 h at 56°C. DNA was subsequently purified using Qiagen MinElute Columns according to manufacturers instructions. DNA concentration was measured using a Qubit (Invitrogen, Grand Island, NY).
The library for sequencing was constructed using Ovation Ultralow IL Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: Primary HUVECS were  infected at passage 4 with a lentivirus containing human PR, then split onto 10cm dishes and grown to confluence (hence they become passage number 5 for the experiment). 3 days after they reached confluence they were treated with progesterone (100nM) for 1 hour--then harvested for the experiment.

value: endothelial cells

tag: passage nr.

value: PR infected

tag: ChIP

value: none, input


title: INPUT_PR_PR_infected

description: INPUT


title: INPUT_PR_PR_infected+Prog

description: INPUT

value: PR infected + Progesterone


title: INPUT_PR_Not_infected

description: INPUT

value: Control


title: IgG_PR_infected

description: PR ChIP

value: PR


title: PR_PR_infected+Prog

description: PR ChIP


title: PR+LPS_8h

description: Sample 4

value: LPS (1μM) for 8 hrs


title: FB.BS

city: Taipei

first: Pao-Yang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
BS-seq reads were aligned to the Tuber_melanosporum_v1.0 genome assembly using BS Seeker
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (seearabidopsis_tair10.fa.log); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
Genome_build: Tuber_melanosporum_v1.0

organism: Tuber melanosporum

source_name: truffle fruit body

extract_protocol:
Genomic DNA from FLM, FB and ECM was extracted by grinding in liquid nitrogen followed by DNeasy Plant Mini kit (QIAGEN) purification
After an additional phenol:chloroform extraction, gDNA was sheared by sonication to generate DNA fragments in the 150-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the EpiTect kit (QIAGEN) was utilized for bisulfite treatment. Two consecutive rounds of conversion were performed for a total of 10 hours. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna Hiseq 2000 sequencer).

value: fruit body


title: FB.RNA

data_processing:
RNA-seq alignment using Tophat 2.0.4, Tuber_melanosporum_v1.0_annot.gff as library junction, allowing 2 mismatches and only uniquely aligned reads, filtering as default by Tophat
abundance counting using HTSeq version 0.5.4p3, using "union" mode for ambiguous reads (default)
calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by Tophat
calculate p-values with DESeq version 2.12
supplementary_files_format_and_content: Two files -- one for the genes (FB_FLM.RNA.txt), one for the repeats (FB_FLM.repeats.txt).
Genome_build: Tuber_melanosporum_v1.0

extract_protocol:
Total RNA from FLM and FB was extracted as described previously (Montanini et al. 2003) and purified with the RNeasy Plant Mini kit and on-column DNase I digestion (QIAGEN) following the manufacturer’s instructions. RNA integrity was verified by a Bioanalyzer: RIN scores of 7.0 and 6.5 for FB and FLM, respectively.
RNA was quantified with the Qubit RNA BR Assay and 1 μg of purified RNA was utilized as starting material for library construction, which was carried out with the Illumina TruSeq RNA Sample Preparation kit following the manufacturer's instructions. Libraries were sequenced using 50-bp single-end reads on the HiSeq 2000 System (Illumina).


title: FLM.BS

source_name: truffle free-living mycelium

value: free-living mycelium


title: neuron_rna_seq


title: NPC_rna_seq


title: tips_rna_seq

source_name: iPSC

value: iPSC


title: PR+P

description: Sample 2

value: primary human umbilical vein endothelial cells

value: Progesterone


title: ppe degradome flower

city: Nanjing

first: Zhihong

last: Gao

state: Jiangsu

address: No. 1, Weigang

department: College of Horticulture

country: China

institute: Nanjing Agricultural University

data_processing:
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
genome_build: The peach genome sequences, CDS sequences and gene annotation information were obtained from GDR (www.rosaceae.org).
After removing low quality reads and trimming adaptor sequences, the high-quality small RNA reads ranging from 18 to 30 nucleotides were obtained from the sRNA raw data.
Small RNA sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam 10 (http://www.sanger.ac.uk/resources/databases/rfam.html) and NCBI Genbank databases were removed.
The remaining sequences were searched against the miRBase database v18.0 (http://www.mirbase.org, release 18) with up to two mismatches, to identify conserved miRNAs.
The sequences that did not map to any miRNAs in miRBase were analysed for predictions to identify novel miRNAs by the program MIREAP (developed by BGI) with default parameters for mapping the peach genome and obtaining all candidate precursors with hairpin-like structures of novel miRNA candidates
Secondary structures of novel miRNAs were also checked using Mfold 3.2
Genome_build: miRBase Release 18
Supplementary_files_format_and_content: all of processed data files format are fasta and content is: one small RNA library and three degradome libraries

organism: Prunus persica

source_name: flowers

growth_protocol: Prunus persica cv. Lovell peach trees were grown in the garden of Nanjing Agricultural University, China

extract_protocol: degradome cDNA libraries construction protocol: German MA, Luo S, Schroth G, Meyers BC, Green PJ (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4: 356-362. The construction of degradome libraries differed considerably from past efforts and followed the procedure of as Ma et al. (Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22: 1090-1103.) with some modifications. (1) Approximately 150 ng of poly (A)+ RNA was used as input RNA and for annealing with biotinylated random primers; (2) Strapavidin capture of RNA fragments was performed via Biotinylated Random Primers; (3) 5´ adaptor ligation was only performed to those RNAs containing 5´-monophosphates; followed by (4) reverse transcription and PCR; (5) libraries were sequenced using the 5´ adapter only, resulting in the sequencing of the first 36 nucleotides of the inserts that represented the 5´ ends of the original RNAs.

tag: cultivar

value: Lovell

value: flowers


title: ppe degradome leave

source_name: young leaves

value: young leaves


title: mixed tissues for small RNA sequencing

data_processing:
After removing low quality reads and trimming adaptor sequences, the high-quality small RNA reads ranging from 18 to 30 nucleotides were obtained from the sRNA raw data. Small RNA sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam 10 (http://www.sanger.ac.uk/resources/databases/rfam.html) and NCBI Genbank databases were removed. The remaining sequences were searched against the miRBase database v18.0 (http://www.mirbase.org, release 18) with up to two mismatches, to identify conserved miRNAs. The sequences that did not map to any miRNAs in miRBase were analysed for predictions to identify novel miRNAs by the program MIREAP (developed by BGI) with default parameters for mapping the peach genome and obtaining all candidate precursors with hairpin-like structures of novel miRNA candidates. Secondary structures of novel miRNAs were also checked using Mfold 3.2.
genome_build: miRBase Release 18
After removing low quality reads and trimming adaptor sequences, the high-quality small RNA reads ranging from 18 to 30 nucleotides were obtained from the sRNA raw data.
Small RNA sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam 10 (http://www.sanger.ac.uk/resources/databases/rfam.html) and NCBI Genbank databases were removed.
The remaining sequences were searched against the miRBase database v18.0 (http://www.mirbase.org, release 18) with up to two mismatches, to identify conserved miRNAs.
The sequences that did not map to any miRNAs in miRBase were analysed for predictions to identify novel miRNAs by the program MIREAP (developed by BGI) with default parameters for mapping the peach genome and obtaining all candidate precursors with hairpin-like structures of novel miRNA candidates
Secondary structures of novel miRNAs were also checked using Mfold 3.2
Genome_build: miRBase Release 18
Supplementary_files_format_and_content: all of processed data files format are fasta and content is: one small RNA library and three degradome libraries

source_name: young leaves, young stems and flower buds

extract_protocol: A low molecular weight (LMW) RNA was isolated from mixed tissues (peach leaves, young stems and flowers) by using CTAB reagent according to the procedure previously described (Wang X, Xiong A, Yao Q, Zhang Z, Qiao Y (2009) Direct isolation of high-quality low molecular weight RNA of pear peel from the extraction mixture containing nucleic acid. Molecular Biotechnology 44: 61-65). The sample was sequenced by the Beijing Genomics Institute (BGI) (Shenzhen, Guangdong Province, China) using the high-throughput pyrosequencing technology developed by Solexa.


title: ppe degradome stem

source_name: young stems

value: young stems


title: Nanog null iPSC G5 -2

city: Cambridge

first: Brandi

middle: Nicole

last: Davis-Dusenbery

state: Massachusetts

address: 7 Divinity Ave

department: SCRB

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2 (v2.0.5) using default parameters. Reference files of the murine genome build mm10, as well as ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn, March 2013 build).
Differential expression was performed using Cuffdiff (v2.1.1) using default parameters and flags  —min-reps-for-js-test 2, GTF from iGenomes was supplied for transcript assembly.
Genome_build: mm10 : ensembl compatible from igenomes (NCBIM37) March 2013 update
Supplementary_files_format_and_content: The FPKM values calculated by cuffdiff are reported as tab-delimited files for each sample (FPKM.txt).  FPKMs calculated across replicates as well as confidence intervals are provided in the FPKM_matrix.txt file.

source_name: Nanog null iPSC clone G5

growth_protocol: Parental Nanog-/- mESCs were obtained from I. Chambers and were cultured on feeders in 2i + LIF conditions as previously described(Chambers et al., 2007;  Silva et al., 2008).  To obtain Nanog-/- MEFs, Nanog-/- mESCs were injected into blastocyst stage embryos.  At E12.5 MEFs were dissected out and sorted for constitutive GFP expression, indicating Nanog-/- genotype (Chambers et al., 2007).   For reprogramming, MEFs were transduced with retroviruses carrying murine Oct4, Sox2, Klf4, +/- c-Myc exactly as described by Ichida et al (Ichida et al., 2009).   On day 20 post-transduction with reprogramming transgenes, iPS colonies were picked and passaged onto feeders and cultured in 2i+LIF conditions with passaging every 5 days (Silva et al., 2008).  MEFs were grown in 10% FBS.

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturers’ directions. RNA quality was determined using BioAnalyzer (Aligent). RNA integrity numbers above 7.5 were deemed sufficiently high quality to proceed with library preparation
RNA sequencing libraries were generated from ~250 ng total RNA using the illumina TruSeq RNA kit v2, according to the manufacturers' directions. Libraries were sequenced at the Broad Institute genomics platform on a HiSeq 2500 or at the Harvard Northwest labs sequencing facility on a HiSeq 2000.

tag: genotype

value: Nanog -/-

tag: strain

tag: clone


title: Nanog null iPSC G5 -1

tag: cell type


title: PtoDC3000(pBAD::hrpL)_2

description: Biological replicate #2

data_processing:
The PtoDC3000, Pph1448A, Por1_6, Pjap, and Pla107 reads produced using a Illumina GA II.  The PsyB728A reads produced using a Illumina HiSeq system.
A GFF file was created for each genome by BLASTing transcripts to the genomic sequences and recoding gene coordinates for optimal hits.  This was done using an in-house script.  All genomes can be accessed and downloaded from NCBI.  Transcriptomes were constructed by NCBI’s gene prediction pipeline for PtoDC3000, PsyB728A, and Pph1448A.  Por1_6, Pla107, Pjap transcriptomes were constructed by JGI’s Integrated Microbial Genomes – Expert Review gene prediction pipeline.
GENEcounter was used to map RNA-seq reads from each strain to the matching genomic sequence.  Used GENEcounter default parameters.
GENEcounter was used to count the number of reads mapped to each gene for each genome and detect differential expression between HrpL and EV samples within each strain.
A slight modification in GENEcounter allowing for random seeding allowed us to bootstrap the normalization.  Bootstrap values were calculated for 100 random normalizations and differential expression analyses.  Median count values and bootstrapped differential expression occurrences are recorded in the final processed data txt files.
Genome_build: The genomes can be accessed using the following NCBI BIoProject IDs.  PtoDC3000 - PRJNA57967; PtoDC3000_draft - in-house; Pph1448A - PRJNA58099; PsyB728A - PRJNA57931; Por1_6 - PRJNA55447; Pjap - PRJNA33209; Pla107 - PRJNA33205.
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each gene in each sample

source_name: bacterial culture

extract_protocol:
RNA isolation was performed by using the RNeasy minikit (Qiagen). Isolated total RNA was treated with TURBO DNase (Ambion). Total RNA of each time point was pooled at 1/3 ratio. 10 μg of pooled RNA was depleted of 16S and 23S ribosomal RNA using RiboMinusTM (Invitrogen). Double stranded cDNA were prepared from ~ 1 μg ribosomal depleted RNA, using random primers (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pathovar

value: tomato

tag: plasmid


title: Nanog null iPSC G2 -2

source_name: Nanog null iPSC clone G2


title: PR_PR_infected [RNA-Seq]

description: RNA-seq

data_processing:
Debarcoding of the multiplex runs was performed using in house shell script
Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.
The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for PR and PR+P endothelial cells were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes

growth_protocol: HUVECs, passages 4-6, were cultured in MCDB-131 (VEC Technologies, Rensselaer, NY) with the addition of 10% fetal bovine serum (Omega Scientific, Tarzana, CA) that was stripped using 0.25% dextran coated charcoal (Sigma, St. Louis, MO).

treatment_protocol: Primary HUVECS were  infected at passage 4 with a lentivirus containing human PR, then split onto 10cm dishes and grown to confluence. Three days after they reached confluence they were treated with progesterone (100nM) for 4 hours, then harvested for the experiment.

value: endothelial cells

tag: treatment

value: PR infected


title: piPSC -1

source_name: partially reprogrammed iPSC

value: WT

value: piPSC


title: piPSC -2


title: Nanog null iPSC G2 -1


title: FLM.RNA

data_processing:
RNA-seq alignment using Tophat 2.0.4, Tuber_melanosporum_v1.0_annot.gff as library junction, allowing 2 mismatches and only uniquely aligned reads, filtering as default by Tophat
abundance counting using HTSeq version 0.5.4p3, using "union" mode for ambiguous reads (default)
calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by Tophat
calculate p-values with DESeq version 2.13
supplementary_files_format_and_content: Two files -- one for the genes (FB_FLM.RNA.txt), one for the repeats (FB_FLM.repeats.txt).
Genome_build: Tuber_melanosporum_v1.0

tag: tissue


title: PR_PR_infected

description: PR ChIP

value: PR


title: iPSC -1

source_name: induced pluripotent stem cell


title: WT ESC -2

source_name: embryonic stem cells

value: ESC


title: PR_Not_infected

description: IgG ChIP

value: Control

value: IgG


title: Nanog null ESC -1

source_name: Nanog null embryonic stem cells


title: TET-TEM1_OFF_REP2

city: Exeter

first: Steven

last: Bates

address: GP Building, Stocker Road

department: Biosciences

institute: University of Exeter

data_processing:
Base calling was with Illumina RTA and CASAVA 1.8.
Fastq files were demultiplexed using CASAVA 1.8.
Demultiplexed fastq files were aligned to the C. albicans genome using Tophat v 2.04.
The Bedtools package (multicov) was used to extract gene counts from the alignment vs GFF ORF features.
A statistical analysis of differential gene expression was conducted using DESeq 1.10.
Genome_build: C. albicans assembly 21 at The Candida Genome Database (http://www.candidagenome.org/) version A21-s02-m01-r24 (3/15/2012)
Supplementary_files_format_and_content: DESeq-group1_vs_group2.txt is a tab deliminated text file, comparing the replicates with TEM1 expression repressed and non-repressed.  The first lines include a legend for the headers.

organism: Candida albicans

source_name: Strain SBC170 (TET-TEM1)

extract_protocol:
RNA extractions were performed by mechanical lysis and purified using the RNeasy mini kit (Qiagen, Crawley, UK), with optional DNase treatment, according to manufacturer’s instructions.  RNA integrity and quantity was checked on a 2100 Bioanalyzer (Agilent, Wokingham, UK).
Sequencing libraries were prepared using the mRNA-Seq sample preparation kit from Illumina (Little Chesterford, UK).

tag: tem1 expression

value: OFF

tag: medium

value: YPD + 20µg/ml Doxycyline


title: WT ESC -1


title: ECM.BS

source_name: truffle ectomycorrhizal root tips

value: ectomycorrhizal root tips


title: TET-TEM1_ON_REP3

value: ON

value: YPD


title: TET-TEM1_ON_REP2


title: TET-TEM1_ON_REP1


title: DF1

status: Public on Dec 31 2013

first: Virginia

last: Savova

address: 450 Brookline Ave.

institute: DFCI

data_processing:
Illumina RTA
Botwie 2.0
Matlab
Excel
Supplementary_files_format_and_content: Series supplementary files include allelic bias calls per gene per sample

source_name: Lymphoblastoid cell line

extract_protocol:
Trizol, Poly(A)Purist™ MAG Kit AM1922
Parkhomchuk et. al. NAR 2009

value: Lymphoblastoid cell line

value: GM12878 clone DF1


title: DF2

value: GM12878 clone DF2


title: KBM7 bio rep2

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

description:
biological replicate 1
strand specific RNA-Seq using UTP/UNG

data_processing:
basecalling
alignment of both technical replicates (TopHat v2.0.3 using Bowtie 2.0.0.6)
Fusion candidate gene were identified using three software algorithms
deFuse(1) (version 0.6.1) and Tophat-Fusion (2) (version 2.0.8) were used with default parameters, for FusionMap (3) (release 2013-02-01) parameter "NonCanonicalSpliceJuncitonPenalty" was set to 2
To reduce false positives only those fusion candidates were validated that could be detected with at least 2 fusion detection software tools
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including the raw output of the fusion transcript detection tools (bio rep2)

growth_protocol: KBM7 cell line was cultured according to standard cell culture procedures

extract_protocol:
Total RNA was extracted using TRIZol (Sigma) and ribosomal RNAs were depleted using RiboZero (Epicentre).
Libraries were constructed using Illumina mRNA library construction KIT with modifications according to: Sultan et al. BBRC 2012 (PMID:22609201)

tag: ploidy

value: haploid

tag: cell line


title: KBM7 bio rep1 tech rep1

description:
technical replicate 1
strand specific RNA-Seq using tagged hexamers

data_processing: basecalling, alignment of both technical replicates (TopHat v2.0.3 using Bowtie 2.0.0.6), genome build: hg19, processed data files format and content: tab delimited text file of RPKM counts (KBM7_RefSeq_RPKM)

extract_protocol:
Total RNA was extracted using TRIZol (Sigma) and ribosomal RNAs were depleted using RiboZero (Epicentre).
Libraries were constructed using the ScriptSeq v1 (Epicentre) KIT.


title: KBM7 bio rep1 tech rep2

description:
technical replicate 2
strand specific RNA-Seq using tagged hexamers


title: shoots

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

institute: Chinese Acadamy of agricultural science

data_processing:
After removing reads with adaptors, unknown nucleotides larger than 10%, and low quality (more than half of the bases’ quality are less than 5), all clean reads were aligned to the genome of S. propinquum (downloaded from ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Sbicolor/assembly) using SOAP with mismatchs no more than 5 bases.
The gene expression level was measured as numbers of reads per kilobase of exon region per million mapped reads (RPKM). The RPKM method can eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression. Therefore, we analyzed the most differentially expressed genes with a log2 RPKM ratio >2 or <-2 and FDR less than 0.001.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Sorghum propinquum

source_name: shoots

growth_protocol: A S. propinquum vegetative clone (unnamed accession) with abundant tillering and strong rhizomes cultured in the greenhouse was used in this experiment. Two organs, shoots and rhizomes, at active tillering stage were collected and flash frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: shoots

tag: developmental stage

value: active tillering stage


title: Nanog null ESC -2

institute: Harvard University

value: Nanog -/-

tag: passage


title: 2nd_tips_rna_seq

value: iPSC


title: Nucleus_RNA_repeat2

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1
The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: HelaS3 cells

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer’s instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS™ Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus™ Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.
Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3’ to 5’ exo- (NEB) to add an “A” base at the 3’end of the DNA fragments, and finally ligated to adapters with a “T” overhang.  Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 × 100 bp paired-end).

value: tumor cells

tag: library

value: nucleus RNA


title: rhizomes

source_name: rhizomes

value: rhizomes


title: Cyto_RNA_repeat1

value: cyto RNA


title: Cyto_RNA_repeat2


title: PR_PR_infected+Prog [RNA-Seq]

description: RNA-seq

source_name: primary HUVECs

value: endothelial cells

tag: passage nr.

value: PR infected + Progesterone


title: TET-TEM1_OFF_REP3

value: OFF

value: YPD + 20µg/ml Doxycyline


title: polyA_RNA_repeat1

value: polyA RNA


title: polyA_RNA_repeat2


title: TET-TEM1_OFF_REP1


title: Nucleus_RNA_repeat1


title: 4sU_RNA_repeat2

value: 4sU RNA


title: CG-SH  gDNA

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

country: Canada

institute: University of Montreal

data_processing:
Illumina Casava1.7 software used for basecalling.
Eland2 was used (through Casava 1.7) for mapping to the human reference genome
Variants were called usign Samtools with a quality filter of 20 and a minimum number of reads equal or greater than 3
Genome Build: hg19
supplementary files format and content: Sequence variants in BCF format

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in IMDM medium with 10% FBS, penicillin (100 U/ml) and streptomycin (100 µg/ml) supplemented with cytokines (human stem cell factor (H-SCF) (100 ng/ml), interleukin 3 (IL-3) (20 ng/ml), granulocyte colony-stimulating factor (G-CSF) (20 ng/ml)

extract_protocol: gDNA was extracted from DNAzol (Invitrogen) according to manufacturers protocol.  gDNA was used to created paired-end libraries using Illumina Truseq V3 kit according to manufacturers protocol.

treatment_protocol: Cells were grown in exponential phase before 1x10^7 cells were collected and placed into either DNAzol or Trizol in order to extract gDNA or RNA respectively

value: CG-SH


title: KW1407-MEA-Control 4 days

city: Vancouver

first: Ye

last: Wang

state: BC

department: Department of Wood Science

institute: University of British Columbia

data_processing:
BWA 0.5.7
Sequenced reads were trimmed for adaptor sequence, and low-quality base pairs, then mapped to Gc reference genome using CLC genomics workbench, v5.0.1
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using CLC genomics workbench. In short, the number of reads falling in the exons of a gene were counted and normalized by the size of the total exon length for that gene, and by the size of the library (or total mapped reads)
Genome_build: Gc reference genome ACXQ00000000.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Leptographium clavigerum

source_name: fungal mycelium

growth_protocol: Inoculum incubated for a week and their spores harvested and germinated on 1% OMEA plates for 3 days before transferred to treatment plates

extract_protocol:
Mycelium was harvested and flash frozen with liquid nitrogen, grinded with mortar & pestle and RNA was extracted using the Qiagen RNA easy mini kit
Polyadenylated (PolyA+) RNA was purified using the uMACS mRNA isolation kit, with on-column DNaseI-treatment. Double-stranded cDNA was synthesized from the purified polyA+RNA using the Superscript Double-Stranded cDNA Synthesis kit. cDNA was fragmented by sonication, purified, then subjected to end-repair and phosphorylation. Picogreen quantification was performed to determine the amount of Illumina PE adapters used in the next step of adapter ligation reaction. The adapter-ligated products were purified then PCR-amplified with Phusion DNA Polymerase using Illumina’s PE primer set. PCR product of desired size range was gel purified.

treatment_protocol: Samples transferred onto MEA were supplied with either 300ul heptane or 200ul (+)-limonene added to filter paper strips (placed on the lid); samples transferred onto YNB were supplied with 200ul terpene added to filter paper strips (placed on the lid). Samples transferred to YNB and Mannose/Oleic Acid/Olive Oil, were added directly the the mixed media.

value: MEA-Control

tag: time

value: 4 d


title: KW1407-YNB-Oleic Acid 5 days

value: YNB-Oleic acid

value: 5 d