title: empty-vector-H3K4me3-ChIP-rep1

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

data_processing:
Sequencing data were aligned to GRCh37-lite genome-plus-junctions reference (http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome) using BWA (version 0.5.7). BWA "aln" and "sampe" were run with default parameters. Reads failing the Illumina chastity filter were flagged with a custom script, and duplicated reads were flagged with Picard Tools (version 1.31, http://broadinstitute.github.io/picard/). Unmapped reads, optical duplicates and PCR duplicates were removed.
Wig files were produced using BAM2WIG (http://www.epigenomes.ca/tools.html).
For assessment of data quality peaks were identified at a false discovery rate of 0.01 using FindPeaks version FP4.0.15
To identify peaks present in ChIP samples that were not present in sequenced input DNA (false discovery rate of 0.05) we used MACS2 version 2.0.10.20131010
Intersects between peak lists were obtained using ChIPseek. Genes associated with peaks were identified using GREAT
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were produced using MACS2 to compare ChIP samples to input control samples. Peak files were produced using FindPeaks version FP4.0.15 for quality control purposes.

source_name: empty vector cells

growth_protocol: Cells were cultured in DMEM with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library construction was carried out on the Bravo liquid handling platform using VWorks Automation Control Software (Agilent Automation). Samples were first subjected to end repair using T4 Polynucleotide Kinase (NEB), T4 DNA Polymerase (NEB) and Klenow DNA Polymerase (NEB) at room temperature for half an hour. DNA was purified using PEG-Sera Mag Speedbeads (Fisher), with 13.87% final PEG concentration.  A-tailing was then performed using Klenow exo minus (NEB) at 37oC for 30 minutes. Products were purified as before. Illumina short sequencing adaptors were ligated to A-tailed product using T4 DNA Ligase (NEB) at room temperature overnight. To remove adaptor dimers and library fragments below 200 bp, products were purified twice using PEG-Sera Mag Speedbeads with 8.89% and 10.91% final PEG concentrations. Adaptor ligated libraries were PCR amplified and barcoded using custom indexing primers, Illumina PCR primer 1.0 and 0.5 U of Phusion Hot Start II (Fisher). The initial denaturation step at 98oC for 30 seconds was followed by 13 cycles of 15 seconds at 98oC, 30 seconds at 65oC and 30 seconds at 72oC, and a final step at 72oC for 5 minutes. Amplified libraries were purified using PEG-Sera Mag Speedbeads with 9.19% final PEG concentration. Libraries were quantified using a Qubit HS DNA assay (Invitrogen) and equal-molar amounts were pooled.  Each pool was quantified for sequencing with Kapa SYBR Fast Complete Universal qPCR kit (Kapa Biosystems). ChIP libraries were sequenced on the Illumina HiSeq 2000/2500 platform using v3 chemistry and HiSeq Control Software version 2.0.10. H3K27ac ChIP libraries were sequenced 5 per lane, H3K4me3 ChIP libraries were sequenced 20 per lane and ChIP input control DNA was sequenced 14 per lane.

treatment_protocol: Cells were treated with DMSO (1.07uL/mL) for 6hrs

tag: treatment

value: DMSO (1.07uL/mL)

value: H3K4me3 (Cell Signaling C42D8)

tag: expression

value: empty-vector


title: Aa_V1 [RNA-Seq]

status: Public on Jul 01 2015

type: SRA

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: North Ave NW

department: School of Biology

country: USA

institute: Georgia Institute of Technology

library_source: transcriptomic

data_processing:
All short reads were aligned to HuRef19 using the TopHat spliced-reads fast mapper in Cufflinks v2.0.1. FPKM (fragments per kilobase of exon per millions) values were obtained and log2 transformed.
Log2 transformed FPKM values were normalized by the Supervised Normalization of Microarray (SNM) algorithm with a model fitting individual's age and BMI as the biological variable, and removing effects of RNA quality, gender and ethnicity
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including SNM normalized log2 FPKM values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Peripheral blood samples (10ml) were collected into EDTA tubes that were frozen for DNA preservation, and Tempus RNA tubes (Life Technologies, Grand Island NY) for preservation of RNA.
Total RNA was isolated from Tempus tubes using the Life Technologies Tempus Spin RNA Isolation Kit following manufacturer's protocols.
Unstranded TruSeq cDNA libraries were prepared using Illumina TruSeq RNA Sample Prep kits (Set A, v2) from total RNA following the manufacturer’s protocols.

tag: tissue

value: Whole blood

tag: gender

value: Female

tag: ethnicity

value: African American


title: Cg_V2 [RNA-Seq]

value: Caucasian


title: WT-MEF2B-input-control-rep2

library_source: genomic

molecule: genomic DNA

source_name: WT MEF2B-V5 cells

tag: cell line

tag: chip antibody


title: empty-vector-input-control-rep2


title: WT-MEF2B-input-control-rep1


title: empty-vector-input-control-rep1


title: empty-vector-H3K4me3-ChIP-rep2


title: WT-MEF2B-H3K4me3-ChIP-rep1


title: D83V-MEF2B-V5-ChIP-input-rep2

data_processing:
Sequencing data were aligned to GRCh37-lite genome-plus-junctions reference (http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome) using BWA (version 0.5.7). BWA "aln" and "sampe" were run with default parameters. Reads failing the Illumina chastity filter were flagged with a custom script, and duplicated reads were flagged with Picard Tools (version 1.31, http://broadinstitute.github.io/picard/). Unmapped reads, optical duplicates and PCR duplicates were removed.
Wig files were produced by BAM2WIG (http://www.epigenomes.ca/tools.html).
For assessment of data quality peaks were identified at a false discovery rate of 0.01 using FindPeaks version FP4.0.15
To identify peaks present in ChIP samples that were not present in sequenced input DNA (false discovery rate of 0.05) we used MACS2 version 2.0.10.20131010
Intersects between peak lists were obtained using ChIPseek. Genes associated with peaks were identified using GREAT
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were produced using MACS2 to compare ChIP samples to input control samples. Peak files were produced using FindPeaks version FP4.0.15 for quality control purposes.

source_name: D83V MEF2B-V5 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and MEF2B-DNA complexes were isolated with antibody.
Library construction was carried out on the Bravo liquid handling platform using VWorks Automation Control Software (Agilent Automation). Samples were first subjected to end repair using T4 Polynucleotide Kinase (NEB), T4 DNA Polymerase (NEB) and Klenow DNA Polymerase (NEB) at room temperature for half an hour. DNA was purified using PEG-Sera Mag Speedbeads (Fisher), with 13.87% final PEG concentration.  A-tailing was then performed using Klenow exo minus (NEB) at 37oC for 30 minutes. Products were purified as before. Illumina short sequencing adaptors were ligated to A-tailed product using T4 DNA Ligase (NEB) at room temperature overnight. To remove adaptor dimers and library fragments below 200 bp, products were purified twice using PEG-Sera Mag Speedbeads with 8.89% and 10.91% final PEG concentrations. Adaptor ligated libraries were PCR amplified and barcoded using custom indexing primers, Illumina PCR primer 1.0 and 0.5 U of Phusion Hot Start II (Fisher). The initial denaturation step at 98oC for 30 seconds was followed by 13 cycles of 15 seconds at 98oC, 30 seconds at 65oC and 30 seconds at 72oC, and a final step at 72oC for 5 minutes. Amplified libraries were purified using PEG-Sera Mag Speedbeads with 9.19% final PEG concentration. Libraries were quantified using a Qubit HS DNA assay (Invitrogen) and equal-molar amounts were pooled.  Each pool was quantified for sequencing with Kapa SYBR Fast Complete Universal qPCR kit (Kapa Biosystems). ChIP libraries were sequenced on the Illumina HiSeq 2000/2500 platform using v3 chemistry and HiSeq Control Software version 2.0.10. MEF2B-V5 ChIP libraries were sequenced 8 per lane. Input DNA was sequenced 14 per lane.


title: D83V-MEF2B-V5-ChIP-input-rep1


title: empty-vector-H3K27ac-ChIP-rep2

value: H3K27ac (Abcam, ab4729)


title: WT-MEF2B-V5-ChIP-input-rep1


title: empty-vector-H3K27ac-ChIP-rep1


title: D83V-MEF2B-V5-ChIP-rep1

value: V5 (Invitrogen, R960-25)


title: WT-MEF2B-H3K4me3-ChIP-rep2


title: K4E-MEF2B-V5-ChIP-input-rep2

source_name: K4E MEF2B-V5 cells


title: WT-MEF2B-V5-ChIP-rep2


title: Ad_V1 [RNA-Seq]


title: WT-MEF2B-H3K27ac-ChIP-rep2


title: WT-MEF2B-V5-ChIP-input-rep2


title: empty-vector-RNAseq-iono

data_processing:
Sequencing data were aligned to GRCh37-lite genome-plus-junctions reference (http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome) using BWA (version 0.5.7). BWA "aln" and "sampe" were run with default parameters. Reads failing the Illumina chastity filter were flagged with a custom script, and duplicated reads were flagged with Picard Tools (version 1.31, http://broadinstitute.github.io/picard/). Unmapped reads, optical duplicates and PCR duplicates were removed.
Wig files were produced using BAM2WIG (http://www.epigenomes.ca/tools.html).
The WIG files were used in an in-house pipeline  to calculate RPKM values for each gene
Differential expression analysis of RNA-seq data used DEseq Release 2.13 (Bioconductor). To enable analysis of data with only one replicate per group, “SharingMode” was set to “fit-only” and “method” was set to “blind”. Default settings were otherwise used.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files contain abundance values (i.e. baseMean scores) calculated using DEseq

source_name: empty-vector

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Invitrogen) as directed.
Plate-based libraries were prepared following the BC Cancer Agency's Michael Smith Genome Sciences Centre (BCGSC) strand specific paired-end protocol on a Biomek FX robot (Beckman-Coulter) with Ampure XP SPRI beads (Beckman-Coulter). First-strand cDNA was synthesized using the Superscript cDNA Synthesis kit (Life Technologies) with random hexamer primers and 1 μg/μL Actinomycin D. The second strand cDNA was synthesized following the Superscript cDNA Synthesis protocol, but substituting dTTP for dUTP. The cDNA was fragmented in an E210 sonicator (Covaris) for 55 seconds, using a duty cycle of 20% and intensity of 5. Purified cDNA was subjected to end-repair and phosphorylation by T4 DNA polymerase, Klenow DNA Polymerase, and T4 polynucleotide kinase in a single reaction, followed by 3’ A-tailing by Klenow fragment (3’ to 5’ exo minus). Products were ligated to Illumina PE adapters. The second strand was then digested using Uracil-N-Glycosylase (Life Technologies), thus achieving strand specificity. After purification, products were PCR-amplified using Phusion DNA Polymerase (Thermo Fisher Scientific) and Illumina’s PE primer set, with cycle conditions of 98°C for 30sec followed by 10-15 cycles of 98°C for 10 seconds, 65°C for 30 seconds and 72°C for 30 seconds, and then 72°C for 5 minutes. Purified PCR products were analysed using a LabChip GX (PerkinElmer). PCR products with a desired size range were purified using a 96-channel size selection robot developed at the BCGSC. The DNA quality was assessed using an Agilent DNA 1000 series II assay. DNA was quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and diluted to 8 nM. RNA libraries were sequenced on the Illumina HiSeq 2000/2500 platform using v3 chemistry and HiSeq Control Software version 2.0.10. RNA libraries were sequenced 2 per lane.

treatment_protocol: Cells were treated with either ionomycin (1.5uM, Sigma I0634) or DMSO (solvent control, 1.07uL/mL) for 6hrs

value: ionomycin (1.5uM)


title: Ab_V2 [RNA-Seq]


title: WT-MEF2B-V5-ChIP-rep1


title: K4E-MEF2B-V5-ChIP-input-rep1


title: D83V-MEF2B-V5-ChIP-rep2


title: K4E-MEF2B-V5-ChIP-rep1


title: Y69H-MEF2B-V5-RNAseq-iono


title: D83V-MEF2B-V5-RNAseq-iono


title: K4E-MEF2B-V5-RNAseq-iono


title: WT-MEF2B-V5-RNAseq-DMSO


title: Y69H-MEF2B-V5-RNAseq-DMSO


title: WT-MEF2B-V5-RNAseq-iono


title: K4E-MEF2B-V5-RNAseq-DMSO


title: empty-vector-RNAseq-DMSO


title: K4E-MEF2B-V5-ChIP-rep2


title: FZD6-dN

city: Beijing

first: Zhenzhen

last: Liu

state: Beijing

address: NO.1 Beichen West Road, Chaoyang Distric

department: Beijing Institute of Genomics

country: China

institute: Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Sequenced reads  were aligned to the reference genome (GRCh37.73/hg19) with the Tophat alignment software tools.
The uniquely aligned reads were used for calculation by Cufflinks software and the gene expression levels were normalized using the FPKM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HCT116 Cell line

growth_protocol: The cells were cultured in McCOY's 5A (Sigma) plus 10% FBS (Hyclone) with penicillin (100 U/ml) plus streptomycin (100 μg/ml) (Sigma) at 37 °C with 5% CO2 in a humidified incubator (Thermo Scientific), and were expanded on a 6-cm dish until the cells were seeded on 96/24-well plates.

extract_protocol:
Total RNA was extracted using a RNA prep Pure Cell/Bacteria Kit (Tiangen). Three milligrams of total RNA from each of the 3 independent experiments was mixed for the whole transcriptome library construction.
The library preparation was performed according to the TruSeq™ RNA Sample Preparation Guide standard protocol.

treatment_protocol: 2×10^3 or  3×10^4 HCT 116 cells were seeded in each well of the 96 or 24-well plates one day before transfection.The transfection was mediated by Lipofectamine™ 2000 (Invitrogen) according to the manufacturer’s instructions.

value: transfect siRNA with double N


title: FZD6-sN

value: transfect siRNA with single N


title: WT-MEF2B-H3K27ac-ChIP-rep1


title: 0C

value: blank control


title: FZD6-0N

value: transfect siRNA without N


title: laryngo-pharyngeal tumor micro rna-seq LP6_Normal (matched normal for LP6_Tumor)

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

country: India

institute: ganit labs foundation

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
3dapc3_miRNA-seq

data_processing:
LifeScope v2.5-r2.5.1 and DeSeq (all with default parameters)
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_Table3.xlsx cotaining read statistics

source_name: normal tissue

extract_protocol:
Purelink RNA-mini and Ambion miRVANa
solid-5500xl

treatment_protocol: tumors and normal samples

tag: patient/sample id

value: matched normal from the same patient


title: R1.CE.8E.ChIP

city: Cambridge

first: Erel

last: Levine

state: MA

address: 52 Oxford St

institute: Harvard University

data_processing:
bwa version 0.7.0-r320 used for alignment to C. elegans genome version ce10
samtools 0.1.18 filtering  to obtain uniquely mapped reads
picard for filtering duplicates
bedtools to create coverage file
Genome_build: ce10
Supplementary_files_format_and_content: wig

organism: Caenorhabditis elegans

source_name: 8E syncrhonized embryos

growth_protocol: Freshly starved synchronized N2 wild type L1 larvae grown in 250 mL S medium with NA22 as a food source and incubated at 20°C with 200 rpm shaking.Worms were harvested and bleached after proximately 56–60 hours incubation, when young adult worms have only 1–2 fertilized embryos in the gonads.

extract_protocol:
Whole embryo lysates were clarified from sonication and PolII-DNA complex were isolated with antibody.
The ChIP-Seq libraries from two wild-type 8E stage Pol II ChIP and one wild-type bean stage Pol II ChIP were generated by using Apollo 324 System and PrepX ILM DNA Library Kit from IntergenX. After adaptor ligation, the input and ChIP DNA were enriched by PCR amplification using Phusion DNA Polymerase (New England Biolab) and Illumina universal PCR primer

tag: strain

value: 4H8 (Covance)


title: Sleeping Beauty (SB) insertions

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

country: Germany

institute: Technische Hochschule MIttelhessen

data_processing:
Reads starting with a valid combination of 4bp barcode and transposon IR-specific primer sequence with up to 1 mismatch were selected. The primer sequences for PB and SB were CGCAGACTATCTTTCTAGGGTTAA and GTAAACTTCCGACTTCAACTGTA, respectively. Barcodes and primers were stripped and the rest of the reads (27bp for SB starting with TA dinucleotide, and 30bp for PB starting with TTAA) were mapped to the human genome using the following procedure to avoid spurious insertion sites: First, we determined all sequencing reads mapping exactly to one or more positions within the reference genome using Bowtie (Langmead et al 2009). The resulting reads were mapped against each other and then clustered such that any two reads with up to two mismatches belong to the same cluster. We kept only reads which occured at least twice and contributed at least one fifths of the total number of reads within their cluster. From the resulting reads we kept only those which mapped exactly to a unique position inside of the reference genome. Reads mapping to the same TA (in the case of SB) or TTAA (in the case of PB) sequence in the genome were then merged together.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files including the chromosome (col 1), the 0-based position (col 2), the number of reads mapped to this position (col 3) and the method variant (restriction enzyme or sonication) with which it was found (col 4). Each row contains one integration site.

source_name: blood

extract_protocol:
Genomic DNA
Sample 1 genomic DNA was digested with DpnI and KpnII, Sample 2 genomic DNA was digested with DpnI and BamHI

tag: cell type

value: primary human CD4+ T cells

tag: transposon

value: Sleeping Beauty


title: piggyBac (PB) insertions

value: piggyBac


title: laryngo-pharyngeal tumor micro rna-seq LP8_Tumor

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
2euocs_miRNA-seq

source_name: tumor tissue

value: laryngo-pharyngeal tumor


title: laryngo-pharyngeal tumor micro rna-seq LP10_Tumor

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
tu2jsy_miRNA-seq


title: R2.CE.8E.ChIP


title: R1.CE.BE.ChIP

source_name: bean syncrhonized embryos


title: D83V-MEF2B-V5-RNAseq-DMSO

value: DMSO (1.07uL/mL)


title: laryngo-pharyngeal tumor micro rna-seq LP6_Tumor

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
0ubur0_miRNA-seq


title: R1.CE.8E.Input

value: none, Input


title: laryngo-pharyngeal tumor micro rna-seq LP8_Normal (matched normal for LP8_Tumor)

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
0rc4rq_miRNA-seq


title: R2.CE.8E.Input


title: R1.CE.BE.Input


title: laryngo-pharyngeal tumor micro rna-seq LP7_tumor

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
g82d35_miRNA-seq


title: laryngo-pharyngeal tumor micro rna-seq LP7_Normal (matched normal for LP7_Tumor)

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
u1fypo_miRNA-seq


title: laryngo-pharyngeal tumor rna-seq LP13_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
9zexjo


title: laryngo-pharyngeal tumor rna-seq LP5_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
itnb4j


title: laryngo-pharyngeal tumor rna-seq LP2_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
emdb4k


title: laryngo-pharyngeal tumor rna-seq LP11_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
uhxr8e


title: laryngo-pharyngeal tumor rna-seq LP3_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
qva3ot


title: laryngo-pharyngeal tumor rna-seq LP6_Normal (matched normal for LP6_Tumor)

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
3dapc3


title: laryngo-pharyngeal tumor rna-seq LP1_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
7t6pux


title: laryngo-pharyngeal tumor rna-seq LP6_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
0ubur0


title: laryngo-pharyngeal tumor rna-seq LP8_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
2euocs


title: laryngo-pharyngeal tumor rna-seq LP10_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
tu2jsy


title: laryngo-pharyngeal tumor rna-seq LP7_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
g82d35


title: laryngo-pharyngeal tumor rna-seq LP10_Normal  (matched normal for LP10_Tumor)

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
lp0dd2


title: laryngo-pharyngeal tumor rna-seq LP9_Normal (matched normal for LP9_Tumor)

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
l983jx


title: laryngo-pharyngeal tumor micro rna-seq LP10_Normal  (matched normal for LP10_Tumor)

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
lp0dd2_miRNA-seq


title: laryngo-pharyngeal tumor rna-seq LP9_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
a6f41n


title: laryngo-pharyngeal tumor rna-seq LP8_Normal  (matched normal for LP8_Tumor)

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
0rc4rq


title: laryngo-pharyngeal tumor rna-seq LP4_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
v152d4


title: miR-seq 8

city: Columbus

first: wei

last: meng

state: Ohio

address: 400 W12 street

department: Radiation Oncology

institute: The Ohio State University

data_processing:
Among the total 64 tissue samples, 10 samples (6 with N0 stage and 4 with N1+ stage) were sequenced using the SOLiD platform. First, all reads were trimmed by removing the 3’ adaptor sequence using the Cutadapt program, and the length distribution of reads for each sample has been plotted . Subsequently, we used a “Sequential Trim Alignment (SeqTrimAlign)” strategy to map all reads to the hg19 reference genome in color space , in which the last one color base of those unmapped reads in the previous alignment round would be trimmed, and re-submited to the next round of alignment using Bowtie, until a minimum read length was reached, in our case 19 color bases. This strategy is believed to fit specifically for solid data and could promote a high mapping ratio without sacrificing much performance. Detection of novel microRNAs was performed by miRDeep2 using the above alignment, which utilizes the position and frequency of reads uniquely aligned to the genome (“signature”) with respect to a putative RNA hairpin and scores the microRNA candidate employing a probabilistic model based on microRNA biogenesis . The more positive the score the more reliable the prediction would be. We chose predicted microRNAs as novel candidates if they had a score >= 2.0 and were present in at least 3 samples. Applying these selection criteria 65 novel microRNAs were identified in our data set, that were then included in the following expression analysis.
Expression analysis of microRNA-Seq data was performed using the R/Bioconductor package EdgeR , which is designed for use with digital gene expression data. First, we counted the number of reads uniquely mapped to microRNA regions according to the reference database miRBase and novel microRNAs identified as above; then the normalization and differential expression between the N0 group and N1+ group was assessed in EdgeR by calculating an exact test p-value analogous to the Fisher’s exact test.
Genome_build: hg19, miRBase 19
Supplementary_files_format_and_content: raw_counts_table.txt and novel_miR_position.txt
Supplementary_files_format_and_content: edgeR_output.txt; columns: logConc: the log2-average concentration/abundance for each tag in the two groups being compared.  logFC: the log2-abundance ratio (N1+ group/N0 group) p.value: exact p-value for differential expression using the NB model (refer to edgeR manual). adj.p.val: the p-value adjusted for multiple testing by Benjamini-Hochberg method.

source_name: lung

extract_protocol:
MicroRNA samples from fresh frozen tissue were extracted using PureLink™ microRNA Isolation Kit (Life Technologies Corporation, Carlsbad, CA). Briefly, 5 mg fresh frozen tissue samples were mixed with 300 μl Binding Buffer (L3) and homogenized using a tissue homogenizer. Homogenized samples were centrifuged, and the supernatants were mixed with 300 μl 70% ethanol. Solutions containing RNA were purified by two rounds of spin column cleanup and RNA was eluted with 50 μl sterile RNase-free water.
Total RNA samples were processed by the flashPAGE fractionator (Ambion) and flashPAGE Clean-Up Kit (Ambion). Enriched small RNA was then processed according to the SOLiD Small RNA Expression Kit protocol (Applied Biosystems) and purified small RNAs were ligated with 5' and 3' adapter Mix using RNA ligase. Ligated products (40–60 bases in length) were reverse transcribed and purified on Novex 10% TBE-Urea gel. Subsequently, 15–18 cycles of PCR were performed by amplifying the purified cDNA with barcoded PCR primer sets provided with the kit, which differed by a unique 6-nucleotide sequence. Amplified products were loaded on Novex 6% TBE gel (Invitrogen) and the gel bands containing 110 to 130bp fragments were excised. Amplified products were purified from the excised gel band and then loaded on the Applied Biosystems SOLiD next generation high throughput sequencing system for data acquisition. The quality of the samples and libraries were verified on the Agilent Bioanalyzer.

tag: histology

value: Lung Adenocarcinoma

tag: lymph node status

tag: age

value: M

tag: Stage


title: miR-seq 10


title: miR-seq 9

value: F


title: GR_032015

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

description:
SRR2045115: raw reads for the bound portion of GR-DNA complex
SRR2045116: raw reads for the unbound portion of GR-DNA complex

data_processing:
Library strategy: Spec-seq
Read sorting: Each binding site sequence was extracted from the variable region from each read; the number of each binding site variant was counted in total.
For each variant, the read number in bound fraction was divided by the corresponding number in unbounded fraction to get the relative affinity value.
The relative affinity for each variant was sorted from high to low (normalized to 100% for the reference sequence), and its logarithmic value corresponds to relative binding energy.
Motif analysis and logo generation: The GR PWM that was generated through this analysis was used to define relative binding energies using the patser program (35), which can be accessed online at (http://stormo.wustl.edu/consensus/cgi-bin/Server/Interface/patser.cgi ). Derived binding affinities are proportional to the inverse of the natural log of the calculated energies.
Paired-end experiments, but only one mate-pair file was used/submitted
Supplementary_files_format_and_content: Processed data files listing final results including binding site, bound&unbound reads, relative affinity, relative binding energy in kT units

molecule: other

source_name: Recombinant human GR protein + 5% positive control DNA sequence + Random DNA library 5

extract_protocol:
Library design: An initial experiment (Dec, 2014) was performed using the putative consensus sequence: AGAACA GGG TGTTCT; randomized library 1: AGAACN NSN NGTTCT [diversity =512]; randomized library 2: AGAANN GGG NNNTCT [diversity = 1024]; randomized library 3: AGAACA GGG TGNNNN [diversity =256]; randomized library 4: AGAACA GGGC NNNTCT [diversity = 64]. The initial total library diversity was ~1853 with a library composition of 10% positive control sequence + randomized libraries 1-4 + 5% negative control sequence. A 5th library containing 2304 (run in March 2015) sequences based on DDNACW KKN KGTTCT, where D="not C", N="any base", W="A or T" and K="G or T" was subsequently prepared and analyzed using similar ratios of control sequences.
Library construction: ssDNA oligo containing the DNA binding site of interest was ordered from IDT, with flanking Illumina PE1 and PE2 sequences on each side for final PCR enrichment. FAM-labelled reversed PE2 primer was used to anneal/extend the ssDNA template to make dsDNA pools. Afterwards ExoI nuclease treatment followed by Qiagen PCR column purification can make sure only dsDNA templates exist in the pool.
DNA separation, extraction, and sample preparation protocol: Binding conditions for EMSA were 100ng FAM-labelled dsDNA+ 0/0.5/1/2/4uM GR DBD protein for each lane, 1X NEB buffer 4. GR DBD was prepared as previously described. The EMSA was performed using a 9% 33:1 acrylamide gel and TB buffer, and was run at 200V for 30mins @ 0 degrees C. The 2uM protein lane used for final sequencing. Gel bands containing each DNA fragment were cut, extracted by acrylamide extraction buffer. No more than 10 rounds of PCR by Illumina PE1-Genetics, indexed PE2 primers can enrich each portion of DNA fragments. All indexed (barcoded) DNA samples were pooled together for Illumina sequencing.

tag: in vitro material


title: Untreated MCF7 cells

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description: Control Cell

data_processing:
The reads were mapped onto the human genome (build 36, Mar 2006) and intersected with microRNAs (mirBase.org) using GeneSifter Software (PerkinElmer, Santa Clara CA).
Reads were normalized to the mapped reads and significant differences in reads were determined using the Likelihood Ratio Test and the Benjamini and Hochberg post-test.
Genome_build: hg18, mirBase release 13
Supplementary_files_format_and_content: miRBase_normalized_reads.txt
Supplementary_files_format_and_content: Supplemental_File_1_Likelihood_Ratio_Test.xlsx

source_name: MCF7 breast cancer cells

growth_protocol: The cells were cultivated in DMEM medium supplemented with exosome-depleted 10 % fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin (Corning/Mediatech, Inc. Manassas, VA). Cells were routinely maintained in a humidified chamber at 37 °C and 5 % CO2.

extract_protocol:
Total RNA was extracted from the cells and exosomes using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), according to the manufacturer’s protocol.
A small RNA library was prepared from 100 ng of total RNA using the TruSeq Small RNA Preparation Kit (Illumina, San Diego, CA).

treatment_protocol: Human breast cancer MCF7 cells were grown in cell culture medium supplemented with exosome-depleted serum for 3 days and treated with 100 μM DHA for 24 h. Whole exosomes were collected from the conditioned medium of DHA-treated and untreated MCF7 cells.

tag: agent

value: control

tag: rna source

value: cells


title: Untreated MCF7 exosomes

description: Control Exosome

source_name: MCF7 breast cancer exosomes

value: exosomes


title: DHA-treated MCF7 exosomes

description: DHA Exosome

value: DHA


title: laryngo-pharyngeal tumor micro rna-seq LP9_Normal (matched normal for LP9_Tumor)

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
l983jx_miRNA-seq


title: DHA-treated MCF7 cells

description: DHA Cell


title: miR-seq 6


title: laryngo-pharyngeal tumor rna-seq LP7_Normal  (matched normal for LP7_Tumor)

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
u1fypo


title: laryngo-pharyngeal tumor rna-seq LP12_Tumor

description:
total RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-sequencing using solid sequencer 5500xl
8zo6l8


title: GR_122314

description:
SRR2045113: raw reads for the bound portion of GR-DNA complex
SRR2045114: raw reads for the unbound portion of GR-DNA complex

source_name: Recombinant human GR protein + 10% positive control DNA sequence + Random DNA libraries 1-4 + 5% negative control DNA sequence


title: miR-seq 3


title: miR-seq 5


title: CAGEScan_nurses

city: Jeddah

first: Vladimir

middle: B

last: Bajic

state: Jeddah

address: Thuwal

department: CEMSE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology (KAUST)

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, reads with no or incorrect adapters were omitted. To estimate the inner distance between paired-end reads, reads were mapped to the honey bee reference genome (version 4.5) using Bowtie2 v2.1.0
Then all reads were mapped to OGS3.2 whole genome using Tophat v2.0.8 with parameters (mean=588,std=767,allowing 2 mismatches and 2 gaps per read)
filtered out mapped reads that had a relatively high probability (p > 0.01/ MAPQ < 20).
Excluded mapped paired reads if they were : 1) both mates mapped to alternate strands, 2) one mate was unmapped, 3) the mates mapped to different scaffolds or 4) there was an inner distance greater than (mean + standard deviation) of the estimated inner distance between paired reads.
Genome_build: Honey Bee Apis Mellifera OGS3.2
Supplementary_files_format_and_content: matrix of read count (rows = genes, columns = samples)

organism: Apis mellifera

source_name: brain

growth_protocol: Total RNA from individual bee heads was prepared by homogenizing the brain tissue using a motorized pestle and

extract_protocol:
extracting the RNA using TRIzol (Life Technologies, Carlsbad, California, USA) and RNeasy Mini spin columns (Qiaqen, Venlo, Limberg, Netherlands), as per manufacturer specifications
CAGEscan libraries were generated from total RNA preparations from individual brains (in total 16 samples from 8 nurses and 8 foragers each), and barcoded cDNAs were pooled into two libraries for sequencing. prior to CAGEscan library preparation, total RNA samples were incubated with a 5´-Phosphate-Dependent Exonuclease (Terminator, Epicentre, Madison, USA) as per manufacturer instructions to remove rRNA and truncated mRNAs. During cDNA synthesis a reverse-transcription primer and “template-switching” oligonucleotide with individual barcodes plus specific sequences for template switching at the 5’ cap of mRNA were incorporated into the first strand cDNA by a reverse transcriptase

treatment_protocol: All samples were treated with DNase (Qiagen)

value: brain

tag: developmental stage

value: nurse


title: CAGEScan_foragers

tag: tissue

value: forager


title: miR-seq 4

tag: gender


title: HP26695 ML B1 HS1 -TEX

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.5, Förstner et al., 2014)
Read mapping using segemehl version 0.1.7 (READemption 0.3.5, Förstner et al., 2014)
Coverage calculation and normalization (READemption 0.3.5, Förstner et al., 2014)
Coverage normalization by TSSpredator (http://it.inf.uni-tuebingen.de/TSSpredator)
Genome_build: NC_000915.1
Supplementary_files_format_and_content: wiggle

organism: Helicobacter pylori 26695

source_name: Helicobacter pylori 26695 wildtype

growth_protocol: Helicobacter pylori wild type strain 26695 (CSS-0065, kindly provided by D. Scott Merrell, Bethesda, MD) was grown on GC-agar (Oxoid) plates supplemented with 10% (V/V) donor horse serum (Biochrom AG), 1% (V/V) vitamin mix, 10 μg/ml vancomycin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin. For liquid cultures, 15 or 50 ml Brain Heart Infusion medium (BHI, Becton, Dickinson and Company) supplemented with 10% (V/V) FBS (Biochrom AG) and 10 μg/ml vancomycin, 5 μg/ml trimethoprim, and 1 μg/ml nystatin were inoculated with H. pylori grown on plates to a final OD600 of 0.02 – 0.05 and grown under agitation at 140 rpm in 25 cm³ or 75 cm³ cell culture flasks (Corning). Bacteria were grown at 37°C in a HERAcell 150i incubator (Thermo scientific) in a microaerophilic environment (10% CO2, 5 % O2, and 85 % N2). When the cultures reached mid-log phase (OD600  ~0.6), culture volumes of cells corresponding to a total amount of 4 OD600, were mixed with 0.2 volumes of stop-mix (95% EtOH and 5% phenol, V/V), frozen in liquid N2 and stored at −80°C until RNA extraction. In total, three biological replicates of bacteria grown to mid-log phase (ML) were harvested: B1 which was grown separately from B2 and B3 which were grown on the same day.

extract_protocol:
Frozen cell pellets were thawed on ice and re-suspended in lysis solution containing 600 µl of 0.5 mg/ml lysozyme in TE buffer (pH 8.0) and 60 µl 10% SDS. Bacterial cells were lysed by incubating the samples for 1–2 minutes at 65°C. Afterwards, total RNA was extracted using the hot-phenol method described previously (Sharma et al. 2010, Bloomberg 1990, EMBO J). DNaseI (Fermentas) treatment was performed on total RNA according to manufacturer’s instruction. Afterwards, ~200 ng RNA samples were poly(A)-tailed using 2.5 U E.coli poly(A) polymerase (NEB) for 5 min at 37°C. Terminator exonuclease treatment (+TEX) and mock treatment without the enzyme (-TEX) were carried out after poly(A)-tailing. In brief, poly(A)-tailed RNA was denatured for 2 min at 90˚C, cooled on ice for 5 min and treated with 1.5U of Terminator Exonuclease (Epicentre) for 30 min at 30˚C.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). At first, the 5'-PPP structures were removed using tobacco acid pyrophosphatase (TAP). TAP treatment was performed by incubating TEX-treated (+TEX) and untreated control (−TEX) samples with 5U TAP for 15 min at 37˚C.  Afterwards, an RNA adapter (5' Illumina sequencing adapter, 5'-UUUCCCUACACGACGCUCUUCCGAUCU-3') was ligated to the 5´-phosphate of the TAP-treated, poly(A)-tailed RNA for 30 min at 25°C. First-strand cDNA was synthesized by using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (AffinityScript, Agilent) by incubation at 42°C for 20 min, ramp to 55°C followed by 55°C for 5 min. In a PCR-based amplification step using a high fidelity DNA polymerase (Herculase II Fusion DNA Polymerases, Agilent)  the cDNA concentration was increased to 10-20 ng/μl (initial denaturation at 95°C for 2 min, 10-15 cycles 95°C for 20 sec and 68°C for 2 min). The TruSeq index primers for PCR amplification were according to the instructions of Illumina. For all libraries the Agencourt AMPure XP kit (Beckman Coulter Genomics) was used to purify the DNA (1.8 x sample volume), and cDNA sizes were examined by capillary electrophoresis on a MultiNA microchip electrophoresis system (Shimadzu). A library-specific barcode for multiplex sequencing was included as part of a 3'-sequencing adapter.

tag: treatment

value: untreated


title: miR-seq 2


title: miR-seq 7


title: HP26695 ML B1 HS1 +TEX

treatment_protocol: When the cultures reached mid-log phase (OD600  ~0.6), culture volumes of cells corresponding to a total amount of 4 OD600, were mixed with 0.2 volumes of stop-mix (95% EtOH and 5% phenol, V/V), frozen in liquid N2 and stored at −80°C until RNA extraction.

value: TEX treated


title: miR-seq 1


title: 2045_SF/SCL

city: Pirassununga

first: Mario

last: Binelli

state: SP

address: Rua Duque de Caxias Norte, 255

department: department of animal reproduction

country: Brazil

institute: University of Sao Paulo (USP)

data_processing:
CASAVA v1.8.2
The 100bp paired end (PE) reads were filtered using a perl script which removed all reads with a mean quality under 26. The reads were mapped with Bowtie2 v2.1.0 on the masked bovine genome assembly (Bos taurus UMD 3.1, NCBI).
The mapping file was sorted using SAMTools v 0.1.18 and read counts were obtained using the script from HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
The differential expression analysis was performed with package DESEq v1.12.1, from R. Using the function estimateSizeFactors, the normalized counts were obtained (baseMean values, which are the number of reads divided by the size factor or normalization constant). The standard deviation along the baseMean values was also calculated for each transcript.
In order to avoid artifacts caused by low expression profiles and high expression variance, only transcripts that had an average of baseMean > 5 and the mean greater than the standard variation were analyzed. The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR-Benjamini-Hochberg.
genome_build:  Bos taurus (assembly Bos_taurus_UMD_3.1.1)
supplementary_files_format_and_content: Mesquita data.txt: abundance measurements

organism: Bos indicus

source_name: Endometrium

extract_protocol:
Approximately 30 mg of endometrial tissue were ground in liquid nitrogen using a stainless steel apparatus and immediately mixed with buffer RLT from the RNeasy Mini columns kit (Qiagen, São Paulo, SP, Brazil), as per manufacturer’s instructions. To maximize lysis, tissue suspension was passed at least ten times through a 21 G needle, and centrifuged at 13,000 x g for 3 minutes for removal of debris, prior to supernatant loading and processing in RNeasy columns. Columns were eluted with 40 l of RNase free water, and elution was repeated using the same 40 l initially used to increase RNA concentration. Concentration of total RNA on extracts was measured by a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, USA). Prior to reverse-transcription, 1 g of total RNA was treated with DNAse I (Life Technologies, São Paulo, SP, Brazil) for 15 minutes at room temperature in a 10 l reaction, followed by addition of 1l of EDTA (25mM) and heating at 65C for 10 minutes to inactivate DNase I. DNase I treatment was immediately followed by reverse-transcription (High Capacity cDNA Reverse Transcription Kit, Life Technologies) according to manufacturer’s instructions. Briefly, 9 l of master mix containing RT buffer, dNTP mix, random primers, RNase inhibitor and reverse transcriptase were added to the 11 l of DNase I treatment reaction. Immediately, samples were incubated at 25 C for 10 minutes, followed by incubation at 37 C for 2 hours and reverse-transcriptase inactivation at 85C for 5 minutes and storage at -20C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seventy-four multiparous, nonlactating, presynchronized Nelore cows received a progesterone-releasing device and estradiol benzoate on Day–10 (D−10). Animals received cloprostenol (large follicle-large CL group; LF-LCL; N = 35) or not (small follicle-small CL group; SF-SCL; N = 39) on D−10. Progesterone devices were withdrawn and cloprostenol administered 42 to 54 hours (LF-LCL) or 30 to 36 hours (SF-SCL) before GnRH treatment (D0). Endometrial tissue was collected at slaughter on D7.

value: multiparous cows

tag: health status

value: Healthy

tag: breed

value: Nelore


title: 2755_SF/SCL


title: 674_SF/SCL


title: 770_LF/LCL


title: 1499_LF/LCL


title: 1145_LF/LCL


title: m_oleifera_seed_s1

city: Rome

first: Stefano

last: Pirro'

address: Via della Ricerca Scientifica

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

description: smallRNA

data_processing:
Illumina adapter clipped using FASTX-Toolkit
Sequencing artifacts were removed and the remaining reads were trimmed on the 3p and 5p ends in order to cut low- quality bases
BLASTn v 2.2.30 was used to strictly compare reads with the Rfam database, allowing us to remove non-coding RNA (rRNA, tRNA, snRNA, snoRNA) and degradation fragments of mRNA
Reads highlighted as possible miRNAs were aligned against a specific-plant miRBASE with a low-redundancy rate, using BLASTn v 2.2.30
Sequences with homology rate equal to 100% and abundance value higher then 10 copies, were considered conserved M. oleifera miRNAs.
Supplementary_files_format_and_content: text files have been generated using a custom ruby script which manipulate the BLASTn output. We report the miRNA name, the abundance in our sample (number of copies) and the sequence

organism: Moringa oleifera

source_name: sRNA extract of seed tissue

growth_protocol: Germination by placing the seeds on paper soaked in sterile water

extract_protocol:
Total RNA was isolated by using mirVana kit (Ambion, USA), according to the manufacturer’s protocol.
Indexed libraries were prepared from 1 ug/ea purified RNA with TruSeq SmallRNA Sample Prep Kit (Illumina, U.S.A.) according to the manufacturer’s instructions.

value: seed


title: SREB-3xHA B Input

city: Madison

first: Gregory

middle: M

last: Gauthier

state: WI

address: 1550 Linden Drive

department: Medicine

institute: University of Wisconsin - Madison

description: Input DNA

data_processing:
ChIP and input reads were aligned using Bowtie  (version 0.12.7 with parameters  “-p 4  -q -v 2 -a --best --strata   -m 2”) to the genome sequence of Blastomyces dermatitidis (blastomyces_dermatitidis_atcc_26199_1_supercontigs.fasta  downloaded from www.broadinstitute.org/annotation/genome/blastomyces_dermatitidis/MultiDownloads.html [Langmead B et al., Genome Biol 2009;10:R25; Kuan P et al. J Am Stat Assoc 2011;106:891-903; Sun G et al., Methods Mol Biol 2013;1038:193-212].  We performed quality control analysis of the data using the quality metrics from Landt et al. [Landt SG et al., Genome Res 2012;22:1813-1831].  We then used the R package mosaics in the two sample analysis with input data mode to call peaks [Sun G et al., Methods Mol Biol 2013;1038:193-212]. The specific parameters of mosaics were set as follows: bin size = 150; fragment size = 150, fdr = 0.1; thres = 97.5th percentile of the bin-level ChIP read count distribution.  The peaks were further filtered by taking into account the ChIP signal at the summit.  Specifically, for each peak, a window size of 1000 bps around the mid-point of the original peak was used and defined as the highest read coverage point as the summit of the peak.  Peaks were annotated by overlapping them with the 500 bps upstream of the transcription start sites using the 9180 TSS groups defined in blastomyces_dermatitidis_atcc_26199_1_transcripts.gtf (www.broadinstitute.org).
Genome_build: blastomyces_dermatitidis_atcc_26199_1_transcripts.gtf (www.broadinstitute.org)
Supplementary_files_format_and_content: TXT files contain peak intensities, location (supercontig number including location of the peak within the contig (start, end), width of the peak, peak quality, and upstream gene

organism: Blastomyces dermatitidis ATCC 26199

source_name: Yeast

growth_protocol: B. dermatitidis ATCC 26199 and SREB-3xHA cells were grown in liquid Histoplasma macrophage medium (HMM) containing 10 μM iron sulfate (FeSO4) at 37oC overnight prior to cross-linking.

extract_protocol:
B. dermatitidis ATCC 26199 and SREB-3xHA cells were grown in liquid HMM containing 10 μM iron sulfate (FeSO4) at 37oC overnight and treated with 1% formaldehyde for 30 minutes.  Formaldehyde cross-linking was quenched with 0.125 M glycine for 5 minutes. Cells were washed with ice-cold 1x phosphate buffered saline (PBS) containing a protease inhibitor cocktail (PIC; Sigma Aldrich), flash frozen in liquid nitrogen, ground to a fine powder using a a mortar and pestle, and resuspended in FA lysis buffer with PIC plus PMSF.  Chromatin was sheared using probe sonication (Misonix S-4000) for a total of 25 minutes of "on time".  Each round of sonication was divided into 15 seconds (amplitude 30) x 4 with intervening rest periods on ice lasting 30 seconds.  Prior to each round of sonication, cells were chilled for approximately 10 seconds in a dry-ice ethanol bath to prevent overheating.  From each sample, 50 μl was saved as the "input" sample and 50 μl was analyzed for efficacy of chromatin shearing by 0.8% agarose gel electrophoresis.  For chromatin immunoprecipitation (ChIP), protein A agarose beads (without salmon sperm DNA) were prepared according to the manufacturers instructions (Millipore) and resuspended in FA lysis buffer containing PIC and PMSF.  Sonicated chromatin (300 μg measured by nanodrop spectophotometer) was pre-cleared for 1 hour at 4oC prior to adding 10 μl ChIP-grade anti-HA tag antibody (Abcam, catalogue # ab9110) along with freshly prepared beads.  Following overnight incubation at 4oC, samples were washed with with buffer #1 (FA lysis buffer), once with buffer #2 (FA lysis buffer with 0.5 M NaCl), once with buffer #3 (10 mM Tris pH8, 0.25M LiCl, 1 mM EDTA, 0.5% Nonidet P-40, 0.5% sodium deoxycholate), and three times with Tris-EDTA pH 8.  All washes were 3 minutes at 4oC with orbital rotation.  ChIP'd samples were treated with proteinase K for 2 hours at 45oC and then 65oC overnight. Input samples were treated with proteinase K at 55oC x 4 hours then 65oC overnight.  DNA was isolated and purified according to the protocol in Mukhopadhyay et al. [Nat Protocol 2008;3:698-70] and resuspended in Tris-HCl pH 8.  The DNA from 3 technical replicates of ChIP'd or input samples were pooled for each biological replicate of ATCC 26199 and SREB-3xHA.  There were 2 biological replicates for ATCC 26199 and SREB-3xHA.
Immunoprecipitated and input DNA were submitted to the University of Wisconsin Biotechnology Center in Madison, WI for sequencing using Illumina HiSeq 2000 platform.

value: ATCC 26199 containing SREB-3xHA construct

tag: antibody

value: Input sample


title: SREB-3xHA A Input

description: Input DNA

tag: strain


title: SREB-3xHA B ChIP

description: ChIP'd DNA

value: Chip Antibody:Anti-HA tag antibody (Abcam, ab9110)


title: SREB-3xHA A ChIP

description: ChIP'd DNA


title: 26199 B ChIP

description: ChIP'd DNA

value: ATCC 26199 - wild type (untagged) strain


title: 26199 B Input

description: Input DNA


title: 26199 A Input

description: Input DNA


title: 26199 A ChIP

description: ChIP'd DNA


title: Total RNA control 2

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Raw reads were processed using Trimmomatic v 0.32.
Reads were aligned to a modified tRNA reference genome based on hg19 using bowtie2 with the parameters -D 20 -R 3 -N 1 -i S,1,0.50.
Reads aligning to multiple tRNA isodecoders were removed, and fragments shorter than 18 bp aligning were also culled due to redundant gene_ID calls.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing gene IDs and raw read counts

source_name: Total RNA control 2

growth_protocol: Human HEK293T cell line was cultured in DMEM (Thermo) media supplemented with 10% FBS and 1% 100 × Pen Strep (Gibco)

extract_protocol:
Total RNA was isolated by using mirVana miRNA Isolation Kit (Life Technologies). Purified total RNA was deacylated by incubating in 0.1 M tris-HCl, pH 9 at 37°C for 45 min. When necessary, total tRNA was subsequently isolated using a denaturing 10% polyacrylamide gel followed by passive gel elution and ethanol precipitation.
Homemade protocol based on Illumina protocols. Deacylated RNAs with or without the demethylation were first treated with T4 Polynucleotide Kinase (Epicentre) at 37C° for 30 min to further warrant a free 3' hydroxyl group for template switching. Template-switching reactions were performed as described7. Briefly, we used an initial template-primer substrate consisting of a 41-nt RNA oligonucleotide (5’-AGA UCG GAA GAG CAC ACG UCU AGU UCU ACA GUC CGA CGA UC/3SpC3/-3’) that contains Illumina Read1 and Read2 primer-binding sites and a 3’ blocking group (three carbon spacer; IDT) annealed to a complementary 32P-labeled DNA primer with a single-nucleotide 3’ overhang, T, which facilitates the template switch to full-length tRNA that mostly contain a 3’ CCA end. For g2RT template-switching reactions, average 100 ng of demethylated tRNAs or 1 μg of demethylated total RNA were mixed with the initial template-primer substrate (100 nM) and g2RT (1 μM of TeI4cΔEn or 500 nM of GsI-IIC RT) in reaction medium containing 450 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.5, and DTT (1 mM for TeI4cΔEn or 5 mM for GsI-IIC RT). For template-switching with TeI4cΔEn RT, the reactions were pre-incubated at room temperature for 30 min, initiated by adding 25 mM dNTPs to a final concentration of 1 mM and incubating at 60°C for 30 min. For template-switching with GsI-IIC RT, the pre-incubation step is not required. The reactions were terminated by adding 5 M NaOH to a final concentration of 0.25 M, incubating at 95°C for 3 min, and neutralizing with 5M HCl. The cDNAs resulting from template switching were analyzed in a denaturing 6% polyacrylamide gel, electroeluted using a D-tube Dialyzer Maxi with MWCO of 6-8 kDa (EMD Millipore), and ethanol precipitated with 0.3 M sodium acetate in the presence of 25 µg of linear acrylamide (Life Technologies). The purified cDNAs were then circularized with CircLigase II (Epicentre) using manufacture’s protocol with extended incubation time of 5 hours at 60°C, phenol-CIA extracted, ethanol precipitated and amplified with Phusion-HF (Thermo Scientific) using Illumina multiplex (5’- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GAC GAT C -3’) and barcode (5’- CAA GCA GAA GAC GGC ATA CGA GAT BARCODE GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T -3’) primers for 12 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The PCR products were sequenced on Illumina HiSeq 1000 system.

tag: cell line

value: no AlkB-derived enzyme mixture


title: Total RNA control 1

source_name: Total RNA control 1


title: tRNA treated 2

description: tRNA

source_name: tRNA treated 2

value: AlkB-derived enzyme mixture


title: Total RNA treated 2

source_name: Total RNA treated 2


title: tRNA control 1

description: tRNA

source_name: tRNA control 1


title: tRNA control 2

description: tRNA

source_name: tRNA control 2


title: Cyc_1

first: Jordan

last: Lewandowski

address: 7 Divinity Ave

data_processing:
tophat (v2.0.9) used to align the reads to the reference genome, supplied with  transcript annotation data (genes.gtf) from UCSC mm10, with options  --bowtie1 --color --quals --library-type fr-secondstrand --no-coverage-search
SAMtools used to organize, sort the BAM files and create SAM files
htseq-count (v0.5.4p5) used to get read counts for genes, nes.gtf) from UCSC mm10, with options -s no
edgeR (v3.4.2) used to normalize counts across samples, and to do differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab separated .txt file includes gene name, log fold change, log count-per-million, Pvalue and FDR
Supplementary_files_format_and_content: comma separated .csv file includes normalized counts for all 4 samples (Cyc_1,Cyc_2,Ctrl_1,Ctrl_2)

organism: Mus musculus

source_name: E10.25 forelimb cyclopmaine treated

extract_protocol:
At the end of the culture period, limb buds were immediately processed for RNA extraction using TRIzol
RNA libraries were prepared for sequencing using standard ABI SOLiD protocols

value: Swiss Webster

value: Forelimb

tag: genotype/variation

value: wild type

value: cyclopmaine


title: Total RNA treated 1

source_name: Total RNA treated 1


title: Cyc_2


title: laryngo-pharyngeal tumor micro rna-seq LP9_Tumor

description:
micro RNA was isolated from either tumor tissue or matched normal tissue, further subjected to rna-seq experiment using solid sequencer 5500xl
a6f41n_miRNA-seq

source_name: tumor tissue

tag: patient/sample id

value: laryngo-pharyngeal tumor


title: L08

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

country: France

institute: INRA

description:
Total RNA was extracted from ~150 mg of mammary tissue collected and frozen at the slaughterhouse.
FD: Fed ad-libitum during a 2-week pre-experimental period and food deprived during the 48 hours experimental period.
Small RNA-seq using Solexa's Illumina technic.

data_processing:
Images analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2.
Sequenced reads were trimmed for poly-A stretches, then filtered for their size (17-28 nt). The cleaned sequences were clustered into unique reads and then mapped to the goat genome (CHIR1.0) using the mapper.pl module from miRDeep2 with default parameters.
Novel miRNA and precursors were identified using miRDeep2 core module miRDeep2.pl using default parameters. Potential miRNA dataset was created by adding known goat miRNA (miRBase v21) to miRNA corresponding/associated to predicted precursors with a miRDeep2 score≥ 0. The same operation was done to create the dataset of potential precursors.
Quantification was achieved using quantifier.pl module from miRDeep2 with default parameters using the unique reads, potential miRNA and precursors datasets.
Results were then filtered with a custom Perl script parse_miRDeep2_outputs.pl (https://mulcyber.toulouse.inra.fr/projects/bioinfoutils/) to eliminate redundancy between known and putative novel miRNA.
Genome_build: CHIR1.0 (http://goat.kiz.ac.cn/GGD/index.htm)
Supplementary_files_format_and_content: Quantification files (*_quantification.txt) are the resulting files generated by the quantifier.pl module of miRDeep2. These tab-delimited text files include for each miRNA its associated precursor, raw abundance measurements, normalized abundance, and sequence.
Supplementary_files_format_and_content: Prediction file (chi_novel_miRNAs_miRDeep2_prediction.txt) is the resulting file generated by the miRDeep2 prediction process (miRDeep2.pl). This tab-delimited text file includes predicted miRNA and precursors, associated miRDeep2 scores, and their genome location.

organism: Capra hircus

source_name: Mammary gland, food deprived

extract_protocol: Total RNA were isolated from ~150 mg of goats mammary gland using TRIzol® Reagent (Life Technologies) and further purified with the SV Total RNA Isolation system (Promega) to eliminate contaminating genomic DNA.

treatment_protocol: The goats were fed an orchard grass hay-based diet with a 35:65 forage to concentrate ratio during a 2-week pre-experimental period. For 48 h before slaughtering, 4 goats consumed this diet ad libitum (Control) and the 6 others were food deprived (FD). Goats were milked at 0800 and 1600. Goats were housed in individual stalls, had free access to water, and were fed twice daily (except during the deprivation) just after milking.

value: Alpine

value: mammary gland

tag: physiology

value: peak of lactation (48 ± 2 days post-partum)

value: food deprived


title: Ctrl_2

source_name: E10.25 forelimb

tag: age

value: control


title: L06

description:
Total RNA was extracted from ~150 mg of mammary tissue collected and frozen at the slaughterhouse.
Control: Fed ad-libitum during a 2-week pre-experimental period and during the 48 hours experimental period.
Small RNA-seq using Solexa's Illumina technic.

source_name: Mammary gland, control


title: hf348 [SIRS-AKI-HD]

city: Albuquerque

first: Raymond

middle: J

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

description: Raw Reads Per Million - relevantly expressed genes

data_processing:
CAPSOD experimental samples were sequenced without multiplexing on Illumina GAIIx instruments (54-cycle singleton reads).This yielded 13.4 million reads, totaling 718.4 Mbp of sequence, and 9-fold average coverage. Base calling was performed using Illumina Pipeline software v1.4, except for 14 samples performed with v1.3. Approximately 500 million high quality reads were generated per sample.
Genome_build: Results were aligned to the NCBI human nuclear genome reference build GRCh37/hg19 using GSNAP and Alpheus
Supplementary_files_format_and_content: mRNA sequencing for 133 subjects to an average depth of 13.5 million reads/sample yielded relative levels of transcription of 32,358 genes (of which 18,618 mRNAs were detected in >50% of subjects). Patient values were normalized as reads per million. Expression in less than 50% of the subjects were removed from analysis. A log2(x+1) transformation was performed prior to ANONA analysis

molecule: polyA RNA

source_name: Whole Blood Cells

extract_protocol:
Whole blood was collected in PAXgene RNA tubes (Qiagen, CA) to stabilize intracellular RNA and subsequently stored at -80°C until use. RNA was prepared using a PaxGene Blood RNA kit (Qiagen) according to the manufacturer’s instructions.
mRNA sequencing libraries were prepared from total RNA using the Illumina mRNA-Seq Sample Prep Kit (Illumina, catalog # RS‐100‐0801), according to manufacturers’ recommend protocols

tag: patient id

tag: sirs outcomes

value: Hemodialysis


title: L09


title: hf275 [SIRS-AKI-HD]


title: L07


title: tRNA treated 1

description: tRNA

source_name: tRNA treated 1


title: hf295 [SIRS-AKI-HD]


title: L04


title: RNA-Seq S3KO CD4 aIFNg d1

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: +IL-21 for 1 day, with aIFNg

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.8 and unpublished python scripts

source_name: Pre-activated CD4+ T cells

growth_protocol: Mouse CD4+ T cells were prepared by passing spleens through a cell strainer, and erythrocytes were removed by ACK lysis buffer.  Total CD4+ T cells were isolated by negative selection (Miltenyi Biotc.), with cell purity of 90-95%

extract_protocol:
For ChIP-Seq, Cells were fixed with 1% formaldehyde at 37°C for 10 min, and chromatin from 2.5 x 107 cells was sonicated for 20 cycles (15 sec on/45 sec off) to produce 250-450 bp fragments. STAT3- or STAT1-linked chromatin was immunoprecipitated using anti-STAT3 (13-7000, Invitrogen) or anti-STAT1 (sc-346, Santa Cruz Biotechnology) antibody bound to Dynabeads.  The ends of isolated DNA were repaired using the DNA END-Repair kit (Epicentre Biotechnologies), and a 3’ “A” nucleotide was added with Taq polymerase.  Two mixed Solexa adaptors (Illumina) were ligated to DNA ends and primers complementary to these adaptors (PE 1.0 and 2.0, Illumina) were used to amplify the DNA for 18 cycles.  DNA fragments of 250-450 bp were purified from 2% E-gels and used for cluster generation and sequencing. For RNA-Seq,  Total RNA was isolated, and 5 μg per sample were used for mRNA purification using Dynal oligo(dT) beads (Invitrogen).  Double-stranded cDNA was synthesized with random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (Invitrogen) and fragmented by Bioraptor.  After end repair (Epicentre DNA END-Repair kit) and the addition of an “A” nucleotide to the 3’ ends with Taq DNA polymerase, two mixed Solexa adaptors (Illumina) were ligated to DNA ends using T4 DNA ligase (New England Biolabs).  250-450 bp fragments were isolated on 2% E-Gels (Invitrogen) and amplified for 18 cycles using PE 1.0 and 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).  PCR products were run on a gel, and 250-450 bp fragments were purified
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Total mouse splenic CD4+ T cells were preactivated with plate-bound anti-CD3 + anti-CD28 for 3 days, washed and rested overnight, and not stimulated or stimulated with IL-21 for 1h (ChIP-Seq) or indicated time points (RNA-Seq)

value: Spleen

tag: genotype

value: CD4 aIFNg d1

tag: cell type

value: Pre-activated CD4+ T cells


title: L03


title: d84 [SIRS-AKI-HD]


title: Ctrl_1

tag: agent


title: RNA-Seq S3KO CD4 aIFNg d0

description: untreated, with aIFNg

tag: tissue

value: CD4 aIFNg d0


title: L10


title: hf162 [SIRS-AKI-HD]


title: RNA-Seq WT CD4 aIFNg d3

description: +IL-21 for 3 day, with aIFNg

value: WT

value: CD4 aIFNg d3


title: RNA-Seq WT CD4 aIFNg d1

description: +IL-21 for 1 day, with aIFNg


title: RNA-Seq S3KO CD4 aIFNg d3

description: +IL-21 for 3 day, with aIFNg


title: RNA-Seq S3KO CD4 d1

description: +IL-21 for 1 day, no aIFNg

value: CD4 d1


title: hf174 [SIRS-AKI-HD]


title: RNA-Seq S3KO CD4 d3

description: +IL-21 for 3 day, no aIFNg

value: CD4 d3


title: L02


title: RNA-Seq S3KO CD4 d0

description: untreated, no aIFNg

value: CD4 d0


title: hf138 [SIRS-AKI-HD]


title: hf59 [SIRS-AKI-HD]


title: L01


title: hf258 [SIRS-AKI-HD]


title: RNA-Seq WT CD4 aIFNg d0

description: untreated, with aIFNg


title: RNA-Seq WT CD4 d1

description: +IL-21 for 1 day, no aIFNg


title: hf325 [SIRS-AKI-HD]


title: hf33 [SIRS-AKI-HD]


title: L05


title: RNA-Seq WT CD4 d0

description: untreated, no aIFNg


title: RNA-Seq WT CD4 d3

description: +IL-21 for 3 day, no aIFNg


title: ML60

city: Urbana

first: William

last: Metcalf

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois at Urbana Champaign

data_processing:
CLC Genomics Workbench (version 7.0)( Aarhus, Denmark) is used to perform all subsequent bioinformatic analysis.
Briefly, fastq files were imported as high-throughput data, and trimmed for quality (Quality: 0.001, Ambiguous: 2, Discard: min 30, max 100) and to remove adapter sequences.
After trimming, remaining reads that mapped to stable RNAs (16s, 23s, 5s rRNA and all tRNAs) were bioinformatically removed (similarity: 0.9, length: 0.85, mismtach: 2, insertion: 3, deletion: 3; global alignment and stand-alone read).
Remaining reads were then mapped to the genome for RNA-seq analyses (mapping parameters:  0.9, length: 0.85, mismatch: 2; insertion: 3; deletion: 3; maximum number of hits for a read: 10).
Expression analysis was set up in CLC before the data were normalized and statistical analysis were done using empirical analysis of DGE (digital gene expression), with total counter filter cutoff set as  5.0. From here, the xlsx files were generated.
Genome_build: M. barkeri Fusaro genome
Supplementary_files_format_and_content: Excel files (xlsx) include raw data (normalized values for each sample) and data sorted by p-value ≤ 0.05, fold-change ≥ 3 and normalized mean ≥ 50

organism: Methanosarcina barkeri str. Fusaro

growth_protocol: Cells were adapted for at least 30 generations in the substrate of interest, before performing the RNA extraction.

extract_protocol:
Total RNA was isolated from mid exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and  the ZR Fungal/Bacterial RNA MiniPrep kit  (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes.
Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA).

tag: growth medium

value: HS medium with 125 mM methanol


title: ML61


title: hf86 [SIRS-AKI-HD]


title: ML58

value: Dhpt::fC31int-attP, pycC1


title: CD4.S3KO.IL21.STAT1

description: ChIP against STAT1

tag: chip antibody

value: STAT1 (Santa Cruz, sc-346)

tag: treatment

value: IL21 STAT1


title: hf99 [SIRS-AKI-HD]


title: CD4.S3KO.Cont.STAT1

description: ChIP against STAT1

value: Cont STAT1


title: ML59


title: hf240 [SIRS-AKI-HD]


title: CD4.WT.IL21.STAT1

description: ChIP against STAT1


title: ML56


title: ML57


title: hf101 [SIRS-AKI-HD]


title: CD4.WT.Cont.STAT1

description: ChIP against STAT1


title: hf194 [SIRS-AKI-HD]


title: d309 [SIRS-AKI-HD]


title: ML54


title: Rib_Chondrocyte_p300_ChIPSeq

city: Los Angeles

first: Xinjun

last: He

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

data_processing:
ChIP libraries were sequenced on Illumina Genome Analyzer II for samples (Rib_Chondrocyte_Sox9_ChIPseq, Rib_Chondrocyte_H3K4me2_ChIPSeq, Rib_Chondrocyte_H3K4me3_ChIPSeq, Rib_Chondrocyte_H3K27me3_ChIPSeq, Rib_Chondrocyte_H3K36me3_ChIPSeq, Rib_Chondrocyte_H3K27ac_ChIPSeq, Rib_Chondrocyte_RNA_Pol_II_ChIPseq, Rib_Chondrocyte_Input_Control_ChIpseq, Rib_Chondrocyte_IgG_Control_ChIpseq), or Hiseq 2000  for samples ( Rib_Chondrocyte_Input_Control_for_p300_ChIPseq, Rib_Chondrocyte_p300_ChIPSeq)
the first 25nt of sequence reads were aligned with Eland software (Illumina), allowing not more than 2 mismatches per reads to mouse genome version mm9/Build 37
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008; Jiang et al., 2010) with a P-value cutoff of 10e-5, by comparing with the input control without antibody immunoprecipitation or an IgG control. Peaks were incorporated into further analysis displaying an FDR<0.01.
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed

source_name: p1 mouse rib chondrocytes

growth_protocol: Neonatal ICR wild-type mice embryonic day 17.5 nasal septum or postnatal day 1 rib

extract_protocol:
Embryonic day 17.5 (E17.5) nasal septum or postnatal day 1 (p1) rib chondrocytes isolated from wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature, then 0.125 M Glycine was added to quench formaldehyde.  20,000,000 cells were used for a ChIP reaction. Chromatin was sonicated by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson sonifier 250D (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. One hundred microlitters of Dynabeads M-280 Sheep anti-Mouse IgG or anti-Rabbit IgG was combined with 9 μg of antibodies for targets of interest.
ChIPseq libraries were constructed from input control samples (input DNA and IgG controls) as well as ChIP DNA using ChIP-seq DNA Sample Prep Kit (IP-102-1001; Illumina Inc., San Diego, CA), according to manufacturer’s instruction. Adaptor-modified DNA fragments were enriched by 18 cycles of PCR.

treatment_protocol: Wild type, not treated

tag: strain background

value: ICR

tag: isolation stage

value: Enzyme digested rib chondrocytes

tag: chip antibody vandor

value: Santa Cruz

tag: chip antibody cat. #


title: Rib_Chondrocyte_Input_Control_for_p300_ChIPseq


title: d307 [SIRS-AKI-HD]

value: Hemodialysis


title: hf57 [SIRS-AKI-HD]


title: hf103 [SIRS-AKI-HD]


title: ML52-2

tag: strain

value: Pyr+

value: Low Salt Imidazole buffered medium with 125 mM methanol, 100mM pyruvate, 120 mM acetate


title: ML52-1


title: RNA130926RH_47

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

description: Sample name: 47

data_processing:
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
STAR 2.4.0 was used for read alignment with the following parameters: outFilterMismatchNmax 3 outFilterScoreMinOverLread 0.33 outFilterMatchNminOverLread 0.33 outFilterMismatchNoverLmax 0.03 outFilterMultimapNmax 1
Normalization: Gene and exon expression data were imported into the R (version 3.0.2 - Linux) application environment and samples were normalized using the upper-quartile normalization factor generated for each sample by the edgeR (version 3.4.2) Bioconductor package. Following normalization, genes which had counts less than 20 in more than half of the samples were filtered from the analysis and exons with counts less than 5 in more than half of the samples were set to 0.
Genome_build: mm9
Supplementary_files_format_and_content: RNA130926RH_normalizedGeneCounts.csv: first column has the ENSEMBL Gene ID, subsequent 48 columns provide the normalized reads for each sample for each gene
Supplementary_files_format_and_content: RNA130926RH_normalizedExonCounts.csv first column has the ENSEMBL Exon ID (i.e., GeneID_FeatureStart), subsequent 48 columns provide the normalized reads for each sample for each gene exon

source_name: Dissected Tissue - Nucleus Accumbens Shell (Brain)

extract_protocol:
Brain nucleus accumbens shell was dissected via laser microdissection. Total RNA was extracted by using acturus picopure RNA extraction columns.
RNA libraries were prepared for sequencing using TruSeq PolyA Illumina protocol: PolyA(+) RNA was recovered from 1 ug of total RNA using oligo-dT attached to magnetic beads. PolyA(+) RNA was chemically fragmented. Double stranded DNA was made from the fragmented RNA using random hexamers. All ends were repaired.  A single A was added to each of the 3’ ends of each fragment. Illumina adaptors were ligated to the fragments.  Concentration was determined by real time PCR. Samples were mixed for multiplexing. Samples were diluted to target 180 million templates per lane on the flow cell

value: heterogeneous stock-collaborative cross (HS-CC)

value: brain nucleus accumbens shell

tag: behavioral phenotype

value: Low ethanol Preference

tag: gender

value: M


title: hf104 [SIRS-AKI-HD]


title: RNA130926RH_46

description: Sample name: 46

value: F


title: RNA130926RH_45

description: Sample name: 45

value: High ethanol Preference


title: hf286 [SIRS-AKI-HD]

value: Acute Kidney Injury stage 2/3


title: ML55

value: HS medium with 125 mM methanol


title: RNA130926RH_44

description: Sample name: 44


title: ML23


title: hf102 [SIRS-AKI-HD]


title: ML21


title: hf190 [SIRS-AKI-HD]


title: hf6 [SIRS-AKI-HD]


title: RNA130926RH_43

description: Sample name: 43


title: ML33

value: wild type


title: hf270 [SIRS-AKI-HD]


title: ML41


title: RNA130926RH_41

description: Sample name: 41


title: RNA130926RH_48

description: Sample name: 48


title: d364 [SIRS-AKI-HD]


title: ML53


title: ML32


title: hf81 [SIRS-AKI-HD]


title: ML25


title: hf327 [SIRS-AKI-HD]


title: RNA130926RH_39

description: Sample name: 39


title: RNA130926RH_40

description: Sample name: 40


title: d29 [SIRS-AKI-HD]


title: ML42


title: RNA130926RH_38

description: Sample name: 38


title: d347 [SIRS-AKI-HD]


title: RNA130926RH_37

description: Sample name: 37


title: ML49

value: Low Salt Imidazole buffered medium with 125 mM methanol, 100mM pyruvate


title: ML50


title: ML40


title: RNA130926RH_35

description: Sample name: 35


title: hf79 [SIRS-AKI-HD]


title: RNA130926RH_42

description: Sample name: 42


title: ML22


title: RNA130926RH_36

description: Sample name: 36


title: hf22 [SIRS-AKI-HD]


title: hf207 [SIRS-AKI-HD]


title: RNA130926RH_34

description: Sample name: 34


title: ML39


title: hf230 [SIRS-AKI-HD]


title: ML20


title: ML30


title: RNA130926RH_33

description: Sample name: 33


title: hf346 [SIRS-AKI-HD]


title: hf11 [SIRS-AKI-HD]


title: ML24


title: ML31


title: hf201 [SIRS-AKI-HD]


title: RNA130926RH_32

description: Sample name: 32


title: RNA130926RH_29

description: Sample name: 29


title: RNA130926RH_30

description: Sample name: 30


title: RNA130926RH_31

description: Sample name: 31


title: hf225 [SIRS-AKI-HD]

value: Acute Kidney Injury stage 1


title: ML48

value: Low Salt Imidazole buffered medium with 125 mM methanol, 120mM acetate


title: RNA130926RH_27

description: Sample name: 27


title: hf184 [SIRS-AKI-HD]


title: ML17


title: RNA130926RH_26

description: Sample name: 26


title: hf202 [SIRS-AKI-HD]


title: hf314 [SIRS-AKI-HD]


title: ML15


title: RNA130926RH_25

description: Sample name: 25


title: ML13


title: hf83 [SIRS-AKI-HD]


title: ML6


title: hf310 [SIRS-AKI-HD]


title: hf188 [SIRS-AKI-HD]


title: RNA130926RH_24

description: Sample name: 24


title: hf301 [SIRS-AKI-HD]


title: RNA130926RH_23

description: Sample name: 23


title: d194 [SIRS-AKI-HD]


title: RNA130926RH_22

description: Sample name: 22


title: ML3


title: RNA130926RH_21

description: Sample name: 21


title: hf287 [SIRS-AKI-HD]


title: ML10


title: ML44

value: Low Salt Imidazole buffered medium with 125 mM methanol


title: RNA130926RH_20

description: Sample name: 20


title: RNA130926RH_19

description: Sample name: 19


title: ML8


title: RNA130926RH_17

description: Sample name: 17


title: hf195 [SIRS-AKI-HD]


title: ML43


title: RNA130926RH_18

description: Sample name: 18


title: ML35


title: ML36


title: hf260 [SIRS-AKI-HD]


title: hf206 [SIRS-AKI-HD]


title: RNA130926RH_15

description: Sample name: 15


title: hf192 [SIRS-AKI-HD]


title: hf246 [SIRS-AKI-HD]


title: RNA130926RH_16

description: Sample name: 16


title: ML34


title: ML29


title: ML26


title: RNA130926RH_14

description: Sample name: 14


title: RNA130926RH_28

description: Sample name: 28


title: RNA130926RH_13

description: Sample name: 13


title: ML18


title: hf292 [SIRS-AKI-HD]


title: hf40 [SIRS-AKI-HD]


title: ML1


title: ML47

value: Low Salt Imidazole buffered medium with 120 mM acetate


title: RNA130926RH_12

description: Sample name: 12


title: RNA130926RH_11

description: Sample name: 11


title: ML9


title: d37 [SIRS-AKI-HD]


title: RNA130926RH_10

description: Sample name: 10


title: d387 [SIRS-AKI-HD]


title: ML16


title: d360 [SIRS-AKI-HD]


title: ML38


title: RNA130926RH_8

description: Sample name: 8


title: ML12


title: hf82 [SIRS-AKI-HD]


title: ML28


title: hf265 [SIRS-AKI-HD]


title: hf25 [SIRS-AKI-HD]


title: hf161 [SIRS-AKI-HD]


title: hf189 [SIRS-AKI-HD]


title: RNA130926RH_7

description: Sample name: 7


title: RNA130926RH_6

description: Sample name: 6


title: ML27


title: RNA130926RH_5

description: Sample name: 5


title: hf244 [SIRS-AKI-HD]


title: RNA130926RH_4

description: Sample name: 4


title: ML19


title: RNA130926RH_3

description: Sample name: 3


title: RNA130926RH_2

description: Sample name: 2


title: ML5


title: hf311 [SIRS-AKI-HD]


title: ML2


title: hf319 [SIRS-AKI-HD]


title: RNA130926RH_9

description: Sample name: 9


title: RNA130926RH_1

description: Sample name: 1


title: hf18 [SIRS-AKI-HD]


title: hf213 [SIRS-AKI-HD]


title: hf10 [SIRS-AKI-HD]


title: RNA-Seq STAT3WT.IL21.4h

description: treated with IL-21 for 4h

extract_protocol:
For ChIP-Seq, Cells were fixed with 1% formaldehyde at 37°C for 10 min, and chromatin from 2.5 x 107 cells was sonicated for 20 cycles (15 sec on/45 sec off) to produce 250-450 bp fragments. STAT3-linked chromatin was immunoprecipitated using anti-STAT3 (13-7000, Invitrogen) antibody bound to Dynabeads.  The ends of isolated DNA were repaired using the DNA END-Repair kit (Epicentre Biotechnologies), and a 3’ “A” nucleotide was added with Taq polymerase.  Two mixed Solexa adaptors (Illumina) were ligated to DNA ends and primers complementary to these adaptors (PE 1.0 and 2.0, Illumina) were used to amplify the DNA for 18 cycles.  DNA fragments of 250-450 bp were purified from 2% E-gels and used for cluster generation and sequencing. For RNA-Seq,  Total RNA was isolated, and 5 μg per sample were used for mRNA purification using Dynal oligo(dT) beads (Invitrogen).  Double-stranded cDNA was synthesized with random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (Invitrogen) and fragmented by Bioraptor.  After end repair (Epicentre DNA END-Repair kit) and the addition of an “A” nucleotide to the 3’ ends with Taq DNA polymerase, two mixed Solexa adaptors (Illumina) were ligated to DNA ends using T4 DNA ligase (New England Biolabs).  250-450 bp fragments were isolated on 2% E-Gels (Invitrogen) and amplified for 18 cycles using PE 1.0 and 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).  PCR products were run on a gel, and 250-450 bp fragments were purified
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Total mouse splenic CD4+ T cells were preactivated with plate-bound anti-CD3 + anti-CD28 for 3 days, washed and rested overnight, and not stimulated or stimulated with IL-21 for 1h (ChIP-Seq) or 4h (RNA-Seq)

value: Spleen

value: Pre-activated CD4+ T cells

value: treated with IL-21 for 4h


title: RNA-Seq STAT3KO.IL21.4h

description: treated with IL-21 for 4h


title: RNA-Seq STAT3KO.untreat

description: untreated

value: untreated


title: hf217 [SIRS-AKI-HD]


title: d68 [SIRS-AKI-HD]


title: hf2 [SIRS-AKI-HD]


title: hf20 [SIRS-AKI-HD]


title: hf126 [SIRS-AKI-HD]


title: RNA-Seq STAT1KO.untreat

description: untreated


title: RNA-Seq STAT3WT.untreat

description: untreated


title: RNA-Seq STAT1KO.IL21.4h

description: treated with IL-21 for 4h


title: RNA-Seq STAT1WT.IL21.4h

description: treated with IL-21 for 4h


title: hf136 [SIRS-AKI-HD]

value: Acute Kidney Injury stage 0


title: hf193 [SIRS-AKI-HD]


title: CD4.S1KO.IL21.STAT3

description: ChIP against STAT3

value: STAT3 (Invitrogen, 13-7000)


title: CD4.S1KO.Cont.STAT3

description: ChIP against STAT3


title: Shh_2

city: Cambridge

institute: Harvard University

data_processing:
tophat (v2.0.9) used to align the reads to the reference genome, supplied with  transcript annotation data (genes.gtf) from UCSC mm10, with options  --b2-sensitive (default preset option for alginment)
SAMtools used to organize, sort the BAM files and create SAM files
htseq-count (v0.5.4p5) used to get read counts for genes, nes.gtf) from UCSC mm10, with options -s no
edgeR (v3.4.2) used to normalize counts across samples, and to do differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab separated .txt file includes gene name, log fold change, log count-per-million, Pvalue and FDR
Supplementary_files_format_and_content: comma separated .csv file includes normalized counts for all 4 samples (WT_1, WT_2, Shh_1, Shh_2)

source_name: Shh null E10.5 mouse forelimb

extract_protocol:
Forelimbs were harvested and were immediately processed for RNA extraction using TRIzol
RNA libraries were prepared for sequencing using standard Illumina Hi-Seq protocols

value: Swiss Webster

value: Forelimb

tag: age

tag: genotype/variation

value: Shh null


title: hf155 [SIRS-AKI-HD]

tag: patient id

tag: sirs outcomes


title: hf98 [SIRS-AKI-HD]


title: CD4.WT.Cont.STAT3

description: ChIP against STAT3

tag: cell type

tag: genotype

value: WT


title: d155 [SIRS-AKI-HD]


title: hf231 [SIRS-AKI-HD]


title: Shh_1

tag: tissue


title: WT_2

source_name: Wild-type E10.5 mouse forelimb


title: WT_1


title: RNA-Seq STAT1WT.untreat

description: untreated


title: hf45 [SIRS-AKI-HD]


title: hf274 [SIRS-AKI-HD]


title: hf27 [SIRS-AKI-HD]


title: d326 [SIRS-AKI-HD]


title: hf120 [SIRS-AKI-HD]


title: d61 [SIRS-AKI-HD]


title: Proximal LGR5 2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Hi-Seq 2000 for sequencing
Sequenced reads were trimmed of adaptors and barcodes, filtered of reads with quality threshold <= 30, multiply mapped reads, and number of N's > 0.  Remaining reads were aligned to the mm9 genome in GeneSpring NGS
Reads per kilobase per megabase (RPKM) was calculated, and normalized using the DeSeq normalization procedure, thresholding the number of reads per entity to 1.
Normalized expression values were baselined to the median of all samples
Genome_build: MGSCv37
Supplementary_files_format_and_content: tab-delimited text files containing RPKM values (*RPKM.txt), and normalized and baselined RPKM values, for each sample.

source_name: Jejenum LGR5 stem cells

growth_protocol: Cells sorted with FACSaria II were collected, pelleted, and embedded in Matrigel™ (BD Biosciences) supplemented with 750 ng/mL EGF, 1,5 µg/mL Noggin and 1 µM Jagged-1 Fc chimera (R&D). Each well was overlaid with culture medium containing 1 mM N-acetylcysteine (Sigma), 2,5 µM Thiazovivin and 2,5 µM CHIR99021 (Stemgent, Cambridge, MA). Culture medium was replaced 2 days after the sorting by culture medium supplemented with 1 μg/mL R-Spondin1 (Preprotech), 1 μM Jagged-1 Fc chimera, 50 ng/mL EGF and 100 ng/mL Noggin (R&D). Medium then was changed every 4 days and EGF, Noggin, R-spondin1 were added at original concentrations.

extract_protocol:
Illumina TruSeq RNA preparation kit
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq 2000 with single-end 50-bp reads (Illumina, San Diego, CA)

value: Jejenum LGR5 stem cells

tag: stem cell selection

value: LGR5 stem cells

tag: location

value: Jejenum

value: 6-12 weeks

value: Male


title: Proximal 166 1

source_name: Jejunum 166 stem cells

value: Jejunum 166 stem cells

value: CD44+/CD24lo/CD166+ stem cells


title: CD4.WT.IL21.STAT3

description: ChIP against STAT3

value: Spleen

tag: chip antibody


title: Distal 166 2

source_name: Ileal 166 stem cells

value: Ileal 166 stem cells

value: Ileum


title: Proximal LGR5 1


title: Distal 166 1


title: hf307 [SIRS-AKI-HD]


title: hf156 [SIRS-AKI-HD]


title: hf179 [SIRS-AKI-HD]


title: Distal LGR5 1

source_name: Ileal LGR5 stem cells

value: Ileal LGR5 stem cells


title: Proximal Crypt 3

source_name: Jejenum crypt stem cells

value: Jejenum crypt stem cells

value: Crypt stem cells


title: hf205 [SIRS-AKI-HD]

value: Acute Kidney Injury stage 0


title: Proximal 166 2


title: d91 [SIRS-AKI-HD]


title: hf197 [SIRS-AKI-HD]


title: Proximal Crypt 2


title: Proximal Crypt 1


title: hf317 [SIRS-AKI-HD]


title: hf203 [SIRS-AKI-HD]


title: Distal LGR5 2


title: d25 [SIRS-AKI-HD]


title: d205 [SIRS-AKI-HD]


title: Distal Crypt 2

source_name: Ileal crypt stem cells

value: Ileal crypt stem cells


title: Distal Crypt 1


title: hf347 [SIRS-AKI-HD]


title: d284 [SIRS-AKI-HD]


title: d121 [SIRS-AKI-HD]


title: d366 [SIRS-AKI-HD]


title: hf13 [SIRS-AKI-HD]


title: d187 [SIRS-AKI-HD]


title: d161 [SIRS-AKI-HD]


title: hf196 [SIRS-AKI-HD]


title: hf241 [SIRS-AKI-HD]


title: d38 [SIRS-AKI-HD]


title: d249 [SIRS-AKI-HD]


title: d39 [SIRS-AKI-HD]


title: hf111 [SIRS-AKI-HD]


title: hf330 [SIRS-AKI-HD]


title: d303 [SIRS-AKI-HD]


title: hf124 [SIRS-AKI-HD]


title: Distal Crypt 3


title: d246 [SIRS-AKI-HD]


title: hf100 [SIRS-AKI-HD]


title: hf236 [SIRS-AKI-HD]


title: hf158 [SIRS-AKI-HD]


title: hf296 [SIRS-AKI-HD]


title: hf304 [SIRS-AKI-HD]


title: d253 [SIRS-AKI-HD]


title: d283 [SIRS-AKI-HD]


title: d299 [SIRS-AKI-HD]


title: hf159 [SIRS-AKI-HD]


title: d188 [SIRS-AKI-HD]


title: hf76 [SIRS-AKI-HD]


title: hf106 [SIRS-AKI-HD]


title: hf37 [SIRS-AKI-HD]


title: hf97 [SIRS-AKI-HD]


title: hf107 [SIRS-AKI-HD]


title: hf216 [SIRS-AKI-HD]


title: hf210 [SIRS-AKI-HD]


title: hf128 [SIRS-AKI-HD]


title: Imatinib

city: La Jolla

first: Jean

middle: YJ

last: Wang

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: University of California San Diego

data_processing:
Illumina Casava1.7 software used for basecalling. Clipping/statistics/qc is by ea-utils toolbox.
Reads were clipped using the fastq-mcf tool and miRNA were quantified from reads using mirna-quant, both from the open source ea-utils toolbox.
Alignment was done with bowtie
miRNA species were annotated using miRBase
Read counts were normalized with the upper quartile method by Bullard et al., BMC Bioinformatics 2010, 11:94
Genome_build: miRbase
Supplementary_files_format_and_content: tab-delimited text files include normalized read count for each miRNA

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells are routinely cultured in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. Cells are in 70% confluency at the time of treatment

extract_protocol:
Total RNA extraction with Trizol
RNA libraries were prepared for sequencing using "TruSeq RNA Sample Prep Kit" from Illumina

treatment_protocol: Vehicle: distilled water in same volume and duration as the imatinib or doxorubicin. Imatinib: 10 μM for 2 h. Doxorubicin: 0.5 μg/ml at 2 h following the vehicle or imatinib treatment, and last for 24 h

tag: cell line

tag: treatment

value: Imatinib


title: Vehicle

value: Vehicle


title: Doxorubicin

value: Doxorubicin


title: Imatinib + Doxorubicin

value: Imatinib + Doxorubicin


title: d315 [SIRS-AKI-HD]


title: hf68 [SIRS-AKI-HD]


title: NGS 17

city: Jacksonville

first: Michael

middle: Patrick

last: Walsh

state: Florida

address: 4500 San Pablo Road

department: Cancer Basic Science

institute: Mayo Clinic Jacksonville

data_processing:
Aligment was performed using Tophat version 2
Gene counts were calculated using HTSeq
Genome_build: HG19
Supplementary_files_format_and_content: csv file containing reads mapped to genes

source_name: Thyroid tumor

extract_protocol:
PicoPure Kit
Illumina TrueSeq v 2

value: Thyroid cancer

tag: Sex

value: female

tag: tumor stage

value: BRAF-wt


title: NGS 9

value: BRAF-mut


title: NGS 7


title: NGS 15


title: NGS 12


title: NGS 18

value: BRAF - mut


title: NGS 13

value: male


title: NGS 5


title: NGS 10


title: NGS 16


title: NGS 19


title: NGS 14


title: NGS 6


title: NGS 11


title: NGS 20


title: NGS 4


title: NGS 2


title: NGS 3


title: Nasal_Chondrocyte_Sox9_ChIPseq

source_name: E17.5 Nsal chondrocytes

tag: strain background

value: ICR

tag: isolation stage

value: Enzyme digested nasal septum chondrocytes

tag: chip antibody vandor

value: Millipore

tag: chip antibody cat. #


title: TR2-105 - rep2 - 0% glucose

city: Leuven

first: Kevin

last: Verstrepen

address: Gaston Geenslaan 1

country: Belgium

institute: VIB/KULeuven

description:
glu0-TR2-105.2
TR2_105repeats_0%Glu_FC.txt

data_processing:
Raw reads were filtered using FASTX-Toolkit with Q30 cutoff.
Sequenced reads were trimmed to remove adaptor sequences and low quality reads and then aligned to the S. cerevisiae reference genome (GeneBank version 64) using Tophat 2.0.7 to obtain read numbers
The Trimmed Mean of M-values method (Robinson and Oshlack, Genome Biology 2010) was used to normalize the data and the edgeR Bioconductor package used to determine differentially expressed genes (in each TR2 variant relative to the WT - TR2-63)
Genome_build: SacCer_May2010
Supplementary_files_format_and_content: Tab delimited text files including Log2 fold change in gene expression relative to the WT sample (TR2-63)

organism: Saccharomyces cerevisiae

source_name: cells grown in glucose-starved medium

growth_protocol: Cells were grown  in YP medium supplemented with 4% glucose until exponential phase. Half the volume of each culture was harvested and the second half transferred to medium without glucose for 2 hours before harvest.

extract_protocol:
Cells were lysed with glass beads and total RNA was extracted using the Phenol-Chloroform standard method.
polyA RNA libraries were prepared from 1 ug total RNA using standard illumina protocols and sequenced on an Illumina HiSeq2000

tag: growth protocol

value: glucose-starved medium

tag: strain

tag: growth stage

value: exponential

tag: harvest time

value: 2 hours after medium switch

tag: tandem repeat number

value: 105 repeats


title: Rib_Chondrocyte_IgG_Control_ChIpseq

tag: cell type

value: Enzyme digested rib chondrocytes

value: rabbit IgG

value: Invitrogen


title: TR2-90 - rep2 - 0% glucose

description:
glu0-TR2-90.2
TR2_90repeats_0%Glu_FC.txt

value: 90 repeats


title: TR2-90 - rep1 - 0% glucose

description:
glu0-TR2-90.1
TR2_90repeats_0%Glu_FC.txt


title: Rib_Chondrocyte_Input_Control_ChIpseq


title: Nasal_Chondrocyte_Input_Control_ChIPseq


title: Rib_Chondrocyte_RNA_Pol_II_ChIPseq

value: Abcam


title: NGS 8

tag: tissue

value: Thyroid cancer

tag: age

value: female

tag: genotype/variation


title: TR2-63 (WT) - rep2 - 0% glucose

value: 63 repeats (WT)


title: TR2-55 - rep1 - 0% glucose

description:
glu0-TR2-55.1
TR2_55repeats_0%Glu_FC.txt

value: 55 repeats


title: Rib_Chondrocyte_H3K27ac_ChIPSeq

tag: chip antibody


title: Rib_Chondrocyte_H3K4me2_ChIPSeq


title: TR2-55 - rep2 - 0% glucose

description:
glu0-TR2-55.2
TR2_55repeats_0%Glu_FC.txt


title: Rib_Chondrocyte_Sox9_ChIPseq


title: Rib_Chondrocyte_H3K36me3_ChIPSeq


title: TR2-63 (WT) - rep1 - 0% glucose


title: TR2-33 - rep1 - 0% glucose

description:
glu0-TR2-33.1
TR2_33repeats_0%Glu_FC.txt

value: 33 repeats


title: TR2-33 - rep2 - 0% glucose

description:
glu0-TR2-33.2
TR2_33repeats_0%Glu_FC.txt


title: TR2-14 - rep1 - 0% glucose

description:
glu0-TR2-14.1
TR2_14repeats_0%Glu_FC.txt

value: 14 repeats


title: TR2-27 - rep2 - 0% glucose

description:
glu0-TR2-27.2
TR2_27repeats_0%Glu_FC.txt

value: 27 repeats


title: TR2-20 - rep1 - 0% glucose

description:
glu0-TR2-20.1
TR2_20repeats_0%Glu_FC.txt

value: 20 repeats


title: Rib_Chondrocyte_H3K27me3_ChIPSeq

value: ICR

value: Millipore


title: TR2-0 - rep2 - 0% glucose

description:
glu0-TR2-0.2
TR2_0repeats_0%Glu_FC.txt

value: glucose-starved medium

value: exponential

value: 2 hours after medium switch

value: 0 repeats


title: TR2-27 - rep1 - 0% glucose

description:
glu0-TR2-27.1
TR2_27repeats_0%Glu_FC.txt


title: TR2-0 - rep1 - 0% glucose

description:
glu0-TR2-0.1
TR2_0repeats_0%Glu_FC.txt


title: TR2-105 - rep2 - 4% glucose

description:
glu4-TR2-105.2
TR2_105repeats_4%Glu_FC.txt

source_name: cells grown in glucose-rich medium

value: glucose-rich medium

value: 105 repeats


title: TR2-14 - rep2 - 0% glucose

description:
glu0-TR2-14.2
TR2_14repeats_0%Glu_FC.txt


title: TR2-63 (WT) - rep2 - 4% glucose


title: TR2-90 - rep1 - 4% glucose

description:
glu4-TR2-90.1
TR2_90repeats_4%Glu_FC.txt

value: 90 repeats


title: TR2-105 - rep1 - 0% glucose

description:
glu0-TR2-105.1
TR2_105repeats_0%Glu_FC.txt


title: TR2-63 (WT) - rep1 - 4% glucose


title: TR2-55 - rep2 - 4% glucose

description:
glu4-TR2-55.2
TR2_55repeats_4%Glu_FC.txt


title: NGS 1

value: Thyroid cancer

value: BRAF-mut


title: TR2-20 - rep2 - 0% glucose

description:
glu0-TR2-20.2
TR2_20repeats_0%Glu_FC.txt


title: Rib_Chondrocyte_H3K4me3_ChIPSeq

value: Enzyme digested rib chondrocytes


title: TR2-33 - rep2 - 4% glucose

description:
glu4-TR2-33.2
TR2_33repeats_4%Glu_FC.txt


title: TR2-55 - rep1 - 4% glucose

description:
glu4-TR2-55.1
TR2_55repeats_4%Glu_FC.txt

value: 55 repeats


title: TR2-33 - rep1 - 4% glucose

description:
glu4-TR2-33.1
TR2_33repeats_4%Glu_FC.txt

value: 33 repeats


title: TR2-27 - rep1 - 4% glucose

description:
glu4-TR2-27.1
TR2_27repeats_4%Glu_FC.txt


title: TR2-0 - rep2 - 4% glucose

description:
glu4-TR2-0.2
TR2_0repeats_4%Glu_FC.txt


title: TR2-0 - rep1 - 4% glucose

description:
glu4-TR2-0.1
TR2_0repeats_4%Glu_FC.txt


title: TR2-14 - rep1 - 4% glucose

description:
glu4-TR2-14.1
TR2_14repeats_4%Glu_FC.txt

value: 14 repeats


title: TR2-27 - rep2 - 4% glucose

description:
glu4-TR2-27.2
TR2_27repeats_4%Glu_FC.txt

value: 27 repeats


title: TR2-105 - rep1 - 4% glucose

description:
glu4-TR2-105.1
TR2_105repeats_4%Glu_FC.txt