title: hMeDIP-Seq (JBP-1)

city: Irvine

first: Xueguang

last: Sun

state: CA

address: 17062 Murphy Ave

institute: zymo research corp

data_processing:
RRHP reads was aligned back to hg18 assembly using bowtie 0.12.8 and its default parameters with --best. Aligned reads with CCGG tag at 5’ end were counted.
RRBS reads was aligned back to hg 18 assembly using Bismark with default parameter.
hMeDIP-Seq (JBP-1) reads was aligned back hg18 assembly using bowtie 0.12.8 and its default parameters with --best, and analyzed for enrichment peak calling in MACS.
Genome_build: hg18
Supplementary_files_format_and_content: bed file and wig file

source_name: hMeDIP-Seq (JBP-1)

extract_protocol:
gDNA from human male cerebellum was purified via phenol::chloroform extraction
gDNA was digested by MspI, the resulting fragment was ligated with specifically designed RRHP adapater and then subjected with the second round MspI digestion, followed by a limited cycles of amplifcation

value: brain


title: NTHi 86-028NPrpsL∆fur∆hrrF3' bio rep 1

status: Public on Aug 26 2014

type: SRA

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

country: USA

institute: The Research Institute at Nationwide Children's Hospital

library_source: transcriptomic

data_processing:
Base calls and initial quality scoring of data produced by the Illumina HiSeq2000 were performed using Illumina RTA 1.12.4
Base call files were converted to fastq files using Illumina CASAVA 1.8.2
Read alignment was performed using Burrows-Wheelr Aligner v0.78 allowing up to four mismatches with multiple aligned reads counted only once
Processing the read alignemnt file was done using samtools v0.1.19 with default parameters
Gene expression measurement was determiend using NGSUtlis v.0.55 with default parameters
Differential gene expression analysis was performed using edgeR v3.6.1
Genome_build: NC_007146
Supplementary_files_format_and_content: Processed data for all strains is contained in a matrix in an excel spreadsheet. For each gene expression comparision there is logCounts/million reads, fold change calculation of gene expression, an FDR calculation, and a P-value for the associated comparison. Additionally for each open reading frame and RNA annotation there are raw counts in each strain and their associated biological replicate used in comparison.

molecule: total RNA

organism: Haemophilus influenzae

source_name: Bacterial cells

growth_protocol: All strains were grown in an RPMI-based defined iron source medium, DIS. Strains were plated onto Chocolate II agar plates (Fisher Scientific) overnight. Cells from plates were diluted into DIS medium for the purpose of iron depletion and grown statically at 37˚C, 5% CO2 for 12-13 hours. Iron-depleted cells were transferred to DIS supplemented with 10µg human hemoglobin/ml and grown at 37˚C with shaking at 50rpm to mid-logarithmic phase.

extract_protocol:
Total RNA was extracted via hot phenol once bacterial cultures were in mid-logarithmic phase.
cDNA libraries were prepared using the Illumina TruSeq RNA sample prep kit according to the manufacturers protocol.

tag: strain background

tag: strain type

value: Nontypeable Haemophilus influenzae (NTHi)

tag: genotype/variation

value: isogenic fur mutant of 86-028NPrpsL also containing a deletion of only the 3' portion of hrrF


title: NTHi 86-028NPrpsL∆fur∆hrrF3' bio rep 3


title: Shoot-Salinity stress

status: Public on Aug 27 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Chickpea genome v1.0 (http://nipgr.res.in/CGAP/download/genome_sequencing/genome_sequence/)
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

organism: Cicer arietinum

source_name: 10-day-old seedlings

growth_protocol: Seedlings were grown in a culture room

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

treatment_protocol: Root and shoot tissues of 10-day-old seedlings were subjected to control (in water), desiccation (on folds of tissue paper), salinity (in 150 mM NaCl solution) and cold (in water at 4 ± 1°C) stress treatments for 5 h

tag: genotype

tag: age

value: 10 days

tag: tissue

value: shoot


title: E13_5_WT1

city: Montpellier

first: Brigitte

last: Boizet-Bonhoure

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: CNRS

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 1.5.15) and Real-Time Analysis component (RTA 1.13.48).
Demultiplexing, alignment and RNA counting was performed using CASAVA 1.8.2 (Illumina). Alignment was made with eland_rna on the mm9 version of mouse genome and on several contaminants (the ribosomal RNA sequences 28S, Rn18s and Rn5s, the mitochondrial chromosome, the PhiX genome and the Illumina adaptors). The transcript annotation was retrieved from UCSC (refFlat file) on January 15, 2012.
Differentially expressed genes were identified using the Bioconductor package edgeR (v2.6.2). Genes with less than 15 reads (cumulating the two analysed samples) were filtered and thus removed from the analysis. Data were normalized using  Upper Quartile normalization factors. Genes with adjusted p-value less than 1% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Table with 5 columns for gene description. The next columns correspond to the normalized abundance measurements (Upper Quartile normalization using edgeR statistical package) for each sample

organism: Mus musculus

extract_protocol:
E13.5  gonads were dissected from staged embryos from 6 different WT and L/H-Pgds-/- littermates, were rapidly frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-Seq libraries were prepared the 'TruSeq RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

tag: strain

value: male gonad

value: wild type


title: NTHi 86-028NPrpsL∆fur∆hrrF3' bio rep 2


title: NTHi 86-028NPrpsL∆fur∆hrrF bio rep 3

value: isogenic fur mutant of 86-028NPrpsL also containing a full deletion of hrrF


title: NTHi 86-028NPrpsL∆fur∆hrrF bio rep 2


title: NTHi 86-028NPrpsL∆fur bio rep 3

value: isogenic fur mutant of 86-028NPrpsL


title: Foc1_48h

city: Shenzhen

first: Fan

middle: ding

last: ding

address: yantian shashen Road

country: China

institute: EasyATCG

description: infect Musa acuminata 48 hour

data_processing:
Used Fusarium oxysporum f. sp. cubense tropical race 1 and 4 genomes, PRJNA174275 and PRJNA174274, respectively. Sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 10 -I 10000  --segment-mismatches 3  --segment-length 24 --solexa1.3-quals
Cnnnnn identifiers found in the .wig files represent contigs.

organism: Fusarium oxysporum f. sp. cubense

extract_protocol: Total RNA is extracted by TRIzol Reagent. For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: tropical race

tag: time point

tag: infection

value: Musa acuminata


title: NTHi 86-028NPrpsL∆fur bio rep 1


title: NTHi 86-028NPrpsL bio rep 2

value: rpsL mutant of 86-028NP


title: NTHi 86-028NPrpsL bio rep 1


title: NTHi 86-028NPrpsL bio rep 3


title: NTHi 86-028NPrpsL∆fur bio rep 2


title: RRHP-Liver-Cancer

library_source: genomic

data_processing:
Library strategy: RRHP-Seq
RRHP reads were aligned back to hg19 assembly using bowtie 0.12.8 and its default parameters with --best. Aligned reads with CCGG tag at 5’ end were counted.
Genome_build: hg19
Supplementary_files_format_and_content: bed file

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver Cancer tissue

extract_protocol:
gDNA was purified via phenol::chloroform extraction
gDNA was digested by MspI, the resulting fragment was ligated with specifically designed RRHP adapater and then subjected with the second round MspI digestion, followed by a limited cycles of amplifcation

value: Liver

tag: retriction enzyme

value: MspI


title: RRHP-Liver-Normal

source_name: Liver Cancer adjacent normal tissue


title: ELT-2 RNAi Normoxia

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 240 E. Huron St.

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

data_processing:
After sequencing, the reads were demultiplexed by removing adapters and filtered by censoring the reads with poor quality.
Reads were aligned to the C. elegans reference genome (ce10 from UCSC) using TopHat (v2.0.8b) in conjunction with the ce10 gene annotation data obtained from UCSC.
After alignment, transcripts were quantified and a differential expression analysis was performed using Cufflinks (v2.1.1), which calculates gene expression as RPKM values.
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data file (.xls) reports RPKM values.

organism: Caenorhabditis elegans

source_name: C. elegans whole RNA extract

growth_protocol: Synchronized C. elegans were grown until day 1 of adulthood and then exposed to 36hrs of transient hypoxia or normoxia

extract_protocol:
RNA was isolated using TriZol extraction and isopropanol precipitation
RNA was evaluated for integrity using an Agilent Bioanalyzer 2100 and 100 bp paired-end cDNA sequencing libraries were prepared separately for each sample using indexed adapters.  All four samples were multiplexed onto a single lane of an Illumina HiSeq2000.

treatment_protocol: Animals were exposed to 36h 0.5% O2/bal N2 in an airthight chamber at room temperature

tag: developmental stage

value: adult

tag: stress

value: Normoxia

tag: media

value: NGM modified RNAi media

tag: treatment

value: fed ELT-2 RNAi

tag: temperature


title: RRHP-HpaII

description: RRHP library

source_name: RRHP-HpaII

value: brain

value: HpaII


title: RRHP-MspI-3

description: RRHP library


title: RRHP-MspI-2

description: RRHP library


title: RRHP-(- βgt control )

description: RRHP library

source_name: RRHP-(- βgt control )


title: RRHP-Breast-Cancer

source_name: Breast Cancer tissue

value: Breast


title: RRHP-MspI-1

description: RRHP library


title: RRHP-Breast-Normal

source_name: Breast Cancer adjacent normal tissue


title: adaptation response nitrite (TestAR)

status: Public on Aug 25 2014

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL, Department of Microbiology

country: Germany

institute: Technical University Munich

description:
pooled samples were sequenced on six lanes (raw files 1-6)  (see Library construction protocol)
nitriteadaptation_counts_DE.txt

data_processing:
For each sample, *_n.csfasta and *_n.qual files (n=01-06) from the 3 or 6 lanes were merged into single *.csfasta and *.qual files for further analysis.
*.csfasta and *.qual files were converted to fastq using Convert (version 1.0.0) in Galaxy.
*.fastq files were mapped to the genome of S. Typhimurium 14028 (chromosome and plasmid) using Map with Bowtie for SOLiD (version 1.1.2) with default settings in Galaxy.
Unmapped reads were filtered using SAM Tools' Filter SAM (version 1.0.0) in Galaxy.
SAM format was converted to BAM format using SAM Tools' SAM-to-BAM (version 1.1.2) in Galaxy.
The counts of each gene (number of reads overlapping a gene on the same strand) were calculated in Artemis 15.0.0 based on the GenBank file of the reference genome. Raw counts of all protein-coding genes were normalized to the total number of reads mapping to protein-coding genes in the corresponding library, and are presented as counts per million (cpm) in the processed data files.
Differential gene expression analysis was performed by processing raw counts of all protein-coding genes (according to the .ptt files) with edgeR in R (version 3.0.2). Genes with less than 10 counts per million (cpm) in both conditions were filtered before TMM (trimmed mean of M values) normalization was applied. The exact test function was used with a common dispersion 0.1, as suggested for genetically identical model organisms in the edgeR user’s guide (revised version from 4 May 2012).
Genes with BH (Benjamini and Hochberg) adjusted p-values < 0.05 were selected as differentially expressed genes in acidified NaNO2 treated cultures compared to control cultures.
Genome_build: NC_016856.1 (chromosome), NC_016855.1 (plasmid)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and normalized counts (cpm) of the control and acidified NaNO2 treated samples for each protein-coding gene and log2 fold-changes (acidified NaNO2 treated vs control) with corresponding BH adjusted p-values from the edgeR analysis

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial culture

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) and RNeasy Mini Kit (Qiagen). Briefly, RNA was extracted with TriReagent, and 90 µg of TRI Reagent-extracted RNA was further subjected to the column-based purification steps of the RNeasy Mini Kit. 16S and 23S ribosomal RNA (rRNA) was removed from 5 µg total RNA using the MicrobExpress Kit (Ambion). In addition to the capture oligonucleotide mix supplied with the kit, two additional oligonucleotides targeting fragments of the S. Typhimurium 23S rRNA (5’-xCCTCGGGGTACTTAGATGTTTCA-3’, 5’-xGTCGGTTCGGTCCTCCAGTTAGT-3’; x = sequence needed for hybridization to Oligo MagBeads) were added (2 µl of a 10 µM mix, corresponding to 20 pmol of each probe) and annealing was performed for 30 min. The mRNA enriched sample was then treated with the TURBO DNA-free Kit (Ambion) to remove residual DNA and concentrated by ethanol precipitation.
The sequencing library was constructed with the SOLiD Total RNA-Seq Kit and the SOLiD Transcriptome Multiplexing Kit (Applied Biosystems). Briefly, 500 ng RNA was fragmented with RNase III for 9 min and cleaned up with the miRNeasy Mini Kit (Qiagen). Further steps were performed according to the SOLiD manual. Sequencing on the SOLiD 5500xl system was conducted by CeGaT GmbH (Tübingen, Germany). Samples of the adaptive and shock response were sequenced in independent runs. Differentially barcoded libraries derived from acidified NaNO2 treated and control samples were pooled and sequenced on three (shock response) or six lanes (adaptive response) of one SOLiD slide, along with four additional libraries that do not fall within the scope of this study.

treatment_protocol: After the indicated time or after reaching the final OD600, 20 ml of the cultures were collected by centrifugation (8 min, 4186 × g, room temperature) and the cell pellets were shock frozen immediately in liquid nitrogen. The cell pellets were stored at -80 °C until further processing.

tag: growth protocol

value: A 50 ml culture in LB pH 5.5 (adjusted with 90% lactic acid (Merck) prior to autoclaving) was grown with shaking (160 rpm) at 24°C to OD600 = 0.80-0.85. 150 mg/l NaNO2 were added, and the culture was further grown to OD600 = 1.45-1.55.

tag: culture type

value: culture treated with 150 mg/l NaNO2 at OD600 = 0.85, cells were harvested at 1.46


title: adaptation response control (CtrlAR)

value: A 50 ml culture in LB pH 5.5 (adjusted with 90% lactic acid (Merck) prior to autoclaving) was grown with shaking (160 rpm) at 24°C to OD600 = 1.45-1.55.

value: control culture, cells were harvested at OD600 = 1.47


title: shock response control (CtrlSR)

description:
pooled samples were sequenced on three lanes (raw files 1-3) (see Library construction protocol)
nitriteshock_counts_DE.txt

value: A 150 ml culture in LB pH 5.5 (adjusted with 90% lactic acid (Merck) prior to autoclaving) was grown with shaking (160 rpm) at 24°C. At OD600 = 0.80-0.85, 50 ml of the culture was transferred to a new flask and further incubated for 10 min with shaking (160 rpm) at 24°C.

value: control culture


title: SNM8_WT_pol_WT_MMR

city: Research Triangle Park

first: Scott

middle: Alexander

last: Lujan

state: NC

address: 101 T.W. Alexander Drive

department: LMG/LSB

institute: NIEHS

data_processing:
Basecalls performed using CASAVA version 1.8
DNA-seq reads aligned using CLC Bio Genomics Workbench version 5.1.5
Variant calls were performed using a custom CLC Bio plugin and filtered using a custom Excel-based tool
MNase-seq read pairs aligned using bowtie 0.12.8 (-m1 -v2 -X1000)
Aligned MNase-seq pairs were filtered to exclude those originating from fragments smaller than 120 or greater than 180 nt
Nucleosome postions were determined using NOrMAL (s_max 200, v_d 0.1, v_max 30)
Genome_build: L03 reference v2 (see supplementary files)
Supplementary_files_format_and_content: tab-delimited text files contain nucleosome positions as well as variant calls for all samples

organism: Saccharomyces cerevisiae

source_name: whole cells

growth_protocol: 30 bottleneck passages were performed by streaking each strain for single cell-derived colonies on complete solid media enriched with adenine. After bottlenecks 0, 1, 4, 10, 16, 22, and 30, each sample was split into three parts: one part was used to inoculate a 1 mL overnight culture and then a freezer stock; one part was re-streaked to initiate the next passage; the last inoculated a patch on solid media, which was replicated on selective media to test for all marker genes, mating type (as a proxy for ploidy), and ability to metabolize glycerol. Accumulation was stopped no later than passage 30, or earlier if most colonies in the streak were small, indicative of accumulation of multiple mutations affecting growth rate, which could skew generation estimates and mutation rate calculations.

extract_protocol:
Cells were harvested from 10 mL cultures. Genomic DNA was isolated via the Epicentre MasterPure Yeast DNA Purification Kit (MPY80200), including the optional RNase A treatment step.
The DNA libraries were prepared according to Illumina TruSeqTM DNA Sample Prep protocol. Total cellular DNA was fragmented to sizes between 200 and 800 bp by using Covaris S2 sonicator according to the Illumina TruSeq DNA protocol and then libraries were prepared using Illumina TruSeqTM DNA Sample Prep Kit on Tecan Freedom EVO 150 Automated Liquid Handling System. Libraries were size selected for insert fragments around 300 base pairs using Pippin Prep automatic DNA size selection system (Sage Science). Libraries were analyzed and quantified using a Qubit (fluorometric detection – Invitrogen) and Experion automated electrophoresis system (Biorad). Quantified libraries were diluted to 15 nM concentration and pooled for sequencing. The Paired-End sequencing (2 × 100 cycles) was performed on HiSeq2000 sequencers (Illumina).

tag: pol genotype

value: WT

tag: mmr genotype

tag: passages


title: TAK280_pol3-L612M_MSH2-


title: NTHi 86-028NPrpsL∆fur∆hrrF bio rep 1

tag: strain background

tag: strain type

value: Nontypeable Haemophilus influenzae (NTHi)

tag: genotype/variation

value: isogenic fur mutant of 86-028NPrpsL also containing a full deletion of hrrF


title: TAK215_pol3-L612M_MSH2-


title: TAK162_pol3-L612M_MSH2-


title: TAK163_pol3-L612M_MSH2-


title: TAK142_pol3-L612M_WT_MMR


title: TAK143_pol3-L612M_WT_MMR


title: TAK134_pol3-L612M_WT_MMR


title: TAK135_pol3-L612M_WT_MMR


title: TAK133_pol3-L612M_WT_MMR


title: TAK131_pol3-L612M_WT_MMR


title: TAK130_pol3-L612M_WT_MMR


title: TAK132_pol3-L612M_WT_MMR


title: TAK077_pol3-L612M_WT_MMR


title: TAK206_pol2-M644G_MSH3-_MSH6-

value: msh3- msh6-


title: TAK076_pol3-L612M_WT_MMR


title: TAK279_pol3-L612M_MSH2-


title: TAK069_pol2-M644G_MSH3-_MSH6-


title: TAK068_pol2-M644G_MSH3-_MSH6-


title: TAK217_pol2-M644G_MSH2-


title: shock response nitrite (TestSR)

description:
pooled samples were sequenced on three lanes (raw files 1-3)  (see Library construction protocol)
nitriteshock_counts_DE.txt

tag: strain

value: A 150 ml culture in LB pH 5.5 (adjusted with 90% lactic acid (Merck) prior to autoclaving) was grown with shaking (160 rpm) at 24°C. At OD600 = 0.80-0.85, 50 ml of the culture was transferred to a new flask and 150 mg/l NaNO2 was added. The culture was further incubated for 10 min with shaking (160 rpm) at 24°C .

value: culture treated with 150 mg/l NaNO2 at OD600 = 0.83


title: TAK180_pol2-M644G_MSH2-


title: TAK281_pol3-L612M_MSH2-


title: TAK152_pol2-M644G_MSH2-


title: TAK141_pol2-M644G_WT_MMR


title: TAK151_pol2-M644G_MSH2-


title: TAK170_pol2-M644G_MSH2-


title: TAK140_pol2-M644G_WT_MMR


title: TAK166_pol2-M644G_MSH2-


title: TAK129_pol2-M644G_WT_MMR


title: TAK126_pol2-M644G_WT_MMR


title: TAK125_pol2-M644G_WT_MMR


title: TAK127_pol2-M644G_WT_MMR


title: TAK128_pol2-M644G_WT_MMR


title: TAK075_pol2-M644G_WT_MMR


title: TAK271_pol1-L868M_MSH2-


title: TAK074_pol2-M644G_WT_MMR


title: TAK272_pol1-L868M_MSH2-


title: TAK159_pol2-M644G_MSH3-_MSH6-


title: TAK273_pol1-L868M_MSH2-


title: TAK264_pol1-L868M_MSH2-


title: TAK124_pol2-M644G_WT_MMR


title: TAK150_pol1-L868M_MSH2-


title: TAK199_pol1-L868M_MSH2-


title: TAK139_pol1-L868M_WT_MMR


title: TAK216_pol1-L868M_MSH2-


title: TAK269_pol1-L868M_MSH2-


title: T_P0_WT_2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using TopHat v2.0.6 (with Bowtie 2.0.5.0) using default settings.
All samples were modeled using cuffdiff with options -p 6 --no-update-check and the UCSC mm10 genes.gtf file from the Illumina iGenomes site
Raw cuffdiff output files were loaded into the R package cummeRbund
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: fpkm-replicates-WT.txt: FPKM abundance measurements for WT samples.

molecule: polyA RNA

extract_protocol:
Cortical dissections were performed under RNAse free conditions on ice in PBS or HBSS. Cortices were either used immediately or stored at -80C until use. Isolated neocortices were lysed in polysome extraction buffer (PEB: 20mM Tris-HCl, 100mM KCl, 10mM MgCl2, 0.3% Igepal Sigma-Aldrich #CA-630) supplemented with EDTA free protease inhibitor (Santa Cruz Biotechnology #sc-29131) RNAase inhibitor (Invitrogen #100000840), 20mM DTT (Invitrogen #NP0009), and 0.1mg/ml cycloheximide (Santa Cruz Biotechnology #sc-3508A) immediately before use, for 10 minutes on ice with occasional pipetting to mix and homogenize tissue. Then, lysate was cleared by centrifugation (Sorvall Biofuge fresco) for 10 minutes at 4C. Total lysate RNA level was determined on spectrophotometer (NanoDrop ND-1000). 250ug or 50ug total RNA weight was loaded onto 11ml or 2ml columns respectively. Ultracentrifugation for 11ml tubes was performed at 39,000 rpm for 90 minutes (Sorvall Discovery 100 with SW41 rotor and buckets) or for 2ml tubes at 39,000rpm for 50 minutes (Sorvall Discovery M120SE with S-55-S rotor and buckets). Then, samples were immediately placed in tube piercer (Brandel #621140007) connected to a syringe pump (Brandel syringe pump) and fractionated into 14 equal volume fractions while recording the absorbance (Brandel UA-6 absorbance detector). Fractions were processed for RNA by Trizol-LS extraction according to manufacturer’s protocol. Equal volumes of RNA isolated from polysome fractions 4,5,6 and 7 were pooled together for 40S-60S-80S region RNA. Similarly, equal volumes of RNA extracted from polysome fractions 9,10,11 and 12 were pooled together for polysome RNA.
Sequencing libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 according to the manufacturer's protocol. Libraries were quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems), then diluted and symmetrically pooled. We performed 2x100bp paired-end sequencing on the Illumina Hiseq2500 in rapid run mode.

tag: tissue

value: brain neocortex

tag: age

tag: rna fraction

value: Total


title: TAK175_pol1-L868M_MSH2-


title: TAK149_pol1-L868M_MSH2-


title: T_P0_WT_1


title: TAK121_pol1-L868M_WT_MMR


title: TAK123_pol1-L868M_WT_MMR


title: T_E13_WT_0


title: T_E13_WT_1


title: P_P0_WT_2

value: Polysome


title: TAK119_pol1-L868M_WT_MMR


title: P_P0_WT_1


title: P_P0_WT_0


title: TAK118_pol1-L868M_WT_MMR


title: P_E13_WT_1


title: TAK073_pol1-L868M_WT_MMR


title: P_E13_WT_0


title: M_P0_WT_1

value: Monosome


title: M_P0_WT_0


title: TAK138_pol1-L868M_WT_MMR


title: TAK266_WT_pol_MSH2-


title: TAK072_pol1-L868M_WT_MMR


title: P493-6 treated with doxycycline(Myc Low)

city: La Jolla

first: Jonathan

middle: Ross

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

data_processing:
Basecalls performed using CASAVA version v1.8.2
Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20
Aligned with STAR 2.3.0 to HG19 with Gencode v19 junctions followed by generation of a new genome using the detected junctions and realignment(2 pass alignment)
Samtools 0.1.19-44428cd to make a bam, sort, index
Raw counts were generated using htseq_count 0.6.1 using the UCSC HG19 known gene transcripts from Illumina iGenomes
edgeR 3.2.4 in R 3.1.0 were used to normalize counts between samples and to make comparisons between groups.
Genome_build: HG19
Supplementary_files_format_and_content: Gene by sample normalized counts with comparisons between sample groups as additional columns(log2FC, p.value, and BH FDR corrected q.values)

source_name: B cell line

growth_protocol: P493-6 cells grown in RPMI-1640 supplemented with 10% tetracycline free FBS and 1x Pen/Strep/L-Glutamine supplement

extract_protocol:
RNA was extracted using a Maxwell 16 instrument using simplyRNA LEV reagents
Life Technology Ribominus kits were used to remove rRNA from total RNA samples. 1 ug total RNA input was used for each sample. RNAseq libraries were prepared from ribo-depleted RNA samples using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s protocols

treatment_protocol: Cells were seeded in 4mL of media at a density of 100k/mL and treated with compounds immediately after seeding.  Cells were grown for 48 hours

tag: cell line

tag: cell type

value: B cells

tag: doxycycline treatment

value: TRUE

tag: kj-pyr-9 treatment

value: FALSE

tag: control


title: M_E13_WT_0


title: P493-6 treated with KJ-Pyr-9 and doxycycline


title: P493-6 (Myc High/No treatment control)


title: M_E13_WT_1


title: T_P0_WT_0


title: TAK259_WT_pol_MSH2-


title: HGDP00967

city: Stanford

first: Carlos

middle: D.

last: Bustamante

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Basecalls performed using Illumina CASAVA version 1.4
Reads were mapped to the human reference genome (hg19) using bowtie-2.0.0 and tophat-2.0.4 split read mapping algorithms using the “-b2-very-sensitive” parameters
Reads were filtered to include only properly paired reads.
Transcript level quantification was performed with cufflinks-2.0.2 to produce gene and transcript FPKM estimates
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for gene and isoform FPKM values for each sample

source_name: Lymphoblast cell line

extract_protocol:
Total RNA was extracted from lymphoblastoid using an RNeasy Mini Kit (Qiagen). mRNAs were purified using magnetic oligo-dT beads and randomly fragmented to 300-400 nucleotides in length.
First-strand cDNA synthesis was performed using random hexamers and reverse transcriptase. This was followed second-strand cDNA synthesis with dUTP via the dUTP strand-marking protocol. Illumina TruSeq adaptors were ligated to the ends of the double-stranded cDNA fragments followed by digestion with uracil N-glycosylase (UNG) to remove second strand cDNA. A 300-400 bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. Libraries were paired-end sequenced with an average insert size of ~200bp

value: Lymphoblast cells

tag: population

value: Yakut

tag: Sex

value: Female


title: HGDP00959


title: HGDP00964

value: Male


title: HGDP00955


title: HGDP00950


title: TAK148_WT_pol_MSH2-

tag: pol genotype

value: WT


title: HGDP01036

value: San


title: HGDP00948


title: HGDP01029


title: M_P0_WT_2


title: TAK260_WT_pol_MSH2-

tag: mmr genotype


title: P493-6 treated with KJ-Pyr-9


title: HGDP00258

value: Pathan


title: HGDP00247


title: HGDP00992


title: HGDP00222


title: HGDP00239


title: TAK262_WT_pol_MSH2-

tag: passages


title: HGDP00232


title: TAK136_WT_pol_WT_MMR


title: TAK117_WT_pol_WT_MMR


title: TAK137_WT_pol_WT_MMR


title: HGDP00987


title: HGDP00237


title: HGDP00213


title: TAK113_WT_pol_WT_MMR


title: TAK258_WT_pol_MSH2-


title: TAK116_WT_pol_WT_MMR


title: TAK147_WT_pol_MSH2-


title: HGDP01275

value: Mozabite


title: TAK114_WT_pol_WT_MMR


title: HGDP01277


title: TAK112_WT_pol_WT_MMR


title: MPP_R3

city: Heidelberg

first: Christoph

last: Plass

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: bisulfite converted genomic DNA

data_processing:
Basecalling was performed using Ilumina Real-Time Analysis (RTA) Software 1.13.48.
Sequencing reads were trimmed for adapter sequence (SeqPrep v0.4 ) and then mapped with BWA (bwa-0.6.1-tpx) with default parameters except the quality threshold for read trimming ( -q) of 20 and the Smith-Waterman for the unmapped mate disabled (-s).
Duplicate reads were removed using Picard (version 1.61) and reads with alignment scores less than 1 were filtered before subsequent analysis.
At each cytosine position, reads that maintain the cytosine status were considered methylated, and the reads that have cytosine converted to thymine were considered unmethylated.
Only bases with Phred-scaled quality score of ≥20 were considered. The first 9 bp of the second read and last 9 bp before the adapter in the first read were excluded from methylation calling.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CpG coordinates, the numbers of methylated cytosines and the coverage at the CpG postion, as well as smoothed methylation level estimates using bsseq (version 0.8.0; default parameters)

source_name: primary murine hematopoietic multipotent progenitor cells

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA Micro Kit (Qiagen, Germany) and polyacryl precipitation carrier (Molecular Research Center Inc., Cincinnati, OH, USA).
Tagmentation-based whole-genome bisulfite sequencing (TWGBS) was performed as recently published (Wang et al., Nat. Prot., 2013). We used 8-30 ng genomic mouse DNA as input.


title: TAK115_WT_pol_WT_MMR


title: MPP_R2

description: bisulfite converted genomic DNA


title: HGDP01274


title: HGDP01264


title: TAK071_WT_pol_WT_MMR


title: MPP_R1

description: bisulfite converted genomic DNA


title: HGDP01262


title: Sep1_Bort_ChIPSeq

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: data are an aggregate of two biological experiments

data_processing:
Base calls from Illumina MiSeq (FASTQ files)
Data from all biological replicates were clubbed into one FASTQ file
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v1.16) using Bowtie2_2.1.0 (Langmead et al., 2009)
The resulting SAM file was processed to BAM file and all duplicates were removed using samtools v0.1.18 (Li et al., 2009).
Peak detection was conducted by HOMER tools using default settings (Heinz et al., 2010). The Untagged ChIP-Seq experiment was used as the control dataset for finding peaks.
Genome_build: Schizosaccharomyces_pombe.ASM294v1.16.dna.toplevel.fa (Reference sequence, ftp://ftp.ensemblgenomes.org/pub/fungi/release-16/fasta/schizosaccharomyces_pombe/dna/); Schizosaccharomyces_pombe.ASM294v1.16; .fa - genome file, .fa.fai - genome index, .gtf - annotation files
Supplementary_files_format_and_content: Peaks File (.txt): Contains Peaks identified by homer and gives statistics for the IP experiment and individual peaks

organism: Schizosaccharomyces pombe

source_name: JLP1670 Strain

extract_protocol:
Variations introduced in the ChIP experimental method from Keogh et al. A) 1600 μl (60 ml initial culture) of prepared chromatin (TAP-tagged protein) and 20μl of beads (GE IgG Sepharose 6 Fast Flow) were used for IP. Pre-clearance of the beads with ascites fluid was not performed. IP was carried out for 2-3 hours at 4C. B) The following variations were introduced in the wash buffers used: Wash Buffer 1 – 1X FA-Lysis Buffer, 0.1% SDS, 1 M NaCl (Final Salt Concentration); Wash Buffer 2 – 1X FA-Lysis Buffer, 0.1% SDS, 500 mM NaCl (Final Salt Concentration). C) For each Wash Buffer, two rinses (invert 30 times) and one 4 minute wash on rotator was conducted. Beads were collected in between each step by centrifugation at 1000 rpm for 30 sec. While changing the Wash Buffer, beads were transferred to a fresh microcentrifuge tube (total 3 tube changes). D) Purified IP’ed DNA was re-suspended in 40 μl DNase free water. 10 μl of this IP’ed DNA was used for qPCR’s (Roche Lightcycler 480 SYBR Green I Master, Machine: Eppendorf Realplex2 Mastercycler ep Gradient S) and Illumina sequencing libraries were made from the remaining 30 μl.
A) End Polish (final conc.): IP’ed DNA, 1X T4 DNA Ligase Buffer (NEB), 3U T4 DNA Polymerase (NEB), 10U T4 Polynucleotide Kinase (NEB), 0.4 mM dNTP’s. Reaction was kept at 20C for 30 minutes. It was subsequently cleaned up with QIAquick PCR Purification Kit and eluted in 20 μl water. B) A-tail addition (final conc.): Previously eluted DNA, 5U Klenow Fragment (3’-5’ exo-) (NEB), 33.33 μM dATP, 1X NE Buffer 2 (NEB). Total volume was 30 μl. The reaction was incubated at 37C for 30 minutes. The enzyme was inactivated by heating at 75C for 20 minutes and was ramped down (rate=10%) to 4C. C) Adaptor Ligation (final conc.): previous volume, 750U T4 DNA Ligase (Rapid) (Enzymatics), 1X T4 DNA Ligase Buffer, 37.5 nM Illumina adaptor (sequences and detailed method for adaptors, below) (Iossifov et al., 2012). The reaction was kept at 25C for 1 hr and inactivated at 65C for 10 minutes. The reaction was cleaned up twice using 0.8X volume of Agencourt Ampure beads (1st elution volume: 40 μl H2O, second elution volume: 15 μl H2O). D) PCR Amplification: eluted DNA, 1X Phusion Master Mix (NEB M0531), 2U Phusion Enzyme (NEB M0530), 200 μM dNTP’s, 1 μM each library amplification primers. The libraries were amplified between 18-21 cycles (annealing temp., 65C for 30 sec.; polymerization time, 30 sec.). E) The amplified products were purified using 0.8X volume of Agencourt Ampure beads. Eluted DNA was size-selected using 2% agarose gel electrophoresis followed by cutting out the 250-350 bp region. The DNA was purified from the gel using QIAquick Gel Extraction kit (Qiagen). Eluted DNA was quantitated on Qubit (Invitrogen) and size range was checked using Bioanalyzer 2100.

tag: epitope tag

value: C-terminal TAP Tagged Sep1

tag: starting material

value: ChIP from prepared chromatin

tag: chip antibody

tag: growth conditions

value: Asynchronous culture

tag: growth medium

value: YES medium

tag: treatment

value: 1mM bortezomib (45 min.)


title: HGDP01081

value: Mbuti Pygmy


title: HGDP00467


title: HGDP00462


title: Sak1_ChIPSeq

source_name: JLP1792 Strain

tag: strain

value: C-terminal TAP Tagged Sak1


title: Fkh2_ChIPSeq

source_name: JLP1586 Strain

value: C-terminal TAP Tagged Fkh2


title: HGDP00471

tag: cell line


title: Untagged_ChIPSeq

description:
data are an aggregate of two biological experiments
Control for Peak detection

value: Untagged control strain


title: HGDP00857

tag: cell type

value: Lymphoblast cells

value: Maya


title: HGDP00877


title: HGDP00858

value: Female


title: Tumor RiboTag Profiling C

first: Peter

last: Sims

state: NEW YORK

address: 3960 Broadway blvd

institute: Columbia Medical Center

description:
Ribosome profiling library preparation
RNA footprint library

data_processing:
For ribosome profiling libraries: basecalls performed using Illumina CASAVA
Samples were demultiplexed and the adapter clipped with fastx_clipper.
Bowtie 2 was used to map rRNA; these were filtered out. Tophat was used to map reads to the mouse transcriptome.
HTSeq was used to compute read counts for reads that mapped uniquely to the  mouse transcriptome in the CDS, 5’-leader (5’-UTR), 3’-UTR, and total exonic sequence for each gene.
For RNA-Seq: we received fastq files containing demultiplexed, single-end 100 base reads for each sample from the Columbia Sulzberger Genome Center.
Tophat 2 was used to map the reads to the mouse transcriptome
HTSeq to compute read counts for reads that mapped uniquely to the mouse transcriptome in the total exonic sequence for each gene
Genome_build: mm10
Supplementary_files_format_and_content: gene, counts, gene length

source_name: tumor

growth_protocol: Tumors were induced by PDGF/Cre retroviral infection.

extract_protocol:
Tumor and normal tissues were homogenized using a glass dounce homogenizer. Lysates were clarified and one half used for poly(A)+ RNA extraction and the other to generate and isolate ribosome-protected RNA fragments.
For RNA-Seq libraries: Standard RNA-Seq library preparation. For ribosome profiling libraries: Ribosome footpring libraries were prepared by ligating a 3' adapter, reverse transcribing, and circularizing. The circles were then used for PCR amplification of the footprints.

tag: tissue

value: PDGF/Cre tumor

tag: Stage

value: end-stage


title: HGDP00868


title: HGDP00856

value: Male


title: HGDP00449


title: HGDP00456


title: Tumor Homogenate Profiling C


title: Tumor Homogenate Profiling A


title: HGDP00855


title: TAK070_WT_pol_WT_MMR

value: WT


title: Tumor Homogenate Profiling B


title: Tumor RiboTag Profiling A


title: Tumor RiboTag Profiling B


title: Tumor Homogenate RNA-Seq C

description:
TruSeq V2 RNA-Seq preparation.
Poly(A) RNA library


title: HGDP00854


title: HGDP01259

value: Mozabite


title: Tumor Homogenate RNA-Seq B


title: HGDP00721

value: Cambodian


title: Tumor Homogenate RNA-Seq A


title: HGDP00476


title: HGDP00715


title: HGDP00720


title: Normal Homogenate Profiling  A

source_name: normal brain

value: normal brain


title: HGDP00716


title: Normal Homogenate Profiling B


title: HGDP00713


title: Normal Homogenate RNA-Seq A


title: Normal Homogenate RNA-Seq C


title: HGDP00712


title: Normal Homogenate RNA-Seq B


title: Log Phase 2 Nat +CMC

status: Public on Aug 24 2014

first: Alexander

middle: F

last: Lovejoy

address: 279 Campus Drive

department: Biochemistry

description: PSI-seq

data_processing:
Aligned to the S. cerevisiae genome using bowtie-0.12.5.  Conditions -p 6 -v 3 -q -a --best --strata
Counted reads stopping at each nucleotide in each sequencing run.  Merged these data into one table, then sorted the table to get sorted_genomic_reads.txt
Genome_build: saccer3

extract_protocol:
Hot phenol chloroform extraction, 2x poly(A) purification with Ambion polyA Purist Kit
PSI-seq.  Libraries were constructed as described in Lovejoy et al.

tag: growth condition

value: Log phase:OD260 = 0.8

value: +CMC


title: Log Phase 2 IVT -CMC

description: PSI-seq

value: -CMC


title: Heat Shock Nat +CMC

description: PSI-seq

value: Log phase, then 30 min heat shock at 45C


title: Log Phase 2 IVT +CMC

description: PSI-seq


title: Heat Shock IVT +CMC

description: PSI-seq


title: Heat Shock IVT -CMC

description: PSI-seq


title: Stationary Nat -CMC

description: PSI-seq

value: Stationary phase:OD260 = 4


title: Stationary IVT +CMC

description: PSI-seq


title: Stationary IVT -CMC

description: PSI-seq


title: Log Phase 2 Nat -CMC

description: PSI-seq


title: Log Phase 1 IVT +CMC

description: PSI-seq


title: Log Phase 1 IVT -CMC

description: PSI-seq


title: Heat Shock Nat -CMC

description: PSI-seq


title: Log Phase 1 Nat -CMC

description: PSI-seq


title: Log Phase 1 Nat +CMC

description: PSI-seq


title: Normal Homogenate Profiling C


title: hGFAP-Gnas-7

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
tophat was used to  base-calling, alignment, filtering, peak-calling, generation of normalized abundance measurements,  with the defaut parameters.
cufflinks was used to generate the FPKM values and comparison of the gene transcript abudence
Genome_build: mm9
Supplementary_files_format_and_content: Table containg the FPKM value and fold change

source_name: cerebellum

extract_protocol:
cerebellums were removed, flash frozen in liquid nitrogen, and RNA was harvested by using Trizol reagent. RNeasy Mini Kit (Qiagen cat# 74104 ) was used to purify the RNA.
Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2201) was used to generate the libraries from 1 ug of total RNA. RNA libraries were prepared for sequencing using standard Illumina protocols

value: cerebellum

tag: age

value: post natal day 60

tag: genotype

value: Gsa conditional knockout mediated by hGFAPCre


title: hGFAP-Gnas-8


title: HGDP00711

value: Lymphoblast cells

tag: population

tag: Sex


title: hGFAP-Gnas-5


title: hGFAP-Gnas-6


title: hGFAP-Gnas-4


title: hGFAP-Gnas-2


title: hGFAP-Gnas-3


title: hGFAP-Gnas-1


title: Olig1-Gnas-8

value: Gsa conditional knockout mediated by Olig1Cre


title: Stationary Nat +CMC

description: PSI-seq


title: Olig1-Gnas-6


title: Olig1-Gnas-1


title: Olig1-Gnas-5


title: Ctrl-2

value: wild type


title: Ctrl-3


title: Olig1-Gnas-3


title: Olig1-Gnas-2


title: Olig1-Gnas-4


title: Ctrl-1


title: 6 h starvation A replicate

status: Public on Aug 22 2014

city: Nottingham

first: David

middle: B

last: Archer

address: University Park

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
The Life Technologies LifeScope (v2.5.1) Whole Transcriptome (WT) Pipeline was used to filter, then map the SOLiD reads to the reference genome sequence using the mate-pair read WT pipeline.
Reads were initially filtered against library adaptor and barcode sequences as well as A. niger rRNA 5.8S, 16S, 18S & 28S sequences obtained from Genbank.
Reads that passed the filter were then mapped to the reference genome sequence, and to a library of exon junction sequences derived from the genome sequence using known exon coordinates. This allowed reads that spanned exon junctions (spliced reads) to be determined.
Read counts per gene were determined using the program Htseq-count (http://www-huber.embl.de/users/anders/HTSeq) using uniquely aligned reads with ≥MAPQ20. For paired read alignments from this dataset, only the forward read (F3) were counted. The count information was then used to calculate normalized gene expression values as RPKM (Mortazavi et al., 2008).
Genome_build: The reference genome and gene models used here are mainly from the genome sequence and gene models of the Aspergillus niger ATCC1015 strain version 3 from the JGI. This was supplemeted with gene models and sequence from the CBS513.88 strain where the gene model and/or genomic sequence was absent from the ATCC1015 strain genome sequence and/or gene models.
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each sample

organism: Aspergillus niger

source_name: mycelia from Aspergillus niger cultured in medium without a carbon source

growth_protocol:
A. niger strain N402 (Bos et al., 1988) was routinely grown on potato dextrose agar (PDA, Oxoid) (Delmas et al., 2012). Medium contained 1 % (w/v) glucose or 1 % ball milled wheat straw (Delmas et al., 2012) as the sole carbon source. Fungal strains were grown on agar slopes at 28 °C to produce spores, which were harvested using 0.1% (v/v) Tween 20. For liquid cultures, 100 ml medium in a 250 ml flask was inoculated with 1x10^6 spores ml-1 and incubated at 28 °C, 150 RPM. For cultivation on wheat straw or in medium without carbon source, AMM containing glucose was inoculated with spores and incubated for 48 h to generate mycelium. Mycelium was collected by filtration over Miracloth (Calbiochem), washed with AMM without carbon source and subsequently 1.5 g wet weight of mycelium was transferred to a flask with the appropriate medium.
References: Bos, C. J., et al., 1988. Genetic analysis and the construction of master strains for assignment of 781 genes to six linkage groups in Aspergillus niger. Curr. Genet. 14, 437-443. Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A et al: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing. PLoS Genet 2012, 8(8):e1002875.

extract_protocol:
Total RNA was extracted from mycelia using the Plant/Fungi total RNA Purification Kit (Norgen Biotek, Canada) including the on-column DNAase treatment step.
10 ug of Total RNA was depleted of ribosomal RNA using the Ribominus Eukaryotic kit (Invitrogen). The KAPA library quantification kit for Applied Biosystems SOLiD platform was used to quantify the libraries by qPCR. SOLiD whole transcriptome libraries were made as outlined in the SOLiD Whole transcriptome kit protocol (Applied Biosystems). Emulsion PCR and bead-based enrichment was carried out using the SOLiD EZ bead system. Using a SOLiD 5500xl ABi sequencer, 50bp/35bp paired-end reads were generated in colour space.

value: mycelia


title: 6 h starvation B replicate


title: 24 h starvation A replicate


title: 24 h starvation B replicate


title: 48 h glucose B replicate

source_name: mycelia from Aspergillus niger cultured in glucose medium


title: 6 h wheat straw A replicate

source_name: mycelia from Aspergillus niger cultured in wheat straw medium


title: 6 h wheat straw B replicate


title: 48 h glucose A replicate


title: Olig1-Gnas-7


title: with FK506 immunosuppression for 7d

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: small RNAs

data_processing: After indexing and trimming of linker sequences, those reads of at least 15 nt in length that had less than three terminal mismatches in the sequence were sorted and counted for the following analysis. The clean read datasets were blasted with the BOWTIE software according to the following criteria: a 5′ and 3′ linker match of at least 15 nt and an appropriate length (15–30 nt). The pre-miRNAs and mature miRNAs in the miRBase v.20.0 were searched with BLAST to identify Mus musculus miRNAs.

source_name: serum

growth_protocol: All the housing conditions and the surgical procedures, analgesia, and assessments were in accordance with national and institutional guidelines, and an Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC)–accredited SPF facility was used. The animals were monitored to ensure appropriate feeding and diet after surgery.

extract_protocol:
Total RNA was extracted from the harvested serum using a mirVana miRNA Isolation Kit (Ambion, USA). The purified RNA yield was determined by the absorbance at 260 nm with an SSP-3000 NanoDrop spectrophotometer (Infinigen Biotech, USA), and RNA quality was evaluated with a BioAnalyzer 2100 system (Agilent Technologies, USA).
RNA smaller than 200 base pairs (bp) was enriched with the mirVana miRNA isolation kit (Ambion). The small RNA samples were sent to GeneTech Biotech Co., Ltd (GeneTech, Taiwan) for small RNA cloning. The population of miRNAs with a length of 15–30 nucleotides (nt) was passively eluted from polyacrylamide gels. The RNA was then precipitated with ethanol and dissolved in water. Small RNAs had linkers ligated to them and bar-coded cDNAs were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina, USA) following the manufacturer’s instructions. Individual libraries were analyzed on a BioAnalyzer (Agilent) for the presence of linked cDNA at the appropriate size (135–165 bp) and 11 bar-coded libraries were pooled into 1 sample by mixing 2.0 ng of the 135–165 bp peak from each sample, as determined by the BioAnalyzer.
Sequencing of the pooled libraries was performed in 1 lane of the Illumina HiSeq2000 Sequencer. Fifty bp single-end reads of the libraries were obtained. After indexing and trimming of linker sequences, those reads of at least 15 nt in length that had less than three terminal mismatches in the sequence were sorted and counted for the following analysis. The clean read datasets were BLASTed with the BOWTIE software according to the following criteria: a 5′ and 3′ linker match of at least 15 nt and an appropriate length (15–29 nt). The pre-miRNAs and mature miRNAs in the miRBase v.20.0 were searched with BLAST to identify Mus musculus miRNAs.

treatment_protocol: The mice were anesthetized by intraperitoneal injection of an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine. The anesthetized mice were restrained in a supine position on a heated pad to maintain the body temperature at 37°C. Under aseptic conditions, with sterile povidone/iodine preparation and 70% ethanol and sterile instruments and drapes, the skin over the proximal right hindlimb was incised, and the underlying biceps femoris muscle was bluntly dissected to expose the sciatic nerve. An established mouse sciatic nerve allotransplantation model was used. In brief, 1-cm Balb/c donor sciatic nerve grafts were transplanted in reverse orientation into 0.5-cm sciatic nerve gaps created in the recipient Balb/c mice. Tension-free repair was then performed under an operating microscope with three 11–0 nylon (Ethicon Inc., Somerville, NJ) interrupted epineurial sutures under 40X magnification. The muscle was closed with 5–0 vicryl sutures, and the skin with interrupted 5–0 nylon sutures. FK506 was administered subcutaneously at 1 mg/(kg•d) throughout the experimental course.

tag: time

value: 7 d

tag: sample type

value: serum


title: without FK506 immunosuppression for 7d

description: small RNAs


title: with FK506 immunosuppression for 3d

description: small RNAs

value: 3 d


title: HGDP01258

value: Mozabite

value: Male


title: without FK506 immunosuppression for 3d

description: small RNAs


title: EutV-NoFlag_EA

city: Paris

first: Jeffrey

last: Mellin

address: 25 rue Docteur Roux

institute: Institut Pasteur

data_processing:
For RNA-seq; Reads were mapped to the corresponding reference genome (NC_003210) using Novoalign (Novocraft V3.02.02) and RPM were calculated with in-house perl scripts
For CLIP-Seq; Raw sequence files (fastq) were cleaned of 3' Adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG), and low quality (cutoff 28) and short sequence (15nt) reads were removed using AdapterRemoval v1.5.2 (Lindgreen et. al, 2012) software. Reads were aligned against the reference genome (NC_003210) with bowtie v1.0.0 (Langmead et al., 2009) using default parameters, counted with HTSeq v0.6.0 and normalized to reads per million.
Genome_build: NC_003210
Supplementary_files_format_and_content: The *cov.txt contains three columns; the 1st column describes the concerned chromosome/contig, the 2nd the position on the specified region and the last the normalised coverage (in reads per million)

organism: Listeria monocytogenes EGD-e

source_name: Bacteria

growth_protocol:
growth supplemented with 10 mM ethanolamine (Sigma, 98136)
Listeria monocytogenes strains were grown in LB broth with shaking at 200 rpm in Erlenmeyer flasks at 37° C

extract_protocol:
CLIP-Seq : Flag-tagged proteins where immunoprecipitated and directional libraries where constructed following a ligation based protocol fully described in the manuscript.
For all RNA isolations, 25 ml cultures of L. monocytogenes were grown to an OD600 of 0.3 – 0.5 and subsequently pelleted by centrifugation at 4000 rpm for 20 mins in 50 ml Falcon tubes with swing bucket rotor. Pellets were resuspended in 1ml Tri Reagent (Sigma, 93289), transferred to 2 ml Lysing Matrix Tubes (MP Biomedicals, 6911) and mechanically lysed by bead beating in a FastPrep apparatus (45 secs, speed 6.5 followed by an additional 30 secs, speed 6.5). Subsequently tubes were centrifuged for 5 min at 8000 X G, 4° C in a tabletop centrifuge to separate beads from lysates. Lysates were drawn off and transferred to 2 ml Eppendorf tubes. RNA isolation proceeded according to the manufacturers instructions. Briefly, 200 μl Chloroform (Carlo Erba Reagents, 438601) was added to the lysate, shaken and incubated for 10 minutes at room temperature followed by centrifugation for 15 min at 13,000 X G, 4° C. The upper aqueous phase was removed and transferred to a new 1.5 ml Eppendorf tube and RNA was precipitated by the addition of 500 μl Isopropanol and incubation at room temperature for 5-10 mins. RNA was pelleted by centrifuging for 10 mins at 13,000 X G, 4° C. The supernatant was discarded and the pellet was washed twice with 75% ethanol. RNA pellets were resuspended in 50 μl water.

tag: genotype/variation

value: EutVNOFLAG

tag: growth medium supplemented with

value: 10 mM ethanolamine


title: EutV-Flag_B12_EA

growth_protocol:
growth supplemented with 10 mM ethanolamine (Sigma, 98136) and 20 nm Vitamin B12 (Sigma. C0884)
Listeria monocytogenes strains were grown in LB broth with shaking at 200 rpm in Erlenmeyer flasks at 37° C

value: EutVFLAG

value: 10 mM ethanolamine and 20 nM Vitamin B12


title: EutV-NoFlag_B12_EA


title: EA_WT

extract_protocol:
10µg of total RNA was ribodepleted and non-directional libraries were constructed using a random hexamer priming approach fully described in the manuscript
For all RNA isolations, 25 ml cultures of L. monocytogenes were grown to an OD600 of 0.3 – 0.5 and subsequently pelleted by centrifugation at 4000 rpm for 20 mins in 50 ml Falcon tubes with swing bucket rotor. Pellets were resuspended in 1ml Tri Reagent (Sigma, 93289), transferred to 2 ml Lysing Matrix Tubes (MP Biomedicals, 6911) and mechanically lysed by bead beating in a FastPrep apparatus (45 secs, speed 6.5 followed by an additional 30 secs, speed 6.5). Subsequently tubes were centrifuged for 5 min at 8000 X G, 4° C in a tabletop centrifuge to separate beads from lysates. Lysates were drawn off and transferred to 2 ml Eppendorf tubes. RNA isolation proceeded according to the manufacturers instructions. Briefly, 200 μl Chloroform (Carlo Erba Reagents, 438601) was added to the lysate, shaken and incubated for 10 minutes at room temperature followed by centrifugation for 15 min at 13,000 X G, 4° C. The upper aqueous phase was removed and transferred to a new 1.5 ml Eppendorf tube and RNA was precipitated by the addition of 500 μl Isopropanol and incubation at room temperature for 5-10 mins. RNA was pelleted by centrifuging for 10 mins at 13,000 X G, 4° C. The supernatant was discarded and the pellet was washed twice with 75% ethanol. RNA pellets were resuspended in 50 μl water.


title: DRGFP-4C-1

city: Bethesda

first: Philipp

last: Oberdoerffer

state: MD

address: 41 Library Drive

department: CCR

institute: National Cancer Institute

data_processing:
4C amplified DNA was subjected to Illumina Hi-seq 2000 High throughput 100bp paired end sequencing
Sequenced tags containing the HindIII-proximal primer sequence were sorted for downstream analysis.  HindIII proximal reads were trimmed by 30 bp at the 5’ end to remove the bait sequence and by 12 bp at the 3’ end to remove the low quality bases
The resulting 58 bp reads were mapped to the human genome (hg18) using the Illumina single-end algorithm
Normalized read counts were binned using SeqMonk software to create 50KB wide non-overlapping windows across the genome
Genome_build: Hg18
Supplementary_files_format_and_content: Tab-delimited file converted to MS-Excel spreadsheet, with genome-wide normalized read counts in 50KB wide non-overlapping windows in each of the two replicates (DRGFP-4C-1 and DRGFP-4C-2)

source_name: osteosarcoma

growth_protocol: U2OS cells were grown in DMEM supplemented with 10% FBS and passaged when ~80 % confluent, approximatley every three days.

extract_protocol:
10 million DRGFP-U2OS cells were crosslinked with 2 % formaldehyde and lysed (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitors (Roche)) at 4°C for 1 hour. Lysed cells were washed with restriction enzyme (RE) buffer (New England Biolabs buffer 2) and incubated at 37°C for 1 hour in RE buffer containing 0.3% SDS. SDS was sequestered by Triton X-100 (1.8%). RE digestion was performed with 400 U of HindIII (New England Biolabs) overnight. Following enzyme inactivation, the reaction was ligated using 100 U T4 DNA Ligase (Roche) at 16°C overnight. Following reversal of crosslinks, the DNA was purified by phenol extraction and ethanol precipitation. For circularization, the DNA was digested with Csp6I (Fermentas) at 37°C overnight. Following enzyme inactivation, phenol extraction and DNA re-ligation, 3.2 µg of the 4C contacts library was amplified for 30 PCR cycles. Inverted PCR primers recognized an I-SceI proximal HindIII-Csp6I fragment on the integrated DRGFP transgene (Csp6I-proximal: GACGTTGTGGCTGTTGTAGTTG, HindIII-proximal: CGGCATCAAGGTGAACTTC).
PCR amplified 4C DNA was sequenced using Illumina standard protocols for genomic DNA. After adapter ligation the library was amplified for eight cycles and sequenced.

tag: transgenes

value: DRGFP, TRE-I-SceI, Tet-On (Clontech)


title: LB_WT

growth_protocol: Listeria monocytogenes strains were grown in LB broth with shaking at 200 rpm in Erlenmeyer flasks at 37° C

value: none  (LB control)


title: B12_WT

growth_protocol:
growth supplemented with 20 nm Vitamin B12 (Sigma. C0884)
Listeria monocytogenes strains were grown in LB broth with shaking at 200 rpm in Erlenmeyer flasks at 37° C

value: 20 nm Vitamin B12


title: BOTH_B12EA_WT


title: without FK506 immunosuppression for 14d

description: small RNAs


title: 12129_1-24OBM

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

description:
Sample_7
methylation calls

data_processing:
Reads were created by CASAVA 1.8.2 from the  HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011)( http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to whole genome using the bismark(http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: hg18
Supplementary_files_format_and_content: *myCpG.txt = tab delimited file with the following column heades: chrBase chr base strand coverage freqC freqT

source_name: Normal CD34+ bone marrow cells

extract_protocol: ERRBS libraries were constructed as described in 18. Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia. PLOS Genetics 8, in press (2012).

value: Normal CD34+ bone marrow cells

value: Normal

tag: flowcell id

tag: lane #


title: 12135_YBM2

description:
Sample_6
methylation calls


title: 20122

description:
Sample_4
methylation calls

source_name: AML blasts

value: AML blasts

value: TET2 mutated


title: with FK506 immunosuppression for 14d

description: small RNAs

tag: strain

tag: treatment


title: DRGFP-4C-2

tag: cell line


title: 18907

description:
Sample_3
methylation calls

tag: cell type

value: IDH and TET2 wild type


title: 12133_YBM1

description:
Sample_5
methylation calls


title: 12131_3-7OBM

description:
Sample_8
methylation calls


title: T29_DGE

status: Public on Aug 21 2014

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
Library strategy: DGE-seq
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
All DGE clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)
Genome_build: UCSC hg18
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample.

source_name: ovarian epithelial cell line

extract_protocol:
Genomic RNA was extracted using the genomic RNA extraction kit (TIANGEN, Beijing, China)
DGE libraries from both T29 and T29H cells were prepared by using the Illumina Gene Expression Sample Prep Kit. Briefly, mRNA for each sample was reverse-transcripted to cDNA. Then, the resulted cDNAs were ligated to sequencing adapters and the products were purified and enriched with PCR to create the final cDNA libraries, which were then sequenced using the Illumina GAII System

value: immortalized but non-transformed ovarian epithelial cell line

tag: passages

tag: tissue

value: ovarian epithelial


title: in vivo rep3

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
The reads were processed using BWA software.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization.
Genome_build: ASM2264v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Burkholderia glumae BGR1

source_name: In rice, BGR1

growth_protocol: B. glumae BGR1 was used to inoculate 2 ml of LB broth and then incubated at 37°C overnight with shaking, after which it was subcultured at 37°C for 4 to 5 h in 2 ml of fresh LB broth to reach the mid-logarithmic phase. Cultured bacteria cells were then collected by centrifugation, washed twice with sterile water and resuspended in distilled water, after which the suspension was adjusted to OD600 = 0.5 using a colorimeter (Biochrom WPA CO8000 Cell Density Meter, Biochrom). Next, stems of rice at the vegetative stage were inoculated with bacterial suspensions using a syringe. Inoculated plants were grown in a greenhouse for 8 days, at which time rice stems with symptoms of B. glumae BGR1 were collected.

extract_protocol:
The infected rice stem segments were centrifuged directly at 4°C and 2,000 × g for 5 min in 15-ml conical tubes to obtain bacteria pellets. Each pellet contained 2.5 × 108 to 3.3 × 108 CFU/ml, which was primarily composed of B. glumae BGR1 (data not shown). For later RNA extraction, the collected pellets were suspended in 2 ml of RNAprotectTM Bacteria Reagent (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type

tag: condition

value: in vivo


title: 14877

description:
Sample_1
methylation calls


title: in vivo rep1

tag: genotype


title: input_HEK

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Ribosome Profiling

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Genome_build: mm10 with Ensembl release 72 transcripts; hg19 with Gencode v17 transcripts
Supplementary_files_format_and_content: CSV text files contain five columns: 1. feature name; 2. - 5. read counts on the whole transcript, CDS, 5’ UTR, and 3’ UTR

source_name: HEK cell

extract_protocol:
Rnase I footprinting, size exclusion chromatography, RNA extraction
RNA extraction with Trizol, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

value: DMEM + 10% FBS

value: HEK


title: in vivo rep2


title: T29H_DGE

value: RasV12-transformed human ovarian epithelial cell line


title: in vitro rep3

data_processing:
The reads were processed using BWA software.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization.
Genome_build: Burkholderia glumae BGR1 ASM2264v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

source_name: Bacteria culture, BGR1, 6hr

value: in vitro


title: in vitro rep1


title: EutV-Flag_EA

value: EutVFLAG

value: 10 mM ethanolamine


title: 17065

description:
Sample_2
methylation calls

value: IDH mutated


title: RAD21 ChIA-PET in K562

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: immortalized myelogenous leukemia cell line

extract_protocol: See Fullwood et al., 2010 (PMID:20069536) and Fullwood et al., 2009 (PMID:19890323)


title: bound_HEK

description: Ribosome Profiling

extract_protocol:
Rnase I footprinting, size exclusion chromatography, streptavidin affinity purification of assembled 80S ribosomes by large subunit affinity tag
RNA extraction with Trizol, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification


title: H3K4me1 ChIA-PET in K562


title: H3K4me3 ChIA-PET in K562


title: POL2RA ChIA-PET in K562


title: H3K27ac ChIA-PET in K562


title: H3K4me2 ChIA-PET in K562


title: T29H_RRBS_rep2

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
RRBS-seq reads were aligned to the hg18 genome assembly using SOAP2.21 with two mismatches allowed in the seed (40 bp)
BSMAP was used to process the alignment results to identify the methylcytosines where at least three reads were covered
Genome_build: UCSC hg18
Supplementary_files_format_and_content: Tab-delimited text files include methylation information of each chromosone for each Sample. Scores represent chromosome, position, strand, Cpattern, Csequence, copy number, methylC reads number, unmethylC reads number, binomial expection.

extract_protocol:
Genomic DNA was extracted using the genomic DNA extraction kit (TIANGEN, Beijing, China)
RRBS libraries were constructed for T29 and T29H cell lines, as previously described (31). Briefly, 500 ng of genomic DNA was digested with 20 units of MspI (NEB, NY, USA) in a 20 μl reaction for 20 h at 37 °C. After purification, the digested products were blunt-ended, and then dA was added, followed by methylated-adapter (Illumina, CA, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s standard protocol. The final libraries were generated by amplification with HiFi HotStart Uracil+ ReadyMix (KAPA, MA，USA), and Illumina Multiplexing PCR Primers. The quality and quantity of RRBS libraries were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and RT-PCR, respectively.


title: T29H_RRBS_rep1


title: ribo_chx_mesc

description: Ribosome Profiling

source_name: ES cell

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction with Trizol, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

value: ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml)

tag: genetic background

tag: growth protocol

value: Feeder-free, with LIF


title: T29_RRBS_rep1


title: T29_RRBS_rep2


title: ribo_emet_mesc

description: Ribosome Profiling

value: ES cell feeder-free, w/ LIF 60 s Emetine


title: in vitro rep2


title: RNAseq_SalineShock_rep2

status: Public on Aug 20 2014

city: Cuernavaca

first: Gamaliel

last: Lopez

state: Morelos

address: Ave. Universidad s/n, Chamilpa

department: Genómica Evolutiva

country: Mexico

institute: Centro de Ciencias Genómicas

data_processing:
Basecalls performed using CASAVA version 1.7.0 and CASAVA version 1.8.2
Sequenced duplicates reads were remove using ShortRead packages from Bioconductor, then mapped to Rhizobium etli CFN42 whole genome using bowtie v0.12.2 with parameters  --phred64-- quals
To adjust the values in the biological replicates, the RNA-seq data were pre-processed. We used a variant of RPKM (Reads per Kilobase per Millon), pre-processed the total number of reads from the library for each condition. Perl script was written to determinate the expression values of each gene
Genome_build: Rhizobium etli CFN42
Supplementary_files_format_and_content: Unique* files were generated using ShortRead package in order to eliminate the duplicates reads
Supplementary_files_format_and_content: dfRetli_AllCondi_wReplics_Norm_byLibsize.txt file contains all expression values pre-proceced by the library size of each sample

organism: Rhizobium etli

source_name: cell culture

growth_protocol: all cultures were grown at 30°C, with agitation (200 rpm), in peptone-yeast extract medium, (PY). Aliquots were taken 12 hours post-inoculation (OD600)~0.4 in exponential phase.

extract_protocol:
Total RNA was isolated using RNeasy Midi Kit (QIAGEN) following the manufacturer’s instructions. Ribosomal RNA elimination was done following the RiboMinus Kit protocol with a few modifications: we added a second rRNA elimination step, using the Terminator Exonuclease enzyme (epicenter)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples were incunbated at 30°C for 30min for control condition; 42°C for 30min for the culture subject to heat -shock, and 30min at 30°C in supplementary PY medium with 80mM NaCl2 for the saline shock condition.

value: Saline Shock


title: RNAseq_SalineShock_rep3


title: RNAseq_HeatShock_rep2

value: Heat Shock


title: RNAseq_HeatShock_rep3


title: RNAseq_HeatShock


title: RAD21 ChIA-PET in GM12878

source_name: immortalized lymphoblastoid cell line


title: RNAseq_Reference_rep3

value: Control


title: RNAseq_Reference_rep2


title: RNAseq_Reference


title: wheat root (WRT)

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

institute: Delhi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Purity filtered raw reads were analyzed using Java-based UEA Small RNA Workbench version 2.4  (Stocks et al. 2012). Due to the unavailability of whole genome sequence of Triticum aestivum, sequence datasets from several resources (BACs, GSSs, ESTs available at NCBI and 5X coverage wheat genomic dataset available as EMBL/Genbank SRA accession number ERP000319) were compiled as ‘in-house wheat genome dataset’ to map putative sRNAs. UEA sRNA workbench v2.4 was employed for prediction of miRNAs and miRBase v20 database was used as a reference for identification of conserved, variants of conserved miRNAs and novel miRNAs.
Genome_build: BACs, GSSs, ESTs available at NCBI and 5X coverage wheat genomic dataset available as EMBL/Genbank SRA accession number ERP000319
Supplementary_files_format_and_content: Text files with abundance measurements

organism: Triticum aestivum

source_name: 7-day old whole seedling

growth_protocol: Wheat (Triticum aestivum cv. PBW343) seeds were surface-sterilized with 4% (v/v) sodium hypochlorite solution followed by 5-6 washes with sterile water and planted on muslin cloth for growing hydroponically in controlled conditions (temperature: 25±1ºC; relative humidity: 70-75%; photoperiod: 16h light/8h dark) in a growth room.

extract_protocol:
Total RNA was isolated from various tissues following a modified protocol by Chomzynski and Sacchi (1987). Lithium chloride method was employed for the enrichment of low molecular weight RNA (LMW) fraction (Katiyar-Agarwal and Jin, 2007). Concentration of RNA was determined using spectrophotometer (Bio-Rad, USA) followed by evaluating the quality on MOPS-formaldehyde-agarose gel (total RNA) or TBE-urea-PAGE (LMW RNA).
For small RNA library construction, 50 µg of LMW RNA was resolved on 15% denaturing polyacrylamide gel and sRNAs in the size-range of 18-40 nt were purified from the gel followed by sequential ligation with 5’ adapter and 3’ adapter. After each adapter ligation, size selection was performed using a polyacrylamide gel and ligated product was eluted from the gel. Subsequently, first strand cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, USA) and 3’ adapter-specific RT primer. The cDNA was amplified using adapter-specific sequencing primers and the amplified product was purified. Prior to sequencing, quality and quantity of the amplified small RNA-cDNA libraries was evaluated on Agilent 2100 Bioanalyzer system (Agilent Technologies, USA). Sequencing was performed using Illumina GAIIx sequencing platform at High-throughput Sequencing Facility, University of Delhi South Campus, New Delhi, India according to manufacturer’s instructions (Illumina, USA). All the adapters, RT primer and sequencing primers were procured from Illumina, USA.

treatment_protocol: For the preparation of tissue-specific small RNA libraries, shoot and root tissues were collected separately from hydroponically grown seven-day-old seedlings. Mature leaf and spikelets were collected from field-grown plants 50 days after planting (DAP) and 90 DAP, respectively. Seven-day-old seedlings were employed for abiotic stress-related studies. For heat stress, seedlings were subjected to 35ºC and 40ºC for 30 min, 2 h, 4 h and 8 h each. Salinity stress was induced by treating the seedlings with 150 mM and 250 mM saline solution (sodium chloride) for 3 h, 6 h, 12 h and 24 h each. For water-deficit stress, seedlings were exposed to 20% PEG6000 (polyethylene glycol) and 400 mM mannitol for 1 h, 3 h, 6 h and 12 h each. Tissues for all time-points of each stress were pooled to obtain four samples, which are referred to as: HS (heat stress), SS (salinity stress), WDS (water-deficit stress). A control sample (C) was kept as wheat seedlings grown under controlled conditions along with all the abiotic stress treatments.

tag: cultivar

value: 7-day old whole seedling


title: wheat flower (WFL)

source_name: Flower (spikelets) 50 days after planting


title: wheat shoot (WSH)


title: wheat drought stressed (WDS)


title: B. juncea drought stressed (BJD)

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Images obtained from Illumina GA IIx were converted into text files using genome analyzer pipeline software provided with the genome analyser. The UEA small RNA workbench v2.4 was then used for further analysis. Briefly, after trimming of adapter sequences, tags of length ranging from 16-30 nt were used to remove all non-small RNA sequences like low complexity sequences (simple sequence repeats) and degradation species (fragments of tRNA, rRNA, snRNA, snoRNA). The putative small RNA reads thus obtained were screened for the presence of conserved miRNAs based on their perfect homology with miRBase version 19. The remaining dataset was mapped onto the B. juncea genome reference dataset (generated in our lab by sequencing on Illumina plateform at 8x coverage; manuscript under preparation), B. rapa ver. 1.5  reference dataset (obtained from BrassicaDB) and reference dataset of other Brassicas (obtained from NCBI). The flanking sequences of varying length on both sides of the mapping position were extracted and processed for prediction of secondary hairpin structure. Secondary structures fulfilling the miRNA hairpin structure criteria were listed as conserved (already reported in miRBase v 20) and novel miRNAs.
Genome_build: n/a
Supplementary_files_format_and_content: small RNA sequence abundance

organism: Brassica juncea

growth_protocol: Seeds were surface sterilized with 2% sodium hypochlorite solution for ten minutes, followed by extensive washes with sterile water and hydroponically grown in a plastic container lined at the top with muslin cloth. The trays were placed in a growth room (Vista Biocell, India) maintained at 24°C±1 with a 16 h day/8 h night photoperiod.

extract_protocol:
Tissues obtained from different time points of each stress were pooled and enriched low molecular weight (LMW) RNA was isolated using GITC-LiCl method (Chomczynski and Sacchi, 1987) with some modifications. Tissue was homogenized in liquid nitrogen and total RNA was extracted using GITC buffer and phenol-chloroform purification steps followed by ethanol precipitation. Total RNA was re-precipitated with lithium chloride to extract low molecular weight RNA.
Small RNA libraries were prepared utilizing Illumina small RNA sample preparation kit v1 according to manufacturer’s instructions. Briefly, equal amount of enriched-LMW RNA (50 μg) was size fractionated on 15% TBE-urea gel and small RNA fraction (18-40 nt) was excised and purified. RNA adapters were ligated on both ends using T4 RNA ligase followed by cDNA preparation utilizing Superscript II (Invitrogen, USA). The prepared cDNA was PCR amplified and the amplicon of approximately 100 bp was excised from a 6% TBE gel. The quality and quantity of prepared libraries was evaluated utilizing DNA 1000 kit on a bioanalyzer (Agilent, USA).

treatment_protocol: Seven day old seedlings were subjected to various abiotic stresses. Heat stress was given at two different temperatures, 35°C and 42°C, for 30 min, 2 h, 4 h and 8 h by decanting the water from the growth container and placing it in a BOD incubator (Scientific systems, India). Salinity stress was given at two different concentrations, 150mM NaCl and 250mM NaCl, for 3 h, 6 h, 12 h and 24 h by replacing the water from the container with NaCl solution. Similarly, drought stress was given with 20% PEG and 300mM mannitol for 1 h, 3 h, 6 h and 12 h. Untreated seedlings were taken as control. Intact, equal sized whole seedlings were harvested, snap-frozen in liquid nitrogen and stored at -80°C.

value: varuna

value: whole seedling

tag: age

value: drought stressed


title: wheat salinity stressed (WSS)


title: RNAseq_SalineShock

value: wild-type


title: HEK-293 /STF cells

city: Baltimore

first: Yulian

last: Zhou

address: 725 N. Wolfe Street

institute: JHMI

data_processing:
Raw reads were mapped to the reference genome (hg19) using TopHat (v2.0.8) and the relative abundance of each transcript was calculated with Cufflinks (v2.1.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text/FPKM of every human gene

source_name: cell line

extract_protocol:
Total RNA were extracted using Trizol (Invitrogen) and the RNeasy kit (Qiagen)
TruSeq RNA Sample Prep Kit v2 (Illumina)

value: embryonic kidney 293 cells

tag: reporter

value: canonical Wnt signaling reporter


title: B. juncea control (BJC)

description: small RNA

value: control


title: wheat control (WC)


title: wheat leaf (WLF)

source_name: Leaf 50 days after planting

value: Leaf 50 days after planting


title: B. juncea salinity stressed (BJS)

description: small RNA

value: salinity stressed


title: PHR_RIBO0

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls performed using CASAVA version 1.8. Quality score is phred33 scale.
Sequenced reads were to hg19 whole genome using MapSplice v12_07 with the default configuration.
The number of fragments derived from genes was estimated using RSEM v1.1.13 with the default setting and the reference transcriptome of UCSC hg19 GAF2.1 KnownGenes on standard chromosomes. Estimated counts were then transformed by upper quartile normalization.
Gene abundance was normalized by the upper quartile across all genes within each lane.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalized gene counts for each sample.

Raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns:
http://www.ncbi.nlm.nih.gov/gap/?term=phs000676

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
Ribo-zero: rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit cat# RZH110424. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.

tag: er (1=positive; 0=negative)

tag: pr (1=positive; 0=negative)

tag: node status (1=positive=1 or more nodes; 0=negative)

tag: grade

tag: tumor size (1= <=2cm; 2= >2cm to <=5cm; 3= >5cm; 4=any size with direct extension to chest wall or skin)

tag: rfs event (0=no relapse; 1=relapsed at any site or died of disease)

tag: rfs months

tag: overall survival event (0=alive; 1=dod or doc)

tag: overall suvival months


title: A1-PRIMARYT-FF_DSN

source_name: breast tumor

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
DSN: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries. DSN normalization was then performed to remove rRNA. (ref. Illumina DSN Normalization Sample Preparation Guide)


title: A1-PRIMARYT-FF_mRNA-seq

extract_protocol:
Fresh-frozen: Autopsy breast tissue sample was flash frozen on dry ice. RNA was retrieved using Qiagen RNeasy mini kit.
mRNA-seq: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. rRNA was removed using standard Illumina protocols.


title: PHR2_mRNA-seq


title: PHR_mRNA-seq


title: A1-PRIMARY-FFPE_RIBO0

extract_protocol:
FFPE: Autopsy breast tissue sample was formalin-fixed and praffin-embedded. RNA was retrieved using Roche High Pure RNA paraffin kit, Cat# 03270289001.
Ribo-zero: rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit cat# RZH110424. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.


title: 990141B-FFPE_RIBO0


title: PHR_DSN


title: A7-LIVERMET-FF_RIBO0

source_name: Liver metastasis


title: wheat high temperature stressed (WHTS)

tag: tissue


title: B. juncea high temperature stressed (BJH)

description: small RNA

tag: strain

tag: treatment

value: high temperature stressed


title: A7-LIVERMET-FF_mRNA-seq


title: CP190_mixed_2

city: Boston

first: Ruslan

last: Sadreyev

state: Massachusetts

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description:
nuclei from embryo 5-13h
nuclei from embryo 5-13h

data_processing:
OLB 1.9.0 / RTA 1.13 used for base-calling
CHIPseq reads aligned to dm3 using BWA, allowing up to 1 mismatch and otherwise default settings
Data were filtered for reads aligning to multiple positions, pcr duplicates, and inferred fragment size <100 or >800.
Genome_build: dm3
Supplementary_files_format_and_content: Wig files generated using SPP's "smoothed.density" function, following default guidelines estimating peak separation distance and removing low quality and anomalous tags.

organism: Drosophila melanogaster

growth_protocol: Eggs were harvested 5-13h after laying, nuclei extracted and marked parasegment-specific nuclei sorted by FACS

extract_protocol:
Nuclei were digested with MNase, solubilized and ChIP performed using the appropriate antibody.
Libraries were prepared as described in Bowman et al., 2013.

value: embryo

tag: tissue subtype

value: whole embryo

tag: chip antibody

tag: chip antibody ref.

value: Pai et al, Molecular Cell 2004


title: CP190_mixed_1

tag: age


title: inp_CP190_PS7_1

value: parasegment 7

value: input


title: CP190_PS7_2


title: inp_CP190_mixed_2


title: 990141B-FF_mRNA-seq


title: 9830-020310B-FFPE_DSN

extract_protocol:
FFPE: Autopsy breast tissue sample was formalin-fixed and praffin-embedded. RNA was retrieved using Roche High Pure RNA paraffin kit, Cat# 03270289001.
DSN: Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries. DSN normalization was then performed to remove rRNA. (ref. Illumina DSN Normalization Sample Preparation Guide)


title: A1-PRIMARYT-FF_RIBO0


title: 9830-020310B-FF_DSN


title: inp_CP190_PS7_2


title: 9830-020310B-FFPE_RIBO0


title: 990141B-FF_DSN


title: inp_CP190_mixed_1


title: CP190_PS7_1


title: Cfp1null_Dox_H3Ac_1

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

data_processing:
Basecalls performed using Illumina Basecalling Package  VN:1.13.57.0
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.5.9 and  -q 15
Data were filtered using the following specifications : Only kept reads that mapped to a unique location and as a proper pair. Duplicate reads removed.
Read counts were normalized to “Reads per  10^7 mapped reads” to account for depth of sequencing
When applicable technical replicates were pooled
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were created from BAM using bedtools genomeCoverageBed and UCSC wigToBigWig

source_name: Embryonic stem cells

growth_protocol: ES cells were grown in gelatinized dishes in Glasgow MEM (Gibco) supplemented with 10% foetal bovine serum (Hyclone) , 1× MEM nonessential amino acids, 1 mM sodium pyruvate, 50 μM 2-mercaptoethanol (Gibco) and LIF.

extract_protocol:
ES cells were crosslinked with 1% formaldehyde at room temperature for 10 min, followed by 5 min incubation with 125mM glycine at room temperature. Cells were washed in PBS, flash frozen in liquid nitrogen and stored at –80°C prior to use. Cell pellets were thawed on ice, resuspended in lysis buffer 1 (50mM Hepes KOH, pH 7.9, 140mM NaCl, 1mM EDTA , 10% Glycerol, 0.5% NP-40,  0.25% Triton X-100) and incubated for 10 min on a rotator at 4°C. Cells were washed in TE (10mM Tris-HCl, pH 8, 1mM EDTA). Cells were resuspended in TE containing 0.5% SDS, incubated on ice for 10 min and sonicated using a Bioruptor (Diagenode) on High setting for 18 cycles of 30 sec (30 sec pause between pulses). The sonicated extract was centrifuged at 20000g for 10 min at 4°C and the supernatant diluted 5 fold with ChIP dilution buffer (20mM Tris-HCl, pH 8, 150mM NaCl, 1% Triton X-100, 1mM EDTA).
ChIP DNA was end repaired by incubation at 20°C for 30 min with 3 U of T4 DNA Polymerase (NEB), 10 U of Polynucleotide Kinase (NEB), 2 U DNA Polymerase I Large (Klenow) fragment (NEB), 1x T4 DNA ligase reaction buffer (NEB) and 400 nM dNTPs. The enzymes were then heat inactivated at 75ºC for 20 min, after which the DNA was ethanol precipitated. A tail of 'A' bases was added to the 3’ ends of the DNA by incubation with 5 U Klenow Fragment (3’-5’ exo-; NEB), 200nM dATP and 1x buffer 2 (NEB) at 37°C for 30 min. The enzymes were heat inactivated and cleaned up as before .Barcoded Ilumina paired end adaptors were then ligated to the processed ChIP DNA by incubation with 300 U of T4 DNA ligase (NEB), 1x T4 DNA ligase buffer (NEB), 7.5% PEG-6000 and 2 pmol of annealed Illumina adaptors for 3 hr at room temperature. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 10 μl water. Ligated DNA was amplified by 16-18 cycles of PCR with primers complementary to the adaptor sequences and Phusion 2x premix (Finnzymes). The DNA was purified using QIAquick PCR Purification columns (Qiagen).

treatment_protocol: Doxorubicin was purchased from Sigma and used at a final concentration of 1 μM for 6 hours.

tag: genotype

value: Doxorubicin (1mM,  6 hours)

value: H3K9,K14ac (Millipore, Catalog# 06-599, Lot# 2019589)


title: 9830-020185B-FFPE_RIBO0

tag: er (1=positive; 0=negative)


title: 9830-020185B-FFPE_DSN

tag: pr (1=positive; 0=negative)


title: 9830-020185B-FF_RIBO0

tag: node status (1=positive=1 or more nodes; 0=negative)


title: wtES_H3Ac_1

value: Wildtype (E14Tg2a)

value: Control


title: 9830-020310B-FF_RIBO0

tag: grade


title: 9830-020185B-FF_mRNA-seq

tag: tumor size (1= <=2cm; 2= >2cm to <=5cm; 3= >5cm; 4=any size with direct extension to chest wall or skin)


title: Cfp1null_Dox_H3K4me3_2

description:
Replicate 2
processed data file: m_Cfp1null_Dox_H3K4me3_merge.bigwig

value: H3K4me3 (Abcam, Catalog# ab8580, Lot# GR47272-1)


title: 9830-020310B-FF_mRNA-seq

tag: rfs event (0=no relapse; 1=relapsed at any site or died of disease)


title: Cfp1null_Dox_H3K4me3_1

description:
Replicate 1
processed data file: m_Cfp1null_Dox_H3K4me3_merge.bigwig


title: Cfp1null_H3Ac_1


title: Cfp1null_H3K4me3_2

description:
Replicate 2
processed data file: m_Cfp1null_H3K4me3_merged.bigwig


title: wtES_Dox_H3Ac_1


title: 990141B-FF_RIBO0

tag: rfs months


title: 9830-010255B-FF_RIBO0

tag: overall survival event (0=alive; 1=dod or doc)


title: 9830-010255B-FF_DSN

tag: overall suvival months


title: wtES_Dox_H3K4me3_2

description:
Replicate 2
processed data file: m_wtES_Dox_H3K4me3_merged.bigwig


title: 9830-010214B-FFPE_RIBO0


title: wtES_H3K4me3_2

description:
Replicate 2
processed data file: m_wtES_H3K4me3_merged.bigwig


title: wtES_Dox_H3K4me3_1

description:
Replicate 1
processed data file: m_wtES_Dox_H3K4me3_merged.bigwig


title: 9830-010214B-FF_RIBO0


title: 9830-010214B-FF_mRNA-seq


title: 9830-010214B-FF_DSN


title: wtES_H3K4me3_1

description:
Replicate 1
processed data file: m_wtES_H3K4me3_merged.bigwig


title: Cfp1null_H3K4me3_1

description:
Replicate 1
processed data file: m_Cfp1null_H3K4me3_merged.bigwig


title: Cfp1null_input


title: wtES_input_1


title: 9830-000030B-FF_DSN


title: m_Cfp1null_Dox_RNA_2

description:
rRNA depleted total RNA
biological replicate 2
technical replicate 1
processed data file: m_Cfp1null_Dox_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_Dox_RNA_merged_reverse.bigwig

data_processing:
Basecalls performed using Illumina Basecalling Package  VN:1.13.57.0
RNA-seq reads were aligned to the mm9 genome assembly using STAR 2.2.1 to allow for gapped alignments using default settings
A GTF file containing ensEMBL mouse transcript information (release 67) was used to generate a count table with HTSeq in union mode. This only counts 1 isoform per gene using the longest possible transcript. Counts from technical replicates were pooled.
Size factors for each library were determined using the Bioconductor package DESeq (Anders and Huber 2010) and applied to generate a normalized count table for each biological replicate
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were created from BAM using bedtools GenomeCoverageBed with -split option and UCSC wigToBigWig. Tabular count tables were produced by HTSeq.

extract_protocol:
Cells were lysed in TRI reagent (Sigma). Total RNA was then extracted with chloroform, precipitated with isopropanol and DNAse treated (DNA-free, Ambion). Ribosomal RNA from 5 μg of total RNA was depleted using Ribo-Zero kit (Epicentre).
Strand specific RNA-Seq ibraries were prepared using Script-Seq V2 RNA-Seq library preparation kit (Epicentre) according to manufacturer’s instructions.


title: 9830-000030B-FF_RIBO0


title: m_Cfp1null_Dox_RNA_12

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 2
processed data file: m_Cfp1null_Dox_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_Dox_RNA_merged_reverse.bigwig


title: 982049B-FFPE_RIBO0


title: LJ C2

city: La Jolla

first: Lani

last: Gleason

address: 8750 Biological Grade

department: Marine Biology Research Division

institute: Scripps Institution of Oceanography

description: control

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed.
Sequences were used to construct de novo transcriptome assemblies (CLC Genomics Workbench v.6), one for each population.  The 4 population assemblies were then reciprocally blasted and the resulting contigs were trimmed, so all 4 assemblies were comparable.
Assemblies were annotated using Blast2Go.
Reads were mapped back to these assemblies (CLC Genomics Workbench v.6).
Differential expression between geographic regions and between control and heat stress conditions was examined with the program DESeq in R.
Genome_build: no available genome; reference sequences used was de novo transcriptome assemblies from this study
Supplementary_files_format_and_content: tab-delimited text file include normalized expression values for each of the 12 samples for each of the contigs in the reference assembly

organism: Tegula funebralis

source_name: whole animal

extract_protocol:
Whole animals were frozen in liquid nitrogen, ground to a powder, and the RNA of each individual was extracted using standard Trizol reagent methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the start of each experiment, treatment animals were placed in a temperature-programmable incubator (Thermo Precision Model 818) and air temperature was increased by 3 °C every half hour (starting at 15 °C) to simulate a natural rate of heating that snails experience in the intertidal. This gradual increase was continued until the target temperature of 34 °C was reached; the incubator stayed at this target temperature for the remaining 2 hours and 20 min of the experiment.  Each heat stress trial lasted a total of 5.5 hours (including the ramp time), which is an estimate of a typical low tide period for *C. funebralis *in the intertidal.  Control animals were exposed to 15 °C in air in the same incubator for 5.5 hours.

tag: population

value: southern CA

tag: tissue

value: whole animal

tag: location

value: La Jolla, San Diego County


title: LJ T2

description: treated


title: m_Cfp1null_Dox_RNA_1

description:
rRNA depleted total RNA
biological replicate 1
technical replicate 1
processed data file: m_Cfp1null_Dox_RNA_merged_forward.bigwig
processed data file: m_Cfp1null_Dox_RNA_merged_reverse.bigwig

tag: strain

tag: treatment


title: ABA_Sorghum_Root_BS

status: Public on Aug 29 2014

city: Cold Spring Harbor

first: Andrew

middle: J

last: Olson

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
BS-seq reads were trimmed for adaptor sequence and low quality base call, then aligned to sorghum genome assembly using rmap V2.03  with parameters -Q -v -m 4
Then the C/T counts from aligned BS-seq reads for each cytosine in reference genome were saved in CT count file
genome_build:Sbi1.4
supplementary_files_format_and_content: The CT count files have the first 6 columns the same as a bed file, the 7th col is count of C, the 8th col is count of T, the 9th col is the 3 nt in reference genome, the 10th col is the context of cytosine

organism: Sorghum bicolor

source_name: Roots from 9d sorghum seedings treated with 20µM exogenous ABA for 27 hrs

growth_protocol: Seeds of Sorghum bicolor genotype BTx623 were germinated by soaking in distilled, aerated water overnight and then transferred to moist germination paper for 3 days.  The seedlings were then transferred to 0.5x Hoagland’s solution and allowed to grow for an additional 5 days in a controlled environment chamber with a day length of 12 hrs, 50% humidity, and day and night temperatures of 31˚C and 22˚C, respectively.

extract_protocol: Flash-frozen root tissue was ground under liquid Nitrogen, and high-quality DNA was isolated utilizing the FastDNA SPIN Kit (MP Biomedicals, Santa Ana, CA USA). Library construction and bisulfite conversion were conducted as described previously (Regulski et al., 2013 GSE39232) and sequenced on Illumina GAIIx machines using PE50 protocol.

treatment_protocol: At 8 days, the plants were treated with 20µM exogenous ABA for 27 hours.  Three groups of 10 plant roots each were harvested post-treatment.

tag: germplasm

value: Root

tag: replicate type

value: technical


title: LJ C1

description: control