title: No detectable cancer on biopsy

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Raw sequences were obtained using CASAVA version 1.8.2 software (Illumina).
Adaptor sequences were removed from the reads using Cutadapt (version 1.1) (Martin 2011), with the following parameters: overlap = 2, minimum length = 17, quality cut-off = 28, error rate = 0.2.
The trimmed reads were subsequently mapped to the human genome (UCSC hg18) using Bowtie 2 Version 2.0.0 (Langmead and Salzberg 2012) with default parameters.
Uniquely aligned reads corresponding to small RNA transcripts were quantified using Avadis NGS software (version 1.4.7, build 182206; Strand Scientific Intelligence Inc.; San Francisco, CA, USA), which utilises annotations for miRNAs (miRBase release 18) (Kozomara and Griffiths-Jones 2011),  transfer RNAs (tRNAs; tRNAscan-SE) (Lowe and Eddy 1997), small nuclear RNAs (snRNAs;  Ensembl), small nucleolar RNAs (snoRNAs; Ensembl) and small cytoplasmic RNAs (scRNAs; Ensembl).
Raw counts were normalised using DEseq (Anders and Huber 2010), implemented in the Avadis NGS workflow.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalised, log-transformed miRNA levels.

source_name: Control

extract_protocol:
Seminal fluid samples were collected into 20 ml Hanks’ Balanced Salt Solution (Gibco; Carlsbad, CA, USA) or phosphate buffered saline (PBS). All samples were processed within 2 h of collection. Briefly, mononuclear cells, including prostatic epithelial and urothelial cells, were separated from sperm cells using an isopycnic Percoll (GE Healthcare; Piscataway, NJ, USA) gradient. The mononuclear cell layer was removed and washed twice with PBS. Total RNA was isolated using TRIzol reagent (Invitrogen; Carlsbad, CA, USA) and cleaned up with RNeasy Mini kits (Qiagen, Valencia, CA, USA), including an on-column DNase digestion with the RNase-Free DNase Set (Qiagen), according to the manufacturer’s instructions.
Library construction, using 1 µg of RNA and a TruSeq small RNA sample preparation kit (Illumina; San Diego, CA, USA), was carried out according to the manufacturer's instructions except that library cDNA was size-selected using a Pippin Prep  (Sage Science; Beverly, MA, USA) following the PCR amplification step.

tag: diagnosis

value: healthy

value: Seminal fluid


title: Biopsy-proven cancer

status: Public on Apr 15 2014

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Cancer

value: prostate cancer

tag: tissue type


title: WT_cu+

city: Charlottesville

first: xin

last: zhao

state: VA

address: Department of Biology, 229 Gilmer Hall

department: Biology

country: USA

institute: University of Virginia

data_processing:
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava 1.8.2
RNA-seq reads were aligned to the TAIR10 genome assembly using Tophat, allowing for up to two mismatching nucleotides, max intron length 2000bp, min isoform fraction 0 and no gaps. Only uniquely mapped reads were retained for further analysis.
Cufflinks software was used to identify differentially expressed genes. Parameters were set as following: FDR 0.01; minimum alignment count 50; Quartile normolization True.
genome build: TAIR10
processed data files format and content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

growth_protocol: Seeds were cold-treated at 4°C for 4 day, sowed on standard MS medium or MS medium with 5µM CuSO4, transferred to growth chamber, and allowed to growth at 22°C for 7 day under continuous white light.

extract_protocol:
Whole seedlings were harvested, ground to powder in liquid nitrogen, and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA treated with DNase I for the construction of sequencing libraries.
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit'.

tag: tissue

value: whole seedlings

tag: genotype

value: wild type (Col-0)

tag: age

value: post germination day 7


title: FLAG-SPL7 ChIP-seq

library_source: genomic

data_processing:
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava 1.8.2
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie, allowing for up to two mismatching nucleotides and no gaps. Only uniquely mapped reads were retained for further analysis.
MACS software with customized parameters (bandwidth, 300bp; P valueof, 1.00e-05; mfold, 10-50;nolambda) was used to call peaks representing enriched binding
genome build: TAIR10
processed data files format and content: BED files were generated using MACS; Scores represent fold enrichment

molecule: genomic DNA

source_name: FLAG-SPL7 ChIP-seq

growth_protocol: Seeds of spl7 mutant and 35S:FLAG-SPL7 transgene were cold-treated at 4°C for 4 day, sowed on standard MS medium , transferred to growth chamber, and allowed to growth at 22°C for 7 day under continuous white light.

extract_protocol:
7-day-old whole seedlings were harvested, cross-linked in 1% fomaldehyde, ground to powder in liquid nitrogen, and chromatin was isolated. Chromatin immunoprecipitation was performed with FLAG antibody (Sigma F7425), and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with ChIPed genomic DNA for the construction of sequencing libraries.
The ChIPseq libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 15 cycles.

value: 35S:FLAG-SPL7 transgene


title: WT_MS


title: spl7 ChIP-seq

source_name: spl7 ChIP-seq

value: spl7 mutant


title: mRNA-seq_PRKACA-mutant adrenal tumor

city: New Haven

first: Gerald

last: Goh

state: Connecticut

address: 1 Gilbert St TAC S355

institute: Yale University

data_processing:
Sequences trimmed to 50bp
Sequences aligned using TopHat version 2.08 with parameters -m 2 -g 1 --b2-very-sensitive
Aligned reads assembled into transcript using Cufflinks version 2.0.2
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited isoforms_fpkm_tracking.txt file produced by Cufflinks version 2.0.2

source_name: cortisol-producing adrenal tumor

extract_protocol:
RNA was isolated from tumor tissue using the Allprep kit (Qiagen) following manufacturer’s instructions.
Ribosomal RNA (rRNA) was removed from total RNA using the Ribo-Zero rRNA Removal Kit (Epicenter) according to manufacturer’s instructions. cDNA was synthesized and libraries prepared using the Illumina RNA-Seq kit.

value: adrenal tumor

tag: gender

value: female

value: 61 years

tag: genotype/variation

value: PRKACA p.Leu206Arg mutation


title: NPC_Time_2_rep1

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Reads were aligned to the human (hg19) reference genome assemblies using Tophat2 with default options.
Aligned fragments were used as input for Cuffdiff2 to determine expression levels (FPKM) and differential expression between conditions using the default options.
CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was used to process, index, and visualize the output of the Cuffdiff2 analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CummeRbund diffTable output. Contains log ratios and differential significance test results.
Supplementary_files_format_and_content: see diffTable output for locations on the genome

molecule: polyA RNA

source_name: H1-derived neural progenitor cells

growth_protocol: H1 human neural stem cells were prepared as described previously (Arnold et al., 2008; Goff et al., 2009) and grown at 37°C, 5% CO2 on 1:4 diluted Matrigel-coated wells in neural proliferation medium (NPM; 50% DMEM/F12 Glutamax, 50% Neurobasal medium, 0.5X N2, 0.5X B27 without vitamin A, 20 ng/ml FGF [Life Technologies]). For differentiation, cells were plated at a density of 106 cells per well in a 6-well plate and allowed to proliferate for one day in the NPM medium. Neural induction was then initiated by withdrawal of FGF and addition of BDNF by switching the medium to neural differentiation medium (NDM; 100% Neurobasal medium, 1X B27 without vitamin A [Life Technologies], 10 ng/ml BDNF [Peprotech, Rocky Hill, NJ].) Differentiating cultures were maintained by refreshing NDM every other day until collection. Samples of these cultures were collected at days 0, 1, 2, and 4. Remaining cells (those designated for collection at days 5, 11, and 18) were replated at day 4 at a density 106 cells per well of a Poly-D-lysine/laminin-coated 6-well plate.

extract_protocol:
Cells were harvested with Accutase (Stem Cell Technologies, Vancouver, Canada). Total RNA was isolated using TRIzol (Life Technology, Carlsbad, CA)/chloroform extraction followed by spin-column purification (RNeasy mini kit, Qiagen, Venlo, Netherlands) according to the manufacturer instructions. RNA concentration and purity were determined using a Nanodrop (Thermo Fisher, Waltham, MA). RNA integrity was assessed on a Bioanalyzer (Agilent, Santa Clara, CA) using the RNA 6000 RNA chip. High-quality RNA samples (RNA Integrity Number ≥8) were used for library preparation.
200ng total RNA was used as input for the TruSeq RNA-Seq kit (Illumina) for each of the samples described. Prior to sequencing, libraries were run on a Bioanalyzer DNA7500 chip to assess purity, fragment size, and concentration. Libraries free of adapter dimers and with a peak region area (220–500 bp) ≥80% of the total area were sequenced. Individually barcoded samples were pooled and sequenced on the Illumina HiSeq 2000 platform.

tag: cell line

tag: cell type

value: ES-derived neural progenitor cells

tag: time

value: Day 2


title: 0 kg/ha glyphosate Rep-2

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 ALBRECHT BLVD N

department: Sunflower and Plant Biology Research Unit

institute: United States Department of Agriculture, Agricultural Research Service

description: For more information see linked paper

data_processing:
Basecalling was performed with CASAVA version 1.8.2, which uses Sanger scores.
Adapter sequences and low-quality bases (<30 Phred score) were trimmed from both ends of sequence. Assembly was performed with Trinity (version trinityrnaseq-r2013-02-25) with the sequences of 50 nucleotides and higher.
The abundance of every gene in each of the 8 samples was determined by performing alignment and abundance estimation using the RSEM package (version 1.2.3). Only those genes that had at least one sample with the transcripts per million (TPM) value of ≥ 0.5 were used as input for the next step.
Differential gene expression was performed at the level of genes with the EBSeq package  (version 1.0) using the median normalization approach and 10 iterations of the algorithm used by EBSeq. Genes were called differentially expressed if they had an FDR value of ≤0.05.
Genome_build: N/A
Supplementary_files_format_and_content: tab delimited text files include the TPM and FPKM of each gene, for each of the 8 samples respectively.

organism: Euphorbia esula

source_name: aerial tissue

growth_protocol: Leafy spurge plants were propagated from a uniform biotype (1984-ND001) in cone-tainers and maintained in a greenhouse (25°C with a 16 h:8 h day:night photoperiod; average daily light fluencies were ~ 350 μmol m-2 s-1 and 400 W, high-pressure sodium lamps were used as to extend the day-length) as described by Anderson and Davis (2004).

extract_protocol:
Total RNA was purified from aerial tissue samples according to the pine tree RNA extraction protocol (Chang et al. 1993).
The RNA was treated with amplification grade DNase1 (Invitrogen), quantified by the Qubit® 2.0 Fluorometer, and quality was confirmed by agarose gel electrophoresis. The RNAseq libraries were prepared with the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, Cat. N° RS–122–2101) starting from 1ug of total RNA. The pooled cDNA library was quantitated by qPCR using the Library Quantification kit (Kapa Biosystems, Cat. N° KK4824). The size range of the final cDNA libraries was determined on an Agilent bioanalyzer DNA7500 DNA chip (Agilent Technologies). The cDNA libraries were sequenced on one lane for 151 cycles from each end of the cDNA fragments on a HiSeq2500 using a TruSeq SBS sequencing kit version 1 (Illumina).

treatment_protocol: Aerial tissues of four-month old greenhouse grown leafy spurge plants were treated with 0 or 2.24 kg ha-1 active ingredient glyphosate plus 0.25% surfactant as described by Dogramaci et al. (2014). Plants were returned to growth-conducive conditions in the greenhouse after foliar glyphosate-treatment. Each experiment included four biological replicates; aerial tissues of eight plants from each replicate were decapitated 7 day post-application to determine the vegetative growth rate from crown buds as previously described by Foley et al. (2009). After six weeks of vegetative growth from crown buds of foliar glyphosate-treated and control plants, shoot heights were measured and analysed using the generalized linear mixed model (PROC GLIMMIX) procedure of SAS 9.2. Afterward, the aerial tissues were harvested and flash frozen in liquid nitrogen and stored in -80 C for further experiments i.e., shikimate and phytohormone quantification, and transcript analyses by RNAseq and qPCR.

tag: biotype

value: aerial tissue derived from crown buds

tag: treatment

value: glyphosate treated (0 kg/ha + 0.25% surfactant)

tag: developmental stage

value: 6 weeks of regrowth from crown buds of foliar glyphosate treated (0kg/ha) plants


title: 0 kg/ha glyphosate Rep-4

description: For more information see linked paper


title: NPC_Time_11_rep1

value: Day 11


title: Fermentation 2- NAG 45 min

city: Brisbane

first: Cuauhtemoc

last: Licona-Cassani

state: Queensland

address: Crn College and Cooper rds

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

data_processing:
The initial image processing and base calling was done by a standard Software pipeline provided by Illumina. Reads were aligned to the S. erythraea genome using Burrows-Wheeler Aligner BWA and Bowtie requiring no more than 2 mismatches. Only reads that aligned to one genomic location were retained unless specified for the analysis. We employed CuffDiff to determine gene expression using SAM files resulting from alignment, annotated gene file, upper quantile normalization and masking of rRNA sequences.
Gene expression was normalized between the seven libraries for total alignable reads.
Genome_build: ASM6288v1

organism: Saccharopolyspora erythraea

source_name: cells cultured in Bioreactors

growth_protocol: Bioreactor fermentation using MM-101 chemically defined media.

extract_protocol:
Total RNA was extracted using two cycles of cellular lysis in Rnase-free zirconia beads, followed by column purifications using Qiagen RNAeasy.
Libraries were prepared using DSN treatment, following of mRNA enrichment using MicrobExpress (Ambion)

treatment_protocol: RNA isolation was performed after 8h incubation at 4C in RNA later (Ambion).

tag: strain

tag: growth protocol

value: fermentation (cells cultured in bioreactor) - extraction after 45 mins of NAG induction


title: Fermentation 1

value: fermentation (cells cultured in bioreactor)


title: Fermentation 1- NAG 45 min


title: 0 kg/ha glyphosate Rep-3

description: For more information see linked paper

value: 6 weeks of regrowth from crown buds of foliar glyphosate treated (0 kg/ha) plants


title: 2.24 kg/ha glyphosate Rep-3

description: For more information see linked paper

value: glyphosate treated (2.24 kg/ha + 0.25% surfactant)

value: 6 weeks of regrowth from crown buds of foliar glyphosate treated (2.24 kg/ha) plants


title: 0 kg/ha glyphosate Rep-1

description: For more information see linked paper


title: 2.24 kg/ha glyphosate Rep-4

description: For more information see linked paper


title: RED_uninf_day4

city: Madison

first: Bruce

middle: M

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description: rep pooled

data_processing:
Illumina Casava1.7 software was used for basecalling and demultiplexing.
Sequenced reads were mapped to the combined genomes of Aedes aegypti [VectorBase: AaegL1] and Brugia malayi [GenBank:DS236884-DS264093] using TopHat v1.0.14 with parameters "--solexa1.3-quals --coverage-search --GTF".
Reads aligned to exonic regions were enumerated for each gene using htseq-count v0.4.7 with parameters "-s no -a 5 -q". A set of paired-end reads were counted as one fragment to represent a single sampling event.
Transcript abundance was expressed as fragments per kilobase of exon per million fragments mapped (FPKM). Following Robinson and Oshlack (2010), count data were normalized to account for compositional biases using TMM (trimmed mean of M) method in addition to adjusting for differing library sizes.
Genome_build: Aedes aegypti [VectorBase: AaegL1] and Brugia malayi [GenBank:DS236884-DS264093]
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Aedes aegypti

source_name: uninfected mosquito thorax

growth_protocol: Liverpool (LVP) and RED strains of Aedes aegypti were reared as previously described (Christensen and Sutherland, 1984). Briefly, mosquitoes were maintained on 0.3 M sucrose in an environmental chamber at 26.5±1°C, 75±10% RH, and with a 16 hour light and 8 hour dark photoperiod with a 90 minute crepuscular period at the beginning and end of each light period. Three- to four-day-old mosquitoes were sucrose starved for 14 to 16 hours prior to blood feeding.

extract_protocol:
Dissected tissues were immediately flash-frozen in microfuge tubes on dry ice and stored at -80°C. Total RNA was isolated using MasterPure RNA Purification Kit (Epicenter, Madison, WI) including built-in Proteinase K and DNase treatments. Labgen7b electric tissue grinder (Cole-Parmer, Vernon Hills, IL) was used for tissue homogenization, and RNA purity and concentration were determined spectrophotometrically (NanoDrop ND-1000; Thermo Scientific, Waltham, MA). For all samples, RNA integrity was visually assessed by denaturing gel electrophoresis using GelRed staining (Phenix Research Products, Candler, NC) and further confirmed by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
Multiplex sequencing libraries were generated from 10 µg total RNA (per library) using standard Illumina protocols. Separate libraries were constructed for each replicate sample from infected mosquitoes. Equal amounts of total RNA were pooled from replicates prior to library construction for uninfected blood-fed and non-blood-fed samples.

treatment_protocol: Mosquitoes were exposed to Brugia malayi (originally obtained from NIAID/NIH Filariasis Research Reagent Resource Center) by feeding on ketamine/xylazine anesthetized, dark-clawed Mongolian gerbils, Meriones unguiculatus. Microfilaremias ranged from 90-204 mf per 20 µl of blood as determined in samples obtained by orbital punctures immediately before feeding. Control mosquitoes were exposed to anesthetized, uninfected gerbils. Mosquitoes that fed to repletion were separated and maintained on 0.3 M sucrose in 30×30×30 cm colony cages. Thoracic tissues were collected every 24 hours after exposure from infected and uninfected blood-fed mosquitoes for 4 (RED) and 8 (LVP) consecutive days, and also from non-blood-fed mosquitoes at the time of exposure (i.e., time-zero sample). For each time point, 30 thoraces were collected per strain per condition. At 8 days post infection, thoraces, abdomen, and heads were dissected for each strain as previously described (Erickson et al., 2009) to assess infection intensity and prevalence. A complete set of replicate samples was collected using a separate generation of mosquitoes blood-fed on the same infected animals in an independent exposure.

value: Aedes aegypti RED

value: thorax

tag: infection

value: uninfected

value: post blood-feeding day 4


title: RED_uninf_day3

description: rep pooled

value: post blood-feeding day 3


title: 2.24 kg/ha glyphosate Rep-1

description: For more information see linked paper


title: 2.24 kg/ha glyphosate Rep-2

description: For more information see linked paper


title: RED_uninf_day0

description: rep pooled

value: post blood-feeding day 0


title: LVP_uninf_day8

description: rep pooled

value: Aedes aegypti LVP

value: post blood-feeding day 8


title: LVP_uninf_day7

description: rep pooled

value: post blood-feeding day 7


title: LVP_uninf_day5

description: rep pooled

value: post blood-feeding day 5


title: NPC_Time_0_rep0

value: ES-derived neural progenitor cells

value: Day 0


title: marmoset RNAseq data 4

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

description: polyadenylated RNA fraction

data_processing:
All RNA-seq reads were mapped with TopHat 1.4.0
Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) was then used to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations
Expression levels were normalized across samples and species with a median scaling procedure. In case multiple samples from different male individuals were available for a given tissue, the median expression value across these samples was used for further analyses. Similarly, frontal cortex and cerebellum expression values were combined into a single median “brain” value.
For the elephant samples we mapped all RNA-seq reads with TopHat 1.4.0 and worked with the unmapped reads only
FPKM values were not calculated for the elphant samples because the reference genome and the annotations have not been published yet
Genome_build: ensembl67 (marmoset)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Callithrix jacchus

source_name: cerebellum

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Strand‐specific (marmoset) and non-strand-specific (elephant) RNA-seq libraries were prepared according to the Directional mRNA‐seq Library Prep Pre‐Release Protocols from Illumina for male and female heart, liver, kidney, frontal cortex, cerebellum, ovary and testis (marmoset), and fibroblast (elephant). The testis samples for the common marmoset come from two different individuals. Marmoset tissues were obtained from the German Primate Center ("Deutsches Primatenzentrum") in Göttingen, Germany. Elephant fibroblasts were obtained from the Australian National University, Canberra, Australia. Each of these libraries were sequenced (101 cycles, single‐end) using the Illumina HiSeq 2000 platform, except for marmoset testis samples (individual 2) and both elephant fibroblast samples that were sequenced (79 cycles, single‐end) using the Illumina Illumina Genome Analyzer IIx platform.

value: cerebellum

tag: Sex

value: male

tag: individuals

value: individual 1


title: marmoset RNAseq data 9

description: polyadenylated RNA fraction

source_name: liver

value: liver

value: female


title: marmoset RNAseq data 5

description: polyadenylated RNA fraction

source_name: heart

value: heart


title: marmoset RNAseq data 8

description: polyadenylated RNA fraction

source_name: kidney

value: kidney


title: marmoset RNAseq data 7

description: polyadenylated RNA fraction


title: marmoset RNAseq data 6

description: polyadenylated RNA fraction


title: RED_uninf_day2

description: rep pooled

value: Aedes aegypti RED

value: thorax

value: uninfected

value: post blood-feeding day 2


title: marmoset RNAseq data 2

description: polyadenylated RNA fraction

source_name: frontal cortex

value: frontal cortex


title: LVP_uninf_day4

description: rep pooled

value: Aedes aegypti LVP

value: post blood-feeding day 4


title: LVP_uninf_day0

description: rep pooled

value: post blood-feeding day 0


title: LVP_uninf_day2

description: rep pooled


title: LVP_uninf_day3

description: rep pooled

value: post blood-feeding day 3


title: RED_uninf_day1

description: rep pooled

value: post blood-feeding day 1


title: marmoset RNAseq data 1

description: polyadenylated RNA fraction


title: marmoset RNAseq data 10

description: polyadenylated RNA fraction


title: LVP_uninf_day1

description: rep pooled


title: marmoset RNAseq data 12

description: polyadenylated RNA fraction

source_name: testis

value: testis


title: RED_inf_day4_rep2

description: rep 2

source_name: filarial worm-infected mosquito thorax

value: Brugia malayi infected


title: marmoset RNAseq data 3

description: polyadenylated RNA fraction

value: cerebellum

value: individual 1


title: elephant RNAseq data 2

description: polyadenylated RNA fraction

organism: Loxodonta africana

source_name: fibroblast

value: fibroblast

value: male


title: elephant RNAseq data 1

description: polyadenylated RNA fraction

value: female


title: marmoset RNAseq data 11

description: polyadenylated RNA fraction

source_name: ovary

value: ovary


title: RED_inf_day1_rep2

description: rep 2

value: Aedes aegypti RED

value: thorax


title: LVP_uninf_day6

description: rep pooled

value: uninfected

value: post blood-feeding day 6


title: LVP_inf_day8_rep2

description: rep 2

value: Aedes aegypti LVP

value: post blood-feeding day 8


title: elephant RNAseq data 3

description: polyadenylated RNA fraction

data_processing:
All RNA-seq reads were mapped with TopHat 1.4.0
Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) was then used to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations
Expression levels were normalized across samples and species with a median scaling procedure. In case multiple samples from different male individuals were available for a given tissue, the median expression value across these samples was used for further analyses. Similarly, frontal cortex and cerebellum expression values were combined into a single median “brain” value.
For the elephant samples we mapped all RNA-seq reads with TopHat 1.4.0 and worked with the unmapped reads only
FPKM values were not calculated for the elphant samples because the reference genome and the annotations have not been published yet
Genome_build: ensembl67 (marmoset), ensembl72 (rat), ensembl73 (wallaby)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

value: individual 2


title: LVP_inf_day6_rep2

description: rep 2


title: marmoset RNAseq data 13

description: polyadenylated RNA fraction


title: LVP_inf_day7_rep2

description: rep 2

value: post blood-feeding day 7


title: LVP_inf_day5_rep2

description: rep 2

value: post blood-feeding day 5


title: RED_inf_day3_rep2

description: rep 2

value: post blood-feeding day 3


title: LVP_inf_day3_rep2

description: rep 2

value: Brugia malayi infected


title: LVP_inf_day2_rep2

description: rep 2

value: post blood-feeding day 2


title: RED_inf_day2_rep1

description: rep 1


title: RED_inf_day2_rep2

description: rep 2


title: RED_inf_day4_rep1

description: rep 1

value: post blood-feeding day 4


title: wallaby RNAseq data 1

description:
polyadenylated RNA fraction
wallaby_normalized_all_tissues_FPKM.txt

organism: Notamacropus eugenii

value: liver

value: individual 1


title: RED_inf_day1_rep1

description: rep 1

value: post blood-feeding day 1


title: LVP_inf_day8_rep1

description: rep 1


title: LVP_inf_day7_rep1

description: rep 1


title: LVP_inf_day4_rep1

description: rep 1


title: LVP_inf_day3_rep1

description: rep 1


title: LVP_inf_day2_rep1

description: rep 1


title: WT_Nuc_(20140107_1_1)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Permeabilized WT S.cerevisiae cells were MNase-treated, and DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.

data_processing:
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads obtaining from sequencing S.cervisiae DNA to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads mapped to S.cervisiae. (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig).
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads obtaining from sequencing S.cervisiae DNA to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads mapped to S.cervisiae. (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig).
Genome_build: sacCer3
Supplementary_files_format_and_content: bed and wig peak

organism: Saccharomyces cerevisiae

source_name: MNase-cleaved chromatin.

extract_protocol:
Samples was prepared as described in PMID 22722846. After lyticase treatment and washes, samples were subjected to MNase treatment and needle extraction, and the soluble chromatin was recovered and used for ChIP with a Cse4 anti-rabbit antibody as described in PMID 24336359.
Sequencing libraries were prepared as described in PMID 22025700.

value: spheroplasts

tag: genetic background

value: MATa, his3delta1, leu2delta0, met15delta0, ura3delta0


title: WT_Pell_(20140107_1_5)

description: Permeabilized WT S.cerevisiae cells were MNase-treated, soluble chromatin was extracted and DNA was purified from the insoluble pellet and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: LVP_inf_day1_rep1

description: rep 1

tag: tissue

value: thorax


title: marmoset RNAseq data 14

description: polyadenylated RNA fraction

value: testis

value: male


title: rat RNAseq data 12

description:
polyadenylated RNA fraction
rat_normalized_all_tissues_FPKM.txt

organism: Rattus norvegicus


title: WT_Cse4_IP_(20140107_1_13)

description: Permeabilized WT S.cerevisiae cells were MNase-treated, soluble chromatin was extracted and used for Chromatin immunoprecipitation with a Cse4 anti-rabbit antibody. DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.

tag: genotype


title: LVP_inf_day4_rep2

description: rep 2

value: Aedes aegypti LVP


title: RED_inf_day3_rep1

description: rep 1

value: Aedes aegypti RED


title: LVP_inf_day6_rep1

description: rep 1

value: post blood-feeding day 6


title: LVP_inf_day5_rep1

description: rep 1


title: rat RNAseq data 10


title: rat RNAseq data 11

value: ovary

value: female


title: rat RNAseq data 8

value: kidney


title: WT-OP_Pell_(20140107_1_7)

description: Permeabilized WT S.cerevisiae cells with cysteine substituted for histone H4S47 were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled, MNase-treated, soluble chromatin was extracted and DNA was purified from the insoluble pellet and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: rat RNAseq data 7


title: H4C_Pell_(20140107_1_6)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were MNase-treated, soluble chromatin was extracted and DNA was purified from the insoluble pellet and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.

value: H4S47C, deltaHHF2, BY4741 (MATa, his3delta1, leu2delta0, met15delta0, ura3delta0)


title: WT-OP_Nuc_(20140107_1_3)

description: Permeabilized WT S.cerevisiae cells were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled MNase-treated, and DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: rat RNAseq data 9


title: LVP_inf_day1_rep2

description: rep 2

value: Brugia malayi infected


title: rat RNAseq data 5

value: heart


title: H4C_Cse4_IP_(20140107_1_14)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were MNase-treated, soluble chromatin was extracted and used for Chromatin immunoprecipitation with a Cse4 anti-rabbit antibody. DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: rat RNAseq data 4

value: cerebellum


title: rat RNAseq data 3

value: individual 1


title: H4C-OP_Nuc_(20140107_1_4)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled MNase-treated, and DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: H4C-OP_Cse4_IP_(20140107_1_16)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled, MNase-treated, soluble chromatin was extracted and used for Chromatin immunoprecipitation with a Cse4 anti-rabbit antibody. DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: wallaby RNAseq data 2


title: WT-OP_Cse4_IP_(20140107_1_15)

description: Permeabilized WT S.cerevisiae cells were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled, MNase-treated, soluble chromatin was extracted and used for Chromatin immunoprecipitation with a Cse4 anti-rabbit antibody. DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: rat RNAseq data 2

value: frontal cortex


title: rat RNAseq data 1


title: H4C-OP_Pell_(20140107_1_8)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were N(1,10-phenanthroline-5-yl)iodoacetamide (OP)-labeled, MNase-treated, soluble chromatin was extracted and DNA was purified from the insoluble pellet and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.

value: spheroplasts


title: NPC_Time_5_rep1

value: ES-derived neural progenitor cells

value: Day 5


title: H4C_2_(20130612_1,2_4)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were labeled on cysteines with orthophenantroline complex, which chelates a copper ion. In an oxidizing environment the derivatized residue contacts a deoxyribose CIH and cleaves DNA, and the fragments that are released are purified and subjected to paired-end Illumina sequencing. Biological replicate using KAPA DNA polymerase for library amplification.

data_processing:
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)
Genome_build: sacCer3
Supplementary_files_format_and_content: bed and wig peak

source_name: Chemically cleaved chromatin.

extract_protocol: Samples was prepared as described in PMID 22722846. Sequencing libraries were prepared as described in PMID 22025700.

tag: organelle

value: nuclei

tag: genetick background

value: MATa his3-1 leu2-0 ura3-0,mutant:H4S47C in the HHF1 gene (PMID 22722846 for details)


title: NPC_Time_5_rep0


title: H4C_1_(20130520_1,2_4)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were labeled on cysteines with orthophenantroline complex, which chelates a copper ion. In an oxidizing environment the derivatized residue contacts a deoxyribose CIH and cleaves DNA, and the fragments that are released are purified and subjected to paired-end Illumina sequencing. Technical replicate using Phusion DNA polymerase for library amplification.


title: H4C_3_(20131010_1_8)


title: NPC_Time_4_rep2

value: Day 4


title: ALU_mock_(20120131_3)

description: AluI (New England Biolabs) cleavage reactions were performed according to the manufacturer's instructions on wildtype DNA subjected to mock hydroxy radical cleavage.

data_processing:
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads obtaining from sequencing S.cervisiae DNA mixed with D.melanogaster DNA from a unrelated experiment to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. We also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to S.cervisiae (Supplementary file .bed). 3. We compared the endpoints of the paired reads with the ALU sites in AGCT_V64.bed looking for AG^CT cleavages.
Genome_build: sacCer3
Supplementary_files_format_and_content: bed and wig peak


title: rat RNAseq data 6

value: male


title: NPC_Time_4_rep1


title: ALU_genomic_(20120131_4)

description: AluI (New England Biolabs) cleavage reactions were performed according to the manufacturer's instructions on wildtype DNA directly purified from cells using the Epicentre MasterPure Yeast DNA Purification Kit.


title: HS_mRNAseq

status: Public on Apr 14 2014

city: Shanghai

first: Zhe

last: Wang

address: 3663 N. Zhongshan Rd.

country: China

institute: East China Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
De novo reconstruction of the transcriptome from RNA-seq data was performed using Trinity software, followed by transcript quantification using RSEM software.
NCBI nr database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) was used for gene annotation by Blast.
Gene counts (i.e. gene expression levels) were normalized by TMM method using the edgeR package
Genome_build: NCBI nr database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/)
Supplementary_files_format_and_content: The txt file, GeneCounts_Normalized.txt, includes the normalized gene counts of the 14 samples. The fasta file, GeneNameSeq.fasta, includes the gene common names for the GeneID in the txt file, as well as the mRNA sequences.

organism: Miniopterus schreibersii

source_name: Metatarsals of hindlimb digits I-V

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen), and treated with DNase I using RNase-Free DNase set (Qiagen). TruSeq™ RNA Sample Prep Kit (Illumina), Truseq PE Cluster Kit (Illumina) and Truseq SBS Kit (Illumina) were used for constructing libraries, cluster amplification and final sequencing-by-synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: embryonic stage

value: Fetal stage


title: HW_mRNAseq

source_name: Interdigital tissues between hindlimb digits I and V


title: FL_mRNAseq

source_name: Metacarpals of forelimb digits II-V


title: FW_mRNAseq

source_name: Interdigital tissue between forelimb digits I and II


title: FI_mRNAseq

source_name: Forelimb digit I


title: FF_mRNAseq

source_name: Interdigital tissues between forelimb digits II and V


title: HM_mRNAseq

source_name: Middle part of the Hindlimb bud


title: HA_mRNAseq

source_name: Anterior part of the Hindlimb bud


title: FD_mRNAseq

source_name: Forelimb digits II-V


title: FP_mRNAseq

source_name: Posterior  part of the forelimb bud


title: FM_mRNAseq

source_name: Middle part of the forelimb bud


title: H4C_Nuc_(20140107_1_2)

description: Permeabilized S.cerevisiae cells with cysteine substituted for histone H4S47 were MNase-treated, and DNA was purified and subjected to paired-end Illumina sequencing using Phusion DNA polymerase for library amplification.


title: HpaII-126-N5

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

institute: Albert Einstein College of Medicine

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: The wig files were generated using in house pipeline; Scores represent degree of unmethylation

extract_protocol:
Human Peripheral Blood Mononuclear Cells were separated using Ficoll Hypaque treatment from whole blood. Genomic DNA samples were extracted uisng standard protocol.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII in 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpureXP (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, we did the size selection using gel extraction kit(Qiagen).

tag: clinical phenotype

value: Healthy Control


title: FLM_aza_treated_RNA-seq

city: Taipei

first: Pao-Yang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
RNA-seq alignment using Tophat 2.0.4, Tuber_melanosporum_v1.0_annot.gff as library junction, allowing 2 mismatches and only uniquely aligned reads, filtering as default by Tophat
abundance counting using HTSeq version 0.5.4p3, using "union" mode for ambiguous reads (default)
calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by Tophat
calculate p-values with DESeq version 2.12
RPKM values for treated and untreated samples are contained in aza.txt and aza.repeats.txt found on series entry.
Genome_build: Tuber_melanosporum_v1.0

organism: Tuber melanosporum

growth_protocol: T. melanosporum mycelia (isolate Tmel28) were grown in the dark at 23 °C in synthetic liquid medium (SLM) containing (mg/L) CaCl2 ∙ 2H2O (66), NaCl (25), KH2PO4 (500), (NH4) 2HPO4 (250), MgSO4 ∙ 7H2O (150), FeNa–EDTA (20), thiamine hydrochloride (1), and glucose (5 g/L).

extract_protocol:
Total RNA from FLM and FB was extracted as described previously (Montanini et al. 2003) and purified with the RNeasy Plant Mini kit and on-column DNase I digestion (QIAGEN) following the manufacturer’s instructions. RNA integrity was verified by a Bioanalyzer: RIN scores of 7.0 and 6.5 for FB and FLM, respectively.
RNA was quantified with the Qubit RNA BR Assay and 1 μg of purified RNA was utilized as starting material for library construction, which was carried out with the Illumina TruSeq RNA Sample Preparation kit following the manufacturer's instructions. Libraries were sequenced using 50-bp single-end reads on the HiSeq 2000 System (Illumina).
Tissues were grinded in liquid nitrogen, extracted in the extraction solution [50% Phenol; 50% Extraction buffer (100 mM Tris-HCl pH 8.0; 100 mM NaCl; 20 mM EDTA; 1% SDS] at 65°C for 10‘ and centrifuged at 14,000 rpm for 10’. The aqueous phase was transferred to new tubes and extracted twice with phenol:chloroform (1:1) and once with chloroform. After precipitation with ethanol, samples were resuspended in H20. LiCl (2M) precipitation (2M LiCl) was employed to separate RNA (pellet) from genomic DNA (supernatant). Genomic DNA was precipitated with ethanol and resuspended in H20.

treatment_protocol: 5-azacytidine (5-AZA) dissolved in water was added to growing cultures of T. melanosporum mycelia every 5 days at 100µM final concentration (treatment) for 45 days. The last addition was applied 24 hours before harvesting. In control samples (untreated), the same volume of water was added instead of 5-AZA.

value: wild type

value: mycelia


title: FA_mRNAseq

source_name: Anterior part of the forelimb bud


title: FLM_untreated_RNA-seq

source_name: truffle free-living mycelium_untreated


title: HpaII-110-N26

source_name: Human Peripheral Blood Mononuclear Cells

tag: cell type


title: HpaII-105-N24

value: Human Peripheral Blood Mononuclear Cells


title: FLM_aza_treated_BS

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

extract_protocol:
Genomic DNA was extracted by grinding in liquid nitrogen followed by DNeasy Plant Mini kit (QIAGEN) purification
After an additional phenol:chloroform extraction, gDNA was sheared by sonication to generate DNA fragments in the 150-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the EpiTect kit (QIAGEN) was utilized for bisulfite treatment. Two consecutive rounds of conversion were performed for a total of 10 hours. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna Hiseq 2000 sequencer).
Tissues were grinded in liquid nitrogen, extracted in the extraction solution [50% Phenol; 50% Extraction buffer (100 mM Tris-HCl pH 8.0; 100 mM NaCl; 20 mM EDTA; 1% SDS] at 65°C for 10‘ and centrifuged at 14,000 rpm for 10’. The aqueous phase was transferred to new tubes and extracted twice with phenol:chloroform (1:1) and once with chloroform. After precipitation with ethanol, samples were resuspended in H20. LiCl (2M) precipitation (2M LiCl) was employed to separate RNA (pellet) from genomic DNA (supernatant). Genomic DNA was precipitated with ethanol and resuspended in H20.


title: HpaII-68-N15


title: FLM_untreated_BS


title: HD_mRNAseq

source_name: Hindlimb digits I-V


title: HpaII-67-N14


title: HpaII-59-N11


title: HpaII-66-N13


title: HP_mRNAseq

source_name: Posterior  part of the Hindlimb bud


title: HpaII-99-O21

value: Obese non-asthma


title: HpaII-70-O11


title: HpaII-82-O14


title: HpaII-108-O24


title: HpaII-119-O29


title: HpaII-114-N28


title: HpaII-124-A4

value: Normal-weight Asthma


title: HpaII-64-O9


title: HpaII-104-A32


title: HpaII-103-A31


title: HpaII-69-O10


title: HpaII-125-A5


title: HpaII-76-A24


title: HpaII-75-A23


title: HpaII-57-A20


title: HpaII-123-OA5

value: Obese Asthma


title: HpaII-121-OA1


title: HpaII-122-OA2


title: HpaII-109-OA30


title: HpaII-80-OA29


title: HpaII-60-OA24


title: HpaII-65-OA26


title: HpaII-58-OA23


title: HpaII-71-O12


title: C-33 1E2

city: Bethesda

first: Kui

last: Shen

address: Room 3B62, 31 Center Drive

institute: National Institute of Allergy and Infectious Diseases, NIH

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptors  and masked for low-quality short reads, then mapped to hg19 using tophat with parameters: tophat -p 5 --no-mixed -G hg19_genes.gtf Bowtie2Index sample1_sort_f.fastq sample1_sort_r.fastq
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calcuated by software cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each sample

source_name: Cervix

growth_protocol: C-33 cells were cultured in DMEM, 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was prepared using RNeasy mini prep kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four hours before harvesting, E2 expression was induced with 3 μM CdSO4.

value: HPV1 E2

tag: cell line


title: HpaII-91-A28


title: sh-QKI rep2

first: Jingyi

last: Hui

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The RNA-Seq reads were aligned to the human genome (hg19), annotated splicing-junction sequences, and predicted splicing-junction sequences.
We preformed the alignment with Bowtiev 0.12.8  with parameters -v3 -k2 -m1 --best --strat. The ambiguously aligned reads were excluded from further analysis.
To calculate the gene expression value, the numbers of alignments that located within the exons and covered the exon-junctions were summed and normalized by the total number of mapped reads (per million reads) and the length of exons (per Kbp).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: BEAS2B cells

growth_protocol: The human bronchial epithelial BEAS2B cells were grown in Dulbecco’s Modified Eagle’s medium supplemented with 10% fetal bovine serum.

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

value: bronchial epithelial BEAS2B cells

value: epithelial (virus transformed)

tag: passages

value: lung/bronchus

tag: genotype/variation

value: QKI-knockdown


title: sh-QKI rep1


title: 20091006_1881_X_BMM_LPS_0120_P65

status: Public on Apr 13 2014

first: Theo

last: Knijnenburg

address: 401 Terry Avenue North

institute: Institute for Systems Biology

data_processing:
Reads were aligned to the mouse genome using eland extended with an ELAND SEED LENGTH value of 25 and an ELAND MAX MATCHES value of 15, and with the 3′-most base excluded. Reads aligned to the same position and strand were counted only once to eliminate duplicates from PCR amplification.
For all ChIP-Seq samples, aligned reads were processed into extended fragments of length 158 bp, the estimated typical insert size in the sequencing library. This estimated size was determined by assaying representative ChIP-Seq samples (after the PCR amplification step) using the Agilent Bioanalyzer to determine the typical fragment size in the sequencing library, and subtracting the combined size of the two Illumina adaptor molecules.
For each sample, the multiscale representation (MSR) was derived as explained in the manuscript.
Genome_build: mm9
Supplementary_files_format_and_content: Enriched segments of the MSR pruned with T=1.05 and R = 0.2. BED format

organism: Mus musculus

growth_protocol: The BMMs were cultured from female C57BL/6 mice (age 8-12 weeks)

extract_protocol:
For ChIP–Seq analysis, formaldehyde-fixed cells were sonicated and processed for immunoprecipitation. In brief, 3 × 107 BMMs were fixed for 10 min in 1% formaldehyde in PBS, washed in PBS, and harvested by scraping in PBS. Cells were lysed by resuspending cell pellets in RIPA buffer (10mM Tris-HCl, pH8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% Deoxcholic acid sodium salt) and drawing the cell suspensions three times through a 30 gauge needle.  Chromatin was sheared using a probe sonicator (130 W Ultrasonic Processor with a 3mm tip, 5 × 60s at 30% maximum setting). Sonication quality was checked by gel electrophoresis.  Protein concentrations in the extracts were determined (BioRad DC Protein Assay Kit I # 500-111) and sonicated cell extracts containing 0.5 mg protein were incubated with antibodies overnight at 4oC. Immune complexes were recovered by incubation with a 50%-50% mix of magnetic beads coated with Protein A or Protein G (Dynabeads Protein A Invitrogen # 100.02D, Dynabeads Protein G Invitrogen # 100.04D). The magnetic beads were washed with RIPA buffer and the chromatin was eluted with 1% SDS in TE buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA pH8.0) at 65oC for 15 min. Eluted chromatin was reverse-cross-linked by adding 226 mM NaCl and incubating at 65oC for > 5 hr. Then 36 mM Tris–HCl pH8.0, 9 mM EDTA, and 1.5 U of Proteinase K (Fermentas # EO0491) was added to the samples and they were incubated at 42oC for > 1 hr.  DNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1, v:v:v) extraction. The purified immunoprecipitated DNA was prepared for sequencing with the Illumina ChIP-Seq Sample Prep Kit and processed according to the manufacturer’s instructions (Illumina Part # 11257047 Rev. A).
A sequencing library for the Illumina Genome Analyzer was derived from the IP using the Illumina reagent kit (see systemsimmunology.org). Single-ended, 36-cycle sequencing was performed on an Illumina Genome Analyzer, and the raw image data were processed using the Illumina Genome Analysis Pipeline Software on a dedicated sequence data processing system (see Genome Analyzer Pipeline Software User Guide, Illumina, San Diego, CA, USA, v0.3).

tag: age

value: 8-12 weeks

value: primary murine bone marrow macrophage cells (BMMs)

tag: stimuated with

value: lipopolysaccharide (LPS)

tag: time after lps stimulation

value: 120 minutes

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology Inc.

tag: chip antibody cat.#


title: 20090821_1880_X_BMM_LPS_0060_P65

tag: strain

value: 60 minutes


title: sh-Ctrl rep2

tag: tissue

value: control


title: 20090805_VL04_BMM_LPS_0480_meH3K27

value: wild type

value: 480 minutes

value: Methylated Histone H3K27me3

value: Millipore


title: C-33

description: Sample 1

tag: treatment


title: 20090611_1919_A_BMM_NoStim_0000_PolII

value: none (unstimulated control)

value: 0 (no stim)

value: Anti-RNA polymerase II, clone CTD4H8

value: Upstate


title: 20090625_1923_A_BMM_LPS_0360_PolII

value: 360 minutes


title: 20090709_1866_A_BMM_NoStim_0000_meH3K27


title: 20090805_1958_B_BMM_LPS_0060_PolII


title: sh-Ctrl rep1

value: bronchial epithelial BEAS2B cells

value: epithelial (virus transformed)

value: lung/bronchus


title: 20090625_1921_A_BMM_LPS_0120_PolII

value: 8-12 weeks

value: primary murine bone marrow macrophage cells (BMMs)

value: lipopolysaccharide (LPS)


title: 20090625_1920_A_BMM_LPS_0060_PolII

value: 60 minutes


title: 20090611_1868_A_BMM_LPS_0120_meH3K27

value: 120 minutes


title: 20090529_1938_B_BMM_LPS_0240_AcH4

value: wild type

value: 240 minutes

value: Acetylated Histone H4


title: 20090611_1870_A_BMM_LPS_0240_meH3K27

value: Methylated Histone H3K27me3

value: Millipore


title: 20090529_1935_B_BMM_LPS_0060_AcH4


title: 20090529_1936_B_BMM_LPS_0120_AcH4


title: 20090529_1934_B_BMM_NoStim_0000_AcH4

value: none (unstimulated control)

value: 0 (no stim)


title: 20090529_1922_A_BMM_LPS_0240_PolII

value: Anti-RNA polymerase II, clone CTD4H8

value: Upstate


title: 20090507_1875_A_BMM_LPS_0120_AcH4


title: 20090429_H41877_A_BMM_LPS_0240_AcH4


title: 20090805_VL05_BMM_LPS_0060_7hdelay_meH3K27

value: 480 minutes


title: 20090507_1874_A_BMM_LPS_0060_AcH4


title: 20090805_1960_B_BMM_LPS_0240_PolII


title: 20090116_1420_C_BMM_LPS_0240_ATF3

value: Santa Cruz Biotechnology Inc.


title: Control 2

city: Zürich

first: Katharina

last: Gapp

address: Winterthurerstrasse 190

department: Health Science and Technology

institute: Swiss Federal Institue of Technology

description: 0-50 base pairs

data_processing:
Adapters were removed using Cutadapt (v1)
Fastq files were converted to Fasta using a custom perl script running in Perl v5.12.1
Fasta files were trimmed to remove reads >=15 base pairs and <=30 base pairs using a custom perl script running in Perl v5.12.1
Fasta files were collapsed to unique sequences retaining read counts using the Fastx toolkit module
Supplementary_files_format_and_content: fasta: >seq name_read count

source_name: sperm cell RNA of 5 mice

extract_protocol:
RNA was extracted according to the standard Trizol protocol after purifying samples using elutriation centrifugation. The quantity and quality of RNAs were determined by Qubit® fluorometer (Life Technologies) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively.
Small RNA libraries were prepared according to a modified Illumina v1.5 protocol. Briefly, small RNAs of <50 nt were purified on an acrylamide gel. Universal miRNA cloning linker (New England Biolabs) instead of 3´ adapters and then 5’ Illumina adapters ( CTGTAGGCACCATCAAT)were single-stranded ligated with T4 truncated RNA and T4 ligase respectively. The constructs were purified on an acrylamide gel to remove empty adapters then reverse-transcribed and PCR-amplified. The primers used for cDNA synthesis and PCR were designed to insert an index in the 3- adapter. Multiplexing indexes were as follows: Sample 1: ACACCA, Sample 2: CTTTCT, Sample 3: GAGTTG, Sample 4: CAAGTA, Sample 5: GATGGC, Sample 6: GGCACG, Sample 7: CGACAG.

treatment_protocol: Males were subjected to unpredictable maternal separation combined with unpredictable maternal stress during their first 2 weeks of life, while control males were left undisturbed. Mature sperm samples were collected in adulthood.

tag: sample type

value: sperm cell RNA of 5 mice

tag: stress

tag: gender

value: male


title: 20081229_1349A_C_BMM_LPS_0120_P65

value: 8-12 weeks

value: primary murine bone marrow macrophage cells (BMMs)


title: Control 1

description: 0-50 base pairs

source_name: sperm cell RNA of 1 mouse

value: sperm cell RNA of 1 mouse


title: MSUS 1

description: 0-50 base pairs

value: unpredictable maternal separation combined with unpredictable maternal stress during their first 2 weeks of life


title: 20081022_1345_A_BMM_LPS_0240_ATF3

value: wild type

value: lipopolysaccharide (LPS)


title: 20080731_1343_D_BMM_LPS_0060_P50

value: 60 minutes

value: eBioscience


title: MSUS 2

description: 0-50 base pairs


title: 20080731_1342_D_BMM_NoStim_0000_P50


title: 20081114_1352_B_BMM_LPS_0240_ATF3

value: 240 minutes


title: MSUS 3

description: 0-50 base pairs


title: Control 4

description: 0-50 base pairs


title: 20091124_1879_X_BMM_NoStim_0000_P65

value: none (unstimulated control)


title: Control 3

description: 0-50 base pairs


title: 20080606_1348_B_BMM_LPS_0060_P50


title: 20080723_1273_A_BMM_LPS_0060_P50


title: 20080723_1272_A_BMM_NoStim_0000_P50

value: 0 (no stim)


title: aTreg Input Rep1

status: Public on Apr 12 2014

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: aTreg Input Rep1

data_processing:
Base calling was performed using Illumina software pipeline (Genome Analyzer)
Align to the mouse genome (mm9) using bowtie (version 0.12.7) allowing 1 mismatch and reporting only uniquely aligning hits.
Peak calling was perfomed using SPP and MACS.  Number of peaks was estimated as described in our manuscript.
Genome_build: mm9 (ucsc genome)
Supplementary_files_format_and_content: see README file for additional details

source_name: Activated Treg

extract_protocol:
Cells were harvested from mice that were approximately 8 weeks old.  Lymph nodes and spleen were extracted and sorted based on GFP (Foxp3)
Cells were fixed with formaldehyde, nuclei were extracted and sonicated.  Antibodies were incubated with sonicated chromatin.
Standard illumina kit

value: Activated Treg

tag: antibody

tag: cell source

value: Primary Mouse T cells isolated ex-vivo and sorted


title: AL5_OE

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
base calling and base call quality calibration are accomplished with illumina sequence control software (SCS) during the run
Sequenced reads were trimmed for adaptor sequence
Filtered reads were aligned to the TAIR9 genome using  bowtie version 0.12.7 with parameters -v 2 -m 1
peaks were found using MACS version 1.4.2 with -g 120000000 -s 36 -w .
Genome_build: TAIR9
Supplementary_files_format_and_content: wig files were generated using MACS from each chromosome for each sample

source_name: whole plant

growth_protocol: Seeds of AL5 over-expressing Arabidopsis and al5 T-DNA insertion mutant Salk_075676 (from Arabidopsis Biological Resource Center, ABRC, The Ohio State University) were sterilized with 75% ethanol for 5 min and then with 1% NaClO for 10 min, plated on 1/2 Murashige and Skoog (MS) medium and stratified at 4 °C for 3 d to synchronize germination. The seeds were then germinated at 22 °C and the seedlings were grown with a photoperiod of 16-h light and 8-h dark. Seven-day-old seedlings were transplanted to vermiculite and grown for three weeks.

extract_protocol:
ChIP DNA was extracted following the protocol published on Nature protocol,2008, titled "An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants."
Library were prepared according to the protocol of ChIP-Seq DNA sample Prep Kit (Illumina)

treatment_protocol: No treatment

value: Polyclonal antibody of AL5 protein

tag: genotype

value: AL5 overexpression

value: whole plant


title: 20080723_1440_C_BMM_LPS_0060_P50


title: aTreg Foxp3 ChIP Rep2

description: aTreg Foxp3 ChIP Rep2

tag: cell type

value: Foxp3 antibody is a custom polyclonal antibody that has been affinity purified


title: 20090507_1873_A_BMM_NoStim_0000_AcH4

tag: genotype/variation

value: 8-12 weeks

value: Acetylated Histone H4

value: Millipore


title: al5_mutant

value: AL5 knockout


title: 20081114_1523_A_BMM_LPS_0060_P65

value: wild type

tag: age

value: primary murine bone marrow macrophage cells (BMMs)

value: Santa Cruz Biotechnology Inc.


title: aTreg Foxp3 ChIP Rep3

description: aTreg Foxp3 ChIP Rep3


title: Foxp3GFPKO H3K27me3 ChIP Rep1

description: Foxp3GFPKO H3K27me3 ChIP Rep1

source_name: Foxp3GFPKO (het female)

value: Foxp3GFPKO (het female)

value: H3K27me3 antibody (Upstate 07-449)


title: aTreg Foxp3 ChIP Rep1 (Tech Rep 1)

description: aTreg Foxp3 ChIP Rep1 (Tech Rep 1)


title: 20080723_1438_C_BMM_NoStim_0000_P50

tag: stimuated with

value: none (unstimulated control)

value: eBioscience


title: Foxp3GFPKO H3K27me3 ChIP Rep2

description: Foxp3GFPKO H3K27me3 ChIP Rep2


title: adult_1

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

country: Canada

institute: The University of Victoria

description: Adult

data_processing:
Please refer to TSA: GAZX00000000.1 (http://www.ncbi.nlm.nih.gov/nuccore/604768531)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using CLC Genomics Workbench v6.5
Genome_build: GAZX00000000.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Caligus rogercresseyi

source_name: whole

extract_protocol:
RNA from pooled samples from farmed Atlantic salmon was extracted by mixer-mill (Retsch) homogenization in Trizol (Invitrogen), followed by column clean-up using the RNeasy kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: whole

value: adult


title: aFoxp3GFPKO H3K27me3 ChIP Rep2

description: aFoxp3GFPKO H3K27me3 ChIP Rep2

source_name: Foxp3GFPKO (male)

value: Foxp3GFPKO (male)

value: Primary Mouse T cells isolated ex-vivo and sorted


title: aFoxp3GFPKO H3K27me3 ChIP Rep1

description: aFoxp3GFPKO H3K27me3 ChIP Rep1


title: male_1

description: Male


title: Tn H3K27me3 ChIP Rep2

description: Tn H3K27me3 ChIP Rep2

source_name: Tnaive

value: Tnaive


title: copepodid_1

description: Copepodid

value: copepodid


title: female_1

description: Female


title: chalimus_1

description: Chalimus

value: chalimus


title: eggs_1

description: Eggs

value: egg


title: rTreg H3K27me3 ChIP Rep1

description: rTreg H3K27me3 ChIP Rep1

source_name: Resting Treg

value: Resting Treg


title: aTreg H3K27me3 ChIP Rep1

description: aTreg H3K27me3 ChIP Rep1

value: Activated Treg


title: Tn H3K27me3 ChIP Rep1

description: Tn H3K27me3 ChIP Rep1


title: testis_1

status: Public on Apr 11 2014

description: Testis

data_processing:
Please refer to TSA: GATF00000000.1 (http://www.ncbi.nlm.nih.gov/nuccore/601035834)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using CLC Genomics Workbench v6.5
Genome_build: GATF00000000.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Esox lucius

source_name: Testis

extract_protocol:
All tissues for RNA-seq were extracted from a single, juvenile, male pike caught November 1, 2011 in the Portage Diversion/Assiniboine River Floodway near Portage la Prairie, MB, Canada (N50.00747 W98.38181). The animal was euthanized and then frozen on dry ice until sampling, and subsequently at -80°C. Tissues were extracted by mixer-mill (Retsch) homogenization in Trizol (Invitrogen), followed by column clean-up using the RNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: juvenile

value: Testis

value: male

value: wild type


title: aTreg Foxp3 ChIP Rep1 (Tech Rep 2)

description: aTreg Foxp3 ChIP Rep1 (Tech Rep 2)

value: Foxp3 antibody is a custom polyclonal antibody that has been affinity purified


title: aTreg H3K27me3 ChIP Rep2

description: aTreg H3K27me3 ChIP Rep2

value: H3K27me3 antibody (Upstate 07-449)


title: aTreg Foxp3 ChIP Rep4

description: aTreg Foxp3 ChIP Rep4


title: spleen_1

description: Spleen

source_name: Spleen

value: Spleen


title: nose_1

description: Nose

source_name: Nose

value: Nose


title: liver_1

description: Liver

source_name: Liver

value: Liver


title: kidney_1

description: Kidney

source_name: Kidney

value: Kidney


title: TFAP2A_MCF

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using ELAND software to NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18
Supplementary_files_format_and_content: wig file

growth_protocol: The human breast cancer cell line MCF‐7 was obtained from American Type Culture Collection (ATCC). The cell line was grown in appropriate medium at 37°C in a humidified 5% CO2 incubator.

extract_protocol: One hundred million cells were cross-linked for 10 min at 37°C using 0.7% formaldehyde, 0.125 M glycine. Cells were washed twice with PBS, re-suspended in lysis buffer and incubated for 5 minutes. Cells were collected by centrifugation and cell pellets were frozen in liquid nitrogen and stored at minus 80°C. Cell pellets were thawed in lysis buffer, collected by centrifugation and cell nuclei were re-suspended in RIPA buffer. Chromatin was sonicated using conditions determined empirically for MCF-7 cells to achieve an optimal fragment length between 100 to 400 bp. After sonication, samples were centrifuged at 20,000 × g for 10 min at 4°C. The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml. The sample was immunoprecipitated with 10 μg of TFAP2A with the addition of Dynal sheep anti-mouse Dynabeads and allowed to recognize their antigens overnight at 4°C with rotation. Protein/antibody/DNA complexes were collected magnetically followed by washing and elution. Protein/DNA cross-links were reversed using 200 mmol/L NaCl at 65°C overnight. DNA was treated with Proteinase K and RNase A and was recovered with QIAquick PCR Kit (Qiagen) according to manufacturer's suggested protocol. Purified DNA was quantified by using a NanoDrop ND-1000 (NanoDrop, Wilmington, DE). 100 ng of ChIPed DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.

tag: cell line

value: breast carcinoma cell line MCF-7

value: AP-2α Antibody (3B5) [Santa Cruz, catalog# sc-12726]


title: heart_1

description: Heart

source_name: Heart

value: Heart


title: Teff H3K27me3 ChIP Rep1

description: Teff H3K27me3 ChIP Rep1

source_name: T effector

value: T effector

value: Primary Mouse T cells isolated ex-vivo and sorted


title: rTreg H3K27me3 ChIP Rep2

description: rTreg H3K27me3 ChIP Rep2

value: Resting Treg


title: eye_1

description: Eye

source_name: Eye

value: Eye


title: head_kidney_1

description: Head kidney

source_name: Head kidney

value: juvenile

value: Head kidney


title: TP53_Cisplating_replicate_2

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Fastq files were generated with Illumina pipeline software (CASAVA 1.8.1 using the default chastity base call thresholds) and subsequently filtered to remove PCR duplicates.
Reads were mapped to the GRCh37/hg19 reference genome using bwa allowing for gapped alignment and maximum five alignment locations for each read
MACS peak calling algorithm (version 1.4; p=1e-5, shiftsize=100)used to call peaks comparing to input
Resulting peaks were curated to remove Encode “Dark regions” (Encode Consensus Signal Artifact Regions) and spurious peaks (>1000 reads, mostly in centromeric regions)
Genome_build: hg19
Supplementary_files_format_and_content: .wig files were normalised (per 10 million reads) using wigreader  (https://github.com/rgejman/wigreader)
Supplementary_files_format_and_content: MACS peak files

source_name: Human neonatal foreskin keratinocytes

growth_protocol: Human neonatal foreskin keratinocytes were isolated and cultured in Epilife supplemented with human keratinocyte growth supplement (HKGS)

extract_protocol: p63 or p53 bound DNA was enriched for by chromatin immunoprecipitation .End repaired sequencing libraries were prepared from two independent biological replicatesand matched input control using NEBNext sample preparation kit (New England biolabs)  according to manufacturers instructions.  The resulting adapter ligated DNA was subjected to 16 cycles of adapter mediated pcr using Herculase II Fusion DNA Polymerase (Agilent). The resulting libraries were size fractionated in a 2% agarose gel and purified to obtain 2-400Bp fragments.  Each library was validated using an agilent 2100 bioanalyser and sequenced on the Illumina GAII sequencer according to manufacturers instructions.

treatment_protocol: Cells were treated for 24hrs with 350nM Adrimycin or 25uM Cisplatin

tag: chip antibody

tag: agent

value: 25uM Cisplatin


title: gut_1

description: Gut

source_name: Gut

value: Gut

value: male

value: wild type


title: gill_1

description: Gill

source_name: Gill

value: Gill


title: TP53_Adriamycin_replicate_2

value: 350nM Adrimycin


title: Teff H3K27me3 ChIP Rep2

description: Teff H3K27me3 ChIP Rep2

value: H3K27me3 antibody (Upstate 07-449)


title: TP53_Untreated_replicate_2


title: TP63_Untreated_replicate_2


title: brain_1

description: Brain

source_name: Brain

value: Brain


title: TP53_Adriamycin_replicate_1


title: TP63_Adriamycin_replicate_2


title: muscle_1

description: Muscle

source_name: Muscle

value: Muscle


title: Input


title: TP53_Untreated_replicate_1


title: Prostate_VA-PC-99-85

city: Atlanta

first: Carlos

last: Moreno

state: Georgia

address: 615 Michael St

department: Department of Pathology & Laboratory Medicine

institute: Emory University

data_processing:
filtered in FASTQC, not trimmed, and mapped with a maximum of 2bp mismatch to hg19.
Quality control : FastQC, RNA-SEQc
Mapping : Tophat 2.0.8, Bowtie 2.1.0
FPKM : Cufflinks
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM - tab delimited

source_name: formalin-fixed, paraffin-embedded (FFPE) prostatectomy sample

growth_protocol: FFPE - Formalin fixed Parrafin embedded tissue blocks

extract_protocol:
RNA extraction Omega XP -FFPE from two 1mm cores
Modified TruSeq RNA Sample preparation with Ambion Ribominus step and no poly-A selection

tag: collection site

value: Atlanta VA Medical Center

tag: cgsr id

tag: external id

value: prostate

tag: months to bcr

tag: months total f/u

tag: bcr

tag: prepsa

tag: race

value: W

tag: pstage

tag: gleason score

tag: tgleason

tag: sms

value: Negative

tag: no of uniquely mapped reads

tag: no. of total reads

tag: % mapped


title: Prostate_VA-PC-98-53

tag: tissue

value: B

value: Positive


title: Prostate_VA-PC-96-44


title: TP53_Cisplating_replicate_1

tag: chip antibody

tag: agent


title: TP63_Cisplatin_replicate_1


title: Prostate_VA-PC-97-46

tag: collection site

tag: cgsr id


title: TP63_Untreated_replicate_1


title: TP63_Adriamycin_replicate_1


title: Prostate_VA-PC-96-43

tag: external id

tag: months to bcr


title: Prostate_VA-PC-95-41

tag: months total f/u

tag: bcr


title: Prostate_VA-PC-95-42

tag: prepsa

tag: race

value: unknown


title: TP63_Cisplatin_replicate_2


title: Prostate_VA-PC-95-34

tag: pstage

tag: gleason score


title: Prostate_VA-PC-94-71

tag: tgleason

tag: sms


title: Prostate_VA-PC-93-24

tag: no of uniquely mapped reads

tag: no. of total reads


title: Prostate_VA-PC-93-21

tag: tissue

tag: % mapped


title: Prostate_VA-PC-93-20


title: Prostate_VA-PC-95-37


title: Prostate_VA-PC-92-9


title: Prostate_VA-PC-91-65


title: Prostate_VA-PC-92-11


title: Prostate_VA-PC-00-99


title: Prostate_UTPC170

value: U. Toronto Sunnybrook Research Centre


title: Prostate_VA-PC-90-4


title: Prostate_VA-PC-00-96


title: Prostate_UTPC164


title: Prostate_VA-PC-00-86


title: Prostate_UTPC147


title: Prostate_VA-PC-00-88


title: Prostate_UTPC146


title: Prostate_UTPC132


title: Prostate_UTPC131


title: Prostate_UTPC116


title: Prostate_UTPC127


title: Prostate_UTPC114


title: Prostate_UTPC160


title: Prostate_UTPC104


title: Prostate_UTPC110


title: Prostate_UTPC101


title: stomach_1

description: Stomach

data_processing:
Please refer to TSA: GATF00000000.1 (http://www.ncbi.nlm.nih.gov/nuccore/601035834)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using CLC Genomics Workbench v6.5
Genome_build: GATF00000000.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Stomach

tag: age

value: juvenile

value: stomach

tag: genotype


title: Prostate_UTPC099

tag: collection site

tag: cgsr id


title: Prostate_UTPC093

tag: external id

tag: months to bcr


title: Prostate_UTPC088

tag: months total f/u

tag: bcr


title: Prostate_UTPC058

tag: prepsa

tag: race


title: Prostate_UTPC041

tag: pstage

tag: gleason score


title: Prostate_UTPC021

tag: tgleason

tag: sms


title: Prostate_UTPC034

tag: no of uniquely mapped reads

tag: no. of total reads


title: Prostate_UTPC034-2

tag: tissue

tag: % mapped


title: Prostate_UTPC029-2


title: Prostate_UTPC029


title: Prostate_UTPC141


title: Prostate_UTPC021-2


title: Prostate_UTPC009


title: Prostate_UTPC004


title: Prostate_UTPC009-2


title: Prostate_UTPC019-2


title: Prostate_UTPC019


title: Prostate_MCC-PT220

value: Moffitt Cancer Center


title: Prostate_MCC-PT264


title: Prostate_MCC-PT197


title: Prostate_VA-PC-99-82


title: Prostate_VA-PC-99-81


title: Prostate_VA-PC-99-80


title: Prostate_VA-PC-99-78


title: Prostate_VA-PC-99-79


title: Prostate_VA-PC-99-77


title: Prostate_VA-PC-99-76


title: Prostate_VA-PC-99-75


title: Prostate_VA-PC-99-54


title: Prostate_VA-PC-97-49


title: Prostate_VA-PC-97-50


title: Prostate_VA-PC-99-55


title: Prostate_VA-PC-97-52


title: Prostate_VA-PC-97-74


title: Prostate_VA-PC-97-51


title: Prostate_VA-PC-97-48


title: Prostate_UTPC004-2


title: Prostate_VA-PC-96-45


title: Prostate_VA-PC-94-70


title: Prostate_VA-PC-97-47


title: Prostate_VA-PC-94-28


title: Prostate_VA-PC-93-19


title: Prostate_VA-PC-93-68


title: Prostate_VA-PC-99-84


title: Prostate_VA-PC-99-83


title: Prostate_VA-PC-92-13


title: Prostate_VA-PC-91-64


title: Prostate_VA-PC-92-66


title: Prostate_VA-PC-00-98


title: Prostate_VA-PC-91-62


title: Prostate_VA-PC-00-95


title: Prostate_VA-PC-00-94


title: Prostate_VA-PC-00-93


title: Prostate_VA-PC-00-92


title: Prostate_VA-PC-00-91


title: Prostate_VA-PC-00-90


title: Prostate_UTPC107


title: Prostate_MCC-PT243


title: Prostate_UTPC008


title: Prostate_VA-PC-00-87


title: Prostate_UTPC162


title: Prostate_UTPC020


title: Prostate_MCC-PT199


title: Prostate_MCC-PT236


title: flowthrough_mock

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012).
We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of reads to the human reference genome sequence (hg18).
mRNA half-lives were determined as described in Schwanhaeusser et al. Nature 2011 from the three fractions total/4suRNA/flowthrough
Genome_build: hg18

source_name: HEK293 cell culture

growth_protocol: HEK293 were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen). 4SU residues were biotinylated using EZ-Link biotin-HPDP (Thermo Fisher Scientific). Biotinylated 4SU-labled RNA was separated from non-labeled RNA using μMACS Streptavidin MicroBeads (Miltenyi) and 4SU-labeled RNA was eluted from μColumns by addition of 100 mM DTT. RNA was recovered from the flow-though and 4SU-labeled fractions using MinElute Spin columns (Qiagen). Input (total), flow-though (non-labeled RNA) and eluted (4SU-labled RNA) samples were used for poly(A)+ mRNA library preparation following the TruSeq RNA sample Prep v2 LS protocol (Illumina). The libraries were sequenced on an Illumina HiSeq2500 for 100 cycles (multiplexed 1× 101 + 7 index). mRNA half-lives were computed as previously described (Schwanhausser et al., 2011)

treatment_protocol: For global mRNA for half-life measurements, mock- or MOV10 siRNA transfected HEK293 cells were labeled with 700 µM 4SU for 60 min.

tag: purification

value: oligo(dT) beads

tag: cell line

tag: transfection

value: mock


title: Prostate_VA-PC-92-14

tag: collection site

tag: cgsr id

tag: external id


title: Prostate_MCC-PT081

tag: months to bcr

tag: months total f/u

tag: bcr


title: Prostate_MCC-PT127

tag: prepsa

tag: race

tag: pstage


title: Prostate_MCC-PT168

tag: gleason score

tag: tgleason

tag: sms


title: flowthrough_MOV10siRNA

value: MOV10 siRNA


title: Prostate_VA-PC-91-61

tag: tissue

tag: no of uniquely mapped reads

tag: no. of total reads


title: Prostate_VA-PC-00-97

tag: % mapped


title: 4suRNA_MOV10siRNA

tag: purification

tag: cell line

tag: transfection


title: UPF1_PARCLIP

description:
binding sites
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCGTATGCCGTCTTCTGCTTGT
5' adapter: GTTCAGAGTTCTACAGTCCGACGATCNN, 3' adapter: TCTAAAATCGTATGCCGTCT

data_processing: Adapters were removed with FLEXBAR (the flexible adapter remover: http://sourceforge.net/projects/flexbar/) aligned to hg18 using BWA. Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script. After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340–352 for details.

growth_protocol: Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged MOV10 WT, MOV10 K530A and MOV10 D645N were grown in high glucose SILAC DMEM (PAA) supplemented with 10 % (v/v) dialyzed fetal bovine serum (Sigma-Aldrich), 4 mM Glutamine (PAA), 0.05 mg/mL Lysine (Sigma-Aldrich) and 0.03 mg/mL Arginine (Sigma-Aldrich). Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged UPF1 were grown in high glucose DMEM media (Invitrogen) supplemented with 10 % (v/v) fetal bovine serum (Sigma-Aldrich), 1 % (v/v) 2 mM L-glutamine (Invitrogen), 1 % (v/v) 10,000 U/mL penicillin and 10,000 μg/mL streptomycin (Invitrogen).

extract_protocol: cDNA libraries were generated as described (Hafner et al., 2010), amplified using the Phusion High-Fidelity DNA polymerase (Finnzymes) and gel purified using the QIAquick gel extraction kit (Qiagen).

treatment_protocol: Cells were incubated with 100 μM 4SU (ChemGenes) nucleoside analog for 14 hrs and UV crosslinked as previously described (Hafner et al., 2010), frozen in liquid nitrogen and stored at -80 oC. Cells were lysed in 3 times the cell pellet volume of high salt NP-40 lysis buffer (50 mM Tris pH = 7.2, 500 mM NaCl, 1% (v/v) NP-40, 1 mM DTT, complete EDTA-free protease inhibitor cocktail (Roche)), incubated 30 min on ice followed by 45 sec sonication (80 % amplitude). UPF1 cell pellets were lysed in 3 times the cell pellet volume of low salt NP-40 lysis buffer (50 mM HEPES-KOH pH = 7.5, 150 mM KCl, EDTA-NaOH pH = 8.0,  0.5% (v/v) NP-40, 1 mM DTT, complete EDTA-free protease inhibitor cocktail (Roche)), incubated 20 min on ice. IP  was performed as previously described (Hafner et al., 2010) with the following modifications: (1) The second ribonuclease digestion was performed with a final concentration of 20 U/μL RNaseT1 (Fermentas) for MOV10 WT and MOV10 K530A IPs. The second ribonuclease digestion was performed with a final concentration of 10 U/μL RNaseT1 for MOV10 D645N and UPF1 IPs (2) Proteinase K (Roche) digestion was performed with a final concentration of 2 mg/mL for 1 hr at 55 oC.

tag: antibody

value: FLAG

tag: culture medium

value: DMEM

tag: expression


title: MOV10_D645N_PARCLIP

description:
binding sites
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTCCATTCGTATGCCGTCTTCTGCTTG
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTCGTATCGTATGCCGTCTTCTGCTTG

value: MOV10 D645N


title: MOV10_K530A_PARCLIP

description:
binding sites
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTTTTATCGTATGCCGTCTTCTGCTTG
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTCACGTCGTATGCCGTCTTCTGCTTG

value: MOV10 K530A


title: 4suRNA_mock


title: Prostate_MCC-PT184

tag: collection site

tag: cgsr id

tag: external id

value: prostate

tag: months to bcr

tag: months total f/u

tag: bcr


title: total_MOV10siRNA


title: total_mock


title: SP_Cont2_RNA

status: Public on Apr 10 2014

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: processed data file: SP_Cont_RNA.txt

data_processing:
Illumina Casava 1.8 software was used for basecalling.
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads.
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1)
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Streptococcus pneumoniae

source_name: Untreated S. pneumoniae cells

growth_protocol: Strain DLA3 was grown to OD600 = 0.4 in 5 ml tubes and diluted 1:100 in fresh C+Y medium pH 7.4 . To study the effects of antibiotics, cells grown without antibiotics were compared to cells grown with 0.15 μg/ml HPUra or 28 ug/ml kanamycin. Cells were grown in microtiter plates and growth and competence development (luc-expression) was followed.

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation.
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis.

tag: strain

tag: genotype/variation

value: bgaA::ssbB_luc (DLA3)

tag: treated with

value: none (untreated control)

tag: molecule subtype

value: total RNA, rRNA depleted


title: SP_Kan_RNA

description: processed data file: SP_Kan_RNA.txt

source_name: Kanamycin-treated S. pneumoniae cells

value: 28 ug/ml kanamycin


title: SP_Cont2_DNA

description: processed data file: SP_Cont_DNA.txt

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega).
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: the DNA samples were treated with ultrasound (3-5 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase (9-11 cycles, depending on the sample). Aliquots of the PCR amplified libraries were examined by capillary electrophoresis.


title: SP_HPUra1_DNA

description: processed data file: SP_HPUra_DNA.txt

source_name: HPUra-treated S. pneumoniae cells

value: 0.15 μg/ml HPUra


title: SP_Cont1_DNA

description: processed data file: SP_Cont_DNA.txt


title: SP_HPUra2_RNA

description: processed data file: SP_HPUra_RNA.txt


title: SP_HPUra2_DNA

description: processed data file: SP_HPUra_DNA.txt


title: SP_Kan_DNA

description: processed data file: SP_Kan_DNA.txt


title: SP_HPUra1_RNA

description: processed data file: SP_HPUra_RNA.txt


title: MOV10_WT_PARCLIP

description:
binding sites
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTCCCATCGTATGCCGTCTTCTGCTTG
5' adapter: GTTCAGAGTTCTACAGTCCGACGATC, 3' adapter: TCTGGGATCGTATGCCGTCTTCTGCTTG

value: MOV10 wild type


title: Aid+/+ MEF#2_p3

city: Kyoto

first: Ren

last: Shimamoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Dept. of Reprogramming Science

country: Japan

institute: Center for iPS Cell Research and Application (CiRA)

data_processing:
Basecalls performed using CASAVA version 1.8.1
Data were filtered using Illumina's Quality Filtering and 76th bases in reads were not used.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9rc1 with default parameters.
Peaks were detected using MACS version 1.4.1 with default parameter and without control samples.
Genome_build: mm9
Supplementary_files_format_and_content: Text files which contain peak information were generated using MACS version 1.4.1.

source_name: Aid+/+ MEF#2_p3

growth_protocol: iPS cells and ES cells were cultured in DMEM supplemented with 20% FBS, 0.1 mM non-essential amino acids, 2 mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.11 mM 2-mercaptoethanol, LIF on gelatin coated dishes. Two μg/mL puromycin was to the medium of iPS cells. MEFs were cultured in DMEM supplemented with 10% FBS, 50 U/ml penicillin-streptomycin.

extract_protocol:
Cells were lysed with genome buffer (8.8 mM Tris-HCl pH8.0, 135 mM NaCl, 8.8 mM EDTA, 1% SDS, 200 μg/mL protenase K) and treated with RNase. Subsequently genomic DNA was purified with Phenol-Chloroform Isoamyl Alcohol (PCI) DNA extraction.
Genomic DNA was sonicated to 100-300 bp fragment with Covaris E210 (Covaris). Methylated DNA was enriched with EpiXplore Methylated DNA Enrichment Kit (Takara) according to manufacturer’s protocol. Multiplexed MBD-seq libraries were prepared from 10 ng of metylated DNA fragment using NEBNext ChIP-seq Library Prep Master Mix (New England BioLabs). For sequencing using GAIIx, cluster generation was performed using TruSeq SR Cluster Kit v2. Each lane of flow cells contained one sample. Sequencing was performed by a single-read run mode with total 76 cycles, including 75-bp read and one cycle for phasing.

treatment_protocol: Ｎｏ

tag: genotype

value: Aid+/+

tag: cell type

value: MEF

tag: modification

value: Nanog-GFP

tag: gender

value: male


title: MG1.19_ES cells_cultured on gelatin

source_name: MG1.19_ES cells_cultured on gelatin

value: ES


title: B6 ES_ES cells_cultured on gelatin

source_name: B6 ES_ES cells_cultured on gelatin


title: 979B1_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin

value: iPS


title: 979F1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin

value: Aid-/-

value: Aid disrupted, Nanog-GFP


title: 981E4_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin


title: 967B2_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin


title: 979B3_Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin


title: Aid+/+ MEF#3_p3

source_name: Aid+/+ MEF#3_p3


title: 979F3_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin


title: 967B4 _Aid+/+ iPS cells_Nanog-GFP_p6_cultured on gelatin


title: 981E1_Aid-/- iPS cells_Nanog-GFP_p6_cultured on gelatin


title: dsRNA in DICER kd cells

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: total RNA was digested using T1 nuclease and resulting dsRNA was sequenced

data_processing:
Basecalling was by Illumina's bcl2fastq v1.8.4, with internal chastity filter. Parameters for configureBclToFastq:.pl  --ignore-missing-bcl  --fastq-cluster-count 0  --no-eamss --use-bases-mask "Y*,I8,Y*" --mismatches 1 --ignore-missing-stats --ignore-missing-control
Mapping was by BWA v0.7 followed by stampy v1.0.21. Parameters for bwa:  -t 8 -q10  Parameters for stampy: defaults, except: -t 8  --bamkeepgoodreads
Processed bam file of WTCHG_64954_282 and WTCHG_64954_283 to wiggle type format. Multiple peaks from set 282 were combined into one, if they overlayed one peak in 283 and vice versa. This was done iteratively until the peaks remained constant. "Top peaks" refers to the peaks where the maximum coverage is >1500 in 282 and 283 data simultaneously.
genome build hg19
supplementary files format and content: peak coordinates from overlay step and top peaks

source_name: HEK 293 cells

extract_protocol:
total RNA was prepared using Trizol reagent, digested using T1 nuclease and resulting dsRNA was sequenced
100ng of sample was phosphatase and PNK treated, as in the Illumina mRNA Directional protocol. All clean ups (post-PNK, post-PCR) were done using Ampure XP beads. Following steps were carried out using the NEBNext Small RNA Library Prep Kit but with custom indexes designed by the WTCHG facility (Reference: Improved workflows for high throughput library preparation using the transposome-based nextera system <http://www.biomedcentral.com/1472-6750/13/104> Sarah Lamble, Elizabeth Batty, Moustafa Attar, David Buck, Rory Bowden, Gerton Lunter, Derrick Crook, Bassam El-Fahmawi, Paolo Piazza BMC Biotechnology 2013, 13:104, 20 November 2013). The concentration of each library was determined by realtime using Agilent qPCR Library and a MX3005P instrument (Agilent). Sequencing was performed on an Illumina HiSeq2000, using 50bp paired end reads.

tag: cell line

value: HEK 293

tag: treatment

value: Dicer knockdown

tag: dicer status

value: knockdown


title: SP_Cont1_RNA

description: processed data file: SP_Cont_RNA.txt

value: bgaA::ssbB_luc (DLA3)


title: dsRNA in wt cells

value: wt


title: Aid+/+ MEF#1_p3

source_name: Aid+/+ MEF#1_p3


title: EC_Trim2_RNA

description: processed data file: EC_Trim_RNA.txt

organism: Escherichia coli

source_name: Trimethoprim-treated E. coli cells

growth_protocol: Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim.

value: wild type

value: 0.5 μg/ml trimethoprim

value: total RNA, rRNA depleted


title: RF8_ES cells_p19_cultured on gelatin

source_name: RF8_ES cells_p19_cultured on gelatin


title: EC_Trim1_RNA

description: processed data file: EC_Trim_RNA.txt