title: FRDA05-UT

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling. The reads were demultiplexed, allowing no mismatches in the index sequence.
Sequence reads were aligned to hg19 version of human genome with Tophat 1.4.1 software with parameters -p 8 -r 100 and transcript annotation file supplied.
Gene based counts were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty  --stranded=no
Differential expression analysis was then performed using DESeq Bioconductor package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Count files were obtained using HTSeq count module (version 0.5.3p9) using parameters -m intersection-nonempty  --stranded=no


title: Myc_Idax_ChIP-seq

status: Public on Apr 03 2013

type: SRA

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: genomic

data_processing:
Basecalls performed using 'HiSeq Control Software' version 1.5.15.1
Sequencing reads were mapped against hg19 using bowti (bowtie-0.12.7 -n 2 -l 28 -m 3 -k 1 --best --chunkmbs 512 -p 8 -S -q)
Peaks were called using MACS (1.4.1) using default parameter settings for human (hs)
Enrichment profiles along selected annotations were calculated using custom scripts inside of the R/Bioconductor environment.
Genome_build: hg19
Supplementary_files_format_and_content: wiggle files were generated as follows: i) reads are extended to the length of estimated average fragment length. ii) coverage is calculated in the single nucleotide-level and its normalised by the number of million mapped reads (RPM)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Stable HEK293T cells were generated by transfecting empty vector, wild-type Myc-Idax or DNA-binding mutant of Myc-Idax (Myc-IdaxDBM).

extract_protocol:
Nuclei were isolated and chromatin was sheared using Covaris S2 instrument and protein-DNA complexes were isolated by antibody.
ChIP-seq library was constructed using TruSeq Sample Prep kit (Illumina) and Illumina HiSeq sequencing was performed as per manufacturer's instructions.

tag: cell line

tag: transfection

value: wild-type Myc-Idax

tag: antibody

value: Anti-c-Myc; Sigma, Cat#:A7470-1ML (Agarose Affinity Gel)


title: FRDA05-Nico

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: transcriptomic

molecule: total RNA

source_name: primary cultured lymphocytes

growth_protocol: Primary lymphocytes from FRDA patients were isolated from the blood samples using Ficoll-Hypaque TM gradient (Sigma) by following the manufacturer’s protocol. Human blood samples were obtained from patients in accordance with UK Human Tissue Authority ethical guidelines. Cells were grown in RPMI 1640 (PAA) medium with 2 mM L-glutamine and 10% fetal calf serum (PAA) and supplemented with 1x penicillin/streptomycin solution (GIBCO) at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. TruSeq DNA Sample Prep Kits v2 - Illumina (Cat#FC-121-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary lymphocytes at cell density of 1x10^7cells/ml were treated with 10mM nicotinamide for 3 days. Culture medium with or without (untreated as control) nicotinamide was changed every 24 hours incubation.

tag: tissue

value: PBMC

tag: treatment

value: 10mM nicotinamide


title: Control adult#1 sRNA library

status: Public on Apr 05 2013

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

country: USA

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing: Data tables include the reads and counts after barcode removal and trimming of adaptor sequences.

organism: Caenorhabditis elegans

source_name: N2 wildtype control adults

growth_protocol: Adult control and postdauer animals were collected as previously described (Hall, Beverly, et al 2010). Dauer animals were collected 24 hours after SDS treatment, following the postdauer growth strategy. L3 animals were grown according to the control adult strategy, but collected at the L3 stage.

extract_protocol: Total RNA was extracted with Trizol reagent (Sigma) from flash-frozen staged worms, and 25 ug was subjected to 5'-triphosphate removal treatment with Tobacco Acid Phosphatase (TAP; Epicentre). This treatment left a 5’-monophosphate on siRNAs. Small RNAs between 18-32 nt were size selected and subjected to linker ligation reactions and amplification as described previously (Lau et al 2001 Science). Two biological replicates were sequenced for adult libraries, one biological replicate for L3 larvae and dauer libraries. sRNA libraries were sequenced on an Illumina GAII machine, yielding between 4 and 14 million reads per library that matched to the C. elegans genome.

tag: strain

value: N2 wildtype

tag: Stage

value: control adults

tag: barcode

value: TTAA


title: Wild Type

city: Vienna

first: Javier

last: Martinez

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

description: size selected 37-50nt

data_processing:
basecalling: RTA 1.7.48.0
trimming: cutadapt 1.0 -a GATCGGAAGAGCACACGTCT -a GTTCAGAGTTCTACAGTCCGACGATC -a TCGTATGCCGTCTTCTGCTTG -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG -a AGATCGGAAGAGCGGTTCAGTAGGAATGCCGAGACCG
alignment: bowtie 0.12.5
bedtools annotation by http://gtrnadb.ucsc.edu/Mmusc/
Genome_build: mm9
Supplementary_files_format_and_content: summary table of read count per tRNA

organism: Mus musculus

source_name: primary MEFs

growth_protocol: Primary MEFs were obtained from day 13.5 embryos and grown in complete medium (Dulbecco's modified Eagle's medium) supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin (GIBCO-BRL).

extract_protocol: ~50 μg of total RNA from primary MEFs was separated alongside with a radiolabeled RNA decade marker (Ambion) on a preparative 10% denaturing polyacrylamide gel (20 × 25 cm, 1 mm thick) containing 8 M urea (Sequagel, National Diagnostics). The gel region comprising sizes of 37-50 nucleotides was excised and passively eluted overnight into 0.4 M NaCl. The RNA was precipitated by adding three volumes of ethanol, the pellet was washed once in 85 % ethanol and dissolved in 16 μL H2O. 2 μL (10 U/μL) tobacco acid pyrophosphatase (TAP, Epicentre; in order to hydrolyze the terminal 5' triphosphate group of tRNAs to generate a 5'  monophosphate terminus; alternatively RNA 5' polyphosphatase (Epicentre) was used to produce 5’ monophosphate termini) and 2 μL 10x TAP reaction buffer was added followed by incubation for 1 hour at 37°C. The reaction was deproteinized, and the RNA was extracted with phenol/chloroform and subsequently precipitated with ethanol. Adaptor ligation for high- throughput sequencing was essentially performed as described in Hafner, M. et al. (Methods 44, 3-12 2007.09.009 [2008]) except that the 5' adapter ligation step was performed prior to the 3' adapter ligation. 5' adapter oligonucleotides (5'- GUU CAG AGU UCU ACA GUC CGA CGA UC-3') were ligated using T4 RNA ligase I (NEB) including 15 % polyethylene glycol 8000 on ice overnight. After separation by a preparative 10% denaturing polyacrylamide gel, the gel region corresponding to 60-74 nucleotides was excised, the RNA passively eluted and ethanol precipitated as described above. The RNA was ligated to 3' adapter oligonucleotides (5'- App-UCG UAU GCC GUC UUC UGC UUG UidT-3') using T4 RNA ligase 2 (truncated, NEB) including 15% polyethylene glycol 8000 on ice overnight. RNA was again separated on a 10% denaturing polyacrylamide gel, and RNA was eluted from the gel region corresponding to 80-100 nucleotides. For cDNA preparation, Illumina Rev primer (5'-CAA GCA GAA GAC GGC ATA CGA-3') and Superscript II Reverse Transcriptase kit (Invitrogen) was used. PCR amplification was performed using Phusion High Fidelity Polymerase (NEB) and Illumina Forward (5'- AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3') and Reverse primers. PCR products were subsequently sequenced on an Illumina G2 platform.

tag: genotype

value: Wt

value: primary MEFs


title: Clp1(k/k)

description: size selected 37-50nt


title: S288C_TATLSeq7

city: Cambridge

first: Joshua

middle: A

last: Arribere

address: 31 Ames St

department: Biology

institute: MIT

description: TATL-Seq, fraction 7

data_processing:
TATL-SeqCombined.wig is TATL-SeqFraction1.wig through TATL-SeqFraction7.wig computationally pooled reads (simply the sum of all the other read densities).  Each file is the read abundance at each position of the sacCer3 genome. Reads were mapped to the genome, then annotated splice junctions allowing for 3 mismatches (just as in the associated paper).
Library strategy: TL-Seq
Reads mapped to genome with Bowtie.
Reads assigned to genes. Intergenic reads were assigned to the closest gene, regardless of strand. Antisense reads were ignored for subsequent analyses.
Peaks were called assuming a uniform background distribution, using Poisson distribution to identify regions of high read density.
Genome Build: sacCer3
Supplementary_files_format_and_content: Tab-delimited file of monopeak TL genes giving TL length

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures (Sigma 1278b MAT a ura3 leu2 trp1 his3 and BY4742 Mat α his3∆1 leu2∆0 lys2∆0 ura3∆0) were grown to mid-log (OD600~0.5-1.0) phase in YPAD (1% yeast extract, 2% peptone, 0.01% adenine hemisulfate, 2% glucose) at 30°C in flasks with vigorous shaking.

extract_protocol: 200-1000 µg RNA was subjected to poly(A) selection using oligo dT cellulose as described previously (Sambrook et al.). Poly(A)-selected RNA was fragmented by alkaline hydrolysis (2 mM EDTA, 100mM NaCO3, pH 9.3) for one hour at 95°C. RNA fragments were gel purified and dephosphorylated with 30 U Calf-Intestinal Phosphatase (CIP, NEB) in 50 ml reactions containing 100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9 at 37°C for 60 min, followed by phenol:chloroform extraction and isopropanol precipitation. Purified CIP-treated fragments were treated (or mock-treated) with 25 U Tobacco Acid Pyrophosphatase (TAP, Epicentre) in 50 ml at 37°C for two hours, then precipitated. Next a 5’RNA adaptor (AAUGAUACGGCGACCACCGACAGGUUCAGAGUUCUACAGUCCGACG) was added via ligation in a 20 ml reaction with 20 U of T4 RNA Ligase (NEB) for one hour at 37°C. Gel purification of a higher molecular weight species yielded the ligated RNA, which was then 3’end captured via poly(A) tailing (TL-Seq, as previously described in (Ingolia et al., 2009)) or ligation with preadenylated adaptor (TATL-Seq, as previously described in (Mayr and Bartel, 2009)). cDNA was prepared from ligated RNA (Superscript III, Invitrogen), amplified by 10-12 cycles of PCR (Phusion, Finnzymes), and sequenced on an Illumina Genome Analyzer II.

treatment_protocol: Total RNA was isolated from yeast cell pellets by hot phenol extraction as described (Clarkson et al., 2010). Polysome gradients were prepared and RNA was extracted from gradient fractions as described (Arribere et al., 2011).

tag: rna subtype

value: RNA, polysome purified


title: RNA_Ad5 (RL-7)

description: Processed data files for this Sample: RNA_MeDIP_promoter_genebody_v2.txt

data_processing:
Illumina 1.5 and 1.6 pipelines.
36mer RNA-seq reads were aligned to the mouse genome using Bowtie (version 0.12.5 – parameter set: -n 2 -l 36 -y --chunkmbs 256 --best --strata -k 1 -m 1) against the genomic reference UCSC mm9. Subsequently, reads that did not map to the genome were aligned to the cDNA reference ENSEMBL v58 in order to map reads spanning exon junctions. Then, uniquely mapped reads aligning to the sense strand of a gene were counted.
Annotations using ENSEMBL58.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files. File "RNA_MeDIP_promoter_genebody_v2.txt" contains the RNA-seq raw read counts per Ensembl gene (Version58) and the normalized read counts (rpm, reads per million: number of exon read counts per gene / sum of the exon read counts of the sample x 1 000 000); the raw MeDIP-seq read counts per sample for individual promoter regions (-1 kb to +0.5 kb) and for individual genes (sum of the reads mapping to a gene) and the relative read counts that were calculated relative to the sample with the highest number of reads. In addition, the file contains the results of the edgeR analysis for the RNA-seq and the MeDIP-seq data. For the MeDIP-seq data, also a ratio and a t-test as well as a score (-log10(p.value)*10)*log(ratio) are given for the comparison of the normal intestinal samples (B,N) vs. the adenoma samples. Files "hyper_500bp_Ad_vs_BN_v1.txt", "hypo_500bp_Ad_vs_BN_v1.txt", "hypo_DMR_merged_Ad_vs_BN_v1.txt", "hyper_DMR_merged_Ad_vs_BN_v1.txt" contain the identified differentially methylated regions and the rpm values of the MeDIP-seq data. In brief, mean rpm values were calculated for genome-wide 500 bp windows overlapping by 250 bp using MEDIPS. Subsequently, for each 500 bp window, we applied a Wilcoxon's test in order to assess significance of methylation differences between the 5 ApcMin/+ adenomas (Ad) versus the 3 ApcMin/+ normal intestine (N), 3 Apc+/+ wildtype normal intestine (B). Differentially methylated regions (cDMRs) were identified by filtering for 500 bp windows associated with Wilcoxon p-values < 0.01, a ratio of >1.33 or <0.75 and a minimum average signal of 0.25 rpm for one of the two groups (results for the 500 bp bins in: "hyper_500bp_Ad_vs_BN_v1.txt", "hypo_500bp_Ad_vs_BN_v1.txt"). Overlapping significant 500 bp windows were merged if their methylation status indicated an extending DMR (Results for the merged regions in files "hypo_DMR_merged_Ad_vs_BN_v1.txt", "hyper_DMR_merged_Ad_vs_BN_v1.txt").

source_name: intestine, ileum, adenoma, Apc-Min/+

extract_protocol:
Intestinal samples were excised, transferred to buffer RLT/1mM DTT (Qiagen, Hilden, Germany) and homogenized in a Tissue Lyser (Qiagen) for 2 x 2 min, frequency set to 20 with a steel bead of 5 mm diameter (Qiagen). Samples were snap frozen and stored at -80°C until extraction of DNA and RNA using the Allprep DNA/RNA Mini kit (Qiagen). A DNase digest of the RNA was performed on the columns according to the manufacturer's instructions. RNA-seq and MeDIP-seq libraries were generated from the same samples.
RNA-Seq: 4 µg of total RNA was depleted for ribosomal RNA using the RiboMinus Euaryote Kit for RNA-seq (Invitrogen, #A1083708) following the manufacturer's instructions. The RiboMinus depleted RNA was then used for the generation of single end RNA-seq libraries using the Illumina sample prep kit, oligo only (#FC-102-1004) and a strand-specific protocol as described previously (Parkhomchouk et al., 2009, Nucleic Acids Res 37: e123. doi:10.1093/nar/gkp596). The generated cDNA libraries were size selected on a 2% agarose gel, and fragments of 150-200 nt were excised (corresponding to insert sizes of 80-130 nt) and purified using the QIAquick Gel extraction kit (Qiagen). Libraries were subjected to single-end sequencing.

value: Apc-Min/+

value: intestine, ileum, adenoma

tag: Sex

value: male

tag: age

value: 15-19 weeks

tag: animal id


title: S288C_TATLSeq6

description: TATL-Seq, fraction 6


title: RNA_Ad4-1 (RL-2)


title: RNA_Ad4 (RL-1)


title: S288C_TATLSeq5

description: TATL-Seq, fraction 5


title: Postdauer adult#1 sRNA library

source_name: N2 wildtype postdauer adults

value: postdauer adults

value: GGAA


title: Myc_IdaxDBM_ChIP-seq

value: DNA-binding mutant of Myc-Idax (Myc-IdaxDBM)


title: S288C_TATLSeq4

description: TATL-Seq, fraction 4


title: RNA_N5 (RL-6)

source_name: intestine, ileum, normal tissue, Apc-Min/+

value: intestine, ileum, normal tissue


title: RNA_N4 (RL-3)


title: RNA_B2 (RL-5)

source_name: intestine, ileum, normal tissue, WT

value: Apc-+/+ (wild type)


title: RNA_B1 (RL-4)


title: S288C_TATLSeq1

description: TATL-Seq, fraction 1


title: S288C_TATLSeq2

description: TATL-Seq, fraction 2


title: S288C_TATLSeq3

description: TATL-Seq, fraction 3


title: Sigma_TLSeqControl

description: TL-Seq, -pyrophosphatase

value: Sigma 1278b

value: RNA


title: Input_B3 (Input10-1)

description: Processed data files for this Sample: hyper_500bp_Ad_vs_BN_v1.txt; hypo_500bp_Ad_vs_BN_v1.txt; hypo_DMR_merged_Ad_vs_BN_v1.txt; hyper_DMR_merged_Ad_vs_BN_v1.txt

data_processing:
Illumina 1.5 and 1.6 pipelines.
Single end sequencing reads (36 bp) generated from MeDIP-seq experiments and input samples were aligned to the mouse genome (UCSC mm9) using Bowtie (version 0.12.5 parameter set -q -n 2 -k 1 --best --maxbts 10000 -m 1) allowing up to 2 nucleotide mismatches to the reference genome per seed and returning only uniquely mapped reads. Replicate sequencing reads (i.e., reads with exactly the same starting position) were counted only once.
The analysis of the MeDIP-seq data was performed with a modified version of the MEDIPS package (Chavez et al., 2010, Genome Res;20(10):1441-50). For each sample, the aligned reads were extended in the sequencing direction to a length of 300 nt. The short read coverage of the extended reads was calculated at genome-wide 50 bp bins. Subsequently, the final short read count at each genomic bin is transformed into reads per million format (rpm = number of reads in the bin / number of uniquely aligned reads x 1000000).
Annotations using ENSEMBL58.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files. File "RNA_MeDIP_promoter_genebody_v2.txt" contains the RNA-seq raw read counts per Ensembl gene (Version58) and the normalized read counts (rpm, reads per million: number of exon read counts per gene / sum of the exon read counts of the sample x 1 000 000); the raw MeDIP-seq read counts per sample for individual promoter regions (-1 kb to +0.5 kb) and for individual genes (sum of the reads mapping to a gene) and the relative read counts that were calculated relative to the sample with the highest number of reads. In addition, the file contains the results of the edgeR analysis for the RNA-seq and the MeDIP-seq data. For the MeDIP-seq data, also a ratio and a t-test as well as a score (-log10(p.value)*10)*log(ratio) are given for the comparison of the normal intestinal samples (B,N) vs. the adenoma samples. Files "hyper_500bp_Ad_vs_BN_v1.txt", "hypo_500bp_Ad_vs_BN_v1.txt", "hypo_DMR_merged_Ad_vs_BN_v1.txt", "hyper_DMR_merged_Ad_vs_BN_v1.txt" contain the identified differentially methylated regions and the rpm values of the MeDIP-seq data. In brief, mean rpm values were calculated for genome-wide 500 bp windows overlapping by 250 bp using MEDIPS. Subsequently, for each 500 bp window, we applied a Wilcoxon's test in order to assess significance of methylation differences between the 5 ApcMin/+ adenomas (Ad) versus the 3 ApcMin/+ normal intestine (N), 3 Apc+/+ wildtype normal intestine (B). Differentially methylated regions (cDMRs) were identified by filtering for 500 bp windows associated with Wilcoxon p-values < 0.01, a ratio of >1.33 or <0.75 and a minimum average signal of 0.25 rpm for one of the two groups (results for the 500 bp bins in: "hyper_500bp_Ad_vs_BN_v1.txt", "hypo_500bp_Ad_vs_BN_v1.txt"). Overlapping significant 500 bp windows were merged if their methylation status indicated an extending DMR (Results for the merged regions in files "hypo_DMR_merged_Ad_vs_BN_v1.txt", "hyper_DMR_merged_Ad_vs_BN_v1.txt").

source_name: intestine, ileum, normal tissue, WT, input

extract_protocol:
Intestinal samples were excised, transferred to buffer RLT/1mM DTT (Qiagen, Hilden, Germany) and homogenized in a Tissue Lyser (Qiagen) for 2 x 2 min, frequency set to 20 with a steel bead of 5 mm diameter (Qiagen). Samples were snap frozen and stored at -80°C until extraction of DNA and RNA using the Allprep DNA/RNA Mini kit (Qiagen). RNA-seq and MeDIP-seq libraries were generated from the same samples.
MeDIP-Seq: 8-10 µg genomic DNA were subjected to an RNase A (Sigma, Taufkirchen, Germany) digest for one hour at 37 °C. Next, DNA was sheared to a size range of 100-400 bp and purified using QIAquick PCR columns and buffer QG (Qiagen, Hilden, Germany). Single end libraries were made using 5 µg of fragmented DNA and the genomic DNA sample prep kit, oligo only (#FC-102-1004, Illumina, San Diego, USA), according to the manufacturer's instructions with modifications as described previously (Grimm and Adjaye, 2012, Methods Mol Biol 873: 281–295. doi:10.1007/978-1-61779-794-1_19). In detail, end repair was done in 317 µl total volume with 0.25 mM of each dNTP, 0.1 U/µl T4 DNA polymerase, 0.03 U/µl DNA polymerase I (large fragment) and 0.3 U/µl T4 polynukleotide kinase. A-tailing was performed in the presence of 0.2 mM dATP and 0.5 U/µl Klenow fragment (3'->5'exo-) in a total volume of 88 µl. Adapters were ligated using 29 µl of 'Adapter oligo mix' and 10 µl of Quick T4 DNA Ligase in a total volume of 98 µl. All enzymes were purchased from NEB (Frankfurt/Main, Germany). Subsequently, the libraries were used for methylated DNA immunoprecipitation (see below). After MeDIP, the libraries were amplified prior to size selection in a total volume of 30 µl using Phusion polymerase and 20% of the immunoprecipitated DNA or 40 ng of non-immunoprecipitated library (input) for 6 PCR-cycles. Amplified libraries were run on a 2% agarose gel (low range ultra agarose, BioRad, München, Germany) and fragments of 150-400 bp were excised (corresponding to insert sizes of 80-330 bp) and purified using the QIAquick Gel Extraction Kit (Qiagen). Size-selected libraries were quantified using the QuantIt dsHS Assay Kit on a Qubit fluorometer (Invitrogen, Darmstadt, Germany). For MeDIP, 10 µl of monoclonal antibody against 5-methylcytidine (#BI-MECY, Eurogentec, Cologne, Germany) were incubated over night with 40 µl Dynabeads M-280 sheep anti-mouse IgG (Invitrogen, Darmstadt, Germany) in 500 µl 0.5% BSA/PBS, washed two times with 0.5% BSA/PBS and one time with IP-buffer (10 mM sodium phosphate (pH7.0), 140 mM NaCl, 0.25 % Triton X100). Prior to immunoprecipitation, the sequencing libraries were denatured for 1 min at 95°C. 4 µg denatured library was immunoprecipitated for 4h at 4°C using the 5-methylcytidine antibody coupled to Dynabeads in a total volume of 230 µl IP-buffer. After immunoprecipitation, the beads were washed three times with 700 µl IP-buffer and then treated with 50 mM Tris-HCl, pH 8.0; 10 mM EDTA, 1% SDS for 15 min at 65 °C. The supernatant containing the methylated DNA (200 µl) was diluted with 200 µl 10 mM Tris pH 8,0, 1 mM EDTA, treated with proteinase K (0.2 µg/µl) for 2 h at 55°C, followed by phenol-chloroform-extraction and ethanol precipitation. Precipitated DNA was resuspended in 20 µl 10 mM Tris pH 8.5.

tag: medip antibody


title: Sigma_TLSeq

description: TL-Seq, +pyrosphosphatase


title: IP2

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

country: Spain

institute: ISCIII

description: immunoprecipitated DNA

data_processing:
Biological replicates were mapped against the human genome using Bowtie and pooled
Genomic intervals bound by macroH2A.1 were called using SICER (Window size= 200, Fragment size= 260, Gap size= 600, FDR= 0.01)
Supplementary_files_format_and_content: bed; bound intervals

source_name: Human Keratinocytes

growth_protocol: Human keratinocytes were cultured using Epilife (invitrogen)

extract_protocol:
About 4 million cells were used for immunoprecipitation using anti HA antibodies (Ab9110 from Abcam).The chromatin immunoprecipitation (ChIP) assays were performed according to the Millipore protocol. Cells were fixed using 1% formaldehyde, harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using the Branson Digital Sonifier to generate fragments of 150 to 500 bp. Soluble chromatin was diluted 8 fold in ChIP RIPA buffer (10 mM Tris–HCl, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated with Dynabeads Protein A (Invitrogen) coupled to specific antibodies against HA (Ab9110 from Abcam). After incubation, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and TE. Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted overnight at 65ºC. Samples were treated with Proteinase K and RNase A and DNA was extracted using the Qiagen PCR purification kit.
Libraries for input and immunoprecipitated material were constructed selecting fragments from 200 to 500 bp and processed in the Solexa GAIIx Sample Sequencing (single reads of 36 nt)

treatment_protocol: Transduced with lentiviral particles pWPI-HA:macroH2A.1

tag: cell type

value: keratinocytes

tag: modification

value: Transduced with HA:macroH2A.1 expressing lentivirus

value: anti HA (Ab9110 from Abcam)


title: IP1

description: immunoprecipitated DNA


title: Input_N4 (Input4-3)

source_name: intestine, ileum, normal tissue, Apc-Min/+, input


title: Input_Ad7 (Input2-1)

source_name: intestine, ileum, adenoma, Apc-Min/+, input


title: Input2

description: input DNA


title: MeDIP_Ad6 (MeDIP10-2)

description: Processed data files for this Sample: RNA_MeDIP_promoter_genebody_v2.txt; hyper_500bp_Ad_vs_BN_v1.txt; hypo_500bp_Ad_vs_BN_v1.txt; hypo_DMR_merged_Ad_vs_BN_v1.txt; hyper_DMR_merged_Ad_vs_BN_v1.txt

source_name: intestine, ileum, adenoma, Apc-Min/+, MeDIP

value: anti-5-methylcytidine-antibody, mouse monoclonal, clone 33D3

tag: antibody vendor; catalog#; lot#

value: Eurogentec; BI-MECY; Lot:250407


title: MeDIP_Ad7 (MeDIP2-1)


title: Input1

description: input DNA

source_name: Human keratinocytes


title: MeDIP_Ad4 (MeDIP4-1)


title: MeDIP_Ad4-1 (MeDIP4-2)


title: MeDIP_N6 (MeDIP9-4)

source_name: intestine, ileum, normal tissue, Apc-Min/+, MeDIP


title: MeDIP_N4 (MeDIP4-3)


title: MeDIP_B3 (MeDIP10-1)

source_name: intestine, ileum, normal tissue, WT, MeDIP


title: MeDIP_B1 (MeDIP4-4)


title: 10 day old leaf explant calli (NAA)

city: Canberra

first: rod

last: eyles

address: Linnaeus Way

country: Australia

institute: Australian National University

description: Six week old leaf tissue was cultivated as explant on P4 media containing 10µM of the synthetic auxin 1-naphthaleneacetic acid (NAA). Leaf explant material treated with NAA only produces callus tissue and, after 14 days, roots. It is thought, at the time of collection, callus tissue produced on media containing only 10µM NAA, contains pluripotent stem cell comitted to root formation

data_processing:
Illumina Casava1.7 software was used for basecalling.
Adaptor trimming and genome alignment was perform using Novoalign v2.07.18
Read collation was performed using a custom PERL script
Read count normalisation was performed using EdgeR
Duplex energy calculations were done using the RNAduplex module of ‘Vienna RNA package’
Individual miRNA hairpin structures were produced using Mfold-quikfold (RNA 3.0, linear)
Genome_build: MedtrA17_3.5 (Medicago truncatula 3.5.1)
Supplementary_files_format_and_content: All_seqs_Planta_normalised1.txt file containing normalised read counts of published sequences

organism: Medicago truncatula

source_name: 10 day old leaf explant calli (NAA)

extract_protocol:
Whole RNA was extracted using the 'Trizol' method. The small RNA component was isolated using a standard precipitation method after the addition of 6 µl 50% PEG (MW 8000) and 7.5 µl 4M NaCl
Small RNA libraries were constructed using a modified version of ‘Preparing Samples for Small RNA Sequencing Using Alternative v1.5 Protocol’ (Part # 15002615 Rev. A, February 2009, Illumina, San Diego, CA, USA). Variations to this protocol were;  200-300 ng low molecular weight RNA was used. 3' and 5' adaptors were ligated in separate reactions.  The 3' adaptor ligation was carried out for 2.5 h at 22 oC and the 5' adaptor ligation was carried out for 1 h at 22 oC and then overnight at 4 oC.

value: auxin induced callus cells treated with root inhibiting cytokinin

tag: cultivar

value: Jemalong A17


title: 3 day old root tissue (Elongation Zone)

description: 10mm region beginning immediately above the root apical meristem (distal 3-13mm region) of three day old seedling root

source_name: 3 day old root tissue (Elongation Zone)

value: non-meristematic root cells


title: 3 day old root tip tissue (Root tip)

description: Distal 3mm of three day old root containing the root apical meristem and root cap.

source_name: 3 day old root tip tissue (Root tip)

value: meristenatic root cells


title: 10 day old leaf explant calli (NAA/BAP )

description: Six week old leaf tissue was cultivated as explant on P4 media containing 10 µM of the synthetic auxin 1-naphthaleneacetic acid (NAA)  plus 4 µM of the synthetic auxin 6-benzylaminopurine (BAP). Leaf explant material grown on media with this hormone combination forms callus tissue but not roots.

value: auxin induced callus cells committed to root formation


title: M+D+_1

status: Public on Apr 02 2013

city: Singapore

first: Weiling

last: Zheng

address: 21 Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

description: SAGE sequencing.

data_processing:
The SOLiD-generated RNA-Seq reads were 27 bp in length. An initial filtering process was performed to remove any non-desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database (Release 39) allowing maxium mismatches using ABI pipeline BioScope v1.0.1.
The expression levels of the mapped transcripts were normalized into transcript per million (TPM) to faciliate comparison among different samples.
Genome_build: RefSeq Release 39
Supplementary_files_format_and_content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.

organism: Danio rerio

source_name: liver tumor, M+D+

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen). Library construction was conducted by Mission Biotech (Taiwan) following the standard ABI SOLiD protocol.

treatment_protocol: Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6-L tanks with around 25 adults and water was changed every other day.

value: Tg(fabp10:TA; TRE:Myc; krt4:GFP)

value: liver

value: doxycycline


title: M+D+_2

description: SAGE sequencing.


title: MeDIP_Ad5 (MeDIP9-3)

value: Apc-Min/+

value: intestine, ileum, adenoma

value: male

value: 15-19 weeks


title: M-D+_1

description:
Wildtype sibling.
SAGE sequencing.

source_name: control liver, M-D+

value: wildtype


title: M-D-_1

description:
Wildtype sibling.
SAGE sequencing.

source_name: control liver, M-D-


title: MeDIP_N5 (MeDIP9-2)

value: intestine, ileum, normal tissue


title: M+D-_2

description: SAGE sequencing.

source_name: control liver, M+D-


title: M-D-_2

description:
Wildtype sibling.
SAGE sequencing.


title: Arabidopsis thaliana Col-0 floral bud 12, biological replicate 2

city: Toronto

first: Stephen

last: Wright

state: Ontario

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

description:
Col_0_floral_br2
PolyA RNA.
Barcode for sample: CATT

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with tophat 1.3.1 and cufflinks 0.9.2.
Genome_build: TAIR9 (available from The Arabidopsis Information Resource)
Supplementary_files_format_and_content: A single tab-delimited text file per sample with gene ids and FPKM values.

organism: Arabidopsis thaliana

source_name: floral bud stage 12

growth_protocol: Plants were grown in Percival AR66L growth chambers under 16 hours of light and 8 hours of dark. Floral buds were collected at stage 12 for RNA preparation. The floral tissue collection methods are as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.

extract_protocol:
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13).

value: flowers

tag: developmental stage

value: floral bud stage 12


title: Arabidopsis thaliana Col-0 floral bud 12, biological replicate 1

description:
Col_0_floral_br1
PolyA RNA.
Barcode for sample: ACGT


title: Arabidopsis lyrata MN47 floral bud 12, biological replicate 2

description:
Alyr_MN47_br_2
PolyA RNA.
Barcode for sample: TGCT

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with tophat 1.3.1 and cufflinks 0.9.2.
Genome_build: Alyrata_107 ('Alyrata_107.fa', which is the nucleotide FASTA format file of the genomic assembly, and 'Alyrata_107_cds.fa', which is the nucleotide FASTA format file of all gene-coding sequences, were downloaded from Phytozome at http://www.phytozome.net/ ). This genome build is as published by Hu et al. 2011. Nat. Genet. 43(5):476-81.
Supplementary_files_format_and_content: A single tab-delimited text file per sample with gene ids and FPKM values.

organism: Arabidopsis lyrata


title: Arabidopsis lyrata MN47 floral bud 12, biological replicate 1

description:
Alyr_MN47_br_1
PolyA RNA.
Barcode for sample: GTAT


title: mRNAseq_STM2683_Cd

city: Montpellier

first: geraldine

last: maynaud

address: Campus International de Baillarguet TA-A82/J

country: France

institute: CIRAD

description: mRNA

data_processing:
Image analyses and basecalling were conducted using the HiSeq Control Software (HCS 1.1.37.8) and RTA component (RTA 1.7.48).
Sequenced reads were mapped to the Mesorhizobium metallidurans STM2683 and STM4661 genomes using ssaha2 version 2.5.1 with parameters -solexa -s (read length)/2.
samtools (version 0.1.12a (r862)) were used to discard reads corresponding to multiple matches and convert ssaha2 SAM output file to generic BAM file.
Transcripts coverage (Read Count Analysis) were performed using the Genomic_Features R package (version 1.4.3) running on R (version 2.13.1).
Differential Expression Analyses were performed using the DESeq R package (version 1.4.1) running on R (version 2.13.1).
Genome_build: STM2683: CAUM01000001-CAUM01000191, BioProject PRJEB1501.
Supplementary_files_format_and_content: Tab-delimited text files containing raw abundance measurements.

organism: Mesorhizobium metallidurans STM 2683

source_name: M. metallidurans STM 2683 bacteria, cadmium treated

growth_protocol: Pre-grown in Ty medium (tryptone, yeast extract and CaCl2) up to mid-exponential phase (up to OD600nm=0.5) in 250-ml Erlenmeyer flasks at 28°C and 145 rpm.

extract_protocol:
After 5 hours incubation, 1/10th volume of ice-cold stop buffer (5% phenol in ethanol) was added to each culture and directly centrifuged at 4°C, 8,000 rpm for 4 minutes. Total RNA was extracted using the RiboPureTM kit (Ambion) following the manufacturer's recommendations. Two successive runs of ribosomal RNA subtractions were performed using the Microbe ExpressTM kit (Ambion) following the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 1004898 Rev. D). Briefly, the first step in the workflow involves fragmentation of mRNA into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers. This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then went through an end-repair process, the addition of a single 'A' base, and then ligation of the adapters. These products were then purified on a gel to select a size range at 200 bp and enriched by PCR to create the final cDNA library. The efficacy of the library construction was checked in a quality control step that involved measuring the adapter-cDNA size and concentration on an Agilent DNA 1000 chip. Sequencing libraries were denatured with sodium hydroxide and diluted to 6 pM in hybridization buffer for loading onto a single lane of an Illumina HiSeq 2000 flowcell V1.5. Cluster formation, primer hybridization and single-read, 36 sequencing cycles were performed on cBot and HiSeq 2000 (Illumina, San Diego, CA), respectively.
mRNAseq Part # 1004898 Rev. D Illumina Cat # RS-930-1001.

treatment_protocol: When the pre-cultures reached the mid-exponential phase (after ca 16 hours), 15 ml were added to an equal volume of pre-warmed TY medium containing either nothing (Control treatments), Zn at 1 mM (Zn treatments, 0.5 mM final concentration) or Cd at 0.05 mM (Cd treatments, 0.025 mM final concentration) and were further incubated for 5 hours at 28°C at 145 rpm.

tag: organism isolated from

value: Anthyllis vulneraria

tag: location isolated

value: Avinieres mine

value: cadmium


title: HCC510N

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing: Expression estimation and tests for differential expression were processed by Cufflinks program v0.8.3. Cufflinks uses the normalized RNA-Seq fragment counts to measure the relative abundances of transcripts. The unit of measurement is Fragments Per Kilobase of exon per Million fragments mapped (FPKM). Reference genome: hg19. For the detection of variants,aligned files from the three different aligners (see publication) were processed with SAMtools and subsequently with VarScan (v2.2) for Single Nucleotide Variations (SNVs) detection.  Variance calling was constrained to locations within gene regions with at least 10X coverage, variation frequency of more than 30% and base quality of more than 15. By subtracting variation between tumor and the matched NT sample, somatic single nucleotide variations were obtained and compared to NCBI dbSNP Build 131.  Lastly, we intersected the somatic SNVs detected from all three aligners to derive a set of high confidence SNVs

source_name: liver tissue, non-tumor

growth_protocol: All paired human HCC and adjacent non-tumor (NT) tissues that surgically removed and snap frozen in liquid nitrogen were obtained from the Cancer Center of Sun Yat-Sen University (Guangzhou, China) along with clinicopathological summaries.

extract_protocol: Total RNA was isolated using mirVanaTM miRNA isolation kit (Applied Biosystems, Carlsbad, CA) and then treated with DNA-free kit for the removal of contaminated genomic DNA. PolyA+ RNA was purified with Dynabeads mRNA purification kit (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions.  About 100ng of mRNA was fragmented by incubation for 5 min at 94°C in 5 × Array Fragmentation Buffer (Ambion, Austin, Texas).  Double strand cDNA was synthesized with the SuperScript Double Stranded cDNA synthesis kit (Invitrogen) using random hexamers.  The reaction was purified on a QiaQuick PCR column (Qiagen, Valencia, CA).  Double strand cDNA fragments were repaired with DNA Terminator End Repair Kit (Lucigen, Middleton, WI) and purified on a QiaQuick PCR column.  The Klenow 3’ to 5’ exo-polymerase (NEB, Ipswich, MA) was used to add a single ‘A’ base to the 3’end of blunt phosphorylated DNA fragments.  Following purification, Illumina PE Adapter (Illumina,San Diego, CA) was ligated to the end of DNA fragments with the Quick Ligation™ Kit (NEB, Ipswich, MA).  About 280 to 300 bp fragments were excised from a 2% low-melting agarose gel.  Fragments were enriched by 10 cycles using AccuPrime™ Pfx DNA Polymerase (Invitrogen).  PCR product was run on Novex 8% TBE polyacrylamide gel (Invitrogen) and stained with SYBR Gold (Invitrogen).  The gel slice containing the 340 to 360-bp fragments was excised and purified by QiaQuick Gel Extraction Kit (Qiagen).  The concentration of gel purified DNA fragments was measured using a ND-1000 UV/Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE).

tag: tissue

tag: phenotype

value: non-tumor


title: mRNAseq_STM2683_TY

description: mRNA

source_name: M. metallidurans STM 2683 bacteria, control treated

tag: strain

tag: treatment

value: medium control


title: HCC473T

source_name: liver tissue, cancerous

value: hepatocellular carcinoma


title: MeDIP_B2 (MeDIP4-5)

tag: genotype

value: Apc-+/+ (wild type)

value: anti-5-methylcytidine-antibody, mouse monoclonal, clone 33D3

value: Eurogentec; BI-MECY; Lot:250407


title: HCC448T

value: liver


title: HCC510T


title: HCC448N


title: mRNAseq_STM4661_Cd

description: mRNA

data_processing:
Image analyses and basecalling were conducted using the HiSeq Control Software (HCS 1.1.37.8) and RTA component (RTA 1.7.48).
Sequenced reads were mapped to the Mesorhizobium metallidurans STM2683 and STM4661 genomes using ssaha2 version 2.5.1 with parameters -solexa -s (read length)/2.
samtools (version 0.1.12a (r862)) were used to discard reads corresponding to multiple matches and convert ssaha2 SAM output file to generic BAM file.
Transcripts coverage (Read Count Analysis) were performed using the Genomic_Features R package (version 1.4.3) running on R (version 2.13.1).
Differential Expression Analyses were performed using the DESeq R package (version 1.4.1) running on R (version 2.13.1).
Genome_build: STM4661: CAAF010000001-CAAF010000089, BioProject PRJEB1502.
Supplementary_files_format_and_content: Tab-delimited text files containing raw abundance measurements.

organism: Mesorhizobium sp. STM 4661

source_name: Mesorhizobium sp. STM 4661 bacteria, cadmium treated

value: Eylie mine


title: mRNAseq_STM4661_Zn

description: mRNA

source_name: Mesorhizobium sp. STM 4661 bacteria, zinc treated

value: zinc


title: mRNAseq_STM4661_TY

description: mRNA

source_name: Mesorhizobium sp. STM 4661 bacteria, control treated


title: M-D+_2

description:
Wildtype sibling.
SAGE sequencing.

value: doxycycline


title: M+D-_1

description: SAGE sequencing.

value: Tg(fabp10:TA; TRE:Myc; krt4:GFP)


title: mRNAseq_STM2683_Zn

description: mRNA

source_name: M. metallidurans STM 2683 bacteria, zinc treated


title: duck_liver_lane_1

status: Public on Apr 01 2013

city: shenzhen

first: wubin

last: qian

address: beishan road

country: China

institute: beijing genomics institute

description: sample for paired-end library with insert size of 500 bp which generates 44 bp paired-end reads

data_processing: Alignment:   After removing reads containing sequencing adapters , we aligned paired-end reads to the duck genome using SOAP 2 allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found. Meanwhile, we set insert of paired reads was 1~10 kb allowing to span introns with varied sizes on genome.

molecule: polyA RNA

organism: Anas platyrhynchos

source_name: cherry valley duck liver

extract_protocol: mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 75 bp of sequence was determined from the both of fragment ends with insert size of 146bp for tissue spleen and 124bp for tissue liver.

value: cherry valley


title: duck_liver_lane_2


title: duck_spleen_lane_2

source_name: cherry valley duck spleen


title: duck_spleen_lane_1


title: HCC473N


title: Short Nodule Rep3 (29)

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

institute: INRA/CNRS

data_processing:
Reads were mapped to the genome using glint (Faraut T. and Courcelle E.; http://lipm-ioinfo.toulouse.inra.fr/download/glint/, unpublished) and parameters were as follow: matches with less than or equal to 2 mismatches, no gap allowed and a minimum length of 18 nt required. We removed all ambiguous matches (reads or read-pairs mapping to two different positions with the same best score) as well as matches of paired-end reads that were separated by more than 1kb.
Genome_build: Sinorhizobium meliloti 2011 submitted to Genbank (pending; GDSub21246)
Supplementary_files_format_and_content: To annotate the Sinorhizobium meliloti genome, we computed the local library specific transcription depth at each position of the sequence (of the chromosome GMI11495-Rm2011G.c and of the megaplasmids GMI11495-Rm2011G.a and GMI11495-Rm2011G.b). The three tabulated files are composed of 20 columns: column 1=position, column2=strand, columns 3-20=local transcription depth for a specific library.

organism:
Sinorhizobium meliloti
Medicago truncatula

source_name: nodule

growth_protocol: RNAs were extracted from bacteria in liquid cultures in exponential and stationary growth phases and from 10-day-old nodules in which bacteria were differentiated in nitrogen fixing bacteroids

extract_protocol:
Harvested cultured bacteria were resuspended and incubated in pre-warmed lysis buffer (1.4% SDS, 4 mM EDTA and 0.4 mg/ml proteinase K) for 20 minutes at 65°C. Lysed cells were then incubated at 4°C for 10 minutes in the presence of 1.5 volumes of 5 M NaCl. Following centrifugation, the pellet containing proteins and cell debris was separated from nucleic acids in the supernatant fraction that were subsequently precipitated by the addition of one volume of isopropanol. Nucleic acid-containing pellets were washed with 70% cold ethanol, dried and resuspended in RNAse free water. Total nucleic acids were processed with mirVana isolation kit (Ambion, Invitrogen) using the total RNA isolation procedure which allowed the extraction of both short and long RNAs. For plant material, root nodules were collected and frozen in liquid nitrogen before ground with a mortar and pestle, and then with a Retsch MM300 mill for 1 min. Total RNA was then immediately extracted with the mirVana Isolation Kit using the total RNA isolation procedure. Bacterial or nodule total RNA preparations were then treated with TURBO DNase (Ambion, Life technologies) to remove residual contaminant DNA. Total RNA preparations were depleted of ribosomal RNAs (rRNAs) by an oligocapture strategy derived from the Plant Ribominus kit (Invitrogen), in which oligonucleotide sets specifically designed to target M. truncatula and S.meliloti rRNAs, as well as the highly abundant S. meliloti tRNA_Ala were used. RNAs were separated in two fractions, short (< 200 nt) and long (> 200 nt), using Zymo Research RNA Clean & Concentrator™-5 columns (Proteigene).
Oriented sequencing with a RNA ligation procedure was carried out by Fasteris SA (Geneva, Switzerland) using procedures recommended by Illumina, with adaptors and amplification primers designed by Fasteris, unless specified (see below). For short RNAs, the Small RNA Sequencing Alternative v1.5 Protocol (Illumina) was used, RNAs were first treated with Tobacco Acid Pyrophosphatase to remove triphosphate at 5’ transcript ends, and purified on acrylamide gel before and after the adaptor ligation step. The 3’ adaptor was the Universal miRNA cloning linker (NEB). For long RNAs, a fragmentation step by zinc during 8 min was included, following the Illumina procedure. The size of selected inserts was 20-120 nt for short RNA libraries and 50-120 nt for long RNA libraries from cultured bacteria and 150-250 nt for long RNA libraries from nodules. Libraries were sequenced either in paired-end or single-end.

tag: development stage

value: 10-day-old nodules

value: Sinorhizobium meliloti 2011

tag: rna fraction

value: short (< 200 nucleotides)

value: Tobacco Acid Pyrophosphatase (TAP)

tag: fragmentation

tag: selected insert size

value: 20-120 nucleotides


title: Short Nodule Rep2 (28)


title: Long Nodule Rep3 (23)

value: long (>200 nucleotides)

value: yes

value: 150-250 nucleotides


title: Short Nodule Rep1 (27)


title: GR ChIP-seq, EtOH [EGR19138]

city: Chicago

first: Joseph

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

data_processing:
ChIP-seq reads were aligned to the hg18 genome assembly using MAQ
Duplicate reads were removed
Reads from the two LCLs were pooled
Peaks were called using MACS with the default settings
Genome_build: hg19

source_name: GR ChIP-seq, EtOH

growth_protocol: LCLs were grown according to standard protocols in RPMI supplemented with 15% charcoal-stripped fetal bovine serum

extract_protocol:
Cells were cross linked with formaldehide and GR or NFkB-chromatin complexes were isolated with antibody
Libraries were constructed using  the Illumina ChIP-seq library preparation protocol according to the manufacturer instructions

treatment_protocol: Cells were treated with either EtOH (vehicle) or 1 micromolar dexamethasone

value: LCL

tag: chip antibody

value: GR

tag: catalog#

tag: vendor

value: Santa Cruz Biotechnology, Inc.

value: EtOH


title: Long Nodule Rep1 (21)


title: Long Nodule Rep2 (22)


title: NFkappaB ChIP-seq, EtOH [EN19138]

source_name: NFkappaB ChIP-seq, EtOH

tag: cell type

value: anti-NFkB p65


title: NFkappaB ChIP-seq, Dex [DN19138]

source_name: NFkappaB ChIP-seq, Dex

value: 1 micromolar dexamethasone


title: NFkappaB ChIP-seq, EtOH [EN19171]


title: NFkappaB ChIP-seq, Dex [DN19171]


title: GR ChIP-seq, Dex [DGR19171]

source_name: GR ChIP-seq, Dex


title: MB_Spt6_ChIPSeq

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

description: Chromatin IP against Spt6

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland)
Peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads in bed format, peak files in bed formats and wig files were generated using filtered reads residing in enriched regions

growth_protocol: C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 20% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and Spt6-DNA or KDM6A-DNA complexes were isolated with antibody
Libraries were prepared according to NuGEN's instructions using Ovation SP Ultralow Library System (Part# 8033-32) on a Mondrian™ SP+ System. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

value: Proliferating Myoblasts


title: MT_KDM6A_ChIPSeq

description: Chromatin IP against KDM6A

value: 48-hours differentiated Myotubes


title: GR ChIP-seq, EtOH [EGR19171]


title: MT_Spt6_ChIPSeq

description: Chromatin IP against Spt6


title: GR ChIP-seq, Dex [DGR19138]


title: MmTKO_Mbd3a

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: NOTE: Curation error resulted in two incorrect runs being added to GSM1089892 on July 8, 2015 (SRR768238 and SRR768239). These runs were withdrawn on March 11, 2016.

data_processing:
basecalls using CASAVA
fastq to fasta conversion
reads from pooled libraries were demultiplexed using Barcodesplitter from FASTX tools, barcodes were removed
reads were aligned to mm9 mouse genome using BOWTIE, allowing up to 2 missmatches
coordinates of reads that map only once to the mouse genome were converted to BED format
Genome_build: mm9
Supplementary_files_format_and_content: bed format, contents: chromosome, start, end, read_name, n times mapped to genome, strand

source_name: embryonic stem cells

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).

extract_protocol: For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 150 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation. ChIP-seq with inline barcodes. Four libraries with different barcodes were pooled at equimolar ratios per lane.

value: embryonic stem cells

value: Dnmt1,Dnmt3a,Dnmt3b triple KO

tag: background strain

value: mixed 129-C57Bl/6


title: MmES_CMV_MeCP2

value: wild type


title: MB(KDM6A KD)_KDM6A_ChIPSeq

description: Chromatin IP against KDM6A

tag: developmental stage


title: MmTKO_Mbd4


title: MB_KDM6A_ChIPSeq

description: Chromatin IP against KDM6A


title: MmES_CMV_Mbd2a


title: MmES_Mbd2a_R181C


title: MmTKO_Mbd2a

tag: mbd protein


title: MmTKO_MeCP2


title: MmTKO_Mbd1b


title: MmES_MeCP2_R106W


title: MmTKO_Mbd1a


title: MmES_Mbd1b_delMBD


title: MmNP_Mbd3a

source_name: neuronal progenitor cells

value: ES-derived neuronal progenitor cells


title: MmES_Mbd1b


title: MmES_Mbd1a_delTRD


title: MmES_MeCP2_R133C


title: MmES_MeCP2_delTRD


title: MmNP_Mbd2a


title: MmTN_MeCP2

source_name: post mitotic neuronal cells

value: ES-derived post mitotic neuronal cells


title: MmES_Mbd1a_R22C


title: MmNP_Mbd4


title: MmES_Mbd4


title: MmES_Mbd3a


title: MmNP_Mbd1a


title: MmES_MeCP2


title: MmES_Mbd1a


title: MmES_Mbd2a


title: MmES_Mbd1a_delMBD


title: H3K4me1_ChIP_sh non targeting

city: Utrecht

first: Richard

last: van Schaik

address: Universiteitsweg 100

department: Molecular Cancer Research

country: Netherlands

institute: UMCUtrecht

description: Sample 6

data_processing:
H3K4me1_w200Rawreads_t10.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

growth_protocol: IB10 (E14 ES) and its derivative BirA mouse embryonic stem cells were cultured on gelatin-coated dishes in high glucose (4.5 g/l) DMEM (Gibco) media supplemented with 15% Fetal bovine serum, 100 µg/ml Pen/Strep, 2 mM L-glutamine, 100 µM β-mercaptoethanol, 1 mM natrium pyruvate, 100 µM non-essential amino acids and leukemia inhibitory factor (LIF). A Kdm5c containing BAC (RP23-391D18) was obtained from BACPAC Resources Center (http://bacpac.chori.org). The triple tag V5-FLAG-BIO cassette was inserted as a C-terminal in-frame fusion using bac recombineering (Ciotta, 2011), details available upon request. BirA ES cells were transfected with the recombineered Kdm5c BAC using Lipofectamine 2000 (Invitrogen) and selected on geneticin (G418 sulphate, Gibco). BirA and transgenic derivatives containing the tagged Kdm5c transgenic BAC were differentiated into NPC cells using the procedure described in Conti et al.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the ChIP Seq Sample preparation Kit (Part# IP-102-1001)

value: IB10 (E14 ES cell subline)

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat #


title: H3K4me1_ChIP_KDM5C_KD_sh3813

description: Sample 5

data_processing:
H3K4me1_sh3813w200Rawreads_t10.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

tag: genotype/variation

value: KDM5C knockdown


title: H3K4me3_ChIP_KDM5C_KD_sh3813

description: Sample 7

data_processing:
H3K4me3_sh3813w200Rawreads_t10.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

tag: strain

value: Millipore


title: KDM5C_ChIP_NPC

description: Sample 3

data_processing:
Jarid1cNeuronw200d4Norm10backg8RatioNCSAR_t2.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

value: NPC derived from the coresponding ES cells

value: transfected with tagged Kdm5c transgenic BAC

value: streptavidin


title: BirA_ChIP_ES

description: Sample 2

data_processing: Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

value: BirA-expressing IB10 (E14 ES cell subline)


title: Non-injected 5 DPI, biol. repl. 4

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

institute: Leiden University

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 4

data_processing:
Base calling was done by the Illumina HCS version 1.15.1
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_63) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Non-injected 5 DPI

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were micro-injected into the yolk (2hpf) with 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. At 5 days post injection 100-200 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: tissue

value: embryo

tag: age

value: 5 days post fertilization


title: H3K4me3_ChIP_sh non targeting

description: Sample 8

data_processing:
H3K4me3_w200Rawreads_t10.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR


title: Non-injected 5 DPI, biol. repl. 2

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 2


title: S. epi mcherry O-47 5 DPI, biol. repl. 4

description: Wildtype; injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 4

source_name: S. epi mcherry O-47 5 DPI


title: S. epi mcherry O-47 5 DPI, biol. repl. 3

description: Wildtype; injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 3


title: Straw + Glucose 5 h 1

city: Nottingham

first: Laure

last: Ries

address: School of Biology, University Park

institute: University of Nottingham

data_processing:
RNA-seq reads from SOLiD 4 from each of the experimental samples were mapped to the T. reesei genome (JGI T. reesei version 2.0 unmasked assembled scaffolds) using the BioScope 1.3.1 Transcriptome Pipeline (LifeTechnologies). Bioscope mapped each read against the complete genome sequence and exon spanning junctions using available gene coordinate information, hence providing the primary read alignment position. Mapping results were recorded in a BAM (binary alignment/map) format.
The amount of reads per gene for each sample was calculated with Htseq-count (http://www.huber.embl.de/users/anders/HTSeq) using the BAM files and the genome annotation. Strand-specific RNA-seq reads, as generated by SOLiD, can be specified for when executing Htseq-count in determining accurate read counts per gene.
Gene counts were used to calculate normalised expression values (reads per kilobase of exon model per million mapped reads = RPKM) for each gene (Mortazavi et al., 2008). Antisense transcription was detected by either excluding or including strand-specificity in the calculations when comparing the Htseq-count generated counts.
Genome_build: JGI T. reesei version 2.0 genes filtered models
Supplementary_files_format_and_content: Tab-delimited text files include Htseq-counts and RPKM values for each sample.

organism: Trichoderma reesei

source_name: Wild-type T. reesei mycelia

growth_protocol: Conidia of T. reesei QM6a were inoculated on potato dextrose agar slopes (PDA: 4.0 g/L potato extract, 15.0 g/L agar, 20.0 g/L) at 28°C until they had grown and sporulated. Spores were resuspended in 2 ml 0.01% (w/v) Tween 80 and and used to inoculate liquid batch cultures at a concentration of 10^5 spores/mL. Strains were cultured in 100 ml Trichoderma Minimal Media [TMM: 15 g/L KH2PO4, 5 g/L (NH4)2SO4, 10 g/L of the respective carbon source, 0.005 g/L FeSO4.7H20, 0.0016 g/L MnSO4.H20, 0.0014 g/L Zn.SO4.H20, 0.0037 g/L CoCl12.6H20, 0.6 g/L MgSO4, 0.6 g CaCl2] in 250 mL Erlenmeyer flasks at 28°C, shaking at 150 rpm. Mycelia were grown for 48 h in 1% (w/v) glucose, after which they were removed by filtration through Miracloth (Merck), washed with double-distilled water (ddH2O), and transferred to fresh media supplemented with 1% w/v of wheat straw for 24 h. Glucose was then added to the wheat straw-incubated cultures to a final concentration of 1% (w/v) and incubation continued for another 5 h.

extract_protocol:
Mycelia from each condition were snap-frozen and ground to a fine powder under liquid N2 using a mortar and pestle. The TRIzol reagent protocol (Invitrogen) was used to extract total RNA from mycelial powder samples. RNA was further purified with the Qiagen RNeasy® Mini Kit (Qiagen) following the instructions of the “RNA clean-up” protocol with on-column DNA digestion.
Ribosomal RNA was degraded in 10 µg of total RNA using the Ribominus Eukaryotic kit (Invitrogen, Cat. No. A10837-08). SOLiD whole transcriptome libraries were made according to the SOLiD Whole transcriptome kit protocol (Applied Biosystems, Cat. No. 4425680) and the library concentrations were measured with the Quant-ut HS dsDNA assay kit (Invitrogen, Cat No. Q32851). Libraries were pooled to equimolar amounts (Invitrogen, Cat. No. Q32851) and gel purified using 2% size-select E-gels to 200-300 bp (Invitrogen). Emulsion PCR (0.5 M final concentration of pooled libraries) and bead-based enrichment was done according to the SOLiD 3+ template bead preparation guide containing library. Sequencing was carried out on a SOLiD 3+ ABi sequencer platform according to manufacturer’s instructions to generate 50 bp reads in colour space.

tag: growth condition

value: Straw + 5 h glucose

value: mycelia


title: Straw 24 h 2

value: 24 h straw


title: Glucose 48 h 1

value: 48 h glucose


title: Glucose 48 h 3


title: BirA_ChIP_NPC

description: Sample 4


title: S. epi mcherry O-47 5 DPI, biol. repl. 2

description: Wildtype; injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 2


title: Non-injected 5 DPI, biol. repl. 1

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 1


title: MmES_Mbd4_R106C

value: embryonic stem cells

tag: genotype

value: wild type

value: mixed 129-C57Bl/6


title: S. epi mcherry O-47 5 DPI, biol. repl. 1

description: Wildtype; injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 1


title: METSIM11401

city: Los Angeles

first: Mete

last: Civelek

state: CA

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

institute: University of California Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.
The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 –k.  Novoalign software trims the adapter sequences while aligning.
We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.
To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA

source_name: adipose tissue

extract_protocol:
Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturer’s instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.
Small RNA libraries were prepared using  the Illumina  TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501)

treatment_protocol: We analyzed samples from 200 male human subjects that are part of the METSIM (METabolic Syndrome In Men) study. The population-based cross-sectional METSIM study included 10,197 men, aged from 45 to 73 years, who were randomly selected from the population register of the Kuopio town in eastern Finland (population 95,000). Every participant had a 1-day outpatient visit to the Clinical Research Unit at the University of Kuopio, including an interview on the history of previous diseases and current drug treatment and an evaluation of glucose tolerance and cardiovascular risk factors. After 12 hours of fasting, a 2-h oral 75-g glucose tolerance test was performed and the blood samples were drawn at 0, 30 and 120 min. Plasma glucose was measured by enzymatic hexokinase photometric assay (Konelab Systems reagents; Thermo Fischer Scientific, Vantaa, Finland). Insulin was determined by immunoassay (ADVIA Centaur Insulin IRI no. 02230141; Siemens Medical Solutions Diagnostics, Tarrytown, NY). Height and weight were measured to the nearest 0.5 cm and 0.1 kg, respectively. Waist (at the midpoint between the lateral iliac crest and lowest rib) and hip circumference (at the level of the trochanter major) were measured to the nearest 0.5 cm. Body composition was determined by bioelectrical impedance (RJL Systems) in subjects in the supine position after a 12-hour fast.

value: adipose tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: Straw + Glucose 5 h 2

tag: strain

tag: growth condition

tag: tissue


title: METSIM11295

tag: age

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)


title: METSIM11138

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: Straw 24 h 1

tag: strain

tag: growth condition

tag: tissue


title: METSIM10346

tag: age

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)


title: METSIM10381

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: METSIM10419

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)


title: Glucose 48 h 2

tag: strain

tag: growth condition

tag: tissue


title: METSIM10062

tag: age

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: Surface_fish_brain

city: Beijing

first: Fanwei

last: Meng

address: 1 Beichen West Road,Chaoyang District

department: State Key Laboratory of Biomembrane and Membrane Biotechnology

institute: Institue of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then de novo assembled or mapped to de novo assembled transcriptome using bowtie v0.12.2 with parameters -v 3 -k 1 -e 100 -a  --best
Reads Per Kilobase of exon per Megabase of library size (RPKM (Reads Per Kilobase of exon per Million mapped sequence reads) were calculated using a protocol from Mortazavi et al., Nat Methods , 2008. In short, we merged the number of reads of surface fish and cavefish that mapped to the same unigene of either our Sinocyclocheilus transcriptome or the zebrafish unigene database, and converted mapped read numbers to RPKM values.
Genome_build: de novo assembled Sinocyclocheilus transcriptome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Sinocyclocheilus angustiporus

source_name: brain

extract_protocol: Total RNA was isolated using a TRIzol reagent (Invitrogen) from whole eye and brain of adult surface and cave species respectively. Two individuals were used in each species. Oligo(dT) selection was performed by using MicroPoly(A) PuristTM (Ambion) according to the manufacturer's protocol. Superscript III First-Strand Synthesis System (Invitrogen) was used to create first-strand cDNA. The second-strand cDNA was synthesized using random primers and Klenow exo- polymerase (Epicentre). cDNA was sheared to short fragments with Biorupter® Sonicator, and then the fragments were connected with sequencing adapters. After size selection, suitable fragments were used as templates for PCR amplification. Finally, four libraries (200 – 400 bp insert) were sequenced using Illumina sequencer GA-II paired-end 80-nt or HiSeq 2000 paired-ed 100-nt (Illumina Inc., San Diego, CA, USA).

tag: tissue

value: brain

tag: age

value: adult

tag: sample type

value: surface fish


title: METSIM10252

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)


title: METSIM8305

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: METSIM8135

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)


title: METSIM8067

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: MmES_Mbd2t

tag: mbd protein

tag: cell type

tag: genotype

tag: background strain


title: KDM5C_ChIP_ES

description: Sample 1

data_processing:
jarid1cES-R2w200d4Norm10backg8RatioNCSAR_t2.wig; genome build: mm9
Sequence reads were mapped to the mouse genome (NCBI37) using SOAPv2 with two or fewer mismatches. Peak detection was performed using CSAR

tag: strain

tag: genotype/variation

tag: chip antibody


title: METSIM7988

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)


title: METSIM10830

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: METSIM10389

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)


title: Non-injected 5 DPI, biol. repl. 3

description: Wildtype: non-injected control; RNA isolated at 5 days post fertilization (=5DPI timepoint). Biological replica 3

tag: tissue

tag: age


title: Straw 24 h 3

tag: strain

tag: growth condition


title: METSIM10277

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: lg10 plasma adiponectin (mg/l)

tag: ogtt fasting plasma free fatty acid (mmol/l)

tag: ogtt 30 min plasma free fatty acid (mmol/l)

tag: ogtt 120 min plasma free fatty acid (mmol/l)

tag: ogtt fasting plasma glucose (mmol/l)

tag: ogtt 30 min plasma glucose (mmol/l)

tag: ogtt 120 min plasma glucose (mmol/l)

tag: log10 serum alanine aminotransfrase (u/l)

tag: log10 creatinine (umol/l)

tag: log10 total cholesterol (mmol/l)

tag: log10 ldl cholesterol (mmol/l)

tag: log10 hdl cholesterol (mmol/l)

tag: log10 total triglycerides (mmol/l)

tag: log10 serum apoa1 (g/l)

tag: log10 serum apob (g/l)

tag: log10 urinary albumin excretion rate (ug/min)


title: METSIM10271

tag: age

tag: tissue

tag: log10 body mass index

tag: log10 basal metabolic rate (kcal)

tag: log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd)

tag: log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr)

tag: plasma free fatty acids under the curve ogtt (mmol/l * min)

tag: fat mass (%)

tag: log10 plasma glucose area under the curve (ogtt) (mmol/l * min)

tag: plasma glucose area under the curve above basal (ogtt) (mmol/l * min)

tag: log10 homair (insulin resistance index based on homa)

tag: log10 homais (insulin secretion index based on homa)

tag: log10 insulin area under the curve (ogtt) (pmol/l * min)

tag: insgenin (insulinogenic index)

tag: log10 insulin area under the curve above basal (ogtt) (pmol/l * min)

tag: log10 matsuda insulin sensitivity index

tag: muscle mass (%)

tag: lg10 serum c-reactive protein (mg/l)

tag: log10 il1 receptor antagonist (pg/ml)

tag: log10 il1 beta (pg/ml)

tag: log10 ogtt fasting plasma insulin (mu/l)

tag: ogtt 30 min plasma insulin (mu/l)

tag: ogtt 120 min plasma insulin (mu/l)

tag: log10 ogtt fasting plasma proinsulin (pm/l)

tag: ogtt 30 min plasma proinsulin (pm/l)

tag: ogtt 120 min plasma proinsulin (pm/l)

tag: log10 bioimpedance

tag: log10 bioimpedance (reactance)

tag: waist to hip ratio

tag: log10 serum bilirubin (umol/l)